greA Resolved · high auto-curated
H37Rv Rv1080c · MTBC0 - ·
164 aa · 1205304–1205798 (-) ·
RefSeq NP_215596.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcription elongation factor GreA |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transcription elongation factor GreA. Pfam: GreA_GreB_N (PF03449.21), GreA_GreB (PF01272.26). |
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 |
P9WMT9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcription elongation factor GreA |
| Curated function | Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreA releases sequences of 2 to 3 nucleotides. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | greA |
| eggNOG description | Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreA releases sequences of 2 to 3 nucleotides |
| Orthologous group | COG0782 |
| KEGG orthology |
K03624
|
| Gene Ontology (17) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0042221, GO:0044424 +5 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 | 0.313 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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_N | PF03449.21 | 2.6e-25 | 8–76 | Transcription elongation factor, N-terminal |
GreA_GreB | PF01272.26 | 8.1e-13 | 82–160 | Transcription elongation factor, GreA/GreB, C-term |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1081c (membrane protein), medium confidence from genomic context alone (score 563 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 943 | 922 | coexpression:472 experimental:819 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 882 | 866 | experimental:798 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 915 | 862 | experimental:818 textmining:414 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 862 | 844 | experimental:793 |
Rv2785c rpsO |
30S ribosomal protein S15 | 565 | 565 | coexpression:560 |
Rv1081c |
membrane protein | 562 | 563 ctx | neighborhood:560 |
Rv3458c rpsD |
30S ribosomal protein S4 | 573 | 554 | coexpression:466 |
Rv0702 rplD |
50S ribosomal protein L4 | 564 | 554 | coexpression:460 |
Rv1082 mca |
mycothiol S-conjugate amidase | 543 | 543 ctx | neighborhood:468 |
Rv2904c rplS |
50S ribosomal protein L19 | 571 | 531 | coexpression:515 |
Rv2783c gpsI |
bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase | 550 | 496 | coexpression:479 |
Rv1298 rpmE |
50S ribosomal protein L31 | 499 | 480 | coexpression:477 |
Rv0704 rplB |
50S ribosomal protein L2 | 476 | 476 | coexpression:475 |
Rv1083 hyp |
hypothetical protein | 453 | 454 ctx | neighborhood:452 |
Rv0639 nusG |
transcription termination/antitermination protein NusG | 746 | 440 | textmining:565 |
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): transcription elongation factor GreA
- Pfam (hmmscan --cut_ga): GreA_GreB_N PF03449.21 (E=3e-25), GreA_GreB PF01272.26 (E=8e-13)
- (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_215596.1)
- Domains: Pfam-A via hmmscan --cut_ga — GreA_GreB_N (PF03449.21), 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 P9WMT9 (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 —
45 functional partner(s); context anchor
Rv1081c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1080c|greA MTDTQVTWLTQESHDRLKAELDQLIANRPVIAAEINDRREEGDLRENGGYHAAREEQGQQEARIRQLQDLLSNAKVGEAPKQSGVALPGSVVKVYYNGDKSDSETFLIATRQEGVSDGKLEVYSPNSPLGGALIDAKVGETRSYTVPNGSTVSVTLVSAEPYHS