Rv1045 Family assigned · medium auto-curated
H37Rv Rv1045 · MTBC0 mtbc0_001122 ·
293 aa · 1175011–1175892 (+) ·
RefSeq NP_215561.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | nucleotidyl transferase AbiEii/AbiGii toxin family protein |
| Revised (this work) | Nucleotidyl transferase AbiEii/AbiGii toxin family protein. Pfam: AbiEii (PF08843.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96356
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nucleotidyl transferase AbiEii/AbiGii toxin family protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Nucleotidyl transferase AbiEii toxin, Type IV TA system |
| Orthologous group | 2DQGD |
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) pseudogene candidate
| pN/pS | 0.119 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 24.28% of strains (35261) · 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 |
|---|---|---|---|---|
AbiEii | PF08843.18 | 1.3e-19 | 49–277 | Nucleotidyl transferase AbiEii toxin, Type IV TA system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2209 (integral membrane protein), high confidence from genomic context alone (score 747 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) |
|---|---|---|---|---|
Rv1044 hyp |
hypothetical protein | 999 | 990 ctx | neighborhood:801 cooccurence:758 coexpression:817 textmining:913 |
Rv2209 |
integral membrane protein | 746 | 747 ctx | cooccurence:745 |
Rv0355c PPE8 |
PPE family protein PPE8 | 746 | 747 ctx | cooccurence:746 |
Rv3350c PPE56 |
PPE family protein PPE56 | 746 | 746 ctx | cooccurence:745 |
Rv3347c PPE55 |
PPE family protein PPE55 | 742 | 742 ctx | cooccurence:741 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 741 | 741 ctx | cooccurence:741 |
Rv1917c PPE34 |
PPE family protein PPE34 | 734 | 734 ctx | cooccurence:734 |
Rv3343c PPE54 |
PPE family protein PPE54 | 732 | 733 ctx | cooccurence:730 |
Rv0304c PPE5 |
PPE family protein PPE5 | 727 | 727 ctx | cooccurence:727 |
Rv1004c |
membrane protein | 727 | 727 ctx | cooccurence:727 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 721 | 721 ctx | cooccurence:721 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 718 | 718 ctx | cooccurence:718 |
Rv1753c PPE24 |
PPE family protein PPE24 | 712 | 713 ctx | cooccurence:712 |
Rv0613c hyp |
hypothetical protein | 709 | 709 ctx | cooccurence:709 |
Rv2082 hyp |
hypothetical protein | 709 | 709 ctx | cooccurence:709 |
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: nucleotidyl transferase AbiEii/AbiGii toxin family protein
- Pfam (hmmscan --cut_ga): AbiEii PF08843.18 (E=1e-19)
- (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_215561.1)
- Domains: Pfam-A via hmmscan --cut_ga — AbiEii (PF08843.18)
- 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
2DQGD - Curated reference: UniProt P96356 (TrEMBL, unreviewed; 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 —
92 functional partner(s); context anchor
Rv2209 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001122|Rv1045| MTKPYSSPPTNLRSLRDRLTQVAERQGVVFGRLQRHVAMIVVAQFAATLTDDTGAPLLLVKGGSSLELRRGIPDSRTSKDFDTVARRDIELIHEQLADAGETGWEGFTAIFTAPEEIDVPGMPVKPRRFTAKLSYRGRAFATVPIEVSSVEAGNADQFDTLTSDALGLVGVPAAVAVPCMTIPWQIAQKLHAVTAVLEEPKVNDRAHDLVDLQLLEGLLLDADLMPTRSACIAIFEARAQHPWPPRVATLPHWPLIYAGALEGLDHLELARTVDAAAQAVQRFVARIDRATKR