Rv1188 Resolved · high auto-curated
H37Rv Rv1188 · MTBC0 mtbc0_001276 ·
329 aa · 1339463–1340452 (+) ·
RefSeq NP_215704.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | proline dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | proline dehydrogenase |
| Revised (this work) | Proline dehydrogenase. Pfam: Pro_dh (PF01619.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O50444
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | proline dehydrogenase |
| EC (curated) |
EC 1.5.5.2
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | putA |
| eggNOG description | Proline dehydrogenase |
| Orthologous group | COG0506 |
| KEGG orthology |
K00318
|
| KEGG pathways |
map00330, map01100, map01110, map01130
|
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) pseudogene candidate
| pN/pS | 1.31 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.45% of strains (2111) · 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 |
|---|---|---|---|---|
Pro_dh | PF01619.25 | 1.6e-30 | 52–312 | Proline dehydrogenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rocA (pyrroline-5-carboxylate dehydrogenase RocA), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1187 rocA |
pyrroline-5-carboxylate dehydrogenase RocA | 999 | 999 ctx | neighborhood:882 cooccurence:650 coexpression:830 database:900 textmining:649 |
Rv0500 proC |
pyrroline-5-carboxylate reductase | 990 | 924 | database:900 textmining:880 |
Rv0840c pip |
proline iminopeptidase | 901 | 902 | database:900 |
Rv1186c hyp |
hypothetical protein | 908 | 840 ctx | neighborhood:783 textmining:451 |
Rv2858c aldC |
aldehyde dehydrogenase AldC | 689 | 669 ctx | fusion:558 |
Rv1249c |
membrane protein | 612 | 612 | coexpression:612 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 576 | 576 ctx | neighborhood:573 |
Rv0768 aldA |
aldehyde dehydrogenase AldA | 579 | 552 | |
Rv3063 cstA |
carbon starvation protein A | 560 | 542 | coexpression:542 |
Rv1190 hyp |
hypothetical protein | 535 | 535 ctx | neighborhood:532 |
Rv0223c |
aldehyde dehydrogenase | 536 | 506 | |
Rv3667 acs |
acetyl-CoAsynthetase | 564 | 501 | coexpression:488 |
Rv0753c mmsA |
methylmalonate-semialdehyde dehydrogenase | 515 | 484 | |
Rv1731 gabD2 |
succinate-semialdehyde dehydrogenase | 485 | 451 | |
Rv0896 gltA2 |
citrate synthase 1 | 483 | 429 | coexpression:429 |
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: proline dehydrogenase
- MTBC0 PGAP product: proline dehydrogenase
- Pfam (hmmscan --cut_ga): Pro_dh PF01619.25 (E=2e-30)
- (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_215704.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pro_dh (PF01619.25)
- 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
COG0506 - Curated reference: UniProt O50444 (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 —
28 functional partner(s); context anchor
rocA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001276|Rv1188| MAGWFAHTLRPAMLAAGRSDRLGRIVERSPLTRGVVRRFVPGDTLDDVVDIVTALRDSGRYLSIDYLGENVTDADDAAAAVRAYLGLLDVLGRRGDIACDGVRPLEVSLKLSALGQALDRDGQKIALDNARAICERAERVGAWVTVDAEDHTTTDSTLSISGDLRVDFPWLGTVVQAYLRRTLADCAELAAVGARVRLCKGAYDEPASVAYRDAAQVTDSYLRCLRVLTAGRGYPMVATHDPVIIAAVPGITRESGRSQGDFEYQMLYGVRDDEQRRLTGAGNHVRVYVPFGTRWYGYFLRRLAERPANLAFFLRALTDRRRARGCAER