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Entry: Defensin_propep (PF00879)

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Pfam summary

Description

Defensin propeptide

 
Literature
 
 
InterPro entry IPR002366
 

Alignment

New Hampshire tree

The seed alignment for this family in the PANDIT database contains 13 aligned sequences:

  DEF1A_CAVPO/1-52   DEF1_MOUSE/1-52   DEF1_RABIT/1-51   DEF1_RAT/1-52   DEF3_HUMAN/1-53   DEF3_RABIT/1-52   DEF4_HUMAN/1-52   DEF4_RAT/1-51   DEF5_HUMAN/1-52   DEF5_MOUSE/1-52   DEF5_RABIT/1-52   DEF6_HUMAN/1-59   DEFA_RAT/1-46  

The full alignment for this family in the Pfam database contains 135 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.

  Homo sapiens (4);   Oryctolagus cuniculus (3);   Rattus norvegicus (3);   Mus musculus (2);   Cavia porcellus (1);  

The full alignment covers 18 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  

-1288.65-1279.943597-1271.854949-1280.308431-1271.870061

Tree Length  

7.267.261337.261337.261337.26133

κ  

2.412.4315092.4967822.4212632.458242

ω-ratio  

ω=0.84526p0=0.323718 ~ ω0=0.264709
p1=0.676282 ~ ω1=1
p0=0.232119 ~ ω0=0.218485
p1=0.727121 ~ ω1=1
p2=0.04076 ~ ω2=4.985928
ω~Β(0.734431,0.253504)p0=0.959207 ~ ω~Β(0.731711,0.22247)
p1=0.040793 ~ ω=4.754064

P-value for testing  
positive selection  

M1 vs M2: P-value=0.000307
family classification: positively selected
M7 vs M8: P-value=0.000216
family classification: positively selected

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:
      Naive Empirical Bayes (NEB) analysis: 25 (0.996); 30 (0.994);
      Empirical Bayes (BEB) analysis: 25 (0.996); 30 (0.995);
   Model M8:
      Naive Empirical Bayes (NEB) analysis: 25 (0.996); 30 (0.994);
      Bayes Empirical Bayes (BEB) analysis: 25 (0.997); 30 (0.997);

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  

-1478.97738-1477.44997

Mean ω-ratio  

ω = 0.90262ω = 1.04462

Coeff. of variation  
of ω-ratio  

CVω = 0.78849CVω = 0.92437
 

Annotations

InteractionsThis family has 0 known interactions:

StructuresThis family has 0 structures:
Notation: PDB_ID (PDB chain, PDB residues)

Gene Ontologies
Biological Process
 defense response[GO:0006952]

KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Lipid Metabolism
Androgen and estrogen metabolism [KEGG]
Glycerolipid metabolism [KEGG]
Sphingolipid metabolism [KEGG]
Amino Acid Metabolism
Lysine degradation [KEGG]
Metabolism of Cofactors and Vitamins
Biotin metabolism [KEGG]
Folate biosynthesis [KEGG]
Xenobiotics Biodegradation and Metabolism
gamma-Hexachlorocyclohexane degradation [KEGG]
Genetic Information Processing
Folding, Sorting and Degradation
Type IV secretion system [KEGG]
Type II secretion system [KEGG]
Environmental Information Processing
Membrane Transport
ABC transporters [KEGG]
Signal Transduction
Two-component system [KEGG]
Signaling Molecules and Interaction
Neuroactive ligand-receptor interaction [KEGG]
Cell adhesion molecules (CAMs) [KEGG]
Cellular Processes
Cell Motility
Flagellar assembly [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
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
 
600753 (1) 601157 (1) 137260 (1) 600472 (1) 125220 (1) 112260 (1) 600471 (1) 604522 (1)