PaperBLAST
PaperBLAST Hits for tr|B1VA15|B1VA15_PHYAS UvrABC system protein B OS=Phytoplasma australiense OX=59748 GN=uvrB PE=3 SV=1 (663 a.a., MNMFKLKTDL...)
Show query sequence
>tr|B1VA15|B1VA15_PHYAS UvrABC system protein B OS=Phytoplasma australiense OX=59748 GN=uvrB PE=3 SV=1
MNMFKLKTDLKPNGDQPQAIKKLVQGFEKGFKEQILLGATGTGKTFTIANIIQHLQQQTL
VIAHNKTLAGQLYNELKMMFPENKVEYFISYYDYYQPEAYVTSSDTYIEKDSKINDEIDQ
LRHNAIVSLLNRKDVIVVASVSCIYGVGDLEDYQSSTLFLQIGDRFERNLFLKKLVELKF
QRNEVNFGRGTFRVRGDIVEIIPSSHKEIGIRIIFFGDEIERIQLFELLNAKVIENLKVT
KIFPASLYAVNAEKIKESIKRIRQELKEQIKHFEKEKNLVAAQKIKMRTSHDLEMLAEMG
HCSGIENYSRHLSLKEQGQPPSTLIDFFDKEFLTIIDESHVTVPQIKGMYFGDFSRKSNL
VNYGFRLPSALDNRPLKFHEFEEKIDKIIYLSATPGDHEIERKLPIIEQIIRPTFVLDPE
IEVKRTQNQMDDLYFEIKKRIQKNQRVLITTLTINMSEDLTAYLKNLGIKVTYLHSEIKS
LQRLEILRDLRLGKYDCLVGVNLLREGLDLPEVSLVAILDADKQGFLRNQRSLIQTIGRA
ARNVDGKVIMYADNTSDAMKLAITETNRRRQIQKDYNQKNQLTPLSLKKNISESVSIQTK
DKATSKKEPMFDLKNINQQIKKLTNDMKKAAEKLDFEKAASLRDLILELEKKDKKAMKKF
SKR
Running BLASTp...
Found 184 similar proteins in the literature:
P56981 UvrABC system protein B from Bacillus caldotenax
59% identity, 97% coverage
ZY05719_04965 excinuclease ABC subunit UvrB from Streptococcus suis
58% identity, 98% coverage
J3U91_00327 excinuclease ABC subunit UvrB from Oenococcus oeni
57% identity, 97% coverage
Cthe_0309 excinuclease ABC subunit B from Clostridium thermocellum ATCC 27405
Clo1313_1918, Cthe_0309 excinuclease ABC subunit UvrB from Acetivibrio thermocellus ATCC 27405
58% identity, 98% coverage
- Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution
Ha-Tran, Microorganisms 2021 - “...mutation was found in the open reading frame of the excinuclease ABC subunit uvrB gene (Cthe_0309), where amino acid His was replaced by Arg at position 402 ( Table S10 ). An indel mutation (deletion of Ala at position 192 causes a frameshift variant) occurred in...”
- Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells
Dumitrache, Scientific reports 2017 - “...DNA repair mechanism, the nucleotide excision repair system. Genes of the UvrABC excinuclease complex (Cthe_0311, Cthe_0309, Cthe_2737) and the UvrD helicase (Cthe_0206) had high transcription levels and up to 41-fold (e.g., UvrC) greater expression in PL cells. Proteases and peptidases Consistent with previous observations, protein damage...”
- Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum
Hebdon, Frontiers in microbiology 2021 - “...DNA repair proteins (Clo1313_0599 and Clo1313_2742), subunits A and B of an excinuclease (Clo1313_1916 and Clo1313_1918) and DNA gyrase B (Clo1313-1922). Three binding sites are also upstream of the LexA-encoding gene ( clo1313_1449 ), as was also the case for B. subtilis LexA ( Au et...”
LBA0688 excinuclease ABC subunit B from Lactobacillus acidophilus NCFM
57% identity, 95% coverage
lp_0772 excinuclease ABC, subunit B from Lactobacillus plantarum WCFS1
lp_0772 excinuclease ABC subunit UvrB from Lactiplantibacillus plantarum WCFS1
58% identity, 98% coverage
B1745_04725 excinuclease ABC subunit UvrB from Lactobacillus amylolyticus
56% identity, 97% coverage
BSU35170 excinuclease ABC subunit B from Bacillus subtilis subsp. subtilis str. 168
P37954 UvrABC system protein B from Bacillus subtilis (strain 168)
57% identity, 97% coverage
SPy1314 putative excinuclease ABC (subunit B) from Streptococcus pyogenes M1 GAS
58% identity, 98% coverage
TTE1971 Helicase subunit of the DNA excision repair complex from Thermoanaerobacter tengcongensis MB4
56% identity, 98% coverage
LSA0523 Excinuclease ABC, subunit B from Lactobacillus sakei subsp. sakei 23K
57% identity, 98% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...RuvA -0.5 LSA0382 dinP DNA-damage-inducible protein P -0.5 LSA0487 recA DNA recombinase A -0.8 -1.1 LSA0523 uvrB Excinuclease ABC, subunit B -0.7 -0.5 LSA0524 uvrA1 Excinuclease ABC, subunit A -1.2 -0.7 LSA0910 rexAN ATP-dependent exonuclease, subunit A (N-terminal fragment), authentic frameshift 0.6 LSA0911 rexAC ATP-dependent exonuclease,...”
UC7_RS15200 excinuclease ABC subunit UvrB from Enterococcus caccae ATCC BAA-1240
57% identity, 98% coverage
- Apigenin Impacts the Growth of the Gut Microbiota and Alters the Gene Expression of Enterococcus
Wang, Molecules (Basel, Switzerland) 2017 - “...Peptidoglycan synthesis UC7_RS12825 phenazine biosynthesis protein PhzF 2.0 Phenazine biosynthesis UC7_RS13565 hypothetical protein 2.0 Unknown UC7_RS15200 excinuclease ABC subunit B 2.0 DNA repair UC7_RS13270 neutral zinc metallopeptidase 1.9 Extracellular metabolism UC7_RS14315 magnesium-transporting ATPase 1.9 Magnesium transportation UC7_RS13560 diaminopimelate dehydrogenase 1.8 Lysine biosynthesis UC7_RS11285 hypothetical protein 1.8...”
SPD_1096 excinuclease ABC, B subunit from Streptococcus pneumoniae D39
57% identity, 98% coverage
SACOL0823 excinuclease ABC, B subunit from Staphylococcus aureus subsp. aureus COL
57% identity, 97% coverage
SAUSA300_0741 excinuclease ABC, B subunit from Staphylococcus aureus subsp. aureus USA300_FPR3757
57% identity, 97% coverage
- Staphylococcus aureus SOS response: Activation, impact, and drug targets
Cheng, mLife 2024 - “...(ATBC) 127 . uvrB /UvrB, a subunit of ABC excinuclease SAOUHSC_00779 a , SAOUHSC_00776 SA0713 SAUSA300_0741 NA uvrB /UvrB, a subunit of ABC excinuclease NA parC /ParC, the subunit A of DNA topoisomerase IV SAOUHSC_01352 SA1189 SAUSA300_1251 NA parC /ParC, the subunit A of DNA topoisomerase...”
- Novel Regulation of Alpha-Toxin and the Phenol-Soluble Modulins by Peptidyl-Prolyl cis/trans Isomerase Enzymes in Staphylococcus aureus
Keogh, Toxins 2019 - “...SAUSA300_0919 MurE 0.32 Cell envelope SAUSA300_1156 ProS 0.32 Protein synthesis SAUSA300_0753 0.30 Conserved hypothetical protein SAUSA300_0741 UvrB 0.29 DNA metabolism SAUSA300_0692 SaeQ 0.27 Conserved hypothetical protein SAUSA300_1523 0.27 Conserved hypothetical protein SAUSA300_2526 PyrD 0.26 Purines, pyrimidines, nucleosides, and nucleotides SAUSA300_0364 YchF 0.26 Unknown function SAUSA300_1144 TrmFO...”
SAB0711 exinuclease ABC subunit B from Staphylococcus aureus RF122
57% identity, 97% coverage
SA0713 excinuclease ABC subunit B from Staphylococcus aureus subsp. aureus N315
57% identity, 97% coverage
- Staphylococcus aureus SOS response: Activation, impact, and drug targets
Cheng, mLife 2024 - “...2[5(methylamino)1,3,4thiadiazol2yl]3Hbenzo[f]chromen3one (ATBC) 127 . uvrB /UvrB, a subunit of ABC excinuclease SAOUHSC_00779 a , SAOUHSC_00776 SA0713 SAUSA300_0741 NA uvrB /UvrB, a subunit of ABC excinuclease NA parC /ParC, the subunit A of DNA topoisomerase IV SAOUHSC_01352 SA1189 SAUSA300_1251 NA parC /ParC, the subunit A of DNA...”
- Regulation of hemolysin expression and virulence of Staphylococcus aureus by a serine/threonine kinase and phosphatase
Burnside, PloS one 2010 - “...geh Lipase precursor, interruption - disrupted reading frame 6 MH ksgA Dimethyladenosine transferase 1 MH SA0713 Hypothetical protein - not conserved 1 MH fruB 1-phosphofructokinase - Glycolysis/gluconeogenesis 1 MH SA1021 Multidrug-efflux transporter, putative 5 MH purL Phosphoribosylformylglycinamidine synthase II 1 MH SA1096 TRK system potassium uptake...”
OB2488 excinuclease ABC subunit B from Oceanobacillus iheyensis HTE831
58% identity, 97% coverage
BC5168 Excinuclease ABC subunit B from Bacillus cereus ATCC 14579
58% identity, 97% coverage
Q8CPZ0 UvrABC system protein B from Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)
57% identity, 97% coverage
lmo2489 excinuclease ABC (subunit B) from Listeria monocytogenes EGD-e
Q8Y4F5 UvrABC system protein B from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
56% identity, 97% coverage
- Listeria monocytogenes utilizes the ClpP1/2 proteolytic machinery for fine-tuned substrate degradation at elevated temperatures
Balogh, RSC chemical biology 2022 - “...addA ) Q8Y511 ATP-dependent helicase/nuclease subunit A lmo2352 Q8Y4T0 Putative LysR family transcriptional regulator a lmo2489 ( uvrB ) Q8Y4F5 UvrABC system protein B, excision nuclease lmo2552 ( murZ ) Q8Y4A2 UDP- N -acetylglucosamine 1-carboxyvinyltransferase 2 lmo2712 Q8Y3W7 Putative gluconate kinase (Pentose phosphate pathway) a a...”
- Listeria monocytogenes Relies on the Heme-Regulated Transporter hrtAB to Resist Heme Toxicity and Uses Heme as a Signal to Induce Transcription of lmo1634, Encoding Listeria Adhesion Protein
Dos, Frontiers in microbiology 2018 - “...and genes encoding the cell division inhibitor YneA ( lmo1303 ), the excinuclease UvrBA ( lmo2489 - lmo2488 ), and the translesion DNA polymerases DinB ( lmo1975 ) and UmuD ( lmo2675 ) ( van der Veen et al., 2010 ). These findings clearly demonstrate that...”
- A detailed view of the intracellular transcriptome of Listeria monocytogenes in murine macrophages using RNA-seq
Schultze, Frontiers in microbiology 2015 - “...repair, e.g., recA ( lmo1398 ) and the excinucleases lmo2050 , lmo2488 ( uvrA )/ lmo2489 ( uvrB ) were differentially expressed during intracellular growth conditions. Antisense Transcription is Altered during Intracellular Growth A benefit of strand-specific RNA-seq studies is the ability to detect antisense transcripts...”
- Transcriptomic and phenotypic responses of Listeria monocytogenes strains possessing different growth efficiencies under acidic conditions
Bowman, Applied and environmental microbiology 2010 - “...2017 by University of California, Berkeley lmo2488, lmo2489 (uvrAB) lmo2504-lmo2508 pH 5.0 SigB lmo2411-lmo2415 lmo2424 (trxA), lmo2426 lmo2478 (trxB)...”
- Genomic and proteomic analysis of the Alkali-Tolerance Response (AlTR) in Listeria monocytogenes 10403S
Giotis, BMC microbiology 2008 - “...regulator, TetR family lmo1398 recA 3.12 0.001 DNA replication, recombination, and repair Recombination protein recA lmo2489 uvrB 3.42 0.026 Excinuclease ABC (subunit B) lmo2676 NA 3.48 0.022 Similar to UV-damage repair protein lmo2717 cydB -3.3 0.004 Electron transport Highly similar to cytochrome D ubiquinol oxidase subunit...”
- Stress Adaptation Responses of a Listeria monocytogenes 1/2a Strain via Proteome Profiling
D'Onofrio, Foods (Basel, Switzerland) 2023 - “...C2, C3, C4 uvrA Q8Y4F6 UvrABC system protein A 956 C1, C2, C3, C4 uvrB Q8Y4F5 UvrABC system protein A 658 C1, C2, C3, C4 ruvA Q8Y6Z7 Holliday junction ATP-dependent DNA helicase RuvA 201 C1, C2, C3 recF Q8YAV8 DNA replication and repair protein RecF 370...”
- Listeria monocytogenes utilizes the ClpP1/2 proteolytic machinery for fine-tuned substrate degradation at elevated temperatures
Balogh, RSC chemical biology 2022 - “...helicase/nuclease subunit A lmo2352 Q8Y4T0 Putative LysR family transcriptional regulator a lmo2489 ( uvrB ) Q8Y4F5 UvrABC system protein B, excision nuclease lmo2552 ( murZ ) Q8Y4A2 UDP- N -acetylglucosamine 1-carboxyvinyltransferase 2 lmo2712 Q8Y3W7 Putative gluconate kinase (Pentose phosphate pathway) a a The functions of not...”
Q71WT9 UvrABC system protein B from Listeria monocytogenes serotype 4b (strain F2365)
56% identity, 97% coverage
- Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach
Srivastava, International journal of peptide research and therapeutics 2021 - “...1.317 Non-allergen 20 Q720T3 0.947 Non-allergen 21 Q722V6 0.505 Non-allergen 22 Q71YI4 0.578 Non-allergen 23 Q71WT9 0.64 Non-allergen 24 Q720J1 1.004 Non-allergen 25 Q71ZD3 0.651 Non-allergen 26 Q71ZZ0 1.285 Non-allergen 27 Q71XV7 1.047 Non-allergen 28 Q71YD8 1.391 Non-allergen 29 Q71XG0 0.986 Non-allergen 30 Q724M5 0.647 Non-allergen...”
- “...DRB1_0701 SGETLSVKV 325.2 2.4375 Antigen DRB1_1301 LRVTPGIRL 32.6 2.4375 Antigen DRB1_1301 FLRVTPGIR 65.4 1.2425 Antigen Q71WT9 DRB1_0701 VSLRVGMEI 216.6 1.6096 Antigen DRB1_1301 IGETERRRK 37.9 1.3502 Antigen Q720J1 DRB1_0701 IEVTPDYLM 299.3 1.7114 Antigen Q71ZZ0 DRB1_1301 THLKTRPKK 20.2 1.3476 Antigen DRB1_1301 LRTHLKTRP 22.8 1.2793 Antigen Q71XV7 DRB1_0101 FLYVVVYSL...”
CAC0502 Excinuclease ABC subunit B (helicase subunit of the DNA excision repair complex) from Clostridium acetobutylicum ATCC 824
56% identity, 98% coverage
- The role of PerR in O2-affected gene expression of Clostridium acetobutylicum
Hillmann, Journal of bacteriology 2009 - “...CAC1993 CAC1994 CAC1995 CAC1996 Nucleic acid repair/metabolism CAC0502 CAC0503 CAC1047 CAC1390 CAC1391 CAC1392 CAC1393 CAC1394 CAC1395 CAC1655 CAC1815 CAC1856...”
- “...to CAC1032, CAC1988 to CAC1990, CAC1991 to CAC1996, CAC0502 to CAC0503, CAC1391 to CAC1395, CAC3276 and CAC3277, CAC3288 to CAC3292, CAC3624 and CAC3625,...”
CDR20291_3234 excinuclease ABC subunit UvrB from Clostridioides difficile R20291
CD3412 excinuclease ABC subunit B from Clostridium difficile 630
56% identity, 98% coverage
- The LexA regulated genes of the Clostridium difficile
Walter, BMC microbiology 2014 - “...GAAC....GTTT 65 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_3234 uvrB Excinuclease ABC subunit B GAAC....GTTC 30 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_0487 rusA Putative RusA-like endodeoxyribonuclease GAAC....GTTT 122 1 4 1...”
- Proteomic analysis of a NAP1 Clostridium difficile clinical isolate resistant to metronidazole
Chong, PloS one 2014 - “...2.00.2 2.10.1 2.10.1 heat-inducible transcription repressor CDR20291_3233 uvrA 1.20.1 1.10.0 1.50.1 excinuclease ABC subunit A CDR20291_3234 uvrB 1.30.1 1.30.1 1.60.1 excinuclease ABC subunit B Metronidazole-treated strains (Met) were compared against respective non-treated strains (c) strains. Fold-change values of selected proteins, with p<0.05, (with Benjamini-Hochberg correction) are...”
- Redefining the Clostridioides difficile σB Regulon: σB Activates Genes Involved in Detoxifying Radicals That Can Result from the Exposure to Antimicrobials and Hydrogen Peroxide
Boekhoud, mSphere 2020 - “...In vitro runoff transcriptions demonstrate direction activation of P cd0350 , P cd2963 , P cd3412 , and P cd3605 by B . Gene expression can directly or indirectly be influenced by B , and to date no attempts have been made to discriminate these possibilities...”
- “...putative hydrolase involved in oxidative stress; Table2 ), cd2963 (encoding an l , d -transpeptidase), cd3412 (encoding UvrB, involved in nucleotide excision repair), cd3605 (encoding a ferredoxin), and cd3614 (encoding a hypothetical protein involved in oxidative stress; Table2 ) were selected on the basis of differential...”
- Genome Location Dictates the Transcriptional Response to PolC Inhibition in Clostridium difficile
van, Antimicrobial agents and chemotherapy 2019 - “...observed is likely independent of B. Finally, CD3412 (uvrB, encoding a subunit of an excinuclease) shows reduced transcriptional upregulation in ACX-362Etreated...”
- Comparative transcriptional analysis of clinically relevant heat stress response in Clostridium difficile strain 630
Ternan, PloS one 2012 - “...included a regulatory endoribonuclease (CD3187, tdcF ), ribonuclease PH (CD3308), an excinuclease ABC subunit B (CD3412, uvrB ), endonuclease III and RNA methylase (CD0565, CD0566), and a putative ATP-dependent RNA helicase (CD0761). These data suggest that overall there is a significant change in the fate of...”
2d7dA / P37954 Structural insights into the cryptic DNA dependent atp-ase activity of uvrb (see paper)
56% identity, 97% coverage
- Ligands: dna; adenosine-5'-diphosphate (2d7dA)
CDR20291_3234 excinuclease ABC subunit B from Clostridium difficile R20291
56% identity, 98% coverage
- The LexA regulated genes of the Clostridium difficile
Walter, BMC microbiology 2014 - “...GAAC....GTTT 65 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_3234 uvrB Excinuclease ABC subunit B GAAC....GTTC 30 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_0487 rusA Putative RusA-like endodeoxyribonuclease GAAC....GTTT 122 1 4 1...”
- Proteomic analysis of a NAP1 Clostridium difficile clinical isolate resistant to metronidazole
Chong, PloS one 2014 - “...2.00.2 2.10.1 2.10.1 heat-inducible transcription repressor CDR20291_3233 uvrA 1.20.1 1.10.0 1.50.1 excinuclease ABC subunit A CDR20291_3234 uvrB 1.30.1 1.30.1 1.60.1 excinuclease ABC subunit B Metronidazole-treated strains (Met) were compared against respective non-treated strains (c) strains. Fold-change values of selected proteins, with p<0.05, (with Benjamini-Hochberg correction) are...”
6o8eA / P56981 Crystal structure of uvrb bound to duplex DNA with adp (see paper)
61% identity, 89% coverage
- Ligands: dna; adenosine-5'-diphosphate (6o8eA)
llmg_0534 UvrABC system protein B from Lactococcus lactis subsp. cremoris MG1363
54% identity, 94% coverage
LLKF_0540 excinuclease ABC subunit B from Lactococcus lactis subsp. lactis KF147
54% identity, 94% coverage
- Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
Dijkstra, PloS one 2016 - “...positive 5.6 LLKF_1812 yraD hypothetical protein positive 1.1 LLKF_1857 ABC transporter ATP-binding protein negative 0.3 LLKF_0540 uvrB excinuclease ABC subunit B positive 2.4 LLKF_1295 hypothetical protein negative 0.5 LLKF_1966 sufC SUF system FeS cluster assembly protein ATP-dependent transporter SufC positive 11.5 LLKF_0052 cysD O-acetyl-L-homoserine sulfhydrolase/O-acetyl-L-serine sulfhydrolase...”
LIC12941 nucleotide excision repair subunit B from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
54% identity, 98% coverage
MXAN_2632 excinuclease ABC, B subunit from Myxococcus xanthus DK 1622
53% identity, 93% coverage
Hore_16230 excinuclease ABC, B subunit from Halothermothrix orenii H 168
54% identity, 95% coverage
HVO_0029 excinuclease ABC subunit B from Haloferax volcanii DS2
52% identity, 93% coverage
- Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair
Wörtz, Frontiers in microbiology 2022 - “...Annotation/Gene name Peptides/Unique spectra counts Replication and repair HVO_0393 UvrABC system protein A, uvrA 73 HVO_0029 UvrABC system protein B, uvrB 32 HVO_0415 repair helicase UvrD, uvrD 38 HVO_0349 DNA-directed RNA polymerase subunit A, rpoA1 56 HVO_0347 DNA-directed RNA polymerase subunit B, rpoB2 44 HVO_0858 DNA-directed...”
- CdrS Is a Global Transcriptional Regulator Influencing Cell Division in Haloferax volcanii
Liao, mBio 2021 - “...Conserved hypothetical protein, containing a signal peptide and a transmembrane domain 42 Between HVO_0027 and HVO_0029 on plus strand Gene not annotated, binding site overlaps with TSS 0 Between HVO_1059 and HVO_1063 on minus strand No TSS in this region NA Between HVO_1182 and HVO_1185 on...”
- Haloferax volcanii-a model archaeon for studying DNA replication and repair
Pérez-Arnaiz, Open biology 2020 - “...described. H. volcanii carries homologues of UvrABC proteins, encoded by genes uvrA (HVO_0393) , uvrB (HVO_0029) and uvrC (HVO_3006) ( figure3 and table1 ) [ 35 ]. The bacterial NER genes are non-essential in H. volcanii and deletion mutants in uvrABC show enhanced sensitivity to UV...”
- “...excision repair. In H. volcanii, bulky DNA adducts (red) are recognized by UvrA (HVO_0393). UvrB (HVO_0029) initiates DNA unwinding around the damage site through its helicase activity. Incisions 5 and 3 to the damaged bases are carried out by the endonuclease UvrC (HVO_3006). Unwinding of the...”
OCU_29740 excinuclease ABC subunit UvrB from Mycobacterium intracellulare ATCC 13950
52% identity, 90% coverage
- Prominent transcriptomic changes in Mycobacterium intracellulare under acidic and oxidative stress
Park, BMC genomics 2024 - “...6.04 OCU_27960 hypothetical protein Conserved hypotheticals 2.34 5.24 OCU_29330 hypothetical protein Conserved hypotheticals 3.10 5.68 OCU_29740 excinuclease ABC subunit B Information pathways 3.04 2.71 OCU_32850 13e12 repeat-containing protein Insertion seqs and phages 4.06 5.55 OCU_34460 LysM domain-containing protein Unknown 2.08 3.40 OCU_36850 hypothetical protein Conserved hypotheticals...”
- “...1.42 3.09 OCU_41260 nei2 (endonuclease) DNA repair 2.26 2.38 OCU_12600 DNA-3-methyladenine glycosylase I 1.56 2.21 OCU_29740 uvrB 3.03 2.71 OCU_39940 uvrD2 1.54 2.22 OCU_39980 Probable ATP-dependent DNA helicase 4.06 5.36 OCU_34590 recA 1.24 2.28 OCU_33030 ruvC -1.38 2.25 OCU_42300 groEL1 Heat shock response 3.47 3.07 OCU_45770...”
DVU1605 excinuclease ABC, B subunit from Desulfovibrio vulgaris Hildenborough
50% identity, 96% coverage
RM25_1449 excinuclease ABC subunit UvrB from Propionibacterium freudenreichii subsp. freudenreichii
51% identity, 95% coverage
SCO1966 excinuclease ABC subunit B from Streptomyces coelicolor A3(2)
51% identity, 91% coverage
- Transcriptomic analysis of liquid non-sporulating Streptomyces coelicolor cultures demonstrates the existence of a complex differentiation comparable to that occurring in solid sporulating cultures
Yagüe, PloS one 2014 - “...protein L4 0.4 2.1 SCO1631 Helicase 1.2 0.8 SCO4712 50S ribosomal protein L14 0.7 1.4 SCO1966 Excinuclease ABC subunit B 1.9 0.1 SCO4734 50S ribosomal protein L13 0.6 1.8 SCO2003 DNA polymerase I 1.8 0.2 SCO5494 NAD-dependent DNA ligase ligA 2.2 0.9 SCO2036 Tryptophan synthase subunit...”
- Pre-sporulation stages of Streptomyces differentiation: state-of-the-art and future perspectives
Yagüe, FEMS microbiology letters 2013 - “...SCO0755 SCO1850 SCO3351 SCO4508 SCO5580 SCO6635 SCP1.110 SCO0756 SCO1852 SCO3369 SCO4585 SCO5603 SCO6677 SCP1.136 SCO0824 SCO1966 SCO3370 SCO4620 SCO5633 SCO6683 SCP1.169 SCO1144 SCO2000 SCO3372 SCO4685 SCO5648 SCO6684 SCP1.205c SCO1147 SCO2257 SCO3418 SCO4797 SCO5668 SCO6719 SCP1.216Ac SCO1148 SCO2259 SCO3453 SCO4803 SCO5734 SCO6720 SCP1.290c SCO1152 SCO2324 SCO3526 SCO4909...”
- Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
Hsiao, Antonie van Leeuwenhoek 2008 - “...DNA glycosylase 0.20485 0.07755 0.083499 0.2824 SCO1827 putative DNA polymerase III 0.559715 0.711265 0.512873 0.343849 SCO1966 ABC excision nuclease subunit B 0.047382 0.06896 1.085903 0.05934 SCO1969 putative DNA-methyltransferase 0.19025 0.12184 0.143367 0.56545 SCO2003 DNA polymerase I 1.172176 0.188493 0.498126 0.201411 SCO2468 DNA primase 0.82715 0.520552 1.25613...”
- Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor
Studholme, BMC microbiology 2004 - “...3, additional file 2 [table3.pdf]). These included genes predicted to encode an ABC excision nuclease (SCO1966), DNA helicase (SCO5761), DNA polymerase (SCO3541 and SCO6084), a DNA gyrase (SCO5836) and a putative primosomal protein (SCO1475). A sequence motif represented by matrix 1744 was found in intergenic regions...”
- “...other genes implicated in nucleic acid metabolism including ABC excision nuclease subunits (SCO1953, SCO1958 and SCO1966), a helicase (SCO6262) and uracil-DNA glycosylase (SCO1343). On further examination of the matrix 1744 match site upstream of S. coelicolor recA , it became apparent that this site overlaps the...”
HI1247 excinuclease ABC, subunit B (uvrB) from Haemophilus influenzae Rd KW20
53% identity, 96% coverage
sll0459 excinuclease ABC subunit B from Synechocystis sp. PCC 6803
52% identity, 97% coverage
PP_1974 excinuclease ABC subunit UvrB from Pseudomonas putida KT2440
PP1974 excinuclease ABC, B subunit from Pseudomonas putida KT2440
51% identity, 97% coverage
- Physiological responses of Pseudomonas putida to formaldehyde during detoxification
Roca, Microbial biotechnology 2008 - “...2.02 1 Y PP_1639 SprT protein, putative 4.91 3 PP_1640 Conserved hypothetical protein 3.23 7 PP_1974 Excinuclease ABC, B subunit uvrB 2.17 1 Y PP_1982 Heatshock protein IbpA ibpA 8.25 2 PP_2302 ATPdependent protease La lon2 2.12 2 PP_2426 d isomer specific 2hydroxy acid dehydrogenase family...”
- “...isomer specific 2hydroxy acid dehydrogenase No growth PP_1617 Esterase, putative 8.7 PP_1629 RecA protein 2.8 PP_1974 Uvr B 2.2 PP_2426 d isomer specific 2hydroxy acid dehydrogenase 9.5 PP_2647 Major facilitator family transporter 8.8 PP_2648 Universal stress protein family 8.2 PP_2695 Transcriptional regulator LysR family 2.5 PP_3425...”
- Cohabitation of two different lexA regulons in Pseudomonas putida
Abella, Journal of bacteriology 2007 - “...PP_2142 (sulA) PP_4616 (yebG) PP_4729 (recN) PP_1203 (dinP) PP_1974 (uvrB) PP_5352 (uvrD) PP_2109 (hp)d PP_2452 (hp) PP_2451 (endA) PP_4019 (topB) PP_5393 (hp)...”
- Physiological responses of Pseudomonas putida to formaldehyde during detoxification
Roca, Microbial biotechnology 2008 - “...esterase Duque etal. (2007a ) PRCC recA (PP1629) RecA protein Duque etal. (2007a ) PRCC (PP1974) Excinuclease ABC, B subunit Duque etal. (2007a ) PRCC (PP2426) d isomer specific 2hydroxy acid dehydrogenase Duque etal. (2007a ) PRCC (PP2646) Conserved hypothetical protein Duque etal. (2007a ) PRCC...”
- “...of enzymes to be induced in response to formaldehyde. Repair and recombination systems, including uvrB (PP1974), uvrC (PP3254) and recA (PP1629), were induced more than twofold in response to sublethal HCOH concentrations ( Table2 ). Table 2 Genes upregulated in P. putida KT2440 (pWW0) 20min after...”
FTN_1176 excinuclease ABC, subunit B from Francisella tularensis subsp. novicida U112
50% identity, 98% coverage
- Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance
Felix, Scientific reports 2021 - “...in ldcF cadA FTN_0504 Lysine decarboxylase 6.135487177 6.5901E12 udp FTN_0652 Uridine phosphorylase 2.442473795 0.000355044 uvrB FTN_1176 Excinuclease ABC subunit B 2.359970258 1.5872E07 yhiP FTN_0885 Proton-dependent oligopeptide transporter (POT) family protein, di- or tripeptide:H+symporter 2.233739832 1.28816E08 FTN_1453 Two-component regulator, sensor histidine kinase 2.225623368 0.000269144 FTN_0705 Abortive infection...”
- “...base excision repair pathways (FTN_1486, Ung and FTN_0838, XthA), one involved in nucleotide excision repair (FTN_1176, UvrB), and two involved in homologous recombination pathways (FTN_1025, RuvA and FTN_1357, RecB). Two of these proteins (UvrB and Ung), which displayed reduced expression levels in ldcF , are enzymes...”
- Francisella-arthropod vector interaction and its role in patho-adaptation to infect mammals
Akimana, Frontiers in microbiology 2011 - “...xseA FTN_1170 Conserved protein of unknown function FTN_1171 Conserved hypothetical lipoprotein FTN_1174 Glutamate racemase murI FTN_1176 Excinuclease ABC, subunit B uvrB FTN_1179 Transcriptional regulator, LysR family FTN_1186 Metallopeptidase family M13 protein, pseudogene FTN_1196 Conserved hypothetical UPF0133 protein ybaB FTN_1198 Guanosine-3,5-bis(diphosphate) 3-pyrophosphohydrolase/(p)ppGpp synthase spoT FTN_1214 Glycosyl transferase,...”
- Exploitation of host cell biology and evasion of immunity by francisella tularensis
Asare, Frontiers in microbiology 2010 - “...ruvC Holliday junction endodeoxyribonuclease FTN_1073 DNA/RNA endonuclease G FTN_1154 Type I restrictionmodification system, subunit S FTN_1176 uvrB Excinuclease ABC, subunit B FTN_1197 recR RecFOR complex, RecR component FTN_1293 rnhB Ribonuclease HII FTN_1357 recB ATP-dependent exoDNase_subunit FTN_1487 Restriction endonuclease TRANSCRIPTION/TRANSLATION FTL_1542 migR Macrophage intracellular growth regulator FTL_1606...”
- Molecular complexity orchestrates modulation of phagosome biogenesis and escape to the cytosol of macrophages by Francisella tularensis
Asare, Environmental microbiology 2010 - “...(restriction) 4 tnfn1_pw060510p04q179 FTN_0838 xthA exodeoxyribonuclease III 3 tnfn1_pw060419p04q152 FTN_1017 pseudogene: DNA-3-methyladenine glycosylase 5 tnfn1_pw060323p04q111 FTN_1176 uvrB excinuclease ABC, subunit B 2 Transferases tnfn1_pw060420p02q180 FTN_0483 bifunctional NMN adenylyltransferase/Nudix hydrolase 7 tnfn1_pw060510p01q158 FTN_0988 prmA 50S ribosomal protein L11, methyltransferase 7 tnfn1_pw060510p02q144 FTN_1234 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase 6 Transcription/Translation...”
- Molecular bases of proliferation of Francisella tularensis in arthropod vectors
Asare, Environmental microbiology 2010 - “...(restriction) 4 tnfn1_pw060510p04q179 FTN_0838 xthA exodeoxyribonuclease III 3 tnfn1_pw060419p04q152 FTN_1017 pseudogene: DNA-3-methyladenine glycosylase 5 tnfn1_pw060323p04q111 FTN_1176 uvrB excinuclease ABC, subunit B 2 Transferases tnfn1_pw060420p02q180 FTN_0483 bifunctional NMN adenylyltransferase/Nudix hydrolase 7 tnfn1_pw060510p01q158 FTN_0988 prmA 50S ribosomal protein L11, methyltransferase 7 tnfn1_pw060510p02q144 FTN_1234 queA S-adenosylmethionine:tRNA ribosyltransferase- isomerase 6...”
6o8hA / P56981 Crystal structure of uvrb mutant bound to duplex DNA (see paper)
57% identity, 89% coverage
FN0224 Excinuclease ABC subunit B from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
53% identity, 97% coverage
- Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
Hendrickson, MicrobiologyOpen 2014 - “...Unchanged 7 4 6 7 8 5 1 Covers: FN0019, FN0047, FN0065, FN0117, FN0157, FN0158, FN0224, FN0268, FN0297, FN0374, FN0462, FN0524, FN0547, FN0592, FN0622, FN0693, FN0705, FN0962, FN1103, FN1149, FN1217, FN1226, FN1304, FN1581, FN1660, FN1717, FN1864, FN2018. 2 Covers: FN1088, FN1123, FN1163, FN1983, FN1984, FN2007, FN2067....”
BCG_1671 Excinuclease ABC subunit B uvrB from Mycobacterium bovis BCG str. Pasteur 1173P2
51% identity, 93% coverage
Rv1633 excinuclease ABC subunit B from Mycobacterium tuberculosis H37Rv
51% identity, 93% coverage
- SNPs in genes related to the repair of damage to DNA in clinical isolates of M. tuberculosis: A transversal and longitudinal approach
Pérez-Martínez, PloS one 2024 - “...24.4 11 16.4 0.012 Rv1420 UvrC 1594594 Gly185Ser 3 13.6 0 0.0 3 4.5 0.032 Rv1633 UvrB 1837613 Asp180Gly 4 18.2 0 0.0 4 6.0 0.010 Rv2464c Nei1 ** - 0 0.0 15 33.3 15 22.4 0.001 Rv2464c Nei1 2766941 Pro242Leu 0 0.0 14 31.1 14...”
- GWAS and functional studies suggest a role for altered DNA repair in the evolution of drug resistance in Mycobacterium tuberculosis
Naz, eLife 2023 - “...the NER pathway upon DNA damage. UvrB, a 698 aa long DNA helicase encoded by rv1633, plays a pivotal role in the NER pathway by interacting with the UvrA and UvrC ( Figure 3d ; Kurthkoti et al., 2008 ). UvrB harbors N and C-terminal helicase...”
- Identification of Mycobacterium tuberculosis Antigens with Vaccine Potential Using a Machine Learning-Based Reverse Vaccinology Approach
Teahan, Vaccines 2021 - “...FadD19 (Rv3515c) DNA Repair RecA (Rv2737c), HtpG (Rv2299c), UvrA (Rv1638), LigD (Rv0938), RecG (Rv2973c), UvrB (Rv1633) Interaction with host immune system FadE5 (Rv0244c), Mce1A (Rv0169), probable aldehyde dehydrogenase (Rv0458), CaeA (Rv2224c), LprA (Rv1270c), FadD30 (Rv0404), EccCa1 (Rv3870), Icl1 (Rv0467), PknH (Rv1266c), MmpL12 (Rv1522c), UvrB (Rv1633), EccB1...”
- “...oxidative stress Mpa (Rv2115c), FtsH (Rv3610c), HtpG (Rv2299c), Tgs4 (Rv3088), Mpt53 (Rv2878c), AccD4 (Rv3799c), UvrB (Rv1633), CysN (Rv1286) Response to starvation halimadienyl diphosphate synthase (Rv3377c), PknD (Rv0931c), CysN (Rv1286) vaccines-09-01098-t003_Table 3 Table 3 Final selection of prospective novel MTB vaccine candidates with sufficiently high Vaxign-ML protegenicity...”
- The unfoldase ClpC1 of Mycobacterium tuberculosis regulates the expression of a distinct subset of proteins having intrinsically disordered termini
Lunge, The Journal of biological chemistry 2020 (secret) - The current state of animal models and genomic approaches towards identifying and validating molecular determinants of Mycobacterium tuberculosis infection and tuberculosis disease
Bucsan, Pathogens and disease 2019 - “...repair DNA damage also have significant defects for growth in the murine model. For example, Rv1633, which encodes for UvrB, forms a critical part of the nucleotide excision repair machinery (Darwin etal . 2003 ). Interestingly, there was a significant defect in the killing of mice...”
- Understanding HIV-Mycobacteria synergism through comparative proteomics of intra-phagosomal mycobacteria during mono- and HIV co-infection
Ganji, Scientific reports 2016 - “...78 information pathways Probable excinuclease ABC (subunit B - helicase) UvrB/Involved in nucleotide excision repair. Rv1633 33 BCG1667 4.78 98.4 information pathways Probable DNA polymerase I PolA/Involved in post-incision events. Rv1629 34 BCG3633c 5.96 33.58 intermediary metabolism and respiration 3,4-DHSA dioxygenase/Catalyzes the extradiol cleavage of 3,4-dihydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione...”
- Global transcriptional profiling of longitudinal clinical isolates of Mycobacterium tuberculosis exhibiting rapid accumulation of drug resistance
Chatterjee, PloS one 2013 - “...(4), Rv2937 (2) Rv0783c (6) DNA repair Rv3014c (6),Rv2737c (6),Rv1633 (6),Rv0630c (7) Rv2736c (2),Rv2720 (5) Rv1633 (7), Rv1638 (12.5),Rv3715c (8), Rv0630c (7),Rv3014c (12), Rv0005 (15) Rv0003 (15), Rv0630c (24), Rv2592c (5) ImmuneFunction Rv3881c (3) TBMG_00064 (2),Rv3891c (2.5) Rv2031c (6) Unknown Rv0756c (2), Rv2137c (2), Rv1871c (3)...”
- Cyclic AMP-dependent protein lysine acylation in mycobacteria regulates fatty acid and propionate metabolism
Nambi, The Journal of biological chemistry 2013 - “...Rv1007c is predicted to be a methionyl tRNA synthetase, Rv1633 is an enzyme involved in nucleotide excision repair, and Rv0640 is a 50 S ribosomal protein, L11....”
- “...FadD13 (Rv3089) were acetylated in a cAMP-dependent manner, Rv1633 and Rv1007c were not acetylated by KATmt. Therefore, we were able to identify KATmt...”
- More
BAB1_1530 DEAD/DEAH box helicase:Helicase, C-terminal:ATP/GTP-binding site motif A (P-loop):UvrB/UvrC protein:Excinuclease ABC, B subunit from Brucella melitensis biovar Abortus 2308
BruAb1_1504 UvrB, excinuclease ABC, B subunit from Brucella abortus biovar 1 str. 9-941
51% identity, 69% coverage
- Intracellular adaptation of Brucella abortus
Lamontagne, Journal of proteome research 2009 - “...mismatches. Two proteins involved in DNA relaxation, the TldD peptidase (BAB1_0490) and the ABC UvrB (BAB1_1530) were also overexpressed early after infection, and dropped to pre-infection levels afterwards. Furthermore, expression of a negative regulator of septum formation, MinD (BAB2_0883) 39 , 40 was reduced early in...”
- “...BAB1_2174 Lipid metabolism FabA 77 BAB2_0975 Lipid metabolism FabC 78 BAB2_1008 Cell division MepA 79 BAB1_1530 Cell division UvrB 80 BAB2_0475 Cell division XseA 81 BAB1_0640 Cell division PleC 82 BAB1_0075 Unknown Conserved 83 BAB1_1612 Unknown Conserved 84 BAB1_0863 Unknown Conserved 85 BAB1_0771 Unknown Conserved 86...”
- Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes
Crasta, PloS one 2008 - “...dehydrogenase family protein 12 2 BAbS19_I18830 1 3 1 FS -_intimin/invasin family protein 13 3 BruAb1_1504 1 1 D->N(yes) L_excinuclease ABC subunit B 14 3 BruAb1_0772 1 1 Q->R(yes) O_arginyl-tRNA-protein transferase 15 3 BruAb1_1114 1 1 E->Q(yes) O_ATP-dependent protease ATP-binding subunit 16 3 BruAb1_0208 1 1...”
- “...Table 7 ) that resulted in the net charge change included excinuclease ABC subunit B (BruAb1_1504), ABC transporter, periplasmic substrate-binding protein (BruAb1_0208), IolC myo-catabolism protein (BruAb2_0517), outer membrane autotransporter (BAbS19_I18870), CTP synthetase (BruAb1_1140), Omp2b, porin (BruAb1_0657), and three hypothetical proteins. We also identified 9 OCDs that...”
P9WFC7 DNA 3'-5' helicase (EC 5.6.2.4) from Mycobacterium tuberculosis (see paper)
51% identity, 90% coverage
APY09_08030 excinuclease ABC subunit UvrB from Schaalia odontolytica
51% identity, 95% coverage
- Ultrasmall epibiont <i>Nanosynbacter lyticus</i> strain TM7x and host bacteria transcriptional activity after initial host parasitism
Hendrickson, Journal of oral microbiology 2024 - “...(APY09_07805), clpB (APY09_01465), clpX (APY09_06360), recG (APY09_08820), recO (APY09_06005), exonuclease ABC subunits B and C (APY09_08030, APY09_07980), DNA polymerase I (APY09_08050), DNA ligase A (APY09_09965), and a heat shock protein (APY09_01500). In the previous study, we also saw chaperones with lower expression compared to XH001n [...”
lpg0072 excinuclease ABC subunit B from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
50% identity, 98% coverage
- Identification of Genes Required for Long-Term Survival of Legionella pneumophila in Water
Aurass, mSphere 2023 - “...lpg0102 fabF 16 NE 4 NE 3-Oxoacyl-(acyl carrier protein) synthase DNA replication, repair, and recombination lpg0072 uvrB 37 NE 10 E Excinuclease ABC subunit B lpg1812 lpg1812 25 NE 15 E UvrD/Rep helicase lpg2645 uvrC 38 NE 12 U Excinuclease ABC subunit C Virulence lpg2639 enhC...”
- “...25 ), in which three of our candidate genes, ykuD ( lpg1697 ), uvrB ( lpg0072 ), and Lon protease gene ( lpg1859 ) are activated, while two, i.e., ppsA and enhC , are repressed by RpoS. Our study suggests that the absence of either of...”
- bdhA-patD operon as a virulence determinant, revealed by a novel large-scale approach for identification of Legionella pneumophila mutants defective for amoeba infection
Aurass, Applied and environmental microbiology 2009 - “...screena Closest homolog (organism) E value lpg0026 lpg0072 lpg0129 lpg0166 lpg0200 lpg0230 lpg0233 lpg0237 lpg0243 lpg0265 lpg0277 lpg0493 lpg0515 lpg0549...”
lpp0086 excinuclease ABC subunit B from Legionella pneumophila str. Paris
50% identity, 98% coverage
- Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease
Gomez-Valero, Genome biology 2014 - “...data sets were created: one based on the concatenated alignment of 29 housekeeping genes ( lpp0086 ( uvrB ), lpp0152 ( pgk ), lpp0419 ( rpoA ), lpp0467 ( ffh ), lpp0575 ( serS ), lpp0749 ( pros ), lpp0791 ( glyA ), lpp1020 ( lig...”
- Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes
Gomez-Valero, BMC genomics 2011 - “...reconstruction Gene Name Product Label a Function Length (nts) a uvrB Excinuclease ABC, subunit B lpp0086 DNA replication, recombination, and repair 1992 pgk Phosphoglycerate kinase lpp0152 Glycolysis/gluconeogenesis 1191 rpoA RNA polymerase, alpha subunit lpp0419 Transcription 993 ffh Signal recognition particle protein, GTPase lpp0467 Transport and binding...”
Krad_2942 excinuclease ABC subunit UvrB from Kineococcus radiotolerans SRS30216 = ATCC BAA-149
49% identity, 93% coverage
PA3138 excinuclease ABC subunit B from Pseudomonas aeruginosa PAO1
50% identity, 97% coverage
CV3152 excinuclease ABC subunit B from Chromobacterium violaceum ATCC 12472
50% identity, 97% coverage
cg1550 excinuclease ABC subunit B from Corynebacterium glutamicum ATCC 13032
51% identity, 90% coverage
rrnAC2996 UvrABC system protein B from Haloarcula marismortui ATCC 43049
50% identity, 95% coverage
BCAL2302 excinuclease ABC subunit B from Burkholderia cenocepacia J2315
51% identity, 93% coverage
BBMN68_740 excinuclease ABC subunit UvrB from Bifidobacterium longum subsp. longum BBMN68
52% identity, 94% coverage
UvrB / b0779 excision nuclease subunit B from Escherichia coli K-12 substr. MG1655 (see 5 papers)
uvrB / P0A8F8 UvrABC excision nuclease subunit B from Escherichia coli (strain K12) (see 2 papers)
UVRB_ECO27 / B7ULX6 UvrABC system protein B; Protein UvrB; Excinuclease ABC subunit B from Escherichia coli O127:H6 (strain E2348/69 / EPEC) (see paper)
UVRB_ECOLI / P0A8F8 UvrABC system protein B; Protein UvrB; Excinuclease ABC subunit B from Escherichia coli (strain K12) (see 2 papers)
NP_415300 UvrABC excision nuclease subunit B from Escherichia coli str. K-12 substr. MG1655
b0779 excinuclease ABC subunit B from Escherichia coli str. K-12 substr. MG1655
Z0998 DNA repair; excision nuclease subunit B from Escherichia coli O157:H7 EDL933
EDL933_0900, EDL933_RS04475 excinuclease ABC subunit UvrB from Escherichia coli O157:H7 str. EDL933
51% identity, 96% coverage
- function: The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage.
function: Plays a role in recovery after DNA ADP-ribosylation; a proportion of UvrB becomes immobilized on DNA in cells expressing DNA ADP-ribosyl transferase (darT) mutant G49D.
subunit: Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. - function: The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage.
subunit: Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex - Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom.
Amemiya, Transcription 2021 (no snippet) - Real-time investigation of the roles of ATP hydrolysis by UvrA and UvrB during DNA damage recognition in nucleotide excision repair.
Kraithong, DNA repair 2021 (PubMed)- GeneRIF: Real-time investigation of the roles of ATP hydrolysis by UvrA and UvrB during DNA damage recognition in nucleotide excision repair.
- Recruitment of UvrBC complexes to UV-induced damage in the absence of UvrA increases cell survival.
Springall, Nucleic acids research 2018 - GeneRIF: Recruitment of UvrBC complexes to UV-induced damage in the absence of UvrA increases bacterial survival.
- Evidence for involvement of UvrB in elicitation of 'SIR' phenotype by rpoB87-gyrA87 mutations in lexA3 mutant of Escherichia coli.
Shanmughapriya, DNA repair 2012 (PubMed)- GeneRIF: ATPase domain, ATP binding domain and/or the DNA binding domain of the UvrB protein are required for DNA repair.
- Collaborative dynamic DNA scanning by nucleotide excision repair proteins investigated by single- molecule imaging of quantum-dot-labeled proteins.
Kad, Molecular cell 2010 - GeneRIF: study visualized how UvrA and UvrB interacted with DNA individually or together by single- molecule imaging of quantum-dot-labeled proteins
- Exploring damage recognition models in prokaryotic nucleotide excision repair with a benzo[a]pyrene-derived lesion in UvrB.
Jia, Biochemistry 2009 - GeneRIF: Exploring damage recognition models in prokaryotic nucleotide excision repair with a benzo[a]pyrene-derived lesion in UvrB.
- The unstructured C-terminal extension of UvrD interacts with UvrB, but is dispensable for nucleotide excision repair.
Manelyte, DNA repair 2009 - GeneRIF: found that the N-terminal domain and the unstructured region at the C-terminus of UvrD interact with UvrB.
- Dynamics of the UvrABC nucleotide excision repair proteins analyzed by fluorescence resonance energy transfer.
Malta, Biochemistry 2007 (PubMed)- GeneRIF: In solution, two UvrB subunits bind to UvrA, most likely as part of a UvrA2B2 complex. The UvrA-induced dimerization of the C-terminal domain 4 regions of UvrB serves to shield these domains from premature UvrC binding.
- Structural basis for transcription-coupled repair: the N terminus of Mfd resembles UvrB with degenerate ATPase motifs.
Assenmacher, Journal of molecular biology 2006 (PubMed)- GeneRIF: transcription-repair ATP-dependent coupling factor-N reveals a fold that resembles the three N-terminal domains of the repair enzyme UvrB
- More
- The bile salt deoxycholate induces Campylobacter jejuni genetic point mutations that promote increased antibiotic resistance and fitness
Talukdar, Frontiers in microbiology 2022 - “...(2/3) 33.0%/47.6% Nucleotide excision repair UvrA Cj0342c /CJJ81176_RS01645 b4058 Yes (1/2) 50.5%/67.6% UvrB Cj0680c /CJJ81176_RS03285 b0779 No 50.1%/69.2% UvrC * Cj1246c /CJJ81176_RS06065 b1913 Yes (2/3) 29.1%/49.1% UvrD Cj1101/CJJ81176_RS05350 b3813 Yes (5/13) 34.5%/53.3% Mfd Cj1085c /CJJ81176_RS05270 b1114 Yes (10/15)? 28.2%/46.6% Base excision repair MutY * Cj1620c /CJJ81176_RS07755...”
- Elevated Levels of the Escherichia coli nrdAB-Encoded Ribonucleotide Reductase Counteract the Toxicity Caused by an Increased Abundance of the β Clamp
Babu, Journal of bacteriology 2021 (secret) - The Mutant βE202K Sliding Clamp Protein Impairs DNA Polymerase III Replication Activity
Homiski, Journal of bacteriology 2021 (secret) - The alternative translational profile that underlies the immune-evasive state of persistence in Chlamydiaceae exploits differential tryptophan contents of the protein repertoire
Lo, Microbiology and molecular biology reviews : MMBR 2012 - “...kinase/ flavin adenine dinucleotide synthase 434 b0779 fig|83333.1.peg.765 UvrABC system protein B b4143 fig|83333.1.peg.4055 mopA 60-kDa chaperonin b3326...”
- Functional characterization of excision repair and RecA-dependent recombinational DNA repair in Campylobacter jejuni
Gaasbeek, Journal of bacteriology 2009 - “...b4170 b2831 mutS Cj1052c 21.9 NER uvrA uvrB uvrC b4058 b0779 b1913 uvrA uvrB uvrC Cj0342c Cj0680c Cj1246c 67.6 69.2 49.1 BER ung xthA recJ b2580 b1749 b2892 ung...”
- Analysis of global gene expression and double-strand-break formation in DNA adenine methyltransferase- and mismatch repair-deficient Escherichia coli
Robbins-Manke, Journal of bacteriology 2005 - “...ruvA (b1861) ruvB (b1860) dinI (b1061) uvrA (b4058) uvrB (b0779) chol ydjQ (b1741) dam mutS/WT VOL. 187, 2005 GENE EXPRESSION AND DNA DAMAGE IN dam E. COLI...”
- Role of SeqA and Dam in Escherichia coli gene expression: a global/microarray analysis
Løbner-Olesen, Proceedings of the National Academy of Sciences of the United States of America 2003 - “...Relative expression lacZ b0958 b0680 b4043 b2698 b2699 b4058 b0779 b4044 b4393 b1061 b0243 b1530 b3748 b1037 b2133 b3599 b3702 1.8 (2.1) 1.9 (3.0) 1.3 (0.9) 1.8...”
- Use of in vivo-induced antigen technology for identification of Escherichia coli O157:H7 proteins expressed during human infection
John, Infection and immunity 2005 - “...Z2789 Z3827 Z5977 Z3777 Z5955 Z3491 Z4043 Z4478 Z0998 Z5392 transketolase 1 isozyme (tktA) GroES, 10-kDa chaperone binds to Hsp60 (mopB) fructose-bisphosphate...”
- Transcriptomic and proteomic analysis of the virulence inducing effect of ciprofloxacin on enterohemorrhagic Escherichia coli
Kijewski, PloS one 2024 - “...Protein HokE 3.5 --- --- EDL933_RS03695 EDL933_0757 ybfE Uncharacterized protein YbfE --- 1.0 -1.3 EDL933_RS04475 EDL933_0900 uvrB Excinuclease ABC subunit B --- 1.0 -1.1 EDL933_RS04585 EDL933_0922 dinG ATP-dependent helicase DinG 2.1 1.1 -1.9 EDL933_RS06015 EDL933_1225 sulA Cell division inhibitor SulA 4.6 -1.4 -1.3 EDL933_RS06545 EDL933_1330 yccM...”
- “...hokE Protein HokE 3.5 --- --- EDL933_RS03695 EDL933_0757 ybfE Uncharacterized protein YbfE --- 1.0 -1.3 EDL933_RS04475 EDL933_0900 uvrB Excinuclease ABC subunit B --- 1.0 -1.1 EDL933_RS04585 EDL933_0922 dinG ATP-dependent helicase DinG 2.1 1.1 -1.9 EDL933_RS06015 EDL933_1225 sulA Cell division inhibitor SulA 4.6 -1.4 -1.3 EDL933_RS06545 EDL933_1330...”
XALc_1870 probable excinuclease abc subunit b protein from Xanthomonas albilineans
50% identity, 96% coverage
BL107_06249 excinuclease ABC subunit B from Synechococcus sp. BL107
51% identity, 96% coverage
- A Sample-to-Sequence Protocol for Genus Targeted Transcriptomic Profiling: Application to Marine Synechococcus
Pitt, Frontiers in microbiology 2016 - “...DNA recombination protein RmuC 3.26 0.20 BL107_11686 116,064,969 recD; exodeoxyribonuclease V alpha subunit 1.09 0.39 BL107_06249 116,065,351 uvrB; exonuclease ABC subunit B 1.00 0.28 8: SIGNAL TRANSDUCTION MECHANISMS BL107_13595 116,066,088 typA; GTP-binding protein 1.33 0.21 8.1: CIRCADIAN CLOCK SIGNALING BL107_05064 116,065,114 rpaA; two-component system, OmpR family,...”
NGO0573 UvrB from Neisseria gonorrhoeae FA 1090
50% identity, 95% coverage
NGK_1349 UvrABC system protein B from Neisseria gonorrhoeae NCCP11945
50% identity, 95% coverage
S101446_02949 excinuclease ABC subunit UvrB from Komagataeibacter europaeus
50% identity, 87% coverage
ZMO0362 excinuclease ABC subunit B from Zymomonas mobilis subsp. mobilis ZM4
49% identity, 88% coverage
- Lipid membrane remodeling and metabolic response during isobutanol and ethanol exposure in Zymomonas mobilis
Rivera, Biotechnology for biofuels and bioproducts 2024 - “...levels of UvrABC DNA repair system proteins (Fig. 4 E). Specifically, UvrA (ZMO1588) and UvrB (ZMO0362) were both upregulated in response to the solvent stress. Concurrently, the DNA repair proteins, MutM (ZMO1187) and NrdF (ZMO0443), were also upregulated in response to the ethanol and isobutanol stress....”
- Development and characterization of acidic-pH-tolerant mutants of Zymomonas mobilis through adaptation and next-generation sequencing-based genome resequencing and RNA-Seq
Yang, Biotechnology for biofuels 2020 - “...co-chaperone ZMO1690 ( dnaJ ) as well as ZMO1588 ( uvrA ) and its subunit ZMO0362 ( uvrB ) were upregulated in ZM4 at acidic pH 3.8 than at neutral pH 6.2. Moreover, the expression level of Clp protease complex, ZMO0405 ( clpA ), ZMO0948 (...”
- Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics
Yang, Frontiers in microbiology 2014 - “...three thioredoxin-like genes, and genes associated with DNA repair such as UvrABC system gene uvrB (ZMO0362), mutM (ZMO1187), mutS (ZMO1907) and ZMO1426 (Additional File 13 ). There are more previously documented interactions among the downregulated genes in MM relative to RM compared to the upregulated genes...”
Dgeo_1890 excinuclease ABC, B subunit from Deinococcus geothermalis DSM 11300
49% identity, 96% coverage
- Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria
Sghaier, BMC genomics 2008 - “...Rxyl_1394 Ribonuclease HII n.a. -1.642 DR_2074 Dgeo_1660 Krad_3154 Rxyl_1309 Putative 3-methyladenine DNA glycosylase 3.25 DR_2275 Dgeo_1890 Krad_2942 Rxyl_2021 Excinuclease ABC, subunit B* n.a. -1.767 DR_2285 Dgeo_0019 Krad_0599 Rxyl_2229 A/G-specific adenine glycosylase* 1.85 DR_2340 Dgeo_2138 Krad_1492 Rxyl_1423 RecA protein* n.a. -1.179 DR_2584 Dgeo_0107 Krad_4325 Rxyl_1215 DNA-3-methyladenine glycosidase...”
- Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks
Makarova, PloS one 2007 - “...DR1771 (uvrA) Dgeo_0694 COG0178 +/+ + [46] , [92] Excinuclease ATPase subunit, UvrA. DR2275 (uvrB) Dgeo_1890 COG0556 +/+ n/a [46] , [92] Helicase subunit of the DNA excision repair complex, UvrB. DR1913 (gyrA) Dgeo_1016 COG0188 +/+ n/a [46] , [92] DNA gyrase (topoisomerase II) A subunit....”
- “...Dgeo_0868 49 3.5 TTATGccgccAACAgAA no yes UvrD UvrD Superfamily I helicase DR2275 74 3.87 TTAcGcTgTgggCgTAA Dgeo_1890 87 4.79 TTATGTTtTTggCgTAA no yes UvrB Helicase subunit of the DNA excision repair complex, UvrB DR0596 25 3.84 TTtcGcaAATAgCgTAA Dgeo_0404 25 3.84 TTtcGcaAATAgCgTAA yes yes RuvB Holliday junction resolvasome, helicase...”
SMc04231 PROBABLE EXCINUCLEASE ABC SUBUNIT B PROTEIN from Sinorhizobium meliloti 1021
49% identity, 66% coverage
E2P69_RS14465 excinuclease ABC subunit UvrB from Xanthomonas perforans
49% identity, 96% coverage
BL0990 excinuclease ABC subunit B from Bifidobacterium longum NCC2705
52% identity, 92% coverage
STM14_0926 excinuclease ABC subunit UvrB from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM0798 UvrB with UvrAC is a DNA excision repair enzyme from Salmonella typhimurium LT2
51% identity, 96% coverage
LHK_00960 UvrABC system protein B from Laribacter hongkongensis HLHK9
51% identity, 97% coverage
CC2981 excinuclease ABC, subunit B from Caulobacter crescentus CB15
CCNA_03076 excinuclease ABC subunit B from Caulobacter crescentus NA1000
50% identity, 86% coverage
- Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus
Martins-Pinheiro, BMC microbiology 2007 - “...damage recognition protein UvrA CC2590 716/944 (75%) uvrB (673 aa) DNA damage binding protein UvrB CC2981 481/668 (72%) uvrC (610 aa) excision nuclease UvrC 1-CC2881; 360/608 (59%) UvrC-N-terminal like protein, endonuclease 2-CC3518; absent 3-CC1343; absent 4-CC0707 absent uvrD (720 aa) DNA-dependent ATPase I and helicase II...”
- Iron Deficiency Generates Oxidative Stress and Activation of the SOS Response in Caulobacter crescentus
Leaden, Frontiers in microbiology 2018 - “...UvrABC system, which is part of the SOS response, but these genes (CCNA_02673, CCNA_02975, and CCNA_03076) were not induced in the DP-treated condition. In fact, these genes are poorly induced even in the absence of the lexA repressor ( uvrA , 3.5-fold; uvrC , 1.7-fold, and...”
Deide_03120 putative UvrABC system protein B (Excinuclease ABC, subunit B) from Deinococcus deserti VCD115
49% identity, 97% coverage
- Conservation and diversity of the IrrE/DdrO-controlled radiation response in radiation-resistant Deinococcus bacteria
Blanchard, MicrobiologyOpen 2017 - “...Deide_18720 Conserved protein (+) Deide_19430 CinAlike protein + >2.5 Deide_00120 Singlestranded DNAbinding protein (SSB) + Deide_03120 Excinuclease ABC subunit B (UvrB) + Deide_11446 Putative protein Deide_21600 RtcB family protein not >2.5 Deide_00100 50S ribosomal protein L9 (RplI) (+) Deide_08010 ABC transporter permease Deide_20140 Putative Nacetyltransferase Deide_1p01870...”
- “...uvrA + + + + + + + + + + + + + + Deide_03120 uvrB + + + + + + + + + + + + + + Deide_12100 uvrD + + + + + + + + + + + + Deide_00600...”
- RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti
de, Genome biology and evolution 2014 - “...proteins produced from leadered mRNAs are Ssb (Deide_00120) ( fig. 1 ), UvrA (Deide_12760), UvrB (Deide_03120), GyrA (Deide_12520), GyrB (Deide_15490), TopA (Deide_07410), RecA P1 (Deide_1p01260), HU3 (Deide_00200), DdrB (Deide_02990), PprA (Deide_2p01380), SodA (Deide_07760), catalase (Deide_2p00330), Lon protease (Deide_05670 and Deide_19590), and ClpC (Deide_12680). F ig ....”
DRO_2249, DR_2275 excinuclease ABC subunit UvrB from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
49% identity, 97% coverage
- Structural and functional insights into the activation of the dual incision activity of UvrC, a key player in bacterial NER
Seck, Nucleic acids research 2023 - “...and purification of uvr proteins Cloning, expression and purification of D. radiodurans UvrA1 (DR_1771), UvrB (DR_2275) and UvrC (DR_1354) have been described previously ( 45 ). Truncated constructs (Table S1) of UvrC (DR_1354) were cloned into pProexHtB (EMBL) for expression with a cleavable N-terminal His-tag. A...”
- In vitro reconstitution of an efficient nucleotide excision repair system using mesophilic enzymes from Deinococcus radiodurans
Seck, Communications biology 2022 - “...genome of D. radiodurans encodes for a complete NER pathway 31 : UvrA1 (DR_1771), UvrB (DR_2275), UvrC (DR_1354), and UvrD (DR_1775), but also for a UV-damage endonuclease, UvsE, that efficiently repairs UV-induced pyrimidine dimers 32 . In a uvrA1 knock out strain of D. radiodurans ,...”
- “...and methods Cloning, expression and purification of Uvr proteins Deinococcus radiodurans UvrA1 (DR_1771) and UvrB (DR_2275) genes were cloned into pProexHtB (EMBL). Based on sequence alignment, the first 59 amino acids of D. radiodurans UvrB (drUvrB) were removed and our full-length drUvrB construct thus starts at...”
- Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses
Eugénie, Cells 2021 - “...3, 4, 5 DR2069 DRO_2042 ligA DNA ligase (NAD(+)) LigA 47 ATTCTGCCCTGAACCGAAC yes/yes 5 DR2275 DRO_2249 uvrB , putatively in operon with dr2276 excinuclease ABC subunit B 105 CTTACGCTGTGGGCGTAAA ND X 1,2,3,5 DR2338 DRO_2308 cinA , first gene in operon with ligT and recA Competence inducible...”
- Proteomic Response of Deinococcus radiodurans to Short-Term Real Microgravity during Parabolic Flight Reveals Altered Abundance of Proteins Involved in Stress Response and Cell Envelope Functions
Moors, Life (Basel, Switzerland) 2021 - “...(DR_2069 or LigA) show an increase of more than twofold and exonuclease ABC subunit B (DR_2275 or UvrB) and transcription-repair coupling factor (DR_1532 or Mfd) show an increase of 1.7-fold and 1.59-fold, respectively. These four proteins are part of the nucleotide excision repair (NER) pathway (dra03420),...”
- “...DR_2069 1.04 DNA-directed DNA polymerase DR_1707 1.01 hypothetical protein DR_0428 0.83 exconuclease ABC subunit B DR_2275 0.77 Mrr restriction system protein DR_0508 0.77 hypothetical protein DR_0326 0.68 transcription-repair coupling factor DR_1532 0.67 ParB family chromosome partitioning protein DR_A0002 0.58 Beta sliding clamp DR_0001 0.54 exonuclease SbcC...”
- Proteometabolomic response of Deinococcus radiodurans exposed to UVC and vacuum conditions: Initial studies prior to the Tanpopo space mission
Ott, PloS one 2017 - “...Lon proteases (DR_0349 and DR_1974), DNA repair protein PprA (DR_A0346), UvrABC system protein B UvrB (DR_2275), catalase katA (DR_0146) and tellurium resistance protein TerB (DR_2220). Thus, DR_0997 might act as a positive regulator in response to combined UVC-vacuum stress in D . radiodurans . DdrO, a...”
- A Decade of Biochemical and Structural Studies of the DNA Repair Machinery of Deinococcus radiodurans: Major Findings, Functional and Mechanistic Insight and Challenges
Timmins, Computational and structural biotechnology journal 2016 - “...The genome of D. radiodurans encodes for a complete NER pathway: UvrA1 (DR_1771; drUvrA1), UvrB (DR_2275; drUvrB), UvrC (DR_1354; drUvrC) and UvrD (DR_1775; drUvrD). DrUvrD has been shown to be involved in several DNA repair pathways [59] and will thus be discussed below in Section 6...”
- Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria
Sghaier, BMC genomics 2008 - “...Krad_1405 Rxyl_1394 Ribonuclease HII n.a. -1.642 DR_2074 Dgeo_1660 Krad_3154 Rxyl_1309 Putative 3-methyladenine DNA glycosylase 3.25 DR_2275 Dgeo_1890 Krad_2942 Rxyl_2021 Excinuclease ABC, subunit B* n.a. -1.767 DR_2285 Dgeo_0019 Krad_0599 Rxyl_2229 A/G-specific adenine glycosylase* 1.85 DR_2340 Dgeo_2138 Krad_1492 Rxyl_1423 RecA protein* n.a. -1.179 DR_2584 Dgeo_0107 Krad_4325 Rxyl_1215 DNA-3-methyladenine...”
- Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of Kineococcus radiotolerans SRS30216
Bagwell, PloS one 2008 - “...homologs UvrA ATPase, DNA binding UvrA DR_1771 DR_A0188 Rv1638c Krad_2940 Krad_1787 Krad_0057 UvrB Helicase UvrB DR_2275 Rv1633c Krad_2942 UvrC Nuclease UvrC DR_1354 Rv1420 Krad_2935 UvrD DNA helicase II (DNA-dependent helicase activity) initiates unwinding from a nick; DR_1572 has a frameshift UvrD DR_1775 Rv0949 Rv3198c (putative) Krad_0757...”
DR2275 excinuclease ABC, subunit B from Deinococcus radiodurans R1
49% identity, 89% coverage
- Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses
Eugénie, Cells 2021 - “...2, 3, 4, 5 DR2069 DRO_2042 ligA DNA ligase (NAD(+)) LigA 47 ATTCTGCCCTGAACCGAAC yes/yes 5 DR2275 DRO_2249 uvrB , putatively in operon with dr2276 excinuclease ABC subunit B 105 CTTACGCTGTGGGCGTAAA ND X 1,2,3,5 DR2338 DRO_2308 cinA , first gene in operon with ligT and recA Competence...”
- Novel Sequence Features of DNA Repair Genes/Proteins from Deinococcus Species Implicated in Protection from Oxidatively Generated Damage
Hassan, Genes 2018 - “...Endonuclease III (Nth) DR0928 6 1 Figure S17D Exonuclease III (Xth) DR0354 2 - UvrB DR2275 6 - - UvrC DR1354 3 - - UvsE DR1819 4 - - Rad25 DRA0131 10 2 Figure S17E RecA DR2340 1 - - RecO DR0819 4 2 Figure S17F...”
- Cyclic AMP Receptor Protein Acts as a Transcription Regulator in Response to Stresses in Deinococcus radiodurans
Yang, PloS one 2016 - “...UvsE -5.19 (0.45) -1.36 (0.17) DR1771 excinuclease ABC subunit A UvrA -1.11 (0.30) 0.81 (0.06) DR2275 excinuclease ABC subunit B UvrB -3.21 (0.39) -1.87 (0.21) DR1354 excinuclease ABC subunit C UvrC -5.95 (0.53) -2.99 (0.31) DR1274 Holliday junction DNA helicase RuvA -1.13 (0.02) -0.93 (0.13) DR0596...”
- Identification of new genes contributing to the extreme radioresistance of Deinococcus radiodurans using a Tn5-based transposon mutant library
Dulermo, PloS one 2015 - “...recombination, and repair Nucleotide excision repair UvrA1 DR1771 5.7 0.3 SS s s heterogenote UvrB DR2275 6.2 0.7 SS R R UvrC DR1354 5.0 0.03 S s R Homologous recombination RecG DR1916 23.0 4.1 SS S R RecN DR1477 28.9 5.5 SS S R RuvA DR1274...”
- Gamma radiation-induced proteome of Deinococcus radiodurans primarily targets DNA repair and oxidative stress alleviation
Basu, Molecular & cellular proteomics : MCP 2012 - “...these, only a few: recA (DR2340), uvrA (DR1771), uvrB (DR2275), gyrA (DR1913), and gyrB (DR0906), are well annotated DNA repair 1 The abbreviations used are:...”
- “...(DR0003), ddrD (DR0326), ddrP (DRB0100), or uvrB (DR2275), all identified as strongly up-regulated by transcriptomic analyses, do not affect radiation...”
- Oxidative stress resistance in Deinococcus radiodurans
Slade, Microbiology and molecular biology reviews : MMBR 2011 - “...DR2162 DR2285 DR0493 DR0928 DR2438 DR0289 DR0354 DR1771 DR2275 DdrO? DrRRA DdrO? DR1354 DR1819 DR1532 DRA0131 DR2340 DR1089 DR0819 DR0198 DR1126 DR1477 DR1289...”
- “...of UvrA (UvrA1 [DR1771] and UvrA2 [DRA0188]), UvrB (DR2275), and UvrC (DR1354). UvrA2 does not contribute to UV radiation resistance (603). E. coli UvrA...”
- Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks
Makarova, PloS one 2007 - “...DR1289 ortholog. DR1771 (uvrA) Dgeo_0694 COG0178 +/+ + [46] , [92] Excinuclease ATPase subunit, UvrA. DR2275 (uvrB) Dgeo_1890 COG0556 +/+ n/a [46] , [92] Helicase subunit of the DNA excision repair complex, UvrB. DR1913 (gyrA) Dgeo_1016 COG0188 +/+ n/a [46] , [92] DNA gyrase (topoisomerase II)...”
- “...DR1775 40 4.09 TTAcGcTccTggCAgAA Dgeo_0868 49 3.5 TTATGccgccAACAgAA no yes UvrD UvrD Superfamily I helicase DR2275 74 3.87 TTAcGcTgTgggCgTAA Dgeo_1890 87 4.79 TTATGTTtTTggCgTAA no yes UvrB Helicase subunit of the DNA excision repair complex, UvrB DR0596 25 3.84 TTtcGcaAATAgCgTAA Dgeo_0404 25 3.84 TTtcGcaAATAgCgTAA yes yes RuvB...”
- Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance
Tanaka, Genetics 2004 - “...tag Identifier Gene name/annotation DR0596 DR2340 DR1771 DR2275 DR1913 DR0906 DR2220 DR2224 DR2338 DR2339 DR1262 DR1114 Protein fate Heat-shock protein, HSP20...”
- More
KP13_03032 excinuclease ABC subunit UvrB from Klebsiella pneumoniae subsp. pneumoniae Kp13
51% identity, 96% coverage
RSP_2083 Putative Excinuclease subunit B from Rhodobacter sphaeroides 2.4.1
49% identity, 89% coverage
- Convergence of the transcriptional responses to heat shock and singlet oxygen stresses
Dufour, PLoS genetics 2012 - “...RSP_1546, RSP_2608 Unknown substrate RSP_1895, RSP_2802, RSP_3160 DNA metabolism DNA replication, recombination, and repair RSP_1466, RSP_2083, RSP_2414, RSP_2850, RSP_3077, RSP_3423 Pyrimidine ribonucleotide biosynthesis RSP_3722 Fatty acid and cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides RSP_1491, RSP_2163, RSP_3721 Degradation RSP_0119 Other RSP_0422, RSP_0595, RSP_0855...”
Rxyl_2021 excinuclease ABC, B subunit from Rubrobacter xylanophilus DSM 9941
50% identity, 93% coverage
EAMY_1211 Excinuclease UvrABC subunit B from Erwinia amylovora CFBP1430
50% identity, 95% coverage
YP_1003 excinuclease ABC subunit UvrB from Yersinia pestis biovar Microtus str. 91001
50% identity, 97% coverage
TTHA1892 excinuclease ABC subunit B (UvrB) from Thermus thermophilus HB8
51% identity, 96% coverage
- Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems
Morita, Journal of nucleic acids 2010 - “...but not without UvrA [ 111 ]. In T. thermophilus HB8, the UvrB protein (ttUvrB; TTHA1892) shows ATPase activity at its physiological temperature even in the absence of UvrA (ttUvrA; TTHA1440) [ 112 , 113 ]. Finally, a new pre-incision complex is formed by binding new...”
- “...I, Thermus filiformis DNA ligase, and E. coli TRCF. UvrA (TTHA1440; predicted model) and UvrB (TTHA1892; PDB ID: 1D2M) recognize the DNA lesion. In transcribing strand, TRCF (TTHA0889; predicted model) is also involved in recognition of the lesion. UvrC (TTHA1568; predicted model) incises both sides of...”
MMP0727 excinuclease ABC subunit B from Methanococcus maripaludis S2
50% identity, 98% coverage
RP203 EXCINUCLEASE ABC SUBUNIT B (uvrB) from Rickettsia prowazekii str. Madrid E
49% identity, 98% coverage
Cla_1186 excinuclease ABC, subunit B from Campylobacter lari RM2100
50% identity, 97% coverage
CCO0746 excinuclease ABC, B subunit from Campylobacter coli RM2228
49% identity, 97% coverage
TP0116 excinuclease ABC, subunit B (uvrB) from Treponema pallidum subsp. pallidum str. Nichols
47% identity, 98% coverage
CJJ81176_0703 excinuclease ABC, B subunit from Campylobacter jejuni subsp. jejuni 81-176
48% identity, 97% coverage
Cj0680c excinuclease ABC subunit B from Campylobacter jejuni subsp. jejuni NCTC 11168
48% identity, 97% coverage
WD0839 excinuclease ABC, B subunit from Wolbachia endosymbiont of Drosophila melanogaster
48% identity, 97% coverage
CT586 Exinuclease ABC Subunit B from Chlamydia trachomatis D/UW-3/CX
48% identity, 96% coverage
- Transposon Mutagenesis in Chlamydia trachomatis Identifies CT339 as a ComEC Homolog Important for DNA Uptake and Lateral Gene Transfer
LaBrie, mBio 2019 - “...diverse biological functions. For example, five Tn insertions ( ct298 , ct333 , ct470 , ct586 , and ct575 ) were involved in DNA repair mechanisms, four ( ct054 , ct248 , ct489 , and ct592 ) were were involved in central metabolism, and four (...”
- “...h mutL DNA mismatch repair endonuclease 966365 626/1,731 KQGFI T GWMISPRSDAQWNENSRX [E210T; 228/576] ctl0849 ( ct586 ) uvrB Excinuclease ABC subunit B 979090 848/2,007 EGRPV T GWMISPRSDAQWNENSRX [E284T; 302/668] ctl0853 ( ct590 ) h Hypothetical 986413 2,164/2,865 DKSAI X [I722X; 722/955] ctl0853 ( ct590 ) h...”
- Genomic and phenotypic characterization of in vitro-generated Chlamydia trachomatis recombinants
Jeffrey, BMC microbiology 2013 - “...J/6276 CT569, L2-434 CT570 Recombinant RC-L2/971 RC-L2/55 Region of crossover CT585 ( trpS ) and CT586 ( uvrB ) CT586 ( uvrB ) Coordinates 655362 : 656561 656865 : 657292 Comments L2-434 CT585, J/6276 CT586 F(s)70 - L2-434 hybrid CT586 Table 3 Analysis of independent recombinant...”
- The alternative translational profile that underlies the immune-evasive state of persistence in Chlamydiaceae exploits differential tryptophan contents of the protein repertoire
Lo, Microbiology and molecular biology reviews : MMBR 2012 - “...zero-Trp proteins C. trachomatis locus SEED ID CT586 CT497 CT334 CT491 fig|272561.1.peg.599 uvrB UvrABC system protein B fig|272561.1.peg.678 gyrB2 DNA gyrase...”
jhp1041 EXCINUCLEASE ABC SUBUNIT B from Helicobacter pylori J99
48% identity, 98% coverage
- Genetic analysis of Helicobacter pylori strain populations colonizing the stomach at different times postinfection
Salama, Journal of bacteriology 2007 - “...HPAG1_1337-8, HPAG1_0970 HPAG1_0862, HP0488/HP1116, JHP1044, JHP1041, JHP0440, HPAG1_1054, HPAG1_0464 HP0896, HP0963, HPAG1_0946 1.2 kb, HPAG1_0946 (77)...”
HP1114 excinuclease ABC subunit B (uvrB) from Helicobacter pylori 26695
48% identity, 98% coverage
- The Role of a Dipeptide Transporter in the Virulence of Human Pathogen, Helicobacter pylori
Xu, Frontiers in microbiology 2021 - “...1.2796 HP1038 aroQ 1.0187 HP1055 Predicted gene 1.3617 HP1077 nixA 1.3528 HP1098 Predicted gene 1.0557 HP1114 uvrB 1.6187 HP1162 Predicted gene 2.3026 HP1164 trxB 1.1085 HP1177 hopQ 1.657 HP1180 nupC 1.273 HP1181 Multidrug transporter 1.2283 HP1186 arsR 1.2884 HP1212 atpE 1.662 HP1283 Predicted gene 1.4378 HP1286...”
- The nucleotide excision repair (NER) system of Helicobacter pylori: role in mutation prevention and chromosomal import patterns after natural transformation
Moccia, BMC microbiology 2012 - “...into the ureAB locus (Additional file 4 : Table S3). To do so, the ORFs HP1114 and HP0821 were cloned in the pADC vector [ 45 ] downstream of the strong ureAB promoter, creating the plasmids pSUS2646 and pSUS2644 (Additional file 4 : Table S2 and...”
- “...E. coli K12 EG11061 and S. aureus N315 SA0714). B. UvrB ( H. pylori 26695 HP1114, C. jejuni NCTC11168 Cj0680c, E. coli K12 EG11062 and S. aureus N315 SA0713. C. UvrC ( H. pylori 26695 HP0821, C. jejuni NCTC11168 Cj1246c, E. coli K12 EG11063 and S....”
- New implications on genomic adaptation derived from the Helicobacter pylori genome comparison
Lara-Ramírez, PloS one 2011 - “...strains showed that: other strains have the same genomic structure flanking the orthologs of HP0448; HP1114, HP1117 and their orthologs are conserved in different strains but the sequences between them are distinct, indicating no consistent genomic structure around HP1116; the 1430 bp-repeated fragment within HP0448 or...”
- UvrD helicase suppresses recombination and DNA damage-induced deletions
Kang, Journal of bacteriology 2006 - “...cassette HP1478 interrupted with 100 bp deletion cassette HP1114 interrupted with 0 bp deletion cassette HP1114 interrupted with 100 bp deletion cassette 31 31...”
- Metabolism and genetics of Helicobacter pylori: the genome era
Marais, Microbiology and molecular biology reviews : MMBR 1999 - “...pathway contributes to the repair of DNA damage, and HP1114 (uvrB) is a putative NER gene in H. pylori. An isogenic H. pylori UvrB-negative mutant constructed...”
CTL0849 excinuclease ABC subunit B from Chlamydia trachomatis 434/Bu
48% identity, 96% coverage
BB0836 excinuclease ABC, subunit B (uvrB) from Borrelia burgdorferi B31
50% identity, 96% coverage
- A high-throughput genetic screen identifies previously uncharacterized Borrelia burgdorferi genes important for resistance against reactive oxygen and nitrogen species
Ramsey, PLoS pathogens 2017 - “...(Replicate 1, Replicate 2) DEA/NO chr bb0457 UvrC, excinuclease ABC subunit 0.048 (0.054, 0.041) chr bb0836 UvrB, excinuclease ABC subunit 0.072 (0.110, 0.034) chr bb0839 putative ribonuclease HI 0.074 (0.049, 0.099) chr bb0344 UvrD, DNA helicase II 0.103 (0.108, 0.098) chr bb0467 laccase domain-containing protein 0.162...”
- Correction: Characterization of the RelBbu regulon in Borrelia burgdorferi reveals modulation of glycerol metabolism by (p)ppGpp
PLOS, PloS one 2015 - “...) 4.95 0.001 BB0710 DNA primase ( dnaG ), authentic frameshift 1.26 <0.001 1.33 <0.001 BB0836 excinuclease ABC, B subunit ( uvrB ) 2.35 <0.001 BB0837 excinuclease ABC, A subunit ( uvrA ) 1.04 0.003 Cell division BB0177 glucose inhibited division protein B ( gidB )...”
- Characterization of the RelBbu Regulon in Borrelia burgdorferi Reveals Modulation of Glycerol Metabolism by (p)ppGpp
Bugrysheva, PloS one 2015 - “...) 4.95 0.001 BB0710 DNA primase ( dnaG ), authentic frameshift 1.26 <0.001 1.33 <0.001 BB0836 excinuclease ABC, B subunit ( uvrB ) 2.35 <0.001 BB0837 excinuclease ABC, A subunit ( uvrA ) 1.04 0.003 Cell division BB0177 glucose inhibited division protein B ( gidB )...”
- Nitrosative damage to free and zinc-bound cysteine thiols underlies nitric oxide toxicity in wild-type Borrelia burgdorferi
Bourret, Molecular microbiology 2011 - “...the resistance of B. burgdorferi to RNS, ORF bb0457 ( uvrC ) (476263478074) and ORF bb0836 ( uvrB ) (888297890318) were removed by allelic exchange and replaced with a flgB p ::aadA streptomycin resistance cassette generating the uvrC::aadA and uvrB::aadA strains respectively ( Fig. 4A and...”
- “...Experimental procedures . B. A diagram is shown of the deletion strategy for uvrB ( bb0836 ) and replacement with a flgB p ::aadA resistance cassette using the strategy outlined in (A). C. B31 A3 (WT) and B31 A3 uvrc::aadA ( uvrC ) cells were treated...”
- Toll-like receptors 1 and 2 heterodimers alter Borrelia burgdorferi gene expression in mice and ticks
Fikrig, The Journal of infectious diseases 2009 - “...DNA metabolism b No prediction 1.50 bb0154 Protein and peptide trafficking b Cytoplasm/cytoplasmic membrane 1.50 bb0836 DNA metabolism b Cytoplasm 1.45 bb0803 Protein synthesis b No prediction 4.65 bb0694 Protein/peptide trafficking b Cytoplasm/cytoplasmic membrane 1.50 bb0355 Transcription factors b Cytoplasm 2.45 bb0585 Cell envelope/biosynthesis and degradation...”
- Molecular and immunological analyses of the Borrelia turicatae Bdr protein family
Carlyon, Infection and immunity 2000 - “...the PPM family of eucaryotic protein Ser-Thr phosphatases (BB0836) (9, 20). Regarding the multiallelic nature of the bdr genes, Bdr variation and redundancy...”
MCJ_000340 UvrABC system protein B from Mycoplasma conjunctivae HRC/581
46% identity, 98% coverage
MHO_4730 excinuclease ABC subunit UvrB from Metamycoplasma hominis ATCC 23114
MHO_4730 UvrABC system protein B from Mycoplasma hominis
45% identity, 98% coverage
2fdcA / P56981 Structural basis of DNA damage recognition and processing by uvrb: crystal structure of a uvrb/DNA complex (see paper)
60% identity, 53% coverage
SAOUHSC_00779 excinuclease ABC subunit B, putative from Staphylococcus aureus subsp. aureus NCTC 8325
60% identity, 48% coverage
- Staphylococcus aureus SOS response: Activation, impact, and drug targets
Cheng, mLife 2024 - “...with transcriptionrepaircoupling factor (4DFC) 2[5(methylamino)1,3,4thiadiazol2yl]3Hbenzo[f]chromen3one (ATBC) 127 . uvrB /UvrB, a subunit of ABC excinuclease SAOUHSC_00779 a , SAOUHSC_00776 SA0713 SAUSA300_0741 NA uvrB /UvrB, a subunit of ABC excinuclease NA parC /ParC, the subunit A of DNA topoisomerase IV SAOUHSC_01352 SA1189 SAUSA300_1251 NA parC /ParC, the...”
- “...(SAOUHSC_00777) is inserted between the internal regions of the uvrB gene (Nterminal SAOUHSC_00776 and Cterminal SAOUHSC_00779). It remains unclear whether this inserted fragment affects the downstream expression of UvrA or alters the functionality of UvrABC. If affected, this raises a question about whether the nonresistant strain's...”
SAOUHSC_00776 excinuclease ABC, B subunit from Staphylococcus aureus subsp. aureus NCTC 8325
55% identity, 50% coverage
- Staphylococcus aureus SOS response: Activation, impact, and drug targets
Cheng, mLife 2024 - “...(4DFC) 2[5(methylamino)1,3,4thiadiazol2yl]3Hbenzo[f]chromen3one (ATBC) 127 . uvrB /UvrB, a subunit of ABC excinuclease SAOUHSC_00779 a , SAOUHSC_00776 SA0713 SAUSA300_0741 NA uvrB /UvrB, a subunit of ABC excinuclease NA parC /ParC, the subunit A of DNA topoisomerase IV SAOUHSC_01352 SA1189 SAUSA300_1251 NA parC /ParC, the subunit A of...”
- “...IS5 family transposase (SAOUHSC_00777) is inserted between the internal regions of the uvrB gene (Nterminal SAOUHSC_00776 and Cterminal SAOUHSC_00779). It remains unclear whether this inserted fragment affects the downstream expression of UvrA or alters the functionality of UvrABC. If affected, this raises a question about whether...”
BSU00550 transcription-repair coupling factor from Bacillus subtilis subsp. subtilis str. 168
NP_387936 transcription-repair coupling factor from Bacillus subtilis subsp. subtilis str. 168
P37474 Transcription-repair-coupling factor from Bacillus subtilis (strain 168)
25% identity, 27% coverage
- The Blueprint of a Minimal Cell: MiniBacillus
Reuß, Microbiology and molecular biology reviews : MMBR 2016 - “...Yes mutY polY1 mutM mfd recD2 BSU08630 BSU23870 BSU29080 BSU00550 BSU27480 No No No No No rnhB recA BSU16060 BSU16940 No No Other/unknown ppaC ylaN yitI yitW...”
- Mfd protects against oxidative stress in Bacillus subtilis independently of its canonical function in DNA repair.
Martin, BMC microbiology 2019 - GeneRIF: Mfd mediates error-prone repair of DNA and protects cells against oxidation of proteins by affecting gene expression.
- Transcriptional coupling of DNA repair in sporulating Bacillus subtilis cells.
Ramírez-Guadiana, Molecular microbiology 2013 (PubMed)- GeneRIF: Data propose that the Mfd-dependent repair pathway operates during B. subtilis sporulation and that its function is required to eliminate genetic damage from transcriptionally active genes.
- A high-frequency mutation in Bacillus subtilis: requirements for the decryptification of the gudB glutamate dehydrogenase gene.
Gunka, Journal of bacteriology 2012 - GeneRIF: This idea is supported by the finding that the transcription-repair coupling factor Mfd is required for the decryptification of gudB.
- Transcriptional de-repression and Mfd are mutagenic in stressed Bacillus subtilis cells.
Martin, Journal of molecular microbiology and biotechnology 2011 - GeneRIF: The authors examined the role of Mfd, a transcription elongation factor involved in DNA repair, in this process and showed that proficiency of this factor promotes mutagenic events.
- Novel role of mfd: effects on stationary-phase mutagenesis in Bacillus subtilis.
Ross, Journal of bacteriology 2006 - GeneRIF: Here we demonstrate that the loss of Mfd has a depressive effect on stationary-phase mutagenesis.
- Analysis of the PcrA-RNA polymerase complex reveals a helicase interaction motif and a role for PcrA/UvrD helicase in the suppression of R-loops
Urrutia-Irazabal, eLife 2021 - “...accession code, GN refers to gene name and FC, to fold change. Accession Description LogFC P37474 Transcription-repair-coupling factor GN=mfd 7.887 O34863 UvrABC system protein A GN=uvrA 6.127 O34628 Uncharacterised protein YvlB GN=yvlB 5.779 Q795Q5 Uncharacterised membrane protein YttA GN=yttA 3.735 O34942 ATP-dependent DNA helicase RecG GN=recG...”
GBAA0052 transcription-repair coupling factor from Bacillus anthracis str. 'Ames Ancestor'
BA0052 transcription-repair coupling factor from Bacillus anthracis str. Ames
22% identity, 27% coverage
- Identification of Bacillus anthracis spore component antigens conserved across diverse Bacillus cereus sensu lato strains
Mukhopadhyay, Molecular & cellular proteomics : MCP 2009 - “...15 16 17 18 GBAA3601 GBAA1094 GBAA3677 GBAA0052 GBAA4157 GBAA0887 GBAA3944 GBAA4843 GBAA5583 GBAA0309 GBAA3609 GBAA4184 GBAA0252 GBAA5222 GBAA4539 GBAA0267...”
- “...1185 1186 Locus tag GBAA3601 GBAA1094 GBAA3677 GBAA0052 GBAA4157 GBAA0887 GBAA3944 GBAA4843 GBAA5583 GBAA0309 GBAA3609 GBAA4184 GBAA0252 GBAA5222 Accession no....”
- A Survey of Antimicrobial Resistance Determinants in Category A Select Agents, Exempt Strains, and Near-Neighbor Species
Taitt, International journal of molecular sciences 2020 - “...41) V770-NP1-R, Ames, Smith 1013, Delta Sterne, Vollum 1B, Zimbabwe 89, Pakistan SK-102, Scotland K1811, BA0052, Canadian Bison, Pasteur, RA3, strain 108, Ohio ACB, Turkey 32, A0435, 2000031021, 2002013094, ANR, S1-1, S2-1, S2-3, S3-3, S3-4, S3-5, S3-6, S3-7, S3-8, S3-11, S3-12, S3-17, S3-18 bla1 , bla2...”
- “...SK-102 wt 76.2 1 wt 76.45 1 Scotland K1811 wt 76.2 1 wt 76.57 1 BA0052 wt 76.08 1 wt 76.55 1 Pasteur wt Invalid 2 - wt 76.52 1 RA3 wt 76.15 1 wt 76.52 1 Strain 108 wt 76.03 1 wt 76.55 1 Ohio...”
- Twenty Whole-Genome Bacillus sp. Assemblies
Daligault, Genome announcements 2014 - “...of rRNAs Bacillus anthracis 2000031021 CP007618 Chr. CP007617 pXO2 5,331,737 35.2 303 5,509 96 33 BA0052 CP007704 Chr. CP007703 pXO1 CP007702 pXO2 5,504,355 53.3 897 5,777 95 33 Delta Sterne CP008752 Chr 5,226,650 35.4 579 5,479 107 32 Pasteur-like JNOD00000000 WGS (18) 5,285,189 35.3 305 5,564...”
- Genetic diversity in the protective antigen gene of Bacillus anthracis
Price, Journal of bacteriology 1999 - “...or description Diversity groupa PA genotypeb PA phenotypec BA0052 BA1087 J611 BA1031 BA1043 28 MOZ-3 BA1035 33 A24 K20 26/05/94 BA1033 BA1017 BA1015 93-194C...”
- Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers
Keim, Journal of bacteriology 1997 - “...#20, #28 #25 #38 BA1002 (Vollum-1b) BA1086 BA0015 BA0018 BA0052 BA0003 BA0006 ZIM69 Ames*, Sterne*, Vollum* (cured of pXO1 and pXO2 at USAMRIID) a Contributing...”
- Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates
Jackson, Applied and environmental microbiology 1997 - “...ASC-30, ASC-129, B1965/77, B7227/83, BA0003, BA0006, BA0052, BA0078/BA1008, BA1007, BA1015, BA1017, BA1021, BA1024, BA1031, BA1033, BA1040, BA1087, D9106771,...”
W8YKA7 Transcription-repair-coupling factor from Bacillus thuringiensis DB27
22% identity, 27% coverage
- Role of hsp20 in the Production of Spores and Insecticidal Crystal Proteins in Bacillus thuringiensis
Xie, Frontiers in microbiology 2019 - “...metG Methionine tRNA ligase W8Y8A7 0.45 ndk Nucleoside diphosphate kinase W8Z497 0.44 pdhC Dihydrolipoyllysine-residue acetyltransferase W8YKA7 0.44 mfd Transcription-repair-coupling factor W8YSS4 0.43 purN Phosphoribosylglycinamide formyltransferase W8Y8Z7 0.43 argD Acetylornithine aminotransferase W8YC93 0.41 ftsH ATP-dependent zinc metalloprotease W8YKA3 0.40 spoVG Putative septation protein SpoVG W8XWN5 0.39 adk...”
CTC_00194 transcription-repair coupling factor from Clostridium tetani E88
23% identity, 43% coverage
- Tetanus Toxin Synthesis is Under the Control of A Complex Network of Regulatory Genes in Clostridium tetani
Chapeton-Montes, Toxins 2020 - “...CodY P2289-F CCGCTGCAGGAGGAGTTACAAATGTCATCATTATTA 232 P2290-R GGCCATGGACTACCTTGTCTCTTACTGTCTG CN655/1472 CTC_00222 Spo0 P2361-F CCGCTGCAGGGAGGTATAAAATATATGATA 225 P2362-R GGCCATGGTTATTACACTCTTTAAAGGTGAA CN655/1480 CTC_00194 mfd P2359-F CCGCTGCAGGAGGTGAATTTTATTATGAGAT 236 P2360-R GGCCATGGAATATTTTTTGCTTCTATATCG toxins-12-00328-t003_Table 3 Table 3 Primers used for qRT-PCR, protein expression and promoter regions of tent and tetR for EMSA experiments. Target Gene Primer Nucleotide...”
CTC00194 transcription-repair coupling factor from Clostridium tetani E88
23% identity, 43% coverage
BPUM_0039 transcription-repair coupling factor from Bacillus pumilus SAFR-032
23% identity, 27% coverage
EJ379_00305, WP_000579687 transcription-repair coupling factor from Bacillus cereus
BC0058 Transcription-repair coupling factor from Bacillus cereus ATCC 14579
22% identity, 27% coverage
- Antibacterial Ingredients and Modes of the Methanol-Phase Extract from the Fruit of Amomum villosum Lour
Zhang, Plants (Basel, Switzerland) 2024 - “...significantly inhibited (0.18- to 0.431-fold) ( p < 0.05), e.g., the transcription-repair coupling factor ( EJ379_00305 ), DNA polymerase I ( EJ379_23430 ), NAD-dependent DNA ligase LigA ( EJ379_01760 ), and ATP-dependent helicase ( EJ379_06255 ). For example, LigA is crucial for DNA replication and repair...”
- The bacterial DNA repair protein Mfd confers resistance to the host nitrogen immune response.
Guillemet, Scientific reports 2016 - GeneRIF: Mfd, a typical housekeeping gene, turns out to be a true virulence factor allowing survival and growth of the pathogen in its host, due to its capacity to protect the bacterium against NO, a key molecule of the innate immune defense
- Multi-locus sequence typing and virulence profile in Bacillus cereus sensu lato strains isolated from dairy products
Bianco, Italian journal of food safety 2020 - “...- BC0057 Mozzarella 1665 + - + + + + + + - + - BC0058 Caciocavallo 1986* + + + + + + + + - + - BC0059 Caciocavallo ST-142 complex 4 + + + + + + + + - + - BC0060...”
- The bacterial DNA repair protein Mfd confers resistance to the host nitrogen immune response
Guillemet, Scientific reports 2016 - “...insect larvae. A strain mutated in the trcf gene was identified as avirulent. This gene (Bc0058 in the B. cereus reference strain ATCC 14579) encodes for the Mfd protein. A stable mfd deletion strain was constructed by insertion of a kanamycin-resistance cassette into the mfd gene....”
ZY05719_00040 transcription-repair coupling factor from Streptococcus suis
24% identity, 26% coverage
GK0048 transcription-repair coupling factor from Geobacillus kaustophilus HTA426
21% identity, 27% coverage
LBA0273 transcriptional repair coupling factor from Lactobacillus acidophilus NCFM
24% identity, 21% coverage
SA0461 transcription-repair coupling factor from Staphylococcus aureus subsp. aureus N315
25% identity, 32% coverage
USA300HOU_0497 transcription-repair coupling factor helicase from Staphylococcus aureus subsp. aureus USA300_TCH1516
SAUSA300_0481 transcription-repair coupling factor from Staphylococcus aureus subsp. aureus USA300_FPR3757
SAKOR_00488 transcription-repair coupling factor from Staphylococcus aureus subsp. aureus CN1
25% identity, 32% coverage
- Identification of Genes Regulating Cell Death in Staphylococcus aureus
Yee, Frontiers in microbiology 2019 - “...transporter subunit IIC USA300HOU_0350 ABC transporter ATP-binding protein USA300HOU_2386 Transcription regulators mfd Transcription-repair coupling factor USA300HOU_0497 Transcription regulator USA300HOU_0044 Transcription regulator USA300HOU_2004 GntR family transcription regulator USA300HOU_1209 Peptidases sspA Glutamyl endopeptidase USA300HOU_0996 Peptidase USA300HOU_2590 Metabolism folD Methylenetetrahydrofolate dehydrogenase; Methenyltetrahydrofolate cyclohydrolase USA300HOU_1008 Bifunctional N-acetylmuramoyl-L-alanine amidase, Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase...”
- Histidine transport is essential for the growth of Staphylococcus aureus at low pH
Beetham, PLoS pathogens 2024 - “...permease), SAUSA300_0543 (predicted t-RNA adenosine deaminase), and a slight reduction in growth was seen for SAUSA300_0481 (transcription-repair coupling factor Mfd) and SAUSA300_1518 (DEAD-box ATP dependent DNA helicase CshB) mutants ( Fig 3F and 3G ). However, not all the mutant strains displayed a reduced ability to...”
- High-throughput transposon sequencing highlights the cell wall as an important barrier for osmotic stress in methicillin resistant Staphylococcus aureus and underlines a tailored response to different osmotic stressors
Schuster, Molecular microbiology 2020 - “...(Lee, Buranen, & Ye, 1991 ), yielding strains ANG4326 and ANG4328 and strains NE188 (JE2 SAUSA300_0481 :: Tn ), NE251 (JE2 SAUSA300_0482:: Tn ), NE526 (JE2 SAUSA300_0694 :: Tn ), NE736 (JE2 SAUSA300_0910 :: Tn ), NE1384 (JE2 SAUSA300_0957 :: Tn ) with plasmid piTET (Grndling...”
- “...complementation plasmid piTET 481 for strain NE188 (JE2 SAUSA300_0481::Tn ) was constructed by amplifying the SAUSA300_0481 gene using primers P2378/P2379, digesting the product with AvrII/BglII and ligating the fragment with plasmid piTET cut with the same enzymes. The plasmid was then introduced into E. coli strain...”
- Long-Term Intrahost Evolution of Methicillin Resistant Staphylococcus aureus Among Cystic Fibrosis Patients With Respiratory Carriage
Azarian, Frontiers in genetics 2019 - “...0.00 0.42 (0.22) Phosphatidylglycerol lysyltransferase (Oxacillin resistance-related protein) K14205 Antimicrobial resistance/signaling and cellular processes mfd SAKOR_00488 0.29 0.09 0.00 0.21 Transcription-repair coupling factor (superfamily II helicase) K03723 DNA repair and recombination proteins AGU62445.1 SAKOR_02305 0.11 0.17 0.00 0.21 Metal-dependent membrane protease None No orthology prpC SAKOR_01146...”
LIC11455 transcription-repair coupling factor from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
27% identity, 18% coverage
VF_A0460 transcription-repair coupling factor from Vibrio fischeri ES114
25% identity, 20% coverage
PF0126 DNA repair protein rad25 from Pyrococcus furiosus DSM 3638
31% identity, 28% coverage
SXYL_02427 transcription-repair coupling factor from Staphylococcus xylosus
24% identity, 26% coverage
PG1774 transcription-repair coupling factor from Porphyromonas gingivalis W83
25% identity, 19% coverage
PA14_25230 transcription-repair coupling factor from Pseudomonas aeruginosa UCBPP-PA14
21% identity, 20% coverage
Q9HZK3 Transcription-repair-coupling factor from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA3002 transcription-repair coupling protein Mfd from Pseudomonas aeruginosa PAO1
21% identity, 20% coverage
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - Food for Thought: Proteomics for Meat Safety
Tarbeeva, Life (Basel, Switzerland) 2023 - “...mdtK, mfd P48372, P13364, A0A5E7MVR1 *, Q5BU34, Q9HUK1, Q9HUJ8, A0A5E7FSX8 *, A0A5M9IUB7 *, A0A0B7DI98 *, Q9HZK3 Fluoroquinolones [ 73 , 74 ] mdtD, mdtG, mdtH, glpT, murA A0A5E6SQR7 *, A0A5E6YH70 *, A0A5E6QA20 *, Q9HTV5, Q9Z3Z6 Fosfomycin [ 73 ] vanA O05616 Glycopeptide antibiotics [ 73 ]...”
- Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites
Subedi, Scientific reports 2018 - “...1 1 4 1 1 2 3 2 3 2 2 3 4 1 49 PA3002 mfd 1 2 2 3 2 2 1 1 1 2 1 2 1 2 1 1 2 27 PA3168 gyrA 1 1 1 1 1 2 2 1 1...”
- PA3297 Counteracts Antimicrobial Effects of Azithromycin in Pseudomonas aeruginosa
Tan, Frontiers in microbiology 2016 - “...transposon inserted at PA2840 Liberati et al., 2006 PA3002::Tn PA14 with a transposon inserted at PA3002 Liberati et al., 2006 PA3272::Tn PA14 with a transposon inserted at PA3272 Liberati et al., 2006 PA3297::Tn PA14 with a transposon inserted at PA3297 Liberati et al., 2006 PA3308::Tn PA14...”
- Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains
Kwon, Journal of proteome research 2014 - “...name p value genes mismatch repair 0.015 PA1529, PA1532, PA1816 nucleotide excision repair 0.001 PA1529, PA3002 , PA4234 DNA replication 0.000 PA1529, PA1532, PA1816, PA4931 nicotinate and nicotinamide metabolism 0.004 PA0143, PA3625, PA4920 selenocompound metabolism 0.035 PA0849, PA1642 fatty acid biosynthesis 0.014 PA1609, PA1610, PA2965, PA3645...”
- Mutator genes giving rise to decreased antibiotic susceptibility in Pseudomonas aeruginosa
Wiegand, Antimicrobial agents and chemotherapy 2008 - “...PA14_25230 PA14_25220 PA14_54590 PA4400 PA5147 PA0357 PA0140 PA4609 PA3002 PA3003 PA0750 mutS mutL uvrD mutT mutY mutM ahpF radA mfd ung Polaritya No Yes...”
- “...with disruptions of the two genes of the operon, PA3002 and PA3003, were detected in the tobramycin screen and in the tobramycin and ciprofloxacin screen,...”
- The Pseudomonas aeruginosa proteome during anaerobic growth
Wu, Journal of bacteriology 2005 - “...PA2119 PA2127 PA2323 PA2567 PA2945 PA2991 PA2994 PA2999* PA3002 PA3150 PA3185 PA3391 PA3392 PA3394 PA3438 PA3515 PA3562* PA3694 PA3871 PA3873 PA3874 PA3875...”
TK0928 predicted DNA/RNA repair helicase from Thermococcus kodakaraensis KOD1
29% identity, 28% coverage
- Application of a Euryarchaeota-Specific Helicase from Thermococcus kodakarensis for Noise Reduction in PCR
Fujiwara, Applied and environmental microbiology 2016 - “...within the sequences of the 16S rRNA, Tk0566, or Tk0928 gene are underlined. In the present study, we tested a novel approach to reduce unexpected misannealing...”
- “...genome: Tk0566, bp 486488 to 488986 (negative strand); and Tk0928, bp 806025 to 807410 (negative strand). The Tk0566 and Tk0928 genes were amplified using the...”
- Proteome profiling of heat, oxidative, and salt stress responses in Thermococcus kodakarensis KOD1
Jia, Frontiers in microbiology 2015 - “...ABC-type dipeptide transport system TK1804 15 1.9 4.64 4.8 92.13 92.6 2 DNA/RNA repair helicase TK0928 12 2.1 4.33 4.5 53.15 54.0 3 Thermophile-specific fructose-1,6-bisphosphatase fructose-1,6-bisphosphatase TK2164 15 2.6 5.36 5.4 41.63 43.5 4 Archaeal ATPase TK1465 21 3.0 6.36 6.4 53.84 54.2 5 Zinc-dependent protease...”
- Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork
Grogan, Archaea (Vancouver, B.C.) 2015 - “...] dpo4 S. solfataricus Y-family DNA polymerase Possible sensitivity to cisplatin [ 61 ] xpb TK0928 Tc. kodakarensis NER-related helicase Marginal damage sensitivity [ 36 ] xpd TK0784 Tc. kodakarensis NER-related helicase Marginal damage sensitivity [ 36 ] Group II (no observed impact) xpd SiRe_1685 S....”
Q9V278 DNA repair protein RAD25 from Pyrococcus abyssi (strain GE5 / Orsay)
30% identity, 29% coverage
WP_091502582 transcription-repair coupling factor from Fructobacillus durionis
24% identity, 19% coverage
SERP0141 transcription-repair coupling factor from Staphylococcus epidermidis RP62A
22% identity, 33% coverage
LSEI_1615 RecG-like helicase from Lactobacillus casei ATCC 334
29% identity, 20% coverage
- Functional genomics of Lactobacillus casei establishment in the gut
Licandro-Seraut, Proceedings of the National Academy of Sciences of the United States of America 2014 - “...3): LSEI_0757 and 1539 (nucleotide metabolism), LSEI_1615 and 1488 (DNA replication), LSEI_1668 (transcription), LSEI_1656 (translation), and LSEI_1274...”
- “...We also identified the RecG family helicase RecG (LSEI_1615) and DinG (LSEI_1488), primarily involved in DNA replication and possibly in DNA repair (28)....”
XP_004252562 DEAD-box ATP-dependent RNA helicase 39 from Solanum lycopersicum
26% identity, 36% coverage
Sez_1547 comF operon protein A ComFA from Streptococcus equi subsp. zooepidemicus MGCS10565
29% identity, 22% coverage
LHK_00629 Mfd from Laribacter hongkongensis HLHK9
22% identity, 21% coverage
lmo1811 similar to ATP-dependent DNA helicase recG from Listeria monocytogenes EGD-e
29% identity, 26% coverage
VC1886 transcription-repair coupling factor from Vibrio cholerae O1 biovar eltor str. N16961
24% identity, 20% coverage
- Identification of genes involved in low aminoglycoside-induced SOS response in Vibrio cholerae: a role for transcription stalling and Mfd helicase
Baharoglu, Nucleic acids research 2014 - “...identified in the inactivation screen Replication recombination repair VC2322 RecC RecBCD double-strand break repair a VC1886 Mfd helicase Transcription repair coupling factor a VC0498 RnaseH RNADNA helicase a VC1636 Putative (YejH vc ) DNARNA helicase VC0015a GreA-like putative transcriptional regulator a Gene for which deletion mutants...”
- “...10 ) A321 N16961 hapR+ rpoS::aadA1 ( 10 ) A126 N16961 hapR+ mfd::aadA1 This study (VC1886, Supplementary Table S1 ) B978 N16961 hapR+ uvrA::aadA1 This study ( Supplementary Table S1 ) B742 N16961 hapR+ mutS::aadA1 This study ( Supplementary Table S1 ) A322 N16961 hapR+ dinB::aadA1...”
SACE_0826 transcription-repair coupling factor from Saccharopolyspora erythraea NRRL 2338
26% identity, 10% coverage
- Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain
Peano, Microbial cell factories 2012 - “...Length (amino acids) Gene (locus) Variation a Protein function and notes DNA replication and repair SACE_0826 1195 mfd Frameshift (+A 218/219) Transcription/repair coupling factor SACE_1351 269 mutM, fpg Missense (M199T) Formamidopyrimidine DNA glycosylase SACE_3677 147 ogtl Missense (G41K) Methylated DNA-protein cysteine methyltransferase SACE_4427 183 Frameshift (+G...”
- “...by missense and frameshift mutations affecting genes involved in DNA replication and repair. In particular, SACE_0826 ( mfd ) coding for transcription/repair coupling factor, SACE_4427 ( mug ) coding for G/U mismatch-specific DNA glycosidase and SACE_5437 ( polA ) were inactivated by frameshift mutations, while missense...”
PF3D7_0218400 ATP-dependent RNA helicase DDX47, putative from Plasmodium falciparum 3D7
26% identity, 24% coverage
- A bioinformatic survey of RNA-binding proteins in Plasmodium
Reddy, BMC genomics 2015 - “...organization in P. falciparum Name of the domain architecture Domain architecture Gene IDs Helicase PF3D7_0521700, PF3D7_0218400, PF3D7_1307300, PF3D7_1332700, PF3D7_0827000, PF3D7_1251500, PF3D7_0422700, PF3D7_1021500, PF3D7_1445900, PF3D7_0504200, PF3D7_0903400, PF3D7_1031500, PF3D7_1241800, PF3D7_0320800, PF3D7_0807100, PF3D7_0810600, PF3D7_1459000, PF3D7_1468700, PF3D7_0321600, PF3D7_0209800, PF3D7_0508700, PF3D7_0518500, PF3D7_0703500, PF3D7_0405000, PF3D7_1202000, PF3D7_0411400, PF3D7_0103600, PF3D7_1445200 HelicaseC+Suv3 PF3D7_0623700 Helicase+DUF4217 PF3D7_0721300,...”
- “...in ribosome biogenesis in P. falciparum Gene ID Putative function Named in P. falciparum Remarks PF3D7_0218400 DDX47 (Rrp8p) PfRrp8p *18S rRNA processing, participates in cleavages at A 2 , and to a lesser extent, A 0 and A 1 sites PF3D7_0721300 DDX31 (Dbp7p) PfDbp7p 27S pre-ribosomal...”
- Reduced ribosomes of the apicoplast and mitochondrion of Plasmodium spp. and predicted interactions with antibiotics
Gupta, Open biology 2014 - “...to the DEAD-box family and are predicted to contain sequence elements for organellar import (PF3D7_1445900, PF3D7_0218400, PF3D7_1332700, PF3D7_1418900, PF3D7_0504200, PF3D7_1021500 and PF3D7_1251500) were identified. These proteins have a conserved DEAD-box motif and RNA helicase domain but could not be unambiguously classified as a specific member (SrmB,...”
SAG0008 transcription-repair coupling factor from Streptococcus agalactiae 2603V/R
25% identity, 19% coverage
TTHA1266 DNA helicase RecG from Thermus thermophilus HB8
23% identity, 26% coverage
- Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems
Morita, Journal of nucleic acids 2010 - “...SSB and branch migration mediated by the RuvA-RuvB complex (TTHA0291-TTHA0406; PDB ID: 1IXR) and RecG (TTHA1266) to yield HJs. HJs are cleaved by RuvC resolvase (TTHA1090) and the nicks sealed by LigA (TTHA1097). Newly synthesized DNA is colored in blue. The model structures of T. thermophilus...”
- “...Branch migration complex RuvA (TTHA0291) RuvA Branch migration complex RuvB (TTHA0406) RuvB DNA helicase RecG (TTHA1266) RecG AT2G01440 (RecG) RecA-like ATPase RadA/Sms (TTHA0541) RadA/Sms AT5G50340 RAD54 family DNA translocase, recombinase mediator RAD54 AT3G19210 (ATRad54) Rad54l RAD54L Adenocarcinoma, Non-Hodgkin lymphoma RAD54 family DNA translocase, recombinase mediator RDH54...”
MAP0987 Mfd from Mycobacterium avium subsp. paratuberculosis str. k10
30% identity, 7% coverage
- Identification and characterization of a spore-like morphotype in chronically starved Mycobacterium avium subsp. paratuberculosis cultures
Lamont, PloS one 2012 - “...PCR was performed on dormant MAP cultures to determine the presence of carD (MAP0475 and MAP0987 ) and spo0A ( MAP1002c ). All three genes are upregulated in comparison to log-phase MAP K-10 culture. All samples were conducted in triplicate. C) Multiple sequence alignment of selected...”
- “...16SrRNA, R GGGTGGATCCTCCTT MAP1002c, F CGGGTGTGGAACTACGACTT MAP1002c, R TCTTCTTCCTCAGGTACGAGATGT MAP0475, F GACAAGGTATTCCAGGTGCTG MAP0475, R CTCGGCGACCTTGTTGAC MAP0987, F GCACGACGGCATCGTTAT MAP0987, R GTCAAGTCCGTCCGTCTCGGTGA Motiwala, A.S., et al. Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis: evidence for limited strain diversity, strain sharing, and identification of unique targets for diagnosis....”
LMOf2365_1839 ATP-dependent DNA helicase RecG from Listeria monocytogenes str. 4b F2365
28% identity, 26% coverage
Q55750 Transcription-repair-coupling factor from Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)
24% identity, 18% coverage
YP_629274 transcription-repair coupling factor from Myxococcus xanthus DK 1622
31% identity, 7% coverage
GLH4_CAEEL / O76743 ATP-dependent RNA helicase glh-4; Germline helicase 4; EC 3.6.4.13 from Caenorhabditis elegans (see 4 papers)
NP_491207 ATP-dependent RNA helicase glh-4 from Caenorhabditis elegans
31% identity, 8% coverage
- function: Probable ATP-binding RNA helicase. May act redundantly with the P-granule component glh-1 to regulate the formation of the granular structure of P-granules in embryos (PubMed:21402787, PubMed:24746798). May protect somatic cells from excessive apoptosis during normal development (PubMed:27650246).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Interacts (via C-terminus) with kgb-1.
disruption phenotype: Knockout with RNAi-mediated knockdown of glh-1 results in smaller P-granules and irregular cytoplasmic localization of the P-granule component pgl-3 in embryos (PubMed:21402787). Quadruple RNAi-mediated knockdown with glh-1, pgl-1 and pgl-3 results in offspring that display 27-89% sterility, abnormal oocytes and do not have embryos in the uterus (PubMed:24746798). These sterile offspring still produce sperm (PubMed:24746798). Furthermore, these offspring may have compromised P-granule integrity as there is diffuse cytoplasmic localization of the P-granule component deps-1, which may cause germ cells to initiate somatic reprogramming (PubMed:24746798). RNAi- mediated knockdown in a double ced-1 and hpl-2 mutant background rescues the reduced somatic cell apoptotic cell defect in the ced-1 and hpl-2 double knockout (PubMed:27650246). - Determination of the role of DDX3 a factor involved in mammalian RNAi pathway using an shRNA-expression library
Kasim, PloS one 2013 - “...NP_491963; CeGLH-2, C. elegans GLH-2, NP_491876; CeGLH-3, C. elegans GLH-3, NP_491681; CeGLH-4, C. elegans GLH-4, NP_491207; CeY38A10A.6, C. elegans CeY38A10A.6, NP_504574; ScDbp1p, Saccharomyces cerevisiae Dbp1p, NP_015206; and AraNM_126777, Arabidopsis thaliana putative helicase, NP_178818.G. We examined the subcellular localization of DDX3 in HeLa S3 cells and analyzed...”
MAVA5_05585 transcription-repair coupling factor from Mycobacterium avium subsp. hominissuis A5
29% identity, 7% coverage
- Identification of Bicarbonate as a Trigger and Genes Involved with Extracellular DNA Export in Mycobacterial Biofilms
Rose, mBio 2016 - “...were all in unique sites): MAVA5_03165, encoding a GntR transcriptional regulator (mutants 19d12 and 26e9); MAVA5_05585, encoding a transcription-repair coupling factor (mutants 16e4 and 41c1); MAVA5_10275, encoding a metal-dependent hydrolase (mutants 26e12, 29b11, and 7d3); and MAVA5_10310, encoding a monooxygenase (mutants 43f8 and 5d3) ( TableS2...”
- “...methyltransferase 6,798 40c10 MAVA5_19945 Carbonic anhydrase 6,941 24d3 MAVA5_13900 Hypothetical protein (dehydrogenase domain) 7,105 41c1 MAVA5_05585 Transcription-repair coupling factor 7,184 36d7 MAVA5_05310 (2Fe2S)-binding protein 7,469 40h2 MAVA5_10220 Hypothetical protein (MaoC dehydrogenase domain) 7,581 1e5 MAVA5_10615 SAM-dependent methyltransferase 7,871 36f9 MAVA5_13185 Oxidoreductase 7,932 35c4 MAVA5_01245 Hypothetical protein...”
all5215 transcriptional-repair coupling factor from Nostoc sp. PCC 7120
25% identity, 16% coverage
CD3501 transcription-repair coupling factor from Clostridium difficile 630
22% identity, 25% coverage
- Increased toxin expression in a Clostridium difficile mfd mutant
Willing, BMC microbiology 2015 - “...plasmids revealed the presence of the erm gene and C. difficile DNA encoding the ORF CD3501, indicating this gene as the site where the intron had inserted. Insertion within CD3501 between basepairs 1412 and 1413 was subsequently confirmed by PCR using primers flanking the insertion site,...”
- “...and Southern blot confirmed this to be the only ClosTron insertion site (data not shown). CD3501 encodes mfd , a transcription-repair coupling factor (TCRF) [ 29 ]. TCRFs are widely conserved in nature and function to relieve stalled RNA polymerase molecules at regions of DNA damage,...”
- Transcriptional profiling of Clostridium difficile and Caco-2 cells during infection
Janvilisri, The Journal of infectious diseases 2010 - “...genes encoding the transcriptional repressor nrdR ( CD2640 ) and transcription-repair coupling factor Mfd ( CD3501 ). A large set of genes involved in cellular metabolism, especially in energy production, was also found to be differentially regulated during infection. Examples include genes involved in carbohydrate utilization...”
lmo0214 transcription-repair coupling factor from Listeria monocytogenes EGD-e
20% identity, 27% coverage
- Genome-wide identification of Listeria monocytogenes CodY-binding sites
Biswas, Molecular microbiology 2020 - “...LMRG_RS10020, LMRG_01131) (K D 10 nM), ilvE (lmo0978, LMRG_RS04930, LMRG_02078) (K D 12.5 nM), mfd (lmo0214, LMRG_RS01035, LMRG_02636) (K D 12.5 nM), and lmo0849 ( LMRG_RS04250, LMRG_02272) (K D 12.5 nM) genes ( Fig. 5A F ). All but one of these genes were found in...”
- Comparison of Surface Proteomes of Adherence Variants of Listeria Monocytogenes Using LC-MS/MS for Identification of Potential Surface Adhesins
Tiong, Pathogens (Basel, Switzerland) 2016 - “...inducing protein (70) C/M/S M CM Yes Yes (Sec) 1 Yes Yes (Sec) >1.8 0.80 lmo0214 (3.2) Transcription-repair coupling factor (135) CY CY 0.03 (E,C) CY No No 0 No No <1.8 0.33 lmo0241 (5.2) Hypothetical protein (28) CY CY 1.84 (CY,C,E) CM No No 0...”
- Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling
Schauer, BMC genomics 2010 - “...ATP-dependent helicase possible 2.1 1.0 lmo0799 oxygen/light sensor with PAS domain no 8.3 2.0 mfd (lmo0214) transcription-repair coupling factor possible 8.9 3.7 lmo1508 two-component sensor histidine kinase no 5.2 2.9 lmo0588 DNA photolyase no 9.6 2.0 membrane bioenergetics mutM (lmo1564) formamidopyrimidine-DNA glycosylase no 5.2 1.1 lmo0091...”
SMU_RS00030 transcription-repair coupling factor from Streptococcus mutans UA159
21% identity, 20% coverage
LMRG_RS01035 transcription-repair coupling factor from Listeria monocytogenes 10403S
LMRG_02636 transcription-repair coupling factor from Listeria monocytogenes 10403S
20% identity, 27% coverage
- Genome-wide identification of Listeria monocytogenes CodY-binding sites
Biswas, Molecular microbiology 2020 - “...LMRG_01131) (K D 10 nM), ilvE (lmo0978, LMRG_RS04930, LMRG_02078) (K D 12.5 nM), mfd (lmo0214, LMRG_RS01035, LMRG_02636) (K D 12.5 nM), and lmo0849 ( LMRG_RS04250, LMRG_02272) (K D 12.5 nM) genes ( Fig. 5A F ). All but one of these genes were found in the...”
- “...factor of the binding region Site detection by ChIP-Seq d first gene second gene 1. LMRG_RS01035 mfd 24 8 UPSTREAM 554.0 yes 2. LMRG_RS00580 lmaA 282 7 INTERNAL 335.1 yes 3. LMRG_RS07545,LMRG_RS07550 amtB,glnK 1110 104 6 INTERNAL,UPSTREAM 302.1 no 4. LMRG_RS04970,LMRG_RS04975 797 99 9 INTERNAL,UPSTREAM 288.0...”
- Genome-wide identification of Listeria monocytogenes CodY-binding sites
Biswas, Molecular microbiology 2020 - “...(K D 10 nM), ilvE (lmo0978, LMRG_RS04930, LMRG_02078) (K D 12.5 nM), mfd (lmo0214, LMRG_RS01035, LMRG_02636) (K D 12.5 nM), and lmo0849 ( LMRG_RS04250, LMRG_02272) (K D 12.5 nM) genes ( Fig. 5A F ). All but one of these genes were found in the IDAP-Seq...”
6acxA / A0R3C5 Crystal structure of mycobacterium smegmatis mfd in complex with adp + pi at 3.5 a resolution.
31% identity, 8% coverage
- Ligand: adenosine-5'-diphosphate (6acxA)
MSMEG_5423 transcription-repair coupling factor from Mycobacterium smegmatis str. MC2 155
31% identity, 8% coverage
HMPREF0837_10294 transcription-repair coupling factor from Streptococcus pneumoniae TCH8431/19A
26% identity, 20% coverage
V9J15_02010 DEAD/DEAH box helicase from Candidatus Liberibacter africanus
28% identity, 16% coverage
SPD_0006 transcription-repair coupling factor from Streptococcus pneumoniae D39
34% identity, 8% coverage
BBMN68_773 transcription-repair coupling factor from Bifidobacterium longum subsp. longum BBMN68
33% identity, 7% coverage
Pnuc_0929 transcription-repair coupling factor from Polynucleobacter sp. QLW-P1DMWA-1
22% identity, 22% coverage
PG2099 ATP-dependent RNA helicase, DEAD/DEAH box family from Porphyromonas gingivalis W83
28% identity, 13% coverage
ZMO1646 transcription-repair coupling factor from Zymomonas mobilis subsp. mobilis ZM4
29% identity, 9% coverage
A5DKW3 ATP-dependent RNA helicase DRS1 from Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324)
27% identity, 19% coverage
H375_160 transcription-repair coupling factor from Rickettsia prowazekii str. Breinl
RP598 TRANSCRIPTION-REPAIR COUPLING FACTOR (mfd) from Rickettsia prowazekii str. Madrid E
27% identity, 19% coverage
- Identification and Characterization of Novel Small RNAs in Rickettsia prowazekii
Schroeder, Frontiers in microbiology 2016 - “...Trans Rp </>/< Identified by RNA-seq This study 3 14215 13984 232 R Cis Rp H375_160 Identified by RNA-seq This study 4 15459 15203 257 R Cis TG, TRG, SFG H375_160 Identified by RNA-seq This study 5 19850 19622 229 R Trans TG, TRG >/ <...”
- “...to rickettsial species outside of the typhus group. The corresponding ORF for Rp_ sR3 is H375_160 (a transcription-repair coupling factor), which is present in all other sequenced R. prowazekii strains. For Rp_ sR18, the corresponding ORF is a single-stranded DNA-specific exonuclease (H375_870), which is also conserved...”
- Vaccine development: obligate intracellular bacteria new tools, old pathogens: the current state of vaccines against obligate intracellular bacteria
van, Frontiers in cellular and infection microbiology 2024 - “...). Using a reverse vaccinology approach, Caro-Gomez etal. identified a collection of novel antigens (RP403, RP598, RP739, and RP778) from R. prowazekii based on the presence of CD8+ T cell epitopes ( Caro-Gomez etal., 2014b ). These antigens were recombinantly expressed in SCEV 4-10 cells for...”
- Vaccination against Bacterial Infections: Challenges, Progress, and New Approaches with a Focus on Intracellular Bacteria
Osterloh, Vaccines 2022 - “...SFG rickettsiae: OmpA, OmpB, Adr2, YbgF TG rickettsiae: OmpB, CD8 + T cell antigens: RP403, RP598 RP739, RP778 [ 37 , 146 , 147 , 148 , 149 , 150 , 151 , 152 ] Orientia Sta22, Sta56, ScaA [ 153 , 154 , 155 ,...”
- Vaccine Design and Vaccination Strategies against Rickettsiae
Osterloh, Vaccines 2021 - “...of five antigens from R. prowazekii that are recognized by CD8 + T cells (RP403, RP598, RP739, RP778, RP884) [ 131 , 132 ]. These antigens were expressed in SVEC 410 cells, and immunization of mice with these cells induced antigen-specific CD8 + T cells that...”
- “...cell antigens from R. prowazekii have been identified by bioinformatic approaches in reverse vaccinology (RP403, RP598, RP739, RP778, RP884) [ 131 , 132 ]. These antigens were recombinantly expressed in SVEC 410 cells to be presented by MHCI. Transfected SVEC 410 cells were then used for...”
- Immune Response to Tick-Borne Hemoparasites: Host Adaptive Immune Response Mechanisms as Potential Targets for Therapies and Vaccines
Torina, International journal of molecular sciences 2020 - “...Using an experimental mice model, it has been reported that five antigens (RP739, RP403, RP734, RP598 and RP778) conferred protection against R. typhi infection in mice via the stimulation of CD8 + T cells and IFN--related production. Of interest, RP778 also promoted CD4 + T cells...”
- “..., 64 ] Candidate antigens from R. prowazekii - RP739 - RP403 - RP734 - RP598 - RP778 - Development of CD8 + T cells expressing IFN- - Protection from experimental R. typhi and R. conorii infection (cross-protection) [ 66 ] RP778 - IFN- expression in...”
- The neglected challenge: Vaccination against rickettsiae
Osterloh, PLoS neglected tropical diseases 2020 - “...189 ]. Using these bioinformatic approaches, they identified 5 proteins from R . prowazekii (RP403, RP598, RP739, RP778, and RP884) that may be recognized by CD8 + T cells. They further expressed these proteins in SVEC4-10 ECs. These cells derive from C3H/HeJ mice and express the...”
- Immune response against rickettsiae: lessons from murine infection models
Osterloh, Medical microbiology and immunology 2017 - “...rickettsiae. Very recently, five protective R. prowazekii CD8 + T cell antigens (RP884, RP778, RP739, RP598 and RP403) have been discovered [ 122 , 123 ]. C3H/HeN mice that were immunized with antigen-presenting cells (APCs) expressing these antigens developed CD8 + T cells that expressed IFN...”
- Discovery of novel cross-protective Rickettsia prowazekii T-cell antigens using a combined reverse vaccinology and in vivo screening approach
Caro-Gomez, Vaccine 2014 - “...proteasome-processing as well as MHC class-I-binding predictions. The novel rickettsial vaccine candidate antigens, RP778, RP739, RP598, and RP403, protected mice against a lethal challenge with R. typhi , which is indicative of cross-protective immunity within the typhus group rickettsiae. Together, our findings validate a reverse vaccinology...”
- “...protective effect. Mice were immunized with 4.5 10 5 APCs individually expressing RP739, RP403, RP734, RP598, RP778 or RP559, and challenged as described above. None of the tested ORFs induced significant reduction of Rickettsia load; yet, we did observe remarkable differences in the clinical status of...”
- Phenotype of the anti-Rickettsia CD8(+) T cell response suggests cellular correlates of protection for the assessment of novel antigens
Caro-Gomez, Vaccine 2014 - “...2.3. Immunization with protective antigens For immunization with protective antigens (RP884, RP778, RP739, RP403 and RP598) we used a cell-based system as reported by us [ 23 , 24 ]. Briefly, the endothelial cell line SVEC4-10, modified to express the costimulatory molecules CD80 and CD137L through...”
- “...rickettsial antigens to discover five novel R. prowazekii protective antigens, RP884, RP778, RP739, RP403, and RP598. These antigens stimulate CD8 + T cell responses and result in cross-protection against a lethal challenge with R. typhi, the other member of the typhus group Rickettsia ( supplementary table...”
LGG_01660 ATP-dependent DNA helicase recG, transcription-repair coupling from Lactobacillus rhamnosus GG
26% identity, 21% coverage
Pro1000 Transcription-repair coupling factor from Prochlorococcus marinus str. SS120
23% identity, 20% coverage
TM0178 primosomal protein N' from Thermotoga maritima MSB8
Q9WY22 Primosomal protein N' from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
36% identity, 9% coverage
Psyc_1082 possible ATP-dependent DEAD/DEAH box RNA-helicase from Psychrobacter arcticum 273-4
31% identity, 15% coverage
WP_004044943 DEAD/DEAH box helicase from Haloferax volcanii
HVO_3010 ATP-dependent RNA helicase/nuclease Hef from Haloferax volcanii DS2
28% identity, 18% coverage
- Intracellular dynamics of archaeal FANCM homologue Hef in response to halted DNA replication.
Lestini, Nucleic acids research 2013 - GeneRIF: The studies revealed that Haloferax volcanii Hef proteins formed specific localization foci under regular growth conditions, the number of which specifically increased in response to replication arrest.
- Haloferax volcanii-a model archaeon for studying DNA replication and repair
Pérez-Arnaiz, Open biology 2020 - “...homologues of the bacterial Uvr system. However, it also encodes homologues of endonucleases XPF (Hef, HVO_3010) and XPG (Fen1, HVO_2873) [ 35 ]. Unlike XPF in eukaryotes, Hef in H. volcanii has been shown to play no role in NER, instead being implicated in the restart...”
- “...due to displacement of the invading strand by helicases such as Hel308 (HVO_0014) or Hef (HVO_3010); the free strand anneals with and is ligated to the other end of the DNA break using either LigA (HVO_1565) or LigN (HVO_3000). Alternatively, a Holliday junction is formed that...”
- Characterization of Copy Number Control of Two Haloferax volcanii Replication Origins Using Deletion Mutants and Haloarchaeal Artificial Chromosomes
Maurer, Journal of bacteriology 2018 - “...of origin 1 and the adjacent genes. HVO_3010 encodes the Hef endonuclease (helicase-associated endonuclease for fork-structured DNA), which is known to...”
- “...1592908-1596454 1596454-1597516 2394240-2395718 Deleted gene(s) HVO_3010, HVO_3012, HVO_0001 HVO_0001, HVO_0002, HVO_1723, HVO_1724, HVO_1725 HVO_1725,...”
- Multiplex quantitative SILAC for analysis of archaeal proteomes: a case study of oxidative stress responses
McMillan, Environmental microbiology 2018 - “...McCready et al., 2005 ; Boubriak et al., 2008 ). While Hfx. volcanii , Hef (HVO_3010) is involved in stalled replication fork repair ( Lestini et al., 2010 ; Lestini et al., 2013 ) and was detected in this study, the abundance of Hef was found...”
PBANKA_121770, PBANKA_1217700 ATP-dependent RNA helicase DDX6 from Plasmodium berghei ANKA
PY17X_1220900 ATP-dependent RNA helicase DDX6, putative from Plasmodium yoelii
28% identity, 16% coverage
- Regulators of male and female sexual development are critical for the transmission of a malaria parasite
Russell, Cell host & microbe 2023 - “...cluster 15 was too low. Immunofluorescence microscopy Rabbit antibodies to the DDX6 RNA helicase (DOZI) PBANKA_1217700 were raised (Proteintech) against the highly conserved peptide LAGKNILARAKNGTGKTAA representing positions 95-113 of the mature protein. Antibodies were affinity-purified from serum using protein A sepharose and used at a 1:500...”
- Roles and Cellular Localization of GBP2 and NAB2 During the Blood Stage of Malaria Parasites
Niikura, Frontiers in cellular and infection microbiology 2021 - “...1 7 7 16 PBANKA_0704700 conserved Plasmodium protein, unknown function 17.86 1 7 7 15 PBANKA_1217700 ATP-dependent RNA helicase DDX6 22.63 1 9 9 15 PBANKA_0600351 reticulocyte binding protein, putative 2.45 3 1 7 14 PBANKA_0506100 PHAX domain-containing protein, putative 5.35 1 8 8 14 PBANKA_1234500...”
- “...protein Alba (ALBA) 2 and 4 (PBANKA_1359200 and PBANKA_1360300, respectively), ATP-dependent RNA helicase DDX6 (DOZI; PBANKA_1217700) and trailer hitch homolog (CITH; PBANKA_1301300) were identified as GBP2-interacting proteins ( Table 1 , Supplementary Figure S3 ). A phosphorylated adapter RNA export protein (PHAX) domain-containing protein (PBANKA_0506100), which...”
- Translational regulation during stage transitions in malaria parasites
Cui, Annals of the New York Academy of Sciences 2015 - “...Poly(A)-binding protein PABP PBANKA_143920 PF3D7_1224300 Lsm14 domain protein CITH PBANKA_130130 PF3D7_1474900 DEAD-box RNA helicase DOZI PBANKA_121770 PF3D7_0320800 Conserved Plasmodium protein, unknown function PBANKA_070470 PF3D7_0825900 Homologue of BRUNO HoBo PBANKA_103270 PF3D7_1409800 Conserved Plasmodium protein, unknown function PBANKA_143520 PF3D7_1220000 Homologue of RNA-binding protein Musashi HoMu PBANKA_081770 PF3D7_0916700 eIF4E...”
- Genome-wide RIP-Chip analysis of translational repressor-bound mRNAs in the Plasmodium gametocyte
Guerreiro, Genome biology 2014 - “...line 683cl1 (WT DOZI::GFP; RMgm-133) [ 10 ] expressing a C-terminally GFP-tagged version of dozi (PBANKA_121770); line 909 cl1 (WT CITH::GFP; RMgm-358) [ 11 ] expressing a C-terminally GFP-tagged version of cith (PBANKA_130130); line GFPCON [ 18 ]; line 820cl1m1cl1 [ 11 ]; and line cl15cy1...”
- An ancient protein phosphatase, SHLP1, is critical to microneme development in Plasmodium ookinetes and parasite transmission
Patzewitz, Cell reports 2013 - “...(forward, 5-TTGATTCATGTTGGATTTGGCT-3; reverse, 5-ATCCTTCTTTGCCCTTTCAG-3) as reference genes. shlp1 primers were: forward, 5-CATCACACCAAATTGGCTCTT-3; reverse, 5-AATTCGGATAAGGCTGACCA-3. dozi (PBANKA_121770) primers were: forward, 5- GCAAGAATGTCGCAAACAC-3; reverse, 5-TCTGAGGAAACTAAACATCGAC-3. nek4 (PBANKA_061670) primers were: forward, 5-CTTCAGATGTATGGGCTATTGG-3; reverse, 5- TTCCCTTTGTTGAATGAAATGG-3. cht1 (PBANKA_080050) primers were: forward, 5- ACGTTGACTACCCAACAGGA-3; reverse, 5-ATCCTGGGCAGCTGTATTCG-3. cith (PBANKA_130130) primers were: forward,...”
- A unique protein phosphatase with kelch-like domains (PPKL) in Plasmodium modulates ookinete differentiation, motility and invasion
Guttery, PLoS pathogens 2012 - “...reverse, 5-ACCATCTAGTAACTACATGGCT-3 . nek4 (PBANKA_061670) primers were: forward, 5-CTTCAGATGTATGGGCTATTGG-3 ; reverse, 5- TTCCCTTTGTTGAATGAAATGG-3 . dozi (PBANKA_121770) primers were: forward, 5- GCAAGAATGTCGCAAACAC-3 ; reverse, 5-TCTGAGGAAACTAAACATCGAC-3 . Western blotting Western blot analysis was performed on cell lysates prepared by re-suspending parasite pellets in a 11 ratio of PBS...”
- Plasmodium male gametocyte development and transmission are critically regulated by the two putative deadenylases of the CAF1/CCR4/NOT complex
Hart, PLoS pathogens 2019 - “...8|12|3 0|0|0 0.002 PY17X_1207500 NOT5 7|2|0 0|0|0 0.2196 PY17X_1452400 NOT4 0|1|0 0|0|0 0.8736 Translational Repressors PY17X_1220900 DOZI 12|13|4 0|0|0 0.0011 PY17X_1035100 CELF2 17|21|5 1|0|0 0.0037 Stress Granule PY17X_0311400 CCT8 10|3|3 0|0|0 0.0131 PY17X_0613400 HSP40 subfamily A 15|15|5 0|3|0 0.0368 PY17X_1135600 CCT4 12|5|1 1|0|0 0.0735 PY17X_0913800 TSN...”
- ALBA4 modulates its stage-specific interactions and specific mRNA fates during Plasmodium yoelii growth and transmission
Muñoz, Molecular microbiology 2017 - “...Bruno/HoBo/CELF2* 9|12|7 0.99 Y Y PY17X_0705000 conserved Plasmodium protein, unknown function 8|14|8 0.99 Y Y PY17X_1220900 DOZI 5|9|6 0.98 Y Y PY17X_0821000 Musashi/HoMu 5|6|3 0.96 Y Y PY17X_1336600 eIF4A 4|4|4 0.94 Y PY17X_0808800 HSP90 8|11|3 0.94 Y PY17X_1334000 40S ribosomal protein S3 6|3|4 0.94 Y Y...”
- “...PABP 98|38|78 1.00 PY17X_1208200 GBP2* 34|34|35 1.00 PY17X_1116400 conserved Plasmodium protein unknown function 53|13|64 1.00 PY17X_1220900 DOZI 52|15|36 1.00 PY17X_1364900 ALBA2 72|26|32 1.00 PY17X_1035100 Bruno/HoBo/CELF2* 44|14|35 1.00 PY17X_0705000 conserved Plasmodium protein unknown function 36|17|29 1.00 PY17X_1318600 EF2 52|8|31 1.00 PY17X_1304900 CITH 55|18|29 1.00 PY17X_0524100 alpha tubulin...”
- A bioinformatic survey of RNA-binding proteins in Plasmodium
Reddy, BMC genomics 2015 - “...Gene ID P. yoelii Gene ID RAP55 (CITH) PF3D7_1474900 PVX_118625 PY17X_1304900 RCK/p54 (DOZI) PF3D7_0320800 PVX_095195 PY17X_1220900 Puf2 PF3D7_0417100 PVX_089945 PY17X_0719200 ALBA1 PF3D7_0814200 PVX_123060 PY17X_1425300 ALBA2 PF3D7_1346300 PVX_083215 PY17X_1364900 ALBA3 PF3D7_1006200 PVX_094505 PY17X_1207600 ALBA4 PF3D7_1347500 PVX_083270 PY17X_1366000 RNA degradation is largely initiated through the removal of the...”
FANCM_CHICK / A0A1D5PRR9 Fanconi anemia group M protein; Protein FACM; ATP-dependent RNA helicase FANCM; Fanconi anemia-associated polypeptide of 250 kDa; FAAP250; Protein Hef ortholog; EC 3.6.4.13 from Gallus gallus (Chicken) (see 2 papers)
32% identity, 5% coverage
- function: DNA-dependent ATPase component of the Fanconi anemia (FA) core complex (By similarity). Required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage (PubMed:16116434, PubMed:19465393). In complex with CENPS and CENPX, binds double- stranded DNA (dsDNA), fork-structured DNA (fsDNA) and Holliday junction substrates (By similarity). Its ATP-dependent DNA branch migration activity can process branched DNA structures such as a movable replication fork (By similarity). This activity is strongly stimulated in the presence of CENPS and CENPX (By similarity). In complex with FAAP24, efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates (By similarity). In vitro, on its own, strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA (By similarity).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Component of the Fanconi anemia (FA) core complex. The FA core complex associates with Bloom syndrome (BLM) complex. This supercomplex between FA and BLM complexes has been called BRAFT.
PVX_095195 ATP-dependent RNA helicase, putative from Plasmodium vivax
28% identity, 16% coverage
- A bioinformatic survey of RNA-binding proteins in Plasmodium
Reddy, BMC genomics 2015 - “...vivax Gene ID P. yoelii Gene ID RAP55 (CITH) PF3D7_1474900 PVX_118625 PY17X_1304900 RCK/p54 (DOZI) PF3D7_0320800 PVX_095195 PY17X_1220900 Puf2 PF3D7_0417100 PVX_089945 PY17X_0719200 ALBA1 PF3D7_0814200 PVX_123060 PY17X_1425300 ALBA2 PF3D7_1346300 PVX_083215 PY17X_1364900 ALBA3 PF3D7_1006200 PVX_094505 PY17X_1207600 ALBA4 PF3D7_1347500 PVX_083270 PY17X_1366000 RNA degradation is largely initiated through the removal of...”
- Clinical proteomics of the neglected human malarial parasite Plasmodium vivax
Acharya, PloS one 2011 - “...dehydrogenase complex, putative), PVX_099275 (hypothetical protein), PVX_080555 (hypothetical protein), PVX_086990 (vacuolar ATP synthase subunit E), PVX_095195 (ATP-dependent RNA helicase, putative), PVX_099095 (elongation factor 1B, putative), PVX_121930 (hypothetical protein), PVX_092630 (hypothetical protein), PVX_098620 (hypothetical protein), PVX_124190 (hypothetical protein), PVX_113635 (hypothetical protein), PVX_101480 (hypothetical protein), PVX_087690 (hypothetical protein)...”
PF3D7_0320800 ATP-dependent RNA helicase DDX6 from Plasmodium falciparum 3D7
28% identity, 16% coverage
- The DEAD-box RNA helicase PfDOZI imposes opposing actions on RNA metabolism in Plasmodium falciparum
Min, Nature communications 2024 - “...with a GFP tag at the C-terminus, a 581bp 3 fragment of the pfdozi gene (Pf3D7_0320800) encoding aa 297433 of the PfDOZI protein was PCR amplified from the 3D7 genomic DNA using primers tagF and tagR (Supplementary Data 6 : Table S6 ), and cloned into...”
- The global transcriptome of Plasmodium falciparum mid-stage gametocytes (stages II-IV) appears largely conserved and gametocyte-specific gene expression patterns vary in clinical isolates
Kengne-Ouafo, Microbiology spectrum 2023 - “...0.0000829 18 PF3D7_1007700 AP2-I AP2 domain transcription factor AP2-I (1.9 : 1.5) 2.58E17 0.00000322 19 PF3D7_0320800 DOZI ATP-dependent RNA helicase DDX6 (1.32: 0.71 3.67E07 0.072052301 20 PF3D7_0525900 NEK2 NIMA-related kinase 2 (5.9 :3) 7.91E26 0.000405092 21 PF3D7_1129600 N/A Phosphatidylinositol-4-phosphate 5-kinase, putative (5.6 :3.01) 2.59E51 5.77E08 22...”
- Plasmodium falciparum specific helicase 2 is a dual, bipolar helicase and is crucial for parasite growth
Chauhan, Scientific reports 2019 - “...PF3D7_0514100 (PfUvrD) All DNA 7. PF3D7_0809700 (PfRuvB1) ATP DNA 8. PF3D7_110600 (PfRuvB2) ATP DNA 9. PF3D7_0320800 (PfDozi) ATP RNA 10. PF3D7_0934100 (PfXPD) ATP and UTP DNA 11. PF3D7_0918600 (PfBLM) ATP, CTP and dGTP DNA 12. PF3D7_1429900 (PfWRN) ATP and GTP DNA 13. PF3D7_ 0807100 (PfPSH3) ATP...”
- Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes: molecular insight into sex-specific processes and translational repression
Lasonder, Nucleic acids research 2016 - “...2.8E+01 2.0E+01 FG PF3D7_1474900 trailer hitch homolog (CITH) ( 11 ) 9.7E+01 1.6E+00 1.1E+01 FG PF3D7_0320800 ATP-dep.RNA helicase (DOZI) ( 10 ) 5.3E+01 3.1E+00 1.1E+01 FG PF3D7_0729900 dynein heavy chain, putative ( 9 ) 2.3E+01 5.9E-01 2.3E+00 FG PF3D7_0415600 adenylate kinase (GAK) ( 50 ) 7.0E+00...”
- The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum
Bunnik, Genome biology 2016 - “...into ookinetes in the mosquito midgut [ 23 ]. The ATP-dependent RNA helicase DDX6 (DOZI; PF3D7_0320800) and a homolog of CAR-I in fly and Trailer Hitch in worm (CITH; PF3D7_1474900) regulate the storage of these transcripts into ribonucleoprotein complexes in the cytoplasm of the female gametocyte...”
- Synthetic RNA-protein modules integrated with native translation mechanisms to control gene expression in malaria parasites
Ganesan, Nature communications 2016 - “...the yeast and P. falciparum homologues of Dcp1p, Dhh1p and Pop2p revealed that Dhh1p and PF3D7_0320800 (DOZI) had very high sequence identity and similarity (68% and 80%, respectively), and were similar in size (506 versus 433 amino acids, respectively) ( Supplementary Fig. 1a ). In contrast,...”
- A bioinformatic survey of RNA-binding proteins in Plasmodium
Reddy, BMC genomics 2015 - “...IDs Helicase PF3D7_0521700, PF3D7_0218400, PF3D7_1307300, PF3D7_1332700, PF3D7_0827000, PF3D7_1251500, PF3D7_0422700, PF3D7_1021500, PF3D7_1445900, PF3D7_0504200, PF3D7_0903400, PF3D7_1031500, PF3D7_1241800, PF3D7_0320800, PF3D7_0807100, PF3D7_0810600, PF3D7_1459000, PF3D7_1468700, PF3D7_0321600, PF3D7_0209800, PF3D7_0508700, PF3D7_0518500, PF3D7_0703500, PF3D7_0405000, PF3D7_1202000, PF3D7_0411400, PF3D7_0103600, PF3D7_1445200 HelicaseC+Suv3 PF3D7_0623700 Helicase+DUF4217 PF3D7_0721300, PF3D7_1419100, PF3D7_1418900, PF3D7_0630900 Helicase+ZnF PF3D7_0527900, PF3D7_0909900, PF3D7_1313400 Helicase+UPF_Zn PF3D7_1005500 Helicase+Sec63 PF3D7_1439100, PF3D7_0422500...”
- “...P. vivax Gene ID P. yoelii Gene ID RAP55 (CITH) PF3D7_1474900 PVX_118625 PY17X_1304900 RCK/p54 (DOZI) PF3D7_0320800 PVX_095195 PY17X_1220900 Puf2 PF3D7_0417100 PVX_089945 PY17X_0719200 ALBA1 PF3D7_0814200 PVX_123060 PY17X_1425300 ALBA2 PF3D7_1346300 PVX_083215 PY17X_1364900 ALBA3 PF3D7_1006200 PVX_094505 PY17X_1207600 ALBA4 PF3D7_1347500 PVX_083270 PY17X_1366000 RNA degradation is largely initiated through the removal...”
- Translational regulation during stage transitions in malaria parasites
Cui, Annals of the New York Academy of Sciences 2015 - “...protein PABP PBANKA_143920 PF3D7_1224300 Lsm14 domain protein CITH PBANKA_130130 PF3D7_1474900 DEAD-box RNA helicase DOZI PBANKA_121770 PF3D7_0320800 Conserved Plasmodium protein, unknown function PBANKA_070470 PF3D7_0825900 Homologue of BRUNO HoBo PBANKA_103270 PF3D7_1409800 Conserved Plasmodium protein, unknown function PBANKA_143520 PF3D7_1220000 Homologue of RNA-binding protein Musashi HoMu PBANKA_081770 PF3D7_0916700 eIF4E PBANKA_041280...”
PKNH_0820000 ATP-dependent RNA helicase DDX6, putative from Plasmodium knowlesi strain H
28% identity, 16% coverage
NP_001383930 Fanconi anemia group M protein from Gallus gallus
32% identity, 5% coverage
TpMuguga_02g00613 DEAD-box ATP-dependent RNA helicase 8 from Theileria parva strain Muguga
28% identity, 16% coverage
FOIG_04019 ATP-dependent rRNA helicase RRP3 from Fusarium odoratissimum NRRL 54006
28% identity, 15% coverage
NMB1281 transcription-repair coupling factor from Neisseria meningitidis MC58
25% identity, 10% coverage
- Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence
Joseph, Journal of bacteriology 2010 - “...B (LbpB/NMB1541), a transcription-repair coupling factor (NMB1281), and RNA-binding protein (NMB1826). Classification of strain-specific genes. About 20% of...”
- Diversity in coding tandem repeats in related Neisseria spp
Jordan, BMC microbiology 2003 - “...to contain no copies of the repeat in one of the strains was TR10, mfd (NMB1281), encoding transcription-repair coupling factor. While there are one to three copies of the 207 bp (69 amino acid) repeat in the pathogenic Neisseria spp., N. lactamica strain L12 has none...”
- “...) no TR9 NMA1461 NMB1027 XNG0526 DnaJ protein, truncation ( dnaJ ) no TR10 NMA1491 NMB1281 XNG0596 transcription-repair coupling factor ( mfd ) no TR11 NMA1547 NMB1333 XNG0546 conserved hypothetical protein no TR12 NMA1612 NMB1395 XNG0677 alcohol dehydrogenase, zinc-containing no TR13 NMA1680 NMB1468 XNG0955 hypothetical protein...”
NMA1491 transcription-repair coupling factor from Neisseria meningitidis Z2491
25% identity, 10% coverage
- Diversity in coding tandem repeats in related Neisseria spp
Jordan, BMC microbiology 2003 - “...sucB ) no TR9 NMA1461 NMB1027 XNG0526 DnaJ protein, truncation ( dnaJ ) no TR10 NMA1491 NMB1281 XNG0596 transcription-repair coupling factor ( mfd ) no TR11 NMA1547 NMB1333 XNG0546 conserved hypothetical protein no TR12 NMA1612 NMB1395 XNG0677 alcohol dehydrogenase, zinc-containing no TR13 NMA1680 NMB1468 XNG0955 hypothetical...”
GWCH70_2034 type III restriction protein res subunit from Geobacillus sp. WCH70
26% identity, 22% coverage
NCU04439 ATP-dependent RNA helicase dbp-4 from Neurospora crassa OR74A
29% identity, 11% coverage
SCO2863 helicase from Streptomyces coelicolor A3(2)
29% identity, 11% coverage
- Transcriptional Response of Streptomyces coelicolor to Rapid Chromosome Relaxation or Long-Term Supercoiling Imbalance
Szafran, Frontiers in microbiology 2019 - “...III subunit epsilon uvrA sco1958 69 1.89 Exconuclease ABC subunit A sco1969 67 1.88 DNA-methyltransferase sco2863 18 1.98 Helicase sco3434 27 2.01 DNA polymerase I sco4685 16 3.43 DEAD/DEAH box helicase xseA sco5056 69 1.51 Exodeoxyribonuclease VII large subunit sco5183 12 1.70 ATP-dependent DNA helicase sco5184...”
- A protein architecture guided screen for modification dependent restriction endonucleases
Lutz, Nucleic acids research 2019 - “...that cleaves 5mC and 5hmC modified DNA. To evaluate ScoA3I activity, a C-terminal 6xHig-tagged ScoA3I (Sco2863, 945 aa, from a TTG start codon) was purified through nickel agarose and heparin column chromatography. The purified enzyme was assayed for activity on modified DNA substrates such as: pBR322...”
- “...ScoMcrA) so that a third 5mC-dependent endonuclease might be redundant. It was reported previously that Sco2863 (ScoA3I) expressed in S. lividans was able to restrict Dcm + -modified shuttle vector by about a thousand-fold in transformation efficiency ( 44 ). The discrepancy of ScoA3I expression in...”
- The other face of restriction: modification-dependent enzymes
Loenen, Nucleic acids research 2014 - “...( 46 ); NWMN_2386 SepRPMcrR (+) ( 46 ); SERP2052 ScoA3I (+) ( 37 ); Sco2863 PvuRts1I family +/ + + NT NT ( 47 , 48 ) GmrSD + NT NT ( 49 ) ScoA3II+III (+) () ( 37 ); Sco3261-62 a Modifications: m5C: 5-methylcytosine;...”
- Characterization of the methyl-specific restriction system of Streptomyces coelicolor A3(2) and of the role played by laterally acquired nucleases
González-Cerón, FEMS microbiology letters 2009 (PubMed)- “...nucleases (the products of the SCO4213, SCO4631 and SCO2863 genes, as well as the SCO3261-SCO3262 operon) that are located in the laterally acquired genomic...”
- “...used. Construction of S. coelicolor null mutants lacking SCO2863 and cloning of this gene PCR targeting could not be used to construct a deletion...”
- Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
Hsiao, Antonie van Leeuwenhoek 2008 - “...primase 0.82715 0.520552 1.25613 0.69797 SCO2626 putative DNA repair hydrolase (fragment) 0.289916 0.337365 0.567783 0.326821 SCO2863 putative helicase 0.47935 0.68124 1.92881 0.81052 SCO2952 putative helicase protein 0.513952 0.38864 0.750517 0.379556 SCO3109 putative transcriptional-repair coupling factor 0.87255 0.29611 0.759684 0.33637 SCO3351 putative DNA repair protein 0.95043 0.68521...”
- Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans
Jayapal, BMC genomics 2007 - “...similar to an E. coli methylcytosine-specific restriction enzyme with an HNH endonuclease domain. In addition, SCO2863 a putative helicase, also contains an hsdR -like type I restriction endonuclease domain. Moreover, the absence of two DNA-methylases, SCO6844 and SCO6885 might explain why DNA obtained from S. lividans...”
FOIG_08941 ATP-dependent RNA helicase DBP3 from Fusarium odoratissimum NRRL 54006
33% identity, 11% coverage
CH_124133 ATP-dependent RNA helicase dbp-3 from Magnaporthe grisea 70-15 (see 2 papers)
36% identity, 11% coverage
FANCM_DROME / Q9VDA0 DEAD-box ATP-dependent DNA helicase Fancm; Fanconi anemia group M protein homolog; Protein FACM homolog; EC 5.6.2.4 from Drosophila melanogaster (Fruit fly) (see 2 papers)
NP_001262806 fanconi anemia group M helicase, isoform B from Drosophila melanogaster
36% identity, 5% coverage
- function: A ssDNA-dependent ATPase with 3' to 5' helicase activity (PubMed:27466228). Involved in multiple DNA-damage responses, some that require ATPase and helicase activity and some that are independent of these (PubMed:27466228). Involved in DNA interstrand cross-link repair, probably together with Fancl and other Fanconi anemia pathway homologs (PubMed:25205745). Independent of Fancl involved in DNA double strand break repair, including contributing to the synthesis-dependent strand annealing (SDSA) pathway (PubMed:25205745). Probably contributes to SDSA by unwinding short duplex regions in complex D-loop-like DNA structures (PubMed:27466228).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
catalytic activity: Couples ATP hydrolysis with the unwinding of duplex DNA by translocating in the 3'-5' direction.
disruption phenotype: Increased incidence of spontaneous mitotic crossovers (PubMed:25205745, PubMed:27466228). Increased sensitivity to DNA damage caused by the cross linking agent nitrogen mustard mechlorethamine (HN2), the alkylating agent methyl methanesulfonate (MMS), and double-strand break inducing ionizing radiation (IR) (PubMed:25205745, PubMed:27466228). - Biochemical Activities and Genetic Functions of the Drosophila melanogaster Fancm Helicase in DNA Repair.
Romero, Genetics 2016 - GeneRIF: Using transgenic flies expressing full-length or truncated Fancm, each with either a wild-type or mutated helicase domain, we found that there are helicase-independent and C-terminal-independent functions in responding to DNA damage and in preventing mitotic crossovers
- Drosophila FANCM helicase prevents spontaneous mitotic crossovers generated by the MUS81 and SLX1 nucleases.
Kuo, Genetics 2014 - GeneRIF: spontaneous mitotic crossovers that occur when FANCM is missing are dependent on MUS312 and either MUS81 or SLX1.
GOX0055 Transcription-repair coupling factor from Gluconobacter oxydans 621H
24% identity, 11% coverage
ECs1492 transcription-repair coupling factor from Escherichia coli O157:H7 str. Sakai
20% identity, 21% coverage
Q8BGE5 Fanconi anemia group M protein homolog from Mus musculus
35% identity, 3% coverage
RECG_STRPN / Q54900 ATP-dependent DNA helicase RecG; DNA branch migration protein RecG; Probable DNA 3'-5' helicase RecG; EC 5.6.2.4 from Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (see 2 papers)
SP_1697 ATP-dependent DNA helicase RecG from Streptococcus pneumoniae TIGR4
27% identity, 17% coverage
- function: Binds and unwinds Holliday junction (HJ) and partial replication fork DNA (PubMed:15533834). Unwinds R-loops (PubMed:15533834). Plays a critical role in recombination and DNA repair. Helps process Holliday junction intermediates to mature products by catalyzing branch migration. Has replication fork regression activity, unwinds stalled or blocked replication forks to make a HJ that can be resolved. Has a DNA unwinding activity characteristic of a DNA helicase with 3'-5' polarity (By similarity). Complements a recG deletion mutation in E.coli, restoring UV resistance and poor growth in the presence of mitomycin C (PubMed:8830261).
catalytic activity: Couples ATP hydrolysis with the unwinding of duplex DNA by translocating in the 3'-5' direction.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Monomer (By similarity).
disruption phenotype: Increased sensitivity to UV light and MMS (methyl methane sulphonate), a six- to seven-fold reduction in DNA recombination during transformation (PubMed:8830261). - Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
van, Nature methods 2009 - “...and Fig. 3d ). For instance, given the wild-type doubling time of 38 minutes, mutant SP_1697 should have a doubling time of ~31 minutes ([1/1.22]*38), we measured 31 minutes, and mutant SP_0841 should have a doubling time of ~54 minutes ([1/0.71]*38), we measured 57 minutes. Screening...”
- “...) Three representative growth curves; the wild type strain, a strain with an advantageous deletion (SP_1697, W =1.22) and a strain with a disadvantageous deletion (SP_0841, W =0.71). Figure 4 Genetic interaction network of five query genes. Interactions between two genes ( i and j )...”
MJ0383 ATP-dependent RNA helicase, putative from Methanocaldococcus jannaschii DSM 2661
34% identity, 21% coverage
- Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference
Beloglazova, The EMBO journal 2011 - “...substrates by MJ0384 is stimulated by the Cas3 helicase MJ0383 and ATP. The crystal structure of MJ0384 revealed the active site with two bound metal cations...”
- “...Cas proteins: Cas1 (MJ0378), Cas2 (MJ0386), Cas3 (MJ0376, MJ0383, MJ0384), Cas4 (MJ0377), Cas5 (MJ0382), and Cas6 (MJ0375, MJ1234). The other 11 Cas proteins...”
SPD_1507 ATP-dependent DNA helicase RecG from Streptococcus pneumoniae D39
27% identity, 17% coverage
PF1902 DNA repair helicase putative from Pyrococcus furiosus DSM 3638
33% identity, 13% coverage
lpg0954 transcription repair coupling factor from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
21% identity, 19% coverage
- Transcriptomic changes of Legionella pneumophila in water
Li, BMC genomics 2015 - “...DNA binding protein lpg2441 1.79 RNA polymerase sigma-54 factor lpg0477 1.44 Transcription repair coupling factor lpg0954 mfd 2.04 2.14 Transcriptional regulator lpg0586 1.24 3.75 4.48 Transcriptional regulator, ArsR family lpg2723 3.63 1.18 Transcriptional regulator, AsnC family lpg1486 2.33 Transcriptional regulator, DeoR family lpg2167 1.76 Transcriptional regulator,...”
FZF21_16140 ATP-dependent RNA helicase SrmB from Enterobacter sp. LU1
33% identity, 13% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory