PANDIT+

KeywordFamilyClanGene   

Entry: GTP_CDC (PF00735) * this family does not contain any human sequence in the seed alignment although some of the annotation data are human specific [read more]

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Display a clan
Very fast search for clan entries. The
search can be done either by clan ID
(e.g. CL0192) or by clan name (e.g. GPCR_A).

Pfam summary

Description

Cell division protein

Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerise to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis [2].
 
Literature1. Casamayor A, Snyder M; Mol Cell Biol 2003;23:2762-2777.Molecular dissection of a yeast septin: distinct domains are required for septin interaction, localization, and function. PUBMED:12665577
2. Kinoshita M; Genome Biol 2003;4:236.The septins. PUBMED:14611653
 
Clan

CL0023 (AAA)

The clan contains the following members: PF00004(AAA); PF03029(ATP_bind_1); PF02492(cobW); PF00270(DEAD); PF03796(DnaB_C); PF05127(DUF699); PF00009(GTP_EFTU); PF00271(Helicase_C); PF00225(Kinesin); PF03354(Terminase_1); PF02463(SMC_N); PF00448(SRP54); PF00685(Sulfotransfer_1); PF03567(Sulfotransfer_2); PF01591(6PF2K); PF00005(ABC_tran); PF02456(Adeno_IVa2); PF00709(Adenylsucc_synt); PF00406(ADK); PF03969(AFG1_ATPase); PF04548(AIG1); PF01583(APS_kinase); PF01637(Arch_ATPase); PF00025(Arf); PF03308(ArgK); PF02374(ArsA_ATPase); PF00006(ATP-synt_ab); PF00308(Bac_DnaA); PF01656(CbiA); PF01121(CoaE); PF02572(CobA_CobO_BtuR); PF02283(CobU); PF02224(Cytidylate_kin); PF02499(DNA_pack_C); PF02500(DNA_pack_N); PF01712(dNK); PF03193(DUF258); PF03237(DUF264); PF03266(DUF265); PF03976(PPK2); PF01935(DUF87); PF00350(Dynamin_N); PF00519(PPV_E1_C); PF04257(Exonuc_V_gamma); PF02421(FeoB_N); PF00142(Fer4_NifH); PF01268(FTHFS); PF01580(FtsK_SpoIIIE); PF00503(G-alpha); PF04466(Terminase_3); PF02263(GBP); PF00437(GSPII_E); PF00735(GTP_CDC); PF04670(Gtr1_RagA); PF00625(Guanylate_kin); PF02689(Herpes_Helicase); PF02399(Herpes_ori_bp); PF05049(IIGP); PF01715(IPPT); PF01745(IPT); PF01695(IstB); PF02606(LpxK); PF00493(MCM); PF01078(Mg_chelatase); PF01926(MMR_HSR1); PF03205(MobB); PF00488(MutS_V); PF00063(Myosin_head); PF00931(NB-ARC); PF01057(Parvo_NS1); PF02562(PhoH); PF04665(Pox_A32); PF00485(PRK); PF03215(Rad17); PF00071(Ras); PF00154(RecA); PF04851(ResIII); PF00910(RNA_helicase); PF00158(Sigma54_activat); PF01202(SKI); PF00176(SNF2_N); PF02223(Thymidylate_kin); PF00265(TK); PF00693(Herpes_TK); PF02534(TraG); PF03668(ATP_bind_2); PF02367(UPF0079); PF00580(UvrD-helicase); PF01443(Viral_helicase1); PF05496(RuvB_N); PF05621(TniB); PF05625(PAXNEB); PF05673(DUF815); PF05707(Zot); PF05729(NACHT); PF05783(DLIC); PF05872(DUF853); PF05876(Terminase_GpA); PF05879(RHD3); PF05894(Podovirus_Gp16); PF05970(DUF889); PF06068(TIP49); PF06144(DNA_pol3_delta); PF06309(Torsin); PF06414(Zeta_toxin); PF06418(CTP_synth_N); PF06431(Polyoma_lg_T_C); PF06733(DEAD_2); PF06745(KaiC); PF06858(NOG1); PF06862(DUF1253); PF06990(Gal-3-0_sulfotr); PF07015(VirC1); PF07088(GvpD); PF07517(SecA_DEAD); PF07652(Flavi_DEAD); PF07693(KAP_NTPase); PF07724(AAA_2); PF07726(AAA_3); PF07728(AAA_5); PF07755(DUF1611); PF07931(CPT);
 
InterPro entry IPR000038
 

Alignment
New Hampshire tree

The seed alignment for this family in the PANDIT database contains 16 aligned sequences:

  CDC10_CANAL/34-313   CDC10_YEAST/29-308   CDC11_YEAST/19-305   CDC12_YEAST/31-321   CDC3_CANAL/32-314   CDC3_YEAST/116-418   PNUT_DROME/139-418   SEPT1_DROME/32-311   SEPT1_MOUSE/22-301   SEPT2_MOUSE/34-313   SEPT4_MOUSE/141-421   SPN3_SCHPO/49-332   SPN4_SCHPO/25-303   SPN5_SCHPO/115-377   SPN6_SCHPO/27-304   SPR3_YEAST/106-372  

The full alignment for this family in the Pfam database contains 961 aligned sequences

Species in the seed alignment

List of species covered in the seed alignment. The number in brackets denotes the number of sequences taken from each organism.

  Saccharomyces cerevisiae (5);   Schizosaccharomyces pombe (4);   Mus musculus (3);   Drosophila melanogaster (2);   Candida albicans (2);  

The full alignment covers 104 species.

Pre-computed estimates from Markov codon substitution models (explanation)

Following are maximum-likelihood estimates and log-likelihood scores from codon models M0, M1, M2, M7 and M8, implemented in PAML v.4.1

Model name  

Model M0

Model M1

Model M2

Model M7

Model M8

Log-likelihood score  

-1103.01-1103.014285-1103.014285-1103.014285-1103.014285

Tree Length  

0.006e-056e-056e-056e-05

κ  

0.000.00010.00010.00010.0001

ω-ratio  

ω=0.0001p0=0.999999 ~ ω0=1e-06
p1=1.00000000002876e-06 ~ ω1=1		p0=1 ~ ω0=1e-06
p1=0 ~ ω1=1
p2=0 ~ ω2=1		ω~Β(0.005,99)p0=0.999999 ~ ω~Β(0.005,2.318046)
p1=1e-06 ~ ω=2.987187

P-value for testing  
positive selection  

M1 vs M2: P-value=1
family classification: conserved		M7 vs M8: P-value=1
family classification: conserved

Maximum-likelihood estimates and log-likelihood scores from codon models Nonsynonymous and Dual implemented in HYPHY

Model name  

Model Nonsynonymous

Model Dual

Log-likelihood score  

 -1103.11543-1103.08256

Mean ω-ratio  

ω = 0ω = 0

Coeff. of variation  
of ω-ratio  

 CVω = 0CVω = 0
 

Annotations

InteractionsThis family has 1 known interaction:
PF00735;
StructuresThis family has 7 structures:
Notation: PDB_ID (PDB chain, PDB residues)
Gene Ontologies
Biological Process
 cell cycle[GO:0007049]
Molecular Function
 GTP binding[GO:0005525]
KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Nucleotide Metabolism
Purine metabolism [KEGG]
Pyrimidine metabolism [KEGG]
Amino Acid Metabolism
Methionine metabolism [KEGG]
Xenobiotics Biodegradation and Metabolism
Drug metabolism - other enzymes [KEGG]
Genetic Information Processing
Folding, Sorting and Degradation
Protein export [KEGG]
Type IV secretion system [KEGG]
Type II secretion system [KEGG]
Replication and Repair
DNA replication [KEGG]
Nucleotide excision repair [KEGG]
Mismatch repair [KEGG]
Homologous recombination [KEGG]
Non-homologous end-joining [KEGG]
Environmental Information Processing
Membrane Transport
ABC transporters [KEGG]
Cellular Processes
Cell Motility
Regulation of actin cytoskeleton [KEGG]
Human Diseases
Neurodegenerative Diseases
Parkinson's disease [KEGG]
DisProt- disorder annotation inferred from homologous DisProt sequences
DP00537
 

Expression data (explanation)

 
Bgee expression data - for genes coding for sequences from seed alignment     Click here for overview of Bgee data

The numbers in brackets correspond to the number of genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Mus musculus
HumanProteinpedia expression data - for human genes coding for sequences from full alignment     Click here for overview of Human Proteinpedia data

The numbers in brackets correspond to the number of human genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Healthy tissues
Disease tissues

Human disease association

 
Genetic Association Database - data for human genes coding for sequences from full alignment

The numbers in brackets correspond to the number of genes that are associated with the selected family and are associated with the corresponding disease. Click on the disease name to see all the families possibly associated with that disease and click on the genes to see the corresponding genes.

Associated diseases and disorders
Links to OMIM - for human genes coding for sequences from full alignment
 
603696 (1) 612140 (1) 602207 (1) 604199 (1) 605950 (1) 608087 (1) 601506 (1) 300683 (1) 611562 (1) 300333 (1) 608314 (1) 602724 (1) 608418 (1) 611737 (1) 604061 (1) 603151 (1) 612404 (1)