PANDIT+

KeywordFamilyClanGene   

Entry: Peptidase_S9_N (PF02897)

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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

Prolyl oligopeptidase, N-terminal beta-propeller domain

This unusual 7-stranded beta-propeller domain protects the catalytic triad of prolyl oligopeptidase (see Pfam:PF00326), excluding larger peptides and proteins from proteolysis in the cytosol.
 
Literature1. Fulop V, Bocskei Z, Polgar L; Cell 1998;94:161-170.Prolyl oligopeptidase: an unusual beta-propeller domain regulates proteolysis. PUBMED:9695945
 
Clan

CL0186 (Beta_propeller)

The clan contains the following members: PF01011(PQQ); PF00780(CNH); PF03178(CPSF_A); PF00930(DPPIV_N); PF01839(FG-GAP); PF04762(IKI3); PF03022(MRJP); PF01436(NHL); PF02897(Peptidase_S9_N); PF00400(WD40); PF01731(Arylesterase); PF04053(Coatomer_WDAD); PF02239(Cytochrom_D1); PF05096(Glu_cyclase_2); PF00058(Ldl_recept_b); PF00415(RCC1); PF03088(Str_synth); PF05694(SBP56); PF05787(DUF839); PF06433(Me-amine-dh_H); PF06739(SBBP); PF07433(DUF1513); PF07494(Reg_prop); PF07676(PD40);
 
InterPro entry IPR004106
 

Alignment

New Hampshire tree

The seed alignment for this family in the PANDIT database contains 31 aligned sequences:

  O05748_MYCLE/10-432   O07178_MYCTU/3-407   O07834_PSESP/29-445   O70196_RAT/6-423   O76728_TRYBB/19-433   PPCE_AERHY/8-410   PPCE_BOVIN/6-423   PPCE_FLAME/28-429   PPCE_HUMAN/6-423   PPCE_MOUSE/6-423   PPCE_PIG/6-423   PPCF_FLAME/28-429   PTRB_ECOLI/2-404   PTRB_MORLA/3-405   Q94795_TRYCR/17-432   Q9RBG8_AERPU/9-411   Q9RRI7_DEIRA/5-415   Q9SGR9_ARATH/77-501   Q9SX53_ARATH/6-429   Q9UM02_HUMAN/6-423   Q9V9P5_DROME/27-442   Q9VKW5_DROME/50-467   Q9X5N2_MYXXA/3-406   Q9X6R4_AERPU/9-411   Q9XYH4_LEIMA/26-447   Q9XZR9_DICDI/5-478   Q9ZDP6_RICPR/3-407   Q9ZNM8_9SPHN/40-450   Y4NA_RHISN/20-455   Y4QF_RHISN/39-446   Y4SO_RHISN/7-415  

The full alignment for this family in the Pfam database contains 1170 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.

  Rhizobium sp. NGR234 (3);   Drosophila melanogaster (2);   Homo sapiens (2);   Arabidopsis thaliana (2);   Aeromonas punctata (2);   Leishmania major (1);   Rattus norvegicus (1);   Mycobacterium tuberculosis (1);   Deinococcus radiodurans (1);   Trypanosoma cruzi (1);   Escherichia coli K12 (1);   Sus scrofa (1);   Novosphingobium capsulatum (1);   Bos taurus (1);   Dictyostelium discoideum (1);   Trypanosoma brucei brucei (1);   Myxococcus xanthus (1);   Pseudomonas sp. (1);   Mycobacterium leprae (1);   Moraxella lacunata (1);   Elizabethkingia miricola (1);   Mus musculus (1);   Elizabethkingia meningoseptica (1);   Rickettsia prowazekii (1);   Aeromonas hydrophila (1);  

The full alignment covers 442 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  

-28796.79-28793.552588-28793.552588-28549.391737-28549.391897

Tree Length  

179.53179.53496179.53496179.53496179.53496

κ  

1.551.5573381.5573351.5576431.55764

ω-ratio  

ω=0.0424p0=0.991553 ~ ω0=0.043133
p1=0.00844699999999998 ~ ω1=1
p0=0.991554 ~ ω0=0.043133
p1=0.008446 ~ ω1=1
p2=0 ~ ω2=35.6694
ω~Β(2.850261,56.979039)p0=0.999999 ~ ω~Β(2.850245,56.974979)
p1=1e-06 ~ ω=20.03607

P-value for testing  
positive selection  

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

-34680.91252-34608.6039

Mean ω-ratio  

ω = 0.0691ω = 0.06832

Coeff. of variation  
of ω-ratio  

CVω = 2.40336CVω = 1.07276
 

Annotations

InteractionsThis domain has 2 known interactions:
PF00326; PF02897;

StructuresThis domain has 20 structures:
Notation: PDB_ID (PDB chain, PDB residues)

Gene Ontologies
Biological Process
 proteolysis[GO:0006508]
Molecular Function
 serine-type endopeptidase activity[GO:0004252]

KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Energy Metabolism
Nitrogen metabolism [KEGG]
Amino Acid Metabolism
Glutamate metabolism [KEGG]
Lysine degradation [KEGG]
Phenylalanine, tyrosine and tryptophan biosynthesis [KEGG]
Metabolism of Cofactors and Vitamins
Biotin metabolism [KEGG]
Genetic Information Processing
Folding, Sorting and Degradation
Ubiquitin mediated proteolysis [KEGG]
Cellular Processes
Cell Growth and Death
Cell cycle - yeast [KEGG]
 

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.

Homo sapiens
Drosophila melanogaster
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
 
Associated diseases and disorders

Links to OMIM - for human genes coding for sequences from full alignment
 
600400 (1) 609557 (1)