serB1 Resolved · high auto-curated
H37Rv Rv0505c · MTBC0 - ·
373 aa · 595464–596585 (-) ·
RefSeq YP_177732.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphoserine phosphatase SerB |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Phosphoserine phosphatase SerB. Pfam: Hydrolase (PF00702.33), HAD (PF12710.14), Hydrolase_3 (PF08282.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WGJ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphoserine phosphatase SerB1 |
| EC (curated) |
EC 3.1.3.3
|
| Curated function | Likely catalyzes the dephosphorylation of O-phospho-L-serine into L-serine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | serB1 |
| eggNOG description | Hydrolase |
| Orthologous group | COG0560 |
| Gene Ontology (12) |
GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0016020, GO:0016021, GO:0031224, GO:0031226, GO:0044425, GO:0044459, GO:0044464, GO:0071944
|
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 | 0.289 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (176) · 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 |
|---|---|---|---|---|
Hydrolase | PF00702.33 | 1.1e-15 | 123–313 | haloacid dehalogenase-like hydrolase |
HAD | PF12710.14 | 4.6e-28 | 124–310 | haloacid dehalogenase-like hydrolase |
Hydrolase_3 | PF08282.19 | 1.5e-05 | 276–319 | haloacid dehalogenase-like hydrolase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cmaA2 (cyclopropane mycolic acid synthase), high confidence from genomic context alone (score 732 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0508 hyp |
hypothetical protein | 803 | 804 ctx | neighborhood:766 |
Rv0504c hyp |
hypothetical protein | 754 | 754 ctx | neighborhood:747 |
Rv0503c cmaA2 |
cyclopropane mycolic acid synthase | 732 | 732 ctx | neighborhood:731 |
Rv0884c serC |
phosphoserine aminotransferase | 889 | 726 | database:500 textmining:611 |
Rv1605 hisF |
imidazole glycerol phosphate synthase subunit HisF | 609 | 584 | coexpression:570 |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 607 | 584 | database:500 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 606 | 583 | database:500 |
Rv0509 hemA |
glutamyl-tRNA reductase | 534 | 534 ctx | neighborhood:531 |
Rv0510 hemC |
porphobilinogen deaminase | 531 | 531 ctx | neighborhood:527 |
Rv2335 cysE |
serine acetyltransferase | 555 | 520 | database:500 |
Rv1602 hisH |
imidazole glycerol phosphate synthase subunit HisH | 537 | 517 | coexpression:501 |
Rv0507 mmpL2 |
transmembrane transport protein MmpL2 | 515 | 516 ctx | neighborhood:511 |
Rv0506 mmpS2 |
membrane protein MmpS2 | 513 | 514 ctx | neighborhood:511 |
Rv1603 hisA |
1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | 528 | 506 | coexpression:489 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 505 | 506 ctx | neighborhood:489 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): phosphoserine phosphatase SerB
- Pfam (hmmscan --cut_ga): Hydrolase PF00702.33 (E=1e-15), HAD PF12710.14 (E=5e-28), Hydrolase_3 PF08282.19 (E=2e-05)
- (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 YP_177732.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydrolase (PF00702.33), HAD (PF12710.14), Hydrolase_3 (PF08282.19)
- 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
COG0560 - Curated reference: UniProt P9WGJ3 (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 —
41 functional partner(s); context anchor
cmaA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0505c|serB1 MGLTCWPRTAAGRVHDESRCGLANFDTALGLQINPRQPRAPPRICRIGLITAAASATGQAPRLGVMMVSSHLGSPDQAGHVDLASPADPPPPDASASHSPVDMPAPVAAAGSDRQPPIDLTAAAFFDVDNTLVQGSSAVHFGRGLAARHYFTYRDVLGFLYAQAKFQLLGKENSNDVAAGRRKALAFIEGRSVAELVALGEEIYDEIIADKIWDGTRELTQMHLDAGQQVWLITATPYELAATIARRLGLTGALGTVAESVDGIFTGRLVGEILHGTGKAHAVRSLAIREGLNLKRCTAYSDSYNDVPMLSLVGTAVAINPDARLRSLARERGWEIRDFRIARKAARIGVPSALALGAAGGALAALASRRQSR