Rv1048c Still unknown · low auto-curated
H37Rv Rv1048c · MTBC0 mtbc0_001124 ·
371 aa · 1178377–1179492 (-) ·
RefSeq NP_215564.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 4rgu-assembly1_A-2 Crystal Structure of Putative MarR Family Transcrip (prob 0.95, TM 0.60). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96353
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein conserved in bacteria |
| Orthologous group | COG4861 |
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 | 0.804 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 88.9 (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 |
|---|---|---|---|---|
4rgu-assembly1_A-2 |
0.95 | 0.60 | 1.3e-01 | 4rgu-assembly1_A-2 Crystal Structure of Putative MarR Family Transcriptional Regulator HcaR from Acinetobacter sp. ADP complexed with ferulic acid |
5kk1-assembly1_A |
0.90 | 0.61 | 2.2e-01 | 5kk1-assembly1_A Structure of pNOB8 AspA-DNA complex. |
3k0l-assembly1_B |
0.90 | 0.60 | 2.1e-01 | 3k0l-assembly1_B Crystal Structure of Putative MarR Family Transcriptional Regulator from Acinetobacter sp. ADP |
3g3z-assembly1_B |
0.90 | 0.63 | 3.1e-01 | 3g3z-assembly1_B The structure of NMB1585, a MarR family regulator from Neisseria meningitidis |
3bj6-assembly1_B |
0.89 | 0.62 | 3.3e-01 | 3bj6-assembly1_B Crystal structure of MarR family transcription regulator SP03579 |
2ve9-assembly1_B |
0.87 | 0.72 | 5.5e-01 | 2ve9-assembly1_B Xray structure of KOPS bound gamma domain of FtsK (P. aeruginosa) |
3nrv-assembly2_D |
0.87 | 0.63 | 3.7e-01 | 3nrv-assembly2_D Crystal structure of MarR/EmrR family transcriptional regulator from Acinetobacter sp. ADP1 |
4rgu-assembly1_B-2 |
0.82 | 0.55 | 2.0e-01 | 4rgu-assembly1_B-2 Crystal Structure of Putative MarR Family Transcriptional Regulator HcaR from Acinetobacter sp. ADP complexed with ferulic acid |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1049 (transcriptional repressor), medium confidence from genomic context alone (score 483 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) |
|---|---|---|---|---|
Rv1049 |
transcriptional repressor | 570 | 483 ctx | neighborhood:469 |
Rv2528c mrr |
restriction system protein | 575 | 100 | textmining:547 |
Rv3833 |
AraC family transcriptional regulator | 494 | 70 | textmining:479 |
Rv0326 hyp |
hypothetical protein | 635 | 55 | textmining:630 |
Rv0327c cyp135A1 |
cytochrome P450 Cyp135A1 | 477 | 55 | textmining:470 |
Rv0213c |
methyltransferase | 653 | 51 | textmining:650 |
Rv1833c dhmA2 |
haloalkane dehalogenase | 633 | 50 | textmining:630 |
Rv2529 hyp |
hypothetical protein | 655 | 49 | textmining:653 |
Rv0325 hyp |
hypothetical protein | 514 | 47 | textmining:511 |
Rv1767 hyp |
hypothetical protein | 653 | 46 | textmining:652 |
Rv1829 hyp |
hypothetical protein | 625 | 46 | textmining:624 |
Rv3365c hyp |
hypothetical protein | 598 | 45 | textmining:597 |
Rv2527 vapC17 |
ribonuclease VapC17 | 513 | 45 | textmining:511 |
Rv2534c efp |
elongation factor P | 652 | 44 | textmining:651 |
Rv1766 hyp |
hypothetical protein | 652 | 44 | textmining:651 |
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: hypothetical protein
- Foldseek best: 4rgu-assembly1_A-2 Crystal Structure of Putative MarR Family Transcriptional Reg (prob 0.95, E=1e-01, TM=0.60)
- (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_215564.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG4861 - Curated reference: UniProt P96353 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 88.9, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
26 functional partner(s); context anchor
Rv1049 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001124|Rv1048c| MQASDRTWQSNFIRRWYFTETVEYRPLVKYDASMSWDERTVSALEGAFRSEVRARRVNGPHRDVIVSLDGAEFLVRWLTTGWPRQVAEALHATSRPDILAAPTMSPGARKAAHDAGVGWVDESGAADIHYRNTSTGTTLVIETKGAPPAPLDARIGWRRATLAVCEALLANIAGPTVASVVEATGLSMGSSAQALKFLEKNGHLASATARGPKSARLIVDRDALLDAYAEAADKLRSPISISTGVLWRDPTAGVVKAGQLWDAAGIEWAATSALSASLLAPMQTEIAPMEIYVPGRSWSDLRRAAMAAGLQEIAGGRLILRFFPTPACARLTEQNLQGFRSMLWPRVYADLRTAGVRGEDAAEHLREAMTK