PaperBLAST

PaperBLAST Hits for SO0109 (77 a.a., MSQYIPDYQL...)

Show query sequence

>SO0109
MSQYIPDYQLDMVGEPCPYPAVATLEAMPTLKPGEILEVISDCPQSINNIPLDAKNHGYK
VLEIEQNGPTIRYLIQR

Running BLASTp...

Found 29 similar proteins in the literature:

YedF / b1930 putative sulfurtransferase YedF from Escherichia coli K-12 substr. MG1655 (see 4 papers)
b1930 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
NP_460919 putative transcriptional regulator from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
ECs2669 hypothetical protein from Escherichia coli O157:H7 str. Sakai
82% identity, 100% coverage

• A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex
  Tanabe, Protein science : a publication of the Protein Society 2024
  • “...related proteins from sulfur oxidizers and E. coli . Ec, E. coli (TusA, b3470, YedF, b1930, YeeD, and b2012); Ts, Ts. sibirica (ThisiDRAFT_0966, according to JGI IMG); Tk, Thioalkalivibrio sp. K90mix (TK90_0631); Av, Ac. vinosum (Alvin_2600); Hd, Hm. denitrificans (Hden_0698); Aq, Aq. aeolicus (Aq_388a); Mc, Ms....”
• First insights into the pleiotropic role of vrf (yedF), a newly characterized gene of Salmonella Typhimurium.
  Ballesté-Delpierre, Scientific reports 2017
  • GeneRIF: yedF is involved in the regulation of Salmonella pathogenesis and contributes to the activation of the virulence machinery.
• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...yecH -2.94 6 ECs2146 ydeJ 2.05 2 ECs2668 yedE -2.15 1 ECs2150 ydfZ -5.10 4 ECs2669 yedF -2.78 1 ECs2281 O157 2.30 2 ECs2670 yedK 2.55 2 ECs2292 - 3.22 2 ECs2693 - 2.62 2 ECs2295 ynfG -2.81 6 ECs2785 erfK 2.37 2 ECs2820 hisG -2.80...”

APL_1976 hypothetical protein from Actinobacillus pleuropneumoniae L20
APP7_2064 hypothetical protein from Actinobacillus pleuropneumoniae serovar 7 str. AP76
70% identity, 85% coverage

• Host-pathogen interactions of Actinobacillus pleuropneumoniae with porcine lung and tracheal epithelial cells
  Auger, Infection and immunity 2009
  • “...California, Berkeley APL_1833 APL_1435 APL_1285 APL_0145 APL_1976 APL_0116 APL_0093 APL_1374 APL_0465 APL_1919 APL_1138 APL_0443 APL_1656 APL_1203 APL_1609...”
• The ClpP protease is required for the stress tolerance and biofilm formation in Actinobacillus pleuropneumoniae
  Xie, PloS one 2013
  • “...transporter, ATP-binding protein APP7_0104 1.037253 hypothetical protein Down-regulated genes APP7_0616 2.30679 pyridoxal biosynthesis lyase PdxS APP7_2064 2.12199 tRNA 2-thiouridine synthesizing protein A APP7_1497 1.78015 hypothetical protein APP7_0617 1.5762 glutamine amidotransferase subunit PdxT APP7_0418 1.44626 RNA polymerase sigma-70 factor APP7_0419 1.33961 putative sigma-E factor negative regulatory protein...”

YP_001672735 SirA family protein from Shewanella halifaxensis HAW-EB4
71% identity, 94% coverage

• Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation
  Zhao, PloS one 2010
  • “...One system was composed of ,, subunits conserved in S. pealeana and coliform bacteria (YP_001672725- YP_001672735) such as E. coli ATCC 8739, Enterobacter sp. 638, and Citrobacter koseri ATCC BAA-895. Two other systems were composed of -subunits conserved in P. profundum SS9 and 4Fe-4S ferredoxin binding...”

C8J_1404 hypothetical protein from Campylobacter jejuni subsp. jejuni 81116
67% identity, 15% coverage

• Selenium-dependent biogenesis of formate dehydrogenase in Campylobacter jejuni is controlled by the fdhTU accessory genes
  Shaw, Journal of bacteriology 2012
  • “...are fused into a single open reading frame (C8J_1404), although the translational signals (ribosome binding site, GTG start codon) for translation of the Cj1501...”
  • “...jejuni strain NCTC 11168, and the cj1500-cj1501 fusion gene C8J_1404 in strain 81116. The majority of the coding sequences of the cj1500, cj1501, and C8J_1404...”

Cj1501 hypothetical protein Cj1501 from Campylobacter jejuni subsp. jejuni NCTC 11168
YP_002344880 hypothetical protein from Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
69% identity, 91% coverage

• Exploration of genes associated with induction of the viable but non-culturable state of Campylobacter jejuni
  Ohno, Archives of microbiology 2024
  • “...fold change (low temperature) Microarray fold change (high-osmotic pressure) cj1500 fdhT (FDH subunit) + + cj1501 fdhU (FDH subunit) cj1507 regulator cj1508 fdhD (FDH subunit) cj1509 fdhC (FDH subunit) cj1510 fdhB (FDH subunit) cj1511 fdhA (FDH subunit) + cj1513 cofactor cj1514 fdhM (FDH subunit) +, increased...”
• Defining the metabolic requirements for the growth and colonization capacity of Campylobacter jejuni
  Hofreuter, Frontiers in cellular and infection microbiology 2014
  • “...The FDH activity of C. jejuni is controlled by the accessory proteins FdhT (Cj1500), FdhU (Cj1501) and a high-affinity TupABC-like tungstate transporter (Cj1538-Cj1540) indicating that tungstate might be incorporated into the FDH complex (Smart et al., 2009 ; Pryjma et al., 2012 ; Shaw et al.,...”
• Selenium-dependent biogenesis of formate dehydrogenase in Campylobacter jejuni is controlled by the fdhTU accessory genes
  Shaw, Journal of bacteriology 2012
  • “...study we investigated the function of the cj1500 and cj1501 genes of C. jejuni, demonstrate that they are involved in selenium-controlled production of FDH, and...”
  • “...study we have investigated the function of the C. jejuni cj1501 gene, which encodes a SirA-like protein that we have named FdhU, and report on the role of the...”
• Transcriptional regulation of the CmeABC multidrug efflux pump and the KatA catalase by CosR in Campylobacter jejuni
  Hwang, Journal of bacteriology 2012
  • “...Cj0243c Cj0249 Cj0391c Cj0428 Cj0520 Cj0742 Cj0873c Cj1242 Cj1501 Cj1650 Cj0040 Cj0069 Cj0070c Cj0243c Cj0249 Cj0391c Cj0428 Cj0520 Cj0742 Cj0873c Cj1242 Cj1501...”
• FdhTU-modulated formate dehydrogenase expression and electron donor availability enhance recovery of Campylobacter jejuni following host cell infection
  Pryjma, Journal of bacteriology 2012
  • “...were two other uncharacterized genes, designated cj1500 and cj1501 in the first sequenced C. jejuni strain, 11168, and CJJ81176_1492 and CJJ81176_1493 in the...”
• Selenium-dependent biogenesis of formate dehydrogenase in Campylobacter jejuni is controlled by the fdhTU accessory genes.
  Shaw, Journal of bacteriology 2012
  • GeneRIF: The authors demonstrate that the cj1500 and cj1501 genes of Campylobacter jejuni are involved in selenium-controlled production of the formate dehydrogenase enzyme, and propose the names fdhT and fdhU, respectively.

CJJ81176_1493 hypothetical protein from Campylobacter jejuni subsp. jejuni 81-176
67% identity, 91% coverage

• Investigating the Campylobacter jejuni Transcriptional Response to Host Intestinal Extracts Reveals the Involvement of a Widely Conserved Iron Uptake System
  Liu, mBio 2018
  • “...value Fold change P value Respiration CJJ81176_1492 fdhT Membrane protein, putative 2.9 8.27E03 6.4 1.29E10 CJJ81176_1493 fdhU Conserved hypothetical protein 2.4 3.00E02 3.3 8.96E05 Iron uptake CJJ81176_0211 cfbpA Iron ABC transporter, periplasmic iron-binding protein 2.8 1.56E02 CJJ81176_1351 ceuB Enterochelin ABC transporter, permease protein 2.9 1.58E02 CJJ81176_1603...”
• FdhTU-modulated formate dehydrogenase expression and electron donor availability enhance recovery of Campylobacter jejuni following host cell infection
  Pryjma, Journal of bacteriology 2012
  • “...genes that we designated fdhT (CJJ81176_1492) and fdhU (CJJ81176_1493) is conserved in many bacterial species. Deletion of fdhT or fdhU in C. jejuni resulted...”
  • “...sequenced C. jejuni strain, 11168, and CJJ81176_1492 and CJJ81176_1493 in the virulent, invasive strain 81-176 used in our laboratory. We have designated these...”

PA3632 hypothetical protein from Pseudomonas aeruginosa PAO1
52% identity, 87% coverage

• Pseudomonas aeruginosa PA1006 is a persulfide-modified protein that is critical for molybdenum homeostasis
  Tombline, PloS one 2013
  • “...yedF , and yeeD genes. In Pae , in addition to PA1006 , PA1564 and PA3632 are also present. These proteins do not appear to be functionally redundant in either organism since mutation of either the yhhP/tusA gene in E. coli [10] , [11] or PA1006...”
  • “...to be essential in Pae strain PAO1 since several attempts to delete it failed, and PA3632 is not required for anaerobic growth with nitrate (data not shown). 10.1371/journal.pone.0055593.g001 Figure 1 PA1006 is an ortholog of the E. coli YhhP/TusA protein that functions in sulfur trafficking. (A)...”

TRQ2_1812 SirA family protein from Thermotoga sp. RQ2
TM0983 conserved hypothetical protein from Thermotoga maritima MSB8
49% identity, 89% coverage

• A pipeline for completing bacterial genomes using in silico and wet lab approaches
  Puranik, BMC genomics 2015
  • “...hypothetical protein TM0981 TRQ2_1814 CTN_1597 Disrupted hypothetical protein TM0982 TRQ2_1813 CTN_1596 Present hypothetical protein TM0983 TRQ2_1812 CTN_1595 Disrupted hypothetical protein TM0984 TRQ2_1811 CTN_1594 Disrupted hypothetical protein TM0985 TRQ2_1810 CTN_1593 Present hypothetical protein TM0986 TRQ2_1809 CTN_1592 & CTN_1591 Present hypothetical protein TM0987 TRQ2_1808 CTN_1590 Disrupted hypothetical protein...”
• A pipeline for completing bacterial genomes using in silico and wet lab approaches
  Puranik, BMC genomics 2015
  • “...Present hypothetical protein TM0981 TRQ2_1814 CTN_1597 Disrupted hypothetical protein TM0982 TRQ2_1813 CTN_1596 Present hypothetical protein TM0983 TRQ2_1812 CTN_1595 Disrupted hypothetical protein TM0984 TRQ2_1811 CTN_1594 Disrupted hypothetical protein TM0985 TRQ2_1810 CTN_1593 Present hypothetical protein TM0986 TRQ2_1809 CTN_1592 & CTN_1591 Present hypothetical protein TM0987 TRQ2_1808 CTN_1590 Disrupted hypothetical...”
• Stationary phase and nutrient levels trigger transcription of a genomic locus containing a novel peptide (TM1316) in the hyperthermophilic bacterium Thermotoga maritima
  Frock, Applied and environmental microbiology 2013
  • “...medium included a putative sulfur relay operon (TM0979 to TM0983). TM0981, TM0980, and TM0979 are homologous to DsrEFH and TusBCD, which are involved in sulfur...”
  • “...TM0977 66 N 98 N 1.2 1.7 1.2 1.8 TM1732 0.1 0.5 0.2 0.6 TM0983 79 N 59 N 0.8 1.1 0.3 0.2 TM1786 1.1 1.2 0.7 1.3 TM0994 37 Y 30 N 0.6 0.7 0.4 0.5 TM1829 -0.1 0.1...”
• Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex
  Ravcheev, Journal of bacteriology 2012
  • “...TM0012 TM0179 TM0201 TM0227 TM0379 TM0423 TM0686 TM0983 TM1400 TM1420 TM1586 TM1814 TRQ2_0578 hycABC-TM0009 TM0179 hycD hycE-hycC2 noxE gldA...”
  • “...of gene regions containing Rex-binding sites: TM0012, TM0201, TM0983, TM1586 (A); TRQ2-0578 (1), TRQ2-0578 (2), TM0228 (B); TM1420, TM0423, TM0686, TM1400 (C);...”
• An NMR approach to structural proteomics
  Yee, Proceedings of the National Academy of Sciences of the United States of America 2002
  • “...1JSB; BMRB, 5106), Mth1880 (PDB, 1IQO; BMRB, 5129), TM0983 (PDB, 1JDQ; BMRB, 5060), YedF_ecoli (PDB, 1JE3; BMRB, 5059), Yjbj_ecoli (PDB, 1JYG; BMRB, 5106),...”
  • “...place of the C-terminal strand in the PDZ domain. TM0983 and YedF_ecoli (which are members of the same COG) formed a two-layered fold that is structurally...”

CTN_1595 hypothetical protein from Thermotoga neapolitana DSM 4359
49% identity, 85% coverage

• A pipeline for completing bacterial genomes using in silico and wet lab approaches
  Puranik, BMC genomics 2015
  • “...protein TM0981 TRQ2_1814 CTN_1597 Disrupted hypothetical protein TM0982 TRQ2_1813 CTN_1596 Present hypothetical protein TM0983 TRQ2_1812 CTN_1595 Disrupted hypothetical protein TM0984 TRQ2_1811 CTN_1594 Disrupted hypothetical protein TM0985 TRQ2_1810 CTN_1593 Present hypothetical protein TM0986 TRQ2_1809 CTN_1592 & CTN_1591 Present hypothetical protein TM0987 TRQ2_1808 CTN_1590 Disrupted hypothetical protein TM0988...”

BC0795 Molybdopterin biosynthesis MoeB protein from Bacillus cereus ATCC 14579
34% identity, 88% coverage

• Identification of Bacillus cereus genes specifically expressed during growth at low temperatures
  Brillard, Applied and environmental microbiology 2010
  • “...1 BC0749 (6) RZC02927 H Metabolism CIP16 1,473 2 BC0795 RZC01484 O BC0796 RZC01487 P Cellular processes and signaling Metabolism CIP30 558 1 BC1235 (6) RZC03344...”

BAS0740 conserved hypothetical protein from Bacillus anthracis str. Sterne
35% identity, 88% coverage

• Crystal structure and catalytic properties of Bacillus anthracis CoADR-RHD: implications for flavin-linked sulfur trafficking
  Wallen, Biochemistry 2009
  • “...it lacks this third CoADR isoform, does have CoADR-RHD (BAS0736), SirA-RHD (BAS0738; YrkF homolog), SirA (BAS0740; TusA homolog), and DsrE-like (BAS0743; YrkE homolog) protein-encoding loci clustered together. 2 In B. anthracis , the ThiI protein is also known to lack the C-terminal RHD found in E....”

Mcup_0683 sulfurtransferase TusA family protein from Metallosphaera cuprina Ar-4
35% identity, 85% coverage

• A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex
  Tanabe, Protein science : a publication of the Protein Society 2024
  • “...Av, Ac. vinosum (Alvin_2600); Hd, Hm. denitrificans (Hden_0698); Aq, Aq. aeolicus (Aq_388a); Mc, Ms. cuprina (Mcup_0683). Triangles indicate the cysteines that were exchanged to serine in this work. Asterisk, fully conserved residues; colon, conservation between groups of strongly similar properties; dot, conservation between groups of weakly...”
• Thiosulfate transfer mediated by DsrE/TusA homologs from acidothermophilic sulfur-oxidizing archaeon Metallosphaera cuprina
  Liu, The Journal of biological chemistry 2014
  • “...for a potential sulfide:quinone oxidoreductase (Mcup_1723) and TusA (Mcup_1722). Mcup_0682 and a further tusA homolog (Mcup_0683) immediately precede the hdrC1B1AhyphdrC2B2 cluster ( Fig. 2 B ). Mcup_0681 is transcribed in the opposite direction to Mcup_0682 and resides upstream of a genetic cluster that encodes a putative...”
  • “...had 34% (100% coverage) and 35% (86% coverage) identity to AFE_2556 and Alvin_2601, respectively. TusA (Mcup_0683) of M. cuprina Ar-4 has 39% (88% coverage) and 34% (91% coverage) identity to TusA (AFE_2557) of A. ferrooxidans and TusA (Alvin_2600) of A. vinosum , respectively. Cloning, Site-directed Mutagenesis,...”

BSU26500 hypothetical protein from Bacillus subtilis subsp. subtilis str. 168
35% identity, 94% coverage

• Comparison of Bacillus subtilis transcriptome profiles from two separate missions to the International Space Station
  Morrison, NPJ microgravity 2019
  • “...anchoring/assembly protein AbrB, LutR, RemA, SigA, SinR BSU26490 yrkJ 1.73 1.85 1.96 1.92 Unknown Unknown BSU26500 yrkI 2.32 2.50 2.22 2.48 Unknown Unknown BSU26510 yrkH 2.63 2.80 2.50 2.89 Unknown Unknown BSU26530 yrkF 3.22 3.62 2.77 3.84 Unknown Unknown BSU26540 yrkE 3.16 3.47 2.76 3.65 Unknown...”

Teth39_2157 SirA family protein from Thermoanaerobacter ethanolicus ATCC 33223
42% identity, 81% coverage

• A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E
  Clarkson, Biotechnology for biofuels 2014
  • “...Hypothetical protein 0.041 Teth39_0842 -36.68 Hypothetical protein 0.000 Nucleotide related Teth39_1357 -2.51 Metal-dependent phosphohydrolase 0.002 Teth39_2157 -9.29 SirA family protein 0.000 Redox proteins Teth39_0445 -2.19 Thioredoxin reductase 0.002 Teth39_1916 -2.73 Oxidoreductase FAD/NAD(P)-binding domain 0.001 Teth39_1917 -4.88 4Fe-4S ferredoxin, iron-sulfur binding domain 0.000 Teth39_2155 -4.30 FAD-dependent pyridine...”

M9U7N8 Putative redox protein, regulator of disulfidebond formation from Sulfolobus islandicus LAL14/1
35% identity, 96% coverage

• Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics
  Vorontsov, Molecular & cellular proteomics : MCP 2016
  • “...in the top-down mode. Cysteine-containing putative redox proteins M9U7N8 and M9UCV1 appear to bear methylthio groups (-SMe, 45.99 Da) on their cysteine-18 and...”

8j4cB / G0GAP6 Yeee(tsua)-yeed(tsub) complex for thiosulfate uptake (see paper)
38% identity, 17% coverage

• Ligand: thiosulfate (8j4cB)

BSU26530 putative rhodanese-related sulfur transferase from Bacillus subtilis subsp. subtilis str. 168
34% identity, 37% coverage

• Comparison of Bacillus subtilis transcriptome profiles from two separate missions to the International Space Station
  Morrison, NPJ microgravity 2019
  • “...yrkI 2.32 2.50 2.22 2.48 Unknown Unknown BSU26510 yrkH 2.63 2.80 2.50 2.89 Unknown Unknown BSU26530 yrkF 3.22 3.62 2.77 3.84 Unknown Unknown BSU26540 yrkE 3.16 3.47 2.76 3.65 Unknown Unknown BSU29440 argH 2.57 2.67 1.25 1.22 Argininosuccinate lyase AhrC BSU29450 argG 2.50 2.61 1.29 1.30...”

tusA / P0A890 sulfur transfer protein TusA from Escherichia coli (strain K12) (see 12 papers)
TUSA_ECOLI / P0A890 Sulfur carrier protein TusA; Sulfur mediator TusA; Sulfur transfer protein TusA; tRNA 2-thiouridine synthesizing protein A from Escherichia coli (strain K12) (see 4 papers)
TUSA_ECO57 / P0A892 Sulfur carrier protein TusA; Sulfur mediator TusA; Sulfur transfer protein TusA; tRNA 2-thiouridine synthesizing protein A from Escherichia coli O157:H7 (see paper)
tusA sulfurtransferase TusA; EC 2.8.1; EC 2.8.1.- from Escherichia coli K12 (see 7 papers)
B21_RS17320 sulfurtransferase TusA from Escherichia coli BL21(DE3)
NP_417927 sulfur transfer protein TusA from Escherichia coli str. K-12 substr. MG1655
UTI89_C3986 possible RNA-binding protein required for wild-type FtsZ ring formation on rich media from Escherichia coli UTI89
b3470 cell developmental protein SirA from Escherichia coli str. K-12 substr. MG1655
32% identity, 89% coverage

• function: Sulfur carrier protein involved in sulfur trafficking in the cell. Part of a sulfur-relay system required for 2-thiolation during synthesis of 2-thiouridine of the modified wobble base 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) in tRNA (PubMed:16387657). Interacts with IscS and stimulates its cysteine desulfurase activity (PubMed:16387657, PubMed:23281480). Accepts an activated sulfur from IscS, which is then transferred to TusD, and thus determines the direction of sulfur flow from IscS to 2-thiouridine formation (PubMed:16387657). Also appears to be involved in sulfur transfer for the biosynthesis of molybdopterin (PubMed:23281480). Seems to affect the stability of sigma-S, particularly during the logarithmic growth phase (PubMed:9555915).
  subunit: Interacts with IscS.
  disruption phenotype: Cells lacking this gene are not capable of growing in standard laboratory rich medium (i.e., Luria broth), and show filamentous shape (PubMed:9555915). FtsZ-ring formation appears to be severely impaired in tusA-deficient cells, resulting in the formation of a non-divided filamentous cell (PubMed:10830496). A tusA deletion mutant lacks the 2-thio modification of mnm5s2U in tRNA and has a severe growth defect (PubMed:16387657). Deletion of tusA has a pleiotropic effect on transcription, including increased expression of molybdenum cofactor biosynthesis genes (moaABCDE operon), but leads to reduced activity of molybdoenzymes, an overall low molybdopterin content and an accumulation of the molybdopterin precursor cyclic pyranopterin monophopshate (cPMP) (PubMed:23281480).
• function: Sulfur carrier protein involved in sulfur trafficking in the cell. Part of a sulfur-relay system required for 2-thiolation during synthesis of 2-thiouridine of the modified wobble base 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) in tRNA. Interacts with IscS and stimulates its cysteine desulfurase activity. Accepts an activated sulfur from IscS, which is then transferred to TusD, and thus determines the direction of sulfur flow from IscS to 2-thiouridine formation. Also appears to be involved in sulfur transfer for the biosynthesis of molybdopterin.
  subunit: Forms a heterotetramer with IscS. Certain pairs of proteins can bind simultaneously to IscS but TusA does not seem to be one of them. IscU can displace TusA from IscS.
• Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress
  Chen, mSystems 2021
  • “...involved in metal transport (B21_RS09935 and B21_RS17315), ferric iron import (B21_RS02785 and B21_RS22395), sulfur metabolism (B21_RS17320, B21_RS13610, B21_RS13605, B21_RS13600, and B21_RS07750), stress response (B21_RS19915), sugar import (B21_RS20540, B21_RS20565, and B21_RS21625), cell wall remodeling (B21_RS05900), and energy production and conversion (B21_RS21615) ( Fig.2A ). In S. cerevisiae...”
• The sulfur carrier protein TusA has a pleiotropic role in Escherichia coli that also affects molybdenum cofactor biosynthesis.
  Dahl, The Journal of biological chemistry 2013
  • GeneRIF: sulfur carrier protein TusA has a pleiotropic role in Escherichia coli that also affects molybdenum cofactor biosynthesis
• TusA (YhhP) and IscS are required for molybdenum cofactor-dependent base-analog detoxification.
  Kozmin, MicrobiologyOpen 2013
  • GeneRIF: TusA (YhhP) and IscS are required for molybdenum cofactor-dependent base-analog detoxification.
• Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions.
  Shi, PLoS biology 2010
  • GeneRIF: study determined the crystal structures of IscS-IscU and IscS-TusA complexes providing the first insight into their different modes of binding and the mechanism of sulfur transfer
• Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections
  García, Microbial genomics 2021
  • “...Outer membrane protein A Ion transport/host-virus interaction/conjugation (M) 2.20 UTI89_C3110 UTI89_C3110 Hypothetical protein (NI) 2.19 UTI89_C3986 sira (tusA) Possible RNA-binding protein required for wild-type FtsZ ring formation on rich media tRNA processing (J) 2.18 UTI89_C2311 rfbD dTDP-4-dehydrorhamnose reductase LPS biosynthesis (F) 2.12 UTI89_C2826 guaB Inosine-5'-monophosphate dehydrogenase...”
• A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex
  Tanabe, Protein science : a publication of the Protein Society 2024
  • “...TusA and related proteins from sulfur oxidizers and E. coli . Ec, E. coli (TusA, b3470, YedF, b1930, YeeD, and b2012); Ts, Ts. sibirica (ThisiDRAFT_0966, according to JGI IMG); Tk, Thioalkalivibrio sp. K90mix (TK90_0631); Av, Ac. vinosum (Alvin_2600); Hd, Hm. denitrificans (Hden_0698); Aq, Aq. aeolicus (Aq_388a);...”
• The sulfur carrier protein TusA has a pleiotropic role in Escherichia coli that also affects molybdenum cofactor biosynthesis
  Dahl, The Journal of biological chemistry 2013
  • “...protein 2-thiouridine formation b1133 b3343 b3470 mnmA tusB tusA tRNA-specific 2-thiouridylase 2-Thiouridine-synthesizing protein B 2-Thiouridine-synthesizing...”

G0GAP7 SirA-like domain-containing protein from Spirochaeta thermophila (strain ATCC 700085 / DSM 6578 / Z-1203)
39% identity, 86% coverage

• YeeD is an essential partner for YeeE-mediated thiosulfate uptake in bacteria and regulates thiosulfate ion decomposition
  Ikei, PLoS biology 2024
  • “...IDs of YeeD sequences used are as follows: E . coli YeeD, P33014; Spirochaeta_thermophila YeeD, G0GAP7; Candidatus Sodalis pierantonius YeeD, W0HL40; Klebsiella_sp . _WP3-W18-ESBL-02 YeeD, A0A7I6Q8F8; Methanosarcinales archaeon YeeD, A0A822J3Z6, Streptococcus thermophilus YeeD, A0A8D6XUG1; Koleobacter methoxysyntrophicus YeeD, A0A8A0RNL6; Wohlfahrtiimonas chitiniclastica YeeD, L8Y0N6; Paenibacillus alvei YeeD, A0A383RJV0;...”

TC 9.B.102.1.12 / Q8FLY1 YeeE/YedE protein with 9 TMSs and a C-terminal SirA/YedF/YeeD/YvrY domain of about 100 aas. The hydrophilic SirA α/β sandwich from Corynebacterium efficiens (strain DSM 44549 / YS-314 / AJ 12310 / JCM 11189 / NBRC 100395)
33% identity, 13% coverage

• substrates: sulfur
  tcdb comment: domain has been suggested to be involved in surface attachement and biofilm formation in enteric bacteria (Teplitski et al. 2006; Salazar et al. 2013). However, SirA/TusA/YhhP proteins bind FMN, catalyze sulfur transfer, and are important for sulfur oxidation, tRNA thiomodification and molybdenum cofactor biosynthesis (Dahl et al. 2013; Lee et al. 2013; Higgins et al. 2015) Homologues have been shown to bind sulfur via a cysteyl residue, and growth on sullfide in sufur oxidation bacteria requires such a homologue (Stockdreher et al. 2014). Genes encoding homologues of YeeD are often found sandwiched in between the two genes encoding half sized YeeE homologues of 4 or 5 TMSs

TRQ2_1817 ArsR family transcriptional regulator from Thermotoga sp. RQ2
38% identity, 37% coverage

• A pipeline for completing bacterial genomes using in silico and wet lab approaches
  Puranik, BMC genomics 2015
  • “...hypothetical protein TM0976 Absent Present* Present hypothetical protein TM0977 Absent CTN_1601 Present hypothetical protein TM0978 TRQ2_1817 CTN_1600 Present hypothetical protein TM0979 TRQ2_1816 CTN_1599 Present hypothetical protein TM0980 TRQ2_1815 CTN_1598 Present hypothetical protein TM0981 TRQ2_1814 CTN_1597 Disrupted hypothetical protein TM0982 TRQ2_1813 CTN_1596 Present hypothetical protein TM0983 TRQ2_1812...”

tusA / D3RPC0 TusA sulfur-carrier protein from Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D) (see 2 papers)
TUSA_ALLVD / D3RPC0 Sulfur carrier protein TusA from Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D) (Chromatium vinosum) (see 2 papers)
Alvin_2600 SirA family protein from Allochromatium vinosum DSM 180
28% identity, 92% coverage

• function: Sulfur carrier protein involved in sulfur trafficking for oxidative dissimilatory sulfur metabolism. Component of a sulfur relay system that starts with the sulfur-mobilizing rhodanese-like protein Rhd_2599 (Alvin_2599), which transfers the sulfur from a low-molecular- weight thiol, maybe glutathione, to the TusA protein (Alvin_2600); TusA serves as the sulfur donor for DsrEFH, which persulfurates DsrC; persulfurated DsrC very probably serves as a direct substrate for reverse-acting sulfite reductase, DsrAB. TusA seems to be not exclusively dedicated to sulfur oxidation and may have other important roles in the cell. Might also act as a sulfur mediator required for 2- thiouridine formation of tRNA.
  subunit: Mostly a monomer, a small portion forms homodimer via intermolecular disulfide bonds. Tightly interacts with DsrEFH.
  disruption phenotype: A mutant strain lacking rhd_2599, tusA and dsrE2, although not viable in liquid culture, is clearly sulfur oxidation negative upon growth on solid media containing sulfide, and shows massive accumulation of intercellular sulfur globules.
• Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source
  Alarcon, Applied and environmental microbiology 2024
  • “...Biopolymer transport protein ExbD/TolR 135 Alvin_2551 2.64 5.0E-03 Photosynthetic reaction centre cytochrome c subunit 136 Alvin_2600 2.63 7.8E-23 SirA family protein 137 Alvin_0744 2.63 6.5E-11 Aigma54 specific transcriptional regulator, Fis family 138 Alvin_2432 2.62 8.7E-30 Triosephosphate isomerase 139 Alvin_0805 2.60 1.4E-23 2-Oxo-acid dehydrogenase E1 subunit, homodimeric...”
• The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways
  Petushkova, Microorganisms 2024
  • “...the transfer of sulfur from a low-molecular-weight thiol (probably from glutathion) to the TusA protein (Alvin_2600); TusA serves as a sulfur donor for DsrEFH (genes Alvin_1253, Alvin_1254, and Alvin_1255), which in its turn perform the persulfation of DsrC (Alvin_1256); persulfated DsrC is likely to serve as...”
• A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex
  Tanabe, Protein science : a publication of the Protein Society 2024
  • “...Ts. sibirica (ThisiDRAFT_0966, according to JGI IMG); Tk, Thioalkalivibrio sp. K90mix (TK90_0631); Av, Ac. vinosum (Alvin_2600); Hd, Hm. denitrificans (Hden_0698); Aq, Aq. aeolicus (Aq_388a); Mc, Ms. cuprina (Mcup_0683). Triangles indicate the cysteines that were exchanged to serine in this work. Asterisk, fully conserved residues; colon, conservation...”
• A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum
  Weissgerber, Applied and environmental microbiology 2014
  • “...from the low-molecular-weight thiol to the TusA protein (Alvin_2600). TusA serves as a sulfur donor for DsrEFH, which persulfurates DsrC. The latter very...”
  • “...rhodanese-like protein Alvin_ 2599, A. vinosum TusA (Alvin_2600), and possibly also the membrane-bound DsrE2 protein (Alvin_2601) as components of a cytoplasmic...”
• Thiosulfate transfer mediated by DsrE/TusA homologs from acidothermophilic sulfur-oxidizing archaeon Metallosphaera cuprina
  Liu, The Journal of biological chemistry 2014
  • “...(88% coverage) and 34% (91% coverage) identity to TusA (AFE_2557) of A. ferrooxidans and TusA (Alvin_2600) of A. vinosum , respectively. Cloning, Site-directed Mutagenesis, and Expression of dsrE2B, dsrE3A, and tusA from M. cuprina in E. coli N-terminally His-tagged DsrE3A (Mcup_0681), DsrE2B (Mcup_0682), and TusA (Mcup_0683)...”
• New proteins involved in sulfur trafficking in the cytoplasm of Allochromatium vinosum
  Stockdreher, The Journal of biological chemistry 2014
  • “...Proteins--For the amplification of the Alvin_2599 (rhd_2599), Alvin_2600 (tusA), and Alvin_2601 (dsrE2) genes, genomic DNA of A. vinosum served as the...”
  • “...no extra copies for tusA or tusBCD apart from Alvin_2600 and dsrEFH, respectively. The tusE homolog dsrC is present with five genomic copies. This implies that...”
• Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds
  Weissgerber, Journal of bacteriology 2013
  • “...and approximately 150-bp fragments of Alvin_0258, Alvin_2600, Alvin_2601, Alvin_3028, and the reference locus, Alvin_0486, encoding a uroporphyrinogen...”
  • “...Alvin_2500 Alvin_2501 Alvin_2507 Alvin_2515 Alvin_2572 Alvin_2600 Alvin_2601 Alvin_2651 Alvin_2661 Alvin_2667 Alvin_2705 Alvin_2962 Alvin_2965 Alvin_2980...”

TM0978 conserved hypothetical protein from Thermotoga maritima MSB8
CTN_1600 SirA family protein from Thermotoga neapolitana DSM 4359
38% identity, 37% coverage

• A pipeline for completing bacterial genomes using in silico and wet lab approaches
  Puranik, BMC genomics 2015
  • “...Disrupted hypothetical protein TM0976 Absent Present* Present hypothetical protein TM0977 Absent CTN_1601 Present hypothetical protein TM0978 TRQ2_1817 CTN_1600 Present hypothetical protein TM0979 TRQ2_1816 CTN_1599 Present hypothetical protein TM0980 TRQ2_1815 CTN_1598 Present hypothetical protein TM0981 TRQ2_1814 CTN_1597 Disrupted hypothetical protein TM0982 TRQ2_1813 CTN_1596 Present hypothetical protein TM0983...”
• A pipeline for completing bacterial genomes using in silico and wet lab approaches
  Puranik, BMC genomics 2015
  • “...protein TM0976 Absent Present* Present hypothetical protein TM0977 Absent CTN_1601 Present hypothetical protein TM0978 TRQ2_1817 CTN_1600 Present hypothetical protein TM0979 TRQ2_1816 CTN_1599 Present hypothetical protein TM0980 TRQ2_1815 CTN_1598 Present hypothetical protein TM0981 TRQ2_1814 CTN_1597 Disrupted hypothetical protein TM0982 TRQ2_1813 CTN_1596 Present hypothetical protein TM0983 TRQ2_1812 CTN_1595...”

LGS26_02870 sulfurtransferase TusA family protein from Dissulfurimicrobium hydrothermale
34% identity, 80% coverage

• Genetic Potential of Dissulfurimicrobium hydrothermale, an Obligate Sulfur-Disproportionating Thermophilic Microorganism
  Yvenou, Microorganisms 2021
  • “...is a non-sulfate reducing organism capable of growth by ISC-disproportionation. Indeed (i) a sulfurtransferase TusA (LGS26_02870) protein is encoded and shares the highest protein sequence homology with TusA from Dissulfurirhabdus thermomarina , (ii) a YeeE/YedE family protein (LGS26_02865) is present and shares the highest protein sequence...”

Q2FWL8 UPF0033 domain-containing protein from Staphylococcus aureus (strain NCTC 8325 / PS 47)
SAOUHSC_02271 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_1997 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
NWMN_1951 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
37% identity, 77% coverage

• Antibacterial Activity of Juglone against Staphylococcus aureus: From Apparent to Proteomic
  Wang, International journal of molecular sciences 2016
  • “...50.20 0.761 0.022 Others Q2FVB3 antibiotic transport system permease SAOUHSC_02821 1 1 28.90 1.299 0.007 Q2FWL8 transcriptional regulator SAOUHSC_02271 2 2 8.20 1.448 0.001 Q2G2L6 pf09954 family protein SAOUHSC_02812 1 1 16.00 1.383 0.019 Q2FZ07 uncharacterized protein SAOUHSC_01264 2 2 8.20 0.809 0.000 Q2FV28 uncharacterized conserved...”
• Teg58, a small regulatory RNA, is involved in regulating arginine biosynthesis and biofilm formation in Staphylococcus aureus
  Manna, Scientific reports 2022
  • “...1066 341 3.13 SAOUHSC_00075 Siderophore staphylobactin biosynthesis protein, sbnA 92 21 4.41 Transcriptional regulatory proteins SAOUHSC_02271 Transcriptional regulator, yedF 1214 268 4.53 SAOUHSC_00706 Fructose repressor, glcR 18,040 5240 3.44 SAOUHSC_02570 Transcription regulator, HP 2238 580 3.86 Uncharacterized proteins SAOUHSC_00410 Uncharacterized conserved protein 19,136 2907 6.58 SAOUHSC_00355...”
• Antibacterial Activity of Juglone against Staphylococcus aureus: From Apparent to Proteomic
  Wang, International journal of molecular sciences 2016
  • “...Others Q2FVB3 antibiotic transport system permease SAOUHSC_02821 1 1 28.90 1.299 0.007 Q2FWL8 transcriptional regulator SAOUHSC_02271 2 2 8.20 1.448 0.001 Q2G2L6 pf09954 family protein SAOUHSC_02812 1 1 16.00 1.383 0.019 Q2FZ07 uncharacterized protein SAOUHSC_01264 2 2 8.20 0.809 0.000 Q2FV28 uncharacterized conserved protein SAOUHSC_02911 2...”
• Cigarette Smoke Extract-Exposed Methicillin-Resistant Staphylococcus aureus Regulates Leukocyte Function for Pulmonary Persistence
  Kulkarni, American journal of respiratory cell and molecular biology 2016
  • “...SAUSA300_0177 SAUSA300_2454 SAUSA300_2364 SAUSA300_0173 SAUSA300_1997 SAUSA300_1998 SAUSA300_1052 SAUSA300_2489 SAUSA300_0386 SAUSA300_0776 SAUSA300_0387...”
  • “...SAUSA300_2343 SAUSA300_2321 SAUSA300_2097 SAUSA300_1998 SAUSA300_1997 SAUSA300_1938 SAUSA300_1937 SAUSA300_1936 SAUSA300_1935 SAUSA300_1934 SAUSA300_1395...”
• Comparative Transcriptome Analysis Reveals Differentially Expressed Genes Related to Antimicrobial Properties of Lysostaphin in Staphylococcus aureus
  Yan, Antibiotics (Basel, Switzerland) 2022
  • “...BAF66470 0.92 5.12 0.00 0.03 GntR NWMN_0738 BA67010 0.71 8.16 0.00 0.04 Conserved hypothetical protein NWMN_1951 BAF68223 1.08 4.81 0.00 0.04 oxidoreductase lukF BAF68199 0.95 6.15 0.00 0.04 gamma-hemolysin subunit B NWMN_2209 BAF68481 0.83 6.91 0.00 0.04 conserved hypothetical protein Up-regulated gene (lower expression in WT)...”
• Sulfide Homeostasis and Nitroxyl Intersect via Formation of Reactive Sulfur Species in Staphylococcus aureus
  Peng, mSphere 2017
  • “...e 4.8 ABC transporter: cystine (cystine binding) e + NWMN_1877 SA1755 chp 32.7 Chemotaxis-inhibiting protein NWMN_1951 SA1849 9.8 4.4 TusA-like (SirA/YedF/YeeD) protein + NWMN_1952 SA1850 14.2 5.0 Putative thiosulfate (TS) importer + NWMN_2049 SA1949 czrA 15.9 Zinc-specific repressor (ArsR family) NWMN_2050 SA1950 czrB 14.0 Zinc cation...”
  • “...(NWMN_0246 to NWMN_0428) and cystine (NWMN_0374 and NWMN_1749 to NWMN_1751) ABC transporters and an operon (NWMN_1951 to NWMN_1952) encoding a TusA-like sulfurtransferase and a putative thiosulfate importer are also repressed ( 3 ). Loss of cymR in a cymR mutant results in overexpression of the CymR...”
• Hydrogen Sulfide and Reactive Sulfur Species Impact Proteome S-Sulfhydration and Global Virulence Regulation in Staphylococcus aureus
  Peng, ACS infectious diseases 2017
  • “...S2C ); those that do include genes are either strongly repressed ( cysK ; NWMN_0115; NWMN_1951) or derepressed ( cstAB ) by exogenous sulfide treatment. 24 A bioinformatics analysis reveals that S -sulfhydrated proteins can be mapped to distinct metabolic pathways. For example, proteins known to...”

TK90_0631 SirA family protein from Thioalkalivibrio sp. K90mix
25% identity, 92% coverage

• A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex
  Tanabe, Protein science : a publication of the Protein Society 2024
  • “...YeeD, and b2012); Ts, Ts. sibirica (ThisiDRAFT_0966, according to JGI IMG); Tk, Thioalkalivibrio sp. K90mix (TK90_0631); Av, Ac. vinosum (Alvin_2600); Hd, Hm. denitrificans (Hden_0698); Aq, Aq. aeolicus (Aq_388a); Mc, Ms. cuprina (Mcup_0683). Triangles indicate the cysteines that were exchanged to serine in this work. Asterisk, fully...”
• Complete genome sequence of Thioalkalivibrio sp. K90mix
  Muyzer, Standards in genomic sciences 2011
  • “...]. However, we found a gene cluster encoding two sulfur transferases ( rhd, TK90_0630; sirA, TK90_0631) and a heterodisulfide reductase complex (TK90_0632 - TK90_0637) consisting of hdrA, hdrB, and hdrC ( Figure 6 ). dsrE was missing in this cascade, but was present at 3 other...”

SA1849 hypothetical protein from Staphylococcus aureus subsp. aureus N315
36% identity, 77% coverage

• Sulfide Homeostasis and Nitroxyl Intersect via Formation of Reactive Sulfur Species in Staphylococcus aureus
  Peng, mSphere 2017
  • “...4.8 ABC transporter: cystine (cystine binding) e + NWMN_1877 SA1755 chp 32.7 Chemotaxis-inhibiting protein NWMN_1951 SA1849 9.8 4.4 TusA-like (SirA/YedF/YeeD) protein + NWMN_1952 SA1850 14.2 5.0 Putative thiosulfate (TS) importer + NWMN_2049 SA1949 czrA 15.9 Zinc-specific repressor (ArsR family) NWMN_2050 SA1950 czrB 14.0 Zinc cation diffusion...”

W0HL40 YeeD from Candidatus Sodalis pierantonius str. SOPE
31% identity, 79% coverage

• YeeD is an essential partner for YeeE-mediated thiosulfate uptake in bacteria and regulates thiosulfate ion decomposition
  Ikei, PLoS biology 2024
  • “...are as follows: E . coli YeeD, P33014; Spirochaeta_thermophila YeeD, G0GAP7; Candidatus Sodalis pierantonius YeeD, W0HL40; Klebsiella_sp . _WP3-W18-ESBL-02 YeeD, A0A7I6Q8F8; Methanosarcinales archaeon YeeD, A0A822J3Z6, Streptococcus thermophilus YeeD, A0A8D6XUG1; Koleobacter methoxysyntrophicus YeeD, A0A8A0RNL6; Wohlfahrtiimonas chitiniclastica YeeD, L8Y0N6; Paenibacillus alvei YeeD, A0A383RJV0; Shigella flexneri YeeD, A0A384L8W9; Streptococcus...”

Hden_0698 sulfurtransferase TusA family protein from Hyphomicrobium denitrificans ATCC 51888
29% identity, 95% coverage

• A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex
  Tanabe, Protein science : a publication of the Protein Society 2024
  • “...to JGI IMG); Tk, Thioalkalivibrio sp. K90mix (TK90_0631); Av, Ac. vinosum (Alvin_2600); Hd, Hm. denitrificans (Hden_0698); Aq, Aq. aeolicus (Aq_388a); Mc, Ms. cuprina (Mcup_0683). Triangles indicate the cysteines that were exchanged to serine in this work. Asterisk, fully conserved residues; colon, conservation between groups of strongly...”
• In the Alphaproteobacterium Hyphomicrobium denitrificans SoxR Serves a Sulfane Sulfur-Responsive Repressor of Sulfur Oxidation
  Li, Antioxidants (Basel, Switzerland) 2023
  • “...between the lipX (Hden_0687) and dsrE3C (Hden_0688) genes, a 176-bp fragment located between the tusA (Hden_0698) and hyp (Hden_0697) genes, and a 151-bp fragment situated between the soxA (Hden_0703) and soxY (Hden_0704) genes. All primers used are listed in Table S1 . Native 6% polyacrylamide gels...”

New Search

Statistics

How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.