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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 disease0.0001191Least InformativeDirect
Disease Ontology (DO)disease of mental health0.00000000294Moderately InformativeDirect
Disease Ontology (DO)brain disease0.0916Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.09645Moderately InformativeInherited
Disease Ontology (DO)schizophrenia0.000000000004126InformativeDirect
Disease Ontology (DO)focal epilepsy0.04185InformativeInherited
Disease Ontology (DO)motor neuron disease0.04405InformativeInherited
Disease Ontology (DO)developmental disorder of mental health0.515InformativeInherited
Disease Ontology (DO)temporal lobe epilepsy0.000004083Highly InformativeDirect
Disease Ontology (DO)lateral sclerosis0.000005459Highly InformativeDirect
Disease Ontology (DO)amyotrophic lateral sclerosis0.00003496Highly InformativeDirect
Disease Ontology (DO)bipolar disorder0.00004214Highly 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 morphology0.02619Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.1012Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of central motor function0.0008298Moderately InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.0775Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.2356Moderately InformativeInherited
Phenotypic Abnormality (PA)Upper motor neuron dysfunction0.00003067InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the cerebral white matter0.003592InformativeInherited
Phenotypic Abnormality (PA)Abnormal nervous system electrophysiology0.01111InformativeInherited
Phenotypic Abnormality (PA)Hypoplasia of the corpus callosum0.0009857Highly 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 phenotype0.0001259Least InformativeDirect
Mammalian Phenotype (MP)abnormal nervous system physiology0.01572Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.1452Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal CNS synaptic transmission0.000000000001102InformativeDirect
Mammalian Phenotype (MP)abnormal learning/memory/conditioning0.0000384InformativeDirect
Mammalian Phenotype (MP)abnormal touch/ nociception0.0006382InformativeDirect
Mammalian Phenotype (MP)seizures0.0007641InformativeDirect
Mammalian Phenotype (MP)abnormal emotion/affect behavior0.003204InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.163InformativeInherited
Mammalian Phenotype (MP)abnormal glutamate-mediated receptor currents0.0000002158Highly InformativeDirect
Mammalian Phenotype (MP)abnormal exploration in a new environment0.000006814Highly InformativeDirect
Mammalian Phenotype (MP)abnormal locomotor activation0.000008062Highly InformativeDirect
Mammalian Phenotype (MP)abnormal synaptic plasticity0.0001959Highly InformativeDirect
Mammalian Phenotype (MP)tonic-clonic seizures0.0007285Highly InformativeDirect
Mammalian Phenotype (MP)abnormal synaptic depression0.08458Highly 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 variant0.004602Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.04654Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.7803Least InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.09186Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.1351Moderately InformativeInherited
Worm Phenotype (WP)chemotaxis variant0.000002967InformativeDirect
Worm Phenotype (WP)lipid metabolism variant0.0004941InformativeDirect
Worm Phenotype (WP)organism temperature response variant0.05358InformativeInherited
Worm Phenotype (WP)sodium chloride chemotaxis variant0.0000001293Highly InformativeDirect
Worm Phenotype (WP)aqueous positive chemotaxis defective0.0000002272Highly InformativeDirect
Worm Phenotype (WP)thermotaxis variant0.00001283Highly InformativeDirect
Worm Phenotype (WP)organism starvation response variant0.00002258Highly InformativeDirect
Worm Phenotype (WP)pharyngeal pumping rate variant0.0002319Highly 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 defective0.004087Moderately InformativeInherited
Fly Phenotype (FP)neurophysiology defective0.0000002566InformativeDirect
Fly Phenotype (FP)sensory perception defective0.0001692InformativeDirect
Fly Phenotype (FP)feeding behavior defective0.00006079Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)sensory system0.07711Moderately InformativeInherited
Fly Anatomy (FA)chemosensory system0.000006281InformativeDirect
Fly Anatomy (FA)chemosensory sensory organ0.00002115Highly 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 stage0.1701Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.5384InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 35 and 360.0005987Highly 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)Lyases0.0006624Least 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)Carboxy-lyases1InformativeInherited
Enzyme Commission (EC)Intramolecular transferases1InformativeInherited
Enzyme Commission (EC)Acting on polysaccharides0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
DomainSignal0Least InformativeDirect

Document: KW 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) · UniProtKB KeyWords (KW) ]

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 292 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 292 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) · UniProtKB KeyWords (KW) · Internal database links ]