Rv2136c Resolved · high auto-curated
H37Rv Rv2136c · MTBC0 mtbc0_002269 ·
276 aa · 2423271–2424101 (-) ·
RefSeq NP_216652.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | undecaprenyl-diphosphatase |
|---|---|
| MTBC0 PGAP re-annotation | undecaprenyl-diphosphate phosphatase |
| Revised (this work) | Undecaprenyl-diphosphate phosphatase. Pfam: BacA (PF02673.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFF9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Undecaprenyl-diphosphatase |
| EC (curated) |
EC 3.6.1.27
|
| Curated function | Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| Preferred name | uppP |
| eggNOG description | Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin |
| Orthologous group | COG1968 |
| EC number |
EC 3.6.1.27
|
| KEGG orthology |
K06153
|
| KEGG pathways |
map00550
|
| Gene Ontology (4) |
GO:0006950, GO:0008150, GO:0050896, GO:0051409
|
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 | 0.621 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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 |
|---|---|---|---|---|
BacA | PF02673.25 | 1.4e-79 | 7–262 | Bacitracin resistance protein BacA |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cysQ (3'(2'),5'-bisphosphate nucleotidase CysQ), medium confidence from genomic context alone (score 561 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2156c murX |
phospho-N-acetylmuramoyl-pentappeptidetransferase | 926 | 919 | database:900 |
Rv2135c hyp |
hypothetical protein | 958 | 912 ctx | neighborhood:882 textmining:549 |
Rv2134c hyp |
hypothetical protein | 806 | 807 ctx | neighborhood:800 |
Rv2137c hyp |
hypothetical protein | 841 | 801 ctx | neighborhood:800 |
Rv2133c hyp |
hypothetical protein | 801 | 801 ctx | neighborhood:798 |
Rv2131c cysQ |
3'(2'),5'-bisphosphate nucleotidase CysQ | 560 | 561 ctx | neighborhood:544 |
Rv1302 rfe |
decaprenyl-phosphate N-acetylglucosaminephosphotransferase | 598 | 556 | database:500 |
Rv3859c gltB |
glutamate synthase large subunit | 546 | 547 ctx | neighborhood:544 |
Rv2130c mshC |
cysteine:1D-myo-inosityl 2-amino-2-deoxy--D-glucopyranoside ligase | 525 | 526 ctx | neighborhood:519 |
Rv2138 lppL |
lipoprotein LppL | 509 | 510 ctx | neighborhood:505 |
Rv2361c uppS |
decaprenyl diphosphate synthase | 565 | 506 | database:500 |
Rv2139 pyrD |
dihydroorotate dehydrogenase | 424 | 423 ctx | neighborhood:407 |
Rv2124c metH |
methionine synthase | 430 | 402 | |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 578 | 311 | textmining:413 |
Rv2157c murF |
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | 445 | 216 |
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: undecaprenyl-diphosphatase
- MTBC0 PGAP product: undecaprenyl-diphosphate phosphatase
- Pfam (hmmscan --cut_ga): BacA PF02673.25 (E=1e-79)
- (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_216652.1)
- Domains: Pfam-A via hmmscan --cut_ga — BacA (PF02673.25)
- 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
COG1968 - Curated reference: UniProt P9WFF9 (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
cysQ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002269|Rv2136c| MSWWQVIVLAAAQGLTEFLPVSSSGHLAIVSRIFFSGDAGASFTAVSQLGTEAAVVIYFARDIVRILSAWLHGLVVKAHRNTDYRLGWYVIIGTIPICILGLFFKDDIRSGVRNLWVVVTALVVFSGVIALAEYVGRQSRHIERLTWRDAVVVGIAQTLALVPGVSRSGSTISAGLFLGLDRELAARFGFLLAIPAVFASGLFSLPDAFHPVTEGMSATGPQLLVATLIAFVLGLTAVAWLLRFLVRHNMYWFVGYRVLVGTGMLVLLATGTVAAT