Rv0576 Family assigned · medium auto-curated
H37Rv Rv0576 · MTBC0 mtbc0_000606 ·
434 aa · 673399–674703 (+) ·
RefSeq NP_215090.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | TIGR03086 family metal-binding protein |
| Revised (this work) | TIGR03086 family metal-binding protein. Pfam: HTH_20 (PF12840.14), HTH_5 (PF01022.27), Polyketide_cyc2 (PF10604.16), AHSA1 (PF08327.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53773
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG0640 |
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 | 0.92 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (242) · 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 |
|---|---|---|---|---|
HTH_20 | PF12840.14 | 7.4e-12 | 6–52 | Helix-turn-helix domain |
HTH_5 | PF01022.27 | 7.0e-13 | 8–52 | Bacterial regulatory protein, arsR family |
Polyketide_cyc2 | PF10604.16 | 1.9e-08 | 105–203 | Polyketide cyclase / dehydrase and lipid transport |
AHSA1 | PF08327.18 | 7.9e-28 | 115–228 | Activator of Hsp90 ATPase homolog 1-like protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0575c (oxidoreductase), medium confidence from genomic context alone (score 561 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0577 TB27.3 hyp |
hypothetical protein | 767 | 767 ctx | neighborhood:755 |
Rv0575c |
oxidoreductase | 561 | 561 ctx | neighborhood:552 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 526 | 524 ctx | cooccurence:492 |
Rv2640c |
ArsR family transcriptional regulator | 505 | 505 ctx | cooccurence:458 |
Rv2487c PE_PGRS42 |
PE-PGRS family protein PE_PGRS42 | 492 | 492 ctx | cooccurence:492 |
Rv2098c PE_PGRS36 |
PE-PGRS family protein PE_PGRS36; Rv2098c, (MTCY49.38c), len: 434 aa. PE_PGRS36,Member of the Mycobacterium tuberculosis PE family, PGRS sub | 473 | 474 ctx | cooccurence:450 |
Rv1725c hyp |
hypothetical protein | 450 | 449 | |
Rv2305 hyp |
hypothetical protein | 430 | 431 ctx | cooccurence:428 |
Rv1931c |
transcriptional regulator | 423 | 423 | |
Rv3328c sigJ |
ECF RNA polymerase sigma factor SigJ | 419 | 416 | |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 411 | 323 |
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: transcriptional regulator
- MTBC0 PGAP product: TIGR03086 family metal-binding protein
- Pfam (hmmscan --cut_ga): HTH_20 PF12840.14 (E=7e-12), HTH_5 PF01022.27 (E=7e-13), Polyketide_cyc2 PF10604.16 (E=2e-08), AHSA1 PF08327.18 (E=8e-28)
- (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_215090.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_20 (PF12840.14), HTH_5 (PF01022.27), Polyketide_cyc2 (PF10604.16), AHSA1 (PF08327.18)
- 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
COG0640 - Curated reference: UniProt O53773 (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 —
11 functional partner(s); context anchor
Rv0575c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000606|Rv0576| MLEVAAEPTRRRLLQLLAPGERTVTQLASQFTVTRSAISQHLGMLAEAGLVTARKQGRERYYRLDERGVLRLRALMESFWSDELDRLVADAAHYPPSQGDCAMPFEKAVVVPLDPTSTFALITQPDRLRRWMAVAARIELRTGGAYRWTVTPGHSAAGTVIDVDPGKRVVFTWGWEDHGDPPPGGSTVTITLTPVDGGTEVRLVHDGLTAQQAARHAKGWNHFLDRLVVAGQHGDAGPDEWAAAPDPLDELSCAEATLAVLQHVLRGIGASDLTRQTPCTEYDVSQLADHLLRSLAIIGAAAGAQLAPRDVDAPLETQVADAAQAVMEAWRRRGLAGTVELNSNQVPATVPVGILCLEFLVHAWDFAIATGSQVIASEPVSEYVLAVAGKVITPATRNSAGFAAPAAVGSFAPVLDRLIAFTGRQPTAGHVSAT