engA Resolved · high auto-curated
H37Rv Rv1713 · MTBC0 mtbc0_001823 ·
463 aa · 1952303–1953694 (+) ·
RefSeq NP_216229.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | GTPase Der |
|---|---|
| MTBC0 PGAP re-annotation | ribosome biogenesis GTPase Der |
| Revised (this work) | Ribosome biogenesis GTPase Der. Pfam: MMR_HSR1 (PF01926.30), FeoB_N (PF02421.25), GTP_EFTU (PF00009.34), KH_dom-like (PF14714.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNL3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | GTPase Der |
| Curated function | GTPase that plays an essential role in the late steps of ribosome biogenesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | der |
| eggNOG description | GTPase that plays an essential role in the late steps of ribosome biogenesis |
| Orthologous group | COG1160 |
| KEGG orthology |
K03977
|
| Gene Ontology (10) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0040007, GO:0044464, GO:0071944
|
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 | 2.547 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 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 | 1.4e-23 | 29–143 | 50S ribosome-binding GTPase |
FeoB_N | PF02421.25 | 5.0e-14 | 201–362 | Ferrous iron transport protein B |
GTP_EFTU | PF00009.34 | 1.3e-08 | 265–369 | Elongation factor Tu GTP binding domain |
KH_dom-like | PF14714.12 | 7.6e-25 | 375–453 | KH-domain-like of EngA bacterial GTPase enzymes, C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cmk (cytidylate kinase), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1712 cmk |
cytidylate kinase | 999 | 999 ctx | neighborhood:881 fusion:887 coexpression:849 textmining:917 |
Rv1711 |
RNA pseudouridine synthase | 995 | 993 ctx | neighborhood:881 cooccurence:704 coexpression:810 |
Rv1710 scpB |
segregation and condensation protein ScpB | 981 | 971 ctx | neighborhood:881 coexpression:723 |
Rv1709 scpA |
segregation and condensation protein ScpA | 937 | 928 ctx | neighborhood:881 |
Rv1708 |
initiation inhibitor protein | 883 | 883 ctx | neighborhood:881 |
Rv2343c dnaG |
DNA primase | 873 | 866 | coexpression:863 |
Rv2982c gpdA2 |
glycerol-3-phosphate dehydrogenase | 853 | 833 ctx | fusion:407 coexpression:708 |
Rv0541c |
integral membrane protein | 808 | 808 | coexpression:808 |
Rv0564c gpdA1 |
glycerol-3-phosphate dehydrogenase | 812 | 788 | coexpression:704 |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 781 | 757 | coexpression:738 |
Rv1707 |
transmembrane protein | 743 | 744 ctx | neighborhood:744 |
Rv0542c menE |
2-succinylbenzoic acid--CoA ligase | 736 | 736 | coexpression:734 |
Rv2364c era |
GTPase Era | 761 | 735 ctx | cooccurence:704 |
Rv2916c ffh |
signal recognition particle protein | 743 | 716 ctx | cooccurence:671 |
Rv1389 gmk |
guanylate kinase | 764 | 710 ctx | cooccurence:607 |
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: GTPase Der
- MTBC0 PGAP product: ribosome biogenesis GTPase Der
- Pfam (hmmscan --cut_ga): MMR_HSR1 PF01926.30 (E=1e-23), FeoB_N PF02421.25 (E=5e-14), GTP_EFTU PF00009.34 (E=1e-08), KH_dom-like PF14714.12 (E=8e-25)
- (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_216229.1)
- Domains: Pfam-A via hmmscan --cut_ga — MMR_HSR1 (PF01926.30), FeoB_N (PF02421.25), GTP_EFTU (PF00009.34), KH_dom-like (PF14714.12)
- 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
COG1160 - Curated reference: UniProt P9WNL3 (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 —
82 functional partner(s); context anchor
cmk - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001823|Rv1713|engA MTQDGTWVDESDWQLDDSEIAESGAAPVVAVVGRPNVGKSTLVNRILGRREAVVQDIPGVTRDRVCYDALWTGRRFVVQDTGGWEPNAKGLQRLVAEQASVAMRTADAVILVVDAGVGATAADEAAARILLRSGKPVFLAANKVDSEKGESDAAALWSLGLGEPHAISAMHGRGVADLLDGVLAALPEVGESASASGGPRRVALVGKPNVGKSSLLNKLAGDQRSVVHEAAGTTVDPVDSLIELGGDVWRFVDTAGLRRKVGQASGHEFYASVRTHAAIDSAEVAIVLIDASQPLTEQDLRVISMVIEAGRALVLAYNKWDLVDEDRRELLQREIDRELVQVRWAQRVNISAKTGRAVHKLVPAMEDALASWDTRIATGPLNTWLTEVTAATPPPVRGGKQPRILFATQATARPPTFVLFTTGFLEAGYRRFLERRLRETFGFDGSPIRVNVRVREKRAGKRR