Rv1084 Family assigned · medium auto-curated
H37Rv Rv1084 · MTBC0 mtbc0_001164 ·
673 aa · 1215905–1217926 (+) ·
RefSeq NP_215600.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | thioredoxin domain-containing protein |
| Revised (this work) | Thioredoxin domain-containing protein. Pfam: Thioredox_DsbH (PF03190.22), Thioredoxin_7 (PF13899.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53432
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; 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
|
|---|---|
| eggNOG description | Protein of unknown function, DUF255 |
| Orthologous group | COG1331 |
| KEGG orthology |
K06888
|
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 | 0.187 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 5 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 |
|---|---|---|---|---|
Thioredox_DsbH | PF03190.22 | 4.5e-68 | 9–164 | Protein of unknown function, DUF255 |
Thioredoxin_7 | PF13899.13 | 5.4e-11 | 30–119 | Thioredoxin-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mca (mycothiol S-conjugate amidase), high confidence from genomic context alone (score 885 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) |
|---|---|---|---|---|
Rv1082 mca |
mycothiol S-conjugate amidase | 885 | 885 ctx | neighborhood:882 |
Rv1083 hyp |
hypothetical protein | 882 | 882 ctx | neighborhood:881 |
Rv1081c |
membrane protein | 781 | 781 ctx | neighborhood:780 |
Rv0519c |
membrane protein | 664 | 652 | experimental:652 |
Rv1987 |
chitinase | 537 | 518 | experimental:465 |
Rv0062 celA1 |
cellulase CelA | 536 | 517 | experimental:465 |
Rv1090 celA2b |
Rv1090, (MTV017.43), len: 151 aa. Probable celA2b,second part of cellulase (endoglucanase), similar to C-terminus of others e.g. O08468 cell | 591 | 498 | experimental:449 |
Rv1080c greA |
transcription elongation factor GreA | 417 | 417 ctx | neighborhood:413 |
Rv3895c eccB2 |
ESX-2 secretion system protein EccB | 407 | 406 | |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 403 | 403 | |
Rv1782 eccB5 |
ESX-5 type VII secretion system protein EccB5 | 403 | 403 | |
Rv3450c eccB4 |
ESX-4 secretion system protein EccB4 | 402 | 401 | |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 402 | 401 | |
Rv2075c hyp |
hypothetical protein | 402 | 401 | |
Rv3616c espA |
ESX-1 secretion-associated protein EspA | 401 | 400 |
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: thioredoxin domain-containing protein
- Pfam (hmmscan --cut_ga): Thioredox_DsbH PF03190.22 (E=4e-68), Thioredoxin_7 PF13899.13 (E=5e-11)
- (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_215600.1)
- Domains: Pfam-A via hmmscan --cut_ga — Thioredox_DsbH (PF03190.22), Thioredoxin_7 (PF13899.13)
- 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
COG1331 - Curated reference: UniProt O53432 (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 —
35 functional partner(s); context anchor
mca - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001164|Rv1084| MSPANPSGTNTLALATSPYLRQHADNPVHWQQWTPQALAEAAARAVPILLSVGYAACHWCHVMAHESFDDDEVAAAMNAGFVCIKVDREERPDIDAVYMNATVALTGQGGWPMTCFLTPNGRPFFCGTYYPKAAFLQLLSAISETWRERRAEVEQASDHIAAELRSMASGLPGGGPEVAPELCDDAVAGVLREQDTAHGGFGGAPKFPPSALLEALMRHYERTRSPAALEAVARTGNAMARGGIYDQLGGGFARYSVDGAWVVPHFEKMLYDNALLLRAYAHWARRTGDPLARRVAAQTARFLLDELGSKAPADMFTSSLDADADGREGSTYVWTPVQLTEVLGGDDGRWAAEVFGVTEAGTFEHGTSVLQLPADPDDAARLDRVRAALLVARLARAQPARDDKVVTSWNGLAITALAEASVALDDPALAHAARRCATRLLDLHVVDGRLRRASLGGVVGDSAAILEDHAMLATGLLALYQLTSEGAWLTAATGLLDTAVAHFGDPQRPGRWFDTADDAERLMLRPSDPLDGATPSGASSIAEALLTAGHVVDGARAERYWQLAADTLRAHAVLLARAPRSAGHWLAVAEAVVRGPLQIAVACDLPRSSLLADARRLAPGGAIVVGGAAGSSALLVGRDRVAGADAAYVCRGRVCDLPVTSAAELATALGVPG