Rv0862c Family assigned · medium auto-curated
H37Rv Rv0862c · MTBC0 mtbc0_000917 ·
756 aa · 963545–965815 (-) ·
RefSeq NP_215377.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | helicase-associated domain-containing protein |
| Revised (this work) | Helicase-associated domain-containing protein. Pfam: Helicase_C_3 (PF13625.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53874
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 |
K Transcription
|
|---|---|
| eggNOG description | Helicase conserved C-terminal domain |
| Orthologous group | COG2378 |
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 | 0.736 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 15 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 |
|---|---|---|---|---|
Helicase_C_3 | PF13625.12 | 5.5e-41 | 479–601 | Helicase conserved C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ercc3 (DNA helicase Ercc3), high confidence from genomic context alone (score 932 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) |
|---|---|---|---|---|
Rv0861c ercc3 |
DNA helicase Ercc3 | 931 | 932 ctx | neighborhood:738 cooccurence:743 |
Rv0866 moaE2 |
molybdopterin synthase catalytic subunit 2 | 792 | 792 ctx | neighborhood:789 |
Rv0863 hyp |
hypothetical protein | 792 | 792 ctx | neighborhood:792 |
Rv0865 mog |
molybdopterin biosynthesis protein | 790 | 790 ctx | neighborhood:789 |
Rv0864 moaC2 |
cyclic pyranopterin monophosphate synthase accessory protein | 601 | 600 ctx | neighborhood:599 |
Rv3669 |
transmembrane protein | 596 | 596 ctx | cooccurence:596 |
Rv3268 hyp |
hypothetical protein | 570 | 571 ctx | cooccurence:566 |
Rv1486c hyp |
hypothetical protein | 532 | 533 ctx | cooccurence:530 |
Rv1234 |
transmembrane protein | 524 | 524 ctx | cooccurence:504 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 522 | 523 | experimental:431 |
Rv3015c hyp |
hypothetical protein | 518 | 519 ctx | cooccurence:516 |
Rv2175c |
DNA-binding protein | 512 | 512 ctx | cooccurence:509 |
Rv1312 hyp |
hypothetical protein | 497 | 497 ctx | cooccurence:497 |
Rv3196 hyp |
hypothetical protein | 482 | 482 ctx | cooccurence:473 |
Rv2712c hyp |
hypothetical protein | 464 | 465 ctx | cooccurence:464 |
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: helicase-associated domain-containing protein
- Pfam (hmmscan --cut_ga): Helicase_C_3 PF13625.12 (E=6e-41)
- (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_215377.1)
- Domains: Pfam-A via hmmscan --cut_ga — Helicase_C_3 (PF13625.12)
- 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
COG2378 - Curated reference: UniProt O53874 (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 —
38 functional partner(s); context anchor
ercc3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000917|Rv0862c| MTEHTPDIPLGSWLAALPDERLTQLLELRPDLAQPPPGSIAALAARAQARQSVKAATDELDFLRLAVFDALLVLQADTAPVPIVRLLAVIGDRAAQADVLGALADLKQRALAWGETAVRVATDAGTALPWHPGQVTLEGSSRSGDQLADLIAGLDPAQRDVLDKLLQGSPVGRTRDAAPGAPSDRPVPRLLAMGLLRRIDAETVILPRHVGQVLRGEQPGPMELTAPDPVVSTTTPDDADAAAAGAVIDLLREVDVLLENLGATPVAELRSGGLGVREFKRLAKATGIDEPRLGLILEIAAAAGLIASGMPDPEPPHSDGPFWAPTVAADRFATMSPAERWHLLASAWLDLPGRPALIGTRGPDAKPYGALSDSLFSTAAPLDRRLLLGMLAELPAGAGVDASRASATLIWRRPRWARRLQPAPIADLLTEGHALGLVGRGAISTPARALLDEALEPATAPAAAVGVMARALPKPIDHFLVQADLTVVVPGPLQRELADDLTTVATVESAGTAMVYRVSEQSIRHALDVGKSRDWLQEFFANRSKTPVPQGLTYLIDDVARRHGQLRIGMAASFVRCEDPTLLAQVVAAPEADGLALRALAPTVAVSPAPISEVLVTLRGAGFAPAAEDSTGAVVDVRTRGARVPTPQRRRPYRPPPRPNSEALKAVVAVLREVTAAPFANVRVDPAVTMSLLQRAAKDQATLVISYLDAAGVATQRVVAPITLRGGQLVAFDSSSGRLRDFAIHRITSVVSAHDR