serC Resolved · high auto-curated
H37Rv Rv0884c · MTBC0 mtbc0_000939 ·
376 aa · 984638–985768 (-) ·
RefSeq NP_215399.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphoserine aminotransferase |
|---|---|
| MTBC0 PGAP re-annotation | phosphoserine transaminase |
| Revised (this work) | Phosphoserine transaminase. Pfam: Aminotran_5 (PF00266.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ73
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphoserine aminotransferase |
| EC (curated) |
EC 2.6.1.52
|
| Curated function | Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | serC |
| eggNOG description | Catalyzes the reversible conversion of 3- phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4- phosphonooxybutanoate to phosphohydroxythreonine |
| Orthologous group | COG1932 |
| EC number |
EC 2.6.1.52
|
| KEGG orthology |
K00831
|
| KEGG pathways |
map00260, map00680, map00750, map01100, map01120, map01130, map01200, map01230
|
| KEGG modules |
M00020, M00124
|
| Gene Ontology (59) |
GO:0001505, GO:0003674, GO:0003824, GO:0004760, GO:0005575, GO:0005576, GO:0005622, GO:0005623, GO:0005737, GO:0005777, GO:0005886, GO:0006082 +47 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 | 0.347 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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 |
|---|---|---|---|---|
Aminotran_5 | PF00266.26 | 2.0e-14 | 42–335 | Aminotransferase class-V |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fprB (ferredoxin/ferredoxin--NADP reductase), high confidence from genomic context alone (score 748 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2996c serA1 |
D-3-phosphoglycerate dehydrogenase | 992 | 979 | coexpression:729 database:900 textmining:628 |
Rv0728c serA2 |
D-3-phosphoglycerate dehydrogenase SerA | 992 | 977 | coexpression:728 database:900 textmining:698 |
Rv1295 thrC |
threonine synthase | 951 | 943 | database:900 |
Rv3042c serB2 |
phosphoserine phosphatase SerB | 992 | 936 | database:900 textmining:888 |
Rv3684 |
lyase | 920 | 908 | database:900 |
Rv2334 cysK1 |
O-acetylserine sulfhydrylase | 918 | 907 | database:900 |
Rv0848 cysK2 |
cysteine synthase CysK | 913 | 906 | database:900 |
Rv0885 hyp |
hypothetical protein | 951 | 758 ctx | neighborhood:756 textmining:807 |
Rv0883c sepH hyp |
hypothetical protein | 751 | 752 ctx | neighborhood:749 |
Rv0886 fprB |
ferredoxin/ferredoxin--NADP reductase | 749 | 748 ctx | neighborhood:742 |
Rv0505c serB1 |
phosphoserine phosphatase SerB | 889 | 726 | database:500 textmining:611 |
Rv0889c citA |
citrate synthase 2 | 740 | 724 ctx | fusion:587 |
Rv3227 aroA |
3-phosphoshikimate 1-carboxyvinyltransferase | 733 | 677 | coexpression:650 |
Rv1307 atpH |
ATP synthase subunit b/delta | 616 | 616 | coexpression:615 |
Rv1600 hisC1 |
histidinol-phosphate aminotransferase | 583 | 560 ctx | cooccurence:442 |
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 aminotransferase
- MTBC0 PGAP product: phosphoserine transaminase
- Pfam (hmmscan --cut_ga): Aminotran_5 PF00266.26 (E=2e-14)
- (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_215399.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_5 (PF00266.26)
- 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
COG1932 - Curated reference: UniProt P9WQ73 (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 —
89 functional partner(s); context anchor
fprB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000939|Rv0884c|serC MADQLTPHLEIPTAIKPRDGRFGSGPSKVRLEQLQTLTTTAAALFGTSHRQAPVKNLVGRVRSGLAELFSLPDGYEVILGNGGATAFWDAAAFGLIDKRSLHLTYGEFSAKFASAVSKNPFVGEPIIITSDPGSAPEPQTDPSVDVIAWAHNETSTGVAVAVRRPEGSDDALVVIDATSGAGGLPVDIAETDAYYFAPQKNFASDGGLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVENSLKNQTYNTPAIATLALLAEQIDWLVGNGGLDWAVKRTADSSQRLYSWAQERPYTTPFVTDPGLRSQVVGTIDFVDDVDAGTVAKILRANGIVDTEPYRKLGRNQLRVAMFPAVEPDDVSALTECVDWVVERL