Rv2813 Family assigned · medium auto-curated
H37Rv Rv2813 · MTBC0 mtbc0_002993 ·
270 aa · 3140649–3141461 (+) ·
RefSeq NP_217329.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | ExeA family protein |
| Revised (this work) | ExeA family protein. Pfam: AAA_22 (PF13401.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XFD1
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | ORC1/DEAH AAA+ ATPase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| eggNOG description | SMART AAA ATPase |
| Orthologous group | COG3267 |
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 | 0.526 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.27% of strains (389) · clonal |
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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
AAA_22 | PF13401.13 | 1.1e-20 | 44–173 | AAA domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2812 (transposase), high confidence from genomic context alone (score 977 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2812 |
transposase | 977 | 977 ctx | neighborhood:882 cooccurence:643 |
Rv3638 |
transposase | 774 | 775 | coexpression:772 |
Rv2811 hyp |
hypothetical protein | 624 | 624 ctx | neighborhood:620 |
Rv2810c |
Probable transposase; Rv2810c, (MTCY16B7.33), len: 133 aa. Probable transposase for IS1555, similar to C-terminal domain of transposases for | 588 | 588 ctx | neighborhood:451 |
Rv3859c gltB |
glutamate synthase large subunit | 546 | 546 ctx | neighborhood:544 |
Rv1755c plcD |
Rv1755c, (MT1799, MTCY28.21c), len: 280 aa. Probable plcD, phospholipase C 4 (fragment) (see citations below),highly similar to C-terminus o | 536 | 93 | textmining:510 |
Rv3327 |
transposase fusion protein | 811 | 90 | textmining:801 |
Rv0197 |
oxidoreductase | 812 | 87 | textmining:803 |
Rv0796 |
Putative transposase for insertion sequence element IS6110; Involved in the transposition of the insertion sequence. | 641 | 79 | textmining:627 |
Rv2814c |
Probable transposase; Rv2814c, (MTCY16B7.29), len: 328 aa. Probable transposase subunit for IS6110. Identical to many other M. tuberculosis | 874 | 77 | textmining:870 |
Rv3212 hyp |
hypothetical protein | 815 | 76 | textmining:809 |
Rv2820c csm4 |
CRISPR type III-associated RAMP protein Csm4 | 527 | 71 | textmining:512 |
Rv1777 cyp144 |
cytochrome P450 Cyp144 | 428 | 71 | textmining:410 |
Rv0578c PE_PGRS7 |
PE-PGRS family protein PE_PGRS7 | 805 | 59 | textmining:802 |
Rv0279c PE_PGRS4 |
PE-PGRS family protein PE_PGRS4 | 520 | 59 | textmining:511 |
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 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: hypothetical protein
- MTBC0 PGAP product: ExeA family protein
- Pfam (hmmscan --cut_ga): AAA_22 PF13401.13 (E=1e-20)
- (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_217329.1)
- Domains: Pfam-A via hmmscan --cut_ga — AAA_22 (PF13401.13)
- 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
COG3267 - Curated reference: UniProt I6XFD1 (TrEMBL, unreviewed; Predicted)
- 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 —
23 functional partner(s); context anchor
Rv2812 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002993|Rv2813| MMHKLISYYGFSRMPFGRDLAPGMLHRHSAHNEAVARIGWCIADRRIGVITGEVGAGKTVAVRAALASLDRSRHTVIYLPDPTVGVQGIHHRIVASLGGQPLTHHATLAPQAADALAAEQAERGRTPVVVVEEAHLLGYDQLEALRLLTNHDLDSSSPFACLLIGQPTLRRRMKLGVLAALDQRIGLRYAMPPMTDTNTGSYLRHHLKLAGRDDALFSDDAIGLIHQTSRGYPRAVNNLALQALVAAFAADKAIVDESTTRTAIAEVTAD