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 (2,976) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 9,864 27,804 19
Proteins 9,797 27,757 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 6.308e-12 Least Informative Direct
Biological Process (BP) localization 0.0008306 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) protein metabolic process 0.1249 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.6871 Least Informative Inherited
Biological Process (BP) developmental process 0.5489 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.7341 Least Informative Inherited
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) macromolecule catabolic process 0.0006433 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.1457 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.6329 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1822 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.001687 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.003598 Moderately Informative Inherited
Biological Process (BP) cytoskeleton organization 3.67e-09 Informative Direct
Biological Process (BP) microtubule-based process 0 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 6.743e-08 Informative Direct
Biological Process (BP) hexose metabolic process 7.021e-08 Informative Direct
Biological Process (BP) cell cycle process 1.931e-15 Informative Direct
Biological Process (BP) protein catabolic process 3.985e-05 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0004358 Informative Direct
Biological Process (BP) organelle localization 6.305e-09 Informative Direct
Biological Process (BP) mitochondrion organization 0.1351 Informative Inherited
Biological Process (BP) cellular component movement 0.3015 Informative Inherited
Biological Process (BP) proteolysis 0.001164 Informative Inherited
Biological Process (BP) chromosome organization 1 Informative Inherited
Biological Process (BP) microtubule cytoskeleton organization 0.0001452 Highly Informative Direct
Biological Process (BP) protein folding 7.892e-07 Highly Informative Direct
Biological Process (BP) chromosome segregation 4.144e-07 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 8.383e-08 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 1.977e-07 Highly Informative Direct
Biological Process (BP) cell division 7.02e-07 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.5966 Highly Informative Inherited
Biological Process (BP) developmental maturation 0.001413 Highly Informative Inherited
Molecular Function (MF) binding 0.6094 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.8244 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.00452 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 0.0001235 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 6.12e-06 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 3.771e-06 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.004808 Informative Inherited
Cellular Component (CC) intracellular 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 0.7865 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.5834 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.4478 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.3068 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 8.731e-11 Informative Direct
Cellular Component (CC) plastid 0.01446 Informative Inherited
Cellular Component (CC) external encapsulating structure 0.03037 Informative Inherited
Cellular Component (CC) cell wall 0.0003672 Highly Informative Direct
Cellular Component (CC) mitochondrial outer membrane 5.961e-05 Highly Informative Direct
Cellular Component (CC) centrosome 0.0003813 Highly Informative Direct
Cellular Component (CC) spindle 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic microtubule 0 Highly Informative Direct
Cellular Component (CC) chloroplast stroma 2.742e-06 Highly Informative Direct
Cellular Component (CC) microtubule organizing center part 7.873e-07 Highly Informative Direct
Cellular Component (CC) cell body 0.01289 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 health0.02842Moderately InformativeInherited
Disease Ontology (DO)schizophrenia0.0008309InformativeDirect

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 the skeletal system0Least 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 callosum8.437e-06Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the brainstem1.938e-05Highly 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 variant1.806e-09Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.0007391Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.005149Least InformativeInherited
Worm Phenotype (WP)protein aggregation variant3.373e-11Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal1.684e-05Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant6.973e-05Moderately 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 variant2.856e-08InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant3.995e-08InformativeDirect
Worm Phenotype (WP)nicotine response variant1.017e-07InformativeDirect
Worm Phenotype (WP)exploded through vulva7.293e-05InformativeDirect
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 variant1.035e-09Highly InformativeDirect
Worm Phenotype (WP)touch resistant1.698e-08Highly InformativeDirect
Worm Phenotype (WP)mitotic spindle defective early emb8.964e-07Highly InformativeDirect
Worm Phenotype (WP)presynaptic region morphology variant4.435e-06Highly InformativeDirect
Worm Phenotype (WP)alae morphology variant1.902e-05Highly InformativeDirect
Worm Phenotype (WP)miRNA expression variant2.354e-05Highly 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)fertile0.04491Least InformativeInherited
Fly Phenotype (FP)male fertile1.664e-07InformativeDirect
Fly Phenotype (FP)wild-type0.0007177InformativeDirect

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)cell0.1333Least InformativeInherited
Fly Anatomy (FA)multi-tissue structure0.1494Least InformativeInherited
Fly Anatomy (FA)reproductive system0.01448Moderately InformativeInherited
Fly Anatomy (FA)male germline cell0.03465InformativeInherited
Fly Anatomy (FA)testis0.0718InformativeInherited
Fly Anatomy (FA)spermatid5.152e-05Highly 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 tissue0.3228Least InformativeInherited
Xenopus ANatomical entity (XAN)cell0.3469Least InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.3997Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.517Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.7303Least InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.9345Least InformativeInherited
Xenopus ANatomical entity (XAN)surface structure0.2033Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.2579Moderately InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.4183Moderately InformativeInherited
Xenopus ANatomical entity (XAN)skin0.1129InformativeInherited
Xenopus ANatomical entity (XAN)neuron1.19e-07Highly InformativeDirect
Xenopus ANatomical entity (XAN)epidermis0.0001919Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial nerve0.0002192Highly InformativeDirect
Xenopus ANatomical entity (XAN)zygote0.0002226Highly InformativeDirect
Xenopus ANatomical entity (XAN)intersomitic region0.0003609Highly InformativeDirect
Xenopus ANatomical entity (XAN)pancreas0.0004679Highly 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0Moderately InformativeDirect
Biological processAntibiotic resistance0.0002638InformativeDirect
Biological processSeptation0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentMitochondrion0.2707Moderately InformativeInherited
Cellular componentMicrotubule0InformativeDirect
Cellular componentMitochondrion outer membrane0.0007197InformativeDirect
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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]