Rv2345 Family assigned · medium auto-curated
H37Rv Rv2345 · MTBC0 mtbc0_002497 ·
660 aa · 2648571–2650553 (+) ·
RefSeq NP_216861.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | TPM domain-containing protein |
| Revised (this work) | TPM domain-containing protein. Pfam: TPM_phosphatase (PF04536.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFJ5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UPF0603 protein Rv2345 |
| Curated function | May play a role in septum formation. |
UniProt still lists this protein as UPF0603 protein Rv2345; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | TPM domain |
| Orthologous group | COG1512 |
| Gene Ontology (14) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0005887, GO:0016020, GO:0016021, GO:0030312, GO:0031224, GO:0031226, GO:0044425, GO:0044459 +2 more
|
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 | 0.562 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 9 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 |
|---|---|---|---|---|
TPM_phosphatase | PF04536.21 | 8.2e-20 | 36–153 | TPM domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dgt (deoxyguanosine triphosphate triphosphohydrolase), high confidence from genomic context alone (score 787 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 787 | 788 | experimental:783 |
Rv2344c dgt |
deoxyguanosine triphosphate triphosphohydrolase | 787 | 787 ctx | neighborhood:785 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 786 | 787 | experimental:783 |
Rv2200c ctaC |
cytochrome C oxidase subunit II | 785 | 785 | experimental:783 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 770 | 771 | experimental:747 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 750 | 751 | experimental:747 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 750 | 750 | experimental:747 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 749 | 749 | experimental:747 |
Rv2343c dnaG |
DNA primase | 676 | 676 ctx | neighborhood:673 |
Rv2876 |
transmembrane protein | 590 | 591 | experimental:484 |
Rv3244c lpqB |
lipoprotein LpqB | 580 | 581 ctx | cooccurence:577 |
Rv3584 lpqE |
lipoprotein LpqE | 552 | 552 | experimental:431 |
Rv3517 hyp |
hypothetical protein | 524 | 524 ctx | cooccurence:524 |
Rv1482c hyp |
hypothetical protein | 511 | 512 ctx | cooccurence:511 |
Rv2468A hyp |
hypothetical protein | 502 | 502 | experimental:484 |
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: transmembrane protein
- MTBC0 PGAP product: TPM domain-containing protein
- Pfam (hmmscan --cut_ga): TPM_phosphatase PF04536.21 (E=8e-20)
- (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_216861.1)
- Domains: Pfam-A via hmmscan --cut_ga — TPM_phosphatase (PF04536.21)
- 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
COG1512 - Curated reference: UniProt P9WFJ5 (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 —
36 functional partner(s); context anchor
dgt - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002497|Rv2345| MRLVRLLGMVLTILAAGLLLGPPAGAQPPFRLSNYVTDNAGVLTSSGRTAVTAAVDRLYADRRIRLWVVYVENFSGQSALNWAQRTTRTSELGNYDALLAVATTGREYAFLVPSAMPGVSEGQVDNVRRYQIEPALHDGDYSGAAVAAANGLNRSPSSSSRVVLLVTVGIIVIVVAVLLVVMRHRNRRRRADELAAARRVDPTNVMALAAVPLQALDDLSRSMVVDVDNAVRTSTNELALAIEEFGERRTAPFTQAVNNAKAALSQAFTVRQQLDDNTPETPAQRRELLTRVIVSAAHADRELASQTEAFEKLRDLVINAPARLDLLTQQYVELTTRIGPTQQRLAELHTEFDAAAMTSIAGNVTTATERLAFADRNISAARDLADQAVSGRQAGLVDAVRAAESALGQARALLDAVDSAATDIRHAVASLPAVVADIQTGIKRANQHLQQAQQPQTGRTGDLIAARDAAARALDRARGAADPLTAFDQLTKVDADLDRLLATLAEEQATADRLNRSLEQALFTAESRVRAVSEYIDTRRGSIGPEARTRLAEAKRQLEAAHDRKSSNPTEAIAYANAASTLAAHAQSLANADVQSAQRAYTRRGGNNAGAILGGIIIGDLLSGGTRGGLGGWIPTSFGGSSNAPGSSPDGGFLGGGGRF