Rv1148c Family assigned · medium auto-curated
H37Rv Rv1148c · MTBC0 - ·
482 aa · 1276300–1277748 (-) ·
RefSeq NP_215664.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains DUF222 (PF02720.23), HNH (PF01844.30) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WM55
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1148c |
UniProt still lists this protein as Uncharacterized protein Rv1148c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| eggNOG description | Domain of unknown function (DUF222) |
| Orthologous group | COG1403 |
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 | 0.364 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 11 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 |
|---|---|---|---|---|
DUF222 | PF02720.23 | 5.9e-111 | 66–389 | Domain of unknown function (DUF222) |
HNH | PF01844.30 | 1.5e-04 | 392–432 | HNH endonuclease |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1150 (Possible transposase (fragment); Rv1150, (MTCI65.17), len: 183 aa. Possible fragment of transposase (pseudogene). Identical to C-terminal pa), medium confidence from genomic context alone (score 528 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) |
|---|---|---|---|---|
Rv1945 hyp |
hypothetical protein | 829 | 828 | coexpression:827 |
Rv0336 hyp |
hypothetical protein | 949 | 749 ctx | cooccurence:734 textmining:808 |
Rv0515 hyp |
hypothetical protein | 918 | 747 ctx | cooccurence:735 textmining:689 |
Rv3776 hyp |
hypothetical protein | 785 | 737 ctx | cooccurence:688 |
Rv0393 hyp |
hypothetical protein | 732 | 733 ctx | cooccurence:730 |
Rv2100 hyp |
hypothetical protein | 942 | 717 ctx | cooccurence:680 textmining:805 |
Rv2015c hyp |
hypothetical protein | 651 | 652 ctx | cooccurence:586 |
Rv1765c hyp |
hypothetical protein | 636 | 636 ctx | cooccurence:617 |
Rv1378c hyp |
hypothetical protein | 739 | 562 ctx | cooccurence:514 textmining:430 |
Rv3074 hyp |
hypothetical protein | 612 | 531 ctx | cooccurence:500 |
Rv1150 |
Possible transposase (fragment); Rv1150, (MTCI65.17), len: 183 aa. Possible fragment of transposase (pseudogene). Identical to C-terminal pa | 528 | 528 ctx | neighborhood:526 |
Rv1149 |
transposase | 528 | 527 ctx | neighborhood:526 |
Rv1303 hyp |
hypothetical protein | 492 | 492 ctx | cooccurence:492 |
Rv0756c hyp |
hypothetical protein | 487 | 487 ctx | cooccurence:480 |
Rv3843c |
transmembrane protein | 452 | 452 ctx | cooccurence:449 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): DUF222 PF02720.23 (E=6e-111), HNH PF01844.30 (E=1e-04)
- (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_215664.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF222 (PF02720.23), HNH (PF01844.30)
- 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
COG1403 - Curated reference: UniProt P9WM55 (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 —
27 functional partner(s); context anchor
Rv1150 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1148c| MSETFCLTDHSEPMTARFLSVVLRRIRGMRSDTREEISAALDAYHASLSRVLDLKCDALTTPELLACLQRLEVERRRQGAAEHALINQLAGQACEEELGGTLRTALANRLHITPGEASRRIAEAEDLGERRALTGEPLPAQLTATAAAQREGKIGREHIKEIQAFFKELSAAVDLGIREAAEAQLAELATSRRPDHLHGLATQLMDWLHPDGNFSDQERARKRGITMGKQEFDGMSRISGLLTPELRATIEAVLAKLAAPGACNPDDQTPLVDDTPDADAVRRDTRSQAQRNHDAFLAALRGLLASGELGQHKGLPVTIVVSTTLKELEAATGKGVTGGGSRVPMSDLIRMASHANHYLALFDGAKPLALYHTKRLASPAQRIMLYAKDRGCSRPGCDAPAYHSEVHHVTPWTTTHRTDINDLTLACGPDNRLVEKGWKTRKNAHGDTEWLPPPHLDHGQPRINRYHHPAKILCEQDDDEPH