tatB Resolved · high auto-curated
H37Rv Rv1224 · MTBC0 mtbc0_001312 ·
131 aa ·
1375907–1376302 MTBC0
(+) ·
RefSeq NP_215740.1
Genomic neighbourhood (genome browser)
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Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Sec-independent protein translocase protein TatB |
|---|---|
| MTBC0 PGAP re-annotation | Sec-independent protein translocase protein TatB |
| Revised (this work) | Sec-independent protein translocase protein TatB. Pfam: TatA_B_E (PF02416.22). |
| Functional category (TubercuList) | cell wall and cell processes |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
In the literature (TB corpus sweep) 5 publications
5 TB publications mention this gene. 5 publication(s) discuss this gene (5 in a M. tuberculosis context, 4 in other mycobacteria — M. smegmatis (3), M. leprae (1)).
| Publication | Date |
|---|---|
| Identification of novel loci associated with mycobacterial isoniazid resistance. doi:10.1016/j.tube.2015.09.008 | 2016 |
| Identifying novel mycobacterial stress associated genes using a random mutagenesis screen in Mycobacterium smegmatis. doi:10.1016/j.gene.2015.07.063 | 2015 |
| A TatABC-type Tat translocase is required for unimpaired aerobic growth of Corynebacterium glutamicum ATCC13032. doi:10.1371/journal.pone.0123413 | 2015 |
| Inactivation of Rv2525c, a substrate of the twin arginine translocation (Tat) system of Mycobacterium tuberculosis, increases beta-lactam susceptibility and virulence. doi:10.1128/JB.00631-06 | 2006 |
| Characterization of the twin-arginine translocase secretion system of Mycobacterium smegmatis. doi:10.1128/JB.188.4.1332-1340.2006 | 2006 |
This layer CITES the literature and adds context; it does not change the verdict or the function stated elsewhere in this fiche. This distinguishes a gene that is dark because nobody has looked from one that is dark despite having been studied. Source: PubMed (whole): H37Rv locus tag + GENE NAME + ortholog identifiers (Mb…, MMAR_…, MSMEG_…, ML…, MAB_…), under a mycobacterial context filter; hits verified against the abstract text. Species-context counts distinguish M. tuberculosis literature from literature on other mycobacteria. phase76/phase77, 2026-07-13.
Intrinsic disorder (sequence + structure) partially disordered
| Predicted disorder | 29% of residues (metapredict) · mean AlphaFold pLDDT 73.8 |
|---|---|
| Disordered regions | 1 IDR(s), longest 39 aa [92-131] |
carries a substantial disordered region (39/131 residues); disorder is a property, not a function
A property (biophysics), not a function. No LLPS/condensate claim is made from disorder alone. Verdict unchanged. Source: metapredict v3 (Emenecker/Holehouse) per-residue disorder + AlphaFold mean pLDDT (annotation_mtbc P16.13).
CRISPRi vulnerability
Vulnerability index -9.11 (95% CI -10.02 to -8.19). A more negative index = more vulnerable to knockdown (better drug-target quality); indicative threshold VI ≤ -6 = highly vulnerable.
Quantitative CRISPRi knockdown, graded (finer than binary Tn-seq essentiality). Source: CRISPRi vulnerability index (Bosch 2021, pebble.rockefeller.edu).
Legacy record & comparison (Mycobrowser)
| Mycobrowser function | Involved in proteins export. This sec-independent pathway is termed tat for twin-arginine translocation system. This system mainly transports proteins with bound cofactors that require folding prior to export. |
|---|
The legacy Mycobrowser record is shown for verification. Mycobrowser is no longer maintained; its EC numbers predate recent nomenclature revisions, so a class change usually reflects re-numbering, not a conflict.
Orthologues (reciprocal best hits across mycobacteria)
| M. bovis |
Mb1256
· 99.2% identity |
|---|---|
| M. leprae |
ML1079
· 73.3% identity |
| M. marinum |
MMAR_4213
· 75.0% identity |
| M. smegmatis |
MSMEG_5069
· 68.9% identity |
| M. orygis |
RJtmp_001289
· 99.2% identity |
| M. abscessus |
MAB_1365
· 55.6% identity |
Reciprocal-best-hit orthologues (DIAMOND) against the Mycobrowser reference proteomes. A missing species is informative: e.g. a gene absent from M. leprae was likely lost in its reductive genome evolution. Locus tags link to Mycobrowser.
Curated reference (UniProt)
| UniProt |
P9WG99
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Sec-independent protein translocase protein TatB |
| Curated 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. Together with TatC, TatB is part of a receptor directly interacting with Tat signal peptides. TatB may form an oligomeric binding site that transiently accommodates folded Tat precursor proteins before their translocation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| Preferred name | tatB |
| eggNOG description | 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. Together with TatC, TatB is part of a receptor directly interacting with Tat signal peptides. TatB may form an oligomeric binding site that transiently accommodates folded Tat precursor proteins before their translocation |
| Orthologous group | COG1826 |
| KEGG orthology |
K03117
|
| KEGG pathways |
map03060, map03070
|
| KEGG modules |
M00336
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Outgroup conservation (beyond the MTBC) Corynebacteriales
| M. canettii dN/dS (deep-divergence selection) |
inf (low power)
· 1 consensus substitution(s) low power (1 canettii-consensus substitution(s)); present in M. canettii but dN/dS not reliable |
|---|---|
| Genus-wide presence (~53 non-MTBC Mycobacterium) |
present in 53/53 (100%) · mean identity 73.6%
· 4/4 closest MTBAP relatives conserved across the genus (present in 53/53 non-MTBC Mycobacterium genomes, incl. distant relatives) — an ancient core gene predating the genus radiation |
| Phylostratum (deepest detected homolog) |
MTBC-specific → Mycobacterium → Mycobacteriaceae → Corynebacteriales → Actinomycetia → Bacteria detected in 7/13 non-Mycobacterium reference genomes (down to Corynebacteriales) · mean identity 52.4% detected across the order Corynebacteriales (Corynebacterium/Nocardia/Rhodococcus/…) but not in more distant Actinomycetia — a Corynebacteriales-level gene |
Two orthogonal outgroup signals. M. canettii (the immediate outgroup) gives a deep-divergence dN/dS (a low value confirms a constrained, real gene; shown as confident only at ≥8 substitutions, else flagged low-power). Genus-wide presence/absence (tblastn vs assembled non-MTBC genomes) places the gene on the ancient-core ↔ MTBC-specific axis: a gene absent even from the closest MTBAP relatives is a candidate MTBC-specific innovation (possible host-adaptation factor, to confirm by synteny). The phylostratum extends that axis outside the genus (tblastn vs 13 reference genomes spanning Mycobacteriaceae → Corynebacteriales → Actinomycetia → outside the phylum): it is the deepest clade in which a homolog is still detected, i.e. a proxy for gene age. Read it with the null model in mind: a shallow (young) stratum can also reflect homology-detection failure for short or fast-evolving ORFs, so it is a descriptive axis, not a proof of novelty.
Essentiality (transposon mutagenesis) GD — not strictly essential
| DeJesus 2017 call | GD · growth-defect |
|---|---|
| What the call means | growth-defect: insertions tolerated but fitness reduced; NOT essential |
| TA sites (Himar1) | 6 in the ORF — 0 in the essential state, 5 growth-defect, 1 non-essential, 0 growth-advantage. Saturation 0.667, mean read count 54.75. A region of the protein devoid of TA sites is invisible to this assay: nothing can be inferred about it, in either direction. |
| Caveat | `essential: true` here is the broad union (ES+ESD+GD) kept for backward compatibility; this gene is NOT strictly essential. Read n_sites_* before writing anything about essentiality. Read with some caution: only 6 TA (Himar1) sites in the whole ORF (atlas median 13). The DeJesus 2017 call rests on fewer independent observations than for a longer gene. If this gene overlaps a neighbour (see Genomic-neighbour overlap section below), some of these 6 sites may fall inside the neighbour's ORF rather than its own, leaving even fewer truly informative sites than the raw count suggests. (P20.3) |
Genome-wide Himar1 transposon essentiality in H37Rv (DeJesus 2017). An essential call (ES/ESD/GD) is strong, independent evidence that a "hypothetical" locus encodes a functional, selectively required gene — orthogonal to intra-species conservation.
Proteomics (mass spectrometry) detected
| MS detection | detected in 9 of 16 independent MS datasets |
|---|---|
| Integrated abundance | 36.3 ppm · rank 1973/3519 (44.0th percentile) |
Detection by mass spectrometry is direct, experimental evidence that the protein product exists — orthogonal to sequence conservation and to Tn-seq essentiality, and especially decisive for a "hypothetical" locus. Reproducible detection across several independent datasets (PaxDb) makes the existence claim robust; the integrated abundance places the protein in the proteome's dynamic range.
Physico-chemical properties (computed, ProtParam)
| Length | 131 aa |
|---|---|
| Molecular weight | 14.0 kDa |
| Theoretical pI | 4.76 |
| GRAVY | -0.202 (hydrophilic) |
| Aliphatic index | 86.5 |
| Aromaticity | 0.061 |
| Instability index | 35.0 (stable) |
Computed from the ancestral MTBC0 sequence with the ExPASy ProtParam method (Biopython). Descriptive biophysical context: a positive GRAVY flags a hydrophobic (often membrane) protein, a high instability index (>40) predicts a short in-vitro half-life, an extreme pI hints at compartment or binding partner.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
TatA_B_E | PF02416.22 | 7.7e-14 | 4–49 | mttA/Hcf106 family |
Genomic context (neighbours & predicted operon) operon of 2
| Upstream (5' on genome) | htrA (+ strand, 1 bp gap) |
|---|---|
| Downstream (3' on genome) | Rv1225c (- strand, 32 bp gap) |
| Predicted operon |
htrA · tatB
|
Neighbours from the H37Rv annotation (+ strand). The operon is predicted by co-directional intergenic distance (same strand, gaps ≤50 bp) — a transcription-unit hypothesis, not a mapped TSS. For a "hypothetical", co-transcription with a characterised operon is a concrete functional lead (complements the STRING neighborhood channel below).
Functional interaction network (STRING v12, guilt-by-association)
Explore full network →Node colour = verdict, dashed = hypothetical; edge colour = evidence (green experimental, orange genomic-context, grey co-expression), width ∝ score. Click a partner to open its page; "Explore full network" to walk the graph.
Closest characterised functional partner: htrA (serine protease HtrA), high confidence from genomic context alone (score 966 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1223 htrA |
serine protease HtrA | 967 | 966 ctx | neighborhood:881 coexpression:730 |
Rv3396c guaA |
GMP synthase | 935 | 933 | coexpression:921 |
Rv2093c tatC exp |
Sec-independent protein translocase transmembrane protein TatC | 984 | 930 | coexpression:710 experimental:629 textmining:782 |
Rv1222 rseA |
anti-sigma E factor RseA | 804 | 804 ctx | neighborhood:659 |
Rv1337 exp |
integral membrane protein | 680 | 652 | experimental:467 |
Rv1221 sigE |
ECF RNA polymerase sigma factor SigE | 509 | 509 ctx | neighborhood:490 |
Rv3335c yhjD |
integral membrane protein | 509 | 490 ctx | cooccurence:415 |
Rv0110 exp |
integral membrane protein | 511 | 468 | experimental:467 |
Rv3221A rshA |
anti-sigma factor RshA | 454 | 455 | |
Rv2553c mltG |
membrane protein | 449 | 449 | coexpression:449 |
Rv0846c mmcO exp |
oxidase | 469 | 436 | experimental:415 |
Rv0799c hyp |
hypothetical protein | 822 | 435 | coexpression:403 textmining:698 |
Rv2122c hisE |
phosphoribosyl-ATP pyrophosphatase | 425 | 426 | |
Rv3607c folB |
dihydroneopterin aldolase | 425 | 425 | coexpression:423 |
Rv3013 hyp |
hypothetical protein | 422 | 422 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The exp badge marks an experimentally-supported partner (measured interaction, experimental/database channel ≥400) as opposed to a purely predicted one — but note that the M. tuberculosis experimental interactome is dominated by a noisy bacterial-two-hybrid screen, so a strong measured link that contradicts the operon/localisation context is likely a false positive. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: Sec-independent protein translocase protein TatB
- MTBC0 PGAP product: Sec-independent protein translocase protein TatB
- Pfam (hmmscan --cut_ga): TatA_B_E PF02416.22 (E=8e-14)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215740.1)
- Domains: Pfam-A via hmmscan --cut_ga — TatA_B_E (PF02416.22)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG1826 - Curated reference: UniProt P9WG99 (SwissProt, reviewed; Inferred from homology)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
48 functional partner(s); context anchor
htrA - Essentiality: genome-wide transposon mutagenesis in H37Rv — DeJesus et al. 2017 (mBio, doi:10.1128/mBio.02133-16, CC BY)
- Proteomics: integrated mass-spectrometry abundance from PaxDb 5.0 (Huang et al. 2023, doi:10.1016/j.mcpro.2023.100640), taxon 83332 — weighted average of 16 datasets, incl. Schubert et al. 2013 (doi:10.1016/j.chom.2013.04.008) and Albrethsen et al. 2013 (doi:10.1074/mcp.M112.018846)
- Functional category: TubercuList scheme (Cole et al. 1998, doi:10.1038/31159), via Mycobrowser (Kapopoulou et al. 2011, doi:10.1016/j.tube.2010.09.006)
- Orthologues: reciprocal best hits (DIAMOND, Buchfink et al. 2021, doi:10.1038/s41592-021-01101-x) against Mycobrowser release 5 reference proteomes
- Genomic context / operon: H37Rv annotation; operon predicted by co-directional intergenic distance (Salgado et al. 2000, doi:10.1073/pnas.030539397)
- Physico-chemical properties: ExPASy ProtParam method via Biopython (Gasteiger et al. 2005), computed from the MTBC0 sequence
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001312|Rv1224|tatB MFANIGWGEMLVLVMVGLVVLGPERLPGAIRWAASALRQARDYLSGVTSQLREDIGPEFDDLRGHLGELQKLRGMTPRAALTKHLLDGDDSLFTGDFDRPTPKKPDAAGSAGPDATEQIGAGPIPFDSDAT
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