citE Family assigned · medium auto-curated
H37Rv Rv2498c · MTBC0 mtbc0_002660 ·
273 aa · 2835245–2836066 (-) ·
RefSeq NP_217014.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | citrate (pro-3S)-lyase subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | citrate (pro-3S)-lyase subunit beta |
| Revised (this work) | Citrate (pro-3S)-lyase subunit beta. Pfam: HpcH_HpaI (PF03328.21), C-C_Bond_Lyase (PF15617.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPE1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Citrate lyase subunit beta-like protein |
| EC (curated) |
EC 4.1.-.-
|
| Curated function | May play a role in fatty acid biosynthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | citE |
| eggNOG description | Belongs to the HpcH HpaI aldolase family |
| Orthologous group | COG2301 |
| EC number |
EC 4.1.3.34
|
| KEGG orthology |
K01644
|
| KEGG pathways |
map02020
|
| Gene Ontology (17) |
GO:0000287, GO:0003674, GO:0005488, GO:0006082, GO:0006107, GO:0008150, GO:0008152, GO:0009987, GO:0019752, GO:0043167, GO:0043169, GO:0043436 +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 | 0.238 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 4 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 |
|---|---|---|---|---|
HpcH_HpaI | PF03328.21 | 9.7e-28 | 11–211 | HpcH/HpaI aldolase/citrate lyase |
C-C_Bond_Lyase | PF15617.13 | 8.1e-07 | 187–267 | C-C_Bond_Lyase of the TIM-Barrel fold |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2499c (oxidase regulatory-like protein), high confidence from genomic context alone (score 993 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2499c |
oxidase regulatory-like protein | 998 | 993 ctx | neighborhood:882 cooccurence:760 coexpression:761 textmining:816 |
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha | 990 | 981 ctx | neighborhood:881 coexpression:826 textmining:528 |
Rv2500c fadE19 |
acyl-CoA dehydrogenase FadE19 | 995 | 977 ctx | neighborhood:881 coexpression:787 textmining:830 |
Rv3075c hyp |
hypothetical protein | 949 | 926 | database:900 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 991 | 907 ctx | neighborhood:881 textmining:916 |
Rv2503c scoB |
succinyl-CoA:3-ketoacid-CoA transferase subunit B | 945 | 886 ctx | neighborhood:881 textmining:540 |
Rv2504c scoA |
succinyl-CoA:3-ketoacid-CoA transferase subunit A | 987 | 885 ctx | neighborhood:881 textmining:899 |
Rv2506 |
TetR family transcriptional regulator | 918 | 776 ctx | neighborhood:714 textmining:651 |
Rv2495c bkdC |
branched-chain keto acid dehydrogenase E2 component | 887 | 770 ctx | neighborhood:723 textmining:533 |
Rv2497c bkdA |
3-methyl-2-oxobutanoate dehydrogenase subunit alpha | 840 | 740 ctx | neighborhood:724 textmining:411 |
Rv2496c bkdB |
3-methyl-2-oxobutanoate dehydrogenase subunit beta | 746 | 737 ctx | neighborhood:723 |
Rv0727c fucA |
L-fuculose phosphate aldolase FucA | 731 | 732 | coexpression:732 |
Rv2505c fadD35 |
fatty-acid--CoA ligase FadD35 | 850 | 568 ctx | neighborhood:567 textmining:667 |
Rv1130 prpD |
2-methylcitrate dehydratase | 543 | 524 | |
Rv0216 |
hydratase | 524 | 501 ctx | fusion:401 |
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: citrate (pro-3S)-lyase subunit beta
- MTBC0 PGAP product: citrate (pro-3S)-lyase subunit beta
- Pfam (hmmscan --cut_ga): HpcH_HpaI PF03328.21 (E=1e-27), C-C_Bond_Lyase PF15617.13 (E=8e-07)
- (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_217014.1)
- Domains: Pfam-A via hmmscan --cut_ga — HpcH_HpaI (PF03328.21), C-C_Bond_Lyase (PF15617.13)
- 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
COG2301 - Curated reference: UniProt P9WPE1 (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 —
31 functional partner(s); context anchor
Rv2499c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002660|Rv2498c|citE MNLRAAGPGWLFCPADRPERFAKAAAAADVVILDLEDGVAEAQKPAARNALRDTPLDPERTVVRINAGGTADQARDLEALAGTAYTTVMLPKAESAAQVIELAPRDVIALVETARGAVCAAEIAAADPTVGMMWGAEDLIATLGGSSSRRADGAYRDVARHVRSTILLAASAFGRLALDAVHLDILDVEGLQEEARDAAAVGFDVTVCIHPSQIPVVRKAYRPSHEKLAWARRVLAASRSERGAFAFEGQMVDSPVLTHAETMLRRAGEATSE