Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | AraC/XylS family transcriptional regulator |
|---|
| MTBC0 PGAP re-annotation | AraC family transcriptional regulator |
|---|
| Revised (this work) | AraC family transcriptional regulator. Pfam: Arabinose_bd (PF12625.13), HTH_18 (PF12833.14). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O69703
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Transcriptional regulatory protein |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|
| eggNOG description | Transcriptional regulatory protein (Probably AraC XylS-family) |
|---|
| Orthologous group | COG2207 |
|---|
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 |
0.825 · relaxed/neutral
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
4 synonymous, 9 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 |
|---|
Arabinose_bd | PF12625.13 |
8.0e-38 | 20–204 |
Arabinose-binding domain of AraC transcription regulator, N-term |
HTH_18 | PF12833.14 |
5.4e-14 | 251–328 |
Helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv1931c |
transcriptional regulator |
884 |
879 |
coexpression:831 |
Rv1985c lysG |
HTH-type transcriptional regulator |
872 |
865 |
coexpression:840 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr |
865 |
860 |
coexpression:860 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR |
862 |
860 |
coexpression:860 |
Rv3840 |
transcriptional regulator |
860 |
860 |
coexpression:860 |
Rv3263 |
DNA methylase |
860 |
860 |
coexpression:860 |
Rv0212c nadR |
transcriptional regulator NadR |
860 |
860 |
coexpression:860 |
Rv1267c embR |
transcriptional regulator EmbR |
859 |
859 |
coexpression:859 |
Rv0339c iniR |
transcriptional regulator |
859 |
854 |
coexpression:802 |
Rv1151c cobB |
NAD-dependent protein deacylase |
861 |
853 |
coexpression:848 |
Rv1725c hyp |
hypothetical protein |
853 |
853 |
coexpression:853 |
Rv1674c |
transcriptional regulator |
859 |
851 |
coexpression:848 |
Rv3167c |
TetR family transcriptional regulator |
850 |
848 |
coexpression:848 |
Rv1359 |
transcriptional regulator |
846 |
846 |
coexpression:846 |
Rv2488c |
LuxR family transcriptional regulator |
850 |
842 |
coexpression:841 |
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: AraC/XylS family transcriptional regulator
- MTBC0 PGAP product: AraC family transcriptional regulator
- Pfam (hmmscan --cut_ga): Arabinose_bd PF12625.13 (E=8e-38), HTH_18 PF12833.14 (E=5e-14)
- (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_218253.1)
- Domains: Pfam-A via hmmscan --cut_ga — Arabinose_bd (PF12625.13), HTH_18 (PF12833.14)
- 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
COG2207
- Curated reference: UniProt
O69703
(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 —
89 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003961|Rv3736|
MSVVRGTALANYPSLVAGLGGDPATLLRAAGVRDQDVGNYDAFISIRAAIRAIESAAAVTATMDFGRRLAQRQGIEILGPVGVAARTAATVGDALAIFNTFMAAYSPVIAIRITPLAGQRSFIALEFLLDEPASYPQTMELALGVALGVIRLLLGADYAPLAVHLPHDPLTPEAFYLQYFGCRPYFAERVGGFTMRTADLSRPLNRDDVAHRVVVDYLSSITPLGEGIVESVRTIVRQLLPTGAATLNVVAEQFHLHPKTLQRRLAEENTTFVILVDRVRKDVADRYLRTTGIGLTHLARELGYAEQSVLTRSCKRWFGTGPAAYRNQARLQTTVSAPGSGRGPNPGNVSVSC
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