Rv1480 Family assigned · low
H37Rv Rv1480 · MTBC0 mtbc0_001583 ·
317 aa · 1680218–1681171 (+) ·
RefSeq NP_215996.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF58 domain-containing protein |
| Revised (this work) | DUF58; fold of the BatB/DUF58 family (PDB 3IBS); putative integrity/assembly protein. |
Curated reference (UniProt)
| UniProt |
P9WLX5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1480 |
UniProt still lists this protein as Uncharacterized protein Rv1480; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | conserved protein (some members contain a von Willebrand factor type A (vWA) domain) |
| Orthologous group | COG1721 |
| Gene Ontology (13) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044424, GO:0044444, GO:0044464 +1 more
|
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 | 2.15 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 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 |
|---|---|---|---|---|
DUF58 | PF01882.26 | 8.2e-85 | 61–275 | Protein of unknown function DUF58 |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 89.5 (confident). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
3ibs-assembly1_B |
1.00 | 0.61 | 3.2e-07 sig | 3ibs-assembly1_B Crystal structure of conserved hypothetical protein BatB from Bacteroides thetaiotaomicron |
4jdu-assembly1_A |
1.00 | 0.56 | 2.5e-06 sig | 4jdu-assembly1_A The crystal structure of an aerotolerance-related membrane protein from Bacteroides fragilis NCTC 9343 with multiple mutations to serines. |
8ft6-assembly1_A |
1.00 | 0.65 | 3.1e-04 sig | 8ft6-assembly1_A The von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone, Ala-Ala linker variant, SUMO tag-free preparation. |
8zmn-assembly1_A |
1.00 | 0.61 | 1.7e-04 sig | 8zmn-assembly1_A Crystal structure of ANTXR1 |
8jtl-assembly1_B |
1.00 | 0.57 | 1.6e-04 sig | 8jtl-assembly1_B Structure of OY phytoplasma SAP05 binding with AtRpn10 |
8j4a-assembly1_B |
1.00 | 0.55 | 1.0e-04 sig | 8j4a-assembly1_B Crystal structure of OY phytoplasma SAP05 in complex with AtRPN10 |
8amz-assembly1_W |
1.00 | 0.59 | 5.1e-04 sig | 8amz-assembly1_W Spinach 19S proteasome |
5oqm-assembly1_6 |
1.00 | 0.46 | 2.2e-04 sig | 5oqm-assembly1_6 STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1481 (membrane protein), high confidence from genomic context alone (score 994 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) |
|---|---|---|---|---|
Rv1481 |
membrane protein | 994 | 994 ctx | neighborhood:874 cooccurence:774 coexpression:819 |
Rv1479 moxR1 |
transcriptional regulator MoxR1 | 986 | 984 ctx | neighborhood:882 cooccurence:742 coexpression:414 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 667 | 613 ctx | cooccurence:448 |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 648 | 591 ctx | cooccurence:433 |
Rv1477 ripA |
peptidoglycan endopeptidase RipA | 587 | 587 ctx | neighborhood:576 |
Rv2902c rnhB |
ribonuclease HII | 586 | 587 | coexpression:580 |
Rv1478 ripB |
peptidoglycan endopeptidase RipB | 573 | 573 ctx | neighborhood:563 |
Rv1484 inhA |
NADH-dependent enoyl-[ACP | 554 | 554 ctx | neighborhood:544 |
Rv1485 hemZ |
ferrochelatase | 550 | 551 ctx | neighborhood:544 |
Rv1483 fabG1 |
3-oxoacyl-ACP reductase FabG | 550 | 551 ctx | neighborhood:544 |
Rv0049 hyp |
hypothetical protein | 408 | 409 ctx | cooccurence:405 |
Rv1474c |
transcriptional regulator | 404 | 404 | |
Rv2468c hyp |
hypothetical protein | 406 | 390 | |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 438 | 87 | textmining:411 |
Rv3680 |
anion transporter ATPase | 742 | 64 | textmining:736 |
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
- MTBC0 PGAP product: DUF58 domain-containing protein
- Pfam: DUF58 PF01882.26
- Foldseek best: 3ibs-assembly1_B Crystal structure of conserved hypothetical protein BatB from B (prob 1.00, E=3e-07, TM=0.61)
- (structure-only promotion reviewed by hand, 2026-06-01)
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_215996.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF58 (PF01882.26)
- 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
COG1721 - Curated reference: UniProt P9WLX5 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 89.5, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
24 functional partner(s); context anchor
Rv1481 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001583|Rv1480| MTESKAPAVVHPPSMLRGDIDDPKLAAALRTLELTVKQKLDGVLHGDHLGLIPGPGSEPGESRLYQPGDDVRRMDWAVTARTTHPHVRQMIADRELETWLVVDMSASLDFGTACCEKRDLAVAAAAAITFLNSGGGNRLGALIANGAAMTRVPARTGRQHQHTMLRTIATMPQAPAGVRGDLAVAIDALRRPERRRGMAVIISDFLGPINWMRPLRAIAARHEVLAIEVLDPRDVELPDVGDVVLQDAESGVVREFSIDPALRDDFARAAAAHRADVARTIRGCGAPLLSLRTDRDWLADIVRFVASRRRGALAGHQ