SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


Periplasmic binding protein-like I superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Periplasmic binding protein-like I [ 53821]
Superfamily:   Periplasmic binding protein-like I [ 53822]
Families:   L-arabinose binding protein-like [ 53823] (16)


Superfamily statistics
Genomes (2,635) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 45,984 348,398 47
Proteins 45,374 346,251 47


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Phosphorus-oxygen lyases1InformativeInherited
Enzyme Commission (EC)Guanylate cyclase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)nervous system disease0.00002636Least InformativeDirect
Disease Ontology (DO)disease of mental health0.00000000009921Moderately InformativeDirect
Disease Ontology (DO)brain disease0.01874Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.6524Moderately InformativeInherited
Disease Ontology (DO)schizophrenia0.00000000002407InformativeDirect
Disease Ontology (DO)motor neuron disease0.0002694InformativeDirect
Disease Ontology (DO)focal epilepsy0.009729InformativeInherited
Disease Ontology (DO)developmental disorder of mental health0.3545InformativeInherited
Disease Ontology (DO)temporal lobe epilepsy0.0000000007771Highly InformativeDirect
Disease Ontology (DO)amyotrophic lateral sclerosis0.0000001912Highly InformativeDirect
Disease Ontology (DO)bipolar disorder0.00004982Highly InformativeDirect
Disease Ontology (DO)autistic disorder0.0001622Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.2528Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.04189Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental delay0.1434Moderately InformativeInherited
Phenotypic Abnormality (PA)Epileptic encephalopathy0.0003491InformativeDirect
Phenotypic Abnormality (PA)Neurological speech impairment0.1098InformativeInherited
Phenotypic Abnormality (PA)Delayed speech and language development0.02088Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.00000002825Least InformativeDirect
Mammalian Phenotype (MP)abnormal nervous system physiology0.003733Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.03715Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal learning/memory/conditioning0.0000002225InformativeDirect
Mammalian Phenotype (MP)abnormal behavioral response to xenobiotic0.00004646InformativeDirect
Mammalian Phenotype (MP)abnormal touch/ nociception0.0001559InformativeDirect
Mammalian Phenotype (MP)abnormal physiological response to xenobiotic0.0005469InformativeDirect
Mammalian Phenotype (MP)seizures0.0007681InformativeDirect
Mammalian Phenotype (MP)abnormal emotion/affect behavior0.002027InformativeInherited
Mammalian Phenotype (MP)abnormal CNS synaptic transmission0.1459InformativeInherited
Mammalian Phenotype (MP)abnormal consumption behavior0.1735InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.182InformativeInherited
Mammalian Phenotype (MP)decreased alcohol consumption0.00004552Highly InformativeDirect
Mammalian Phenotype (MP)abnormal glutamate-mediated receptor currents0.00006163Highly InformativeDirect
Mammalian Phenotype (MP)decreased fear-related response0.0001059Highly InformativeDirect
Mammalian Phenotype (MP)absence seizures0.0006769Highly InformativeDirect
Mammalian Phenotype (MP)abnormal synaptic plasticity0.0009879Highly InformativeDirect
Mammalian Phenotype (MP)taste/olfaction phenotype0.009186Highly InformativeInherited
Mammalian Phenotype (MP)abnormal synaptic depression0.1122Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism behavior variant0.000000002743Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.000000006056Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant1Least InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.1487Moderately InformativeInherited
Worm Phenotype (WP)metabolic pathway variant0.2944Moderately InformativeInherited
Worm Phenotype (WP)electrophysiology variant0.0000184InformativeDirect
Worm Phenotype (WP)pharyngeal pumping variant0.00006367InformativeDirect
Worm Phenotype (WP)mechanosensation variant0.0003351InformativeDirect
Worm Phenotype (WP)positive chemotaxis variant0.001146InformativeInherited
Worm Phenotype (WP)second messenger mediated signaling variant0.000000003147Highly InformativeDirect
Worm Phenotype (WP)isothermal tracking behavior variant0.0000002638Highly InformativeDirect
Worm Phenotype (WP)carbon dioxide avoidance variant0.000004567Highly InformativeDirect
Worm Phenotype (WP)alkaline pH chemotaxis variant0.000007572Highly InformativeDirect
Worm Phenotype (WP)social behavior variant0.0004578Highly InformativeDirect
Worm Phenotype (WP)aqueous positive chemotaxis defective0.03303Highly InformativeInherited
Worm Phenotype (WP)pharyngeal pumping irregular0.08266Highly InformativeInherited
Worm Phenotype (WP)pharyngeal pumping rate variant0.2039Highly InformativeInherited
Worm Phenotype (WP)odorant positive chemotaxis variant1Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)neurophysiology defective0.0001441InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)nervous system0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)peripheral nervous system0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus DEvelopment stage (XDE)embryonic stage0.03936Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.02546InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 35 and 360.0001823Highly InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Phosphorus-oxygen lyases1InformativeInherited

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 120 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Periplasmic binding protein-like I domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 120 hidden Markov models representing the Periplasmic binding protein-like I superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]