pbpB Resolved · high auto-curated
H37Rv Rv2163c · MTBC0 mtbc0_002299 ·
679 aa · 2452413–2454452 (-) ·
RefSeq NP_216679.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | penicillin-binding membrane protein PbpB |
|---|---|
| MTBC0 PGAP re-annotation | D%2CD-transpeptidase PbpB |
| Revised (this work) | D%2CD-transpeptidase PbpB. Pfam: PBP_dimer (PF03717.21), Transpeptidase (PF00905.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
L0T911
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Penicillin-binding protein PbpB |
| Curated function | Synthesis of cross-linked peptidoglycan from the lipid intermediates. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | ftsI |
| eggNOG description | Cell division protein FtsI |
| Orthologous group | COG0768 |
| EC number |
EC 3.4.16.4
|
| KEGG orthology |
K03587
|
| KEGG pathways |
map00550, map01501
|
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 | 0.428 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 5 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 |
|---|---|---|---|---|
PBP_dimer | PF03717.21 | 9.8e-10 | 131–295 | Penicillin-binding Protein dimerisation domain |
Transpeptidase | PF00905.28 | 1.3e-84 | 339–654 | Penicillin binding protein transpeptidase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ftsW (lipid II flippase FtsW), high confidence from genomic context alone (score 961 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2164c hyp |
hypothetical protein | 988 | 979 ctx | neighborhood:881 coexpression:806 textmining:475 |
Rv2154c ftsW |
lipid II flippase FtsW | 998 | 961 ctx | neighborhood:544 cooccurence:753 experimental:589 textmining:964 |
Rv2165c rsmH |
rRNA small subunit methyltransferase H | 972 | 945 ctx | neighborhood:881 coexpression:500 textmining:520 |
Rv0016c pbpA |
penicillin-binding protein PbpA | 948 | 921 | database:900 |
Rv2151c ftsQ |
cell division protein FtsQ | 994 | 916 ctx | neighborhood:544 experimental:781 textmining:940 |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 953 | 889 ctx | neighborhood:544 cooccurence:711 textmining:603 |
Rv2166c mraZ |
transcriptional regulator MraZ | 951 | 886 ctx | neighborhood:816 textmining:594 |
Rv2158c murE |
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase | 943 | 875 ctx | neighborhood:544 cooccurence:532 coexpression:445 textmining:565 |
Rv2156c murX |
phospho-N-acetylmuramoyl-pentappeptidetransferase | 882 | 875 ctx | neighborhood:544 cooccurence:697 |
Rv2157c murF |
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | 927 | 859 ctx | neighborhood:544 cooccurence:547 textmining:507 |
Rv0017c rodA |
cell division protein RodA | 984 | 857 ctx | cooccurence:562 experimental:589 textmining:899 |
Rv2155c murD |
UDP-N-acetylmuramoylalanine--D-glutamate ligase | 937 | 854 ctx | neighborhood:544 cooccurence:535 textmining:588 |
Rv2153c murG |
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol-N-acetylglucosamine transferase | 964 | 787 ctx | neighborhood:544 cooccurence:499 textmining:839 |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 889 | 787 ctx | cooccurence:601 experimental:419 textmining:504 |
Rv1315 murA |
UDP-N-acetylglucosamine 1-carboxyvinyltransferase | 837 | 693 ctx | cooccurence:680 textmining:494 |
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: penicillin-binding membrane protein PbpB
- MTBC0 PGAP product: D%2CD-transpeptidase PbpB
- Pfam (hmmscan --cut_ga): PBP_dimer PF03717.21 (E=1e-09), Transpeptidase PF00905.28 (E=1e-84)
- (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_216679.1)
- Domains: Pfam-A via hmmscan --cut_ga — PBP_dimer (PF03717.21), Transpeptidase (PF00905.28)
- 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
COG0768 - Curated reference: UniProt L0T911 (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 —
74 functional partner(s); context anchor
ftsW - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002299|Rv2163c|pbpB MSRAAPRRASQSQSTRPARGLRRPPGAQEVGQRKRPGKTQKARQAQEATKSRPATRSDVAPAGRSTRARRTRQVVDVGTRGASFVFRHRTGNAVILVLMLVAATQLFFLQVSHAAGLRAQAAGQLKVTDVQPAARGSIVDRNNDRLAFTIEARALTFQPKRIRRQLEEARKKTSAAPDPQQRLRDIAQEVAGKLNNKPDAAAVLKKLQSDETFVYLARAVDPAVASAICAKYPEVGAERQDLRQYPGGSLAANVVGGIDWDGHGLLGLEDSLDAVLAGTDGSVTYDRGSDGVVIPGSYRNRHKAVHGSTVVLTLDNDIQFYVQQQVQQAKNLSGAHNVSAVVLDAKTGEVLAMANDNTFDPSQDIGRQGDKQLGNPAVSSPFEPGSVNKIVAASAVIEHGLSSPDEVLQVPGSIQMGGVTVHDAWEHGVMPYTTTGVFGKSSNVGTLMLSQRVGPERYYDMLRKFGLGQRTGVGLPGESAGLVPPIDQWSGSTFANLPIGQGLSMTLLQMTGMYQAIANDGVRVPPRIIKATVAPDGSRTEEPRPDDIRVVSAQTAQTVRQMLRAVVQRDPMGYQQGTGPTAGVPGYQMAGKTGTAQQINPGCGCYFDDVYWITFAGIATADNPRYVIGIMLDNPARNSDGAPGHSAAPLFHNIAGWLMQRENVPLSPDPGPPLVLQAT