Rv0907 Family assigned · medium auto-curated
H37Rv Rv0907 · MTBC0 - ·
532 aa · 1010136–1011734 (+) ·
RefSeq NP_215422.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Beta-lactamase (PF00144.30), DUF3471 (PF11954.14) 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 |
O05900
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 |
V Defense mechanisms
|
|---|---|
| eggNOG description | beta-lactamase |
| Orthologous group | COG1680 |
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 | 2.385 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 98.93% of strains (143662) · reference-fixed |
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 |
|---|---|---|---|---|
Beta-lactamase | PF00144.30 | 1.4e-61 | 63–402 | Beta-lactamase |
DUF3471 | PF11954.14 | 5.7e-14 | 439–512 | Domain of unknown function (DUF3471) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ctpE (metal cation transporter ATPase E), high confidence from genomic context alone (score 903 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) |
|---|---|---|---|---|
Rv0908 ctpE |
metal cation transporter ATPase E | 939 | 903 ctx | neighborhood:881 |
Rv0399c lpqK |
lipoprotein LpqK | 738 | 739 ctx | cooccurence:736 |
Rv0906 hyp |
hypothetical protein | 636 | 637 ctx | neighborhood:620 |
Rv0905 echA6 |
enoyl-CoA hydratase EchA6 | 601 | 601 ctx | neighborhood:589 |
Rv0909 |
antitoxin | 546 | 546 ctx | neighborhood:544 |
Rv0904c accD3 |
acetyl-CoAcarboxylase carboxyl transferase subunit beta | 588 | 446 ctx | neighborhood:444 |
Rv0180c |
transmembrane protein | 422 | 422 ctx | cooccurence:413 |
Rv1367c hyp |
hypothetical protein | 782 | 349 | textmining:679 |
Rv1922 |
lipoprotein | 470 | 292 | |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 476 | 80 | textmining:454 |
Rv0050 ponA1 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 531 | 78 | textmining:513 |
Rv3626c hyp |
hypothetical protein | 807 | 64 | textmining:803 |
Rv1178 dapC |
aminotransferase | 659 | 61 | textmining:652 |
Rv1845c blaR |
sensor-transducer protein BlaR | 658 | 60 | textmining:652 |
Rv0016c pbpA |
penicillin-binding protein PbpA | 465 | 58 | textmining:456 |
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): Beta-lactamase PF00144.30 (E=1e-61), DUF3471 PF11954.14 (E=6e-14)
- (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_215422.1)
- Domains: Pfam-A via hmmscan --cut_ga — Beta-lactamase (PF00144.30), DUF3471 (PF11954.14)
- 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
COG1680 - Curated reference: UniProt O05900 (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 —
25 functional partner(s); context anchor
ctpE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0907| MATICGHDQTSGNGRHGDVADVNGCGSTHQALGPPSGLPDASPNERSAIQIPAGRIDDAVAKVDGLVGELMQNTGIPGMAVAIVHGGKTLYAKGFGVRDVGKGGGPDNKVDADTVFQLASVSKSVGATVVAHAVTDNVVTWDTPVVSKLPWFALRDPYVTGQVTIADLYSHRSGLPDHAGDLLEDLGYDRRQVLQRLKYLPLAPFRISYAYTNFGVTAAAEAVAAAAGQSWEDLSDEVLYRPLGMGSTSSRFTDFLARPNHAVNHVKVADRWEARYQRDPDAQSPAGGVSSSLNDMTHWLAMVLADGVYNGRRITSPEALLPVYTPQVISRHPVSPRARASFYGYGFNVGVTSSGRTEYSHSGAFGLGAAANFVVLPSEDLAIIALTNAGPIGVPETLTAEFMDLVQYGQVREDWAALYKKAFAPLNELAGSLVGKQSPANPAPSRPLNDYVGVYANDYWGPATVTYHDGQLRLSLGPKNQTFDLTHWDGDTFTFTLSTENALPGSISKATFAGDTLNLEYYDADKLGTFTR