Rv3837c Family assigned · medium auto-curated
H37Rv Rv3837c · MTBC0 mtbc0_004067 ·
232 aa · 4335120–4335818 (-) ·
RefSeq NP_218354.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphoglycerate mutase |
|---|---|
| MTBC0 PGAP re-annotation | histidine phosphatase family protein |
| Revised (this work) | Histidine phosphatase family protein. Pfam: His_Phos_1 (PF00300.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96241
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable phosphoglycerate mutase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | pgmB |
| eggNOG description | Belongs to the phosphoglycerate mutase family |
| Orthologous group | COG0406 |
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 | 0.34 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (380) · 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 |
|---|---|---|---|---|
His_Phos_1 | PF00300.28 | 1.1e-33 | 5–202 | Histidine phosphatase superfamily (branch 1) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pheA (prephenate dehydratase), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3838c pheA |
prephenate dehydratase | 884 | 884 ctx | neighborhood:882 |
Rv0563 htpX |
protease HtpX | 811 | 812 | coexpression:806 |
Rv3839 hyp |
hypothetical protein | 783 | 782 ctx | neighborhood:781 |
Rv0983 pepD |
serine protease PepD | 760 | 761 | coexpression:757 |
Rv3840 |
transcriptional regulator | 538 | 538 ctx | neighborhood:532 |
Rv2066 cobIJ |
bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase | 540 | 520 | coexpression:459 |
Rv1437 pgk |
phosphoglycerate kinase | 639 | 512 | database:500 |
Rv1023 eno |
enolase | 749 | 504 | database:500 textmining:515 |
Rv2743c hyp |
hypothetical protein | 470 | 471 | |
Rv2373c dnaJ2 |
chaperone protein DnaJ | 459 | 460 | |
Rv2609c |
membrane protein | 437 | 438 | |
Rv0255c cobQ1 |
cobyric acid synthase | 456 | 431 | coexpression:412 |
Rv2869c rip |
zinc metalloprotease | 416 | 416 | |
Rv1747 |
ABC transporter ATP-binding protein/permease | 409 | 410 | |
Rv3214 gpm2 |
phosphoglycerate mutase | 693 | 361 | textmining:540 |
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: phosphoglycerate mutase
- MTBC0 PGAP product: histidine phosphatase family protein
- Pfam (hmmscan --cut_ga): His_Phos_1 PF00300.28 (E=1e-33)
- (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_218354.1)
- Domains: Pfam-A via hmmscan --cut_ga — His_Phos_1 (PF00300.28)
- 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
COG0406 - Curated reference: UniProt P96241 (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 —
27 functional partner(s); context anchor
pheA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004067|Rv3837c| MSGRLVLLRHGQSYGNVERRLDTLPPGTALTPLGRDQARAFARSGCRRPALLAHSVAIRAYQTAAVVAAELDMVAHEVAGIHEVQVGELENRNDDEAVAEFNATYSRWHRGELDVPLPGGETANDVLDRYLPVLADLRMRYLDDGDWDGDIVVVSHSAAIRLAAAVLAGVDGNFVLDNHLENVESVVLAPITDGRWSCVQWGLRKPPFCPDPAEAAASPVTHAVTSSTDPMG