SUPERFAMILY 1.75 HMM library and genome assignments server


HIT-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   HIT-like [ 54196] (2)
Superfamily:   HIT-like [ 54197] (4)
Families:   HIT (HINT, histidine triad) family of protein kinase-interacting proteins [ 54198] (7)
  Hexose-1-phosphate uridylyltransferase [ 54207]
  mRNA decapping enzyme DcpS C-terminal domain [ 102745]
  CDH-like [ 159882]


Superfamily statistics
Genomes (3,186) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 12,111 47,080 25
Proteins 10,842 41,822 20


Functional annotation
General category Metabolism
Detailed category Carbohydrate metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular aromatic compound metabolic process1.961e-052.871e-13Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.00025287.563e-10Least InformativeDirect
Biological Process (BP)heterocycle metabolic process1.753e-051.382e-13Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process8.545e-051.27e-09Least InformativeDirect
Biological Process (BP)response to stimulus0.92591Least InformativeInherited
Biological Process (BP)regulation of cellular process0.69731Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.010040.5393Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process1.021e-050.0002288Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process7.355e-091.249e-05Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process1.167e-092.028e-05Moderately InformativeDirect
Biological Process (BP)signal transduction0.009290.9417Moderately InformativeInherited
Biological Process (BP)programmed cell death1.361e-070.000809InformativeDirect
Biological Process (BP)intracellular signal transduction4.546e-060.01808InformativeInherited
Biological Process (BP)intrinsic apoptotic signaling pathway2.073e-131.009e-09Highly InformativeDirect
Molecular Function (MF)hydrolase activity5.365e-065.613e-10Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.037460.3043Least InformativeInherited
Cellular Component (CC)protein complex0.57831Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)nuclear part0.19410.2535Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.029320.4647Moderately InformativeInherited
Cellular Component (CC)nucleoplasm part0.00035170.3087InformativeInherited
Cellular Component (CC)histone deacetylase complex2.036e-126.276e-07Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 2.871e-13 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 7.563e-10 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.382e-13 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.27e-09 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.5393 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.6661 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.0002288 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000768 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 1.249e-05 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 8.232e-06 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 2.028e-05 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 2.745e-05 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.388 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.9417 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.8201 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.02268 Moderately Informative Inherited
Biological Process (BP) gene expression 0.3127 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.0002143 Informative Direct
Biological Process (BP) programmed cell death 0.000809 Informative Direct
Biological Process (BP) hexose metabolic process 7.159e-08 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 5.092e-05 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0002615 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.07399 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.01808 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.09587 Informative Inherited
Biological Process (BP) RNA processing 0.04571 Informative Inherited
Biological Process (BP) galactose metabolic process 0 Highly Informative Direct
Biological Process (BP) RNA splicing 0.0002284 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 1.009e-09 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.01054 Highly Informative Inherited
Biological Process (BP) mRNA processing 0.09239 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 5.613e-10 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.000525 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 1 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.1802 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0009097 Informative Direct
Molecular Function (MF) nuclease activity 9.3e-08 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.3043 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0.2535 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.4647 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.3087 Informative Inherited
Cellular Component (CC) histone deacetylase complex 6.276e-07 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases8.856e-13Least InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details) Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least 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 structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorous-containing groups0.000761Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases1.72e-10Moderately InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0Moderately InformativeDirect
Biological processApoptosis1.672e-14Moderately InformativeDirect
Biological processCarbohydrate metabolism4.318e-12Moderately InformativeDirect
Biological processDNA damage8.905e-07Moderately InformativeDirect
Biological processLipid biosynthesis0InformativeDirect
Biological processmRNA splicing5.03e-07InformativeDirect
Biological processPhospholipid metabolism0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMembrane0.05268Least InformativeInherited
Cellular componentCell membrane1.389e-07Moderately InformativeDirect
Cellular componentCell inner membrane1.619e-09InformativeDirect
DomainTransmembrane0.005513Least InformativeInherited
DomainZinc-finger7.923e-06Moderately InformativeDirect
Molecular functionZinc2.669e-11Least InformativeDirect
Molecular functionDNA-binding8.577e-05Moderately InformativeDirect
Molecular functionIron0.0005817Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNucleotidyltransferase2.475e-11Moderately InformativeDirect
Post-translational modificationAcetylation4.176e-07Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)lipid metabolism2.274e-16Least InformativeDirect
UniPathway (UP)carbohydrate metabolism2.848e-06Least InformativeDirect
UniPathway (UP)phospholipid metabolism0InformativeDirect
UniPathway (UP)galactose metabolism0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR011146 SSF54197 Protein matches
Abstract

The histidine triad motif (HIT) is related to the sequence H-phi-H-phi-H-phi-phi (where phi is a hydrophobic amino acid). Proteins containing HIT domains form a superfamily of nucleotide hydrolases and transferases that act on the alpha-phosphate of ribonucleotides [PubMed12119013]. HIT-containing proteins fall into three families:

  • Hint family of protein kinase-interacting proteins. These include adenosine 5'-monophosphoramide hydrolases (e.g. HIT-nucleotide-binding protein, or HINT) and diadenosine polyphosphate hydrolases (e.g. fragile HIT protein, or FINT). These HIT domains have a topology similar to that found in the N-terminal of protein kinases [PubMed15904496].
  • GalT family. These include specific nucleoside monophosphate transferases (e.g. galactose-1-phosphate uridylyltransferase, diadenosine tetraphosphate phosphorylase, and adenylyl sulphate:phosphate adenylytransferase). These HIT domains are a duplication consisting of 2 HIT-like motifs. This family binds zinc and iron.
  • mRNA decapping enzyme family. These include enzymes such as DcpS and Dcp2. The HIT-domain is usually C-terminal in these proteins [PubMed15273322].

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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 13 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 HIT-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 13 hidden Markov models representing the HIT-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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]