Rv0588 Family assigned · medium auto-curated
H37Rv Rv0588 · MTBC0 mtbc0_000618 ·
295 aa · 689479–690366 (+) ·
RefSeq NP_215102.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter permease |
| Revised (this work) | ABC transporter permease. Pfam: MlaE (PF02405.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07790
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Conserved hypothetical integral membrane protein YrbE2B |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | yrbE1B |
| eggNOG description | Permease MlaE |
| Orthologous group | COG0767 |
| KEGG orthology |
K02066
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00210, M00669, M00670
|
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 | 1.139 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.48% of strains (699) · clonal |
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 |
|---|---|---|---|---|
MlaE | PF02405.22 | 2.5e-54 | 76–279 | Permease MlaE |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mce2A (Mce family protein Mce2A), high confidence from genomic context alone (score 994 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) |
|---|---|---|---|---|
Rv0589 mce2A |
Mce family protein Mce2A | 998 | 994 ctx | neighborhood:786 cooccurence:761 coexpression:843 textmining:688 |
Rv0590 mce2B |
Mce-family protein Mce2B; Rv0590, (MTCY19H5.32c), len: 275 aa. Mce2B; belongs to 24-membered Mycobacterium tuberculosis Mce protein family ( | 994 | 994 ctx | neighborhood:791 cooccurence:772 coexpression:832 |
Rv0587 yrbE2A hyp |
hypothetical protein | 991 | 989 ctx | neighborhood:882 coexpression:806 |
Rv0655 mkl |
ABC transporter ATP-binding protein | 990 | 987 ctx | cooccurence:774 coexpression:456 experimental:505 database:800 |
Rv0591 mce2C |
Mce family protein Mce2C | 987 | 983 ctx | neighborhood:881 cooccurence:767 |
Rv0592 mce2D |
Mce family protein Mce2D | 970 | 970 ctx | neighborhood:781 cooccurence:770 |
Rv0594 mce2F |
Mce family protein Mce2F | 984 | 969 ctx | neighborhood:781 cooccurence:764 textmining:529 |
Rv0593 lprL |
Mce family lipoprotein LprL | 971 | 969 ctx | neighborhood:781 cooccurence:769 |
Rv0586 mce2R |
HTH-type transcriptional regulator Mce2R | 958 | 886 ctx | neighborhood:882 textmining:653 |
Rv0590A |
Mce-family related protein; Rv0590A, len: 84 aa. Probable continuation of mce2B|Rv0590. Can find no frameshift to account for this. Possible | 884 | 880 ctx | neighborhood:791 |
Rv1967 mce3B |
Mce family protein Mce3B | 881 | 878 ctx | cooccurence:771 |
Rv0171 mce1C |
Mce family protein Mce1C | 884 | 875 ctx | cooccurence:758 |
Rv3497c mce4C |
Mce family protein Mce4C | 879 | 875 ctx | cooccurence:772 |
Rv1971 mce3F |
Mce family protein Mce3F | 901 | 874 ctx | cooccurence:770 |
Rv0170 mce1B |
Mce family protein Mce1B | 877 | 873 ctx | cooccurence:772 |
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: ABC transporter permease
- Pfam (hmmscan --cut_ga): MlaE PF02405.22 (E=3e-54)
- (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_215102.1)
- Domains: Pfam-A via hmmscan --cut_ga — MlaE (PF02405.22)
- 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
COG0767 - Curated reference: UniProt O07790 (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 —
42 functional partner(s); context anchor
mce2A - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000618|Rv0588| MVESSTASAAAVLRARYPRTAASLDRYGGGTARRLERTGTFARFTRISVVQIGWALRRYRRETLRLVAEIGMGTGAMAVVGGTVAIIGFVTLSGGSLIAIQGFASLGNIGVEAFTGFFAALANTRVAAPIVSGVALAATVGAGATAQLGAMRISEEIDALEVMGIKSISFLVSTRILGGLVVIMPLYALALDMAFTSGQVVTTVFYGQSNGTYEHYFRTFLRPEDVGWSVVEVVIIAVVVMITHCYYGYTASGGPVGVGQAVGRSMRFSLVSVVVVVLLAELALYGVDPNFNLTV