Rv1357c Resolved · high auto-curated
H37Rv Rv1357c · MTBC0 mtbc0_001457 ·
307 aa · 1535995–1536918 (-) ·
RefSeq NP_215873.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | cyclic diguanylate phosphodiesterase |
| Revised (this work) | Cyclic diguanylate phosphodiesterase. Pfam: EAL (PF00563.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WM07
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv1357c |
UniProt still lists this protein as Uncharacterized protein Rv1357c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | EAL domain |
| Orthologous group | COG2200 |
| Gene Ontology (57) |
GO:0003674, GO:0003824, GO:0006139, GO:0006725, GO:0006753, GO:0006793, GO:0006796, GO:0006807, GO:0008081, GO:0008150, GO:0008152, GO:0009056 +45 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 | 0.643 · 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 |
|---|---|---|---|---|
EAL | PF00563.26 | 3.0e-66 | 61–298 | EAL domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1354c hyp |
hypothetical protein | 948 | 903 | coexpression:858 textmining:487 |
Rv1356c hyp |
hypothetical protein | 864 | 864 | coexpression:860 |
Rv1358 |
transcriptional regulator | 871 | 863 | coexpression:804 |
Rv1364c |
sigma factor regulatory protein | 868 | 862 | coexpression:843 |
Rv1355c moeY |
molybdopterin biosynthesis protein MoeY | 848 | 848 | coexpression:848 |
Rv0894 |
transcriptional regulator | 731 | 731 | coexpression:731 |
Rv0895 |
diacyglycerol O-acyltransferase | 554 | 555 | coexpression:553 |
Rv1359 |
transcriptional regulator | 534 | 534 | coexpression:404 |
Rv1353c |
HTH-type transcriptional regulator | 450 | 449 | coexpression:449 |
Rv3287c rsbW |
anti-sigma factor RsbW | 416 | 417 | coexpression:410 |
Rv1173 fbiC |
FO synthase | 416 | 417 | coexpression:417 |
Rv3657c |
membrane protein | 411 | 412 | coexpression:409 |
Rv0990c hyp |
hypothetical protein | 411 | 412 | coexpression:403 |
Rv3658c |
transmembrane protein | 408 | 408 | coexpression:405 |
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: cyclic diguanylate phosphodiesterase
- Pfam (hmmscan --cut_ga): EAL PF00563.26 (E=3e-66)
- (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_215873.1)
- Domains: Pfam-A via hmmscan --cut_ga — EAL (PF00563.26)
- 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
COG2200 - Curated reference: UniProt P9WM07 (SwissProt, reviewed; 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 — 14 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001457|Rv1357c| MDRCCQRATAFACALRPTKLIDYEEMFRGAMQARAMVANPDQWADSDRDQVNTRHYLSTSMRVALDRGEFFLVYQPIIRLADNRIIGAEALLRWEHPTLGTLLPGRFIDRAENNGLMVPLTAFVLEQACRHVRSWRDHSTDPQPFVSVNVSASTICDPGFLVLVEGVLGETGLPAHALQLELAEDARLSRDEKAVTRLQELSALGVGIAIDDFGIGFSSLAYLPRLPVDVVKLGGKFIECLDGDIQARLANEQITRAMIDLGDKLGITVTAKLVETPSQAARLRAFGCKAAQGWHFAKALPVDFFRE