Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | GntR family transcriptional regulator |
|---|
| MTBC0 PGAP re-annotation | FCD domain-containing protein |
|---|
| Revised (this work) | FCD domain-containing protein. Pfam: GntR (PF00392.28), FCD (PF07729.18). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95098
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Probable transcriptional regulatory protein |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|
| eggNOG description | FCD domain |
|---|
| Orthologous group | COG2186 |
|---|
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 |
0.409 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
6 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|
GntR | PF00392.28 |
3.5e-07 | 14–71 |
Bacterial regulatory proteins, gntR family |
FCD | PF07729.18 |
5.0e-17 | 103–226 |
FCD domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv3855 ethR |
HTH-type transcriptional repressor EthR |
842 |
837 |
coexpression:837 |
Rv3183 higA3 |
transcriptional regulator |
824 |
817 |
coexpression:817 |
Rv3263 |
DNA methylase |
813 |
814 |
coexpression:774 |
Rv0792c |
transcriptional regulator |
811 |
805 |
coexpression:764 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR |
809 |
804 |
coexpression:772 |
Rv3055 |
TetR family transcriptional regulator |
804 |
798 |
coexpression:750 |
Rv3830c |
TetR family transcriptional regulator |
802 |
796 |
coexpression:732 |
Rv0273c |
transcriptional regulator |
793 |
788 |
coexpression:753 |
Rv1019 |
transcriptional regulator |
779 |
772 |
coexpression:772 |
Rv1725c hyp |
hypothetical protein |
772 |
772 |
coexpression:772 |
Rv1985c lysG |
HTH-type transcriptional regulator |
781 |
770 |
coexpression:770 |
Rv1167c |
transcriptional regulator |
777 |
770 |
coexpression:705 |
Rv3840 |
transcriptional regulator |
759 |
759 |
coexpression:759 |
Rv1395 |
HTH-type transcriptional regulator |
758 |
758 |
coexpression:757 |
Rv0624 vapC30 |
ribonuclease VapC30 |
748 |
748 |
coexpression:748 |
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: GntR family transcriptional regulator
- MTBC0 PGAP product: FCD domain-containing protein
- Pfam (hmmscan --cut_ga): GntR PF00392.28 (E=3e-07), FCD PF07729.18 (E=5e-17)
- (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_217576.1)
- Domains: Pfam-A via hmmscan --cut_ga — GntR (PF00392.28), FCD (PF07729.18)
- 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
COG2186
- Curated reference: UniProt
P95098
(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 —
77 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003252|Rv3060c|
MSTEPDAVWTDKRASKIARRIEADIVRRGWPIGASLGSESALQQRFCVSRSVLREAVRLVEHHQVARMRRGPNGGLFICEPNAGPATRAVVIYLEYLGTTIGDLLGARLVLEPLAASLAAEHIDEPGIERLRAVLRAEERWRPGLPPPPEQFYRVLAEQSKNPVLQLFIDILMRLTKRYVQKSGTQSAGEAVEAAGQVHNEHSDIVAAVTAGDSAWAKTLSERHVEAVAGWLQQHQRGNDAAVRNGGRAREPRRAQQLILGAPRGKLAEVLAATIGDDIAASGWQVGSVFGTETALLERYQVSRAVLREAVRLLEYHAIAHMRRGPGGGLVVTTPQPQASIDTIALYLQYRKPSREDLRCVRDAIEIDNVAKVVKRRSEPEVASFLDTLGRPRLDNPTDDVRAAAVEEFRFHVGLARAAGNTMLDLFLLILVELFRRHLSSTEQALPTWSDVVAVGHAHVRILEAIGSGDDSLARCRTRRHLDAAASWWL
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