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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

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 the musculature0.04908Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.2663Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle tone0.00315Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of central motor function0.007917Moderately InformativeInherited
Phenotypic Abnormality (PA)Upper motor neuron dysfunction0.0003059InformativeDirect
Phenotypic Abnormality (PA)Abnormal nervous system electrophysiology0.01214InformativeInherited
Phenotypic Abnormality (PA)Encephalopathy0.01434InformativeInherited
Phenotypic Abnormality (PA)Epileptic encephalopathy0.0004276Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.00000002865Least InformativeDirect
Mammalian Phenotype (MP)abnormal nervous system physiology0.003677Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.03708Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal learning/memory/conditioning0.0000002217InformativeDirect
Mammalian Phenotype (MP)abnormal behavioral response to xenobiotic0.00004641InformativeDirect
Mammalian Phenotype (MP)abnormal touch/ nociception0.000156InformativeDirect
Mammalian Phenotype (MP)abnormal physiological response to xenobiotic0.0005451InformativeDirect
Mammalian Phenotype (MP)seizures0.0007677InformativeDirect
Mammalian Phenotype (MP)abnormal emotion/affect behavior0.002026InformativeInherited
Mammalian Phenotype (MP)abnormal CNS synaptic transmission0.1458InformativeInherited
Mammalian Phenotype (MP)abnormal consumption behavior0.1735InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.1821InformativeInherited
Mammalian Phenotype (MP)decreased alcohol consumption0.00004542Highly InformativeDirect
Mammalian Phenotype (MP)abnormal glutamate-mediated receptor currents0.00006156Highly InformativeDirect
Mammalian Phenotype (MP)decreased fear-related response0.0001058Highly InformativeDirect
Mammalian Phenotype (MP)absence seizures0.0006758Highly InformativeDirect
Mammalian Phenotype (MP)abnormal synaptic plasticity0.000987Highly InformativeDirect
Mammalian Phenotype (MP)taste/olfaction phenotype0.009179Highly 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 environmental stimulus response variant0.0000000001232Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.00000002329Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant1Least InformativeInherited
Worm Phenotype (WP)movement variant0.000012Moderately InformativeDirect
Worm Phenotype (WP)locomotion variant0.0001196Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.09309Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.2995Moderately InformativeInherited
Worm Phenotype (WP)metabolic pathway variant0.4686Moderately InformativeInherited
Worm Phenotype (WP)chemotaxis variant0.000000000001099InformativeDirect
Worm Phenotype (WP)electrophysiology variant0.00001987InformativeDirect
Worm Phenotype (WP)mechanosensation variant0.00007751InformativeDirect
Worm Phenotype (WP)odorant chemosensory response variant1InformativeInherited
Worm Phenotype (WP)second messenger mediated signaling variant0.000000003227Highly InformativeDirect
Worm Phenotype (WP)thermotaxis variant0.000001271Highly InformativeDirect
Worm Phenotype (WP)carbon dioxide avoidance variant0.00000512Highly InformativeDirect
Worm Phenotype (WP)alkaline pH chemotaxis variant0.000007314Highly InformativeDirect
Worm Phenotype (WP)AWC odorant chemotaxis variant0.00002857Highly InformativeDirect
Worm Phenotype (WP)social behavior variant0.0002979Highly InformativeDirect
Worm Phenotype (WP)aqueous positive chemotaxis defective0.02813Highly InformativeInherited
Worm Phenotype (WP)pharyngeal pumping irregular0.0943Highly InformativeInherited
Worm Phenotype (WP)pharyngeal pumping rate variant0.2074Highly InformativeInherited
Worm Phenotype (WP)odorant positive chemotaxis defective1Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)neurophysiology defective0.000171InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
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 stage0.009684Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.02578InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 35 and 360.0001912Highly 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 ]