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 (3,193) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 12,221 47,080 25
Proteins 10,933 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 process0.000004790.000000000000003707Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.000076510.0000000004051Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.0000043540Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.000023420.000000000753Least InformativeDirect
Biological Process (BP)response to stimulus0.87811Least InformativeInherited
Biological Process (BP)single-organism cellular process0.60631Least InformativeInherited
Biological Process (BP)regulation of cellular process0.69511Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.032270.0009691Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.0000032210.00005567Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.00000000150.000006818Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process0.0000000000088280.000000000002117Moderately InformativeDirect
Biological Process (BP)signal transduction0.007060.851Moderately InformativeInherited
Biological Process (BP)apoptotic process0.000000036650.0001418InformativeDirect
Biological Process (BP)intracellular signal transduction0.0000037160.01462InformativeInherited
Biological Process (BP)intrinsic apoptotic signaling pathway0.00000000000012670.0000000004406Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.0000031080.000000001359Least InformativeDirect
Molecular Function (MF)transferase activity10.9531Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.18060.00006589Moderately InformativeInherited
Molecular Function (MF)nucleotidyltransferase activity0.00059880InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.021680.0769Least InformativeInherited
Cellular Component (CC)protein complex0.53261Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)nuclear part0.16750.1444Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.020420.2176Moderately InformativeInherited
Cellular Component (CC)nucleoplasm part0.00017770.1043InformativeInherited

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 0.000000000000003707 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000000004051 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0009691 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000000753 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.6672 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.00005567 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000826 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.000006818 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000003236 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.000000000002117 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00001266 Moderately Informative Direct
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.851 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.3248 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.745 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.02458 Moderately Informative Inherited
Biological Process (BP) gene expression 0.2208 Moderately Informative Inherited
Biological Process (BP) apoptotic process 0.0001418 Informative Direct
Biological Process (BP) hexose metabolic process 0.00000000583 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00001568 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0003666 Informative Direct
Biological Process (BP) intracellular signal transduction 0.01462 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.05841 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.08532 Informative Inherited
Biological Process (BP) RNA processing 0.05714 Informative Inherited
Biological Process (BP) galactose metabolic process 0 Highly Informative Direct
Biological Process (BP) RNA splicing 0.0002442 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 0.0000000004406 Highly Informative Direct
Biological Process (BP) mRNA processing 0.09033 Highly Informative Inherited
Biological Process (BP) DNA catabolic process 0.00939 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.000000001359 Least Informative Direct
Molecular Function (MF) transferase activity 0.9531 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.00006589 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 1 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.1798 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0.00000007013 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) RNA binding 0.002014 Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.0769 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 0.1444 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.2176 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.1043 Informative Inherited

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)Nucleotidyltransferases0.0000000000008856Least 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 groups0.000343Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0.00000000002969Moderately 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 processApoptosis0.00000000000001988Moderately InformativeDirect
Biological processCarbohydrate metabolism0.00000000000553Moderately InformativeDirect
Biological processDNA damage0.000001064Moderately InformativeDirect
Biological processLipid biosynthesis0InformativeDirect
Biological processPhospholipid metabolism0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMembrane0.05421Least InformativeInherited
Cellular componentCell membrane0.0000001921Moderately InformativeDirect
Cellular componentCell inner membrane0.000000001538InformativeDirect
DomainTransmembrane0.005595Least InformativeInherited
DomainZinc-finger0.000007589Moderately InformativeDirect
Molecular functionZinc0.00000000004083Least InformativeDirect
Molecular functionDNA-binding0.00009772Least InformativeDirect
Molecular functionIron0.0006484Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNucleotidyltransferase0.00000000000366Moderately InformativeDirect
Post-translational modificationAcetylation0.0000008158Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)lipid metabolism2.278e-16Least InformativeDirect
UniPathway (UP)carbohydrate metabolism0.000002817Least 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 ]