rodA Resolved · high auto-curated
H37Rv Rv0017c · MTBC0 mtbc0_000021 ·
469 aa · 20231–21640 (-) ·
RefSeq NP_214531.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cell division protein RodA |
|---|---|
| MTBC0 PGAP re-annotation | cell shape-determining peptidoglycan glycosyltransferase RodA |
| Revised (this work) | Cell shape-determining peptidoglycan glycosyltransferase RodA. Pfam: FTSW_RODA_SPOVE (PF01098.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN99
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Peptidoglycan glycosyltransferase RodA |
| EC (curated) |
EC 2.4.99.28
|
| Curated function | Transglycosylase involved in peptidoglycan cell wall formation. Required for the regulation of cell length. Plays critical roles for the survival of the pathogen inside the host. Required for both bacterial survival and formation of granuloma structures in a guinea pig infection model. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| Preferred name | rodA |
| eggNOG description | Belongs to the SEDS family |
| Orthologous group | COG0772 |
| KEGG orthology |
K03588
|
| KEGG pathways |
map04112
|
| Gene Ontology (35) |
GO:0002682, GO:0002684, GO:0008150, GO:0009605, GO:0009607, GO:0009987, GO:0035821, GO:0043207, GO:0044003, GO:0044403, GO:0044419, GO:0048518 +23 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 | 0.377 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
FTSW_RODA_SPOVE | PF01098.25 | 2.7e-101 | 81–444 | Cell cycle protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pbpA (penicillin-binding protein PbpA), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0016c pbpA |
penicillin-binding protein PbpA | 999 | 1000 ctx | neighborhood:882 fusion:894 cooccurence:749 coexpression:418 experimental:589 database:500 textmining:869 |
Rv0014c pknB |
serine/threonine-protein kinase PknB | 993 | 940 ctx | neighborhood:881 textmining:894 |
Rv0015c pknA |
serine/threonine-protein kinase PknA | 987 | 914 ctx | neighborhood:882 textmining:858 |
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 982 | 910 ctx | neighborhood:882 textmining:815 |
Rv2163c pbpB |
penicillin-binding membrane protein PbpB | 984 | 857 ctx | cooccurence:562 experimental:589 textmining:899 |
Rv0019c fhaB |
FHA domain-containing protein FhaB | 933 | 851 ctx | neighborhood:780 textmining:574 |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 869 | 817 ctx | cooccurence:551 database:500 |
Rv2156c murX |
phospho-N-acetylmuramoyl-pentappeptidetransferase | 833 | 781 ctx | cooccurence:596 coexpression:463 |
Rv2864c |
penicillin-binding lipoprotein | 782 | 768 | experimental:589 |
Rv0050 ponA1 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 778 | 758 ctx | cooccurence:449 database:500 |
Rv0020c fhaA |
FHA domain-containing protein FhaA | 885 | 747 ctx | neighborhood:700 textmining:564 |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 813 | 728 ctx | cooccurence:511 coexpression:437 |
Rv2151c ftsQ |
cell division protein FtsQ | 970 | 702 | coexpression:458 experimental:443 textmining:905 |
Rv2157c murF |
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | 792 | 672 | coexpression:412 |
Rv2153c murG |
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol-N-acetylglucosamine transferase | 934 | 669 | coexpression:492 textmining:810 |
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: cell division protein RodA
- MTBC0 PGAP product: cell shape-determining peptidoglycan glycosyltransferase RodA
- Pfam (hmmscan --cut_ga): FTSW_RODA_SPOVE PF01098.25 (E=3e-101)
- (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_214531.1)
- Domains: Pfam-A via hmmscan --cut_ga — FTSW_RODA_SPOVE (PF01098.25)
- 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
COG0772 - Curated reference: UniProt P9WN99 (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 —
56 functional partner(s); context anchor
pbpA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000021|Rv0017c|rodA MTTRLQAPVAVTPPLPTRRNAELLLLCFAAVITFAALLVVQANQDQGVPWDLTSYGLAFLTLFGSAHLAIRRFAPYTDPLLLPVVALLNGLGLVMIHRLDLVDNEIGEHRHPSANQQMLWTLVGVAAFALVVTFLKDHRQLARYGYICGLAGLVFLAVPALLPAALSEQNGAKIWIRLPGFSIQPAEFSKILLLIFFSAVLVAKRGLFTSAGKHLLGMTLPRPRDLAPLLAAWVISVGVMVFEKDLGASLLLYTSFLVVVYLATQRFSWVVIGLTLFAAGTLVAYFIFEHVRLRVQTWLDPFADPDGTGYQIVQSLFSFATGGIFGTGLGNGQPDTVPAASTDFIIAAFGEELGLVGLTAILMLYTIVIIRGLRTAIATRDSFGKLLAAGLSSTLAIQLFIVVGGVTRLIPLTGLTTPWMSYGGSSLLANYILLAILARISHGARRPLRTRPRNKSPITAAGTEVIERV