modA Family assigned · medium auto-curated
H37Rv Rv1857 · MTBC0 mtbc0_001970 ·
261 aa · 2123023–2123808 (+) ·
RefSeq NP_216373.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | molybdate ABC transporter substrate-binding lipoprotein ModA |
|---|---|
| MTBC0 PGAP re-annotation | molybdate ABC transporter substrate-binding protein |
| Revised (this work) | Molybdate ABC transporter substrate-binding protein. Pfam: SBP_bac_11 (PF13531.12), SBP_bac_1 (PF01547.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGU3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Molybdate-binding protein ModA |
| Curated function | Involved in the transport of molybdenum into the cell. Part of the binding-protein-dependent transport system ModABCD (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | modA |
| eggNOG description | ABC transporter, periplasmic molybdate-binding protein |
| Orthologous group | COG0725 |
| KEGG orthology |
K02020
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00189
|
| Gene Ontology (21) |
GO:0003674, GO:0005488, GO:0005575, GO:0005623, GO:0008150, GO:0030288, GO:0030313, GO:0030973, GO:0031975, GO:0040007, GO:0042597, GO:0043167 +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 | 0.369 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 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 |
|---|---|---|---|---|
SBP_bac_11 | PF13531.12 | 7.2e-48 | 41–258 | Bacterial extracellular solute-binding protein |
SBP_bac_1 | PF01547.31 | 7.8e-26 | 46–249 | Bacterial extracellular solute-binding protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: modB (molybdenum ABC transporter permease ModB), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1858 modB |
molybdenum ABC transporter permease ModB | 999 | 999 ctx | neighborhood:816 cooccurence:772 coexpression:886 database:800 textmining:902 |
Rv1859 modC |
molybdenum ABC transporter ATP-binding protein ModC | 987 | 984 ctx | neighborhood:882 database:800 |
Rv2399c cysT |
sulfate ABC transporter permease CysT | 969 | 964 ctx | cooccurence:623 experimental:895 |
Rv1860 apa hyp |
hypothetical protein | 682 | 652 ctx | neighborhood:652 |
Rv2398c cysW |
sulfate ABC transporter permease CysW | 769 | 627 ctx | cooccurence:617 textmining:408 |
Rv1856c |
oxidoreductase | 582 | 579 ctx | neighborhood:573 |
Rv0869c moaA2 |
molybdenum cofactor biosynthesis protein MoaA | 746 | 544 ctx | cooccurence:424 textmining:468 |
Rv1855c |
oxidoreductase | 507 | 508 ctx | neighborhood:507 |
Rv3859c gltB |
glutamate synthase large subunit | 539 | 474 | coexpression:403 |
Rv0865 mog |
molybdopterin biosynthesis protein | 588 | 435 | |
Rv2920c amt |
ammonium transporter integral membrane protein | 480 | 420 | coexpression:417 |
Rv2397c cysA1 |
sulfate ABC transporter ATP-binding protein CysA | 552 | 382 | |
Rv3111 moaC1 |
cyclic pyranopterin monophosphate synthase accessory protein | 553 | 381 | |
Rv0984 moaB2 |
pterin-4-alpha-carbinolamine dehydratase | 646 | 368 | textmining:464 |
Rv0868c moaD2 |
cyclic pyranopterin monophosphate synthase | 489 | 345 |
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: molybdate ABC transporter substrate-binding lipoprotein ModA
- MTBC0 PGAP product: molybdate ABC transporter substrate-binding protein
- Pfam (hmmscan --cut_ga): SBP_bac_11 PF13531.12 (E=7e-48), SBP_bac_1 PF01547.31 (E=8e-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_216373.1)
- Domains: Pfam-A via hmmscan --cut_ga — SBP_bac_11 (PF13531.12), SBP_bac_1 (PF01547.31)
- 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
COG0725 - Curated reference: UniProt P9WGU3 (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 —
38 functional partner(s); context anchor
modB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001970|Rv1857|modA MRWIGLSTGLVSAMLVAGLVACGSNSPASSPAGPTQGARSIVVFAAASLQSAFTQIGEQFKAGNPGVNVNFAFAGSSELATQLTQGATADVFASADTAQMDSVAKAGLLAGHPTNFATNTMVIVAAAGNPKKIRSFADLTRPGLNVVVCQPSVPCGSATRRIEDATGIHLNPVSEELSVTDVLNKVITGQADAGLVYVSDALSVATKVTCVRFPEAAGVVNVYAIAVLKRTSQPALARQFVAMVTAAAGRRILDQSGFAKP