sdaA Resolved · high auto-curated
H37Rv Rv0069c · MTBC0 mtbc0_000076 ·
461 aa · 76382–77767 (-) ·
RefSeq NP_214583.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | L-serine dehydratase |
|---|---|
| MTBC0 PGAP re-annotation | L-serine ammonia-lyase |
| Revised (this work) | L-serine ammonia-lyase. Pfam: SDH_beta (PF03315.22), SDH_alpha (PF03313.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGT5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | L-serine dehydratase |
| EC (curated) |
EC 4.3.1.17
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | sdaA |
| eggNOG description | L-serine dehydratase |
| Orthologous group | COG1760 |
| EC number |
EC 4.3.1.17
|
| KEGG orthology |
K01752
|
| KEGG pathways |
map00260, map00270, map01100, map01110, map01130, map01200, map01230
|
| Gene Ontology (12) |
GO:0003674, GO:0003824, GO:0003941, GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0016829, GO:0016840, GO:0016841, 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 | 3.142 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 9 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 |
|---|---|---|---|---|
SDH_beta | PF03315.22 | 4.4e-55 | 4–156 | Serine dehydratase beta chain |
SDH_alpha | PF03313.22 | 1.5e-90 | 187–451 | Serine dehydratase alpha chain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glyA2 (serine hydroxymethyltransferase), high confidence from genomic context alone (score 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0070c glyA2 |
serine hydroxymethyltransferase | 998 | 997 ctx | neighborhood:801 coexpression:839 database:900 textmining:518 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 964 | 925 | database:900 textmining:547 |
Rv1559 ilvA |
threonine dehydratase IlvA | 960 | 922 | database:900 textmining:518 |
Rv1077 cbs |
cystathionine beta-synthase | 926 | 905 | database:900 |
Rv1613 trpA |
tryptophan synthase subunit alpha | 908 | 905 | database:900 |
Rv3042c serB2 |
phosphoserine phosphatase SerB | 973 | 904 | database:900 textmining:737 |
Rv0436c pssA |
CDP-diacylglycerol--serine O-phosphatidyltransferase | 901 | 902 | database:900 |
Rv2335 cysE |
serine acetyltransferase | 956 | 901 | database:900 textmining:579 |
Rv1612 trpB |
tryptophan synthase subunit beta | 904 | 901 | database:900 |
Rv1296 thrB |
homoserine kinase | 860 | 843 | database:800 |
Rv1294 thrA |
homoserine dehydrogenase | 846 | 839 | database:800 |
Rv3341 metA |
homoserine O-acetyltransferase | 800 | 801 | database:800 |
Rv1832 gcvB |
glycine dehydrogenase | 872 | 668 | coexpression:403 textmining:631 |
Rv3002c ilvN |
acetolactate synthase small subunit | 651 | 631 | database:500 |
Rv1295 thrC |
threonine synthase | 636 | 600 | database:500 |
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: L-serine dehydratase
- MTBC0 PGAP product: L-serine ammonia-lyase
- Pfam (hmmscan --cut_ga): SDH_beta PF03315.22 (E=4e-55), SDH_alpha PF03313.22 (E=2e-90)
- (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_214583.1)
- Domains: Pfam-A via hmmscan --cut_ga — SDH_beta (PF03315.22), SDH_alpha (PF03313.22)
- 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
COG1760 - Curated reference: UniProt P9WGT5 (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 —
38 functional partner(s); context anchor
glyA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000076|Rv0069c|sdaA MTISVFDLFTIGIGPSSSHTVGPMRAANQFVVALRRRGHLDDLEAMRVDLFGSLAATGAGHGTMSAILLGLEGCQPETITTEHKERRLAEIAASGVTRIGGVIPVPLTERDIDLHPDIVLPTHPNGMTFTAAGPHGRVLATETYFSVGGGFIVTEQTSGNSGQHPCSVALPYVSAQELLDICDRLDVSISEAALRNETCCRTENEVRAALLHLRDVMVECEQRSIAREGLLPGGLRVRRRAKVWYDRLNAEDPTRKPEFAEDWVNLVALAVNEENASGGRVVTAPTNGAAGIVPAVLHYAIHYTSAGAGDPDDVTVRFLLTAGAIGSLFKERASISGAEVGCQGEVGSAAAMAAAGLAEILGGTPRQVENAAEIAMEHSLGLTCDPIAGLVQIPCIERNAISAGKAINAARMALRGDGIHRVTLDQVIDTMRATGADMHTKYKETSAGGLAINVAVNIVEC