fic Family assigned · medium auto-curated
H37Rv Rv3641c · MTBC0 mtbc0_003856 ·
211 aa · 4103630–4104265 (-) ·
RefSeq NP_218158.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cell filamentation protein Fic |
|---|---|
| MTBC0 PGAP re-annotation | Fic/DOC family protein |
| Revised (this work) | Fic/DOC family protein. Pfam: Fic (PF02661.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YCN3
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | protein adenylyltransferase |
| EC (curated) |
EC 2.7.7.108
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| Preferred name | fic |
| eggNOG description | Fic/DOC family |
| Orthologous group | COG2184 |
| KEGG orthology |
K04095
|
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 | 0.316 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (373) · 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 |
|---|---|---|---|---|
Fic | PF02661.24 | 1.8e-13 | 64–162 | Fic/DOC family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3640c (transposase), medium confidence from genomic context alone (score 490 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3642c hyp |
hypothetical protein | 877 | 877 ctx | neighborhood:875 |
Rv3640c |
transposase | 490 | 490 ctx | neighborhood:488 |
Rv2970A hyp |
hypothetical protein | 476 | 476 | coexpression:403 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 412 | 413 | coexpression:413 |
Rv1884c rpfC |
resuscitation-promoting factor RpfC | 410 | 411 | coexpression:411 |
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 410 | 411 | coexpression:411 |
Rv2450c rpfE |
resuscitation-promoting factor RpfE | 410 | 410 | coexpression:410 |
Rv0887c hyp |
hypothetical protein | 433 | 408 | coexpression:408 |
Rv2971 |
oxidoreductase | 402 | 403 | coexpression:402 |
Rv2389c rpfD |
resuscitation-promoting factor RpfD | 402 | 403 | coexpression:403 |
Rv0867c rpfA |
resuscitation-promoting factor RpfA | 400 | 401 | coexpression:401 |
Rv2515c hyp |
hypothetical protein | 405 | 199 | |
Rv0207c hyp |
hypothetical protein | 829 | 171 | textmining:803 |
Rv3662c hyp |
hypothetical protein | 587 | 113 | textmining:554 |
Rv0366c hyp |
hypothetical protein | 764 | 86 | textmining:753 |
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: cell filamentation protein Fic
- MTBC0 PGAP product: Fic/DOC family protein
- Pfam (hmmscan --cut_ga): Fic PF02661.24 (E=2e-13)
- (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_218158.1)
- Domains: Pfam-A via hmmscan --cut_ga — Fic (PF02661.24)
- 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
COG2184 - Curated reference: UniProt I6YCN3 (TrEMBL, unreviewed; Predicted)
- 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 —
23 functional partner(s); context anchor
Rv3640c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003856|Rv3641c|fic MPHPWDTGDHERNWQGYFIPAMSVLRNRVGARTHAELRDAENDLVEARVIELREDPNLLGDRTDLAYLRAIHRQLFQDIYVWAGDLRTVGIEKEDESFCAPGGISRPMEHVAAEIYQLDRLRAVGEGDLAGQVAYRYDYVNYAHPFREGNGRSTREFFDLLLSERGSGLDWGKTDLEELHGACHVARANSDLTGLVAMFKGILDAEPTYDF