Rv2135c Family assigned · medium auto-curated
H37Rv Rv2135c · MTBC0 mtbc0_002268 ·
236 aa · 2422564–2423274 (-) ·
RefSeq NP_216651.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| 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 |
O06240
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 |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Phosphoglycerate mutase |
| Orthologous group | COG0406 |
| EC number |
EC 5.4.2.11
|
| KEGG orthology |
K01834
|
| KEGG pathways |
map00010, map00260, map00680, map01100, map01110, map01120, map01130, map01200, map01230, map04922, map05230
|
| KEGG modules |
M00001, M00002, M00003
|
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 | 0.722 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 |
|---|---|---|---|---|
His_Phos_1 | PF00300.28 | 1.6e-43 | 3–198 | Histidine phosphatase superfamily (branch 1) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: uppP (undecaprenyl-diphosphatase), high confidence from genomic context alone (score 912 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) |
|---|---|---|---|---|
Rv2133c hyp |
hypothetical protein | 950 | 951 ctx | neighborhood:798 cooccurence:760 |
Rv2134c hyp |
hypothetical protein | 933 | 934 ctx | neighborhood:800 cooccurence:677 |
Rv2136c uppP |
undecaprenyl-diphosphatase | 958 | 912 ctx | neighborhood:882 textmining:549 |
Rv2137c hyp |
hypothetical protein | 800 | 801 ctx | neighborhood:800 |
Rv2130c mshC |
cysteine:1D-myo-inosityl 2-amino-2-deoxy--D-glucopyranoside ligase | 675 | 676 ctx | neighborhood:544 |
Rv2419c gpgP |
glucosyl-3-phosphoglycerate phosphatase | 944 | 592 ctx | cooccurence:591 textmining:870 |
Rv2131c cysQ |
3'(2'),5'-bisphosphate nucleotidase CysQ | 573 | 549 ctx | neighborhood:544 |
Rv0254c cobU |
bifunctional cobinamide kinase/cobinamide phosphate guanylyltransferase | 571 | 546 ctx | cooccurence:419 |
Rv1695 ppnK |
inorganic polyphosphate/ATP-NAD kinase | 546 | 546 | database:500 |
Rv2066 cobIJ |
bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase | 543 | 523 | coexpression:462 |
Rv2138 lppL |
lipoprotein LppL | 520 | 520 ctx | neighborhood:513 |
Rv3199c nudC |
NADH pyrophosphatase | 511 | 512 | database:500 |
Rv2208 cobS |
adenosylcobinamide-GDP ribazoletransferase | 536 | 508 | |
Rv0255c cobQ1 |
cobyric acid synthase | 523 | 501 | coexpression:415 |
Rv3214 gpm2 |
phosphoglycerate mutase | 926 | 457 ctx | cooccurence:452 textmining:870 |
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: histidine phosphatase family protein
- Pfam (hmmscan --cut_ga): His_Phos_1 PF00300.28 (E=2e-43)
- (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_216651.1)
- 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 O06240 (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 —
30 functional partner(s); context anchor
uppP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002268|Rv2135c| MTVILLRHARSTSNTAGVLAGRSGVDLDEKGREQATGLIDRIGDLPIRAVASSPMLRCQRTVEPLAEALCLEPLIDDRFSEVDYGEWTGRKIGDLVDEPLWRVVQAHPSAAVFPGGEGLAQVQTRAVAAVREHDRRLADQHGHDVLWLACTHGDVIKAVIADAFGMHLDSFQRITADPGSVSVVRYTQLRPFVLHVNHTGARLAPALQAAASAQGASPEPNAAVPPGDAVIGGSTD