Family Search for PF04480 (DUF559)
PF04480 hits 32 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
YcjD / b1289 DUF559 domain-containing protein YcjD from Escherichia coli K-12 substr. MG1655
b1289 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 3:111 / 117 (93.2%), covers 99.1% of PF04480, 167.0 bits
Q9JXX1 DUF559 domain-containing protein from Neisseria meningitidis serogroup B (strain MC58)
Aligns to 14:121 / 129 (83.7%), covers 97.2% of PF04480, 164.5 bits
NGO0050 hypothetical protein from Neisseria gonorrhoeae FA 1090
Aligns to 13:121 / 129 (84.5%), covers 98.2% of PF04480, 164.4 bits
- Crystal structure of the 5hmC specific endonuclease PvuRts1I
Kazrani, Nucleic acids research 2014 - “...between the N-terminal domain of PvuRts1I and several PD-(D/E)XK endonucleases (DALI Z-scores of 6.9 for Ngo0050 from Neisseria gonorrhoeae , 4.9 for V.EcoKDcm, 4.2 for Hjc, 2.7 for PspGI and 2.5 for NgoMIV), in agreement with the inclusion of PvuRts1I in a bioinformatic survey of highly...”
P44116 Uncharacterized protein HI_1162 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI1162 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 26:134 / 157 (69.4%), covers 98.2% of PF04480, 161.5 bits
DR0221, DR_0221 conserved hypothetical protein from Deinococcus radiodurans R1
Aligns to 58:167 / 167 (65.9%), covers 97.2% of PF04480, 152.8 bits
- N 4-Cytosine DNA Methylation Is Involved in the Maintenance of Genomic Stability in Deinococcus radiodurans
Li, Frontiers in microbiology 2019 - “...protein DR_B0099 3.3137 5.88E-18 Poly ADP-ribose glycohydrolase, PARG DR_1297 3.09 6.24E-12 Uncharacterized membrane protein, MutK DR_0221 2.7957 1.35E-07 Endonuclease domain-containing protein (DUF559) DR_0596 2.6105 2.51E-14 DNA helicase subunit, RuvB DR_1902 2.6449 2.96E-11 ATP-dependent RecD-like DNA helicase, RecD2 DR_2586 2.4528 0.0001281 Exonuclease VII small subunit, XseB DR_1039...”
- Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation
Liu, Proceedings of the National Academy of Sciences of the United States of America 2003 - “...involved in very short patch repair (24), were activated (DR0221, DR2566, and DRB0135; Table 4). The ComEA system, which has been identified PNAS April 1, 2003...”
- Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics
Makarova, Microbiology and molecular biology reviews : MMBR 2001 - “...Gene nameb Gene_ID DRA0344, DRA0074 ycjD BS_dinB DR0221, DR2566 13 homologs (see Fig. 5) ham1/yggV DR0179 uve1/BS_ywjD DR1819 yejH/rad25 DRA0131 DR0690...”
P44075 Uncharacterized protein HI_0925 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI0925 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 6:116 / 121 (91.7%), covers 98.2% of PF04480, 152.8 bits
- Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
Shahbaaz, PloS one 2013 - “...Peptidase M50 (metalloendopeptidase) 142. HP HI0920 950624 P44938 Undecaprenyl pyrophosphate synthetase 143. HP HI0925 950812 P44075 type I restriction enzyme M protein 144. HP HI0926 949651 P44076 glutaredoxin-like protein (electron transport) 145. HP HI0929 949927 P44940 Bifunctionalglutathionylspermidine synthetase/amidase 146. HP HI0930 949932 P44077 Prokaryotic membrane lipoprotein...”
- Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
Shahbaaz, PloS one 2013 - “...949920 P44936 Peptidase M50 (metalloendopeptidase) 142. HP HI0920 950624 P44938 Undecaprenyl pyrophosphate synthetase 143. HP HI0925 950812 P44075 type I restriction enzyme M protein 144. HP HI0926 949651 P44076 glutaredoxin-like protein (electron transport) 145. HP HI0929 949927 P44940 Bifunctionalglutathionylspermidine synthetase/amidase 146. HP HI0930 949932 P44077 Prokaryotic...”
- Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae
Gladitz, Nucleic acids research 2005 - “...cytosine/adenosine deaminase) HI0906 41 173 39.17 PM 0.3 72.95 Conserved hypothetical protein (homol. to methylases) HI0925 36 122 47.52 HFDY 0 76.27 H.influenzae predicted coding region HI0983 HI0983 35 194 40.33 HFRD 0 71.52 H.influenzae predicted coding region HI1055 (type III restriction modification endonulase-like, strong homology...”
CCNA_02930 cytosolic protein from Caulobacter crescentus NA1000
CC2838 conserved hypothetical protein from Caulobacter crescentus CB15
Aligns to 56:161 / 177 (59.9%), covers 98.2% of PF04480, 142.9 bits
NP_946397 conserved hypothetical protein from Rhodopseudomonas palustris CGA009
Aligns to 8:118 / 144 (77.1%), covers 95.4% of PF04480, 125.2 bits
M.PspMBI7II Type I methyltransferase recognizing GTCANNNNNNTRCC with methylation at 4(m6A),-4(m6A) from Pokkaliibacter species MBI-7
Aligns to 479:589 / 679 (16.3%), covers 96.3% of PF04480, 121.3 bits
Lsp6406VI Type IIG restriction enzyme/methyltransferase recognizing CRAGCAC, ?; GTGCTYG with methylation at 6(m6A) from Leptolyngbya sp. PCC 6406
Aligns to 693:801 / 1204 (9.1%), covers 96.3% of PF04480, 120.4 bits
FTL_0977 hypothetical protein from Francisella tularensis subsp. holarctica
Aligns to 9:117 / 128 (85.2%), covers 95.4% of PF04480, 98.3 bits
IHMA87_01755 endonuclease domain-containing protein from Pseudomonas aeruginosa
Aligns to 5:85 / 92 (88.0%), covers 66.1% of PF04480, 82.5 bits
SGL_RS19135 endonuclease domain-containing protein from Synechocystis sp. PCC 6803
Aligns to 1:69 / 78 (88.5%), covers 61.5% of PF04480, 73.5 bits
- Expression of tardigrade disordered proteins impacts the tolerance to biofuels in a model cyanobacterium Synechocystis sp. PCC 6803
Zhang, Frontiers in microbiology 2022 - “...Resolvase ( slr8029 ), cNMP-binding ( slr0607 ), Radical_SAM ( sll1876 ), and DUF559 ( SGL_RS19135 ). Table 4 Top20 up-regulated and down-regulated DEGs in 1321DP8. Regulation Gene ID log2FoldChange Value of p Gene description TF family Up-regulated slr5013 6.948 0.000 Hypothetical protein slr8044 5.862 0.023...”
- “...substrate-binding protein sll0419 1.880 0.033 Hypothetical protein sll1876 1.818 0.000 Oxygen-independent coproporphyrinogen III oxidase Radical_SAM SGL_RS19135 1.806 0.000 DUF559 domain-containing protein DUF559 Down-regulated slr5082 6.447 0.002 Rpn family recombination-promoting nuclease/putative transposase sll5062 6.447 0.002 Hypothetical protein slr6103 6.161 0.007 Protein of unknown function DUF45 DUF45 sll1005...”
VCHC1A2_1623 RecQ family ATP-dependent DNA helicase from Vibrio cholerae HC-1A2
Aligns to 521:597 / 1558 (4.9%), covers 56.9% of PF04480, 38.6 bits
HD1445 hypothetical protein from Haemophilus ducreyi 35000HP
Aligns to 77:164 / 167 (52.7%), covers 53.2% of PF04480, 34.9 bits
Cp1002B_0894 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein from Corynebacterium pseudotuberculosis
D9QCC1 DUF559 domain-containing protein from Corynebacterium pseudotuberculosis (strain C231)
Aligns to 167:268 / 294 (34.7%), covers 80.7% of PF04480, 30.1 bits
I-Bth0305I homing endonuclease recognizing ATGTAAACTCACGCTTCGGTGATCCAAACGTGACAACTG, 20; CAGTTGTCACGTTTGGATCACCGAAGCGTGAGTTTACAT, 17 from Bacillus thuringiensis bacteriophage 0305phi8-36
Aligns to 165:258 / 266 (35.3%), covers 63.3% of PF04480, 29.7 bits
CTK_C00980 AAA domain-containing protein from Clostridium tyrobutyricum
Aligns to 1241:1342 / 1368 (7.5%), covers 71.6% of PF04480, 29.6 bits
MSMEG_5314 hypothetical protein from Mycobacterium smegmatis str. MC2 155
Aligns to 223:289 / 304 (22.0%), covers 49.5% of PF04480, 28.1 bits
- Pathogen roid rage: cholesterol utilization by Mycobacterium tuberculosis
Wipperman, Critical reviews in biochemistry and molecular biology 2014 - “...MSMEG_6004 oxidoreductase ? Induced, Essential KstR2 Rv3554 - fdxB ferridoxin B ? Induced Induced Rv3555c MSMEG_5314 conserved hypothetical protein Induced Induced Rv3556c MSMEG_6008 fadA6 thiolase ? Essential Induced, Essential KstR2 Rv3557 MSMEG_6009 kstR2 transcriptional repressor (TetR-like) Induced KstR2 Rv3558 - PPE64 PPE family of glycine rich...”
NGK_0449 putative very-short-patch-repair endonuclease from Neisseria gonorrhoeae NCCP11945
NGO0300 putative very-short-patch-repair endonuclease from Neisseria gonorrhoeae FA 1090
Aligns to 73:135 / 137 (46.0%), covers 38.5% of PF04480, 27.3 bits
A1S_2347 hypothetical protein from Acinetobacter baumannii ATCC 17978
Aligns to 5:98 / 100 (94.0%), covers 51.4% of PF04480, 26.1 bits
- ppGpp signaling plays a critical role in virulence of Acinetobacter baumannii
Kim, Virulence 2021 - “...genes, an iron acquisition siderophore gene (A1S_2387) was most upregulated (+ 42.11 fold change), and A1S_2347 that encodes a hypothetical protein was the most downregulated ( 11.27 fold change) in the mutant strain. Genes that show at least 2-fold changes in expression in the ppGpp-deficient strain...”
TGME49_269830 RAP domain-containing protein from Toxoplasma gondii ME49
Aligns to 761:849 / 861 (10.3%), covers 45.0% of PF04480, 24.4 bits
A1S_1148 hypothetical protein from Acinetobacter baumannii ATCC 17978
Aligns to 2:96 / 98 (96.9%), covers 54.1% of PF04480, 24.0 bits
cg0328 hypothetical protein from Corynebacterium glutamicum ATCC 13032
Aligns to 171:281 / 288 (38.5%), covers 55.0% of PF04480, 23.6 bits
MSMEG_0881 hypothetical protein from Mycobacterium smegmatis str. MC2 155
Aligns to 202:271 / 277 (25.3%), covers 56.9% of PF04480, 23.6 bits
- bkaR is a TetR-type repressor that controls an operon associated with branched-chain keto-acid metabolism in Mycobacteria
Balhana, FEMS microbiology letters 2013 - “...protein MSMEG_1548 3.0 4.3E-02 Dehydratase (propanediol utilization) MSMEG_1543 3.2 2.3E-02 Rv0458 Rv0458 EPTC-Inducible aldehyde dehydrogenase MSMEG_0881 3.4 2.2E-02 Hypothetical protein MSMEG_0066 3.3 2.2E-02 esxA Rv3875 Early secretory antigenic target The genes in bold are those directly regulated by bkaR . * Occurrence of the motif. Venugopal...”
- “..., MSMEG_1885 , MSMEG_1548 , MSMEG_1543 , MSMEG_0066 ) or significantly repressed ( MSMEG_4005 , MSMEG_0881 ) are not associated with a motif. We conclude that these are not likely to be under the direct control of BkaR. The changes in expression in these genes may...”
PF3D7_0518100 protein AMR2 from Plasmodium falciparum 3D7
Aligns to 1252:1350 / 1379 (7.2%), covers 76.1% of PF04480, 23.4 bits
- A mutagenesis screen for essential plastid biogenesis genes in human malaria parasites
Tang, PLoS biology 2019 - “...for a cytoplasmic pathway for apicoplast biogenesis, and truncations of three proteins of unknown function (Pf3D7_0518100, Pf3D7_1305100, and Pf3D7_1363700) ( Table 1 ). The remaining candidates contained point mutations and had no known prior function in apicoplast biogenesis or localization to the organelle. 10.1371/journal.pbio.3000136.t001 Table 1...”
- “...FtsH1 Ile437Ser No ND Yes c Pf3D7_1126100 Atg7, putative Gln719 * Yes ND Yes d Pf3D7_0518100 RAP protein, putative Leu1419 * No Yes ND Pf3D7_1305100 Conserved Plasmodium protein, unknown function Lys859 * Yes ND ND Pf3D7_1363700 Conserved Plasmodium protein, unknown function Tyr4669 * Yes Yes ND...”
- Widespread occurrence of lysine methylation in Plasmodium falciparum proteins at asexual blood stages
Kaur, Scientific reports 2016 - “...ANAIITnLYLDGTLIIEnk PF3D7_0517500 UTPglucose-1-phosphate uridylyltransferase, putative K19(Dimethyl) HILIC ANAIITNLYLDGTLIIENk PF3D7_0517500 UTPglucose-1-phosphate uridylyltransferase, putative C-Term(Methyl) HILIC VQSINSTkHNNNIK PF3D7_0518100 RAP protein, putative K8(Methyl) HILIC nETLEEYWWcVESALTWGDGDDNGPDMIVDDGGDATLLVHk PF3D7_0520900 S-adenosyl-L-homocysteine hydrolase (SAHH) K41(Methyl) HILIC EDkENLNDMYSVNVTNHnDEk PF3D7_0521300 conserved Plasmodium protein, unknown function K3(Trimethyl); C-Term(Methyl) IP QNLNASNSSGQENkQnESDGK PF3D7_0524600 50S ribosomal protein L12, apicoplast, putative...”
DR2566, DR_2566 hypothetical protein from Deinococcus radiodurans R1
Aligns to 85:159 / 168 (44.6%), covers 47.7% of PF04480, 22.4 bits
- Comparative genomics of Deinococcus radiodurans: unveiling genetic discrepancies between ATCC 13939K and BAA-816 strains
Jeong, Frontiers in microbiology 2024 - “...restored in ATCC 13939K and other R1 strains ( Supplementary Table S4 ). The protein DR_2566, which includes the domain of unknown function (DUF) 2,726 ( Supplementary Table S2 ), is presumed to be a very short patch repair (VSR)-like nuclease ( Slade and Radman, 2011...”
- Oxidative stress resistance in Deinococcus radiodurans
Slade, Microbiology and molecular biology reviews : MMBR 2011 - “...repair)-like nuclease possibly involved in very-short-patch repair (DR2566), mutT (DR0261 and DR1776), ruvB (DR0596), and ssb (DR0099) (368). The maximum...”
- Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation
Liu, Proceedings of the National Academy of Sciences of the United States of America 2003 - “...in very short patch repair (24), were activated (DR0221, DR2566, and DRB0135; Table 4). The ComEA system, which has been identified PNAS April 1, 2003 vol. 100...”
- Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics
Makarova, Microbiology and molecular biology reviews : MMBR 2001 - “...Gene nameb Gene_ID DRA0344, DRA0074 ycjD BS_dinB DR0221, DR2566 13 homologs (see Fig. 5) ham1/yggV DR0179 uve1/BS_ywjD DR1819 yejH/rad25 DRA0131 DR0690 DR1721...”
YkrI Type II methyl-directed restriction enzyme recognizing C, 11; G, -9 from Yersinia kristensenii
Aligns to 4:119 / 289 (40.1%), covers 76.1% of PF04480, 22.4 bits
P36434 Type II nicking enzyme V.HpaIIP from Haemophilus parainfluenzae
Aligns to 88:136 / 141 (34.8%), covers 39.4% of PF04480, 22.2 bits
NCgl2593 DUF559 domain-containing protein from Corynebacterium glutamicum ATCC 13032
Aligns to 194:302 / 317 (34.4%), covers 88.1% of PF04480, 22.2 bits
OCU_05560 DUF559 domain-containing protein from Mycobacterium intracellulare ATCC 13950
Aligns to 171:273 / 278 (37.1%), covers 41.3% of PF04480, 22.0 bits
- Prominent transcriptomic changes in Mycobacterium intracellulare under acidic and oxidative stress
Park, BMC genomics 2024 - “...hypothetical protein Conserved hypotheticals 4.05 5.42 OCU_04530 hypothetical protein Insertion seqs and phages 4.49 18.01 OCU_05560 hypothetical protein Conserved hypotheticals 3.82 2.29 OCU_06830 zinc transporter Slc39a7 Cell wall and cell processes -2.95 -2.13 OCU_06840 hypothetical protein Regulatory proteins -3.42 -3.24 OCU_08780 hypothetical protein Conserved hypotheticals 4.88...”
Rv3555c hypothetical protein from Mycobacterium tuberculosis H37Rv
Aligns to 206:283 / 289 (27.0%), covers 44.0% of PF04480, 21.5 bits
- Comprehensive Comparative Analysis of Cholesterol Catabolic Genes/Proteins in Mycobacterial Species
van, International journal of molecular sciences 2019 - “...c possible oxidoreductase / 2-nitropropane dioxygenase fdxB Rv3554 e possible electron transfer protein / ferredoxin Rv3555c e CHP kstR2 Rv3557c e Tet-R transcriptional regulator (repressor) PPE64 Rv3558 e PPE Rv3559c c probable oxidoreductase fadD3 Rv3561 c acyl-CoA synthetase (AMP forming) fadE31 Rv3562 e probable acyl-CoA dehydrogenase...”
- “...None None None None Positive mtv None None None None Positive mtc None None None Rv3555c Positive mra None None None None Positive mtf None None None Rv3566A Positive mtb None None None Rv3566A Positive mtk None None None Rv3566A Positive mtz None None None Rv3566A...”
- Non-replicating Mycobacterium tuberculosis elicits a reduced infectivity profile with corresponding modifications to the cell wall and extracellular matrix
Bacon, PloS one 2014 - “...vivo or in vitro data sets used for this comparison ( Table 3 ). Genes Rv3555c, Rv2642, Rv0083 were induced in the human granuloma [27] and gene Rv0251c, encoding heat shock protein hsp , was the only gene induced under all the conditions compared. 10.1371/journal.pone.0087329.t003 Table...”
- “...dehydrogenase 75 days starvation [10] Rv3173c 4 Transcriptional regulator, tetR acrR-family 75 days starvation [10] Rv3555c 3 Conserved hypothetical protein Human granuloma v in vitro culture in 7H9, Human granuloma v pericavity [27] Table 3 Genes that were up-regulated at 48 h in macrophages [26] and...”
- Whole genome sequencing of Mycobacterium tuberculosis reveals slow growth and low mutation rates during latent infections in humans
Colangeli, PloS one 2014 - “...- - G Rv3519 - - - - - - A - - - T Rv3555c - - - - - - - - C - G Rv1081c - - - - A - - - - - C mutA - - - - - -...”
- Pathogen roid rage: cholesterol utilization by Mycobacterium tuberculosis
Wipperman, Critical reviews in biochemistry and molecular biology 2014 - “...Rv3553 MSMEG_6004 oxidoreductase ? Induced, Essential KstR2 Rv3554 - fdxB ferridoxin B ? Induced Induced Rv3555c MSMEG_5314 conserved hypothetical protein Induced Induced Rv3556c MSMEG_6008 fadA6 thiolase ? Essential Induced, Essential KstR2 Rv3557 MSMEG_6009 kstR2 transcriptional repressor (TetR-like) Induced KstR2 Rv3558 - PPE64 PPE family of glycine...”
- Transcriptional profiling of mycobacterium tuberculosis during infection: lessons learned
Ward, Frontiers in microbiology 2010 - “..., rv1952 , rv2005c , rv2160c , rv2262c , rv2557 , rv2603c , rv3412 , rv3555c , rv3626c , rv3706c , rv3776 , rv3860 , rv3861 rv0150c , rv1190 , rv1291c , rv1518 , rv1587c , rv1734c , rv1945 , rv3706c , rv3845 *Genes were identified...”
Or search for genetic data about PF04480 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory