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Periplasmic binding protein-like II superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Periplasmic binding protein-like II [ 53849]
Superfamily:   Periplasmic binding protein-like II [ 53850] (3)
Families:   Phosphate binding protein-like [ 53851] (40)
  Transferrin [ 53888] (3)
  PG0945 N-terminal domain-like [ 159818]


Superfamily statistics
Genomes (3,242) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 156,134 1,360,444 216
Proteins 153,945 1,345,480 192


Functional annotation
General category Processes_IC
Detailed category Ion metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0.00008606Least InformativeDirect
Enzyme Commission (EC)Isomerases1Least InformativeInherited
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases1Moderately InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)Acting on polysaccharides0InformativeDirect
Enzyme Commission (EC)Transferring other groups0.258InformativeInherited
Enzyme Commission (EC)Chorismate mutase0Highly InformativeDirect
Enzyme Commission (EC)Prephenate dehydratase0Highly 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 disease0.0001188Least InformativeDirect
Disease Ontology (DO)disease of mental health0.000000002876Moderately InformativeDirect
Disease Ontology (DO)brain disease0.09097Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.09644Moderately InformativeInherited
Disease Ontology (DO)schizophrenia0.000000000004034InformativeDirect
Disease Ontology (DO)focal epilepsy0.04172InformativeInherited
Disease Ontology (DO)motor neuron disease0.04478InformativeInherited
Disease Ontology (DO)developmental disorder of mental health0.5151InformativeInherited
Disease Ontology (DO)temporal lobe epilepsy0.000004016Highly InformativeDirect
Disease Ontology (DO)lateral sclerosis0.000005378Highly InformativeDirect
Disease Ontology (DO)amyotrophic lateral sclerosis0.00003444Highly InformativeDirect
Disease Ontology (DO)bipolar disorder0.00004147Highly 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 physiology0.1008Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal nervous system electrophysiology0.06712InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.000126Least InformativeDirect
Mammalian Phenotype (MP)abnormal nervous system physiology0.0158Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.1449Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal learning/memory/conditioning0.00003922InformativeDirect
Mammalian Phenotype (MP)abnormal touch/ nociception0.0006422InformativeDirect
Mammalian Phenotype (MP)seizures0.0007667InformativeDirect
Mammalian Phenotype (MP)abnormal emotion/affect behavior0.003219InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.1635InformativeInherited
Mammalian Phenotype (MP)abnormal glutamate-mediated receptor currents0.0000002155Highly InformativeDirect
Mammalian Phenotype (MP)abnormal exploration in a new environment0.000006835Highly InformativeDirect
Mammalian Phenotype (MP)abnormal locomotor activation0.000008138Highly InformativeDirect
Mammalian Phenotype (MP)abnormal synaptic plasticity0.0001959Highly InformativeDirect
Mammalian Phenotype (MP)tonic-clonic seizures0.0007297Highly InformativeDirect
Mammalian Phenotype (MP)abnormal synaptic depression0.08447Highly InformativeInherited
Mammalian Phenotype (MP)abnormal aggression-related behavior0.1457Highly 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 variant0.02238Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.09311Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.716Least InformativeInherited
Worm Phenotype (WP)chemical response variant0.00009307Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.06024Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.08094Moderately InformativeInherited
Worm Phenotype (WP)lipid metabolism variant0.0004266InformativeDirect
Worm Phenotype (WP)pharyngeal pumping variant0.0005629InformativeDirect
Worm Phenotype (WP)positive chemotaxis variant0.2613InformativeInherited
Worm Phenotype (WP)sodium chloride chemotaxis variant0.00000006843Highly InformativeDirect
Worm Phenotype (WP)aqueous positive chemotaxis defective0.0000002101Highly InformativeDirect
Worm Phenotype (WP)response to food variant0.000003211Highly InformativeDirect
Worm Phenotype (WP)isothermal tracking behavior variant0.00002469Highly InformativeDirect
Worm Phenotype (WP)pharyngeal pumping rate variant0.000176Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)behavior defective0.007095Moderately InformativeInherited
Fly Phenotype (FP)neurophysiology defective0.00001698InformativeDirect
Fly Phenotype (FP)sensory perception defective0.0004491InformativeDirect
Fly Phenotype (FP)feeding behavior defective0.000001286Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)anatomical group0.3062Least InformativeInherited
Fly Anatomy (FA)chemosensory system0.0001603InformativeDirect

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 stage0.1493Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)tailbud stage0.04706InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 35 and 360.0003775Highly 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)Lyases0.00008402Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Pentosyltransferases0InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Intramolecular transferases1InformativeInherited
Enzyme Commission (EC)Acting on polysaccharides0Highly InformativeDirect

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) · Yeast Phenotype (YP) · 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 83 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 II 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 83 hidden Markov models representing the Periplasmic binding protein-like II 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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]