PANDIT+

KeywordFamilyClanGene   

Entry: Glyco_hydro_57 (PF03065) * 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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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

Glycosyl hydrolase family 57

This family includes alpha-amylase (EC:3.2.1.1), 4--glucanotransferase (EC:2.4.1.-) and amylopullulanase enzymes.
 
Literature1. Laderman KA, Davis BR, Krutzsch HC, Lewis MS, Griko YV, Privalov PL, Anfinsen CB; J Biol Chem 1993;268:24394-24401.The purification and characterization of an extremely thermostable alpha-amylase from the hyperthermophilic archaebacterium Pyrococcus furiosus. PUBMED:8226989
 
Clan

CL0158 (GH_CE)

The clan contains the following members: PF01522(Polysacc_deac_1); PF01074(Glyco_hydro_38); PF03065(Glyco_hydro_57); PF03746(LamB_YcsF);
 
InterPro entry IPR004300
 

Alignment

New Hampshire tree

The seed alignment for this family in the PANDIT database contains 23 aligned sequences:

  AMY1_DICTH/7-293   AMYA_METJA/6-319   AMYA_PYRHO/7-291   MALQ_PYRKO/7-291   O50094_PYRHO/6-394   O58106_PYRHO/3-316   O66934_AQUAE/7-429   O83182_TREPA/12-351   Q55545_SYNY3/8-468   Q8TIT8_METAC/38-312   Q8TIT9_METAC/7-321   Q8TZQ1_PYRFU/35-537   Q8U136_PYRFU/6-395   Q8YXA5_ANASP/8-473   Q8ZT36_PYRAE/22-486   Q8ZT57_PYRAE/6-321   Q972N0_SULTO/342-681   Q973T0_SULTO/7-324   Q97BM4_THEVO/7-311   Q97ZD2_SULSO/7-324   Q9HL91_THEAC/8-289   Q9HLU6_THEAC/262-747   Q9KD04_BACHD/7-382  

The full alignment for this family in the Pfam database contains 526 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.

  Pyrococcus horikoshii (3);   Thermoplasma acidophilum (2);   Pyrobaculum aerophilum (2);   Pyrococcus furiosus (2);   Sulfolobus tokodaii (2);   Methanosarcina acetivorans (2);   Thermococcus kodakarensis KOD1 (1);   Methanocaldococcus jannaschii (1);   Thermoplasma volcanium (1);   Synechocystis sp. PCC 6803 (1);   Aquifex aeolicus (1);   Dictyoglomus thermophilum (1);   Bacillus halodurans (1);   Sulfolobus solfataricus (1);   Nostoc sp. PCC 7120 (1);   Treponema pallidum (1);  

The full alignment covers 202 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  

-13495.22-13483.303772-13483.260076-13384.446312-13383.086094

Tree Length  

186.50186.49868186.49868186.49868186.49868

κ  

1.691.6721811.6663391.6972811.680878

ω-ratio  

ω=0.03977p0=0.983993 ~ ω0=0.040487
p1=0.016007 ~ ω1=1
p0=0.984155 ~ ω0=0.042967
p1=0.015822 ~ ω1=1
p2=2.3e-05 ~ ω2=999
ω~Β(3.313244,70.590385)p0=0.993683 ~ ω~Β(3.440886,67.830596)
p1=0.006317 ~ ω=5.503563

P-value for testing  
positive selection  

M1 vs M2: P-value=0.957245
family classification: conserved
M7 vs M8: P-value=0.256605
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  

-27258.61012-27050.73907

Mean ω-ratio  

ω = 0.21776ω = 0.07981

Coeff. of variation  
of ω-ratio  

CVω = 2.10545CVω = 0.96859
 

Annotations

InteractionsThis family has 3 known interactions:
PF03065; PF09094; PF09095;

StructuresThis family has 6 structures:
Notation: PDB_ID (PDB chain, PDB residues)

Gene Ontologies
Biological Process
 carbohydrate metabolic process[GO:0005975]
Molecular Function
 catalytic activity[GO:0003824]

KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Carbohydrate Metabolism
Starch and sucrose metabolism [KEGG]
Glycan Biosynthesis and Metabolism
Other glycan degradation [KEGG]
 

Expression data (explanation)

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

none


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