SUPERFAMILY 1.75 HMM library and genome assignments server

Tubulin nucleotide-binding domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Tubulin nucleotide-binding domain-like [ 52489]
Superfamily:   Tubulin nucleotide-binding domain-like [ 52490]
Families:   Tubulin, GTPase domain [ 52491] (3)


Superfamily statistics
Genomes (3,022) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,613 42,782 19
Proteins 10,526 42,709 19


Functional annotation
General category Processes_IC
Detailed category Cell motility

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) single-organism cellular process 0.0003621 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.7872 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.1873 Least Informative Inherited
Biological Process (BP) developmental process 0.6845 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.8211 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) localization 0.0028 Least Informative Inherited
Biological Process (BP) cellular localization 0.000001551 Moderately Informative Direct
Biological Process (BP) single-organism organelle organization 0.0000000000000742 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.6827 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.6546 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1315 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.005124 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.1443 Moderately Informative Inherited
Biological Process (BP) cytoskeleton organization 0.00000001099 Informative Direct
Biological Process (BP) microtubule-based process 0 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00000009746 Informative Direct
Biological Process (BP) hexose metabolic process 0.00000002213 Informative Direct
Biological Process (BP) cell cycle process 0 Informative Direct
Biological Process (BP) protein catabolic process 0.00004415 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0006164 Informative Direct
Biological Process (BP) cell division 0.00000000000001414 Informative Direct
Biological Process (BP) organelle localization 0.000000007443 Informative Direct
Biological Process (BP) single-organism cellular localization 0.0000004346 Informative Direct
Biological Process (BP) cellular component movement 0.03284 Informative Inherited
Biological Process (BP) proteolysis 0.00124 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.1866 Informative Inherited
Biological Process (BP) mitochondrion organization 0.09875 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.004459 Informative Inherited
Biological Process (BP) chromosome organization 1 Informative Inherited
Biological Process (BP) glucose metabolic process 0.000000003634 Highly Informative Direct
Biological Process (BP) protein folding 0.0000008358 Highly Informative Direct
Biological Process (BP) spindle organization 0.000000161 Highly Informative Direct
Biological Process (BP) chromosome segregation 0.00000004699 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 0.0000001663 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.0000004517 Highly Informative Direct
Biological Process (BP) protein polymerization 0.00000000000005988 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.3041 Highly Informative Inherited
Molecular Function (MF) binding 0.7119 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.755 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.0005679 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0098 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.001473 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 0.0002181 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0.0000112 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.000007123 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.001844 Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) membrane 0.8664 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 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 0.4959 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.2972 Moderately Informative Inherited
Cellular Component (CC) bounding membrane of organelle 0.003377 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.000000000003273 Informative Direct
Cellular Component (CC) plastid 0.009949 Informative Inherited
Cellular Component (CC) spindle 0.00000000003316 Highly Informative Direct
Cellular Component (CC) chloroplast stroma 0.000003107 Highly Informative Direct
Cellular Component (CC) organelle outer membrane 0.00001335 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0.1691 Highly Informative Inherited
Cellular Component (CC) cell body 0.01461 Highly Informative Inherited

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)disease of mental health0.0297Moderately InformativeInherited
Disease Ontology (DO)schizophrenia0.0008798InformativeDirect

Document: DO 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 nervous system morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the skull0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of brain morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skull size0InformativeDirect
Phenotypic Abnormality (PA)Intellectual disability0InformativeDirect
Phenotypic Abnormality (PA)Seizures0InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0InformativeDirect
Phenotypic Abnormality (PA)Neurodevelopmental delay0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the cerebrum1InformativeInherited
Phenotypic Abnormality (PA)Polymicrogyria0Highly InformativeDirect
Phenotypic Abnormality (PA)Agenesis of corpus callosum0.000008345Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the brainstem0.00001979Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.000000001806Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.0007391Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.005149Least InformativeInherited
Worm Phenotype (WP)protein aggregation variant0.00000000003373Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.00001684Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant0.00006973Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.04651Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.05181Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.09361Moderately InformativeInherited
Worm Phenotype (WP)cell death variant0.2864Moderately InformativeInherited
Worm Phenotype (WP)cell migration variant0.00000002856InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.00000003995InformativeDirect
Worm Phenotype (WP)nicotine response variant0.0000001017InformativeDirect
Worm Phenotype (WP)exploded through vulva0.00007293InformativeDirect
Worm Phenotype (WP)mechanosensation variant0.0003025InformativeDirect
Worm Phenotype (WP)cell division variant0.0007981InformativeDirect
Worm Phenotype (WP)cell corpse number variant0.000988InformativeDirect
Worm Phenotype (WP)copulation variant0.004847InformativeInherited
Worm Phenotype (WP)neuron development variant0.01458InformativeInherited
Worm Phenotype (WP)RNA expression variant0.1576InformativeInherited
Worm Phenotype (WP)male behavior variant1InformativeInherited
Worm Phenotype (WP)distal tip cell migration variant0.000000001035Highly InformativeDirect
Worm Phenotype (WP)touch resistant0.00000001698Highly InformativeDirect
Worm Phenotype (WP)mitotic spindle defective early emb0.0000008964Highly InformativeDirect
Worm Phenotype (WP)presynaptic region morphology variant0.000004435Highly InformativeDirect
Worm Phenotype (WP)alae morphology variant0.00001902Highly InformativeDirect
Worm Phenotype (WP)miRNA expression variant0.00002354Highly InformativeDirect
Worm Phenotype (WP)cytoskeleton organization biogenesis variant0.005831Highly InformativeInherited
Worm Phenotype (WP)pronucleus centrosomes defective early emb0.06953Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)fertile0.0443Moderately InformativeInherited
Fly Phenotype (FP)wild-type0.0005254InformativeDirect
Fly Phenotype (FP)male fertile0.0000001221Highly InformativeDirect

Document: FP 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)cell0.1281Least InformativeInherited
Fly Anatomy (FA)multi-tissue structure0.1367Least InformativeInherited
Fly Anatomy (FA)reproductive system0.01177Moderately InformativeInherited
Fly Anatomy (FA)germline cyst0.01946InformativeInherited
Fly Anatomy (FA)male germline cell0.03375InformativeInherited
Fly Anatomy (FA)male reproductive system0.06327InformativeInherited
Fly Anatomy (FA)spermatid0.00006665Highly InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)portion of tissue0.3287Least InformativeInherited
Xenopus ANatomical entity (XAN)cell0.3513Least InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.4014Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.5164Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.74Least InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.9347Least InformativeInherited
Xenopus ANatomical entity (XAN)surface structure0.206Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.2681Moderately InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.4424Moderately InformativeInherited
Xenopus ANatomical entity (XAN)skin0.113InformativeInherited
Xenopus ANatomical entity (XAN)neuron0.0000001675Highly InformativeDirect
Xenopus ANatomical entity (XAN)epidermis0.0002059Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial nerve0.0003437Highly InformativeDirect
Xenopus ANatomical entity (XAN)zygote0.0003872Highly InformativeDirect
Xenopus ANatomical entity (XAN)pancreas0.0004842Highly InformativeDirect
Xenopus ANatomical entity (XAN)intersomitic region0.0006242Highly InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0.1928Least InformativeInherited
Plant ANatomical entity (PAN)vascular system0.005109InformativeInherited

Document: AP annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)antineoplastic agents0.000001685Moderately InformativeDirect
Drugbank ATC_code (DB)anthelmintics0.00001761InformativeDirect
Drugbank ATC_code (DB)vinca alkaloids and analogues0.000000000000006795Highly InformativeDirect
Drugbank ATC_code (DB)benzimidazole derivatives0.0000001921Highly InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0Moderately InformativeDirect
Biological processAntibiotic resistance0.0002645InformativeDirect
Biological processSeptation0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentMitochondrion0.2642Moderately InformativeInherited
Cellular componentMicrotubule0InformativeDirect
Cellular componentMitochondrion outer membrane0.0007735InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationNitration0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR003008 SSF52490 Protein matches
Abstract

This domain is found in all tubulin chains, as well as the bacterial FtsZ family of proteins. These proteins are involved in polymer formation. Tubulin is the major component of microtubules, while FtsZ is the polymer-forming protein of bacterial cell division, it is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases, this entry is the GTPase domain. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in bacteria and archaea.


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-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · DrugBank ATC (DB) · 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 7 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 Tubulin nucleotide-binding domain-like 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 7 hidden Markov models representing the Tubulin nucleotide-binding domain-like 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-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · Internal database links ]