rpoA Family assigned · medium auto-curated
H37Rv Rv3457c · MTBC0 mtbc0_003675 ·
347 aa · 3903348–3904391 (-) ·
RefSeq NP_217974.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA-directed RNA polymerase subunit alpha |
|---|---|
| MTBC0 PGAP re-annotation | DNA-directed RNA polymerase subunit alpha |
| Revised (this work) | DNA-directed RNA polymerase subunit alpha. Pfam: RNA_pol_L (PF01193.30), RNA_pol_A_bac (PF01000.32), RNA_pol_A_CTD (PF03118.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGZ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA-directed RNA polymerase subunit alpha |
| EC (curated) |
EC 2.7.7.6
|
| Curated function | DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | rpoA |
| eggNOG description | DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates |
| Orthologous group | COG0202 |
| EC number |
EC 2.7.7.6
|
| KEGG orthology |
K03040
|
| KEGG pathways |
map00230, map00240, map01100, map03020
|
| KEGG modules |
M00183
|
| Gene Ontology (54) |
GO:0003674, GO:0003824, GO:0003899, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006139, GO:0006351 +42 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 | 0.687 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 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 |
|---|---|---|---|---|
RNA_pol_L | PF01193.30 | 7.4e-21 | 24–219 | RNA polymerase Rpb3/Rpb11 dimerisation domain |
RNA_pol_A_bac | PF01000.32 | 1.1e-38 | 54–169 | RNA polymerase Rpb3/RpoA insert domain |
RNA_pol_A_CTD | PF03118.22 | 7.4e-26 | 245–302 | Bacterial RNA polymerase, alpha chain C terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sigA (RNA polymerase sigma factor SigA), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2703 sigA |
RNA polymerase sigma factor SigA | 999 | 1000 ctx | cooccurence:508 experimental:999 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 999 | 1000 ctx | cooccurence:575 coexpression:957 experimental:999 database:844 textmining:970 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 999 | 1000 | coexpression:805 experimental:999 database:844 textmining:878 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 999 | 1000 ctx | cooccurence:481 coexpression:970 experimental:999 database:844 textmining:973 |
Rv3460c rpsM |
30S ribosomal protein S13 | 999 | 999 ctx | neighborhood:578 fusion:673 cooccurence:499 coexpression:926 experimental:808 |
Rv0718 rpsH |
30S ribosomal protein S8 | 999 | 999 ctx | cooccurence:612 coexpression:967 experimental:895 |
Rv3458c rpsD |
30S ribosomal protein S4 | 999 | 999 ctx | neighborhood:750 cooccurence:509 coexpression:958 experimental:902 textmining:413 |
Rv0707 rpsC |
30S ribosomal protein S3 | 999 | 999 ctx | cooccurence:702 coexpression:967 experimental:912 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 999 | 999 | experimental:999 |
Rv3459c rpsK |
30S ribosomal protein S11 | 999 | 999 ctx | neighborhood:578 fusion:691 cooccurence:495 coexpression:891 experimental:895 |
Rv0721 rpsE |
30S ribosomal protein S5 | 998 | 999 ctx | cooccurence:548 coexpression:968 experimental:901 |
Rv0704 rplB |
50S ribosomal protein L2 | 998 | 998 ctx | cooccurence:552 coexpression:975 experimental:850 |
Rv0705 rpsS |
30S ribosomal protein S19 | 998 | 998 ctx | cooccurence:434 coexpression:969 experimental:902 |
Rv3456c rplQ |
50S ribosomal protein L17 | 998 | 998 ctx | neighborhood:838 coexpression:969 experimental:474 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 998 | 998 ctx | cooccurence:510 coexpression:958 experimental:910 |
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: DNA-directed RNA polymerase subunit alpha
- MTBC0 PGAP product: DNA-directed RNA polymerase subunit alpha
- Pfam (hmmscan --cut_ga): RNA_pol_L PF01193.30 (E=7e-21), RNA_pol_A_bac PF01000.32 (E=1e-38), RNA_pol_A_CTD PF03118.22 (E=7e-26)
- (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_217974.1)
- Domains: Pfam-A via hmmscan --cut_ga — RNA_pol_L (PF01193.30), RNA_pol_A_bac (PF01000.32), RNA_pol_A_CTD (PF03118.22)
- 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
COG0202 - Curated reference: UniProt P9WGZ1 (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 —
347 functional partner(s); context anchor
sigA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003675|Rv3457c|rpoA MLISQRPTLSEDVLTDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTEIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPSFDPSEVAGYDVATGTWSTEGAYDEQDYAETEQL