ychF Resolved · high auto-curated
H37Rv Rv1112 · MTBC0 mtbc0_001194 ·
357 aa · 1246695–1247768 (+) ·
RefSeq NP_215628.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | GTP-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | redox-regulated ATPase YchF |
| Revised (this work) | Redox-regulated ATPase YchF. Pfam: MMR_HSR1 (PF01926.30), FeoB_N (PF02421.25), YchF-GTPase_C (PF06071.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53459
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribosome-binding ATPase YchF |
| Curated function | ATPase that binds to both the 70S ribosome and the 50S ribosomal subunit in a nucleotide-independent manner. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | ychF |
| eggNOG description | ATPase that binds to both the 70S ribosome and the 50S ribosomal subunit in a nucleotide-independent manner |
| Orthologous group | COG0012 |
| KEGG orthology |
K06942
|
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 | 2.109 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 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 |
|---|---|---|---|---|
MMR_HSR1 | PF01926.30 | 3.6e-22 | 5–114 | 50S ribosome-binding GTPase |
FeoB_N | PF02421.25 | 1.5e-08 | 6–47 | Ferrous iron transport protein B |
YchF-GTPase_C | PF06071.20 | 1.0e-38 | 273–356 | Protein of unknown function (DUF933) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lepA (GTP-binding protein LepA), high confidence from genomic context alone (score 842 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2404c lepA |
GTP-binding protein LepA | 879 | 842 ctx | cooccurence:719 coexpression:417 |
Rv1299 prfA |
peptide chain release factor PrfA | 845 | 821 ctx | cooccurence:477 coexpression:644 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 862 | 820 | coexpression:710 |
Rv1111c hyp |
hypothetical protein | 786 | 787 ctx | neighborhood:786 |
Rv3396c guaA |
GMP synthase | 810 | 751 | coexpression:656 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 856 | 725 | coexpression:662 textmining:500 |
Rv1292 argS |
arginine--tRNA ligase | 751 | 674 | coexpression:663 |
Rv0684 fusA1 |
elongation factor G | 732 | 674 ctx | cooccurence:511 |
Rv2614c thrS |
threonine--tRNA ligase | 720 | 635 ctx | cooccurence:532 |
Rv0683 rpsG |
30S ribosomal protein S7 | 717 | 631 | coexpression:500 |
Rv1113 vapB32 |
antitoxin VapB32 | 598 | 599 ctx | neighborhood:594 |
Rv1114 vapC32 |
ribonuclease VapC32 | 595 | 595 ctx | neighborhood:594 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 591 | 592 | coexpression:558 |
Rv3442c rpsI |
30S ribosomal protein S9 | 678 | 580 | coexpression:408 |
Rv1437 pgk |
phosphoglycerate kinase | 598 | 578 ctx | cooccurence:539 |
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: GTP-binding protein
- MTBC0 PGAP product: redox-regulated ATPase YchF
- Pfam (hmmscan --cut_ga): MMR_HSR1 PF01926.30 (E=4e-22), FeoB_N PF02421.25 (E=1e-08), YchF-GTPase_C PF06071.20 (E=1e-38)
- (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_215628.1)
- Domains: Pfam-A via hmmscan --cut_ga — MMR_HSR1 (PF01926.30), FeoB_N (PF02421.25), YchF-GTPase_C (PF06071.20)
- 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
COG0012 - Curated reference: UniProt O53459 (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 —
121 functional partner(s); context anchor
lepA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001194|Rv1112|ychF MSLSLGIVGLPNVGKSTLFNALTRNNVVAANYPFATIEPNEGVVSLPDPRLDKLAELFGSQRVVPAPVTFVDIAGLVKGASEGAGLGNKFLAHIRECDAICQVVRVFVDDDVTHVTGRVDPQSDIEVVETELILADLQTLERATGRLEKEARTNKARKPVYDAALRAQQVLDAGKTLFAAGVDAAALRELNLLTTKPFLYVFNADEAVLTDPARVGELRALVAPADAVFLDAAIESELTELDDESAAELLESIGQSERGLDALARAGFHTLKLQTFLTAGPKEARAWTIHQGDTAPKAAGVIHSDFEKGFIKAEIVSYDDLVAAGSMAAAKAAGKVRIEGKDYVMADGDVVEFRFNV