Rv3788 Family assigned · medium auto-curated
H37Rv Rv3788 · MTBC0 mtbc0_004016 ·
161 aa · 4258901–4259386 (+) ·
RefSeq NP_218305.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | GreA/GreB family elongation factor |
| Revised (this work) | GreA/GreB family elongation factor. Pfam: GreA_GreB (PF01272.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKW7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv3788 |
UniProt still lists this protein as Uncharacterized protein Rv3788; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcription elongation factor, GreA/GreB, C-term |
| Orthologous group | COG0782 |
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 | 0.923 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 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 |
|---|---|---|---|---|
GreA_GreB | PF01272.26 | 2.0e-09 | 89–158 | Transcription elongation factor, GreA/GreB, C-term |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3789 (GtrA family protein), high confidence from genomic context alone (score 777 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) |
|---|---|---|---|---|
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 956 | 944 | coexpression:423 experimental:906 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 938 | 913 | experimental:905 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 915 | 905 | experimental:895 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 910 | 898 | experimental:892 |
Rv3789 |
GtrA family protein | 776 | 777 ctx | neighborhood:768 |
Rv1963c mce3R |
transcriptional repressor Mce3R | 760 | 751 ctx | cooccurence:747 |
Rv3790 dprE1 |
decaprenylphosphoryl-beta-D-ribose oxidase | 744 | 745 ctx | neighborhood:732 |
Rv3793 embC |
arabinosyltransferase C | 736 | 736 ctx | neighborhood:732 |
Rv3791 dprE2 |
decaprenylphosphoryl-D-2-keto erythropentose reductase | 735 | 736 ctx | neighborhood:732 |
Rv3792 aftA |
arabinofuranosyltransferase | 733 | 734 ctx | neighborhood:732 |
Rv0538 |
membrane protein | 725 | 726 ctx | cooccurence:724 |
Rv1775 hyp |
hypothetical protein | 713 | 713 ctx | cooccurence:713 |
Rv3903c cpnT hyp |
hypothetical protein | 703 | 702 ctx | cooccurence:700 |
Rv2113 |
integral membrane protein | 673 | 674 ctx | cooccurence:667 |
Rv1937 |
oxygenase | 657 | 656 ctx | cooccurence:627 |
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: GreA/GreB family elongation factor
- Pfam (hmmscan --cut_ga): GreA_GreB PF01272.26 (E=2e-09)
- (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_218305.1)
- Domains: Pfam-A via hmmscan --cut_ga — GreA_GreB (PF01272.26)
- 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
COG0782 - Curated reference: UniProt P9WKW7 (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 —
52 functional partner(s); context anchor
Rv3789 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004016|Rv3788| MSEKVESKGLADAARDHLAAELARLRQRRDRLEVEVKNDRGMIGDHGDAAEAIQRADELAILGDRINELDRRLRTGPTPWSGSETLPGGTEVTLRFPDGEVVTMHVISVVEETPVGREAETLTARSPLGQALAGHQPGDTVTYSTPQGPNQVQLLAVKLPS