Rv2148c Family assigned · medium auto-curated
H37Rv Rv2148c · MTBC0 mtbc0_002284 ·
258 aa · 2434219–2434995 (-) ·
RefSeq NP_216664.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | YggS family pyridoxal phosphate-dependent enzyme |
| Revised (this work) | YggS family pyridoxal phosphate-dependent enzyme. Pfam: Ala_racemase_N (PF01168.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFQ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Pyridoxal phosphate homeostasis protein |
| Curated function | Pyridoxal 5'-phosphate (PLP)-binding protein, which is involved in PLP homeostasis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Pyridoxal 5'-phosphate (PLP)-binding protein, which is involved in PLP homeostasis |
| Orthologous group | COG0325 |
| KEGG orthology |
K06997
|
| Gene Ontology (17) |
GO:0003674, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0008144, GO:0019842, GO:0030170, GO:0036094, GO:0043167, GO:0043168, GO:0044464 +5 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) pseudogene candidate
| pN/pS | 0.238 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 21.21% of strains (30805) · 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 |
|---|---|---|---|---|
Ala_racemase_N | PF01168.27 | 2.3e-09 | 20–252 | Alanine racemase, N-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sepF (cell division protein SepF), high confidence from genomic context alone (score 965 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) |
|---|---|---|---|---|
Rv2147c sepF |
cell division protein SepF | 969 | 965 ctx | neighborhood:831 coexpression:800 |
Rv2149c yfiH |
laccase domain-containing protein | 978 | 960 ctx | neighborhood:882 coexpression:672 textmining:496 |
Rv2150c ftsZ |
cell division protein FtsZ | 901 | 892 ctx | neighborhood:879 |
Rv2157c murF |
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | 793 | 793 ctx | neighborhood:597 coexpression:508 |
Rv2146c |
transmembrane protein | 812 | 782 ctx | neighborhood:571 coexpression:513 |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 772 | 772 ctx | neighborhood:713 |
Rv2145c wag31 |
cell wall synthesis protein Wag31 | 745 | 729 ctx | neighborhood:423 coexpression:549 |
Rv2153c murG |
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol-N-acetylglucosamine transferase | 724 | 706 ctx | neighborhood:678 |
Rv2151c ftsQ |
cell division protein FtsQ | 704 | 687 ctx | neighborhood:677 |
Rv2158c murE |
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase | 645 | 646 ctx | neighborhood:597 |
Rv2154c ftsW |
lipid II flippase FtsW | 651 | 630 ctx | neighborhood:608 |
Rv2156c murX |
phospho-N-acetylmuramoyl-pentappeptidetransferase | 653 | 600 ctx | neighborhood:597 |
Rv2155c murD |
UDP-N-acetylmuramoylalanine--D-glutamate ligase | 621 | 588 ctx | neighborhood:559 |
Rv2927c sepIVA hyp |
hypothetical protein | 597 | 572 | coexpression:547 |
Rv1712 cmk |
cytidylate kinase | 548 | 548 | coexpression:448 |
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: YggS family pyridoxal phosphate-dependent enzyme
- Pfam (hmmscan --cut_ga): Ala_racemase_N PF01168.27 (E=2e-09)
- (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_216664.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ala_racemase_N (PF01168.27)
- 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
COG0325 - Curated reference: UniProt P9WFQ7 (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 —
29 functional partner(s); context anchor
sepF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002284|Rv2148c| MAADLSAYPDRESELTHALAAMRSRLAAAAEAAGRNVGEIELLPITKFFPATDVAILFRLGCRSVGESREQEASAKMAELNRLLAAAELGHSGGVHWHMVGRIQRNKAGSLARWAHTAHSVDSSRLVTALDRAVVAALAEHRRGERLRVYVQVSLDGDGSRGGVDSTTPGAVDRICAQVQESEGLELVGLMGIPPLDWDPDEAFDRLQSEHNRVRAMFPHAIGLSAGMSNDLEVAVKHGSTCVRVGTALLGPRRLRSP