Rv0990c Family assigned · medium auto-curated
H37Rv Rv0990c · MTBC0 mtbc0_001061 ·
218 aa · 1114779–1115435 (-) ·
RefSeq NP_215505.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | SAF domain-containing protein |
| Revised (this work) | SAF domain-containing protein. Pfam: SAF (PF08666.18), ChapFlgA (PF13144.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05573
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | SAF domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| eggNOG description | Flagellar basal body P-ring biosynthesis protein |
| Orthologous group | COG3745 |
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 | 1.66 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.30% of strains (432) · 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 |
|---|---|---|---|---|
SAF | PF08666.18 | 3.0e-13 | 55–113 | SAF domain |
ChapFlgA | PF13144.12 | 1.2e-06 | 55–113 | Chaperone for flagella basal body P-ring formation |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3657c (membrane protein), high confidence from genomic context alone (score 824 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) |
|---|---|---|---|---|
Rv1364c |
sigma factor regulatory protein | 931 | 931 | coexpression:931 |
Rv3657c |
membrane protein | 844 | 824 ctx | cooccurence:450 coexpression:675 |
Rv3658c |
transmembrane protein | 812 | 788 | coexpression:676 |
Rv3660c ssd hyp |
hypothetical protein | 754 | 754 ctx | cooccurence:740 |
Rv3655c hyp |
hypothetical protein | 751 | 728 | coexpression:706 |
Rv0991c hyp |
hypothetical protein | 909 | 717 ctx | neighborhood:645 textmining:692 |
Rv3753c hyp |
hypothetical protein | 665 | 665 ctx | cooccurence:665 |
Rv3013 hyp |
hypothetical protein | 649 | 650 ctx | cooccurence:648 |
Rv1354c hyp |
hypothetical protein | 625 | 625 | coexpression:602 |
Rv0989c grcC2 |
polyprenyl-diphosphate synthase GrcC | 632 | 618 ctx | neighborhood:616 |
Rv0996 |
transmembrane protein | 593 | 593 ctx | cooccurence:406 |
Rv0481c hyp |
hypothetical protein | 587 | 587 ctx | cooccurence:587 |
Rv2905 lppW |
lipoprotein LppW | 555 | 556 ctx | cooccurence:554 |
Rv1332 |
transcriptional regulator | 551 | 551 ctx | cooccurence:550 |
Rv2712c hyp |
hypothetical protein | 547 | 548 ctx | cooccurence:545 |
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: SAF domain-containing protein
- Pfam (hmmscan --cut_ga): SAF PF08666.18 (E=3e-13), ChapFlgA PF13144.12 (E=1e-06)
- (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_215505.1)
- Domains: Pfam-A via hmmscan --cut_ga — SAF (PF08666.18), ChapFlgA (PF13144.12)
- 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
COG3745 - Curated reference: UniProt O05573 (TrEMBL, unreviewed; Predicted)
- 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 —
43 functional partner(s); context anchor
Rv3657c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001061|Rv0990c| MAESSLNPSLVSRISAFLRPDWTRTVRARRFAAAGLVMLAGVAALRSNPEDDRAEVVVAAHDLRPGTALTPGDVRLEKRSATTLPDGSQADLDAVVGSTLASPTRRGEVLTDVRLLGSRLAESTAGPDARIVPLHLADSALVDLVRVGDVVDVLAAPVTDSPAALRLLATDAIVVLVSAQQKAQAADSDRVVLVALPARLANTVAGAALGQTVTLTLH