rocA Resolved · high auto-curated
H37Rv Rv1187 · MTBC0 mtbc0_001275 ·
543 aa · 1337832–1339463 (+) ·
RefSeq NP_215703.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | pyrroline-5-carboxylate dehydrogenase RocA |
|---|---|
| MTBC0 PGAP re-annotation | L-glutamate gamma-semialdehyde dehydrogenase |
| Revised (this work) | L-glutamate gamma-semialdehyde dehydrogenase. Pfam: Aldedh (PF00171.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O50443
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | L-glutamate gamma-semialdehyde dehydrogenase |
| EC (curated) |
EC 1.2.1.88
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | pruA |
| eggNOG description | Dehydrogenase |
| Orthologous group | COG1012 |
| EC number |
EC 1.2.1.88
|
| KEGG orthology |
K00294
|
| KEGG pathways |
map00250, map00330, map01100
|
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 | 0.432 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
Aldedh | PF00171.28 | 3.5e-91 | 53–522 | Aldehyde dehydrogenase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1188 (proline dehydrogenase), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1188 |
proline dehydrogenase | 999 | 999 ctx | neighborhood:882 cooccurence:650 coexpression:830 database:900 textmining:649 |
Rv2322c rocD1 |
Rv2322c, (MTCY3G12.12), len: 221 aa. Probable rocD1,ornithine aminotransferase, highly similar to N-terminal region of other ornithine amino | 941 | 939 | database:900 |
Rv3859c gltB |
glutamate synthase large subunit | 940 | 917 | database:900 |
Rv3432c gadB |
glutamate decarboxylase GadB | 921 | 917 | database:900 |
Rv3858c gltD |
glutamate synthase small subunit | 915 | 911 | database:900 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 909 | 907 | database:900 |
Rv2220 glnA1 |
glutamine synthetase | 910 | 906 | database:900 |
Rv2860c glnA4 |
glutamine synthetase | 909 | 906 | database:900 |
Rv1878 glnA3 |
glutamine synthetase GlnA | 909 | 906 | database:900 |
Rv0500 proC |
pyrroline-5-carboxylate reductase | 957 | 905 | database:900 textmining:570 |
Rv2222c glnA2 |
glutamine synthetase | 910 | 905 | database:900 |
Rv2439c proB |
glutamate 5-kinase protein | 914 | 902 | database:900 |
Rv2427c proA |
gamma-glutamyl phosphate reductase | 907 | 901 | database:900 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 901 | 901 | database:900 |
Rv2211c gcvT |
aminomethyltransferase | 865 | 840 | database:800 |
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: pyrroline-5-carboxylate dehydrogenase RocA
- MTBC0 PGAP product: L-glutamate gamma-semialdehyde dehydrogenase
- Pfam (hmmscan --cut_ga): Aldedh PF00171.28 (E=3e-91)
- (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_215703.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aldedh (PF00171.28)
- 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
COG1012 - Curated reference: UniProt O50443 (TrEMBL, unreviewed; 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 —
82 functional partner(s); context anchor
Rv1188 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001275|Rv1187|rocA MDAITQVPVPANEPVHDYAPKSPERTRLRTELASLADHPIDLPHVIGGRHRMGDGERIDVVQPHRHAARLGTLTNATHADAAAAVEAAMSAKSDWAALPFDERAAVFLRAADLLAGPWREKIAAATMLGQSKSVYQAEIDAVCELIDFWRFNVAFARQILEQQPISGPGEWNRIDYRPLDGFVYAITPFNFTSIAGNLPTAPALMGNTVIWKPSITQTLAAYLTMQLLEAAGLPPGVINLVTGDGFAVSDVALADPRLAGIHFTGSTATFGHLWQWVGTNIGRYHSYPRLVGETGGKDFVVAHASARPDVLRTALIRGAFDYQGQKCSAVSRAFIAHSVWQRMGDELLAKAAELRYGDITDLSNYGGALIDQRAFVKNVDAIERAKGAAAVTVAVGGEYDDSEGYFVRPTVLLSDDPTDESFVIEYFGPLLSVHVYPDERYEQILDVIDTGSRYALTGAVIADDRQAVLTALDRLRFAAGNFYVNDKPTGAVVGRQPFGGARGSGTNDKAGSPLNLLRWTSARSIKETFVAATDHIYPHMAVD