smc Resolved · high auto-curated
H37Rv Rv2922c · MTBC0 mtbc0_003104 ·
1205 aa · 3255186–3258803 (-) ·
RefSeq NP_217438.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | chromosome partition protein Smc |
|---|---|
| MTBC0 PGAP re-annotation | chromosome segregation protein SMC |
| Revised (this work) | Chromosome segregation protein SMC. Pfam: AAA_15 (PF13175.13), SMC_N (PF02463.26), AAA_23 (PF13476.13), SMC_hinge (PF06470.19), AAA_21 (PF13304.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGF3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Chromosome partition protein Smc |
| Curated function | Required for chromosome condensation and partitioning. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| Preferred name | smc |
| eggNOG description | Required for chromosome condensation and partitioning |
| Orthologous group | COG1196 |
| KEGG orthology |
K03529
|
| Gene Ontology (13) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0030312, GO:0044424, GO:0044444, GO:0044464 +1 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 | 1.841 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 21 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 |
|---|---|---|---|---|
AAA_15 | PF13175.13 | 6.6e-09 | 1–53 | AAA ATPase domain |
SMC_N | PF02463.26 | 4.7e-74 | 2–1185 | RecF/RecN/SMC N terminal domain |
AAA_23 | PF13476.13 | 9.0e-17 | 5–200 | AAA domain |
SMC_hinge | PF06470.19 | 3.3e-18 | 514–626 | SMC proteins Flexible Hinge Domain |
AAA_21 | PF13304.13 | 1.4e-08 | 1056–1164 | AAA domain, putative AbiEii toxin, Type IV TA system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: scpA (segregation and condensation protein ScpA), high confidence from genomic context alone (score 952 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1709 scpA |
segregation and condensation protein ScpA | 983 | 952 ctx | cooccurence:764 experimental:788 textmining:670 |
Rv2923c hyp |
hypothetical protein | 878 | 878 ctx | neighborhood:876 |
Rv2922A acyP |
acylphosphatase | 933 | 877 ctx | neighborhood:876 textmining:479 |
Rv2921c ftsY |
signal recognition particle receptor FtsY | 872 | 872 ctx | neighborhood:814 |
Rv1710 scpB |
segregation and condensation protein ScpB | 938 | 814 ctx | cooccurence:770 textmining:681 |
Rv2924c fpg |
formamidopyrimidine-DNA glycosylase | 769 | 770 ctx | neighborhood:765 |
Rv2925c rnc |
ribonuclease III | 704 | 705 ctx | neighborhood:662 |
Rv2926c hyp |
hypothetical protein | 690 | 691 ctx | neighborhood:662 |
Rv0005 gyrB |
DNA gyrase subunit B | 652 | 615 | |
Rv2920c amt |
ammonium transporter integral membrane protein | 627 | 613 ctx | neighborhood:613 |
Rv2927c sepIVA hyp |
hypothetical protein | 608 | 588 ctx | neighborhood:587 |
Rv2524c fas |
fatty acid synthase | 567 | 551 ctx | neighborhood:490 |
Rv3198c uvrD2 |
ATP-dependent DNA helicase UvrD | 512 | 492 | |
Rv3899c hyp |
hypothetical protein | 529 | 487 | experimental:423 |
Rv2082 hyp |
hypothetical protein | 526 | 485 | experimental:423 |
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 partition protein Smc
- MTBC0 PGAP product: chromosome segregation protein SMC
- Pfam (hmmscan --cut_ga): AAA_15 PF13175.13 (E=7e-09), SMC_N PF02463.26 (E=5e-74), AAA_23 PF13476.13 (E=9e-17), SMC_hinge PF06470.19 (E=3e-18), AAA_21 PF13304.13 (E=1e-08)
- (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_217438.2)
- Domains: Pfam-A via hmmscan --cut_ga — AAA_15 (PF13175.13), SMC_N (PF02463.26), AAA_23 (PF13476.13), SMC_hinge (PF06470.19), AAA_21 (PF13304.13)
- 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
COG1196 - Curated reference: UniProt P9WGF3 (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 —
35 functional partner(s); context anchor
scpA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003104|Rv2922c|smc MYLKSLTLKGFKSFAAPTTLRFEPGITAVVGPNGSGKSNVVDALAWVMGEQGAKTLRGGKMEDVIFAGTSSRAPLGRAEVTVSIDNSDNALPIEYTEVSITRRMFRDGASEYEINGSSCRLMDVQELLSDSGIGREMHVIVGQGKLEEILQSRPEDRRAFIEEAAGVLKHRKRKEKALRKLDTMAANLARLTDLTTELRRQLKPLGRQAEAAQRAAAIQADLRDARLRLAADDLVSRRAEREAVFQAEAAMRREHDEAAARLAVASEELAAHESAVAELSTRAESIQHTWFGLSALAERVDATVRIASERAHHLDIEPVAVSDTDPRKPEELEAEAQQVAVAEQQLLAELDAARARLDAARAELADRERRAAEADRAHLAAVREEADRREGLARLAGQVETMRARVESIDESVARLSERIEDAAMRAQQTRAEFETVQGRIGELDQGEVGLDEHHERTVAALRLADERVAELQSAERAAERQVASLRARIDALAVGLQRKDGAAWLAHNRSGAGLFGSIAQLVKVRSGYEAALAAALGPAADALAVDGLTAAGSAVSALKQADGGRAVLVLSDWPAPQAPQSASGEMLPSGAQWALDLVESPPQLVGAMIAMLSGVAVVNDLTEAMGLVEIRPELRAVTVDGDLVGAGWVSGGSDRKLSTLEVTSEIDKARSELAAAEALAAQLNAALAGALTEQSARQDAAEQALAALNESDTAISAMYEQLGRLGQEARAAEEEWNRLLQQRTEQEAVRTQTLDDVIQLETQLRKAQETQRVQVAQPIDRQAISAAADRARGVEVEARLAVRTAEERANAVRGRADSLRRAAAAEREARVRAQQARAARLHAAAVAAAVADCGRLLAGRLHRAVDGASQLRDASAAQRQQRLAAMAAVRDEVNTLSARVGELTDSLHRDELANAQAALRIEQLEQMVLEQFGMAPADLITEYGPHVALPPTELEMAEFEQARERGEQVIAPAPMPFDRVTQERRAKRAERALAELGRVNPLALEEFAALEERYNFLSTQLEDVKAARKDLLGVVADVDARILQVFNDAFVDVEREFRGVFTALFPGGEGRLRLTEPDDMLTTGIEVEARPPGKKITRLSLLSGGEKALTAVAMLVAIFRARPSPFYIMDEVEAALDDVNLRRLLSLFEQLREQSQIIIITHQKPTMEVADALYGVTMQNDGITAVISQRMRGQQVDQLVTNSS