PaperBLAST
PaperBLAST Hits for tr|H8H045|H8H045_DEIGI Permease OS=Deinococcus gobiensis (strain DSM 21396 / JCM 16679 / CGMCC 1.7299 / I-0) OX=745776 GN=DGo_PA0211 PE=3 SV=1 (399 a.a., MTAPPPAPPF...)
Show query sequence
>tr|H8H045|H8H045_DEIGI Permease OS=Deinococcus gobiensis (strain DSM 21396 / JCM 16679 / CGMCC 1.7299 / I-0) OX=745776 GN=DGo_PA0211 PE=3 SV=1
MTAPPPAPPFAALRRLWTWPLFQLAVVLLLLWGLLRVMGEVRAVLLSVAVAYLIAHLTNP
VLRWLSARRVPRPLGITLLFLALLGLLAALSPLIVTTAREVQSLAAQAPQLLDRLNAELR
SLSAHSPLLAGAQTQLSDWITQNAHTLPARLSRSAGELLSPRGALVSGVLGAFGLLGHAF
ITLVISIYMMAIYPQIGPFLLRLLPLRYQPGALELSGHVGRAVGGYFRGQITVALILGAL
LAAGLTLLGVPSGLAVGFLAALLNIVPYLGVVMSLIPALLLALPLGGLKVALVGLLFLAV
NQLEGHVISPRVVSHSTNLSPLGVLLAILFGVELFGILGAIVAVPFVALVKALMEAYYYP
SAGYRAGAGAGGPTATGEGRTVVASAAPPSAAGPGQPRA
Running BLASTp...
Found 86 similar proteins in the literature:
DR0252 conserved hypothetical protein from Deinococcus radiodurans R1
41% identity, 91% coverage
lp_2217 transport protein from Lactobacillus plantarum WCFS1
27% identity, 83% coverage
- CRISPR Interference for Rapid Knockdown of Essential Cell Cycle Genes in Lactobacillus plantarum
Myrbråten, mSphere 2019 - “...CozE homologs; Lp_1247 (35% identity and 60% similarity to CozE from S. pneumoniae ) and Lp_2217 (29% identity and 52% similarity to CozE from S. pneumoniae ). We constructed CRISPRi strains targeting each of these and analyzed the morphologies of the knockdown strains by microscopy. However,...”
- “...of plasmids harboring sgRNA to knock down expression of cozE homologs lp_1247 (strain IM141) and lp_2217 (strain IM142) and double knockdown of lp_1247 and lp_2217 (strain IM130). The restriction sites utilized for construction of the double-sgRNA plasmids are indicated (see Materials and Methods for details). (B)...”
SAUSA300_1254 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
SA1192 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAV1359 hypothetical protein from Staphylococcus aureus subsp. aureus Mu50
SAOUHSC_01358 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
YP_499885 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
25% identity, 84% coverage
- Inactivation of the Monofunctional Peptidoglycan Glycosyltransferase SgtB Allows Staphylococcus aureus To Survive in the Absence of Lipoteichoic Acid
Karinou, Journal of bacteriology 2019 - “...independently in 3 suppressor strains ( Table 1 ). Another strain had a mutation in SAUSA300_1254, coding for a hypothetical membrane protein, and SAUSA300_RS11150, encoding MazE, the antitoxin component of a type II toxin-antitoxin module ( Table 1 ). In the original study by Corrigan et...”
- “...20179522018187 DEL SAUSA300_1855; monofunctional glycosyltransferase SgtB ANG3712 (S2- mazE ) 1380637 INS G 100 38.5 SAUSA300_1254; hypothetical membrane protein Ile291FS 1380639 SNV C A 100 38.7 Ser292Tyr 1380641 REP C AG 100 38.4 Pro293fs 21884372188446 DEL TATCGGAAAA SAUSA300_RS11150; antitoxin component of type II toxin-antitoxin module mazEF...”
- Inhibition of the ATP Synthase Eliminates the Intrinsic Resistance of Staphylococcus aureus towards Polymyxins
Vestergaard, mBio 2017 - “...SAUSA300_1089 64 256 Diacylglycerol glucosyltransferase SAUSA300_0918 64 >256 Hypothetical protein SAUSA300_1802 64 >256 Hypothetical protein SAUSA300_1254 48 192 Hypothetical protein SAUSA300_0980 48 >256 Hypothetical protein SAUSA300_1495 64 >256 Interestingly, inactivation of multiple genes encoding subunits of the ATP synthase displayed increased sensitivity towards polymyxins: the genes...”
- Repurposing of the antimalarial agent tafenoquine to combat MRSA
She, mSystems 2023 - “...8 32 ATCC 25923 8 16 Newman 8 32 LZB1 8 16 SA1191 16 16 SA1192 8 16 SA1193 8 32 SA1195 8 16 SA0645 a 16 16 SA2174 a 16 16 S. epidermidis ATCC 12228 4 64 RP62A 4 64 E. faecalis ATCC 19212 8...”
- Exploring the transcriptome of Staphylococcus aureus in its natural niche
Chaves-Moreno, Scientific reports 2016 - “...vivo (up to 11,970rpm). Evidently, also genes encoding various membrane proteins (SAV0374, SAV0574, SAV1030 and SAV1359) were extremely differently expressed under in vivo versus in vitro 24 conditions ( Supplementary Dataset S2 and Fig. 3D ). A further protein where the encoding gene showed a 2...”
- The function of CozE proteins is linked to lipoteichoic acid biosynthesis in Staphylococcus aureus
Barbuti, mBio 2024 - “...( 12 ), re-sequencing of ltaS deletion mutants resulted in potential suppressor mutations in cozEb (SAOUHSC_01358). This prompted us to investigate a potential link between CozE proteins and LTA synthesis. To screen for potential functional links between cozE and LTA synthesis genes, sgRNAs targeting ltaS and...”
- The function of CozE proteins is linked to lipoteichoic acid biosynthesis inStaphylococcus aureus
Barbuti, 2023 - c-di-AMP is a new second messenger in Staphylococcus aureus with a role in controlling cell size and envelope stress
Corrigan, PLoS pathogens 2011 - “...all five suppressor strains; SAOUHSC_01104, encoding for the succinate dehydrogenase SdhA, a TCA cycle enzyme; SAOUHSC_01358, which encodes for a putative permease; SAOUHSC_02001, a conserved hypothetical protein with weak homology to a fusaric acid transporter, and SAOUHSC_02407, a conserved hypothetical protein with homology to DisA, a...”
- “...Mutations present in SEJ1 ltaS suppressor strains. S. aureus NCTC8325 gene number Strain SAOUHSC_00015 SAOUHSC_01104 SAOUHSC_01358 SAOUHSC_02001 SAOUHSC_02407 4S4 Inverted 18,92419,002 (AA203227 flipped) C 1,065,691 G (Thr119Arg) C 1,300,654 G (Pro287Arg) WT C 2,235,383 A (Leu193Phe) 4S5 G 19,114 A (Gly266Asp) WT G 1,300,870 A (Gly359Asp)...”
- CozEa and CozEb play overlapping and essential roles in controlling cell division in Staphylococcus aureus.
Stamsås, Molecular microbiology 2018 (PubMed)- GeneRIF: These results show that CozEa and Cozeb proteins mediate control of cell division in S. aureus and S. pneumoniae, likely via interactions with key cell division proteins such as EzrA.
F8FLY5 AI-2E family transporter from Paenibacillus mucilaginosus (strain KNP414)
27% identity, 85% coverage
- Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism
Khera, The EMBO journal 2022 - “...AI2 exporters from E.coli (TqsA, YhhT, and PerM), Brucella abortus (UniProt: A0A7U8JIH7), Paenibacillus mucilaginosus (UniProt: F8FLY5), and Bacillus subtilis (YueF, UniProt: O32095). Similarly, homologs considered for Upf0118 group include proteins from H.andaensis (Upf0118, UniProt: A0A1W5X0D5), B.subtilis (YtvI, UniProt O50485), Bacillus pseudofirmus (YCT2, UniProt: Q04454), and Clostridium...”
SP_1505 hypothetical protein from Streptococcus pneumoniae TIGR4
spr1357 Conserved hypothetical protein from Streptococcus pneumoniae R6
SPD_1332 hypothetical protein from Streptococcus pneumoniae D39
25% identity, 83% coverage
- CRISPRi-TnSeq maps genome-wide interactions between essential and non-essential genes in bacteria
Jana, Nature microbiology 2024 - “...5 , respectively. Strain CG89 ( S. pneumoniae TIGR4, bgaA ::P Zn - m(sf)gfp - sp_1505 ) was constructed by transformation of S. pneumoniae TIGR4 wild type with plasmid pCG15. This plasmid was built by ligating the product amplified by PCR with primers SP1505_F-SpeI and SP1505-R-NotI...”
- “...was built by transformation of TIGR4 wild type with product kan-m(sf)gfp-sp1505 to replace the original SP_1505 gene. The DNA product was obtained by Gibson assembly of three PCR fragments: (1) m(sf)gfp-sp1505 amplified with primers SP_1505-up-Htra-GFP-F and SP_1505-down-R on CG89 genomic DNA; (2) kan , kanamycin resistance...”
- A genome-wide atlas of antibiotic susceptibility targets and pathways to tolerance
Leshchiner, Nature communications 2022 - “...ideal if the gene is also important for survival in vivo. A strong candidate is SP_1505, which in the interaction network is most tightly linked to cell wall metabolism and cell-division genes (Fig. 4a ). After we previously hypothesized that it may play a role in...”
- “...Jaccard similarity index was set to 0.5, and nodes in different landscapes were retained. CozEb (SP_1505) cloning and protein expression Cloning and expression of SP_1505 was undertaken commercially (Genscript). Codon-optimized SP_1505 was cloned into pET28a with a C-terminal His-tag. E. coli BL21 (DE3) was transformed with...”
- The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages
Mariano, Scientific reports 2016 - “...hypothetical protein 2.5 3 orf51 Hypothetical protein SP_1672 recombination protein RecR 0.5 6 orf58 Holin SP_1505 membrane protein 1 1 orf58 Holin SP_1731 conserved hypothetical protein 2.5 3 orf58 Holin SP_1606 glycosyl transferase, family 2 25 3 orf58 Holin SP_1751 putative transporter, CorA family 25 5...”
- A CozE Homolog Contributes to Cell Size Homeostasis of Streptococcus pneumoniae
Stamsås, mBio 2020 - “...( 29 ). Here, we report that S. pneumoniae also encodes a second CozE homolog (Spr1357 in strain R6, SPD_1332 in strain D39). For clarity and consistency with the S. aureus study and our phylogenetic analysis, this protein is termed CozEb and the original CozE (Spr0777...”
- “...CozEa) ( 26 ) as the query showed that S. pneumoniae encodes a second protein (Spr1357) belonging to the same family (Pfam PF01594) ( 28 ). Spr1357 displays 28% identity and 54% similarity with CozEa ( Fig.S1A ). In addition, the two proteins have similar predicted...”
- Search for genes essential for pneumococcal transformation: the RADA DNA repair protein plays a role in genomic recombination of donor DNA
Burghout, Journal of bacteriology 2007 - “...i.e., spr0459-spr0460, spr0777, spr0838, spr1259-spr1260, and spr1357, resulted in reduced, albeit modest, transformation rates. No connection to pneumococcal...”
- “...spr0460 spr0777 spr0838 spr0857 spr0881 spr1259 spr1260 spr1357 spr1779 spr1858 spr1859 spr1863 spr1864 spr2011 spr2013 spr2014 spr2042 spr2046 Positively...”
- A CozE Homolog Contributes to Cell Size Homeostasis of Streptococcus pneumoniae
Stamsås, mBio 2020 - “...we report that S. pneumoniae also encodes a second CozE homolog (Spr1357 in strain R6, SPD_1332 in strain D39). For clarity and consistency with the S. aureus study and our phylogenetic analysis, this protein is termed CozEb and the original CozE (Spr0777 in strain R6, SPD_0768...”
ABUW_0982 chloramphenicol efflux transporter CxpE from Acinetobacter baumannii
28% identity, 78% coverage
- Genomic Diversity, Antimicrobial Susceptibility, and Biofilm Formation of Clinical Acinetobacter baumannii Isolates from Horses
Rühl-Teichner, Microorganisms 2023 - “...the chloramphenicol acetyltransferase gene catA1 was detected in only 26.9% of the isolates, we identified ABUW_0982 in all isolates. This gene was recently described as a primary determinant of intrinsic CHL resistance in the human MDR A. baumannii strain 5075 [ 47 ]. The 30 GEN-resistant...”
- “...aph(3)-VIa aph(3)-Ia aph(3)-Ic aph(6)-Id 29.5 32.1 5.1 23.1 30.8 23.1 Phenicols * Chloramphenicol 100 catA1 ABUW_0982 26.9 100 Sulfonamides Trimethoprimsulfamethoxazole 37.2 sul1 sul2 35.9 2.6 Tetracyclines Tetracycline 33.3 tet(A) tet(B) tet(39) 10.3 1.3 1.3 Fluoroquinolones Enrofloxacin Marbofloxacin 37.2 35.9 none # none # Nitrofuran derivates Nitrofurantoin...”
- Acinetobacter baumannii Antibiotic Resistance Mechanisms
Kyriakidis, Pathogens (Basel, Switzerland) 2021 - “...(Ab5075) chloramphenicol resistance has been linked with efflux by an inner membrane permease encoded by ABUW_0982 gene [ 168 ]. Moreover, a recent study identified 8 MDR A. baumannii isolates bearing tet(X5) in plasmids and two isolates with tet(X6) in their chromosomes that displayed resistance to...”
- Multidrug-Resistant Acinetobacter baumannii Chloramphenicol Resistance Requires an Inner Membrane Permease
Karalewitz, Antimicrobial agents and chemotherapy 2018 - “...We identified multiple mutants with mutations in the ABUW_0982 gene, predicted to encode a permease broadly present in A. baumannii isolates with increased...”
- “...such as chloramphenicol acyltransferase genes, we found that ABUW_0982 is the primary determinant of intrinsic CHL resistance in A. baumannii strain 5075...”
O32095 Putative transport protein YueF from Bacillus subtilis (strain 168)
28% identity, 76% coverage
- Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism
Khera, The EMBO journal 2022 - “...and PerM), Brucella abortus (UniProt: A0A7U8JIH7), Paenibacillus mucilaginosus (UniProt: F8FLY5), and Bacillus subtilis (YueF, UniProt: O32095). Similarly, homologs considered for Upf0118 group include proteins from H.andaensis (Upf0118, UniProt: A0A1W5X0D5), B.subtilis (YtvI, UniProt O50485), Bacillus pseudofirmus (YCT2, UniProt: Q04454), and Clostridium difficile (UniProt: Q188A3). The choice of...”
HMPREF0351_10955 AI-2E family transporter from Enterococcus faecium DO
25% identity, 77% coverage
- The LiaFSR and BsrXRS Systems Contribute to Bile Salt Resistance in Enterococcus faecium Isolates
Zhou, Frontiers in microbiology 2019 - “...protein K 3824725 HMPREF0351_11918 N -acetyltransferase GCN5 K 3824372 HMPREF0351_10954 GNAT family acetyltransferase Q 3824373 HMPREF0351_10955 Permease P 3824469 HMPREF0351_11172 Fosfomycin resistance protein FosX S 3824470 HMPREF0351_11173 Hypothetical protein S 3824507 HMPREF0351_11295 Enoyl- acyl-carrier-protein reductase NADH I 3824508 HMPREF0351_11296 3-hydroxydecanoyl-ACP dehydratase I 3824962 HMPREF0351_12672 Hypothetical protein...”
- “...( HMPREF0351_11295 ), secondary metabolites biosynthesis ( HMPREF0351_10954 ), inorganic ion transport and metabolism ( HMPREF0351_10955 ), cell wall maintenance ( HMPREF0351_10944 ), and DNA mismatch repair ( HMPREF0351_11678 ). The other target genes encode hypothetical proteins of unknown functions ( HMPREF0351_11172 , 11173 , 12076...”
Q8Y9E6 Lmo0584 protein from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
lmo0584 conserved hypothetical membrane protein from Listeria monocytogenes EGD-e
27% identity, 80% coverage
- Proteomic Analysis of Listeria monocytogenes FBUNT During Biofilm Formation at 10°C in Response to Lactocin AL705
Melian, Frontiers in microbiology 2021 - “...Hypothetical protein lmo0391 Q8Y9X6 Hypothetical protein lmo0111 Q8YAK7 Hypothetical protein lmo2502 Q8Y4E4 Hypothetical protein lmo0584 Q8Y9E6 Hypothetical protein lmo1452 P53434 Interaction of Differentially Regulated Proteins in L. monocytogenes FBUNT Untreated and Treated Biofilm Cells The protein-protein interaction networks were constructed analyzing proteins that showed differences in...”
- Proteomic Analysis of Listeria monocytogenes FBUNT During Biofilm Formation at 10°C in Response to Lactocin AL705
Melian, Frontiers in microbiology 2021 - “...Q8Y3J2 Hypothetical protein lmo0391 Q8Y9X6 Hypothetical protein lmo0111 Q8YAK7 Hypothetical protein lmo2502 Q8Y4E4 Hypothetical protein lmo0584 Q8Y9E6 Hypothetical protein lmo1452 P53434 Interaction of Differentially Regulated Proteins in L. monocytogenes FBUNT Untreated and Treated Biofilm Cells The protein-protein interaction networks were constructed analyzing proteins that showed differences...”
- Transcriptional and phenotypic responses of Listeria monocytogenes to chlorine dioxide
Pleitner, Applied and environmental microbiology 2014 - “...0.006 0.041 0.031 0.001 0.039 Cell envelope lmo0584 lmo0880 Cellular processes lmo0220 lmo0321 lmo0515 lmo0669 lmo0906 lmo0983 lmo1288 lmo1433 lmo1439 lmo1577...”
- Transcriptomic response of Listeria monocytogenes to iron limitation and Fur mutation
Ledala, Applied and environmental microbiology 2010 - “...or membrane protein-related genes, such as lmo0160, lmo0576, lmo0584, lmo0732, and lmo2522, were downregulated in the absence of iron. Protein sequence analysis...”
- “...surface (3). Analysis of the other sequences showed that Lmo0584 is similar to YubA, a membrane protein of unknown function, whereas Lmo0576 is similar to mucin...”
- Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling
Schauer, BMC genomics 2010 - “...the drug/metabolite transporter (DMT) superfamily possible 4.2 2.3 lmo2694 lysine decarboxylase possible 5.5 0 4 lmo0584 conserved hypothetical membrane protein, putative permease no 7.2 3.0 lmo2770 -glutamylcysteine synthetase and cyanophycin synthetase no 5.8 2.3 lmo0645 amino acid transporter no 4.9 1.5 6 serC (lmo2825) phosphoserine aminotransferase...”
- Listeria monocytogenes {sigma}B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains
Oliver, Applied and environmental microbiology 2010 - “...lmo0398 lmo0399 lmo0400 lmo0401 lmo0402 lmo0439 lmo0449 lmo0584 lmo0589 lmo0590 Productb 4226 OLIVER ET AL. APPL. ENVIRON. MICROBIOL. TABLE 6--Continued Genea...”
LGG_01827 AI-2E family transporter from Lacticaseibacillus rhamnosus GG
26% identity, 97% coverage
PP1667 transporter, putative from Pseudomonas putida KT2440
31% identity, 80% coverage
LMOf2365_0930 hypothetical protein from Listeria monocytogenes str. 4b F2365
26% identity, 86% coverage
c4267 Hypothetical protein yhhT from Escherichia coli CFT073
28% identity, 78% coverage
- Transmissible Gastroenteritis Virus Infection Enhances SGLT1 and GLUT2 Expression to Increase Glucose Uptake
Dai, PloS one 2016 - “...were used in this study: anti-p-EGFR antibody (D7A5; Cell Signaling Technology, Danvers, MA, USA), anti-EGFR (c4267; Cell Signaling Technology, Danvers, MA, USA), anti-SGLT1 (ab14686; Abcam, Cambridge, UK), anti-GLUT2 (sc-7580; Santa Cruz Biotechnology, Dallas, TX, USA), anti--tubulin (E12-043; Enogene Biotech, New York, NY, USA). Membranes were then...”
YhhT / b3474 putative transporter YhhT from Escherichia coli K-12 substr. MG1655 (see 4 papers)
b3474 orf, hypothetical protein from Escherichia coli str. K-12 substr. MG1655
P0AGM0 Putative transport protein YhhT from Escherichia coli (strain K12)
ECs4323 hypothetical protein from Escherichia coli O157:H7 str. Sakai
28% identity, 78% coverage
- Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity
Weber, Journal of bacteriology 2005 - “...b1234 b3453 b3450 b0808 b0815 b1440 b1644 b1806 b1833 b3474 b3522 b2543 b2666 Gene product a OD 4 NaClb pH 5c Alcohol dehydrogenase, propanol preferring...”
- Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.
Paparoditis, Biochimica et biophysica acta 2014 - “...organoanions autoinducer-2 furanosyl borate diester Q7UIW9 6 2.A.86.1.1 P0AFI9 7 organoanions autoinducer-2 Q7USJ9 8 2.A.86.1.2 P0AGM0 7 organoanions autoinducer-2 Q7ULF1 6 2.A.86.1.2 P0AGM0 7 organoanions autoinducer-2 Q7USP8 7 2.A.86.1.2 P0AGM0 7 organoanions autoinducer-2 Q7UYF5 7 2.A.86.2.3 Q3IS50 7 organoanions autoinducer-2 Q7UPF9 8 2.A.93 Unknown BART Superfamily-1...”
- Physiological Response of Escherichia coli O157:H7 Sakai to Dynamic Changes in Temperature and Water Activity as Experienced during Carcass Chilling
King, Molecular & cellular proteomics : MCP 2016 - “..., ECs2695 , ECs2785 , ECs2888 , ECs3588 , ECs4112 , yhfG / ECs4213 , ECs4323 , ysgA / ECs4760 , ECs5089 ). Cluster II contains genes involved in fatty acid and phospholipid metabolism ( fadA / ECs4773 , fadI / ECs3225 ). Genes involved in...”
Bcer98_3102 protein of unknown function UPF0118 from Bacillus cereus subsp. cytotoxis NVH 391-98
22% identity, 76% coverage
- Divergence of the SigB regulon and pathogenesis of the Bacillus cereus sensu lato group
Scott, BMC genomics 2012 - “...signal transduction histidine kinase, ResE bID_Cluster_9721 12 Bcer98_3007 ferric uptake regulator family protein bID_Cluster_3378 13 Bcer98_3102 hypothetical protein bID_Cluster_4858 14 Bcer98_4017 MscS mechanosensitive ion channel All of the SigB-controlled genes originally described by Van Schaik et al. [ 44 ] are found in this core regulon....”
lp_1247 transport protein from Lactobacillus plantarum WCFS1
25% identity, 79% coverage
- CRISPR Interference for Rapid Knockdown of Essential Cell Cycle Genes in Lactobacillus plantarum
Myrbråten, mSphere 2019 - “...studied in rod-shaped bacteria. Homology searches revealed that L. plantarum WCFS1 encodes two CozE homologs; Lp_1247 (35% identity and 60% similarity to CozE from S. pneumoniae ) and Lp_2217 (29% identity and 52% similarity to CozE from S. pneumoniae ). We constructed CRISPRi strains targeting each...”
- “.... (A) Schematic overview of plasmids harboring sgRNA to knock down expression of cozE homologs lp_1247 (strain IM141) and lp_2217 (strain IM142) and double knockdown of lp_1247 and lp_2217 (strain IM130). The restriction sites utilized for construction of the double-sgRNA plasmids are indicated (see Materials and...”
A9WAN6 Permease from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)
28% identity, 82% coverage
- Deciphering the functional role of hypothetical proteins from Chloroflexus aurantiacs J-10-f1 using bioinformatics approach
Thakur, Molecular biology research communications 2020 - “...II like A9WGM3 Lamin tail domain superfamily A9WAT0 1,4 alpha glucan branching enzyme MT3115 like A9WAN6 Transmembrane protein TqsA like A9WJJ6 CCB3/YggT Domain and BLAST analysis characterized HC-HPs role as the member of photosynthetic complex. Four HC-HPs with accession number: A9WC42, A9WC74, A9WD59 and A9WDH7 were...”
- “...4.78 136025 36.45 stable 86.04 -0.08 A9WAT0 485 55746.41 6.08 99935 49.25 unstable 98.6 -0.278 A9WAN6 386 42700.88 8.75 66350 38.79 stable 142.23 0.857 A9WJJ6 85 9584.54 6.53 6990 57.44 unstable 133.06 0.976 MW: Moleular Weight, PI: Isoelectric Point, EC: Extinction Coefficient, IN: Instability index, C:...”
MSMEG_0249 integral membrane protein from Mycobacterium smegmatis str. MC2 155
A0QP26 Integral membrane protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
28% identity, 84% coverage
- New approaches to target the mycolic acid biosynthesis pathway for the development of tuberculosis therapeutics
North, Current pharmaceutical design 2014 - “...]. Genetic analysis of spontaneous BM212-resistant mutants in M. smegmatis revealed alterations in three genes, MSMEG_0249 (integral membrane protein), MSMEG_0250 (MmpL3) and MSMEG_0251 (hypothetical protein). Upon further evaluation, MSMEG_0249 and MSMEG_0251 were identical to wild-type, but MSMEG_0250 contained two non-synonymous mutations translating to A254V and I296L...”
- MmpL3 is the cellular target of the antitubercular pyrrole derivative BM212
La, Antimicrobial agents and chemotherapy 2012 - “...confer resistance to BM212 and contained three genes, MSMEG_0249 (1,140 bp), MSMEG_0250 (3,042 bp), and MSMEG_0251 (699 bp), which code for an integral membrane...”
- “...reference M. smegmatis genome. While the sequences for MSMEG_0249 and MSMEG_0251 were identical to the wild-type sequence, the mmpL3 sequence contained 2...”
- Mycobacterium tuberculosis Small RNA MTS1338 Confers Pathogenic Properties to Non-Pathogenic Mycobacterium smegmatis
Bychenko, Microorganisms 2021 - “...and proline co-importer, conserved transmembrane protein, transmembrane ATP-binding protein, ABC transporter I7FV42, integral membrane protein A0QP26, and integral membrane cytochrome D-II CydB I7GAS8. The expression of Sec-independent protein translocase TatC was also not observed in the MTS1338 strain. Mycobacteria utilize the Tat pathway to transport proteins...”
SCO5030 integral membrane protein from Streptomyces coelicolor A3(2)
28% identity, 68% coverage
- Defining the regulon of genes controlled by σE , a key regulator of the cell envelope stress response in Streptomyces coelicolor
Tran, Molecular microbiology 2019 - “...GGC AACC GCCGCCCGGGGTTTCGT CGTCT C 172 sco4968 Membrane protein CGG AACG GCGTACCAGCCGCTGAA GGTCT A 347 sco5030 Membrane protein CTC AACC TCGCGCAGCCCCTCAC CGTCT T 94 sco5039 HMW PBP, cell wall biosynthesis CAC AACC TTGAACCCCGCTCGTA CGTCG G 335 sco5049 Hypothetical protein GCG AACT GTCCGACTTGAATTTCA CCTTT C 212 sco5213...”
- “...target genes sco2334, sco2897 , sco3044 , sco3712 , sco4134 , sco4471 , sco4847 , sco5030 , sco5358 and the 12gene cwg operon ( sco61796190 ). Class II targets have a single promoter that is partially dependent on E for its transcription (see, for example, Fig....”
PD374_19610 AI-2E family transporter from Pseudomonas sp. WCS374
28% identity, 80% coverage
Rru_A3520 Protein of unknown function UPF0118 from Rhodospirillum rubrum ATCC 11170
29% identity, 74% coverage
DESUT3_31000 AI-2E family transporter from Desulfuromonas versatilis
31% identity, 40% coverage
alr4938 hypothetical protein from Nostoc sp. PCC 7120
25% identity, 80% coverage
alr0242 hypothetical protein from Nostoc sp. PCC 7120
26% identity, 83% coverage
SGO_1657 membrane protein from Streptococcus gordonii str. Challis substr. CH1
SGO_RS08120 AI-2E family transporter from Streptococcus gordonii str. Challis substr. CH1
26% identity, 85% coverage
- Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq
Mutha, Scientific reports 2019 - “...protein (predicted phosphohydrolase enzyme with conserved histidine and/or aspartate residues), respectively, were linked to SGO_RS08120 (SGO_1657), encoding a membrane protein, on the basis of gene co-occurrence and protein homology. In total, 27 of the 69 regulated S. gordonii genes were grouped into networks by STRING DB....”
- Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq
Mutha, Scientific reports 2019 - “...domain protein (predicted phosphohydrolase enzyme with conserved histidine and/or aspartate residues), respectively, were linked to SGO_RS08120 (SGO_1657), encoding a membrane protein, on the basis of gene co-occurrence and protein homology. In total, 27 of the 69 regulated S. gordonii genes were grouped into networks by STRING...”
Q7USJ9 Permease from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
26% identity, 79% coverage
RT0621 possible permease from Rickettsia typhi str. wilmington
21% identity, 80% coverage
BSU31160 putative integral inner membrane protein from Bacillus subtilis subsp. subtilis str. 168
24% identity, 69% coverage
TC 2.A.86.1.7 / O53656 Rv0205 (UFP0118) protein (376 aas, 8 putative TMSs) (may function with a heme uptake transporter) (TC# 2.A.6.5.5) from Mycobacterium tuberculosis (see 2 papers)
Rv0205 PROBABLE CONSERVED TRANSMEMBRANE PROTEIN from Mycobacterium tuberculosis H37Rv
28% identity, 84% coverage
A9WJF9 Permease from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)
25% identity, 81% coverage
- Deciphering the functional role of hypothetical proteins from Chloroflexus aurantiacs J-10-f1 using bioinformatics approach
Thakur, Molecular biology research communications 2020 - “...propeller, TolB like A9WHZ1 Phosphate regulon sensor protein PhoR A9WJM5 RmlC like jelly roll fold A9WJF9 Transmembrane protein TqsA like A9WHC9 Restriction endonuclease type II like A9WGM3 Lamin tail domain superfamily A9WAT0 1,4 alpha glucan branching enzyme MT3115 like A9WAN6 Transmembrane protein TqsA like A9WJJ6 CCB3/YggT...”
- “...8.46 32220 43.84 unstable 120.38 0.313 A9WJM5 613 68498.39 6.16 53830 44.96 unstable 93.72 -0.114 A9WJF9 432 46351.65 5.59 56380 51.47 unstable 128.96 0.743 A9WHC9 377 42791.5 5.22 42400 48.24 unstable 76.87 -0.76 A9WGM3 824 86307.05 4.78 136025 36.45 stable 86.04 -0.08 A9WAT0 485 55746.41 6.08...”
F3M2M2 Putative membrane protein from Paenibacillus sp. HGF5
23% identity, 76% coverage
YP_499501 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SA0870 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAR0979 putative membrane protein from Staphylococcus aureus subsp. aureus MRSA252
SAFDA_0882 lipoteichoic acid biosynthesis protein CozEa from Staphylococcus aureus
22% identity, 87% coverage
- CozEa and CozEb play overlapping and essential roles in controlling cell division in Staphylococcus aureus.
Stamsås, Molecular microbiology 2018 (PubMed)- GeneRIF: These results show that CozEa and Cozeb proteins mediate control of cell division in S. aureus and S. pneumoniae, likely via interactions with key cell division proteins such as EzrA.
- Direct targets of CodY in Staphylococcus aureus
Majerczyk, Journal of bacteriology 2010 - “...ilvA ilvE Methionine SA0431 SA0430 SA0429 SA0428 ilvE metE SA0870 SA2575, 2574 Histidine SA2704 SA2703 SA2702 SA2700 SA2699 hisZ hisG hisD hisB hisH SA2698 hisA...”
- “...ilvA SA0431, SA0430, SA0429, metE, SA0427 SA0427 SA0870 SA2575 SA2574 Serine SA1772 SA1773 SA1774 Genetic organizationb hisZGD, SA2701, BHAFI hisC SA1772,...”
- Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover
Anderson, Journal of bacteriology 2006 - “...SA0692 SA0703 SA0730 SA0755 SA0768 SA0785 SA0821 SA0822 SA0870 SA0871 SA0920 SA1033 SA1044 SA1101 SA1117 SA1191 SA1200 SA1375 SA1418 SA1556 SA1658 SA1659 SA1664...”
- The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
Kenny, PloS one 2009 - “...2.44 8.06E-04 SAR0970 protozoan/cyanobacterial globin family protein 2.38 1.11E-02 SAR0971 conserved hypothetical protein 2.78 1.87E-03 SAR0979 putative membrane protein 2.50 2.25E-03 SAR0981 putative esterase 2.44 1.55E-03 SAR0982 putative restriction-modification system protein 2.44 1.37E-03 SAR0983 putative restriction-modification system protein 2.56 2.42E-03 SAR0985 putative 2,5 RNA ligase family...”
- Understanding the Mechanism of Action of NAI-112, a Lanthipeptide with Potent Antinociceptive Activity
Tocchetti, Molecules (Basel, Switzerland) 2021 - “...SAFDA_0459 to SAFDA_r0004 SNP A to T Non-coding Lysyl-tRNA synthetase5S ribosomal RNA R15.4 R15.5 965417 SAFDA_0882 to SAFDA_0883 SNP C to A b Non-coding Hypothetical proteinNa + alanine symporter R8.1 R15.4 751022 SAFDA_0672 SNP C to A Ala451Ser Di-/tripeptide ABC transporter a Numbering and annotations are...”
Eab7_1321 AI-2E family transporter from Exiguobacterium antarcticum B7
33% identity, 43% coverage
spr0777 Conserved hypothetical protein from Streptococcus pneumoniae R6
Q8DQ98 AI-2E family transporter from Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
SPD_0768 hypothetical protein from Streptococcus pneumoniae D39
24% identity, 85% coverage
- A CozE Homolog Contributes to Cell Size Homeostasis of Streptococcus pneumoniae
Stamsås, mBio 2020 - “...aureus study and our phylogenetic analysis, this protein is termed CozEb and the original CozE (Spr0777 in strain R6, SPD_0768 in strain D39) is referred to as CozEa in this work. Our experiments demonstrated that the deletion of the two genes generates opposing effects on cell...”
- “...cell morphogenesis. RESULTS S. pneumoniae encodes two CozE homologs. Homology searches using the pneumococcal CozE (Spr0777; here referred to as CozEa) ( 26 ) as the query showed that S. pneumoniae encodes a second protein (Spr1357) belonging to the same family (Pfam PF01594) ( 28 )....”
- Pneumococcal Encounter With the Blood-Brain Barrier Endothelium
Anil, Frontiers in cellular and infection microbiology 2020 - “...putative candidates: adhesion lipoprotein, pneumococcal histidine triad protein A (PhtA), endo--N-acetylglucosaminidase, and two hypothetical proteins: Spr0777 and Spr1730 (Jimenez-Munguia et al., 2018 ). Their respective interacting partners on the endothelium, however, remains to be investigated. Figure 1 Major interactions facilitating SPN adhesion to BMECs. Major interactions...”
- The Cell Wall of Streptococcus pneumoniae
Vollmer, Microbiology spectrum 2019 (secret) - Proteomic and bioinformatic pipeline to screen the ligands of S. pneumoniae interacting with human brain microvascular endothelial cells
Jiménez-Munguía, Scientific reports 2018 - “...interactive analysis and literature review, five ligands (adhesion lipoprotein, endo--N-acetylglucosaminidase, PhtA and two hypothetical proteins, Spr0777 and Spr1730) were selected to validate experimentally (ELISA and immunocytochemistry) the ligand-BMECs interaction. In this study, we proposed a high-throughput approach to generate a dataset of plausible bacterial ligands followed...”
- “...of selected bacterial ligands (Adhesion lipoprotein, Spr0996; PhtA, Spr1061; endo--N-acetylglucosaminidase, Spr0440; and two hypothetical proteins, Spr0777 and Spr1730) to BMECs, which may have a crucial role in the commencement of neuroinvasion. This approach could also be used for other pathogens to unfold protein-protein interactions. Results Ligands...”
- Identification of pneumococcal proteins that are functionally linked to penicillin-binding protein 2b (PBP2b)
Straume, Molecular microbiology 2017 (PubMed)- “...phenotypic changes. Four proteins, RodA, MreD, DivIVA and Spr0777, were identified by this approach. Together with PBP2b these proteins are essential for the...”
- “...to CbpD-hypersensitive strains, namely: RodA, MreD, DivIVA and Spr0777. In sum, our results show that together with PBP2b these proteins are essential for the...”
- Search for genes essential for pneumococcal transformation: the RADA DNA repair protein plays a role in genomic recombination of donor DNA
Burghout, Journal of bacteriology 2007 - “...of the eight remaining genes, i.e., spr0459-spr0460, spr0777, spr0838, spr1259-spr1260, and spr1357, resulted in reduced, albeit modest, transformation rates....”
- “...Berkeley Negatively selected spr0025 spr0344 spr0459 spr0460 spr0777 spr0838 spr0857 spr0881 spr1259 spr1260 spr1357 spr1779 spr1858 spr1859 spr1863 spr1864...”
- Regulation of iron transport in Streptococcus pneumoniae by RitR, an orphan response regulator
Ulijasz, Journal of bacteriology 2004 - “...by ritR spr1684 spr1687 spr1928 spr1696 spr1814 spr0777 spr1198 spr0451 spr0502 spr0113 spr0139 spr0322 spr0893 spr1706 spr0866 spr0597 spr1319 spr1824 spr1897...”
- “...spr0757 spr1324 spr1316 piuB piuA spr1928 murI RR479 spr0777 Transposase spr0451 spr0502 spr0113 ugd cpsN spr0893 amiC pyrD rsuA spr1319 rluD pstA map blpC...”
- Proteomic and bioinformatic pipeline to screen the ligands of S. pneumoniae interacting with human brain microvascular endothelial cells
Jiménez-Munguía, Scientific reports 2018 - “...B, E, F 14 Q8CYB8 Hypothetical protein spr1730 Membrane (>1TMD) A, B, E, F 15 Q8DQ98 Hypothetical protein spr0777 Membrane (>1TMD) A, B, E, F 16 Q8DQ02 MesH protein spr0916 Membrane (>1TMD) A, B, E, F 17 Q59947 Immunoglobulin A1 protease (IgA1 protease) (IgA-specific zinc metalloproteinase)...”
- “...50.481 50 3 Q8CZ52 LPXTG-motif cell wall anchor protein spr0440 A276 A1021 111.461 111 4 Q8DQ98 Hypothetical protein spr0777 G88 G159 36.367 36 5 Q8DPQ2 Pneumococcal histidine triad protein A spr1061 G35 S823 118.780 118 Figure 3 Confirmation of interaction between selected ligand candidates and protein...”
- Pivotal Roles for Ribonucleases in Streptococcus pneumoniae Pathogenesis
Sinha, mBio 2021 - “...protein 1.89 4.36E04 SPD_0703 d Hypothetical protein 5.18 1.15E19 SPD_0716 IS630-Spn1, transposase Orf1 1.85 1.70E02 SPD_0768 cozE Coordinator of zonal cell elongation 2.16 2.16E06 SPD_0775 c , g Acetyltransferase 2.81 1.33E03 SPD_0803 f Putative phage shock protein C 2.60 1.24E04 SPD_0806 Hypothetical protein 2.18 5.09E04 SPD_0852...”
- A CozE Homolog Contributes to Cell Size Homeostasis of Streptococcus pneumoniae
Stamsås, mBio 2020 - “...phylogenetic analysis, this protein is termed CozEb and the original CozE (Spr0777 in strain R6, SPD_0768 in strain D39) is referred to as CozEa in this work. Our experiments demonstrated that the deletion of the two genes generates opposing effects on cell size. In addition, we...”
- Redefining the Small Regulatory RNA Transcriptome in Streptococcus pneumoniae Serotype 2 Strain D39
Sinha, Journal of bacteriology 2019 - “...thiE1, spd_0625 spd_0633, thiD spd_0758, spd_0759 spd_0768, spd_0770 spd_0803, spd_0804 spd_0807, spd_0808 spd_0808, cad spd_0846, infC spd_0867, spd_0868...”
- Lipoteichoic acid deficiency permits normal growth but impairs virulence of Streptococcus pneumoniae
Heß, Nature communications 2017 - “...Table 3 ). Two are located in intergenic regions, the two others are placed in spd_0768 (Asp297Gly) and spd_1179 (Ala141Thr), respectively. The latter encodes a predicted lanthionine synthetase, whereas Spd_0768 (CozE) has recently been described as a member of the MreCD complex of S. pneumoniae that...”
- CozE is a member of the MreCD complex that directs cell elongation in Streptococcus pneumoniae
Fenton, Nature microbiology 2016 - “...MreD 2 , 6 , 7 as well as a membrane protein of unknown function (SPD_0768) that we have named CozE (coordinator of zonal elongation). Our results indicate that CozE is a novel member of the MreCD complex of S. pneumoniae that directs the activity of...”
- “...elongation in rod- and ellipsoid-shaped bacteria 2 , 6 , 7 . The third gene, spd_0768 , encodes CozE, a conserved polytopic membrane protein of unknown function that belongs to the widely-distributed UPF0118 protein family 14 ( Fig. 1AC and Supplementary Fig. 23 ). Like MreC,...”
Y11_00031 AI-2E family transporter from Yersinia enterocolitica subsp. palearctica Y11
25% identity, 76% coverage
SCO3797 integral membrane protein from Streptomyces coelicolor A3(2)
28% identity, 91% coverage
FTN_0570 PerM family protein from Francisella tularensis subsp. novicida U112
25% identity, 80% coverage
- Glutamate utilization couples oxidative stress defense and the tricarboxylic acid cycle in Francisella phagosomal escape
Ramond, PLoS pathogens 2014 - “...confirmed that the gadC mutation did not have any polar effect on the downstream gene FTN_0570 by quantitative qRT-PCR ( Figure S1C ). The growth kinetics of the parental F. novicida strain and the gadC mutant were indistinguishable in tryptic soya broth (TSB) and chemically defined...”
- “...following pair of primers was used to amplify the mRNA corresponding to the transcript of FTN_0570 (p13/p14), FTN_0571 (p15/p16), FTN_1700 (p27/9p28), FTN_1701 (p29/p30), FTN_1702 (p31/p32), FTN_1532 (p33/p34), FTN_0127 (p35/p36), FTN_0277 (p37/p38), FTN_0804 (p39/p40), FTN_0593 (p41/p42), FTN_1434 (p43/p44) and FTN_1635 (p45/p46) ( Supplemental Table 1 ). Quantitative...”
- Genotype-phenotype associations in a nonmodel prokaryote
Enstrom, mBio 2012 - “...), suggesting that they may function together. Two additional potential efflux transporters were also identified (FTN_0570 and FTN_1180-1181), as was a potential rhodanese family sulfurtransferase (FTN_0120). Resistance to quinolone antibiotics. The quinolone antibiotics ciprofloxacin and nalidixic acid inhibit DNA gyrase, leading to double-strand DNA breaks. Accordingly,...”
EF1798 hypothetical protein from Enterococcus faecalis V583
26% identity, 65% coverage
- Large-scale screening of a targeted Enterococcus faecalis mutant library identifies envelope fitness factors
Rigottier-Gois, PloS one 2011 - “..., ef0465 , ef0814 , ef1212 , ef1420 , ef1493 , ef1741 , ef1760 , ef1798 or ef2442 . Discussion Bacterial pathogens that invade the animal host are faced with various hostile conditions aimed at their elimination, via products of the host innate and adaptive immune...”
Q8F6G8 Permease from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
27% identity, 78% coverage
MAP3640 hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
38% identity, 34% coverage
O50485 Membrane protein from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
24% identity, 79% coverage
Q7ULF1 Membrane protein-putative a permease from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
26% identity, 84% coverage
lmo1419 conserved hypothetical protein from Listeria monocytogenes EGD-e
25% identity, 79% coverage
SMa0136 hypothetical protein from Sinorhizobium meliloti 1021
24% identity, 45% coverage
- Dual RpoH sigma factors and transcriptional plasticity in a symbiotic bacterium
Barnett, Journal of bacteriology 2012 - “...any of the RpoH promoter consensus sequences SMa0136 SMb20303 SMb21295 SMb21294 SMb21296 SMc00030 SMc00031 SMc00048 SMc00049 SMc00814 SMc00949 SMc00969 SMc00970...”
- “...genes whose expression is indirectly rpoH dependent (SMa0136, SMc00030, SMc00048, SMc00814, SMc00969, SMc01329, SMc02863, and SMc04310 in Table 1). Hence, the...”
MXAN_7270 hypothetical protein from Myxococcus xanthus DK 1622
30% identity, 73% coverage
Gasu_58720 uncharacterized protein from Galdieria sulphuraria
25% identity, 43% coverage
HI0338 conserved hypothetical transmembrane protein from Haemophilus influenzae Rd KW20
27% identity, 76% coverage
VC2162 permease PerM, putative from Vibrio cholerae O1 biovar eltor str. N16961
23% identity, 83% coverage
SVEN_5413 AI-2E family transporter from Streptomyces venezuelae ATCC 10712
24% identity, 75% coverage
NLHAP_HALAA / A0A1W5X0D5 Sodium-lithium/proton antiporter; Na(+) (Li(+))/H(+) antiporter from Halobacillus andaensis (see paper)
22% identity, 73% coverage
- function: Catalyzes the pH-dependent efflux of sodium and lithium in exchange for external protons.
sll1166 hypothetical protein from Synechocystis sp. PCC 6803
22% identity, 92% coverage
- 6S RNA plays a role in recovery from nitrogen depletion in Synechocystis sp. PCC 6803
Heilmann, BMC microbiology 2017 - “...to verify complete segregation of the mutant strain. The location of genes slr1287, slr1288 and sll1166 are depicted upstream and downstream of the ssaA gene. b Complete segregation of the ssaA mutant gene copies and replacement with a kanamycin resistance cassette (Km R ) and its...”
- “...Km_fw/ Km_rv), and (iii) 699bp downstream of ssaA to chromosomal nucleotide position 1,887,765 (primer pair sll1166 _fw/ 3 sll1166 _rv). The ~700bp flanking regions contained non-disrupted segments of loci slr1288 and sll1166, and were used for homologous recombination. The ssaA- mutant was selected on BG11 agar...”
- Systematic and functional identification of small non-coding RNAs associated with exogenous biofuel stress in cyanobacterium Synechocystis sp. PCC 6803
Pei, Biotechnology for biofuels 2017 - “...Hypothetical protein 45 Nc41 (Ncr0480) 0.678 1.053 nc70 1,886,8951,887,070 >>< 47.8 slr1288 Hypothetical protein 158 sll1166 Hypothetical protein 89 Nc70 (6S rRNA) 0.743 0.701 nc7 219,563219,783 <<< 66.9 sll1029 Carbon dioxide concentrating mechanism protein CcmK 46 sll1027 NADH-glutamate synthase small subunit 196 Nc7 1.303 0.632 nc122...”
XF0589 permease from Xylella fastidiosa 9a5c
28% identity, 69% coverage
ECHLIB_RS01065, ECHWAK_RS01070, ECH_RS03745 AI-2E family transporter from Ehrlichia chaffeensis str. Arkansas
21% identity, 45% coverage
- Comparative Genomics of the Zoonotic Pathogen Ehrlichia chaffeensis Reveals Candidate Type IV Effectors and Putative Host Cell Targets
Noroy, Frontiers in cellular and infection microbiology 2016 - “...1 0 0 0 1 0 0 0 1 1 0 0 0 GSRs ECH_RS03745 ECHLIB_RS01065 ECHWAK_RS01070 ECHWP RS03615 AI-2E family transporter 122 1 1 0 0 0 0 0 0 0 1 0 0 0 0 GSRs ECH_RS00450 ECHLIB_RS04345 ECHWAK_RS04360 ECHWP_RS04320 Hypothetica l protein 118...”
- “...; Lin et al., 2007 ; Garcia-Garcia et al., 2009 ; Table S1 ). ECHLIB_RS02190, ECHLIB_RS01065, ECHLIB_RS01605, and ECHLIB_RS01860 are four candidate T4Es presenting homologies with known Coxiella burnetii effectors (Table S1 ). ECHLIB_RS022545 shows homology with a known Legionella pneumophila T4E (lpg2936, 16S ribosomal RNA...”
- “...0 0 0 1 0 0 0 1 1 0 0 0 GSRs ECH_RS03745 ECHLIB_RS01065 ECHWAK_RS01070 ECHWP RS03615 AI-2E family transporter 122 1 1 0 0 0 0 0 0 0 1 0 0 0 0 GSRs ECH_RS00450 ECHLIB_RS04345 ECHWAK_RS04360 ECHWP_RS04320 Hypothetica l protein 118 1...”
- “...1 1 0 0 0 1 0 0 0 1 1 0 0 0 GSRs ECH_RS03745 ECHLIB_RS01065 ECHWAK_RS01070 ECHWP RS03615 AI-2E family transporter 122 1 1 0 0 0 0 0 0 0 1 0 0 0 0 GSRs ECH_RS00450 ECHLIB_RS04345 ECHWAK_RS04360 ECHWP_RS04320 Hypothetica l protein...”
BMB171_RS27155 AI-2E family transporter from Bacillus thuringiensis BMB171
23% identity, 78% coverage
Q7UYF5 Predicted permease from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
24% identity, 81% coverage
HNY42_RS13260 sporulation integral membrane protein YtvI from Exiguobacterium sp. Helios
22% identity, 86% coverage
- Xerotolerance: A New Property in Exiguobacterium Genus
López, Microorganisms 2021 - “...the coat. 87.21% P45693.1 spoIIIAA HNY42_RS12180 QNR21664.1 Uncharacterized AAA domain-containing protein YrvN 48.12% O34528.1 ytvI HNY42_RS13260 QNR21869.1 Unknown 38.58% O34991.1 cwlD HNY42_RS14150 QNR22035.1 N-acetylmuramoyl-L-alanine amidase, spore cortex peptidoglycan synthesis. 24.19% O32041.1 microorganisms-09-02455-t003_Table 3 Table 3 Growth of Exiguobacterium sp. Helios and E. sibiricum 255-15 in different...”
STM2493 putative PerM family permease from Salmonella typhimurium LT2
27% identity, 39% coverage
- High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach
Allard, BMC genomics 2012 - “...AA Position Clade Feature lig STM2427 SEEM020_00085 C/T T 1974 b DNA ligase, NAD-dependent perM STM2493 SEEM020_00410 C/T A 1034 d,e,f permease PerM aroB STM3486 SEEM020_01090 C/T V/A 488 b,c,d,e,f shikimate kinase I yrfI STM3498 SEEM020_01145 C/T T/I 353 b,c,d,e,f heat shock protein gntK STM3542 SEEM020_01330...”
BA1922 membrane protein, putative from Bacillus anthracis str. Ames
29% identity, 34% coverage
HSISS4_00898 AI-2E family transporter from Streptococcus salivarius
25% identity, 72% coverage
CD2273 hypothetical protein from Clostridium difficile 630
24% identity, 74% coverage
N007_01250 sporulation integral membrane protein YtvI from Alicyclobacillus acidoterrestris ATCC 49025
22% identity, 81% coverage
CD2051 hypothetical protein from Clostridium difficile 630
23% identity, 75% coverage
- Genome-wide analysis of cell type-specific gene transcription during spore formation in Clostridium difficile
Saujet, PLoS genetics 2013 - “...0.65 + CD2315 Putative exported protein 0.31 0.38 CD3551.1 Putative membrane protein 0.11 0.18 G CD2051 Putative membrane protein 0.52 CD1789 Putative membrane protein, DUF421 family 0.61 G + CD1789-CD1788 CD1788 Conserved hypothetical protein 0.43 CD2465 Putative amino acid/polyamine transporter 0.36 0.52 G + stress CD1567...”
- “...been recently identified [48] . Nine genes encoding probable membrane proteins (CD0792, CD0793, CD1677, CD1789, CD2051, CD2465, CD2635, CD2636, CD3551.1) were downregulated in the sigG mutant and these proteins may be involved in germination. 55% of our G -controlled genes encode proteins associated to the spore...”
EfmE1162_0375 AI-2E family transporter from Enterococcus faecium E1162
22% identity, 76% coverage
- AsrR is an oxidative stress sensing regulator modulating Enterococcus faecium opportunistic traits, antimicrobial resistance, and pathogenicity
Lebreton, PLoS pathogens 2012 - “...presence of non-competitor DNA ( Figure 1C ). Finally, 69 bp downstream of asrR , EfmE1162_0375 encoded a putative permease of unknown function conserved among enterococci ( Figure 1B ). Oxidative stress inactivates AsrR and modulates asrR and ohr expression Suspecting that asrR expression was modulated...”
- “...a putative anti-recombination endonuclease, respectively, were downregulated in the asrR strain ( Figure 3E ). EfmE1162_0375 encoding a putative permease and located directly downstream of asrR was upregulated in the mutant as well as the gspA paralogous genes encoding general stress proteins ( Figure 3E )....”
Q7UIW9 Predicted permease from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
23% identity, 85% coverage
TE101_15860 AI-2E family transporter from Alteromonas macleodii
30% identity, 45% coverage
CD2376 hypothetical protein from Clostridium difficile 630
30% identity, 31% coverage
- Pleiotropic role of the RNA chaperone protein Hfq in the human pathogen Clostridium difficile
Boudry, Journal of bacteriology 2014 - “...protein CD2144* CD2184* CD2193 cwp24 CD2239 CD2346* CD2376 CD2402 CD2767 CD2852 cwp19 dltB CD3073 CD3228 CD3551 CDIP53/CDIP51 expression ratio 2.07 2.54...”
- Global analysis of the sporulation pathway of Clostridium difficile
Fimlaid, PLoS genetics 2013 - “...observed in sigE , sigG , and sigK mutants ( Figure 6A ). Transcription of cd2376 was reduced by 3-fold in the sigF relative to wild type ( Figure 6A ). Although this correlation was not statistically significant, it approached statistical significance (p=0.065) ( Figure 6A...”
- “...for RNA-Seq. (A) F -dependent genes included gpr , CD0125 ( spoIIQ [13] ) and CD2376 . (B) G -dependent genes included spoVT sspB , and dacF . (C) E -dependent genes included CD3522 , spoIVA , and CD1511 . (D) K -dependent genes included CD1433...”
YfgO / b2493 putative transporter YfgO from Escherichia coli K-12 substr. MG1655 (see 5 papers)
P0AFI9 Putative permease PerM from Escherichia coli (strain K12)
ECs3355 putative permease from Escherichia coli O157:H7 str. Sakai
26% identity, 39% coverage
cce_1269 hypothetical protein from Cyanothece sp. ATCC 51142
29% identity, 64% coverage
- Analysis of Protein Complexes in the Unicellular Cyanobacterium Cyanothece ATCC 51142
Aryal, Journal of proteome research 2018 - “...app 1). The numbers in parenthesis correspond to the R app value. GlgP1; glycogen phosphorylase (cce_1269), Zwf; glucose 6-phosphate dehydrogenase (cce_2536); Pgi; glucose-6-phosphate isomerase (Pgi1; cce_0666, Pgi2; cce_5178), PfkA1; 6-phosphofructokinase (cce_0669), Fda; fructose-bisphosphate aldolase class I (cce_4254), Gap; glyceraldehyde-3-phosphate dehydrogenase (cce_3612), Pgk; phosphoglycerate kinase (cce_4219), Gpm;...”
CD1045 hypothetical protein from Clostridium difficile 630
28% identity, 33% coverage
XF0281 transport protein from Xylella fastidiosa 9a5c
26% identity, 78% coverage
Q7USP8 Membrane protein from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
24% identity, 81% coverage
PA1007 hypothetical protein from Pseudomonas aeruginosa PAO1
PA14_51300 hypothetical protein from Pseudomonas aeruginosa UCBPP-PA14
27% identity, 36% coverage
- The bacterial serine protease inhibitor ecotin inhibits neutrophil elastase enzymatic activity in cystic fibrosis sputa
Fantone, Heliyon 2024 - “...aeruginosa and S. aureus . Kinetic growth curves of P. aeruginosa bacterial strains, PAO1 and PA1007, and S. aureus bacterial strains, USA300 and MRSA24, in the presence of 555.6nM ecotin (without neutrophils). OD, optical density. Statistical differences were considered as , p <0.05. Fig. 7 4...”
- A Selective Culture Medium for Screening Cefiderocol Resistance in Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii
Ibrahim, Journal of clinical microbiology 2023 (secret) - Pseudomonas aeruginosa PA1006, which plays a role in molybdenum homeostasis, is required for nitrate utilization, biofilm formation, and virulence
Filiatrault, PloS one 2013 - “...this manuscript) may be lacking. Given that the PA1006 gene exists in an operon with PA1007 which appears to be a transmembrane protein, it is possible that the PA1007 protein may cooperate with PA1006. To address this point, we obtained and confirmed the PA1007 transposon mutant...”
- “...grow anaerobically with nitrate (data not shown), we did not perform additional analyses of the PA1007 mutant since it displayed non-equivalence with the PA1006 deletion strain. PA1006 is Required for Virulence Pae virulence has been examined by using different animal as well as plant and invertebrate...”
- V-antigen genotype and phenotype analyses of clinical isolates of Pseudomonas aeruginosa
Allmond, Journal of clinical microbiology 2004 - “...pcrV genotype PA103 PA1027 PA1111 PA1085 PA2009 PA2015 PA1007 PA1010 PA1001 PA1100 PA1019 PA1024 PA1034 PA1052 PA1060 PA1063 PA1064 PA1065 PA1067 PA1069 PA1070...”
- “...marker - PA103 PA1027 PA1111 PA1085 PA2009 PA2015 PA1007 PA1010 - negative control - size marker - 1.651.00.65- isolate from acute infection (non-cystic...”
- Intraspecies Signaling between Common Variants of Pseudomonas aeruginosa Increases Production of Quorum-Sensing-Controlled Virulence Factors
Mould, mBio 2020 - “...FIGS7 Anthranilate (AA) supplementation and loss of potential di- and tricarboxylic acid transporters dctA and PA14_51300 did not alter pyocyanin production of the lasR strain. (A) Volcano plot indicating anthranilate metabolism gene expression (orange) in the lasR strain grown in coculture with the WT. (B) Colony...”
- “...RhlR-dependent pyocyanin production in coculture with the WT. (E) The broad TCA cycle intermediate transporter PA14_51300 was not required in the lasR strain for pyocyanin production in coculture with the WT. Download FIGS7, PDF file, 0.5 MB . Copyright 2020 Mould et al. 2020 Mould et...”
Vca1114GL_02777 AI-2E family transporter from Vibrio campbellii
23% identity, 83% coverage
- Popmarker: Identifying Phylogenetic Markers at the Population Level
Ke, Evolutionary bioinformatics online 2017 - “...of Species Rank and the gene trees were reconstructed. However, the pheromone autoinducer 2 transporter (Vca1114GL_02777) was chosen in both Kendall and Spearman methods and was concatenated to the TopN proteins of Species Rank from Kendall and Spearman, respectively. The correlation distances between the gene trees...”
Q04454 Putative transport protein BpOF4_00890 from Alkalihalophilus pseudofirmus (strain ATCC BAA-2126 / JCM 17055 / OF4)
22% identity, 69% coverage
YPO2450 putative membrane protein from Yersinia pestis CO92
24% identity, 83% coverage
EF1365 conserved hypothetical protein from Enterococcus faecalis V583
23% identity, 83% coverage
LBA_RS00210 AI-2E family transporter from Lactobacillus acidophilus NCFM
23% identity, 81% coverage
PPA1574 conserved membrane protein, UPF0118 from Propionibacterium acnes KPA171202
24% identity, 68% coverage
- Identification of Pathogen Signatures in Prostate Cancer Using RNA-seq
Chen, PloS one 2015 - “...ABC subunit B 3 gene1052 YP_055753.1 major facilitator superfamily permease 5 gene1592 YP_056275.1 hypothetical protein PPA1574 3 gene1887 YP_056556.1 elongation factor G 3 Only expressed transcripts with an FPKM > = 1.0 in at least 3 out 10 cancer samples are shown. We tried to find...”
APJL_1147 hypothetical protein from Actinobacillus pleuropneumoniae serovar 3 str. JL03
25% identity, 76% coverage
tqsA / P0AFS5 autoinducer 2 exporter from Escherichia coli (strain K12) (see 5 papers)
TQSA_ECOLI / P0AFS5 AI-2 transport protein TqsA; Transport of quorum-sensing signal protein from Escherichia coli (strain K12) (see 2 papers)
TC 2.A.86.1.4 / P0AFS5 Autoinducer-2 (AI-2) exporter, TqsA (YdgG) (see 5 papers)
tqsA / GB|BAA15335.1 autoinducer 2 exporter TqsA from Escherichia coli W3110 (see 2 papers)
S1754 putative transport protein from Shigella flexneri 2a str. 2457T
b1601 predicted inner membrane protein from Escherichia coli str. K-12 substr. MG1655
25% identity, 76% coverage
- function: Involved in the transport of the quorum-sensing signal autoinducer 2 (AI-2) (PubMed:16385049). Controls the transport of AI-2 either by enhancing its secretion or inhibiting its uptake and consequently represses biofilm formation and motility and affects the global gene expression in biofilms (PubMed:16385049).
catalytic activity: (2R,4S)-2-methyltetrahydrofuran-2,3,3,4-tetrol(in) = (2R,4S)- 2-methyltetrahydrofuran-2,3,3,4-tetrol(out) (RHEA:35147)
disruption phenotype: Cells have a decreased extracellular and increased intracellular concentration of AI-2. Deletion of tqsA results in a 7000-fold increase in biofilm thickness and 574-fold increase in biomass in flow cells. Deletion of tqsA increases cell motility by increasing transcription of flagellar genes. The tqsA deletion mutant shows higher resistance toward crystal violet, spectinomycin, streptomycin sulfate, 2,6-dichloroquinone-4-chloroimide, chloramphenicol and amoxicillin. - substrates: Autoinducer-2
tcdb comment: Plays a role in biofilm formation (Nobre et al. 2009) - Protection of bacteriophage-sensitive Escherichia coli by lysogens
Brown, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...Mal S3137 F- lacI q metA endA hsdR17 supE44 thi1 relA1 gyrA96 fhuA , as S1754 ( 29 ) but fhuA S3207 F- araD139 (argF-lac)169 flhD5301 (fruK-yeiR)725(fruA25) relA1 rpsL150 rbsR22 (fimB-fimE)632(::IS1) deoC1 fhuA (rex::gfp) (rex-galK)::kan S3222 As S3207 but vir r Mal Phage strains cIb221 cI...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Increased antibiotic resistance of Escherichia coli in mature biofilms
Ito, Applied and environmental microbiology 2009 - “...It also included genes encoding other transport proteins (b1601, feoB, ybgH, ydhE, yeaS, yebM, and yhiM), heat shock proteins (dnaJ and hslU), a growth...”
- YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport
Herzberg, Journal of bacteriology 2006 - “...1 fimbriae, and genes with unknown functions, including ydgG (b1601, 344 amino acids [aa]), are induced in biofilms after 7 h (48). The ydgG mutant was chosen...”
- Gene expression in Escherichia coli biofilms
Ren, Applied microbiology and biotechnology 2004 (PubMed)- “...ychM, yefM, ygfA, b1060, b1112, b2377, b3022, b1373, b1601, and b0836). The DNA microarray results were corroborated with RNA dot blotting. For the biofilm...”
- “...met genes Anthranilate synthase component I 37 21 17 8 35 4 7 8 b1601 ygfA b1060 b1373 b0836 ychM yefM 5 5 4 3 3 2 2 6 8 5 1.3 3 3 3 b1601 b2912 b1060 b1373...”
- Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
Sabina, Journal of bacteriology 2003 - “...6.2 6.2 PRM metA ycdU chpR ybeK b1832 phoQ uhpT b1444 b1601 kdpC arp mesJ yfiK xthA yhcR yhaI celC rpmJ b0011 b1447 rpmD b1451 menC yagS b1600 yaeS b2534 hemL...”
- “...b1400 b4013 b1029 b2783 b0651 b1832 b1129 b3666 b1444 b1601 b0696 b4017 b0188 b2578 b1749 b3242 b3104 b1736 b3299 b0011 b1447 b3302 b1451 b2261 b0285 b1600...”
- Global impact of sdiA amplification revealed by comprehensive gene expression profiling of Escherichia coli
Wei, Journal of bacteriology 2001 - “...4.4 b1601 ........................................................................................... 4.0 b1606...”
c1993 Hypothetical protein ydgG from Escherichia coli CFT073
25% identity, 76% coverage
ECs2307 putative transport protein from Escherichia coli O157:H7 str. Sakai
26% identity, 76% coverage
LSA0046 Putative transport protein from Lactobacillus sakei subsp. sakei 23K
25% identity, 80% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...LSA1652 ipk 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase -0.6 -0.7 Secondary metabolites transport and metabolism Transport/binding proteins and lipoproteins LSA0046 lsa0046 Putative transport protein -1.0 -0.6 -1.3 LSA0089 lsa0089 Putative drug transport protein -2.1 -0.9 -0.8 LSA0094 lsa0094 Putative transport protein, Major Facilitator Super (MFS) family transporter -0.7 -0.7 LSA0095...”
Q7UPF9 Probable permease from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
29% identity, 37% coverage
FNP_0388 AI-2E family transporter from Fusobacterium polymorphum ATCC 10953
20% identity, 78% coverage
- Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium
Karpathy, PloS one 2007 - “...possible TonB-dependent iron (Fe) receptor Drug transporters FNP_0174 546224 547564 MOP/MATE family multidrug-resistance efflux pump FNP_0388 760374 759283 perM probable MFS superfamily major facilitator transporter, macrolide symporter FNP_0507 872530 869465 RND superfamily resistance-nodulation-cell division antiporter FNP_0508 873639 872533 RND superfamily resistance-nodulation-cell division antiporter FNP_0622 986693 987907...”
- “...efflux pumps (FNP_0174, FNP_0640, FNP_0890, FNP_1162, FNP_1207, FNP_1299, and FNP_1596), 2 DMT superfamily drug/metabolite transporters (FNP_0388 and FNP_0622) and 2 RND family antiporters (FNP_0507 and FNP_0508). Our annotation did not permit us to predict the substrates of these transporters but it is likely that many of...”
Q188A3 Sporulation integral membrane protein from Clostridioides difficile (strain 630)
CD630_20350 sporulation integral membrane protein YtvI from Clostridioides difficile 630
24% identity, 78% coverage
- Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism.
Khera, The EMBO journal 2022 - “...UniProt: A0A1W5X0D5), B.subtilis (YtvI, UniProt O50485), Bacillus pseudofirmus (YCT2, UniProt: Q04454), and Clostridium difficile (UniProt: Q188A3). The choice of the homologs considered for multiplesequence alignment is based on the subgroups within the AI2 exporter family mentioned in the Upf0118 study (Wang etal , 2020 ). YdiK...”
- Integrated genomic epidemiology and phenotypic profiling of Clostridium difficile across intra-hospital and community populations in Colombia
Muñoz, Scientific reports 2019 - “...encoded by a limited number of genomes (813) were also found, namely, CD630_34990, CD630_26810, and CD630_20350. Figure 5 Genomic and phenotypic characterization of spore producing capacity and new CFU production. ( a ) Proteins involved in the sporulation process detected by comparisons against the sequences of...”
- “...exceptions were found, such as the absence of the gene encoding the integral membrane protein CD630_20350, which was found in only eight of the genomes. This protein has been reported as not strictly required for the sporulation or resistance of spores 40 ; therefore, it may...”
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