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 (326) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 412 342 2
Proteins 412 342 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 1.184e-09 Least Informative Direct
Biological Process (BP) developmental process 1.262e-06 Least Informative Direct
Biological Process (BP) multicellular organismal process 4.972e-06 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 4.488e-05 Least Informative Direct
Biological Process (BP) response to stimulus 0.0007246 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.8341 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.001269 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.02056 Least Informative Inherited
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 9.23e-14 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 5.241e-11 Moderately Informative Direct
Biological Process (BP) reproduction 1.858e-10 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 8.642e-10 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 2.413e-09 Moderately Informative Direct
Biological Process (BP) cell differentiation 4.751e-08 Moderately Informative Direct
Biological Process (BP) immune system process 1.054e-06 Moderately Informative Direct
Biological Process (BP) macromolecule localization 2.529e-06 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 1.562e-05 Moderately Informative Direct
Biological Process (BP) organelle organization 1.777e-05 Moderately Informative Direct
Biological Process (BP) system process 3.693e-05 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 7.9e-05 Moderately Informative Direct
Biological Process (BP) nervous system development 0.0001439 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.0004344 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.000993 Moderately Informative Direct
Biological Process (BP) organ development 0.001335 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.08019 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.004596 Moderately Informative Inherited
Biological Process (BP) tissue development 0.007008 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.007282 Moderately Informative Inherited
Biological Process (BP) organelle assembly 0 Informative Direct
Biological Process (BP) sexual reproduction 0 Informative Direct
Biological Process (BP) organelle localization 0 Informative Direct
Biological Process (BP) microtubule-based process 3.746e-15 Informative Direct
Biological Process (BP) regulation of nucleotide catabolic process 7.333e-15 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 1.086e-14 Informative Direct
Biological Process (BP) cytoskeleton organization 4.755e-14 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 7.325e-14 Informative Direct
Biological Process (BP) single-organism behavior 3.813e-13 Informative Direct
Biological Process (BP) cellular process involved in reproduction 5.651e-13 Informative Direct
Biological Process (BP) protein transport 2.207e-12 Informative Direct
Biological Process (BP) locomotion 1.013e-11 Informative Direct
Biological Process (BP) generation of neurons 1.214e-10 Informative Direct
Biological Process (BP) epithelium development 1.465e-10 Informative Direct
Biological Process (BP) single organism reproductive process 1.475e-10 Informative Direct
Biological Process (BP) cellular component movement 1.88e-10 Informative Direct
Biological Process (BP) central nervous system development 5.932e-10 Informative Direct
Biological Process (BP) secretion by cell 6.585e-10 Informative Direct
Biological Process (BP) actin filament-based process 1.566e-09 Informative Direct
Biological Process (BP) membrane organization 4.505e-09 Informative Direct
Biological Process (BP) transmission of nerve impulse 3.561e-08 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 2.025e-07 Informative Direct
Biological Process (BP) cell-cell signaling 9.453e-07 Informative Direct
Biological Process (BP) cellular component morphogenesis 1.416e-06 Informative Direct
Biological Process (BP) negative regulation of signaling 1.824e-06 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 2.722e-06 Informative Direct
Biological Process (BP) negative regulation of cell communication 3.936e-06 Informative Direct
Biological Process (BP) localization of cell 4.07e-06 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 6.673e-06 Informative Direct
Biological Process (BP) regulation of intracellular protein kinase cascade 0.001608 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.009512 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.002233 Informative Inherited
Biological Process (BP) spermatogenesis 0 Highly Informative Direct
Biological Process (BP) locomotory behavior 0 Highly Informative Direct
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) regulation of Rho protein signal transduction 0 Highly Informative Direct
Biological Process (BP) cellular component disassembly 9.323e-13 Highly Informative Direct
Biological Process (BP) telencephalon development 1.43e-12 Highly Informative Direct
Biological Process (BP) adult behavior 2.226e-12 Highly Informative Direct
Biological Process (BP) cell proliferation 8.43e-12 Highly Informative Direct
Biological Process (BP) cellular component assembly involved in morphogenesis 1.129e-11 Highly Informative Direct
Biological Process (BP) nucleus organization 3.43e-11 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 2.648e-10 Highly Informative Direct
Biological Process (BP) neuromuscular process 4.816e-10 Highly Informative Direct
Biological Process (BP) epithelial cell development 3.733e-09 Highly Informative Direct
Biological Process (BP) microtubule cytoskeleton organization 1.138e-05 Highly Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 8.272e-05 Highly Informative Direct
Molecular Function (MF) binding 7.154e-05 Least Informative Direct
Molecular Function (MF) cytoskeletal protein binding 4.462e-13 Informative Direct
Molecular Function (MF) protein dimerization activity 3.63e-07 Informative Direct
Molecular Function (MF) tubulin binding 0 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 5.051e-13 Least Informative Direct
Cellular Component (CC) protein complex 3.251e-10 Least Informative Direct
Cellular Component (CC) intracellular organelle part 9.085e-05 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.01355 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 1.218e-09 Moderately Informative Direct
Cellular Component (CC) organelle envelope 1.074e-08 Moderately Informative Direct
Cellular Component (CC) cell projection 3.231e-08 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.002235 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 8.262e-14 Informative Direct
Cellular Component (CC) cilium 8.634e-15 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 1.171e-12 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 8.36e-12 Highly Informative Direct
Cellular Component (CC) centrosome 1.648e-11 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 metabolism0.05532Moderately InformativeInherited
Biological processNeurogenesis0InformativeDirect
Biological processMitosis0InformativeDirect
Biological processLipid degradation2.256e-08Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentMicrotubule0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainWD repeat0InformativeDirect
Post-translational modificationDevelopmental protein4.592e-15Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · 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 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 ]