Rv2603c Family assigned · medium auto-curated
H37Rv Rv2603c · MTBC0 mtbc0_002771 ·
251 aa · 2954358–2955113 (-) ·
RefSeq NP_217119.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | YebC/PmpR family DNA-binding transcriptional regulator |
| Revised (this work) | YebC/PmpR family DNA-binding transcriptional regulator. Pfam: TACO1_YebC_N (PF20772.3), Transcrip_reg (PF01709.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGA5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein Rv2603c |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | yebC |
| eggNOG description | transcriptional regulatory protein |
| Orthologous group | COG0217 |
| Gene Ontology (8) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0044424, GO:0044444, GO:0044464
|
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 | 0.951 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
TACO1_YebC_N | PF20772.3 | 1.3e-29 | 5–76 | TACO1/YebC protein N-terminal domain |
Transcrip_reg | PF01709.27 | 8.3e-57 | 84–238 | TACO1/YebC second and third domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tesB2 (acyl-CoA thioesterase II), high confidence from genomic context alone (score 771 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2605c tesB2 |
acyl-CoA thioesterase II | 771 | 771 ctx | neighborhood:757 |
Rv2604c snoP |
glutamine amidotransferase SnoP | 854 | 760 ctx | neighborhood:757 textmining:418 |
Rv2606c snzP |
pyridoxine biosynthesis protein | 846 | 747 ctx | neighborhood:735 textmining:418 |
Rv1630 rpsA |
30S ribosomal protein S1 | 668 | 648 | coexpression:429 |
Rv2904c rplS |
50S ribosomal protein L19 | 641 | 642 | coexpression:459 |
Rv3443c rplM |
50S ribosomal protein L13 | 590 | 590 | coexpression:437 |
Rv2534c efp |
elongation factor P | 568 | 569 | coexpression:423 |
Rv2572c aspS |
aspartate--tRNA ligase | 625 | 566 | coexpression:453 |
Rv2890c rpsB |
30S ribosomal protein S2 | 543 | 544 | coexpression:450 |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 526 | 526 | experimental:410 |
Rv1299 prfA |
peptide chain release factor PrfA | 566 | 525 | |
Rv1307 atpH |
ATP synthase subunit b/delta | 540 | 524 | coexpression:455 |
Rv2462c tig |
trigger factor | 539 | 518 | coexpression:479 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 515 | 515 | |
Rv3456c rplQ |
50S ribosomal protein L17 | 509 | 509 | coexpression:412 |
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: transcriptional regulator
- MTBC0 PGAP product: YebC/PmpR family DNA-binding transcriptional regulator
- Pfam (hmmscan --cut_ga): TACO1_YebC_N PF20772.3 (E=1e-29), Transcrip_reg PF01709.27 (E=8e-57)
- (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_217119.1)
- Domains: Pfam-A via hmmscan --cut_ga — TACO1_YebC_N (PF20772.3), Transcrip_reg (PF01709.27)
- 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
COG0217 - Curated reference: UniProt P9WGA5 (SwissProt, reviewed; Evidence at protein level)
- 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 —
50 functional partner(s); context anchor
tesB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002771|Rv2603c| MSGHSKWATTKHKKAVVDARRGKMFARLIKNIEVAARVGGGDPAGNPTLYDAIQKAKKSSVPNENIERARKRGAGEEAGGADWQTIMYEGYAPNGVAVLIECLTDNRNRAASEVRVAMTRNGGTMADPGSVSYLFSRKGVVTLEKNGLTEDDVLAAVLEAGAEDVNDLGDSFEVISEPAELVAVRSALQDAGIDYESAEASFQPSVSVPVDLDGARKVFKLVDALEDSDDVQNVWTNVDVSDEVLAALDDE