typA Resolved · high auto-curated
H37Rv Rv1165 · MTBC0 mtbc0_001254 ·
628 aa · 1302609–1304495 (+) ·
RefSeq NP_215681.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | GTP-binding translation elongation factor |
|---|---|
| MTBC0 PGAP re-annotation | translational GTPase TypA |
| Revised (this work) | Translational GTPase TypA. Pfam: GTP_EFTU (PF00009.34), EF-G_D2 (PF22042.3), GTP_EFTU_D2 (PF03144.32), EFG_C (PF00679.31), BipA_C (PF21018.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06563
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit assembly factor BipA |
| EC (curated) |
EC 3.6.5.-
|
| Curated function | A 50S ribosomal subunit assembly protein with GTPase activity, required for 50S subunit assembly at low temperatures, may also play a role in translation. Binds GTP and analogs. Binds the 70S ribosome between the 30S and 50S subunits, in a similar position as ribosome-bound EF-G; it contacts a number of ribosomal proteins, both rRNAs and the A-site tRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| Preferred name | typA |
| eggNOG description | GTP-binding protein TypA |
| Orthologous group | COG1217 |
| KEGG orthology |
K06207
|
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 | 0.203 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 4 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 |
|---|---|---|---|---|
GTP_EFTU | PF00009.34 | 1.9e-49 | 2–212 | Elongation factor Tu GTP binding domain |
EF-G_D2 | PF22042.3 | 4.2e-10 | 222–309 | Elongation factor G domain 2 |
GTP_EFTU_D2 | PF03144.32 | 3.4e-12 | 236–309 | Elongation factor Tu domain 2 |
EFG_C | PF00679.31 | 1.2e-21 | 417–501 | Elongation factor G C-terminus |
BipA_C | PF21018.3 | 3.8e-38 | 505–612 | TypA/BipA C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqW (monoacyl phosphatidylinositol tetramannoside-binding protein LpqW), high confidence from genomic context alone (score 901 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 900 | 901 ctx | neighborhood:773 coexpression:580 |
Rv1163 narJ |
nitrate reductase subunit delta | 873 | 838 ctx | neighborhood:785 |
Rv1162 narH |
nitrate reductase subunit beta | 829 | 795 ctx | neighborhood:783 |
Rv1164 narI |
nitrate reductase subunit gamma | 829 | 792 ctx | neighborhood:761 |
Rv1161 narG |
nitrate reductase subunit alpha | 786 | 761 ctx | neighborhood:746 |
Rv0641 rplA |
50S ribosomal protein L1 | 712 | 713 | coexpression:713 |
Rv1713 engA |
GTPase Der | 776 | 707 | coexpression:698 |
Rv3396c guaA |
GMP synthase | 784 | 700 | coexpression:647 |
Rv3442c rpsI |
30S ribosomal protein S9 | 656 | 656 | coexpression:649 |
Rv2890c rpsB |
30S ribosomal protein S2 | 652 | 652 | coexpression:645 |
Rv0702 rplD |
50S ribosomal protein L4 | 667 | 651 | coexpression:651 |
Rv3458c rpsD |
30S ribosomal protein S4 | 629 | 630 | coexpression:617 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 625 | 625 | coexpression:563 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 619 | 587 | coexpression:405 |
Rv2889c tsf |
elongation factor EF-Ts | 703 | 564 | coexpression:506 |
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 translation elongation factor
- MTBC0 PGAP product: translational GTPase TypA
- Pfam (hmmscan --cut_ga): GTP_EFTU PF00009.34 (E=2e-49), EF-G_D2 PF22042.3 (E=4e-10), GTP_EFTU_D2 PF03144.32 (E=3e-12), EFG_C PF00679.31 (E=1e-21), BipA_C PF21018.3 (E=4e-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_215681.1)
- Domains: Pfam-A via hmmscan --cut_ga — GTP_EFTU (PF00009.34), EF-G_D2 (PF22042.3), GTP_EFTU_D2 (PF03144.32), EFG_C (PF00679.31), BipA_C (PF21018.3)
- 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
COG1217 - Curated reference: UniProt O06563 (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 —
103 functional partner(s); context anchor
lpqW - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001254|Rv1165|typA MPFRNVAIVAHVDHGKTTLVDAMLRQSGALRERGELQERVMDTGDLEREKGITILAKNTAVHRHHPDGTVTVINVIDTPGHADFGGEVERGLSMVDGVLLLVDASEGPLPQTRFVLRKALAAHLPVILVVNKTDRPDARIAEVVDASHDLLLDVASDLDDEAAAAAEHALGLPTLYASGRAGVASTTAPPDGQVPDGTNLDPLFEVLEKHVPPPKGEPDAPLQALVTNLDASTFLGRLALIRIYNGRIRKGQQVAWIRQVDGQQTVTTAKITELLATEGVERKPTDAAVAGDIVAVAGLPEIMIGDTLAASANPVALPRITVDEPAISVTIGTNTSPLAGKVGGHKLTARMVRSRLDAELVGNVSIRVVDIGAPDAWEVQGRGELALAVLVEQMRREGFELTVGKPQVVTKTIDGTLHEPFESMTVDCPEEYIGAVTQLMAARKGRMVEMANHTTGWVRMDFVVPSRGLIGWRTDFLTETRGSGVGHAVFDGYRPWAGEIRARHTGSLVSDRAGAITPFALLQLADRGQFFVEPGQQTYEGMVVGINPRPEDLDINVTREKKLTNMRSSTADVIETLAKPLQLDLERAMELCAPDECVEVTPEIVRIRKVELAAAARARSRARTKARG