Rv3404c Resolved · high auto-curated
H37Rv Rv3404c · MTBC0 mtbc0_003618 ·
234 aa · 3849319–3850023 (-) ·
RefSeq NP_217921.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | dTDP-4-amino-4%2C6-dideoxyglucose formyltransferase |
| Revised (this work) | DTDP-4-amino-4%2C6-dideoxyglucose formyltransferase. Pfam: Formyl_trans_N (PF00551.25), N_formyltrans_C (PF18216.7). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKZ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | dTDP-4-amino-4,6-dideoxyglucose formyltransferase |
| EC (curated) |
EC 2.1.2.-
|
| Curated function | Sugar N-formyltransferase that catalyzes the conversion of dTDP-4-amino-4,6-dideoxyglucose into dTDP-4-formamido-4,6-dideoxyglucose using N(10)-formyltetrahydrofolate as the carbon source. Plays a role in virulence. Has no activity on dTDP-3-amino-3,6-dideoxyglucose, dTDP-3-amino-3,6-dideoxygalactose, UDP-4-amino-4-deoxyarabinose, and GDP-4-amino-4,6-dideoxymannose. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| eggNOG description | Formyl transferase |
| Orthologous group | COG0223 |
| Gene Ontology (61) |
GO:0003674, GO:0003824, GO:0004479, GO:0005488, GO:0005515, GO:0006139, GO:0006396, GO:0006399, GO:0006400, GO:0006412, GO:0006413, GO:0006464 +49 more
|
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 | 0.463 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 |
|---|---|---|---|---|
Formyl_trans_N | PF00551.25 | 3.0e-15 | 56–150 | Formyl transferase |
N_formyltrans_C | PF18216.7 | 6.5e-15 | 177–226 | N-formyltransferase dimerization C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3405c (HTH-type transcriptional regulator), medium confidence from genomic context alone (score 642 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) |
|---|---|---|---|---|
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 980 | 970 | coexpression:966 |
Rv3403c hyp |
hypothetical protein | 798 | 799 ctx | neighborhood:746 |
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 748 | 749 | coexpression:703 |
Rv2533c nusB |
N utilization substance protein B | 710 | 683 | coexpression:650 |
Rv3402c hyp |
hypothetical protein | 676 | 657 | |
Rv1402 priA |
primosomal protein N' | 655 | 655 | coexpression:613 |
Rv3405c |
HTH-type transcriptional regulator | 642 | 642 ctx | neighborhood:640 |
Rv3012c gatC |
glutamyl-tRNA(GLN) amidotransferase subunit C | 572 | 556 | |
Rv0429c def |
polypeptide deformylase | 582 | 527 | coexpression:413 |
Rv3356c folD |
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase | 549 | 489 | coexpression:460 |
Rv3025c iscS |
cysteine desulfurase | 460 | 460 | |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 494 | 452 | coexpression:421 |
Rv1901 cinA |
competence damage-inducible protein CinA | 447 | 447 | coexpression:404 |
Rv2879c rlmN |
Conserved hypothetical protein; Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs; Belong | 446 | 447 | coexpression:428 |
Rv2880c |
Rv2880c, (MTCY274.11c), len: 275 aa. Conserved hypothetical protein, highly similar in N-terminus to others e.g. O86754|SC6A9.22c hypothetic | 445 | 445 | coexpression:426 |
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: dTDP-4-amino-4%2C6-dideoxyglucose formyltransferase
- Pfam (hmmscan --cut_ga): Formyl_trans_N PF00551.25 (E=3e-15), N_formyltrans_C PF18216.7 (E=6e-15)
- (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_217921.1)
- Domains: Pfam-A via hmmscan --cut_ga — Formyl_trans_N (PF00551.25), N_formyltrans_C (PF18216.7)
- 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
COG0223 - Curated reference: UniProt P9WKZ3 (SwissProt, reviewed; 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 —
38 functional partner(s); context anchor
Rv3405c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003618|Rv3404c| MTILILTDNVHAHALAVDLQARHGDMDVYQSPIGQLPGVPRCDVAERVAEIVERYDLVLSFHCKQRFPAALIDGVRCVNVHPGFNPYNRGWFPQVFSIIDGQKVGVTIHEIDDQLDHGPIIAQRECAIESWDSSGSVYARLMDIERELVLEHFDAIRDGSYTAKSPATEGNLNLKKDFEQLRRLDLNERGTFGHFLNRLRALTHDDFRNAWFVDASGRKVFVRVVLEPEKPAEA