Rv1488 Family assigned · medium auto-curated
H37Rv Rv1488 · MTBC0 mtbc0_001591 ·
381 aa · 1687202–1688347 (+) ·
RefSeq NP_216004.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | SPFH domain-containing protein |
| Revised (this work) | SPFH domain-containing protein. Pfam: Band_7 (PF01145.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPR9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1488 |
UniProt still lists this protein as Uncharacterized protein Rv1488; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | hflK |
| eggNOG description | COG0330 Membrane protease subunits, stomatin prohibitin homologs |
| Orthologous group | COG0330 |
| Gene Ontology (9) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.262 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (203) · 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 |
|---|---|---|---|---|
Band_7 | PF01145.32 | 1.9e-37 | 29–207 | SPFH domain / Band 7 family |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1487 hyp |
hypothetical protein | 973 | 971 ctx | neighborhood:851 cooccurence:750 |
Rv3610c ftsH |
zinc metalloprotease FtsH | 963 | 959 | coexpression:467 experimental:805 database:633 |
Rv1489 hyp |
hypothetical protein | 878 | 879 ctx | neighborhood:828 |
Rv0038 hyp |
hypothetical protein | 805 | 806 | coexpression:804 |
Rv2115c mpa |
proteasome-associated ATPase | 821 | 804 | coexpression:779 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 783 | 783 | coexpression:783 |
Rv1486c hyp |
hypothetical protein | 777 | 777 ctx | neighborhood:767 |
Rv1019 |
transcriptional regulator | 765 | 765 | coexpression:765 |
Rv1100 hyp |
hypothetical protein | 757 | 757 | coexpression:757 |
Rv2782c pepR |
zinc protease | 778 | 751 | database:594 |
Rv2867c |
GCN5-like N-acetyltransferase | 748 | 748 | coexpression:740 |
Rv2788 sirR |
transcriptional repressor SirR | 734 | 734 | coexpression:734 |
Rv0903c prrA |
two component transcriptional regulator PrrA | 733 | 734 | coexpression:734 |
Rv1337 |
integral membrane protein | 704 | 678 | database:619 |
Rv0110 |
integral membrane protein | 698 | 672 | database:619 |
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: SPFH domain-containing protein
- Pfam (hmmscan --cut_ga): Band_7 PF01145.32 (E=2e-37)
- (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_216004.1)
- Domains: Pfam-A via hmmscan --cut_ga — Band_7 (PF01145.32)
- 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
COG0330 - Curated reference: UniProt P9WPR9 (SwissProt, reviewed; 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 — 67 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001591|Rv1488| MQGAVAGLVFLAVLVIFAIIVVAKSVALIPQAEAAVIERLGRYSRTVSGQLTLLVPFIDRVRARVDLRERVVSFPPQPVITEDNLTLNIDTVVYFQVTVPQAAVYEISNYIVGVEQLTTTTLRNVVGGMTLEQTLTSRDQINAQLRGVLDEATGRWGLRVARVELRSIDPPPSIQASMEKQMKADREKRAMILTAEGTREAAIKQAEGQKQAQILAAEGAKQAAILAAEADRQSRMLRAQGERAAAYLQAQGQAKAIEKTFAAIKAGRPTPEMLAYQYLQTLPEMARGDANKVWVVPSDFNAALQGFTRLLGKPGEDGVFRFEPSPVEDQPKHAADGDDAEVAGWFSTDTDPSIARAVATAEAIARKPVEGSLGTPPRLTQ