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 (3,150) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 11,835 23,825 25
Proteins 10,581 21,037 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 process4.555e-061.431e-14Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process6.343e-051.642e-09Least InformativeDirect
Biological Process (BP)heterocycle metabolic process3.992e-067.333e-15Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process2.122e-052.836e-09Least InformativeDirect
Biological Process (BP)response to stimulus0.86341Least InformativeInherited
Biological Process (BP)regulation of cellular process0.54671Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.0037390.5019Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process2.839e-064.828e-05Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process1.597e-099.315e-06Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process9.676e-101.116e-05Moderately InformativeDirect
Biological Process (BP)signal transduction0.0050210.8286Moderately InformativeInherited
Biological Process (BP)cell death1.076e-070.0006524InformativeDirect
Biological Process (BP)intracellular signal transduction2.05e-060.01034InformativeInherited
Biological Process (BP)intrinsic apoptotic signaling pathway8.261e-144.179e-10Highly InformativeDirect
Molecular Function (MF)hydrolase activity1.095e-065.551e-10Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0099350.226Least InformativeInherited
Cellular Component (CC)protein complex0.4651Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)nuclear part0.084640.2392Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.022420.5117Moderately InformativeInherited
Cellular Component (CC)nucleoplasm part5.815e-050.2367InformativeInherited
Cellular Component (CC)histone deacetylase complex1.191e-123.832e-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 1.431e-14 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.642e-09 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 7.333e-15 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 2.836e-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 metabolic process 0.5019 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.7095 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 4.828e-05 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 9.315e-06 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 6.06e-06 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 1.116e-05 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 8.181e-06 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.2895 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.8286 Moderately Informative Inherited
Biological Process (BP) macromolecule catabolic process 0.001895 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.7043 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.9673 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.02041 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.001717 Moderately Informative Inherited
Biological Process (BP) gene expression 0.4128 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.0001415 Informative Direct
Biological Process (BP) cell death 0.0006524 Informative Direct
Biological Process (BP) hexose metabolic process 2.498e-07 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 3.482e-05 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0002185 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.04931 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.01034 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.08204 Informative Inherited
Biological Process (BP) RNA processing 0.0813 Informative Inherited
Biological Process (BP) galactose metabolic process 0 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.0005555 Highly Informative Direct
Biological Process (BP) RNA splicing 0.0005412 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 4.179e-10 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.01152 Highly Informative Inherited
Biological Process (BP) mRNA processing 0.1458 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 5.551e-10 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.0001589 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 1 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.1397 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0003811 Informative Direct
Molecular Function (MF) nuclease activity 3.563e-08 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.226 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 0.2392 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.5117 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.2367 Informative Inherited
Cellular Component (CC) histone deacetylase complex 3.832e-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 groups0.0003983Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases3.882e-11Moderately 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 processApoptosis1.627e-14Moderately InformativeDirect
Biological processCarbohydrate metabolism3.589e-12Moderately InformativeDirect
Biological processDNA damage9.457e-07Moderately InformativeDirect
Biological processLipid biosynthesis0InformativeDirect
Biological processmRNA splicing4.888e-07InformativeDirect
Biological processPhospholipid metabolism0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMembrane0.05559Least InformativeInherited
Cellular componentCell membrane1.676e-07Moderately InformativeDirect
Cellular componentCell inner membrane1.715e-09InformativeDirect
DomainTransmembrane0.005892Least InformativeInherited
DomainZinc-finger7.682e-06Moderately InformativeDirect
Molecular functionZinc3.171e-11Least InformativeDirect
Molecular functionDNA-binding7.737e-05Least InformativeDirect
Molecular functionIron0.0006933Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNucleotidyltransferase3.946e-12Moderately InformativeDirect
Post-translational modificationAcetylation7.975e-07Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)lipid metabolism6.291e-15Least InformativeDirect
UniPathway (UP)carbohydrate metabolism1.173e-05Least InformativeDirect
UniPathway (UP)phospholipid metabolism0InformativeDirect
UniPathway (UP)galactose metabolism0Highly InformativeDirect
UniPathway (UP)phospholipid degradation0Highly 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 ]