SUPERFAMILY 1.75 HMM library and genome assignments server


RCC1/BLIP-II superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   7-bladed beta-propeller [ 50964] (14)
Superfamily:   RCC1/BLIP-II [ 50985] (2)
Families:   Regulator of chromosome condensation RCC1 [ 50986]
  beta-lactamase inhibitor protein-II, BLIP-II [ 69315]


Superfamily statistics
Genomes (732) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 9,607 8,866 3
Proteins 7,866 7,154 3


Functional annotation
General category Processes_IC
Detailed category Cell cycle, Apoptosis

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)regulation of cellular process0.26410.08692Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.043050.000651Least InformativeInherited
Biological Process (BP)regulation of signal transduction0.0010560.01231Moderately InformativeInherited
Biological Process (BP)regulation of catalytic activity0.001041.405e-07Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.0023790.4827Moderately InformativeInherited
Biological Process (BP)regulation of phosphate metabolic process15.145e-11Moderately InformativeInherited
Biological Process (BP)regulation of nucleoside metabolic process8.022e-070InformativeDirect
Biological Process (BP)regulation of nucleotide catabolic process7.346e-071.992e-05InformativeDirect
Biological Process (BP)regulation of purine nucleotide metabolic process2.782e-060InformativeDirect
Biological Process (BP)regulation of Ras GTPase activity7.47e-090.08164Highly InformativeInherited
Molecular Function (MF)enzyme regulator activity0.00036862.832e-12Moderately InformativeDirect
Molecular Function (MF)GTPase regulator activity1.051e-070InformativeDirect
Molecular Function (MF)guanyl-nucleotide exchange factor activity5.806e-090Highly InformativeDirect
Molecular Function (MF)small GTPase regulator activity1.537e-090.00562Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.62831Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.0015710.2049Least InformativeInherited
Cellular Component (CC)vesicle1.912e-050.0002356Moderately InformativeDirect
Cellular Component (CC)secretory granule1.723e-121.997e-05InformativeDirect
Cellular Component (CC)sperm part5.272e-150Highly 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) regulation of metabolic process 0.000651 Least Informative Direct
Biological Process (BP) protein metabolic process 0.6956 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.7307 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.2722 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.08692 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1199 Least Informative Inherited
Biological Process (BP) developmental process 0.1096 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.005513 Least Informative Inherited
Biological Process (BP) system process 0.000728 Moderately Informative Direct
Biological Process (BP) nervous system development 0.000883 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 2.139e-05 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 5.145e-11 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 1.405e-07 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.2131 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.00191 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.01231 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.4827 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.8162 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.04957 Moderately Informative Inherited
Biological Process (BP) organ development 0.5905 Moderately Informative Inherited
Biological Process (BP) regulation of nucleoside metabolic process 0 Informative Direct
Biological Process (BP) cell projection organization 1.27e-05 Informative Direct
Biological Process (BP) regulation of nucleotide catabolic process 1.992e-05 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0007138 Informative Direct
Biological Process (BP) generation of neurons 1.375e-06 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0004728 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0 Informative Direct
Biological Process (BP) sensory organ development 0.004705 Informative Inherited
Biological Process (BP) organ morphogenesis 0.00256 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.009326 Informative Inherited
Biological Process (BP) protein ubiquitination 1.437e-05 Highly Informative Direct
Biological Process (BP) photoreceptor cell differentiation 0.0003674 Highly Informative Direct
Biological Process (BP) eye morphogenesis 0.0004125 Highly Informative Direct
Biological Process (BP) regulation of Ras GTPase activity 0.08164 Highly Informative Inherited
Biological Process (BP) sensory perception 0.02139 Highly Informative Inherited
Molecular Function (MF) binding 0.6691 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 2.832e-12 Moderately Informative Direct
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 4.313e-07 Informative Direct
Molecular Function (MF) enzyme binding 1.567e-05 Informative Direct
Molecular Function (MF) GTPase regulator activity 0 Informative Direct
Molecular Function (MF) protein dimerization activity 3.502e-06 Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0 Highly Informative Direct
Molecular Function (MF) Ras GTPase binding 7.953e-07 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 2.715e-08 Highly Informative Direct
Molecular Function (MF) protein kinase regulator activity 8.015e-06 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 1.427e-08 Highly Informative Direct
Molecular Function (MF) small GTPase regulator activity 0.00562 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.2049 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.3247 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) vesicle 0.0002356 Moderately Informative Direct
Cellular Component (CC) cell projection 4.181e-08 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.05524 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 9.019e-05 Informative Direct
Cellular Component (CC) secretory granule 1.997e-05 Informative Direct
Cellular Component (CC) centrosome 0.0003617 Highly Informative Direct
Cellular Component (CC) cilium 5.001e-09 Highly Informative Direct
Cellular Component (CC) sperm part 0 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Protein-serine/threonine kinases0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of head and neck0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the skeletal system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of higher mental function0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of pyramidal motor function0InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)cell0Least InformativeDirect
Fly Anatomy (FA)anatomical group0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least 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)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0Moderately InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle5.29e-14Moderately InformativeDirect
Biological processMitosis0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm0.1329Least InformativeInherited
Cellular componentCytoskeleton2.043e-08Moderately InformativeDirect
Cellular componentCell projection8.845e-07Moderately InformativeDirect
Cellular componentCilium1.785e-10Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Post-translational modificationTransferase0.9624Least InformativeInherited
Post-translational modificationLigase1.929e-06Moderately InformativeDirect
Post-translational modificationKinase1.972e-05Moderately InformativeDirect
Post-translational modificationReceptor0.0002266Moderately InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationSerine/threonine-protein kinase3.474e-14InformativeDirect
Post-translational modificationPhosphoprotein6.112e-07Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009091 SSF50985 Protein matches
Abstract

The beta-lactamase-inhibitor protein II (BLIP-II) is a secreted protein produced by the soil bacteria Streptomyces exfoliates SMF19. BLIP-II acts as a potent inhibitor of beta-lactamases such as TEM-1, which is the most widespread resistance enzyme to penicillin antibiotics. BLIP-II binds competitively to TEM-1, but no direct contacts are made with TEM-1 active site residues. BLIP-II shows no sequence similarity with BLIP, even though both bind to and inhibit TEM-1. However, BLIP-II does share significant sequence identity with the regulator of chromosome condensation (RCC1) family of proteins. These two families are clearly related, both having a seven-bladed beta-propeller structure, although they differ in the number of strands per blade, BLIP-II having three antiparallel beta-strands per blade, while RCC1 has four-stranded blades [PubMed11573088]. RCC1 is a eukaryotic nuclear protein that acts as a guanine nucleotide exchange factor for Ran, a member of the Ras GTPase family. RCC1 mediates a Ran-GTP gradient necessary for the regulation of spindle formation and nuclear assembly during mitosis, as well as for the transport of macromolecules across the nuclear membrane during interphase.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · 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 2 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 RCC1/BLIP-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 2 hidden Markov models representing the RCC1/BLIP-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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]