Rv3005c Family assigned · medium auto-curated
H37Rv Rv3005c · MTBC0 mtbc0_003194 ·
279 aa · 3385002–3385841 (-) ·
RefSeq NP_217521.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DoxX family protein |
| Revised (this work) | DoxX family protein. Pfam: DoxX (PF07681.18), MauE (PF07291.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YAV3
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DoxX family protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane |
| Orthologous group | COG2259 |
| KEGG orthology |
K15977
|
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 | 0.121 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 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 |
|---|---|---|---|---|
DoxX | PF07681.18 | 4.6e-20 | 114–194 | DoxX |
MauE | PF07291.17 | 5.5e-07 | 115–194 | Methylamine utilisation protein MauE |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lppZ (lipoprotein LppZ), medium confidence from genomic context alone (score 563 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) |
|---|---|---|---|---|
Rv0435c |
ATPase | 585 | 586 | database:576 |
Rv3868 eccA1 |
ESX-1 secretion system protein EccA1 | 580 | 581 | database:576 |
Rv3884c eccA2 |
ESX-2 secretion system protein EccA | 579 | 580 | database:576 |
Rv0282 eccA3 |
ESX-3 secretion system protein EccA | 578 | 579 | database:576 |
Rv3006 lppZ |
lipoprotein LppZ | 563 | 563 ctx | neighborhood:557 |
Rv0425c ctpH |
metal cation transporting ATPase H | 495 | 495 | |
Rv0908 ctpE |
metal cation transporter ATPase E | 485 | 485 | |
Rv0107c ctpI |
cation-transporter ATPase I | 483 | 483 | |
Rv1997 ctpF |
cation transporter ATPase F | 482 | 483 | |
Rv1305 atpE |
ATP synthase subunit C | 441 | 441 | database:417 |
Rv0412c glnX |
membrane protein | 434 | 435 ctx | cooccurence:421 |
Rv3414c sigD |
ECF RNA polymerase sigma factor SigD | 430 | 420 | |
Rv0732 secY |
preprotein translocase SecY | 406 | 369 | |
Rv3492c |
Mce associated protein | 400 | 274 | |
Rv2704 hyp |
hypothetical protein | 454 | 223 |
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: DoxX family protein
- Pfam (hmmscan --cut_ga): DoxX PF07681.18 (E=5e-20), MauE PF07291.17 (E=6e-07)
- (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_217521.1)
- Domains: Pfam-A via hmmscan --cut_ga — DoxX (PF07681.18), MauE (PF07291.17)
- 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
COG2259 - Curated reference: UniProt I6YAV3 (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 —
24 functional partner(s); context anchor
lppZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003194|Rv3005c| MTSSNDSHWQRPDDSPGPMPGRPVSASLVDPEDDLTPARYAGDFGSGTTTVIPPYDAASSGVGNSGYSLIEAAEPLPYVQPQPGRQVPAGSAGIDMDDDERVRAAGRRGTQNLGLLILRVGLGAVLIAHGLQKLFGWWDGQGLAGFQNSLSDIGYQHAEILAYVSAGGEIVAGVLLVLGLFTPLAAAGALAFLINGLLAGISAQHSRPVAYFLQDGHEYQITLVVMAVAVILSGPGRYGLDAARGWAHRPFIGSFVALLGGIAAGIAVWVLLNGANPLA