Rv1769 Resolved · medium auto-curated
H37Rv Rv1769 · MTBC0 mtbc0_001883 ·
414 aa · 2020637–2021881 (+) ·
RefSeq NP_216285.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | amino acid deaminase/aldolase |
| Revised (this work) | Amino acid deaminase/aldolase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06802
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | Alanine racemase, N-terminal domain |
| Orthologous group | COG3616 |
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 | 0.203 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1771 (L-gulono-1,4-lactone dehydrogenase), high confidence from genomic context alone (score 973 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1771 |
L-gulono-1,4-lactone dehydrogenase | 973 | 973 ctx | neighborhood:881 cooccurence:769 |
Rv1770 hyp |
hypothetical protein | 970 | 971 ctx | neighborhood:881 coexpression:734 |
Rv1768 PE_PGRS31 |
PE-PGRS family protein PE_PGRS31 | 471 | 471 ctx | neighborhood:471 |
Rv1772 hyp |
hypothetical protein | 453 | 453 ctx | neighborhood:451 |
Rv0785 |
KsdD-like steroid dehydrogenase | 443 | 444 ctx | cooccurence:442 |
Rv2004c hyp |
hypothetical protein | 401 | 402 | coexpression:402 |
Rv0988 hyp |
hypothetical protein | 808 | 47 | textmining:807 |
Rv2628 hyp |
hypothetical protein | 652 | 44 | textmining:651 |
Rv0294 tam |
trans-aconitate methyltransferase | 870 | 41 | textmining:870 |
Rv3019c esxR |
ESAT-6 like protein EsxR | 543 | 41 | textmining:543 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 472 | 41 | textmining:472 |
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: hypothetical protein
- MTBC0 PGAP product: amino acid deaminase/aldolase
- (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_216285.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG3616 - Curated reference: UniProt O06802 (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 —
11 functional partner(s); context anchor
Rv1771 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001883|Rv1769| MHEVAAREQRSDGPMRLDAQGRLQRYEEAFADYDAPFAFVDLDAMWGNADQLLARAGDKPIRVASKSLRCRPLQREILDASERFDGLLTFTLTETLWLAGQGFSNLLLAYPPTDRAALRALGELTAKDPDGAPIVMVDSVEHLDLIERTTDKPVRLCLDFDAGYWRAGGRIKIGSKRSPLHTPEQARALAVEIARRPALTLAALMCYEAHIAGLGDNVAGKRVHNAIIRRMQRMSFEELRERRARAVELVREVADIKIVNAGGTGDLQLVAQEPLITEATAGSGFYAPTLFDSYSTFTLQPAAMFALPVCRRPGAKTVTALGGGYLASGVGAKDRMPTPYLPVGLKLNALEGTGEVQTPLSGDAARRLKLGDKVYFRHTKAGELCERFDHLHLVRGAEVVDTVPTYRGEGRTFL