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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 2017_06 genome PDB chains (SCOP 1.75)
Domains 45,984 269,200 47
Proteins 45,374 267,497 47


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)organic substance transport0.0000027051Moderately InformativeInherited
Biological Process (BP)nitrogen compound transport0.22011Moderately InformativeInherited
Biological Process (BP)ion transport0.085610.0000000000005152Moderately InformativeInherited
Biological Process (BP)single-organism transport0.000028941Moderately InformativeInherited
Biological Process (BP)organic acid transport0.00016380.000000001136InformativeDirect
Biological Process (BP)anion transport0.000000000057721InformativeInherited
Biological Process (BP)amino acid transport00.00000000000001597Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.000391Least InformativeInherited
Molecular Function (MF)binding0.38651Least InformativeInherited
Molecular Function (MF)transporter activity0.0000000016460Moderately InformativeDirect
Molecular Function (MF)small molecule binding0.0000041530.00000000000003806Moderately InformativeDirect
Molecular Function (MF)hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.000000000065310.2804Moderately InformativeInherited
Molecular Function (MF)anion binding0.010370.000001381Moderately InformativeInherited
Molecular Function (MF)P-P-bond-hydrolysis-driven transmembrane transporter activity00.0000001422InformativeDirect
Molecular Function (MF)hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances00.00000007394InformativeDirect
Molecular Function (MF)carboxylic acid binding0.00000099080InformativeDirect
Molecular Function (MF)ATPase activity00.009541InformativeInherited
Molecular Function (MF)anion transmembrane transporter activity0.0000000038711InformativeInherited
Molecular Function (MF)amino acid transmembrane transporter activity0.0000000000038230.0000000008445Highly InformativeDirect
Molecular Function (MF)amino acid binding0.00000000043120Highly InformativeDirect
Cellular Component (CC)outer membrane-bounded periplasmic space00.00001974Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) response to stimulus 0.000000001449 Least Informative Direct
Biological Process (BP) biological regulation 0.00000000000002769 Least Informative Direct
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.02139 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) ion transport 0.0000000000005152 Moderately Informative Direct
Biological Process (BP) cell communication 0 Moderately Informative Direct
Biological Process (BP) single organism signaling 0 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.0003998 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.1889 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.9063 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.1815 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.4845 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.8043 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.02144 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.3697 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0.001153 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.3103 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.004035 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.1785 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.102 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.4022 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.001427 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.005222 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.2486 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.01142 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) defense response 1 Moderately Informative Inherited
Biological Process (BP) response to acid chemical 0.0000102 Informative Direct
Biological Process (BP) system process 0 Informative Direct
Biological Process (BP) behavior 0 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.000001698 Informative Direct
Biological Process (BP) organic acid transport 0.000000001136 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.0004838 Informative Direct
Biological Process (BP) regulation of ion transport 0.0001534 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.000000003148 Informative Direct
Biological Process (BP) cation homeostasis 0.00000000002366 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.0000000129 Informative Direct
Biological Process (BP) response to nitrogen compound 0.00004271 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.000000556 Informative Direct
Biological Process (BP) cell surface receptor signaling pathway 0.01341 Informative Inherited
Biological Process (BP) positive regulation of transport 0.1762 Informative Inherited
Biological Process (BP) metal ion transport 0.05374 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.2997 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) inorganic ion homeostasis 0.5463 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.7181 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.6625 Informative Inherited
Biological Process (BP) embryo development 1 Informative Inherited
Biological Process (BP) animal organ morphogenesis 1 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.9142 Informative Inherited
Biological Process (BP) regulation of system process 0.1298 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.01137 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Informative Inherited
Biological Process (BP) intracellular signal transduction 1 Informative Inherited
Biological Process (BP) anion transport 1 Informative Inherited
Biological Process (BP) regulation of secretion 0.008695 Informative Inherited
Biological Process (BP) cell development 1 Informative Inherited
Biological Process (BP) response to radiation 0.04183 Informative Inherited
Biological Process (BP) response to metal ion 0.1049 Informative Inherited
Biological Process (BP) amino acid transport 0.00000000000001597 Highly Informative Direct
Biological Process (BP) G-protein coupled receptor signaling pathway 0.00000000003453 Highly Informative Direct
Biological Process (BP) cell-cell signaling 0 Highly Informative Direct
Biological Process (BP) response to mechanical stimulus 0.00008312 Highly Informative Direct
Biological Process (BP) second-messenger-mediated signaling 0 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0 Highly Informative Direct
Biological Process (BP) response to amino acid 0 Highly Informative Direct
Biological Process (BP) positive regulation of ion transport 0.000116 Highly Informative Direct
Biological Process (BP) regulation of neuron apoptotic process 0.0002396 Highly Informative Direct
Biological Process (BP) single-organism behavior 0 Highly Informative Direct
Biological Process (BP) negative regulation of phosphate metabolic process 0.000299 Highly Informative Direct
Biological Process (BP) nervous system process 0.00000000005273 Highly Informative Direct
Biological Process (BP) regulation of calcium ion transport 0.00003024 Highly Informative Direct
Biological Process (BP) cellular response to acid chemical 0.000000000000007296 Highly Informative Direct
Biological Process (BP) cellular response to organonitrogen compound 0.00000000008246 Highly Informative Direct
Biological Process (BP) divalent inorganic cation transport 0.00000000002166 Highly Informative Direct
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 0.0007662 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 0.2701 Highly Informative Inherited
Biological Process (BP) negative regulation of response to external stimulus 0.02651 Highly Informative Inherited
Biological Process (BP) embryonic organ development 0.528 Highly Informative Inherited
Biological Process (BP) response to alcohol 0.00385 Highly Informative Inherited
Biological Process (BP) regulation of cyclic nucleotide metabolic process 0.005107 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to growth factor stimulus 0.1322 Highly Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 1 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0 Moderately Informative Direct
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.00000000000003806 Moderately Informative Direct
Molecular Function (MF) anion binding 0.000001381 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 1 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.2804 Moderately Informative Inherited
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0.0006541 Informative Direct
Molecular Function (MF) signal transducer activity 0 Informative Direct
Molecular Function (MF) P-P-bond-hydrolysis-driven transmembrane transporter activity 0.0000001422 Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances 0.00000007394 Informative Direct
Molecular Function (MF) passive transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) carboxylic acid binding 0 Informative Direct
Molecular Function (MF) amide binding 0.00007936 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0003374 Informative Direct
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) DNA binding 0.5255 Informative Inherited
Molecular Function (MF) ATPase activity 0.009541 Informative Inherited
Molecular Function (MF) monovalent inorganic cation transmembrane transporter activity 1 Informative Inherited
Molecular Function (MF) anion transmembrane transporter activity 1 Informative Inherited
Molecular Function (MF) metal ion transmembrane transporter activity 0.9506 Informative Inherited
Molecular Function (MF) transmembrane signaling receptor activity 0.000001646 Highly Informative Direct
Molecular Function (MF) ion channel activity 0 Highly Informative Direct
Molecular Function (MF) sodium ion transmembrane transporter activity 0.0000000000001289 Highly Informative Direct
Molecular Function (MF) amino acid transmembrane transporter activity 0.0000000008445 Highly Informative Direct
Molecular Function (MF) amino acid binding 0 Highly Informative Direct
Molecular Function (MF) protein domain specific binding 0.0001767 Highly Informative Direct
Molecular Function (MF) gated channel activity 0.002994 Highly Informative Inherited
Molecular Function (MF) double-stranded DNA binding 0.002847 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding 0.02628 Highly Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.006194 Highly Informative Inherited
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) plasma membrane 0 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0 Moderately Informative Direct
Cellular Component (CC) cell projection 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 1 Moderately Informative Inherited
Cellular Component (CC) vesicle 1 Moderately Informative Inherited
Cellular Component (CC) protein-DNA complex 0.000008201 Informative Direct
Cellular Component (CC) neuron projection 0.0000006025 Informative Direct
Cellular Component (CC) plasma membrane region 0.0000000000002904 Informative Direct
Cellular Component (CC) transporter complex 0 Informative Direct
Cellular Component (CC) plasma membrane bounded cell projection part 0.3889 Informative Inherited
Cellular Component (CC) outer membrane-bounded periplasmic space 0.00001974 Highly Informative Direct
Cellular Component (CC) dendrite 0.000001788 Highly Informative Direct
Cellular Component (CC) intrinsic component of plasma membrane 0 Highly Informative Direct
Cellular Component (CC) receptor complex 0 Highly Informative Direct
Cellular Component (CC) exocytic vesicle 0.000008928 Highly Informative Direct
Cellular Component (CC) presynapse 0.00533 Highly Informative Inherited

Document: GO annotation of SCOP domains

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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processIon transport0Moderately InformativeDirect
Biological processTranscription regulation0Moderately InformativeDirect
Biological processCarbohydrate metabolism1Moderately InformativeInherited
Biological processPurine biosynthesis0InformativeDirect
Biological processSensory transduction0InformativeDirect
Biological processChemotaxis0.0000000000000239InformativeDirect
Biological processCell shape0.0000000009546InformativeDirect
Biological processAmino-acid transport0Highly InformativeDirect
Biological processPeptidoglycan synthesis0.0000000004061Highly InformativeDirect
Biological processOsteogenesis0.0000001837Highly InformativeDirect
Biological processSugar transport0.000003078Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell projection0Moderately InformativeDirect
Cellular componentCell junction0Moderately InformativeDirect
Cellular componentCell membrane0.000000000000004844Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0003027Moderately InformativeDirect
Cellular componentSynapse0InformativeDirect
Cellular componentPeriplasm0InformativeDirect
Cellular componentCell outer membrane0.0000000000007638InformativeDirect
Cellular componentPostsynaptic cell membrane0Highly InformativeDirect
Coding sequence diversityRNA editing0.0000009066Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionNucleotide-binding1Least InformativeInherited
Molecular functionCalcium0Moderately InformativeDirect
Molecular functionGTP-binding0.000000000000001482InformativeDirect
Molecular functionChloride0.00005324InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationLyase0.000000003888Moderately InformativeDirect
Post-translational modificationIon channel0InformativeDirect
Post-translational modificationLigand-gated ion channel0Highly InformativeDirect
Post-translational modificationG-protein coupled receptor0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0.0001026Least InformativeDirect
Post-translational modificationPalmitate0Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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 18 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 18 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]