mkl Family assigned · medium auto-curated
H37Rv Rv0655 · MTBC0 - ·
359 aa · 751517–752596 (+) ·
RefSeq NP_215169.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ABC transporter ATP-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | ABC transporter ATP-binding protein. Pfam: ABC_tran (PF00005.34). |
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 |
P9WQL5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable ribonucleotide transport ATP-binding protein mkl |
| Curated function | Not known, could be involved in the transport of ribonucleotides. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | mkl |
| eggNOG description | ABC transporter |
| Orthologous group | COG1135 |
| KEGG orthology |
K02065
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00210, M00669, M00670
|
| Gene Ontology (21) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006810, GO:0006869, GO:0008150, GO:0010876, GO:0015850, GO:0015918, GO:0016020, GO:0030301 +9 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 | 0.65 · 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 |
|---|---|---|---|---|
ABC_tran | PF00005.34 | 5.6e-28 | 44–191 | ABC transporter |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: yrbE1A (membrane protein), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0167 yrbE1A |
membrane protein | 997 | 996 ctx | cooccurence:773 coexpression:846 experimental:505 database:800 textmining:469 |
Rv0168 yrbE1B |
membrane protein | 997 | 988 ctx | cooccurence:774 coexpression:480 experimental:505 database:800 textmining:810 |
Rv1964 yrbE3A |
integral membrane protein | 991 | 988 ctx | cooccurence:774 coexpression:450 experimental:505 database:800 |
Rv0588 yrbE2B hyp |
hypothetical protein | 990 | 987 ctx | cooccurence:774 coexpression:456 experimental:505 database:800 |
Rv3500c yrbE4B |
integral membrane protein | 990 | 987 ctx | cooccurence:774 coexpression:457 experimental:505 database:800 |
Rv1965 yrbE3B |
integral membrane protein | 989 | 987 ctx | cooccurence:773 coexpression:450 experimental:505 database:800 |
Rv3501c yrbE4A |
integral membrane protein | 987 | 987 ctx | cooccurence:773 coexpression:458 experimental:505 database:800 |
Rv0587 yrbE2A hyp |
hypothetical protein | 987 | 987 ctx | cooccurence:773 coexpression:455 experimental:505 database:800 |
Rv0170 mce1B |
Mce family protein Mce1B | 935 | 914 ctx | cooccurence:765 experimental:431 |
Rv1971 mce3F |
Mce family protein Mce3F | 940 | 900 ctx | cooccurence:759 experimental:431 textmining:424 |
Rv0172 mce1D |
Mce family protein Mce1D | 903 | 899 ctx | cooccurence:746 experimental:431 |
Rv0173 lprK |
Mce family lipoprotein LprK | 941 | 898 ctx | cooccurence:758 experimental:431 textmining:454 |
Rv0171 mce1C |
Mce family protein Mce1C | 930 | 897 ctx | cooccurence:722 experimental:431 |
Rv3497c mce4C |
Mce family protein Mce4C | 895 | 891 ctx | cooccurence:767 experimental:431 |
Rv0169 mce1A |
Mce family protein Mce1A | 964 | 888 ctx | cooccurence:692 experimental:431 textmining:699 |
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): ABC transporter ATP-binding protein
- Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=6e-28)
- (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_215169.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34)
- 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
COG1135 - Curated reference: UniProt P9WQL5 (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 —
56 functional partner(s); context anchor
yrbE1A - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0655|mkl MRYSDSYHTTGRWQPRASTEGFPMGVSIEVNGLTKSFGSSRIWEDVTLTIPAGEVSVLLGPSGTGKSVFLKSLIGLLRPERGSIIIDGTDIIECSAKELYEIRTLFGVLFQDGALFGSMNLYDNTAFPLREHTKKKESEIRDIVMEKLALVGLGGDEKKFPGEISGGMRKRAGLARALVLDPQIILCDEPDSGLDPVRTAYLSQLIMDINAQIDATILIVTHNINIARTVPDNMGMLFRKHLVMFGPREVLLTSDEPVVRQFLNGRRIGPIGMSEEKDEATMAEEQALLDAGHHAGGVEEIEGVPPQISATPGMPERKAVARRQARVREMLHTLPKKAQAAILDDLEGTHKYAVHEIGQ