Rv0988 Family assigned · medium auto-curated
H37Rv Rv0988 · MTBC0 mtbc0_001059 ·
386 aa · 1112452–1113612 (+) ·
RefSeq NP_215503.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | lipocalin-like domain-containing protein |
| Revised (this work) | Lipocalin-like domain-containing protein. Pfam: CrtC (PF07143.18), Lipocalin_9 (PF17186.11). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86370
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible conserved exported protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Lipocalin-like domain |
| Orthologous group | COG5621 |
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 | 0.487 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 13 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.35% of strains (503) · 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 |
|---|---|---|---|---|
CrtC | PF07143.18 | 1.3e-59 | 71–246 | CrtC N-terminal lipocalin domain |
Lipocalin_9 | PF17186.11 | 2.8e-42 | 250–381 | Lipocalin-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0987 (adhesion component ABC transporter permease), high confidence from genomic context alone (score 998 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) |
|---|---|---|---|---|
Rv0987 |
adhesion component ABC transporter permease | 999 | 998 ctx | neighborhood:866 fusion:660 cooccurence:774 coexpression:836 textmining:510 |
Rv0986 |
adhesion component ABC transporter ATP-binding protein | 870 | 862 ctx | neighborhood:833 |
Rv3397c phyA |
phytoene synthase | 445 | 335 | |
Rv1525 wbbL2 |
rhamnosyl transferase WbbL | 590 | 187 | textmining:517 |
Rv0980c PE_PGRS18 |
PE-PGRS family protein PE_PGRS18 | 501 | 156 | textmining:434 |
Rv1664 pks9 |
polyketide synthase | 661 | 53 | textmining:657 |
Rv1769 hyp |
hypothetical protein | 808 | 47 | textmining:807 |
Rv0970 |
integral membrane protein | 435 | 46 | textmining:433 |
Rv0996 |
transmembrane protein | 574 | 42 | textmining:574 |
Rv0294 tam |
trans-aconitate methyltransferase | 803 | 41 | textmining:803 |
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: lipocalin-like domain-containing protein
- Pfam (hmmscan --cut_ga): CrtC PF07143.18 (E=1e-59), Lipocalin_9 PF17186.11 (E=3e-42)
- (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_215503.1)
- Domains: Pfam-A via hmmscan --cut_ga — CrtC (PF07143.18), Lipocalin_9 (PF17186.11)
- 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
COG5621 - Curated reference: UniProt O86370 (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 —
10 functional partner(s); context anchor
Rv0987 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001059|Rv0988| MRKAGLTGVVLVLTLTLVAFWWWQRPRTNAVAADSLVGVLVDENNAGYSLATVPGAIRFPRDLGPHYDYQTEWWYYTGNLETADGRLFGYQLTFFRRALAPPGEGVAIADASSWRTTQVYMAHFAISDISNRGFYPAEKFSRQALGLAGASSEPYAVWLDDWYARESNNNSVQLFARTQNTVLDLTLTQTLPPILQGNAGLSVKGAQPGNASNYYSLVRQESRGTVSVNGDTFMVSGLSWKDHEYMTSALAPEDVGWDWFGLQFYNGTALMLFQIRQADGSVTRFSSGTFVAGDGGVIPLESSDFRIKTTDRWTSDQSGATYPIAWEIEIERIGLTLRGAALMANQELRLSRTYWEGAVALEGRYQGMPISGRGYVEMTGYVQRLS