PANDIT+

KeywordFamilyClanGene   

Entry: Exo_endo_phos (PF03372)

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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

Endonuclease/Exonuclease/phosphatase family

This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3.1.21.1 e.g. Swiss:P24855, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56 Swiss:O43426, Sphingomyelinase EC:3.1.4.12 Swiss:P11889 and Nocturnin Swiss:O35710.
 
Literature1. Dlakic M; Trends Biochem Sci 2000;25:272-273.Functionally unrelated signalling proteins contain a fold similar to Mg2+-dependent endonucleases. PUBMED:10838565
2. Mol CD, Kuo CF, Thayer MM, Cunningham RP, Tainer JA; Nature 1995;374:381-386.Structure and function of the multifunctional DNA-repair enzyme exonuclease III. PUBMED:7885481
3. Lahm A, Suck D; J Mol Biol 1991;222:645-667.DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex. PUBMED:1748997
 
 
InterPro entry IPR005135
 

Alignment
New Hampshire tree

The seed alignment for this family in the PANDIT database contains 174 aligned sequences:

  ANGE_DROME/68-351   APE1_RAT/60-314   APEA_DICDI/105-358   APN2_SCHPO/1-302   APN2_YEAST/17-361   ARP_ARATH/276-534   CC4L_HUMAN/189-538   CCR4_YEAST/505-825   CDTB_ECOLI/23-268   DHP1_HUMAN/22-295   DRN1_BOVIN/23-281   DRN1_CHICK/21-279   DRN1_HUMAN/23-281   DRN1_OREMO/27-283   DRN1_RAT/23-281   DRNG_RAT/26-286   DRNL_HUMAN/19-272   EX3_ECOLI/1-266   EXOA_BACSU/1-250   EXOA_STRPN/1-273   FRA3_ARATH/540-882   I5P1_HUMAN/12-392   I5P2_HUMAN/296-585   INP5E_RAT/304-594   K0759_HUMAN/245-663   LIN1_NYCCO/7-236   NOCT_MOUSE/141-419   NSMA_CAEEL/39-325   NSMA_DROME/6-271   NSMA_HUMAN/9-279   NSMA_MOUSE/9-279   NSMA_SCHPO/9-296   O01419_BOMMO/6-213   O05382_ACTAC/1-266   O13348_MAGGR/14-230   O14306_SCHPO/791-1121   O15921_TRYCR/106-403   O15922_LEIMA/130-444   O16587_CAEEL/317-549   O16589_CAEEL/11-201   O17590_CAEEL/97-410   O18005_CAEEL/307-626   O22148_ARATH/1-229   O26314_METTH/4-255   O27012_METTH/3-229   O29675_ARCFU/2-255   O34095_LEPIN/81-368   O42110_9SAUR/44-259   O44201_BOMMO/5-211   O44767_CAEEL/11-225   O45711_CAEEL/34-286   More...

The full alignment for this family in the Pfam database contains 7967 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.

  Arabidopsis thaliana (22);   Caenorhabditis elegans (14);   Homo sapiens (13);   Drosophila melanogaster (12);   Saccharomyces cerevisiae (9);   Schizosaccharomyces pombe (7);   Rattus norvegicus (7);   Streptomyces coelicolor (7);   Mus musculus (5);   Deinococcus radiodurans (4);   Escherichia coli K12 (3);   Xenopus laevis (3);   Dictyostelium discoideum (3);   Bombyx mori (3);   Gallus gallus (2);   Escherichia coli (2);   Methanothermobacter thermautotrophicus str. Delta H (2);   Trypanosoma cruzi (2);   Aggregatibacter actinomycetemcomitans (2);   Treponema pallidum (2);   Rickettsia prowazekii (2);   Synechocystis sp. PCC 6803 (2);   Leishmania major (2);   Plasmodium falciparum 3D7 (2);   Canis lupus familiaris (1);   Takifugu rubripes (1);   Leptospira interrogans (1);   Drosophila subobscura (1);   Bacillus cereus (1);   Leptospira interrogans serovar Lai (1);   Helicobacter hepaticus (1);   Hydra vulgaris (1);   Rhodnius prolixus (1);   Lymantria dispar (1);   Mycoplasma pulmonis (1);   Oryzias latipes (1);   Campylobacter jejuni (1);   Mycoplasma pneumoniae (1);   Trypanosoma brucei (1);   Cimex lectularius (1);   Drosophila funebris (1);   Nycticebus coucang (1);   Anopheles gambiae (1);   Chlorella vulgaris (1);   Bacillus subtilis (1);   Neurospora crassa (1);   Borrelia burgdorferi (1);   Aedes aegypti (1);   Oreochromis mossambicus (1);   Staphylococcus aureus (1);   Platemys spixii (1);   More...

The full alignment covers 1045 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  

-64246.23-64175.951932-64113.150244-62370.145377-62367.174556

Tree Length  

576.52576.5239576.5239576.5239576.5239

κ  

1.251.3346531.4173991.2495751.238036

ω-ratio  

ω=0.10341p0=0.492749 ~ ω0=0.190825
p1=0.507251 ~ ω1=1		p0=0.636005 ~ ω0=0.235348
p1=0.363476 ~ ω1=1
p2=0.000519 ~ ω2=999		ω~Β(0.835624,6.418846)p0=0.999811 ~ ω~Β(0.836337,5.858828)
p1=0.000189 ~ ω=214.216826

P-value for testing  
positive selection  

M1 vs M2: P-value=0
domain classification: positively selected		M7 vs M8: P-value=0.051261
domain classification: conserved

Positively selected sites - the underlined numbers denote the position in the AA sequence, while the number in brackets denote the estimated probability for having positive selection at that position. Only positions where the estimated probability for positive selection is ≥0.95 are shown.

   Model M2:

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  

 -105290.01992-105206.7981

Mean ω-ratio  

ω = 0.15151ω = 0.19344

Coeff. of variation  
of ω-ratio  

 CVω = 0.42602CVω = 0.69259
 

Annotations

InteractionsThis domain has 3 known interactions:
PF00022; PF03372; PF03498;
StructuresThis domain has 68 structures:
Notation: PDB_ID (PDB chain, PDB residues)
More...
Gene Ontologies
KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Carbohydrate Metabolism
Fructose and mannose metabolism [KEGG]
Aminosugars metabolism [KEGG]
Inositol phosphate metabolism [KEGG]
Lipid Metabolism
Glycerophospholipid metabolism [KEGG]
Ether lipid metabolism [KEGG]
Sphingolipid metabolism [KEGG]
Nucleotide Metabolism
Purine metabolism [KEGG]
Pyrimidine metabolism [KEGG]
Amino Acid Metabolism
Glycine, serine and threonine metabolism [KEGG]
Metabolism of Cofactors and Vitamins
Thiamine metabolism [KEGG]
Riboflavin metabolism [KEGG]
Pantothenate and CoA biosynthesis [KEGG]
Genetic Information Processing
Transcription
RNA polymerase [KEGG]
Replication and Repair
Base excision repair [KEGG]
Environmental Information Processing
Signal Transduction
Phosphatidylinositol signaling system [KEGG]
Cellular Processes
Cell Growth and Death
p53 signaling pathway [KEGG]
Endocrine System
Insulin signaling pathway [KEGG]
Immune System
B cell receptor signaling pathway [KEGG]
Fc epsilon RI signaling pathway [KEGG]
DisProt- disorder annotation inferred from homologous DisProt sequences
DP00007
Intrinsically disordered region starting at position 39 with length 5
Intrinsically disordered region starting at position 62 with length 5
 
ρD/ρO = 2.40912 (p-value = 0)
 

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

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
 
600829 (1) 600106 (1) 608468 (1) 300081 (1) 604297 (1) 605777 (1) 300535 (1) 147264 (1) 606481 (1) 602622 (1) 609410 (1) 608951 (1) 605764 (1) 601582 (1) 107748 (1) 602244 (1) 125505 (1) 603498 (1) 607875 (1)