serB2 Resolved · high auto-curated
H37Rv Rv3042c · MTBC0 mtbc0_003234 ·
409 aa · 3423243–3424472 (-) ·
RefSeq NP_217558.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphoserine phosphatase SerB |
|---|---|
| MTBC0 PGAP re-annotation | phosphoserine phosphatase SerB |
| Revised (this work) | Phosphoserine phosphatase SerB. Pfam: ACT_6 (PF13740.13), ACT_PSP_2 (PF21086.4), 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.
Curated reference (UniProt)
| UniProt |
O53289
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphoserine phosphatase SerB2 |
| EC (curated) |
EC 3.1.3.16, EC 3.1.3.3
|
| Curated function | Catalyzes the dephosphorylation of O-phospho-L-serine into L-serine, a step in the L-serine biosynthetic pathway. Exhibits high specificity for L-phosphoserine compared to substrates like L-phosphothreonine (5% relative activity) and L-phosphotyrosine (1.7% relative activity)..; FUNCTION: In the host, induces significant cytoskeleton rearrangements through cofilin dephosphorylation and its subsequent activation, and affects the expression of genes that regulate actin dynamics. It specifically interacts with HSP90, HSP70 and HSP27 that block apoptotic pathways but not with other HSPs. Also inte. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismT Signal transduction mechanisms
|
|---|---|
| Preferred name | serB |
| eggNOG description | phosphoserine phosphatase |
| Orthologous group | COG0560 |
| EC number |
EC 3.1.3.3
|
| KEGG orthology |
K01079
|
| KEGG pathways |
map00260, map00680, map01100, map01120, map01130, map01200, map01230
|
| KEGG modules |
M00020
|
| Gene Ontology (37) |
GO:0003674, GO:0003824, GO:0004647, GO:0004721, GO:0004722, GO:0005488, GO:0006464, GO:0006470, GO:0006793, GO:0006796, GO:0006807, GO:0008150 +25 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)
| pN/pS | 0.305 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 |
|---|---|---|---|---|
ACT_6 | PF13740.13 | 1.6e-17 | 7–79 | ACT domain |
ACT_PSP_2 | PF21086.4 | 2.6e-30 | 94–170 | ACT domain |
Hydrolase | PF00702.33 | 1.1e-25 | 180–353 | haloacid dehalogenase-like hydrolase |
HAD | PF12710.14 | 6.7e-28 | 182–349 | haloacid dehalogenase-like hydrolase |
Hydrolase_3 | PF08282.19 | 3.9e-11 | 318–372 | haloacid dehalogenase-like hydrolase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3041c (ABC transporter ATP-binding protein), high confidence from genomic context alone (score 871 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0884c serC |
phosphoserine aminotransferase | 992 | 936 | database:900 textmining:888 |
Rv1612 trpB |
tryptophan synthase subunit beta | 928 | 924 | database:900 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 952 | 917 | database:900 textmining:451 |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 949 | 916 | database:900 textmining:421 |
Rv1077 cbs |
cystathionine beta-synthase | 943 | 908 | database:900 textmining:411 |
Rv1613 trpA |
tryptophan synthase subunit alpha | 910 | 908 | database:900 |
Rv1559 ilvA |
threonine dehydratase IlvA | 915 | 907 | database:900 |
Rv0436c pssA |
CDP-diacylglycerol--serine O-phosphatidyltransferase | 906 | 907 | database:900 |
Rv0069c sdaA |
L-serine dehydratase | 973 | 904 | database:900 textmining:737 |
Rv3038c hyp |
hypothetical protein | 879 | 879 ctx | neighborhood:861 |
Rv3040c hyp |
hypothetical protein | 872 | 872 ctx | neighborhood:869 |
Rv3041c |
ABC transporter ATP-binding protein | 871 | 871 ctx | neighborhood:869 |
Rv3039c echA17 |
enoyl-CoA hydratase EchA17 | 870 | 871 ctx | neighborhood:869 |
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 850 | 834 ctx | neighborhood:829 |
Rv2335 cysE |
serine acetyltransferase | 907 | 809 | database:800 textmining:534 |
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: phosphoserine phosphatase SerB
- MTBC0 PGAP product: phosphoserine phosphatase SerB
- Pfam (hmmscan --cut_ga): ACT_6 PF13740.13 (E=2e-17), ACT_PSP_2 PF21086.4 (E=3e-30), Hydrolase PF00702.33 (E=1e-25), HAD PF12710.14 (E=7e-28), Hydrolase_3 PF08282.19 (E=4e-11)
- (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_217558.1)
- Domains: Pfam-A via hmmscan --cut_ga — ACT_6 (PF13740.13), ACT_PSP_2 (PF21086.4), 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 O53289 (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 —
54 functional partner(s); context anchor
Rv3041c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003234|Rv3042c|serB2 MPAKVSVLITVTGMDQPGVTSALFEVLAQHGVELLNVEQVVIRGRLTLGVLVSCPLDVADGTALRDDVAAAIHGVGLDVAIERSDDLPIIRQPSTHTIFVLGRPITAGAFSAVAREVAALGVNIDFIRGISDYPVTGLELRVSVPPGCVGPLQIALTKVAAEEHVDVAVEDYGLAWRTKRLIVFDVDSTLVQGEVIEMLAARAGAQGQVAAITEAAMRGELDFAESLQRRVATLAGLPATVIDDVAEQLELMPGARTTIRTLRRLGFRCGVVSGGFRRIIEPLARELMLDFVASNELEIVDGILTGRVVGPIVDRPGKAKALRDFASQYGVPMEQTVAVGDGANDIDMLGAAGLGIAFNAKPALREVADASLSHPYLDTVLFLLGVTRGEIEAADAGDCGVRRVEIPAD