PaperBLAST
PaperBLAST Hits for DVU1367 (65 a.a., MFGIGFQELL...)
Show query sequence
>DVU1367
MFGIGFQELLVVLVLVLLVFGANKLPEIGGGLGRAIRNFKRAASEPDEIDVTPTDKKDKN
DDKQA
Running BLASTp...
Found 35 similar proteins in the literature:
GSU0781 twin-arginine translocation protein, TatA/E family from Geobacter sulfurreducens PCA
49% identity, 86% coverage
- Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens
Dulay, Frontiers in microbiology 2020 - “...Gene Gene product log(2) FC Metal-binding motif (Pfam) Subcellular localization Folding, secretion, and degradation (1) GSU0781 fdnT Twin-arginine translocation pathway protein, TatA/TatE family 1.95 Inner membrane Carbohydrate metabolism (3) GSU0778 fdnH Periplasmically oriented, membrane-bound formate dehydrogenase, iron-sulfur cluster-binding subunit 2.23 Two [4Fe-4S]-binding (PF13247, PF12800) Inner membrane...”
- “...subunits (GSU07780779) of the trimeric formate dehydrogenase enzyme, FdnGHI, and the associated secretory protein FdnT (GSU0781), which are only needed when growing with formate as electron donor. Another example of a downregulated protein is Prx-2 (GSU3246), a cytoplasmic thioredoxin peroxidase of the 2-cysteine peroxiredoxin subfamily (...”
- Iron Corrosion via Direct Metal-Microbe Electron Transfer
Tang, mBio 2019 - “...dehydrogenase ( fdnG , fdnH , fdnI , fdhD , and fdnT ) (GSU0777 to GSU0781) and Hyb hydrogenase ( hybS , hybA , hybB , hybL , hybP , and hybT ) (GSU0782 to GSU0787) are indicated in green and blue, respectively. Disruption of fdnG...”
- Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens
Leang, BMC genomics 2009 - “...formate dehydrogenase, b -type cytochrome subunit -1.19 GSU0780 formate dehydrogenase accessory protein FdhD N. D. GSU0781 twin-arginine translocation protein, TatA/E family -1.41 Solute transporter Fumarate/succinate exchanger GSU2750 hypothetical protein +1.30 83 GSU2751 ( dcuB ) C 4 -dicarboxylate transporter (DcuB) +1.63 Operon predictions in G. sulfurreducens...”
Hore_03820 twin-arginine translocation protein, TatA subunit from Halothermothrix orenii H 168
45% identity, 91% coverage
asl0845 hypothetical protein from Nostoc sp. PCC 7120
51% identity, 50% coverage
SSCH_170020 twin-arginine translocase TatA/TatE family subunit from Syntrophaceticus schinkii
51% identity, 33% coverage
slr1046 hypothetical protein from Synechocystis sp. PCC 6803
53% identity, 36% coverage
- Genome-Wide Identification and Bioinformatics Characterization of Superoxide Dismutases in the Desiccation-Tolerant Cyanobacterium Chroococcidiopsis sp. CCMEE 029
Napoli, Frontiers in microbiology 2021 - “...Chroococcidiopsis sp. CCMEE 029. ChTat1 and ChTat2 aligned with homologs from Synechocystis sp. PCC 6803 (Slr1046 and Ssl2823) and Escherichia coli (EcTatA and EcTatB). Conserved residues of EcTatA, EcTatB are highlighted in blue. Numbering corresponds to EcTatA and EcTatB. The bioinformatics analysis carried out using the...”
- Impact of RNase E and RNase J on Global mRNA Metabolism in the Cyanobacterium Synechocystis PCC6803
Cavaiuolo, Frontiers in microbiology 2020 - “...a probable thiamine-phosphate pyrophosphorylase), or for only some genes of an operon (e.g., slr1045 and slr1046 coding a hypothetical protein YCF63 and a putative TatA protein, respectively). Another striking example of a gene cluster regulated by RNase E was represented by the two adjacent genes sll1392...”
- Identification and Roles of Photosystem II Assembly, Stability, and Repair Factors in Arabidopsis
Lu, Frontiers in plant science 2016 - “...Cline and Dabney-Smith, 2008 ; Albiniak et al., 2012 ; Walter et al., 2015 Tha4 slr1046 At5g28750 16 14 TM Thylakoid protein targeting: cpTat translocase Insertion and assembly of PSII proteins such as PsbP and PsbQ Cline and Theg, 2007 ; Schunemann, 2007 ; Cline and...”
- Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803
Zhu, Biotechnology for biofuels 2013 - “...signal peptidase I-1 slr0835 1.87 2.17 6.92 MoxR protein homolog slr0994 2.22 1.62 2.30 Octanoyltransferase slr1046 1.86 1.75 1.50 Putative TatA protein slr1204 4.18 2.63 5.57 Putative serine protease HtrA slr1331 2.94 2.26 3.98 Periplasmic processing protease ssr3307 1.76 1.63 2.04 Preprotein translocase SecG subunit Regulatory...”
- “...ssr3307 encoding a preprotein translocase SecG subunit, sll0616 encoding a preprotein translocase SecA subunit and slr1046 encoding a putative TatA protein, were up-regulated by butanol. Genes slr1046 and slr1047 were organized in the same operon. The results confirmed that enhanced protein translocation systems may be an...”
- Proteomic analysis reveals resistance mechanism against biofuel hexane in Synechocystis sp. PCC 6803
Liu, Biotechnology for biofuels 2012 - “...Putative 5-methylthioadenosine phosphorylase Slr0821 1.55 1.59 2.34 2.36 1.74 2.23 Putative sulfur carrier protein slr0821; Slr1046 1.56 Putative T at A protein Sll1440 1.59 Pyridoxamine 5-phosphate oxidase Sll1277 2.25 Recombination protein F Slr1198 1.74 1.54 1.52 Rehydrin Slr1164 3.34 Ribonucleotide reductase subunit alpha Sll0469 1.51 Ribose-phosphate...”
- “...induced the expression of both systems in Synechocystis sp. PCC 6803. The putative TatA protein (Slr1046) of twin arginine translocation pathway and SecF (Slr0775) of the Sec-dependent protein translocation system were both up-regulated (Table 1 ). Regulatory systems regulated by hexane Two-component system (TCS) is an...”
GSU0787 twin-arginine translocation protein, TatA/E family from Geobacter sulfurreducens PCA
45% identity, 78% coverage
- Iron Corrosion via Direct Metal-Microbe Electron Transfer
Tang, mBio 2019 - “...hybS , hybA , hybB , hybL , hybP , and hybT ) (GSU0782 to GSU0787) are indicated in green and blue, respectively. Disruption of fdnG and hybL is indicated by X. aclA and aclB , citrate lyase; lacI , Lac repressor; P/O, tac-lac promoter/ lac...”
- The iron stimulon and fur regulon of Geobacter sulfurreducens and their role in energy metabolism
Embree, Applied and environmental microbiology 2014 - “...GSU3274 4 43.83 5.26 8.34 GSU0787 GSU2075 GSU2678 Periplasmically oriented, membrane-bound [NiFe]-hydrogenase maturation protease Twin-arginine translocation...”
- Adaptation to disruption of the electron transfer pathway for Fe(III) reduction in Geobacter sulfurreducens
Leang, Journal of bacteriology 2005 - “...11, 2017 by University of California, Berkeley GSU0786 GSU0787 GSU1159 VOL. 187, 2005 ADAPTATION TO DISRUPTION IN Fe(III) ELECTRON TRANSFER 5923 TABLE 3. Genes...”
ssl2823 hypothetical protein from Synechocystis sp. PCC 6803
43% identity, 63% coverage
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
39% identity, 70% coverage
SL1344_3927 Sec-independent protein translocase subunit TatA from Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
49% identity, 56% coverage
VP0098 TatA protein from Vibrio parahaemolyticus RIMD 2210633
49% identity, 58% coverage
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)
45% identity, 71% coverage
TATA_PEA / Q9XH46 Sec-independent protein translocase protein TATA, chloroplastic; Protein THYLAKOID ASSEMBLY 4; Protein TWIN-ARGININE TRANSLOCATION A from Pisum sativum (Garden pea) (Lathyrus oleraceus) (see 9 papers)
44% identity, 33% 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 the thylakoid membrane. Involved in delta pH-dependent protein transport required for chloroplast development, especially thylakoid membrane formation. TATC and TATB mediate precursor recognition, whereas TATA facilitates translocation.
subunit: In thylakoid membranes, TATC and TATB form a large receptor complex, containing about eight TATC-TATB pairs, which binds the precursor protein. Twin arginine signal peptide promotes pH-triggered docking of TATA oligomers to TATC-TATB receptor complex, inducing a conformational switch of TATA that results in activation of the translocase. TATA dissociates from TATC-TATB upon completion of translocation. According to PubMed:22564412, it is estimated that the translocase fully saturated with precursor proteins and TATA is an 2.2- megadalton complex that can individually transport eight precursor proteins or cooperatively transport multimeric precursors.
TATA_ARATH / Q9LKU2 Sec-independent protein translocase protein TATA, chloroplastic; Protein THYLAKOID ASSEMBLY 4; Protein TWIN-ARGININE TRANSLOCATION A from Arabidopsis thaliana (Mouse-ear cress) (see paper)
TC 2.A.64.2.1 / Q9LKU2 Tha4, component of The chloroplast Tat translocase (cpTatC/Hcf106/Tha4) from Arabidopsis thaliana (Mouse-ear cress) (see paper)
T32B20.e / RF|NP_198227.1 AT5g28750 from Arabidopsis thaliana (see paper)
AT5G28750 thylakoid assembly protein, putative from Arabidopsis thaliana
44% identity, 31% 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 the thylakoid membrane. Involved in delta pH-dependent protein transport required for chloroplast development, especially thylakoid membrane formation. TATC and TATB mediate precursor recognition, whereas TATA facilitates translocation (By similarity).
subunit: In thylakoid membranes, TATC and TATB form a large receptor complex, containing about eight TATC-TATB pairs, which binds the precursor protein. Twin arginine signal peptide promotes pH-triggered docking of TATA oligomers to TATC-TATB receptor complex, inducing a conformational switch of TATA that results in activation of the translocase. TATA dissociates from TATC-TATB upon completion of translocation. - substrates: proteins
tcdb comment: The precursor mature domain of the substrate protein interacts directly with Tha4 (Pal et al. 2012). Hcf106 is predicted to contain a single amino terminal transmembrane domain followed by a Pro-Gly hinge, a predicted amphipathic alpha-helix (APH), and a loosely structured carboxy terminus. The amphipathic α-helix interacts with the bilayer (Zhang et al., 2013a; Zhang et al. 2013b). TatA has structural plasticity and a capability to adapt to local environments (Pettersson et al. 2018) - Yellow barley xan-m mutants are deficient in the motor unit SECA1 of the SEC1 translocase system
Stuart, Planta 2025 (no snippet) - Defining the heterogeneous composition of Arabidopsis thylakoid membrane
Trotta, The Plant journal : for cell and molecular biology 2025 (no snippet) - Identification and Roles of Photosystem II Assembly, Stability, and Repair Factors in Arabidopsis
Lu, Frontiers in plant science 2016 - “...and Dabney-Smith, 2008 ; Albiniak et al., 2012 ; Walter et al., 2015 Tha4 slr1046 At5g28750 16 14 TM Thylakoid protein targeting: cpTat translocase Insertion and assembly of PSII proteins such as PsbP and PsbQ Cline and Theg, 2007 ; Schunemann, 2007 ; Cline and Dabney-Smith,...”
WP_000508971 Sec-independent protein translocase subunit TatA from Vibrio cholerae
45% identity, 68% 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...”
plu4410 Sec-independent protein translocase protein from Photorhabdus luminescens subsp. laumondii TTO1
40% identity, 64% coverage
VC0086 tatA protein from Vibrio cholerae O1 biovar eltor str. N16961
47% identity, 57% coverage
HBZC1_10870 twin-arginine translocase TatA/TatE family subunit from Helicobacter bizzozeronii CIII-1
49% identity, 45% coverage
LOC102583072 sec-independent protein translocase protein TATA, chloroplastic from Solanum tuberosum
34% identity, 38% coverage
- Canonical and Alternative Auxin Signaling Systems in Mono-, Di-, and Tetraploid Potatoes
Lomin, International journal of molecular sciences 2023 - “...fusion of the StIAA3 gene with two neighboring genes, LOC102582738 (probable prefoldin subunit 4) and LOC102583072 (sec-independent translocase protein TATA, chloroplastic). Therefore, artifactual gene fusion in the processes of gene library creation, DNA sequencing, and/or gene annotation cannot be ruled out. There remain six more StIAA...”
TATA_MAIZE / Q9XFJ8 Sec-independent protein translocase protein TATA, chloroplastic; Protein THYLAKOID ASSEMBLY 4; Protein TWIN-ARGININE TRANSLOCATION A from Zea mays (Maize) (see 2 papers)
44% identity, 26% 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 the thylakoid membrane. Involved in delta pH-dependent protein transport required for chloroplast development, especially thylakoid membrane formation. TATC and TATB mediate precursor recognition, whereas TATA facilitates translocation.
subunit: In thylakoid membranes, TATC and TATB form a large receptor complex, containing about eight TATC-TATB pairs, which binds the precursor protein. Twin arginine signal peptide promotes pH-triggered docking of TATA oligomers to TATC-TATB receptor complex, inducing a conformational switch of TATA that results in activation of the translocase. TATA dissociates from TATC-TATB upon completion of translocation (By similarity).
disruption phenotype: Seedling lethality after the development of three to four leaves. Non-photosynthetic mutants possess near normal pigment levels but lack one or more elements of the electron transport activity in chloroplasts. Defects in protein targeting across chloroplast thylakoid membrane (PubMed:7664731).
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
46% identity, 62% 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
48% identity, 71% coverage
Q7UQP7 Sec-independent protein translocase protein TatA from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
40% identity, 55% coverage
VVMO6_02901 Sec-independent protein translocase subunit TatA from Vibrio vulnificus MO6-24/O
42% identity, 83% 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...”
YPO2597 sec-independent protein translocase protein from Yersinia pestis CO92
YPTB1090 sec-independent protein translocase protein from Yersinia pseudotuberculosis IP 32953
40% identity, 61% coverage
Shew185_0416 twin-arginine translocation protein, TatA/E family subunit from Shewanella baltica OS185
43% identity, 70% 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...”
Q2MGW8 Sec-independent protein translocase protein TatA from Corynebacterium glutamicum
35% identity, 92% coverage
TC 2.A.64.1.3 / Q6ML26 Sec-independent protein translocase protein TatA, component of TatABCE from Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100)
Bd2196 twin-argine protein translocase component from Bdellovibrio bacteriovorus HD100
40% identity, 72% coverage
- substrates: proteins
tcdb comment: The twin-arginine translocation (Tat) system transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. Together with TatB, TatC is part of a receptor directly interacting with Tat signal peptides (Eimer et al. 2015; Kuzniatsova et al. 2016; Cléon et al. 2015) - Quantitative proteome of bacterial periplasmic predation reveals a prey damaging protease
Lai, 2024 - Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria
Hobley, BMC genomics 2012 - “...of the folded-protein secretion- apparatus called the TAT system. Gene tatA has a paralog tatE (bd2196 in HD100), [ 23 ] likely allowing more rapid sequence divergence of tatA as evidenced by the high omega score. A comparison of the HD100 strain Hit locus gene bd0108...”
- The first bite--profiling the predatosome in the bacterial pathogen Bdellovibrio
Lambert, PloS one 2010 - “...system in secreting the many degradative enzymes into the prey cytoplasm. Twin arginine transport gene Bd2196 which encodes a homologue of the TatA pore protein, named TatE [22] is also up-regulated suggesting that some predatory, as well as HI, proteins may be secreted by this alternative...”
Dhaf_2560 twin-arginine translocation protein, TatA/E family subunit from Desulfitobacterium hafniense DCB-2
39% identity, 78% coverage
ATE50_RS18010 twin-arginine translocase TatA/TatE family subunit from Bacillus velezensis
42% identity, 92% coverage
SO4202, SO_4202 Sec-independent protein translocase protein TatA from Shewanella oneidensis MR-1
42% identity, 55% 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...”
msl1085 twin argininte translocase protein A from Mesorhizobium loti MAFF303099
38% identity, 68% coverage
A1S_0466 Sec-independent protein translocase protein from Acinetobacter baumannii ATCC 17978
IX87_RS16610 Sec-independent protein translocase subunit TatA from Acinetobacter baumannii
38% identity, 67% coverage
BSU17710 component of the twin-arginine pre-protein translocation pathway from Bacillus subtilis subsp. subtilis str. 168
NP_389654 component of the twin-arginine pre-protein translocation pathway from Bacillus subtilis subsp. subtilis str. 168
O31804 Sec-independent protein translocase protein TatAc from Bacillus subtilis (strain 168)
37% identity, 92% coverage
- Comparison of Bacillus subtilis transcriptome profiles from two separate missions to the International Space Station
Morrison, NPJ microgravity 2019 - “...1.46 1.19 1.32 Acetoin reductase/butanediol dehydrogenase AbrB BSU10230 yhfH 1.19 1.29 1.59 1.74 Unknown Unknown BSU17710 tatAC 1.30 1.33 1.28 1.33 Component of the twin-arginine translocation pathway Unknown BSU19180 des 1.07 1.07 1.23 1.35 Phosphlipid desaturase DesR, SigA BSU19190 desK 1.08 1.07 1.72 1.85 Two-component sensor...”
- A Tat ménage à trois--The role of Bacillus subtilis TatAc in twin-arginine protein translocation.
Goosens, Biochimica et biophysica acta 2015 (PubMed)- GeneRIF: The role of Bacillus subtilis TatAc in twin-arginine protein translocation
- TatAc, the third TatA subunit of Bacillus subtilis, can form active twin-arginine translocases with the TatCd and TatCy subunits.
Monteferrante, Applied and environmental microbiology 2012 - GeneRIF: findings show that TatAc can form active protein translocases with TatCd and TatCy
- Unanticipated functional diversity among the TatA-type components of the Tat protein translocase
Eimer, Scientific reports 2018 - “...Sequence source: C. glutamicum TatA (Q8NQE4), TatE (Q2MGW8), TatB (Q8NRD0); B. subtilis TatAy (O05522), TatAc (O31804), TatAd (O31467). On the other hand, we found the ExxxxK motif characteristic for E. coli TatE also contained in TatAc, which is one of the three annotated TatA paralogs of...”
TC 2.A.64.1.3 / Q6MGQ8 Putative sec-independent protein translocase protein, component of TatABCE from Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100)
42% identity, 36% coverage
- substrates: proteins
tcdb comment: The twin-arginine translocation (Tat) system transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. Together with TatB, TatC is part of a receptor directly interacting with Tat signal peptides (Eimer et al. 2015; Kuzniatsova et al. 2016; Cléon et al. 2015)
WD0152 mttA/Hcf106 family protein from Wolbachia endosymbiont of Drosophila melanogaster
31% identity, 85% coverage
- Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont
Lindsey, G3 (Bethesda, Md.) 2016 - “...w Tpre_381, and w Tpre_382 all align to sequential portions of the w Pip_Pel gene, WD0152. A single base pair deletion at position 421 in w Tpre_380, relative to w Pip_167, resulted in a premature stop codon. The intergenic spaces between these w Tpre unique genes...”
- “...genes, w Tpre_380, w Tpre_381, and w Tpre_382, are homologous to sequential locations in the WD0152 gene from w Pip_Pel. A frameshift mutation at base pair 421 in w Tpre_380 resulted in a premature stop codon and the subsequent annotation of downstream ORFs (open reading frames),...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory