parA Resolved · high auto-curated
H37Rv Rv3918c · MTBC0 mtbc0_004152 ·
347 aa · 4430739–4431782 (-) ·
RefSeq NP_218434.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | chromosome partitioning protein ParA |
|---|---|
| MTBC0 PGAP re-annotation | chromosome partitioning protein ParA |
| Revised (this work) | Chromosome partitioning protein ParA. Pfam: ParA (PF10609.16), AAA_31 (PF13614.13), MipZ (PF09140.18), CbiA (PF01656.30), ArsA_ATPase (PF02374.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
Q1LVD4
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable chromosome partitioning protein ParA |
| Curated function | May play a role in septum formation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| Preferred name | parA |
| eggNOG description | chromosome partitioning |
| Orthologous group | COG1192 |
| KEGG orthology |
K03496
|
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 | 0.341 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 8 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 |
|---|---|---|---|---|
ParA | PF10609.16 | 1.2e-08 | 84–136 | NUBPL iron-transfer P-loop NTPase |
AAA_31 | PF13614.13 | 5.1e-58 | 85–263 | AAA domain |
MipZ | PF09140.18 | 8.2e-08 | 86–125 | ATPase MipZ |
CbiA | PF01656.30 | 1.1e-29 | 87–313 | CobQ/CobB/MinD/ParA nucleotide binding domain |
ArsA_ATPase | PF02374.22 | 1.2e-07 | 92–221 | Anion-transporting ATPase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: parB (chromosome partitioning protein ParB), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3917c parB |
chromosome partitioning protein ParB | 999 | 998 ctx | neighborhood:882 cooccurence:773 coexpression:892 textmining:580 |
Rv3919c gid |
16S rRNA (guanine(527)-N(7))-methyltransferase RsmG | 982 | 976 ctx | neighborhood:881 coexpression:803 |
Rv3920c hyp |
hypothetical protein | 771 | 772 ctx | neighborhood:758 |
Rv3921c yidC |
membrane protein insertase YidC | 766 | 752 ctx | neighborhood:705 |
Rv3922c yidD |
membrane protein insertion efficiency factor | 697 | 697 ctx | neighborhood:688 |
Rv2647 hyp |
hypothetical protein | 693 | 674 | coexpression:484 |
Rv2748c ftsK |
DNA translocase FtsK | 665 | 649 ctx | cooccurence:637 |
Rv3923c rnpA |
ribonuclease P protein component | 647 | 627 ctx | neighborhood:621 |
Rv0001 dnaA |
chromosomal replication initiator protein DnaA | 725 | 606 | |
Rv3916c hyp |
hypothetical protein | 539 | 538 ctx | neighborhood:524 |
Rv3924c rpmH |
50S ribosomal protein L34 | 519 | 501 ctx | neighborhood:501 |
Rv2916c ffh |
signal recognition particle protein | 478 | 478 | coexpression:409 |
Rv2646 |
integrase | 470 | 444 ctx | cooccurence:420 |
Rv3014c ligA |
DNA ligase A | 439 | 440 | coexpression:421 |
Rv2150c ftsZ |
cell division protein FtsZ | 577 | 437 | coexpression:418 |
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: chromosome partitioning protein ParA
- MTBC0 PGAP product: chromosome partitioning protein ParA
- Pfam (hmmscan --cut_ga): ParA PF10609.16 (E=1e-08), AAA_31 PF13614.13 (E=5e-58), MipZ PF09140.18 (E=8e-08), CbiA PF01656.30 (E=1e-29), ArsA_ATPase PF02374.22 (E=1e-07)
- (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_218434.2)
- Domains: Pfam-A via hmmscan --cut_ga — ParA (PF10609.16), AAA_31 (PF13614.13), MipZ (PF09140.18), CbiA (PF01656.30), ArsA_ATPase (PF02374.22)
- 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
COG1192 - Curated reference: UniProt Q1LVD4 (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 —
30 functional partner(s); context anchor
parB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004152|Rv3918c|parA MSAPWGPVAAGPSALVRSGQASTIEPFQREMTPPTPTPEAAHNPTMNVSRETSTEFDTPIGAAAERAMRVLHTTHEPLQRPGRRRVLTIANQKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNASTALGITDRQSGTPSSYEMLIGEVSLHTALRRSPHSERLFCIPATIDLAGAEIELVSMVARENRLRTALAALDNFDFDYVFVDCPPSLGLLTINALVAAPEVMIPIQCEYYALEGVSQLMRNIEMVKAHLNPQLEVTTVILTMYDGRTKLADQVADEVRQYFGSKVLRTVIPRSVKVSEAPGYSMTIIDYDPGSRGAMSYLDASRELAERDRPPSAKGRP