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 (355) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 426 502 2
Proteins 426 502 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 0.000000001875 Least Informative Direct
Biological Process (BP) developmental process 0.000001447 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.000003473 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00007001 Least Informative Direct
Biological Process (BP) response to stimulus 0.0008273 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.001634 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.002277 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.09116 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.8647 Least Informative Inherited
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.00000000000008678 Moderately Informative Direct
Biological Process (BP) reproductive process 0.00000000003837 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.0000000000661 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.000000001854 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.00000000326 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.00000006925 Moderately Informative Direct
Biological Process (BP) single-organism organelle organization 0.0000001648 Moderately Informative Direct
Biological Process (BP) immune system process 0.000001394 Moderately Informative Direct
Biological Process (BP) regulation of phosphorus metabolic process 0.00001941 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.00008349 Moderately Informative Direct
Biological Process (BP) nervous system development 0.0001736 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0002168 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.001624 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.004236 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.05097 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.001385 Moderately Informative Inherited
Biological Process (BP) organ development 0.001346 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.003518 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.03317 Moderately Informative Inherited
Biological Process (BP) organelle assembly 0 Informative Direct
Biological Process (BP) microtubule-based process 0 Informative Direct
Biological Process (BP) sexual reproduction 0 Informative Direct
Biological Process (BP) organelle localization 0 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0.00000000000001246 Informative Direct
Biological Process (BP) cytoskeleton organization 0.00000000000005349 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.00000000000008202 Informative Direct
Biological Process (BP) neurological system process 0.000000000002689 Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.00000000000311 Informative Direct
Biological Process (BP) cell proliferation 0.000000000005955 Informative Direct
Biological Process (BP) locomotion 0.00000000001192 Informative Direct
Biological Process (BP) cellular component movement 0.00000000004442 Informative Direct
Biological Process (BP) single-organism behavior 0.00000000007536 Informative Direct
Biological Process (BP) generation of neurons 0.0000000001411 Informative Direct
Biological Process (BP) secretion by cell 0.0000000003764 Informative Direct
Biological Process (BP) single organism reproductive process 0.0000000004988 Informative Direct
Biological Process (BP) actin filament-based process 0.000000000512 Informative Direct
Biological Process (BP) central nervous system development 0.0000000008373 Informative Direct
Biological Process (BP) single-organism membrane organization 0.000000004601 Informative Direct
Biological Process (BP) synaptic transmission 0.000000005569 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.00000001012 Informative Direct
Biological Process (BP) single-organism cellular localization 0.0000001274 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.0000002277 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.000001498 Informative Direct
Biological Process (BP) negative regulation of signaling 0.00000306 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.000003205 Informative Direct
Biological Process (BP) localization of cell 0.000003714 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.000004714 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.000006653 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.00001153 Informative Direct
Biological Process (BP) regulation of MAPK cascade 0.0001246 Informative Direct
Biological Process (BP) protein transport 0.000929 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 0.005863 Informative Inherited
Biological Process (BP) regulation of Ras GTPase activity 0 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0 Highly Informative Direct
Biological Process (BP) stem cell proliferation 0 Highly Informative Direct
Biological Process (BP) neuromuscular process 0 Highly Informative Direct
Biological Process (BP) spermatogenesis 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 protein signal transduction 0 Highly Informative Direct
Biological Process (BP) neural precursor cell proliferation 0 Highly Informative Direct
Biological Process (BP) myeloid cell development 0.0000000000001712 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0.0000000000002493 Highly Informative Direct
Biological Process (BP) telencephalon development 0.00000000000227 Highly Informative Direct
Biological Process (BP) cellular component assembly involved in morphogenesis 0.000000000002831 Highly Informative Direct
Biological Process (BP) adult behavior 0.000000000002953 Highly Informative Direct
Biological Process (BP) nucleus organization 0.00000000003594 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0000000003971 Highly Informative Direct
Biological Process (BP) germ cell development 0.00000002625 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular signal transduction 0.000001548 Highly Informative Direct
Molecular Function (MF) binding 0.0001053 Least Informative Direct
Molecular Function (MF) protein complex binding 0.000000000000295 Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0.000000000000555 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0000003771 Informative Direct
Molecular Function (MF) tubulin binding 0 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000000000007687 Least Informative Direct
Cellular Component (CC) protein complex 0.000000005328 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0001131 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.01232 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) organelle envelope 0.000000009275 Moderately Informative Direct
Cellular Component (CC) cell projection 0.00000004087 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.003091 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 0.00000000000005579 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.000000000001869 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 0.000000000006825 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0.000001444 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 metabolism0.05574Moderately InformativeInherited
Biological processNeurogenesis0InformativeDirect
Biological processMitosis0InformativeDirect
Biological processLipid degradation0.000000023Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentMicrotubule0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainWD repeat0InformativeDirect
Post-translational modificationDevelopmental protein0.000000000000004384Moderately 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 ]