hflX Family assigned · medium auto-curated
H37Rv Rv2725c · MTBC0 - ·
495 aa · 3037427–3038914 (-) ·
RefSeq NP_217241.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | GTP-binding protein HflX |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | GTP-binding protein HflX. Pfam: GTP-bdg_N (PF13167.12), GTP-bdg_M (PF16360.11), MMR_HSR1 (PF01926.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O33230
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | GTPase HflX |
| Curated function | GTPase that associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | hflX |
| eggNOG description | GTPase that associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis |
| Orthologous group | COG2262 |
| KEGG orthology |
K03665
|
| Gene Ontology (14) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0016462, GO:0016787, GO:0016817, GO:0016818, GO:0016887, GO:0017111 +2 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 | 0.969 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (169) · 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 |
|---|---|---|---|---|
GTP-bdg_N | PF13167.12 | 4.1e-33 | 90–177 | GTP-binding GTPase N-terminal |
GTP-bdg_M | PF16360.11 | 2.4e-28 | 179–265 | GTP-binding GTPase Middle Region |
MMR_HSR1 | PF01926.30 | 6.9e-21 | 273–395 | 50S ribosome-binding GTPase |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0640 rplK |
50S ribosomal protein L11 | 932 | 921 | experimental:920 |
Rv2904c rplS |
50S ribosomal protein L19 | 919 | 916 | experimental:911 |
Rv2442c rplU |
50S ribosomal protein L21 | 915 | 916 | experimental:912 |
Rv2441c rpmA |
50S ribosomal protein L27 | 916 | 915 | experimental:911 |
Rv0979A rpmF |
50S ribosomal protein L32 | 921 | 912 | experimental:911 |
Rv3456c rplQ |
50S ribosomal protein L17 | 912 | 912 | experimental:911 |
Rv1643 rplT |
50S ribosomal protein L20 | 912 | 912 | experimental:911 |
Rv0701 rplC |
50S ribosomal protein L3 | 919 | 908 | experimental:905 |
Rv0702 rplD |
50S ribosomal protein L4 | 919 | 908 | experimental:906 |
Rv0706 rplV |
50S ribosomal protein L22 | 913 | 908 | experimental:905 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 907 | 908 | experimental:907 |
Rv0704 rplB |
50S ribosomal protein L2 | 910 | 907 | experimental:905 |
Rv0715 rplX |
50S ribosomal protein L24 | 907 | 907 | experimental:905 |
Rv3443c rplM |
50S ribosomal protein L13 | 915 | 906 | experimental:905 |
Rv0708 rplP |
50S ribosomal protein L16 | 904 | 905 | experimental:903 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): GTP-binding protein HflX
- Pfam (hmmscan --cut_ga): GTP-bdg_N PF13167.12 (E=4e-33), GTP-bdg_M PF16360.11 (E=2e-28), MMR_HSR1 PF01926.30 (E=7e-21)
- (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_217241.1)
- Domains: Pfam-A via hmmscan --cut_ga — GTP-bdg_N (PF13167.12), GTP-bdg_M (PF16360.11), MMR_HSR1 (PF01926.30)
- 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
COG2262 - Curated reference: UniProt O33230 (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 — 87 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2725c|hflX MPANSDARPAATCHHRVLAMTYPDPPQTGLSDFTPSLGELALEDRSALRRVAGLSTELADVSEVEYRQLRLERVVLVGVWTEGSAADNRASLAELAALAETAGSQVLEGLIQRRDKPDPSTYIGSGKAAELREVIVATGADTVICDGELSPAQLTALEKAVQVKVIDRTALILDIFAQHATSREGKAQVSLAQMEYMLPRLRGWGESMSRQAGGRAGGSGGGVGLRGPGETKIETDRRRIRERMAKLRRDIRAMKQVRDTQRSRRRHSDVPSIAIVGYTNAGKSSLLNALTGAGVLVQDALFATLEPTTRRAEFGDGRPVVLTDTVGFVRHLPTQLVEAFRSTLEEVVHADLLVHVVDGSDGHPLAQIDAVRQVISEVIADHDGDPPPELLVVNKVDVASDLMLAKLRHGLPGAVFVSARTGDGIDALRRRMAELVVPADTAVDVVIPYDRGDLVARVHADGRIQQAEHKPEGTRIKARVPEALAATLREFAPRA