Rv1455 Family assigned · medium auto-curated
H37Rv Rv1455 · MTBC0 mtbc0_001557 ·
287 aa · 1650432–1651295 (+) ·
RefSeq NP_215971.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains DcsG_N (PF27100.1) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53147
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 |
H Coenzyme transport and metabolismJ Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | dcsG |
| eggNOG description | ligase activity |
| Orthologous group | COG0189 |
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 | 0.595 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
DcsG_N | PF27100.1 | 1.8e-20 | 13–85 | D-cycloserine synthetase DcsG, N-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: qor (quinone reductase), high confidence from genomic context alone (score 792 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) |
|---|---|---|---|---|
Rv1454c qor |
quinone reductase | 878 | 792 ctx | neighborhood:791 textmining:440 |
Rv3810 pirG |
cell surface protein | 538 | 520 ctx | cooccurence:506 |
Rv1987 |
chitinase | 443 | 443 ctx | cooccurence:443 |
Rv3593 lpqF |
lipoprotein LpqF | 412 | 412 ctx | cooccurence:412 |
Rv2672 |
protease | 400 | 378 | |
Rv0678 mmpR5 hyp |
hypothetical protein | 416 | 234 | |
Rv3303c lpdA |
NAD(P)H quinone reductase LpdA | 685 | 44 | textmining:685 |
Rv1453 |
transcriptional activator protein | 870 | 41 | textmining:870 |
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: hypothetical protein
- Pfam (hmmscan --cut_ga): DcsG_N PF27100.1 (E=2e-20)
- (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_215971.1)
- Domains: Pfam-A via hmmscan --cut_ga — DcsG_N (PF27100.1)
- 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
COG0189 - Curated reference: UniProt O53147 (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 —
8 functional partner(s); context anchor
qor - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001557|Rv1455| MKLARPDVFHPRVVLAGWPQQPAGDGDDAGLVAALRHRGLHAGWLSWDDPEIVHADLVILRATRDYPARLDEFLAWTTRVANLLNSRPVVAWNVERRYLRDLMDRGVPTVPGEVYVPGEPVRLPRKGQVFVGPTIGTGTRRCSARFAAEFVAQLHAAGQAVLVQPGGSGDETVLVFLGGEPSHAFTKQADTWRQTEPDFEIWDVGAAAVAGAAAQVGVDPGELLYARAHITGGSRDPRLLELQLVDPSLGWQWLDPDIRNLAQRDFALCVQSALERLGLGPFSHRRP