Rv0843 Family assigned · medium auto-curated
H37Rv Rv0843 · MTBC0 mtbc0_000898 ·
334 aa · 942539–943543 (+) ·
RefSeq NP_215358.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha |
| Revised (this work) | Thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha. Pfam: E1_dh (PF00676.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XWE5
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable dehydrogenase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | Dehydrogenase E1 component |
| Orthologous group | COG1071 |
| EC number |
EC 1.2.4.1
|
| KEGG orthology |
K00161
|
| KEGG pathways |
map00010, map00020, map00620, map01100, map01110, map01120, map01130, map01200, map04066, map04922, map05230
|
| KEGG modules |
M00307
|
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 | 0.96 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 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 |
|---|---|---|---|---|
E1_dh | PF00676.26 | 4.3e-41 | 41–312 | Dehydrogenase E1 component |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: bkdB (3-methyl-2-oxobutanoate dehydrogenase subunit beta), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2496c bkdB |
3-methyl-2-oxobutanoate dehydrogenase subunit beta | 999 | 1000 ctx | fusion:899 cooccurence:774 coexpression:728 experimental:829 database:662 textmining:415 |
Rv2495c bkdC |
branched-chain keto acid dehydrogenase E2 component | 983 | 978 ctx | cooccurence:772 coexpression:599 experimental:415 database:591 |
Rv2215 dlaT |
pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase | 981 | 974 ctx | cooccurence:740 coexpression:597 experimental:415 database:591 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 975 | 966 | coexpression:597 experimental:415 database:844 |
Rv1734c hyp |
hypothetical protein | 940 | 921 | coexpression:601 experimental:415 database:591 |
Rv0842 |
integral membrane protein | 887 | 887 ctx | neighborhood:882 |
Rv0462 lpdC |
dihydrolipoamide dehydrogenase | 900 | 879 ctx | cooccurence:443 coexpression:497 database:580 |
Rv3303c lpdA |
NAD(P)H quinone reductase LpdA | 877 | 870 ctx | cooccurence:414 coexpression:497 database:580 |
Rv2855 mtr |
mycothione reductase | 864 | 852 | coexpression:500 database:580 |
Rv0794c |
oxidoreductase | 857 | 844 | coexpression:502 database:580 |
Rv2713 sthA |
pyridine nucleotide transhydrogenase | 851 | 818 | coexpression:500 database:580 |
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 706 | 697 | database:565 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 705 | 676 | database:632 |
Rv1826 gcvH |
glycine cleavage system protein H | 679 | 659 | database:658 |
Rv2998A |
Rv2998A, len: 67 aa. Probable conserved hypothetical protein, (possibly gene fragment), highly similar to central part of two-component sens | 526 | 505 | database:429 |
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: dehydrogenase
- MTBC0 PGAP product: thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha
- Pfam (hmmscan --cut_ga): E1_dh PF00676.26 (E=4e-41)
- (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_215358.1)
- Domains: Pfam-A via hmmscan --cut_ga — E1_dh (PF00676.26)
- 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
COG1071 - Curated reference: UniProt I6XWE5 (TrEMBL, unreviewed; Predicted)
- 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 —
29 functional partner(s); context anchor
bkdB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000898|Rv0843| MTRTSEGLAAFVVDQLEELYRRMWVLRLLDMALEQLRIEGLINGPLQGGFGQEAVSVGAAAALGEGDVIITTHRPHAQHVGTDAPLGPVIADMLGATAGDLEGADEDAHIADPRAGLPAAIRVVKQSPLLAIGHAYALWLRDTGRVTLCVTQDCDVDADAFNEAADLAAVWQLPVVILVENIRGALSVHLDRYTHEPRVYRRAVAYGMPGVSVDGNDVEAVRDCVANAVVRARAGGGPTLVQAITYRTTDFSGSDRGGYRDLAGSEQFLDPLIFARRRLIAAGTTRGRLDEQERAACQQVADAVAFAKARARPNGGGPISRPTSGWHQQPKTRF