rapZ Resolved · high auto-curated
H37Rv Rv1421 · MTBC0 mtbc0_001521 ·
301 aa · 1605323–1606228 (+) ·
RefSeq NP_215937.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | RNase adapter RapZ |
| Revised (this work) | RNase adapter RapZ. Pfam: RapZ-like_N (PF03668.22), PapZ_C (PF22740.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFQ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nucleotide-binding protein Rv1421 |
| Curated function | Displays ATPase and GTPase activities. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | yvcJ |
| eggNOG description | Displays ATPase and GTPase activities |
| Orthologous group | COG1660 |
| KEGG orthology |
K06958
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.236 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 4 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 |
|---|---|---|---|---|
RapZ-like_N | PF03668.22 | 1.0e-71 | 17–173 | RapZ-like N-terminal domain |
PapZ_C | PF22740.2 | 1.7e-45 | 179–298 | RapZ C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: whiA (transcriptional regulator WhiA), high confidence from genomic context alone (score 941 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) |
|---|---|---|---|---|
Rv1422 cuvA hyp |
hypothetical protein | 972 | 968 ctx | neighborhood:882 coexpression:743 |
Rv1423 whiA |
transcriptional regulator WhiA | 948 | 941 ctx | neighborhood:882 coexpression:431 |
Rv1420 uvrC |
excinuclease ABC subunit UvrC | 893 | 888 ctx | neighborhood:882 |
Rv1417 |
membrane protein | 696 | 696 ctx | neighborhood:682 |
Rv3261 fbiA |
2-phospho-L-lactate transferase | 732 | 692 | coexpression:674 |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 702 | 692 ctx | neighborhood:682 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 689 | 689 ctx | neighborhood:682 |
Rv2444c rne |
ribonuclease E | 700 | 668 | experimental:652 |
Rv1158c hyp |
hypothetical protein | 695 | 663 | experimental:652 |
Rv3441c mrsA |
phosphoglucosamine mutase | 663 | 646 ctx | cooccurence:630 |
Rv1419 hyp |
hypothetical protein | 607 | 608 ctx | neighborhood:607 |
Rv3600c coaX |
type III pantothenate kinase | 464 | 465 ctx | cooccurence:412 |
Rv1418 lprH |
lipoprotein LprH | 442 | 442 ctx | neighborhood:435 |
Rv3241c raiA hyp |
hypothetical protein | 467 | 435 | |
Rv1640c lysX |
bifunctional lysine--tRNA ligase/phosphatidylglycerol lysyltransferase | 429 | 430 |
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: RNase adapter RapZ
- Pfam (hmmscan --cut_ga): RapZ-like_N PF03668.22 (E=1e-71), PapZ_C PF22740.2 (E=2e-45)
- (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_215937.1)
- Domains: Pfam-A via hmmscan --cut_ga — RapZ-like_N (PF03668.22), PapZ_C (PF22740.2)
- 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
COG1660 - Curated reference: UniProt P9WFQ3 (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 —
19 functional partner(s); context anchor
whiA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001521|Rv1421|rapZ MMNHARGVENRSEGGGIDVVLVTGLSGAGRGTAAKVLEDLGWYVADNLPPQLITRMVDFGLAAGSRITQLAVVMDVRSRGFTGDLDSVRNELATRAITPRVVFMEASDDTLVRRYEQNRRSHPLQGEQTLAEGIAAERRMLAPVRATADLIIDTSTLSVGGLRDSIERAFGGDGGATTSVTVESFGFKYGLPMDADMVMDVRFLPNPHWVDELRPLTGQHPAVRDYVLHRPGAAEFLESYHRLLSLVVDGYRREGKRYMTIAIGCTGGKHRSVAIAEALMGLLRSDQQLSVRALHRDLGRE