Rv1944c Family assigned · medium auto-curated
H37Rv Rv1944c · MTBC0 mtbc0_002058 ·
196 aa · 2214460–2215050 (-) ·
RefSeq NP_216460.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | SEC-C domain-containing protein |
| Revised (this work) | SEC-C domain-containing protein. Pfam: SEC-C (PF02810.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95270
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | SEC-C motif |
| Orthologous group | COG3012 |
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 | 0.636 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.23% of strains (333) · 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 |
|---|---|---|---|---|
SEC-C | PF02810.22 | 3.3e-09 | 168–185 | SEC-C motif |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mazE5 (antitoxin MazE5), high confidence from genomic context alone (score 806 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) |
|---|---|---|---|---|
Rv1943c mazE5 |
antitoxin MazE5 | 807 | 806 ctx | neighborhood:801 |
Rv1942c mazF5 |
toxin MazF5 | 802 | 802 ctx | neighborhood:801 |
Rv0732 secY |
preprotein translocase SecY | 816 | 796 | experimental:788 |
Rv1440 secG |
protein-export membrane protein SecG | 812 | 792 | experimental:785 |
Rv0638 secE1 |
preprotein translocase SecE | 797 | 775 | experimental:775 |
Rv1629 polA |
DNA polymerase I | 751 | 659 | coexpression:639 |
Rv1945 hyp |
hypothetical protein | 608 | 591 ctx | neighborhood:588 |
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 672 | 566 | experimental:431 |
Rv0708 rplP |
50S ribosomal protein L16 | 518 | 517 | experimental:431 |
Rv0640 rplK |
50S ribosomal protein L11 | 509 | 508 | experimental:434 |
Rv0703 rplW |
50S ribosomal protein L23 | 524 | 506 | experimental:498 |
Rv0709 rpmC |
50S ribosomal protein L29 | 509 | 490 | experimental:484 |
Rv0979A rpmF |
50S ribosomal protein L32 | 486 | 487 | experimental:431 |
Rv0651 rplJ |
50S ribosomal protein L10 | 489 | 470 | experimental:431 |
Rv3443c rplM |
50S ribosomal protein L13 | 491 | 468 | experimental:431 |
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: SEC-C domain-containing protein
- Pfam (hmmscan --cut_ga): SEC-C PF02810.22 (E=3e-09)
- (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_216460.1)
- Domains: Pfam-A via hmmscan --cut_ga — SEC-C (PF02810.22)
- 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
COG3012 - Curated reference: UniProt P95270 (TrEMBL, unreviewed; 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 —
54 functional partner(s); context anchor
mazE5 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002058|Rv1944c| MISDTEDFAHGDKAAPPRLRASYAACGGDAAGCWTMSDNGASRVPPVDETPAAESAEPITAVSLAWLPAGDYERALDLWPDFAGSDLVTGPDGPVAHPLYCRRMQQKLVEFAEAGFPGLAVAAIRVAPFAAWCAEQGQEPDSPEARAEYAAYLTAHGDHDVMAWPPGRNQQCWCGSGHKYKKCCAAASFIDTEPAP