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 (782) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,971 14,030 3
Proteins 9,010 10,579 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)
Molecular Function (MF)enzyme regulator activity0.0031162.032e-12Moderately InformativeInherited
Molecular Function (MF)GTPase regulator activity1.184e-050InformativeDirect
Molecular Function (MF)guanyl-nucleotide exchange factor activity1.221e-060Highly InformativeDirect
Molecular Function (MF)small GTPase regulator activity4.02e-070.004474Highly InformativeInherited
Cellular Component (CC)membrane0.1171Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.90921Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.0005480.07295Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)endomembrane system0.0015720.237Moderately InformativeInherited
Cellular Component (CC)organelle membrane0.057760.4464Moderately InformativeInherited
Cellular Component (CC)organelle envelope0.018120.1184Moderately InformativeInherited
Cellular Component (CC)nuclear part0.023080.2051Moderately InformativeInherited
Cellular Component (CC)vesicle0.00076650.007506Moderately InformativeInherited
Cellular Component (CC)secretory granule9.165e-121.841e-05InformativeDirect
Cellular Component (CC)nuclear envelope1.547e-060.001927InformativeInherited
Cellular Component (CC)nuclear membrane1.658e-081.657e-05Highly InformativeDirect
Cellular Component (CC)sperm part2.055e-130Highly 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) protein metabolic process 0.8616 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.9161 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.4007 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.00687 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.3394 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.0184 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.06653 Least Informative Inherited
Biological Process (BP) developmental process 0.05283 Least Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.0002557 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 2.163e-09 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 2.716e-07 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.3099 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.1143 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.01041 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.01587 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.508 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.7471 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.01587 Moderately Informative Inherited
Biological Process (BP) system process 0.003793 Moderately Informative Inherited
Biological Process (BP) organ development 0.3704 Moderately Informative Inherited
Biological Process (BP) regulation of nucleoside metabolic process 0 Informative Direct
Biological Process (BP) cell projection organization 4.151e-05 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 9.148e-15 Informative Direct
Biological Process (BP) generation of neurons 7.097e-06 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0003387 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.0001634 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0.0005896 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0 Informative Direct
Biological Process (BP) sensory organ development 0.01254 Informative Inherited
Biological Process (BP) organ morphogenesis 0.01132 Informative Inherited
Biological Process (BP) protein ubiquitination 3.209e-05 Highly Informative Direct
Biological Process (BP) eye morphogenesis 0.0003645 Highly Informative Direct
Biological Process (BP) positive regulation of GTPase activity 0.00283 Highly Informative Inherited
Biological Process (BP) regulation of Ras GTPase activity 0.08045 Highly Informative Inherited
Biological Process (BP) sensory perception 0.0193 Highly Informative Inherited
Molecular Function (MF) binding 0.4092 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 2.032e-12 Moderately Informative Direct
Molecular Function (MF) ligase activity 0.0001552 Informative Direct
Molecular Function (MF) enzyme binding 4.097e-05 Informative Direct
Molecular Function (MF) GTPase regulator activity 0 Informative Direct
Molecular Function (MF) protein dimerization activity 3.414e-05 Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0 Highly Informative Direct
Molecular Function (MF) Ras GTPase binding 1.424e-07 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 4.131e-07 Highly Informative Direct
Molecular Function (MF) protein kinase regulator activity 1.257e-05 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 5.023e-08 Highly Informative Direct
Molecular Function (MF) kinase binding 0.361 Highly Informative Inherited
Molecular Function (MF) small GTPase regulator activity 0.004474 Highly Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.07295 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) cell projection 1.015e-06 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.237 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.4464 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.1184 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.2051 Moderately Informative Inherited
Cellular Component (CC) vesicle 0.007506 Moderately Informative Inherited
Cellular Component (CC) secretory granule 1.841e-05 Informative Direct
Cellular Component (CC) nuclear envelope 0.001927 Informative Inherited
Cellular Component (CC) nuclear membrane 1.657e-05 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 skeletal morphology0Least 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)adult0Least InformativeDirect
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)cell0Least InformativeDirect
Fly Anatomy (FA)anatomical group0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited

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 cycle4.167e-14Moderately InformativeDirect
Biological processMitosis0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm0.136Least InformativeInherited
Cellular componentCytoskeleton2.135e-08Moderately InformativeDirect
Cellular componentCell projection1.051e-06Moderately InformativeDirect
Cellular componentCilium2.108e-10Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Post-translational modificationTransferase0.9605Least InformativeInherited
Post-translational modificationLigase1.828e-06Moderately InformativeDirect
Post-translational modificationKinase2.009e-05Moderately InformativeDirect
Post-translational modificationReceptor0.0002214Moderately InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationSerine/threonine-protein kinase3.435e-14InformativeDirect
Post-translational modificationPhosphoprotein6.159e-07Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)protein ubiquitination0Moderately InformativeDirect

Document: UP 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) · UniProtKB UniPathway (UP) ]

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) · UniProtKB UniPathway (UP) · Internal database links ]