PaperBLAST

PaperBLAST Hits for DDA3937_RS06135 (69 a.a., MEGISIAKLL...)

Show query sequence

>DDA3937_RS06135
MEGISIAKLLVIGALIVLLFGTNKLRSLGSDLGAAIKGFKKSMSDEQPAAKSSAQDEHPA
AISENRPKE

Running BLASTp...

Found 42 similar proteins in the literature:

TatA / b3836 twin arginine protein translocation system - TatA protein from Escherichia coli K-12 substr. MG1655 (see 21 papers)
TatA / P69428 twin arginine protein translocation system - TatA protein from Escherichia coli (strain K12) (see 22 papers)
TATA_ECOLI / P69428 Sec-independent protein translocase protein TatA from Escherichia coli (strain K12) (see 9 papers)
CXG97_RS22995 Sec-independent protein translocase subunit TatA from Escherichia coli
NP_418280 twin arginine protein translocation system - TatA protein from Escherichia coli str. K-12 substr. MG1655
62% identity, 63% coverage

• function: Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin- arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system.
  subunit: The Tat system comprises two distinct complexes: a TatABC complex, containing multiple copies of TatA, TatB and TatC subunits, and a separate TatA complex, containing only TatA subunits. Substrates initially bind to the TatABC complex, which probably triggers association of the separate TatA complex to form the active translocon. A complex containing only TatA and TatB has also been identified. It could be either an assembly intermediate or a disassembly intermediate generated during translocation activity. Each of TatA, TatB and TatC are able to interact in pairs without the third partner; TatA also forms homooligomers.
  disruption phenotype: Disruption of tatA affects the correct localization of multiple enzymes whose precursors bear twin arginine transfer peptides. Export is completely blocked when both tatA and tatE are inactivated.
• Transcriptome profiling of avian pathogenic Escherichia coli and the mouse microvascular endothelial cell line bEnd.3 during interaction
  Wang, PeerJ 2020
  • “...tatC 1.9541 0.00021961 twin-arginine translocase subunit TatC CXG97_RS02115 YajC 1.7879 0.00069815 preprotein translocase subunit YajC CXG97_RS22995 TatA 1.3288 0.012952 twin-arginine translocase subunit TatA CXG97_RS23000 TatB 1.2944 0.014643 twin-arginine translocase subunit TatB CXG97_RS02125 SecF 2.2484 0.020017 protein translocase subunit SecF CXG97_RS21575 SecB 1.237 0.025291 protein-export protein SecB...”
• The polar amino acid in the TatA transmembrane helix is not strictly necessary for protein function.
  Hao, The Journal of biological chemistry 2023
  • GeneRIF: The polar amino acid in the TatA transmembrane helix is not strictly necessary for protein function.
• Hydrophobic mismatch is a key factor in protein transport across lipid bilayer membranes via the Tat pathway.
  Hao, The Journal of biological chemistry 2022
  • GeneRIF: Hydrophobic mismatch is a key factor in protein transport across lipid bilayer membranes via the Tat pathway.
• TatA and TatB generate a hydrophobic mismatch important for the function and assembly of the Tat translocon in Escherichia coli.
  Mehner-Breitfeld, The Journal of biological chemistry 2022
  • GeneRIF: TatA and TatB generate a hydrophobic mismatch important for the function and assembly of the Tat translocon in Escherichia coli.
• Ferric Citrate Regulator FecR Is Translocated across the Bacterial Inner Membrane via a Unique Twin-Arginine Transport-Dependent Mechanism.
  Passmore, Journal of bacteriology 2020
  • GeneRIF: Ferric Citrate Regulator FecR Is Translocated across the Bacterial Inner Membrane via a Unique Twin-Arginine Transport-Dependent Mechanism.
• The TatA component of the twin-arginine translocation system locally weakens the cytoplasmic membrane of Escherichia coli upon protein substrate binding.
  Hou, The Journal of biological chemistry 2018
  • GeneRIF: revealed that substrate binding causes the TatA hinge region and the N-terminal part of the TatA amphipathic helix to move toward the membrane surface
• A signal sequence suppressor mutant that stabilizes an assembled state of the twin arginine translocase.
  Huang, Proceedings of the National Academy of Sciences of the United States of America 2017
  • GeneRIF: It has been concluded that Tat signal peptides play roles in substrate targeting and in triggering assembly of the active TatABC translocase.
• TatA complexes exhibit a marked change in organisation in response to expression of the TatBC complex.
  Smith, The Biochemical journal 2017
  • GeneRIF: Twin-arginine translocation (Tat) system TatA exhibits a uniform distribution throughout the inner membrane and that altering the expression of TatBC shows a uncharacterised distribution of TatA in the inner membrane.
• In vivo experiments do not support the charge zipper model for Tat translocase assembly.
  Alcock, eLife 2017
  • GeneRIF: The authors observe that substitutions of charged residues located in the TatA amphipathic helix lock TatA in an assembled state, suggesting that these charged residues play a critical role in the protein translocation step that follows TatA assembly.
• More
• Biodistribution of ⁸⁹Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
  Li, Poultry science 2023
  • “...production and conversion Cell inner membrane 327 P0ADB1 OSME Function unknown Cell inner membrane 328 P69428 TATA Intracellular trafficking, secretion, and vesicular transport Cell inner membrane 329 P0ABA6 ATPG Energy production and conversion Cell inner membrane 330 P0AC47 FRDB Energy production and conversion Cell inner membrane...”
• Identification of Functional Interactome of Colistin Resistance Protein MCR-1 in Escherichia coli
  Li, Frontiers in microbiology 2020
  • “...Q0TLG8 UPF0325 protein YaeH 15,144 yaeH 25 P0A7T3 30S ribosomal protein S16 9,185 rpsP 26 P69428 Sec-independent protein translocase protein TatA 9,658 tatA 27 P0AG30 Transcription termination factor Rho 47,032 rho 28 P0AGE0 Single-stranded DNA-binding protein 18,963 ssb 29 P02925 Ribose import binding protein RbsB 30,931...”
• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...the amino acid sequences of E. coli TatE (accession number: P0A843), TatB (P69425) and TatA (P69428). N-terminal, charged amino acid residues of TatE and TatB are highlighted in red, other charged residues are in bold. Secondary structural elements are assigned according to the NMR structure of...”
• Large-scale identification of membrane proteins with properties favorable for crystallization
  Kim, Protein science : a publication of the Protein Society 2015
  • “...N Y Y N N N N N N Y N N P69428 P76576 P0AFE4 9658 22162 10838 N N Y cross the membrane only once.32 Interestingly, only 10% of all unique, membrane protein...”
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...Methyl-accepting chemotaxis protein II 5.39/59,943.7 TatA P69428 Sec-independent protein translocase protein 5.73/9,663.98 TatB P69425 5.13/18,420.87 Tdh P07913...”

FPV33_RS18075 twin-arginine translocase subunit TatE from Klebsiella aerogenes
62% identity, 87% coverage

• Transcriptomic analysis of nitrogen metabolism pathways in Klebsiella aerogenes under nitrogen-rich conditions
  Chen, Frontiers in microbiology 2024
  • “...NarK family nitrate/nitrite MFS transporter 1.50 FPV33_RS14980 ntrB Nitrate ABC transporter permease 1.11 Arginine metabolism FPV33_RS18075 tatE Twin-arginine translocase subunit TatE 1.52 FPV33_RS07020 argT Lysine/arginine/ornithine ABC transporter substrate-binding protein ArgT 1.87 FPV33_RS16875 artQ Arginine ABC transporter permease ArtQ 1.50 FPV33_RS16870 artJ Arginine ABC transporter substrate-binding protein...”

YPO2597 sec-independent protein translocase protein from Yersinia pestis CO92
YPTB1090 sec-independent protein translocase protein from Yersinia pseudotuberculosis IP 32953
67% identity, 61% coverage

• Comparative Global Gene Expression Profiles of Wild-Type Yersinia pestis CO92 and Its Braun Lipoprotein Mutant at Flea and Human Body Temperatures
  Galindo, Comparative and functional genomics 2010
  • “...clpB chaperone 2.0 YPCD1.62 putative type III secretion regulatory protein lcrQ/yscM Blocks yop transcription 5.3 YPO2597 sec-independent protein translocase protein tatE Protein and peptide secretion and trafficking 1.7 Stressor response YPO3643 major cold shock protein Cspa2 cspa2 Stress response 3.0 y0224 cold shock-like protein cspI Stress...”
• IscR is essential for yersinia pseudotuberculosis type III secretion and virulence
  Miller, PLoS pathogens 2014
  • “...YPTB0961 ATP-dependent protease lon 2.9 YPTB0995 chaperone Hsp90, heat shock protein C 62.5 htpG 3.3 YPTB1090 sec-independent protein translocase protein tatE 2.9 YPTB1113 putative tRNA-thiotransferase miaB 2.0 YPTB1141 heat shock protein GrpE grpE 2.7 YPTB1417 30S ribosomal protein S1 rpsA 2.2 YPTB1448 putative ribosome modulation factor...”

VP0098 TatA protein from Vibrio parahaemolyticus RIMD 2210633
51% identity, 85% coverage

• QseC Inhibition as a Novel Antivirulence Strategy for the Prevention of Acute Hepatopancreatic Necrosis Disease (AHPND)-Causing Vibrio parahaemolyticus
  Yang, Frontiers in cellular and infection microbiology 2020
  • “...2.03E-50 DUF2383 domain-containing protein VP0096 2.97958 2.04E-23 FIG01200706: hypothetical protein VP0097 3.848639 1.97E-38 Methylglyoxal synthase VP0098 3.289054 3.31E-26 Hemerythrin domain protein VP0099 4.747694 5.81E-34 hypothetical protein VP0100 4.948999 8.06E-56 FIG01201373: hypothetical protein VP0101 4.774471 3.22E-54 inducible periplasmic protein VP0102 2.187439 4.88E-15 sigma-54 interacting response regulator 6...”
• Rapid identification of Vibrio parahaemolyticus by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry
  Hazen, Applied and environmental microbiology 2009
  • “...7,167 10,416 12,569 0 0 0 0 VP3074 VP2780 VP0098 Predicted protein VP2817 VP2331 VP2582 VP0160 VP1210 VP0261 VP1294 VP1283 VP0268 VPA1222 VP2986 VP2923 VP2766...”

plu4410 Sec-independent protein translocase protein from Photorhabdus luminescens subsp. laumondii TTO1
63% identity, 63% coverage

• Genetic and proteomic characterization of rpoB mutations and their effect on nematicidal activity in Photorhabdus luminescens LN2
  Qiu, PloS one 2012
  • “...active drug efflux 6.95 40743.2 1 0 0 0 0 17 Sec-independent protein translocase protein, plu4410 P. luminescens TT01 tatA Sec-independent protein translocase protein 6.18 9289.9 1 0.76 0.81 0.72 0.23 42 Na-binding protein HU-alpha (NS2) (HU-2), plu0492 P. luminescens TT01 dbhA Na-binding protein HU-alpha (NS2)...”

A0KEF9 Sec-independent protein translocase protein TatA from Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049)
62% identity, 72% coverage

• The LysR-Type Transcriptional Regulator YeeY Plays Important Roles in the Regulatory of Furazolidone Resistance in Aeromonas hydrophila
  Fu, Frontiers in microbiology 2020
  • “...under FZ stress by DIA-LC-MS/MS. Accession Gene Description Matched peptides P -value log2( yeeY/WT ) A0KEF9 tatA Sec-independent protein translocase protein TatA 3 5.43E-05 1.762 A0KEY7 glnL Nitrogen regulation protein NR(II) 14 0.000149 2.754 A0KF41 secY Protein translocase subunit SecY 7 1.43E-07 2.724 A0KG12 AHA_0655 Arginine...”

WP_000508971 Sec-independent protein translocase subunit TatA from Vibrio cholerae
50% identity, 83% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog had also been described for the Gram-positive organism Corynebacterium glutamicum 34 . In contrast, the inclusion threshold for TatE homologues that we defined for our database search...”

SL1344_3927 Sec-independent protein translocase subunit TatA from Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
56% identity, 75% coverage

• Role of sapA and yfgA in Susceptibility to Antibody-Mediated Complement-Dependent Killing and Virulence of Salmonella enterica Serovar Typhimurium
  Ondari, Infection and immunity 2017
  • “...147 1,118 2.302 4.84E38 Hypothetical protein SL1344_2377 nupC 204 1,303 2.206 7.05E35 Nucleoside permease NupC SL1344_3927 tatA 408 2,225 2.194 1.73E34 sec-independent protein translocase protein SL1344_3726 slsA 1,288 6,222 2.187 2.89E34 Hypothetical protein SL1344_0091 ksgA 187 1,158 2.132 1.63E32 Dimethyladenosine transferase (adenine1518-N6/adenine1519-N6)-dimethyltransferase SL1344_3928 tatB 1,013 4,552...”

VC0086 tatA protein from Vibrio cholerae O1 biovar eltor str. N16961
57% identity, 68% coverage

• Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation
  Krin, BMC genomics 2018
  • “...ubiquinone (Q) ; 5 : Inner membrane protein 4.5 : Menaquinone and ubiquinone ; 3.7 VC0086 tatA Sec-independent protein translocase TatA t : transporter 4.2.A.64 : The Type V Secretory Pathway or Twin Arginine Targeting (Tat) Family ; 4.S.160 : protein ; 7 : Transport and...”
• Pleiotropic effects of the twin-arginine translocation system on biofilm formation, colonization, and virulence in Vibrio cholerae
  Zhang, BMC microbiology 2009
  • “...genes tatA , tatB , and tatC in chromosome I, and tatA2 in chromosome II (VC0086 and VCA0533 were annotated as tatA and tatA2 , respectively). These genes encode four proteins with a high degree of homology to the E . coli K-12 tat genes, ranging...”

VVMO6_02901 Sec-independent protein translocase subunit TatA from Vibrio vulnificus MO6-24/O
50% identity, 87% coverage

• MARTX Toxin-Stimulated Interplay between Human Cells and Vibrio vulnificus
  Kim, mSphere 2020
  • “...I secretion system, and many sec and tat genes (VVMO6_00227, VVMO6_02445, VVMO6_02446, VVMO6_02568, VVMO6_02900, and VVMO6_02901), which encode Sec (secretion) and Tat (twin-arginine translocation) translocase system proteins, were also expressed at slightly but significantly higher levels in WT V. vulnificus ( TableS5 ). It should be...”

SG0112 sec-independent protein translocase protein TatA from Sodalis glossinidius str. 'morsitans'
68% identity, 53% coverage

• Functional analysis of the twin-arginine translocation pathway in Sodalis glossinidius, a bacterial symbiont of the tsetse fly
  De, Applied and environmental microbiology 2011
  • “...of tatA, tatB, and tatC (GenBank accession no., respectively, SG0112, SG0113, and SG0114), on the circular chromosome with a high level of homology to the...”

YP_3271 Sec-independent protein translocase protein TatA from Yersinia pestis biovar Medievalis str. 91001
YPO3778 Sec-independent protein translocase protein TatA from Yersinia pestis CO92
YPTB0258 Sec-independent protein translocase protein TatA from Yersinia pseudotuberculosis IP 32953
67% identity, 52% coverage

• Comparative Lysine Acetylome Analysis of Y. pestis YfiQ/CobB Mutants Reveals that Acetylation of SlyA Lys73 Significantly Promotes Biofilm Formation of Y. pestis
  Tan, Microbiology spectrum 2023
  • “...HtpG YP_0773 tig Trigger factor YP_2469 ureE Urease accessory protein UreE Nitrogen compound transport (GO:0071705) YP_3271 tatA Sec-independent protein translocase protein TatA YP_3620 secA Protein translocase subunit SecA YP_pCD36 yscU Yop proteins translocation protein U YP_pCD32 yscB Chaperone protein YscB YP_1032 tolB Tol-Pal system protein TolB...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...(pseudogene. inframe deletion) 0.71 (0.035) YPTB0257 (aarF) YPO3779 ubiquinone biosynthesis protein 0.68 (0.048) YPTB0258 (tatA) YPO3778 Sec-independent protein translocase protein tatA 0.685 (0.003) YPTB0327 YPO0270 putative type III secretion apparatus protein 0.658 (0.014) YPTB0331 YPO0274 putative integral membrane protein 2.083 (< 0.001) YPTB0353 (terA) YPO0295 putative...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...division protein (pseudogene. inframe deletion) 0.71 (0.035) YPTB0257 (aarF) YPO3779 ubiquinone biosynthesis protein 0.68 (0.048) YPTB0258 (tatA) YPO3778 Sec-independent protein translocase protein tatA 0.685 (0.003) YPTB0327 YPO0270 putative type III secretion apparatus protein 0.658 (0.014) YPTB0331 YPO0274 putative integral membrane protein 2.083 (< 0.001) YPTB0353 (terA)...”

SO4202, SO_4202 Sec-independent protein translocase protein TatA from Shewanella oneidensis MR-1
66% identity, 53% coverage

• Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation
  Castillo, PloS one 2018
  • “...domain protein 1.02 SO4142 Periplasmic monoheme cytochrome c 1.29 SO4144 otr Octaheme tetrathionate reductase 1.17 SO4202 tatA Twin-arginine translocation protein -1.13 SO4483 Cytochrome b 1.14 SO4484 shp Monoheme cytochrome c 1.13 SO4568 nrfD Nitrite reductase quinol dehydrogenase component 1.50 SO4591 cymA Cytochrome c-type protein -1.45 SO4607...”
• Regulation of Gene Expression in Shewanella oneidensis MR-1 during Electron Acceptor Limitation and Bacterial Nanowire Formation
  Barchinger, Applied and environmental microbiology 2016
  • “...1.97 0.37 1.05 1.38 2.10 0.42 1.07 1.31 Protein translocation SO_4202 SO_4203 SO_4204 SO_0165 SO_1297 SO_1298 tatA tatB tatC gspC gspA gspB 4 4 4 4 3 3 1.57...”
• Mislocalization of Rieske protein PetA predominantly accounts for the aerobic growth defect of Tat mutants in Shewanella oneidensis
  Luo, PloS one 2013
  • “...system ( Fig. 1 ). The rest 7 genes on the fragment, namely tatA ( SO4202 ), tatB ( SO4203 ), tatC ( SO4204 ), SO4205 , SO4206 , SO4207 , and hemB-2 ( SO4208 ), are likely organized into two operons, one of which contains...”
• Profiling the membrane proteome of Shewanella oneidensis MR-1 with new affinity labeling probes
  Tang, Journal of proteome research 2007
  • “...SO3896 SO3906 SO3942 SO3952 SO4012 SO4077 SO4105 SO4202 SO4215 SO4473 SO4513 SO4557 SO4602 SO4719 SOA0048 SOA0099 SOA0106 SOA0161 NIH-PA Author Manuscript...”
• Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins
  Gao, Journal of bacteriology 2006
  • “...encoding components of the Sec-independent protein translocase, so4202 (tatA; 3.4-fold induction), so4203 (tatB; 3.4-fold), and so4204 (tatC; 3.6-fold), were...”

Shew185_0416 twin-arginine translocation protein, TatA/E family subunit from Shewanella baltica OS185
51% identity, 82% coverage

• Adaptation of the Marine Bacterium Shewanella baltica to Low Temperature Stress
  Kloska, International journal of molecular sciences 2020
  • “...gene was upregulated after 90 and 180 min of cold stress, while expression of TatA (Shew185_0416) and TatB (Shew185_0415) encoding genes was downregulated ( Figure 4 ). In our study, expression of the Tat translocon-encoding genes was only slightly regulated upon cold stress at the transcriptional...”

WP_045028541 twin-arginine translocase TatA/TatE family subunit from Photobacterium phosphoreum
48% identity, 94% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...WP_005372432); Photobacterium aquimaris (WP_060996792, WP_060998634); Photobacterium kishitanii (WP_045045764, WP_058120333); Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog had also been described for the Gram-positive organism Corynebacterium glutamicum 34...”

WP_008988792 Sec-independent protein translocase subunit TatA from Photobacterium leiognathi subsp. mandapamensis svers.1.1.
56% identity, 78% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...respectively: Photobacterium angustum (WP_005363978, WP_005372432); Photobacterium aquimaris (WP_060996792, WP_060998634); Photobacterium kishitanii (WP_045045764, WP_058120333); Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog had also been described for the Gram-positive...”

WP_036791541 twin-arginine translocase TatA/TatE family subunit from Photobacterium kishitanii
48% identity, 94% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...WP_058120333); Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog had also been described for the Gram-positive organism Corynebacterium glutamicum 34 . In contrast, the inclusion threshold for TatE...”

WP_045045764 twin-arginine translocase TatA/TatE family subunit from Photobacterium kishitanii
46% identity, 94% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...and TatA _2 paralogs, respectively: Photobacterium angustum (WP_005363978, WP_005372432); Photobacterium aquimaris (WP_060996792, WP_060998634); Photobacterium kishitanii (WP_045045764, WP_058120333); Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog had also been...”

tatE / CAA98158.1 twin-arginine translocation protein E from Pseudomonas stutzeri (see 13 papers)
54% identity, 75% coverage

WP_000508976 twin-arginine translocase TatA/TatE family subunit from Vibrio cholerae O1 biovar El Tor
44% identity, 71% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog had also been described for the Gram-positive organism Corynebacterium glutamicum 34 . In contrast, the inclusion threshold for TatE homologues that we defined...”

WP_060996792 twin-arginine translocase TatA/TatE family subunit from Photobacterium aquimaris
53% identity, 77% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...numbers of their TatA_1 and TatA _2 paralogs, respectively: Photobacterium angustum (WP_005363978, WP_005372432); Photobacterium aquimaris (WP_060996792, WP_060998634); Photobacterium kishitanii (WP_045045764, WP_058120333); Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE...”

JHW33_RS10290 twin-arginine translocase subunit TatE from Rahnella aceris
61% identity, 96% coverage

• Comparative Genomics Assisted Functional Characterization of Rahnella aceris ZF458 as a Novel Plant Growth Promoting Rhizobacterium
  Xu, Frontiers in microbiology 2022
  • “...JHW33_RS25040 WP_013578099.1 WP_119262333.1 100 WP_013578099.1 100 WP_013578099.1 100 WP_014341807.1 94 tatE twin-arginine translocase subunit TatE JHW33_RS10290 WP_013576504.1 WP_013576504.1 100 WP_013576504.1 100 WP_013576504.1 100 WP_013576504.1 100 tatE twin-arginine translocase subunit TatE JHW33_RS15180 WP_013577433.1 WP_013577433.1 100 WP_013577433.1 100 WP_013577433.1 100 WP_013577433.1 100 tatB Sec-independent protein translocase subunit TatB...”

VCA0533 tatA protein from Vibrio cholerae O1 biovar eltor str. N16961
44% identity, 73% coverage

• Pleiotropic effects of the twin-arginine translocation system on biofilm formation, colonization, and virulence in Vibrio cholerae
  Zhang, BMC microbiology 2009
  • “..., tatB , and tatC in chromosome I, and tatA2 in chromosome II (VC0086 and VCA0533 were annotated as tatA and tatA2 , respectively). These genes encode four proteins with a high degree of homology to the E . coli K-12 tat genes, ranging from 43.3...”

JHW33_RS15180 twin-arginine translocase subunit TatE from Rahnella aceris
60% identity, 68% coverage

• Comparative Genomics Assisted Functional Characterization of Rahnella aceris ZF458 as a Novel Plant Growth Promoting Rhizobacterium
  Xu, Frontiers in microbiology 2022
  • “...JHW33_RS10290 WP_013576504.1 WP_013576504.1 100 WP_013576504.1 100 WP_013576504.1 100 WP_013576504.1 100 tatE twin-arginine translocase subunit TatE JHW33_RS15180 WP_013577433.1 WP_013577433.1 100 WP_013577433.1 100 WP_013577433.1 100 WP_013577433.1 100 tatB Sec-independent protein translocase subunit TatB JHW33_RS15175 WP_013577432.1 WP_013577432.1 100 WP_013577432.1 100 WP_013577432.1 100 WP_015699057.1 90 tatC Sec-independent protein translocase subunit...”

WP_006644312 Sec-independent protein translocase subunit TatA from Photobacterium sp. SKA34
51% identity, 80% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...Photobacterium kishitanii (WP_045045764, WP_058120333); Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog had also been described for the Gram-positive organism Corynebacterium glutamicum 34 . In contrast, the inclusion...”

NP_882278 Sec-independent protein translocase protein from Bordetella pertussis Tohama I
BP3777 Sec-independent protein translocase subunit TatA from Bordetella pertussis Tohama I
47% identity, 73% coverage

• A gel-free proteomic-based method for the characterization of Bordetella pertussis clinical isolates
  Williamson, Journal of microbiological methods 2012
  • “...(9) 10 (8) 14 (12) 14 (12) Amino acid metabolism Twin argininte translocase protein A NP_882278 BP3777 tatA 8 U 35 (2) 35 (2) 35 (2) 35 (2) Membrane transport Type II citrate synthase NP_880994 BP2358 qltA 48 C 11 (3) 8 (2) 10 (3) 10...”
• A gel-free proteomic-based method for the characterization of Bordetella pertussis clinical isolates
  Williamson, Journal of microbiological methods 2012
  • “...10 (8) 14 (12) 14 (12) Amino acid metabolism Twin argininte translocase protein A NP_882278 BP3777 tatA 8 U 35 (2) 35 (2) 35 (2) 35 (2) Membrane transport Type II citrate synthase NP_880994 BP2358 qltA 48 C 11 (3) 8 (2) 10 (3) 10 (3)...”

PPUBIRD1_1091 twin-arginine translocase TatA/TatE family subunit from Pseudomonas putida BIRD-1
PP1041 Sec-independent protein translocase TatA from Pseudomonas putida KT2440
44% identity, 77% coverage

• Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria
  Lidbury, Environmental microbiology 2016
  • “...ND Arginine/ornithine antiporter arcD ADR58734 PPUBIRD1_1052 3.04 ND General secretion pathway protein K tatA ADR58773 PPUBIRD1_1091 3.34 ND Alkaline phosphatase phoX ADR58775 PPUBIRD1_1093 5.14 ND 2',3'cyclicnucleotide 2'phosphodiesterase uxpA ADR58776 PPUBIRD1_1094 3.24 ND General secretion pathway protein G tatG ADR58781 PPUBIRD1_1099 4.60 ND Hypothetical protein, conserved ADR59032...”
• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023

TatE / b0627 twin arginine protein translocation system - TatE protein from Escherichia coli K-12 substr. MG1655 (see 3 papers)
TatE / P0A843 twin arginine protein translocation system - TatE protein from Escherichia coli (strain K12) (see 3 papers)
TATE_ECOLI / P0A843 Sec-independent protein translocase protein TatE from Escherichia coli (strain K12) (see 2 papers)
tatE / EW|b0627 sec-independent protein translocase protein tatE from Escherichia coli K12 (see 7 papers)
SF0654 orf, conserved hypothetical protein from Shigella flexneri 2a str. 301
NP_415160 twin arginine protein translocation system - TatE protein from Escherichia coli str. K-12 substr. MG1655
UTI89_C0630 hypothetical protein from Escherichia coli UTI89
73% identity, 74% coverage

• function: Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin- arginine motif in their signal peptide across membranes. TatE shares overlapping functions with TatA.
  disruption phenotype: Disruption of tatE affects the correct localization of multiple enzymes whose precursors bear twin arginine transfer peptides. Export is completely blocked when both tatA and tatE are inactivated.
• Emergence of a new multidrug-resistant serotype X variant in an epidemic clone of Shigella flexneri
  Ye, Journal of clinical microbiology 2010
  • “...X variant 2002017 Locus tag a Lost genes SF0654 SF0721 SF1039 SF1137 SF1494 SF1495 SF1496 SF1497 SF1498 SF1881 SF2066 SF2067 SF2133 SF2135 SF2136 SF2137...”
• TatE as a Regular Constituent of Bacterial Twin-arginine Protein Translocases.
  Eimer, The Journal of biological chemistry 2015
  • GeneRIF: TatE is a regular constituent of the Tat translocase in E. coli
• The twin arginine translocation system is essential for virulence of Yersinia pseudotuberculosis
  Lavander, Infection and immunity 2006
  • “...(YP_026270), TatC (NP_418282), TatD (YP_026271), and TatE (NP_415160) were determined. For identification of potential Tat substrates, pattern searches of the...”
• Biodistribution of ⁸⁹Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
  Li, Poultry science 2023
  • “...Cell inner membrane 372 P0ABI4 CORA Inorganic ion transport and metabolism Cell inner membrane 373 P0A843 TATE Intracellular trafficking, secretion, and vesicular transport Cell inner membrane 374 P0AA47 PLAP Amino acid transport and metabolism Cell inner membrane 375 P69423 TATC Intracellular trafficking, secretion, and vesicular transport...”
• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...A ) Sequence alignment of the amino acid sequences of E. coli TatE (accession number: P0A843), TatB (P69425) and TatA (P69428). N-terminal, charged amino acid residues of TatE and TatB are highlighted in red, other charged residues are in bold. Secondary structural elements are assigned according...”
• High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division
  Mediati, BMC genomics 2018
  • “...17.1 935.0 UTI89_C0349 yahE S UTI89_C0350 yahF C 640,717641,788 UTI89_C0629 ybeM R 1072 4.3 112.5 UTI89_C0630 tatE U UTI89_C0631 lipA H 690,222691,856 UTI89_C0684 glnS J 1635 79.2 8504.0 1,016,1701,016,793 UTI89_C1021 matP MD 624 9.1 575.5 UTI89_C1022 ompA M 1,139,7041,141,232 UTI89_C1147 S 1529 9.6 321.3 UTI89_C1148 (cbeA/yeeU)...”

A1S_0466 Sec-independent protein translocase protein from Acinetobacter baumannii ATCC 17978
IX87_RS16610 Sec-independent protein translocase subunit TatA from Acinetobacter baumannii
44% identity, 69% coverage

• Light Regulates Acinetobacter baumannii Chromosomal and pAB3 Plasmid Genes at 37°C
  Squire, Journal of bacteriology 2022 (secret)
• Acinetobacter baumannii OxyR Regulates the Transcriptional Response to Hydrogen Peroxide
  Juttukonda, Infection and immunity 2019
  • “...TABLE 1 (Continued) Category and locus A1S_1414 A1S_0466 A1S_1665 A1S_3114 A1S_1677 A1S_3381 A1S_0465 A1S_1963 A1S_0464 A1S_1928 A1S_2473 A1S_1224 A1S_0416...”
• Antimicrobial Peptide Cec4 Eradicates Multidrug-Resistant Acinetobacter baumannii in vitro and in vivo
  Peng, Drug design, development and therapy 2023
  • “...Branched-chain amino acid ABC transporter permease 1.84 1.3310 4 IX87_RS18005 MFS transporter 2.78 4.4110 9 IX87_RS16610 Twin-arginine translocase TatA/TatE family subunit 3.0194 1.989510 3 IX87_RS10940 Protein translocase subunit SecA 1.4743 2.137710 3 IX87_RS15635 Preprotein translocase subunit SecE 1.7013 9.473910 4 IX87_RS03860 Type VI secretion system tube...”

BCAL0323 Sec-independent protein translocase protein TatA from Burkholderia cenocepacia J2315
50% identity, 64% coverage

• Genetic Determinants Associated With in Vivo Survival of Burkholderia cenocepacia in the Caenorhabditis elegans Model
  Wong, Frontiers in microbiology 2018
  • “...recG ATP-dependent DNA helicase RecG -7.22 -5.19 BCAL3335 fis DNA-binding protein Fis -3.16 Secretion system BCAL0323 tatA Twin arginine translocase protein A -4.01 BCAL0324 tatB Sec-independent translocase -4.70 -3.38 BCAL0325 tatC Sec-independent protein translocase protein TatC -5.65 -3.42 BCAL0742 secB preprotein translocase subunit SecB -2.90 BCAL3305...”

BPSL3128 Sec-independent protein translocase protein TatA from Burkholderia pseudomallei K96243
50% identity, 64% coverage

• The twin arginine translocation system is essential for aerobic growth and full virulence of Burkholderia thailandensis
  Wagley, Journal of bacteriology 2014
  • “...export system (BTH_I2980, BTH_I2981, and BTH_I2982; BPSL3128, BPSL3127, and BPSL3126; and BMA10229_A1799, BMA10229_A1800, and BMA10229_A1801, respectively). We...”
  • “...viable transposon insertion mutants were found in tatA (BPSL3128), suggesting that this gene is essential for the viability of the bacterium under the...”

BTH_I2982 twin-arginine translocation protein, TatA/E family-related protein from Burkholderia thailandensis E264
50% identity, 64% coverage

• The twin arginine translocation system is essential for aerobic growth and full virulence of Burkholderia thailandensis
  Wagley, Journal of bacteriology 2014
  • “...Tat export system (BTH_I2980, BTH_I2981, and BTH_I2982; BPSL3128, BPSL3127, and BPSL3126; and BMA10229_A1799, BMA10229_A1800, and BMA10229_A1801, respectively)....”

WP_060998634 Sec-independent protein translocase subunit TatA from Photobacterium aquimaris
64% identity, 65% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...of their TatA_1 and TatA _2 paralogs, respectively: Photobacterium angustum (WP_005363978, WP_005372432); Photobacterium aquimaris (WP_060996792, WP_060998634); Photobacterium kishitanii (WP_045045764, WP_058120333); Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog...”

RSc2942 PROBABLE SIGNAL PEPTIDE PROTEIN from Ralstonia solanacearum GMI1000
47% identity, 56% coverage

• PrhG, a transcriptional regulator responding to growth conditions, is involved in the control of the type III secretion system regulon in Ralstonia solanacearum
  Plener, Journal of bacteriology 2010
  • “...operons. Although eight of them (RSc0695, RSc1853, RSc2942, Downloaded from http://jb.asm.org/ on February 18, 2017 by University of California, Berkeley FIG....”

WP_008986002 Sec-independent protein translocase subunit TatA from Photobacterium leiognathi
66% identity, 58% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...Photobacterium angustum (WP_005363978, WP_005372432); Photobacterium aquimaris (WP_060996792, WP_060998634); Photobacterium kishitanii (WP_045045764, WP_058120333); Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog had also been described for the Gram-positive organism...”

WP_058120333 Sec-independent protein translocase subunit TatA from Photobacterium kishitanii
62% identity, 65% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...TatA _2 paralogs, respectively: Photobacterium angustum (WP_005363978, WP_005372432); Photobacterium aquimaris (WP_060996792, WP_060998634); Photobacterium kishitanii (WP_045045764, WP_058120333); Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog had also been described...”

WP_036788465 Sec-independent protein translocase subunit TatA from Photobacterium kishitanii
62% identity, 65% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog had also been described for the Gram-positive organism Corynebacterium glutamicum 34 . In contrast, the inclusion threshold for TatE homologues...”

Reut_A3100 Twin-arginine translocation protein TatA/E from Ralstonia eutropha JMP134
41% identity, 77% coverage

• The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader
  Lykidis, PloS one 2010
  • “...the sec -independent twin-arginine translocation (TAT) system for protein translocation: tatC (Reut_A3098), tatA / E (Reut_A3100), tatB (Reut_3099), and tatD -related components (Reut_A1437 and Reut_A1078). The TAT system is distinguished by the ability to translocate fully-folded proteins and is found also in C. eutropha H16, C....”

WP_006643468 Sec-independent protein translocase subunit TatA from Photobacterium sp. SKA34
66% identity, 52% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...kishitanii (WP_045045764, WP_058120333); Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog had also been described for the Gram-positive organism Corynebacterium glutamicum 34 . In contrast, the inclusion threshold...”

WP_005372432 Sec-independent protein translocase subunit TatA from Photobacterium angustum S14
66% identity, 52% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...the following accession numbers of their TatA_1 and TatA _2 paralogs, respectively: Photobacterium angustum (WP_005363978, WP_005372432); Photobacterium aquimaris (WP_060996792, WP_060998634); Photobacterium kishitanii (WP_045045764, WP_058120333); Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980,...”

NTHI0279 Sec-independent protein translocase protein TatA/E from Haemophilus influenzae 86-028NP
47% identity, 68% coverage

• Genomic sequence of an otitis media isolate of nontypeable Haemophilus influenzae: comparative study with H. influenzae serotype d, strain KW20
  Harrison, Journal of bacteriology 2005
  • “...with twin arginines in their signal peptides (NTHI0279, NTHI0280, and NTHI0282) (15, 119). As previously reported, strain 86-028NP possesses NTHI0585, the...”

WP_045032465 Sec-independent protein translocase subunit TatA from Photobacterium phosphoreum
63% identity, 57% coverage

• Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
  Eimer, Scientific reports 2018
  • “...Photobacterium aquimaris (WP_060996792, WP_060998634); Photobacterium kishitanii (WP_045045764, WP_058120333); Photobacterium leiognathi (WP_008988792, WP_008986002); Photobacterium phosphoreum (WP_045028541, WP_045032465); Photobacterium sp. SKA34 (WP_006644312, WP_006643468); Photobacterium (WP_036791541, WP_036788465); Vibrio cholerae (WP_000508976, WP_000508970/WP_000508978, WP_000508968/WP_000508979, WP_000508969/WP_000508980, WP_000508971). A TatE paralog had also been described for the Gram-positive organism Corynebacterium glutamicum 34 ....”

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.