PaperBLAST
PaperBLAST Hits for metacyc::G12WB-160-MONOMER energy-coupling factor transporter transmembrane protein EcfT (Clostridioides difficile (strain 630)) (267 a.a., MLKDITIGQY...)
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>metacyc::G12WB-160-MONOMER energy-coupling factor transporter transmembrane protein EcfT (Clostridioides difficile (strain 630))
MLKDITIGQYYPTSSAIHKLDPRIKLVATIVFMVSIFVVNKFWPYIVVLLCLLAMIKLAN
IPVKYIVKGVKPLKWIILFTFLINIFFLPGDEIWSFGFLAITKQGLRQAIFMAIRLIFLV
VGTSLLTLTTSPIELTDGIERLLNPFKKIGLPVHELAMMMTIALRFIPTLLDETDKIMKA
QMSRGADFESKNLINRAKNLVPLLVPLFVSAFRRADELAMAMEARCYRGGHNRTKMRESV
ISRRDYMACVFQLVYLGAIIATRFIAI
Running BLASTp...
Found 75 similar proteins in the literature:
cbiQ / Q18CJ3 energy-coupling factor transporter transmembrane protein EcfT from Clostridioides difficile (strain 630) (see 10 papers)
CD0102 ABC transporter, permease protein from Clostridium difficile 630
100% identity, 100% coverage
SFBM_1365 energy-coupling factor transporter transmembrane component T family protein from Candidatus Arthromitus sp. SFB-mouse-Japan
44% identity, 96% coverage
Halsa_1890 energy-coupling factor transporter transmembrane component T family protein from Halanaerobium hydrogeniformans
55% identity, 93% coverage
ECFT_LACP3 / Q035B4 Energy-coupling factor transporter transmembrane protein EcfT; ECF transporter T component EcfT from Lacticaseibacillus paracasei (strain ATCC 334 / BCRC 17002 / CCUG 31169 / CIP 107868 / KCTC 3260 / NRRL B-441) (Lactobacillus paracasei) (see paper)
LSEI_2472 ABC-type cobalt transport system, permease component CbiQ related transporter from Lactobacillus casei ATCC 334
45% identity, 93% coverage
- function: Part of a common energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates including 5-formyltetrahydrofolate and thiamine. Expression of the complex plus FolT or ThiT in Lactococcus lactis subsp. cremoris (strain NZ9000) allows 5-formyltetrahydrofolate or thiamine uptake respectively; 5-formyltetrahydrofolate or thiamine are not taken up in the absence of FolT/ThiT or the EcfA1A2T complex. Deenergized L.lactis subsp. cremoris (treated with 2-deoxyglucose) do not take up substrate.
subunit: Forms a stable energy-coupling factor (ECF) transporter complex probably composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component). This complex interacts with a number of substrate-specific components, including FolT and ThiT for 5- formyltetrahydrofolate and thiamine respectively. May be able to interact with more than 1 S component at a time. - Identification of genes encoding the folate- and thiamine-binding membrane proteins in Firmicutes
Eudes, Journal of bacteriology 2008 - “...contains a gene cluster encoding homologs of BioN (LSEI_2472) and BioM (LSEI_2473 and LSEI_2474), which are thus candidates for shared components of the folate...”
ECFT_BACSU / P70972 Energy-coupling factor transporter transmembrane protein EcfT; ECF transporter T component EcfT from Bacillus subtilis (strain 168) (see paper)
BSU01470 putative permease from Bacillus subtilis subsp. subtilis str. 168
50% identity, 97% coverage
- function: Transmembrane (T) component of an energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates (By similarity). Involved in riboflavin transport.
subunit: Forms a stable energy-coupling factor (ECF) transporter complex composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component). May be able to interact with more than 1 S component at a time (By similarity).
disruption phenotype: Abolishes riboflavin uptake, cell growth less inhibited by roseoflavin, a toxic riboflavin analog. - The Blueprint of a Minimal Cell: MiniBacillus
Reuß, Microbiology and molecular biology reviews : MMBR 2016 - “...Syn3.0c EC no. PDB accession no. Organismd Function(s) BSU01470 No 4HUQ L. brevis Transmembrane T component of ECF transporters NAD nadD BSU25640 Yes 2.7.7.18...”
- Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC
Engelen, BMC genomics 2012 - “..."- energizing coupling factor ABC multiple influx transporter (ATP-binding protein) 3 specific transport group 5 BSU01470 ybaF ecfT "- permease component of the EcfAB influx transporters 3 specific transport group 5 BSU11590 yjbL "- putative phosphatase group 6 BSU11600 yjbM "- (p)ppGpp synthetase group 6 BSU11620...”
BC0162 Cobalt transport protein cbiQ from Bacillus cereus ATCC 14579
48% identity, 89% coverage
lmo2599 highly similar to B. subtilis YbaF protein from Listeria monocytogenes EGD-e
47% identity, 89% coverage
lmo2634 similar to B. subtilis YbaF protein from Listeria monocytogenes EGD-e
43% identity, 97% coverage
LMRG_02179 cobalt transport protein from Listeria monocytogenes 10403S
43% identity, 97% coverage
IUJ47_RS04685 energy-coupling factor transporter transmembrane component T family protein from Enterococcus faecalis
46% identity, 89% coverage
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...EcfT IUJ47_RS09165 0.282 Carbohydrate ABC transporter permease IUJ47_RS11395 0.285 Phosphate ABC transporter ATP-binding protein PstB IUJ47_RS04685 0.288 Energy-coupling factor transporter transmembrane protein EcfT IUJ47_RS01745 0.295 Multidrug efflux ABC transporter subunit EfrA IUJ47_RS10055 0.299 ABC-F type ribosomal protection protein IUJ47_RS08330 0.299 Peptide ABC transporter substrate-binding protein IUJ47_RS11150...”
EF0239 cobalt transport family protein from Enterococcus faecalis V583
46% identity, 89% coverage
TC 3.A.1.26.10 / I7BV49 Energy-coupling factor transporter transmembrane protein EcfT, component of ATP-dependent folic acid uptake porter, FolT/EcfT/EcfA1/EcfA2 from Enterococcus faecalis D32
46% identity, 88% coverage
- substrates: Folic acid
tcdb comment: The crystal structure of FolT has been solved to 3.2 Å resolution in substrate-bound and free conformations, revealing a potential gating mechanism (Zhao et al. 2015)
LSA1735 Putative cobalt ABC transporter, membrane-spanning subunit from Lactobacillus sakei subsp. sakei 23K
45% identity, 93% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...protein -0.6 LSA1703 lsa1703 Putative Na(+)/H(+) antiporter -1.2 LSA1704 lsa1704 Putative calcium-transporting P-type ATPase -0.8 LSA1735 lsa1735 Putative cobalt ABC transporter, membrane-spanning subunit -0.6 LSA1736 lsa1736 Putative cobalt ABC transporter, ATP-binding subunit -0.6 LSA1737 lsa1737 Putative cobalt ABC transporter, ATP-binding subunit -0.7 LSA1838 lsa1838 Putative metal...”
ECFT_LACLM / A2RI03 Energy-coupling factor transporter transmembrane protein EcfT; ECF transporter T component EcfT from Lactococcus lactis subsp. cremoris (strain MG1363) (see paper)
TC 3.A.1.25.4 / A2RI03 Energy-coupling factor transporter transmembrane protein EcfT, component of The biotin uptake system, BioMNY. The 3-d structure of the EcfS subunit, BioY, at 2.1Å resolution is known (Berntsson et al., 2012). BioY and ThiT from L. lactis from Lactococcus lactis subsp. cremoris (strain MG1363)
44% identity, 93% coverage
- function: Part of a common energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. In this organism these probably include biotin, thiamine precursor, niacin, pantothenic acid, queuosine precursor, riboflavin and thiamine. Uptake of niacin or riboflavin into proteosomes containing EcfA1A2T and Niax or RibU has been demonstrated. Uptake requires hydrolyzable Mg-ATP and is substrate-specific; NiaX-containing proteosomes did not transport riboflavin
subunit: Forms a stable energy-coupling factor (ECF) transporter complex possibly composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component). In L.lactis forms a stable complex with EcfA' and EcfT and S components. In E.coli forms a stable complex with EcfA, EcfA' and individually with 3 tested S components (BioY, NiaX and ThiT) with a stoichiometry of 1:1:1:1. The core ECF complex interacts with a number of substrate-specific binding components, including BioY, BioY2, HmpT, NiaX, PanT, QueT, RibU and ThiT. May be able to interact with more than 1 S component at a time. - substrates: Biotin
tcdb comment: show similar N-terminal structures for interaction with the ECF module but divergent C-terminal structures for substrate binding. BioY alone binds biotin but doesn''t transport it (Berntsson et al., 2012). Ala-Arg-Ser and Ala-Arg-Gly signatures in BioN are probably coupling sites to the two BioM ATPase subunits (Neubauer et al., 2011Neubauer et al., 2011)
TC 3.A.1.26.9 / TC 3.A.1.28.2 / Q03PY7 Energy-coupling factor transporter transmembrane protein EcfT, component of The folate transporter, FolT/EcfAA''T (The 3-d structure is known to 3.0Å resolution (Xu et al. 2013; 4HUQ) from Lactobacillus brevis (strain ATCC 367 / JCM 1170)
38% identity, 98% coverage
- substrates: Hydroxymethyl pyrimidine, folate
tcdb comment: Thiamine and riboflavin may also be substrates.. This transporter uses the same ECF energy coupling complex (AA''T) as 3.A.1.28.2
SA2019 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAOUHSC_02481 cobalt transport protein, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_2174 cobalt transport family protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
43% identity, 93% coverage
- Comparative Genomics Identifies Novel Genetic Changes Associated with Oxacillin, Vancomycin and Daptomycin Susceptibility in ST100 Methicillin-Resistant Staphylococcus aureus
Di, Antibiotics (Basel, Switzerland) 2023 - “...+ + + + agrB (accesory gene regulator B) Disrupting gene - - + - SA2019 (hypothetical protein)SA2010 (hypothetical protein) Intergenic + + + + SA2414 (hypothetical protein)SA2415 ( braE , ABC superfamily ATP-binding cassette transporter membrane protein) Intergenic - - + - + Presence of...”
- Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover
Anderson, Journal of bacteriology 2006 - “...SA1798 SA1810 SA1896 SA1956 SA1972 SA1986 SA2019 SA2033 Conserved hypothetical protein Mercuric reductase homologue Conserved hypothetical protein Conserved...”
- Comparison of antibody repertoires against Staphylococcus aureus in healthy individuals and in acutely infected patients
Dryla, Clinical and diagnostic laboratory immunology 2005 - “...protein; SA2006, aerolysin/leukocidin family protein; SA2019, sdrH protein, putative; SA2291, staphyloxanthin biosynthesis protein; SA2236, ribosomal protein...”
- The Energy-Coupling Factor Transporter Module EcfAA'T, a Novel Candidate for the Genetic Basis of Fatty Acid-Auxotrophic Small-Colony Variants of Staphylococcus aureus
Schleimer, Frontiers in microbiology 2018 - “...C G - CTTTATAT - - C ECF transporter transmembrane protein EcfT ( ecf module) SAOUHSC_02481 (99) Frameshift with stop codon after 19 AAs (S114fsX134) Suppressor mutation, frameshift, inframe with WT (L111fsX268 4 ) G (1,153) G A Aminobenzoyl-glutamate utilization protein B SAOUHSC_02374 (99) Missense mutation...”
- Growth and Stress Tolerance Comprise Independent Metabolic Strategies Critical for Staphylococcus aureus Infection
Kim, mBio 2021 - “...+ SAUSA300_1183 4325 * 10229 1010 + + + 1,586 422 *** 225,714 89,230 *** SAUSA300_2174 ecfT 7849 5622 924 + + + + 5,675 5,018 322,500 336,102 * SAUSA300_1016 cyoE 5245 10748 996 + + + + SAUSA300_0539 ilvE 2819 ** 5411 1002 + +...”
- “...** SAUSA300_0959 fmtA 4.8 1.110.03 * 3.09 72.8322.09 * 175.9352.55 *** 69.4117.74 **** 1.210.34 **** SAUSA300_2174 ecfT ABC transport 5.44 1.050.12 3.33 102.9211.60 102.849.79 31.136.64 0.630.15 SAUSA300_2175 cbiO 6.08 1.110.07 * 3.08 109.8328.51 114.0214.85 46.639.47 * 0.930.26 * SAUSA300_0387 pbuX Transport 5.46 0.940.01 2.14 94.4418.10 109.3421.09...”
- Cigarette Smoke Extract-Exposed Methicillin-Resistant Staphylococcus aureus Regulates Leukocyte Function for Pulmonary Persistence
Kulkarni, American journal of respiratory cell and molecular biology 2016 - “...SAUSA300_0012 SAUSA300_2235 SAUSA300_1817 SAUSA300_1567 SAUSA300_0789 SAUSA300_2174 SAUSA300_0541 SAUSA300_1286 SAUSA300_0586 SAUSA300_0503 1.5 1.5 1.5 1.5 1.5...”
SPy2193 conserved hypothetical protein from Streptococcus pyogenes M1 GAS
44% identity, 93% coverage
ECFT_STRT2 / Q5M245 Energy-coupling factor transporter transmembrane protein EcfT; ECF transporter T component EcfT from Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (see paper)
TC 3.A.1.25.6 / Q5M245 Energy-coupling factor transporter transmembrane protein EcfT, component of Riboflavin ECF transport system, EcfAA'T/RibU from Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)
42% identity, 93% coverage
- function: Transmembrane (T) component of an energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. Expression of the complex plus RibU in de- energized E.coli allows riboflavin uptake.
subunit: Forms a stable energy-coupling factor (ECF) transporter complex composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component) upon coexpression of the components in E.coli. May be able to interact with more than 1 S component at a time. - substrates: riboflavin
SpyM3_1844 putative ABC transporter membrane-spanning permease from Streptococcus pyogenes MGAS315
44% identity, 93% coverage
- Novel regulatory small RNAs in Streptococcus pyogenes
Tesorero, PloS one 2013 - “...SPyM3_1838 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA <<< Q, Z SSRC45 SPyM3_1843 hypothetical protein <<< SPyM3_1844 putative ABC transporter membrane-spanning permease <<< Q, Z a SSRC: S. pyogenes Small RNA Candidate. The nucleotide coordinates of SSRC predicted by each computational algorithm are listed in Table S5...”
ID870_09850 energy-coupling factor transporter transmembrane component T family protein from Streptococcus agalactiae CJB111
SAG2149 cobalt transport family protein from Streptococcus agalactiae 2603V/R
43% identity, 91% coverage
LBA0321 ABC transporter permease from Lactobacillus acidophilus NCFM
41% identity, 98% coverage
F1613_RS11960 energy-coupling factor transporter transmembrane component T family protein from Staphylococcus epidermidis
44% identity, 88% coverage
SPSF3K_00021 energy-coupling factor transporter transmembrane component T family protein from Streptococcus parauberis
44% identity, 88% coverage
- Transcriptome analysis unveils survival strategies of Streptococcus parauberis against fish serum
Lee, PloS one 2021 - “...KO number: ko02010, Table 5 ). These include the biotin transporter-encoding genes bioY (SPSF3K_001734), ecfT (SPSF3K_00021 and SPSF3K_00582), and ecfA1 (SPSF3K_00583), the osmoprotectant transporters-encoding genes, proVWX (SPSF3K_001667) and opuC (SPSF3K_01282), as well as the oligopeptide permease transport system-encoding opp operon (SPSF3K_0123841). Many previous studies demonstrated that...”
- “...hpe Biotin bioY SPSF3K_00173 3.22 3.10 2.86 K03523 bioY SPSF3K_00174 3.11 3.04 2.84 K03523 ecfT SPSF3K_00021 - 0.86 - K16785 ecfT SPSF3K_00582 1.68 0.71 - K16785 ecfA1 SPSF3K_00583 2.19 0.83 - K16786 Multidrug resistance / Hemolysin cylA SPSF3K_00217 1.10 0.66 - K11050 cylB SPSF3K_00218 1.34 0.75...”
Q1GBI8 ABC-type vitamin B12 transporter (EC 7.6.2.8) from Lactobacillus delbrueckii subsp. bulgaricus (see paper)
LDB_RS01815 energy-coupling factor transporter transmembrane component T family protein from Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002
36% identity, 98% coverage
- In vitro reconstitution of dynamically interacting integral membrane subunits of energy-coupling factor transporters
Setyawati, eLife 2020 - “...encoding ECF-PanT and ECF-FolT2 from L. delbrueckii subsp. bulgaricus (LDB_RS01805, ecfA ; LDB_RS01810, ecfA ; LDB_RS01815, ecfT ; LDB_RS01970, panT ; LDB_RS07030, folT2 ) were cloned in p2BAD vectors and transformed into Ca 2+ -competent cells of the Escherichia coli strain MC1061 as described before (...”
- Structural insight in the toppling mechanism of an energy-coupling factor transporter
Swier, Nature communications 2016 - “...bulgaricus are annotated as cbiO (both for LDB_RS01805, ecfA and LDB_RS01810 ecfA ) and cbiQ (LDB_RS01815, ecfT ). The ECF module operon was cloned downstream of the first arabinose inducible promoter of the p2BAD vector 29 between the Bsp E1 and Bgl II sites, in-frame with...”
- Bidirectional ATP-driven transport of cobalamin by the mycobacterial ABC transporter BacA
Nijland, Nature communications 2024 - “...the accession codes P37028 for BtuF, B2HSW5 for BacAMm, Q1GBJ0 for EcfA, Q1GBI9 for EcfA, Q1GBI8 for EcfT, Q1G292 for FolT2, and Q1G7W0 for CbrT. The source data underlying Figs. 1 ac, 2 a,b, 3a,b and Supplementary Fig. 2 , Supplementary Fig. 3 and Supplementary Fig....”
- Expulsion mechanism of the substrate-translocating subunit in ECF transporters
Thangaratnarajah, Nature communications 2023 - “...containing the genes encoding EcfA (Uniprot: Q1GBJ0 ), EcfA (Uniprot: Q1GBI9 ) and EcfT (Uniprot: Q1GBI8 ) from L. delbrueckii were cloned downstream of the first arabinose inducible promoter of the p2BAD expression vector into the multiple cloning site between the Bsp E1 and Blg II...”
- “...study are available through UniProt under the accession codes Q1GBJ0 for EcfA, Q1GBI9 for EcfA, Q1GBI8 for EcfT, Q1G930 for FolT1, Q1G292 for FolT2, and Q1G7W0 for CbrT. For the coarse-grained molecular dynamics simulations, data (final snapshots, cleaned trajectories, starting structure/simulation parameters) are available through the...”
SSA_2365 Cobalt transport protein cbiQ, putative from Streptococcus sanguinis SK36
41% identity, 91% coverage
- Genome-wide identification of Streptococcus sanguinis fitness genes in human serum and discovery of potential selective drug targets
Zhu, Molecular microbiology 2021 - “.... The ECF mutant was constructed by replacing the three ECF genes (SSA_2367, SSA_2366, and SSA_2365, in that order) with the aad9 cassette encoding Sc r (Senty Turner et al., 2009 ) by overlap extension PCR (Ho et al., 1989 ). The aad9 cassette, including its...”
- “...as in the earlier annotation. The aad9 cassette extended exactly to the stop codon of SSA_2365, which was 210bp from the downstream ORF, SSA_2364. Based on expression data from multiple RNAseq studies, this ORF appears to be in a separate operon from the ECF genes (data...”
- Availability of Zinc Impacts Interactions between Streptococcus sanguinis and Pseudomonas aeruginosa in Coculture
Li, Journal of bacteriology 2020 (secret)
ZY05719_RS10240 energy-coupling factor transporter transmembrane component T family protein from Streptococcus suis
43% identity, 96% coverage
- hsdS, Belonging to the Type I Restriction-Modification System, Contributes to the Streptococcus suis Serotype 2 Survival Ability in Phagocytes
Xu, Frontiers in microbiology 2017 - “...gene 5, encoding a L-serine dehydratase, locus_tag ZY05719_RS10230; and gene 6, encoding a transporter, locus_tag ZY05719_RS10240. The 307 bp of invert repeats are shown in blue. The arrow is pointing to the TnYLB-1 insertion site. Meanwhile, we found two SS2 ZY05719 genes, which code peptidoglycan-binding proteins,...”
- “...ZY05719_RS10230 lysM-F ATCTGCTACACGCTCTTGG Part of lysM lysM-R CGTAACGGTATCTACATTGGT Part of lysM ZY05719_RS10240-F CCTTCTGAATAAGATTTCCCTC Part of ZY05719_RS10240 ZY05719_RS10240-R CTTGCGTTTTGTACCGACC Part of ZY05719_RS10240 16S RNA-F GTTGCGAACGGGTGAGTAA Part of 16S RNA 16S RNA-R TCTCAGGTCGGCTATGTATCG Part of 16S RNA a Underlined portions of the primers correspond to restriction enzyme recognition...”
CS401_RS07400 energy-coupling factor transporter transmembrane component T family protein from Fusobacterium vincentii
36% identity, 93% coverage
ECFT_LEUMM / Q03ZL4 Energy-coupling factor transporter transmembrane protein EcfT; ECF transporter T component EcfT from Leuconostoc mesenteroides subsp. mesenteroides (strain ATCC 8293 / DSM 20343 / BCRC 11652 / CCM 1803 / JCM 6124 / NCDO 523 / NBRC 100496 / NCIMB 8023 / NCTC 12954 / NRRL B-1118 / 37Y) (see 2 papers)
41% identity, 93% coverage
- function: Part of a common energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates including 5-formyltetrahydrofolate, pantothenate and riboflavin. Upon expression of the complex plus FolT in E.coli allows 5- formyltetrahydrofolate uptake; 5-formyltetrahydrofolate is not taken up in the absence of FolT or the EcfA1A2T complex.
subunit: Forms a stable energy-coupling factor (ECF) transporter complex probably composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component). This complex interacts with a number of substrate-specific components, including FolT, PanT and RibU for 5-formyltetrahydrofolate, pantothenate and riboflavin respectively. May be able to interact with more than 1 S component at a time.
NH16_RS04620 energy-coupling factor transporter transmembrane component T family protein from Leuconostoc mesenteroides subsp. dextranicum
42% identity, 88% coverage
SPD_2046 cobalt ABC transporter, permease protein from Streptococcus pneumoniae D39
spr2024 ABC transporter membrane-spanning permease - unknown substrate from Streptococcus pneumoniae R6
35% identity, 95% coverage
C4N14_03000 energy-coupling factor transporter transmembrane component T family protein from Fusobacterium nucleatum subsp. nucleatum ATCC 23726
36% identity, 92% coverage
- Transcriptome fine-mapping in Fusobacterium nucleatum reveals FoxJ, a new σE-dependent small RNA with unusual mRNA activation activity
Ponath, mBio 2024 - “...Normalized coverage (RPM) of the dRNA-seq and term-seq libraries for the mRNAs of C4N14_02995 and C4N14_03000. The TSS and TTSs are indicated by an arrow and stem-loop, respectively. While dRNA-seq maps 5 UTRs, it does not provide a good annotation of 3 UTRs ( 30 )....”
- “...Interestingly, the 3 UTR of the C4N14_02995 mRNA is transcribed antisense to the downstream gene C4N14_03000, an energy-coupling factor transporter, for which only a few reads could be detected ( Fig. 1G ). This suggests a possible transcriptional regulation through antisense transcription for this specific gene,...”
BL0043 possible fused ATP binding protein and permease of ABC transporter from Bifidobacterium longum NCC2705
34% identity, 29% coverage
- Prediction of Biofilm Inhibiting Peptides: An In silico Approach
Gupta, Frontiers in microbiology 2016 - “...release factor 3 Lactobacillus johnsonii (strainCNCMI-12250) 4 0.47 KKRIHELLRTLK Q8G838 Putative ABC transporter ATP-binding protein BL0043 Bifidobacterium longum (strainNCC2705) 1 0.41 DRIKKAAKKIQN Q74K31 Glucose-6-phosphate isomerase Lactobacillus johnsonii (strainCNCMI-12250) 1 0.38 RIKKAAKKIQND Q74K31 Glucose-6-phosphate isomerase Lactobacillus johnsonii (strainCNCMI-12250) 1 0.38 KQVKKLFKKWGW P80214 Bacteriocin plantaricin-A Lactobacillus plantarum (strainATCCBAA-793)...”
- “...methyl transferase H Lactobacillus johnsonii (strainCNCMI-12250) 4 0.24 AQAKKRIHELLR Q8G838 Putative ABC transporter ATP-binding protein BL0043 Bifidobacterium longum (strainNCC2705) 1 0.23 AKKRIHELLRTL Q8G838 Putative ABC transporter ATP-binding protein BL0043 Bifidobacterium longum (strainNCC2705) 1 0.22 EDKIVKKIFKKY P62471 Ribosomal RNA small subunit methyl transferase H Lactobacillus johnsonii (strainCNCMI-12250)...”
ECFT_THEMA / Q9X2I1 Energy-coupling factor transporter transmembrane protein EcfT; ECF transporter T component EcfT from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see paper)
TC 3.A.1.25.5 / Q9X2I1 ABC-type transporter, integral membrane subunit, component of Biotin/Riboflavin ECF transport system, EcfAA'T/RibU/BioY (Karpowich and Wang 2013). RibU binds riboflavin with high affinity, and the protein-substrate complex is exceptionally stable in solution. The crystal structure of riboflavin-bound RibU reveals an electronegative binding pocket at the extracellular surface in which the substrate is completely buried from Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
TM1868 conserved hypothetical protein from Thermotoga maritima MSB8
35% identity, 87% coverage
- function: Transmembrane (T) component of an energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates (Probable). Expression of the complex plus RibU in E.coli allows riboflavin uptake; uptake does not occur in the absence of RibU or the EcfA1A2T complex.
subunit: Forms a stable energy-coupling factor (ECF) transporter complex composed of 2 membrane-embedded substrate-binding proteins (S component, RibU, BioY), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component) upon coexpression in E.coli. A stable subcomplex with both A and T components are also isolated. This complex interacts with at least 2 substrate-specific components, BioY and RibU. - substrates: Biotin, riboflavin
- Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634
McCleverty, Protein science : a publication of the Protein Society 2008 - “...for cobalt transport have been annotated (TM1663 and TM1868); however, a periplasmic binding domain for the transporter has still not been identified. In...”
Bbr_1329 energy-coupling factor transporter ATPase from Bifidobacterium breve UCC2003
35% identity, 31% coverage
Q8G838 Putative ABC transporter ATP-binding protein BL0043 from Bifidobacterium longum (strain NCC 2705)
34% identity, 30% coverage
- Prediction of Biofilm Inhibiting Peptides: An In silico Approach
Gupta, Frontiers in microbiology 2016 - “...1 0.49 TKKLFKVVKKRG Q74IG8 Peptide chain release factor 3 Lactobacillus johnsonii (strainCNCMI-12250) 4 0.47 KKRIHELLRTLK Q8G838 Putative ABC transporter ATP-binding protein BL0043 Bifidobacterium longum (strainNCC2705) 1 0.41 DRIKKAAKKIQN Q74K31 Glucose-6-phosphate isomerase Lactobacillus johnsonii (strainCNCMI-12250) 1 0.38 RIKKAAKKIQND Q74K31 Glucose-6-phosphate isomerase Lactobacillus johnsonii (strainCNCMI-12250) 1 0.38 KQVKKLFKKWGW...”
- “...subsp. infantis (strainATCC15697) 5 0.30 RKKHVIRVCQDG B3DR08 tRNA(Ile)-lysidine synthase Bifidobacterium longum (strainDJO10A) 5 0.30 QAKKRIHELLRT Q8G838 Putative ABC transporter ATP-bindingproteinBL0043 Bifidobacterium longum (strainNCC2705) 1 0.29 PAAVLLKKAAKV P62435 50S ribosomal protein L11 Lactobacillus johnsonii (strainCNCMI-12250) 1 0.29 DKIVKKIFKKYS P62471 Ribosomal RNA small subunit methyl transferase H Lactobacillus...”
MHO_1990 Cobalt ABC transporter permease protein from Mycoplasma hominis
30% identity, 77% coverage
DSY2722 hypothetical protein from Desulfitobacterium hafniense Y51
32% identity, 88% coverage
slr1978 unknown protein from Synechocystis sp. PCC 6803
25% identity, 89% coverage
- Regulation of Iron Homeostasis and Use in Chloroplasts
Kroh, International journal of molecular sciences 2020 - “...AT4G33460 XP_001703542/Cre03.g164150.t1.1 [ 107 ] sll1623 [ 107 ] ABCI12 AT3G21580 PNW75614/Cre12.g533950.t1.1 [ 107 ] slr1978 [ 107 ] Multiple Antibiotic Resistance 1 (MAR1) AT5G26820 Cre03.g175200.t1.2 lap75 Yellow Stripe Like 4/6 (YSL4/6) (4) AT5G41000, (6) AT3G27020 ROS homeostasis Fe SuperOxide Dismutase (FSD) AT4G25100 AT5G51100 AT5G23310 Cre10.g436050.t1.2...”
Dshi_3687 cobalt transport protein from Dinoroseobacter shibae DFL 12
27% identity, 81% coverage
- Fatal affairs - conjugational transfer of a dinoflagellate-killing plasmid between marine Rhodobacterales
Tomasch, Microbial genomics 2022 - “...lost if genes of a putative biotin ABC transporter operon ( bioYMN , Dshi_3685 to Dshi_3687) were inactivated. This operon is unique for the 191kb plasmid. Biotin is an essential vitamin for dinoflagellates and it is one of the three vitamins provided in L1 medium. However,...”
- The Influence of Genes on the "Killer Plasmid" of Dinoroseobacter shibae on Its Symbiosis With the Dinoflagellate Prorocentrum minimum
Mansky, Frontiers in microbiology 2021 - “...from the three tested transposon mutants (Dshi_3684, Dshi_3685, Dshi_3686) this operon also contains the gene Dshi_3687 and Dshi_3683, for which no transposon mutants was available. Dshi_3687 is annotated as a cobalt/nickel transport protein, EcfT, which is a conserved part of uptake systems ( Rodionov et al.,...”
- “...factor (ECF) ABC-transporter complex. These transporters consist of an ATPase (Dshi_3686), a conserved transmembrane protein (Dshi_3687) as well as a transmembrane substrate-capture protein (Dshi_3685) ( Hebbeln et al., 2007 ). These high-affinity biotin uptake systems were studied in Rhodobacter capsulatus but their role in algae bacteria...”
Synpcc7942_2341 cobalt transport system permease protein from Synechococcus elongatus PCC 7942
26% identity, 88% coverage
- Regulatory Connections Between the Cyanobacterial Factor PipX and the Ribosome Assembly GTPase EngA
Jerez, Frontiers in microbiology 2021 - “..., and proC ) and two other previously unconnected genes: synpcc7942_2340 ( engA ) and synpcc7942_2341 (a putative T component from an energy-coupling factor transporter). Except for PipX, which is only found in cyanobacteria, all network components have homologs outside this phylum. So far, the only...”
- “...(discussed in Labella et al., 2017 ). However, the inferred functional connection between engA and synpcc7942_2341 genes and of these with pipX , unlinked in the S. elongatus genome, has never been predicted by other methods. EngA is an essential GTPase involved in the maturation of...”
O34572 Putative HMP/thiamine permease protein YkoC from Bacillus subtilis (strain 168)
26% identity, 92% coverage
alr0484 hypothetical protein from Nostoc sp. PCC 7120
22% identity, 83% coverage
CCPUN_08380 energy-coupling factor transporter transmembrane component T family protein from Cardinium endosymbiont of Culicoides punctatus
24% identity, 82% coverage
MSMEG_2609 cobalt ABC transporter, permease protein CbiQ from Mycobacterium smegmatis str. MC2 155
28% identity, 82% coverage
MPN431 permease from Mycoplasma pneumoniae M129
25% identity, 47% coverage
IUJ47_RS12860 energy-coupling factor transporter transmembrane component T family protein from Enterococcus faecalis
25% identity, 90% coverage
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...PstC IUJ47_RS11400 0.256 Phosphate ABC transporter ATP-binding protein PstB IUJ47_RS04720 0.265 ABC transporter permease subunit IUJ47_RS12860 0.279 Energy-coupling factor transporter transmembrane protein EcfT IUJ47_RS09165 0.282 Carbohydrate ABC transporter permease IUJ47_RS11395 0.285 Phosphate ABC transporter ATP-binding protein PstB IUJ47_RS04685 0.288 Energy-coupling factor transporter transmembrane protein EcfT IUJ47_RS01745...”
OG1RF_11693 energy-coupling factor transporter transmembrane component T family protein from Enterococcus faecalis OG1RF
25% identity, 90% coverage
SACOL2707 cobalt transport family protein from Staphylococcus aureus subsp. aureus COL
27% identity, 87% coverage
SAR2765 ABC transporter permease protein from Staphylococcus aureus subsp. aureus MRSA252
26% identity, 87% coverage
- Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria
Moody, BMC genomics 2013 - “...analysis to assess their expression profiles (Figure 4 ). Within S. avermitilis, the 89 nucleotide sar2765 was expressed exclusively during vegetative growth (Figure 4 A), while the equivalently sized sar3980 (88 nucleotides) was expressed most highly during vegetative and aerial growth (Figure 4 A). In S....”
- “...species-specific intergenic sRNAs. Expression profiles, northern analyses and structural predictions for: (A) S. avermitilis sRNAs sar2765 (left) and sar3980 (right); (B) S. coelicolor sRNAs scr3716 (left) and scr3931 (right); (C) S. venezuelae sRNA svr5535. For each expression profile, relative sequence reads for genes encoded on the...”
SA2475 hypothetical protein from Staphylococcus aureus subsp. aureus N315
27% identity, 87% coverage
MG_302 metal ion ABC transporter, permease protein, putative from Mycoplasma genitalium G37
24% identity, 70% coverage
IEM_00289 energy-coupling factor transporter transmembrane component T family protein from Bacillus cereus BAG6O-2
28% identity, 57% coverage
- Microbial antigen mimics activate diabetogenic CD8 T cells in NOD mice
Tai, The Journal of experimental medicine 2016 - “...2 uncultured Flavobacteriia bacterium (gram negative, commensal) 303311 F YLKT S VFL W15946 hypothetical protein IEM_00289 Bacillus cereus (gram positive, gut flora) 252260 VYLK V NVF K W15948 NAD synthetase Enterobacter mori LMG 25706 (gram negative) 3240 SYLKTN A FL Bold letters represent the amino acids...”
BION_RHIEC / Q2KBP6 Energy-coupling factor transporter transmembrane protein BioN; ECF transporter T component BioN from Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42) (see paper)
TC 3.A.1.25.1 / Q6GUB1 Permease protein BioN, component of The biotin uptake porter (binding receptor lacking) (see also the VUT or ECF family; BioY; 2.A.88.1.1) (Rodionov et al., 2006; Hebbeln et al., 2007). BioN (the EcfT component of the biotin transporter) appears to be required for intramolecular signaling and subunit assembly (Neubauer et al., 2009). The Ala-Arg-Ser and Ala-Arg-Gly signatures in BioN are coupling sites to the BioM ATPases from Rhizobium etli (see paper)
23% identity, 82% coverage
- function: Involved in biotin uptake.
subunit: Part of a biotin transporter complex composed of BioM, BioN and BioY. - substrates: Biotin
tcdb comment: Subunit stoicheometries have been estimated with the prediction that there are oligomeric forms of BioM and BioY in the BioMNY complex (Finkenwirth et al. 2010)
SAK_1646 nickel/cobalt uptake transporter (NiCoT) family ABC transporter, permease protein from Streptococcus agalactiae A909
30% identity, 57% coverage
YP_001103441 cobalt transport system permease protein from Saccharopolyspora erythraea NRRL 2338
26% identity, 81% coverage
- The biosynthetic gene cluster of zorbamycin, a member of the bleomycin family of antitumor antibiotics, from Streptomyces flavoviridis ATCC 21892
Galm, Molecular bioSystems 2009 - “...shows significant similarity to a cobalt transport system permease protein from Saccharopolyspora erythraea (accession number YP_001103441; 36% identity and 52% similarity). Drug transport is a common resistance mechanism found in antibiotic producing microorganisms, 32 and Zbm-Orf36, Zbm-Orf37 and Zbm-Orf38 may constitute a transport system that provides...”
- “...12 (ZP_01587238) orf37 226 ABC transporter Saccharopolyspora erythraea (YP_001103442) orf38 199 ABC transporter Saccharopolyspora erythraea (YP_001103441) orf39 398 Biotin synthase S. coelicolor (NP_625532) zbmL 337 GDP-mannose-4,6-dehydratase S. hygroscopicus , Hyg5 (ABC42542) Downstream boundary of the ZBM gene cluster orf41-42 (partial) ORFs that are beyond the zbm...”
cg2149 cobalt subfamily permease from Corynebacterium glutamicum ATCC 13032
NCgl1885 energy-coupling factor transporter transmembrane component T family protein from Corynebacterium glutamicum ATCC 13032
25% identity, 84% coverage
- Characterization of the biotin uptake system encoded by the biotin-inducible bioYMN operon of Corynebacterium glutamicum
Schneider, BMC microbiology 2012 - “...Comparative genome analyses suggested that the putative transport system BioYMN encoded by cg2147, cg2148 and cg2149 might be involved in biotin uptake by C. glutamicum . Results By comparison of global gene expression patterns of cells grown with limiting or excess supply of biotin or with...”
- “...from Rhizobium etli . The two genes downstream of bioY ( cg2147 ), cg2148 and cg2149 , encoding components of an ABC transport system with 41% and 25% identity, respectively, to ATP-binding protein BioM and energy-coupling factor transporter transmembrane protein BioN from R. etli , respectively,...”
- The alternative sigma factor SigB of Corynebacterium glutamicum modulates global gene expression during transition from exponential growth to stationary phase
Larisch, BMC genomics 2007 - “...were the biotin biosynthesis and transport genes cg0095 ( bioB ), cg2147 ( bioY )- cg2149 , cg2885 ( bioA ) cg2886 ( bioD ) which were all found stronger expressed in transition phase in the sigB -proficient and the sigB -deficient strain. This expression pattern...”
- “...cg2147 bioY membrane protein, BioY family 3.70 1.51 cg2148 ABC transporter, ATP-binding protein 3.11 1.51 cg2149 permease (cobalt permease subfamily) 1.63 0.75* cg2885 bioA adenosylmethionine-8-amino-7-oxononanoate aminotransferase 2.09 0.91* cg2886 bioD dethiobiotin synthetase protein 1.32 0.76* cg1227 ABC-type cobalt transport system 1.58 1.48 FUNCTION UNKNOWN cg0378 putative...”
- Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect L-Lysine Production in Corynebacterium glutamicum
Kim, International journal of molecular sciences 2016 - “...decreased by approximately 76%, and the three genes involved in biotin transport (NCgl1883, NCgl1884, and NCgl1885) were significantly downregulated. These results will be helpful to improve our understanding of C . glutamicum for industrial amino acid production. biotin Corynebacterium glutamicum l -lysine transcriptome gene ontology (GO)...”
- “...in ATCC13032 ( Table 1 and Figure 3 ). Interestingly, three genes (NCgl1883, NCgl1884, and NCgl1885) involved in biotin transport were also significantly upregulated in ATCC21300 compared to ATCC13032 ( Table 1 and Figure 3 ). 2.3. Effects of bioB Mutation on l -Lysine Production, Growth...”
B7GTQ1 Cobalt transport protein from Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12)
29% identity, 70% coverage
DVU1057 component of nickel ABC transport system from Desulfovibrio vulgaris Hildenborough
24% identity, 89% coverage
lp_0148 ABC transporter, permease protein from Lactobacillus plantarum WCFS1
30% identity, 43% coverage
- Modulation of Lactobacillus plantarum gastrointestinal robustness by fermentation conditions enables identification of bacterial robustness markers
van, PloS one 2012 - “...over pNZ3433 j lp_3297 folE GTP cyclohydrolase I Intracellular + 0.554 1.356 over pNZ7026 i lp_0148 lp_0148 ABC transporter, permease protein, Cobalt (or cobalamine) Multi-transmembrane + 0.523 1.156 over pNZ3433 j lp_2349 hicD3 L-2-hydroxyisocaproate dehydrogenase Intracellular + 0.441 1.001 over pNZ3431 lp_3296 folC2 folylpolyglutamate synthase/dihydrofolate synthase...”
- “...folB - folK - folE - folC2 - xtp2 - folP . j pNZ3433 contains lp_0148 , lp_0149 , and lp_0150 . 10.1371/journal.pone.0039053.g005 Figure 5 Correlation of L. plantarum WCFS1 GI-tract survival and transcript intensity of thrC (A) and pbp2A (B). The eight best and eight...”
BIF_01879 energy-coupling factor transporter transmembrane component T family protein from Bifidobacterium animalis subsp. lactis BB-12
24% identity, 94% coverage
- Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12
Jensen, Microbiology resource announcements 2021 - “...GG) BIF_02260 1832733 1bp Coding(127/180nt) BIF_02260 1832760 1bp Coding(100/180nt) BIF_02260 1850719 3bp13bp Intergenic(100/+17) BIF_00078 / BIF_01879 1851378 +T Coding(71/711nt) BIF_01879 Coding(163/216nt) BIF_02261 1853256 1bp Coding(63/195nt) BIF_02082 1885096 10bp24bp Intergenic(+17/+55) BIF_01746 / BIF_01789 1885634 2bpGC Coding(1,8651,866/2,340nt) BIF_01789 1885679 2bpCT Coding(1,8201,821/2,340nt) BIF_01789 1885686 +G Coding(1,814/2,340nt) BIF_01789 1885711 +G...”
BA2642 cobalt transport protein from Bacillus anthracis str. Ames
26% identity, 86% coverage
TC 3.A.1.26.5 / A7NRG1 Cobalt transport protein, component of ThiW/CbiQ/CbiO homologues (ThiW: 174 aas; 5 putative TMSs) from Roseiflexus castenholzii (strain DSM 13941 / HLO8)
33% identity, 56% coverage
- substrates: thiamin
tcdb comment: Possible thiamin uptake porter (Rodionov et al., 2009)
AB12I_ARATH / Q944H2 Protein ABCI12, chloroplastic; ABC transporter I family member 12; ABC transporter ABCI.12; AtABCI12 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT3G21580 cobalt ion transmembrane transporter from Arabidopsis thaliana
26% identity, 36% coverage
- A Novel Prokaryote-Type ECF/ABC Transporter Module in Chloroplast Metal Homeostasis
Voith, Frontiers in plant science 2019 - “...be 328 aa long with a size of about 36 kDa. In UniProt/InterPro databases (accession Q944H2), At-ABCI12 is annotated to be an ABC/ECF transporter transmembrane component (IPR003339 family). Further, the protein was already mentioned as plant T protein, belonging to a plant-specific ECF transporter T subunit...”
- Regulation of Iron Homeostasis and Use in Chloroplasts
Kroh, International journal of molecular sciences 2020 - “...slr0354 [ 107 ] ABCI10 AT4G33460 XP_001703542/Cre03.g164150.t1.1 [ 107 ] sll1623 [ 107 ] ABCI12 AT3G21580 PNW75614/Cre12.g533950.t1.1 [ 107 ] slr1978 [ 107 ] Multiple Antibiotic Resistance 1 (MAR1) AT5G26820 Cre03.g175200.t1.2 lap75 Yellow Stripe Like 4/6 (YSL4/6) (4) AT5G41000, (6) AT3G27020 ROS homeostasis Fe SuperOxide Dismutase...”
- A Novel Prokaryote-Type ECF/ABC Transporter Module in Chloroplast Metal Homeostasis
Voith, Frontiers in plant science 2019 - “...might contribute to chloroplast metal transport in Arabidopis identified At-ABCI10 (At4g33460), At-ABCI11 (At5g14100), and At-ABCI12 (At3g21580) as promising candidates. All three proteins are predicted to be targeted to chloroplasts and were grouped into the prokaryotic-type CBY/Y179 subfamily of Arabidopsis and rice ABC transport systems ( Garcia...”
- “...that the potential interaction with ABCI12 seems to be specific for ABCI10. For Arabidopsis At-ABCI12 (At3g21580), a chloroplast targeting peptide of 63 aa (ChloroP; Emanuelsson et al., 1999 ) and five -helical transmembrane domains are predicted (Aramemnon database; Schwacke et al., 2003 ). To confirm the...”
- Two essential arginine residues in the T components of energy-coupling factor transporters
Neubauer, Journal of bacteriology 2009 - “...proteins (e.g., the T proteins encoded by the locus AT3G21580 in the Arabidopsis thaliana genome and by the gene Os05g0400600 of Oryza sativa) may be localized...”
AZC_3756 putative cobalt transport system permease protein from Azorhizobium caulinodans ORS 571
26% identity, 55% coverage
BIF_00363 ATP-binding cassette domain-containing protein from Bifidobacterium animalis subsp. lactis BB-12
26% identity, 18% coverage
- Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12
Jensen, Microbiology resource announcements 2021 - “...1470322 AC Intergenic(+487/73) BIF_00011 / BIF_02078 1470328 TC Intergenic(+493/67) BIF_00011 / BIF_02078 1474821 +G Coding(7/2,349nt) BIF_00363 1474832 +C Coding(18/2,349nt) BIF_00363 1494471 + TGAAGCGGC Intergenic(+15/+59) BIF_00354 / BIF_02081 1494477 TG Intergenic(+21/+53) BIF_00354 / BIF_02081 1494479 1bpTG Intergenic(+23/+51) BIF_00354 / BIF_02081 1507139 7bp21bp Intergenic(+39/+35) BIF_00355 / BIF_00882 1516347...”
RL1003 putative transmembrane component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
23% identity, 69% coverage
MA0869 ABC transporter, permease protein from Methanosarcina acetivorans C2A
22% identity, 80% coverage
PF0067 cobalt transport ABC transporter, integral membrane component from Pyrococcus furiosus DSM 3638
33% identity, 60% coverage
MMP1483 Cobalt transport protein Q from Methanococcus maripaludis S2
27% identity, 81% coverage
BION_RHOCB / D5ARG9 Energy-coupling factor transporter transmembrane protein BioN; ECF transporter T component BioN from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (see paper)
TC 3.A.1.25.7 / D5ARG9 Energy-coupling factor transporter transmembrane protein BioN, component of The riboflavin uptake system, BioMNY from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
25% identity, 80% coverage
- function: Probably involved in biotin uptake, although complementation experiments in E.coli do not indicate a clear role.
subunit: Part of a biotin transporter holocomplex composed of BioM, BioN and BioY. BioMN complexes can be readily purified, but not BioNY complexes. Only the BioMNY complex has ATPase activity. - substrates: riboflavin
tcdb comment: BioM, EtcA, ATPase, 234 aas; BioN, EtcT, 190 aas, 5 TMSs; BioY, EtcS, 210 aas, 5 TMSs BioY can also function as a secondary carrier and is therefore listed separately under TC# 2.A.88.1.3. ATP-dependent conformational changes drive substrate capture and release when BioMNY are together in a complex (Finkenwirth et al. 2015)
cg1229 ABC-type cobalt transport system, permease component CbiQ from Corynebacterium glutamicum ATCC 13032
26% identity, 58% coverage
SSO1892 Conserved hypothetical protein from Sulfolobus solfataricus P2
27% identity, 32% coverage
sll0384 unknown protein from Synechocystis sp. PCC 6803
22% identity, 84% coverage
- A global transcriptional activator involved in the iron homeostasis in cyanobacteria
Liu, Science advances 2024 - “...Motif-1, -3 slr0327 , FutB, periplasmic binding protein-dependent ABC transporter Motif-1, -3 Other metal transferrelated sll0384 , CbiQ, cobalt/nickel transport system permease protein Others sll0382 , Slr0382, nickel transport protein Motif-1 sll1598 , MntC, Mn transporter MntC Others Sugar transport slr1202 , Slr1202, permease protein of...”
- In-vivo turnover frequency of the cyanobacterial NiFe-hydrogenase during photohydrogen production outperforms in-vitro systems
Gutekunst, Scientific reports 2018 - “...Co 2+ did not have any effect. This strongly suggests that nikKLMQO (sll0381, sll0382, sll0383, sll0384, and sll0385) encodes a nickel uptake system in Synechocystis . Hydrogenase and urease activity Synechocystis possesses two known nickel-containing enzymes: a bidirectional NiFe-hydrogenase and a urease. In order to further...”
- “...genes PCR products containing the up- and downstream regions of the nikKLMQO (sll0381, sll0382, sll0383, sll0384 and sll0385) gene cluster and the kanamycin resistance cassette were prepared by PCR fusion as described previously 35 . The following primers were used P1nik CCGTGGGCAAAATCTACCCT and P2nik CTTTCTGGCTGGATGATGGGGCGATTAAAGGCGATCAGCAAACTGTGGG for...”
- Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium
Liberton, Molecular & cellular proteomics : MCP 2016 - “...Slr1149 Slr1216 Slr1423 Slr1515 Slr1575 Sll0267 Sll0283 Sll0384 Sll0505 Sll0602 Sll0727 Sll1608 Sll2003 Slr0060 Slr0594 Slr0625 Slr0818 Slr0960 Slr1257 Slr1875...”
- Metals in cyanobacteria: analysis of the copper, nickel, cobalt and arsenic homeostasis mechanisms
Huertas, Life (Basel, Switzerland) 2014 - “...), HupE ( slr2135 ), NrsR ( sll0797 ), NrsS ( sll0798 ), CbiO ( sll0384 ), CbiQ ( sll0385 ) and CbiM ( sll0383 ). OM, outer membrane; PM, plasma membrane. The cobalt resistance system is composed of CorR (or CoaR), a MerR homolog that...”
- RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803
Wang, Biotechnology for biofuels 2012 - “...7.09 29.09 sll0368 uracil phosphoribosyltransferase 2.33 2.00 sll0374 urea transport system ATP-binding protein 2.80 3.60 sll0384 Cations and iron carrying protein 2.31 1.70 sll0450 cytochrome b subunit of nitric oxide reductase 1.62 4.26 sll0536 probable potassium channel protein 2.00 1.93 sll0540 phosphate-binding protein PstS homolog 1.57...”
- “...channel protein, sll1428 encoding a probable sodium-dependent transporter, slr2131 encoding a RND multidrug efflux transporter, sll0384 encoding a cation and iron carrying protein, sll1041 encoding a sulfate transport ATP-binding protein CysA, sll0374 encoding a urea transport system ATP-binding protein, and slr0678 encoding a biopolymer transport ExbD...”
Rv2325c hypothetical protein from Mycobacterium tuberculosis H37Rv
27% identity, 77% coverage
Amuc_1199 cobalt ABC transporter, inner membrane subunit CbiQ from Akkermansia muciniphila ATCC BAA-835
24% identity, 86% coverage
- Omics-based analysis of <i>Akkermansia muciniphila</i> cultivation in food-grade media
Geerlings, Microbiome research reports 2024 - “...well as peptide, aliphatic sulfonate, nitrate/sulfonate/bicarbonate, cobalt and manganese ABC transporters (Amuc_0672, AMUC_1297, Amuc_0408, Amuc_1198, Amuc_1199, Amuc_0056, Amuc_1380 and Amuc_1186) with an increase > 5-fold. In addition, genes involved in oxygen stress response were found to be higher in soy medium including rubrerythrin (Amuc_2055 and Amuc_2056),...”
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