SUPERFAMILY 1.75 HMM library and genome assignments server


Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [ 109924]
Superfamily:   Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [ 109925]
Families:   Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [ 109926]


Superfamily statistics
Genomes (349) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 416 502 2
Proteins 416 502 2


Functional annotation
General category Other
Detailed category Unknown function

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) localization 0.00000002283 Least Informative Direct
Biological Process (BP) developmental process 0.00001347 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.00005017 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0002113 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.001213 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.02161 Least Informative Inherited
Biological Process (BP) response to stimulus 0.003143 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.837 Least Informative Inherited
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.0000000000006422 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.000000000284 Moderately Informative Direct
Biological Process (BP) reproduction 0.000000001426 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.000000003034 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.00000001154 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0000003082 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.000002495 Moderately Informative Direct
Biological Process (BP) immune system process 0.000004186 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 0.0000163 Moderately Informative Direct
Biological Process (BP) organelle organization 0.00001744 Moderately Informative Direct
Biological Process (BP) system process 0.00003867 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.00008202 Moderately Informative Direct
Biological Process (BP) nervous system development 0.0001473 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.0004181 Moderately Informative Direct
Biological Process (BP) organ development 0.001534 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.001034 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.07922 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.004543 Moderately Informative Inherited
Biological Process (BP) tissue development 0.007315 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.007843 Moderately Informative Inherited
Biological Process (BP) organelle assembly 0 Informative Direct
Biological Process (BP) organelle localization 0 Informative Direct
Biological Process (BP) sexual reproduction 0.000000000000001922 Informative Direct
Biological Process (BP) microtubule-based process 0.000000000000007281 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0.00000000000003915 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.0000000000002617 Informative Direct
Biological Process (BP) cytoskeleton organization 0.0000000000003049 Informative Direct
Biological Process (BP) cellular process involved in reproduction 0.000000000000541 Informative Direct
Biological Process (BP) cellular component disassembly 0.000000000001162 Informative Direct
Biological Process (BP) single-organism behavior 0.0000000000018 Informative Direct
Biological Process (BP) protein transport 0.000000000008384 Informative Direct
Biological Process (BP) locomotion 0.00000000007507 Informative Direct
Biological Process (BP) cellular membrane organization 0.00000000009225 Informative Direct
Biological Process (BP) single organism reproductive process 0.0000000001632 Informative Direct
Biological Process (BP) cellular component movement 0.0000000002186 Informative Direct
Biological Process (BP) secretion by cell 0.0000000006023 Informative Direct
Biological Process (BP) central nervous system development 0.0000000006111 Informative Direct
Biological Process (BP) epithelium development 0.0000000006227 Informative Direct
Biological Process (BP) generation of neurons 0.0000000006281 Informative Direct
Biological Process (BP) actin filament-based process 0.000000001526 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.000000007281 Informative Direct
Biological Process (BP) transmission of nerve impulse 0.00000004329 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.000000188 Informative Direct
Biological Process (BP) developmental process involved in reproduction 0.0000002396 Informative Direct
Biological Process (BP) cell-cell signaling 0.000001158 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.000001457 Informative Direct
Biological Process (BP) negative regulation of signaling 0.000001958 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.000004217 Informative Direct
Biological Process (BP) localization of cell 0.000004488 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.000004884 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.000006992 Informative Direct
Biological Process (BP) regulation of response to stress 0.000631 Informative Direct
Biological Process (BP) regulation of intracellular protein kinase cascade 0.001525 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.01004 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.002239 Informative Inherited
Biological Process (BP) spermatogenesis 0 Highly Informative Direct
Biological Process (BP) neural precursor cell proliferation 0 Highly Informative Direct
Biological Process (BP) locomotory behavior 0 Highly Informative Direct
Biological Process (BP) learning or memory 0 Highly Informative Direct
Biological Process (BP) regulation of Rho GTPase activity 0 Highly Informative Direct
Biological Process (BP) stem cell proliferation 0 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0 Highly Informative Direct
Biological Process (BP) telencephalon development 0.000000000001525 Highly Informative Direct
Biological Process (BP) adult behavior 0.000000000002043 Highly Informative Direct
Biological Process (BP) cellular component assembly involved in morphogenesis 0.00000000001082 Highly Informative Direct
Biological Process (BP) nucleus organization 0.00000000002843 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0000000002793 Highly Informative Direct
Biological Process (BP) neuromuscular process 0.0000000005088 Highly Informative Direct
Biological Process (BP) epithelial cell development 0.000000003794 Highly Informative Direct
Biological Process (BP) microtubule cytoskeleton organization 0.00001174 Highly Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.0000955 Highly Informative Direct
Molecular Function (MF) binding 0.001518 Least Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0.0000000000005657 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0000003927 Informative Direct
Molecular Function (MF) tubulin binding 0 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.00000000006694 Least Informative Direct
Cellular Component (CC) protein complex 0.000000003033 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0001426 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.01028 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.000000001408 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.000000008716 Moderately Informative Direct
Cellular Component (CC) cell projection 0.00000002719 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.006277 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0 Informative Direct
Cellular Component (CC) nuclear envelope 0 Informative Direct
Cellular Component (CC) cell leading edge 0.00000000000005683 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.000000000001568 Highly Informative Direct
Cellular Component (CC) centrosome 0.000000000007475 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 0.00000000001158 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processCell cycle0Moderately InformativeDirect
Biological processDifferentiation0Moderately InformativeDirect
Biological processLipid metabolism0.05474Moderately InformativeInherited
Biological processNeurogenesis0InformativeDirect
Biological processMitosis0InformativeDirect
Biological processLipid degradation0.00000002255Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentMicrotubule0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainWD repeat0InformativeDirect
Post-translational modificationDevelopmental protein0.000000000000004594Moderately InformativeDirect

Document: KW annotation of SCOP domains

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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 1 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 Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain 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 1 hidden Markov models representing the Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain 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-coverage) · UniProtKB KeyWords (KW) · Internal database links ]