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Xylose isomerase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   TIM beta/alpha-barrel [ 51350] (33)
Superfamily:   Xylose isomerase-like [ 51658] (7)
Families:   Endonuclease IV [ 51659]
  IolI-like [ 75090] (3)
  Hypothetical protein YgbM (EC1530) [ 75093]
  L-rhamnose isomerase [ 51662]
  Xylose isomerase [ 51665]
  UxuA-like [ 110377]
  KguE-like [ 141854]


Superfamily statistics
Genomes (2,793) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 13,415 93,306 36
Proteins 13,391 93,205 36


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)single-organism metabolic process0.30990.2041Least InformativeInherited
Biological Process (BP)primary metabolic process0.32380.5619Least InformativeInherited
Biological Process (BP)response to stimulus11Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.56850.3615Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.70320.4946Least InformativeInherited
Biological Process (BP)macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.57180.3486Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.90510.7399Least InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.000026850.00001391Moderately InformativeDirect
Biological Process (BP)single-organism catabolic process0.013490.007643Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.03830.03979Moderately InformativeInherited
Biological Process (BP)cellular response to stress0.010050.008862Moderately InformativeInherited
Biological Process (BP)monosaccharide metabolic process0.000000039480.00000002329InformativeDirect
Biological Process (BP)DNA metabolic process0.00077190.0007428InformativeDirect
Biological Process (BP)cellular response to DNA damage stimulus0.00017750.00006786InformativeDirect
Biological Process (BP)carbohydrate catabolic process0.0024710.000773InformativeInherited
Biological Process (BP)monosaccharide catabolic process0.0000046060.00000452Highly InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)hydrolase activity0.90720.7615Least InformativeInherited
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)metal ion binding0.028210.009579Moderately InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds0.020950.000449Moderately InformativeInherited
Molecular Function (MF)nuclease activity0.0000047540.00000002429InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity0.15650.0591InformativeInherited
Molecular Function (MF)racemase and epimerase activity0.03240.01626InformativeInherited
Molecular Function (MF)racemase and epimerase activity, acting on carbohydrates and derivatives0.000000000037090.0000000000002843Highly InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity, interconverting aldoses and ketoses0.00000000000056540.000000000000003188Highly InformativeDirect
Molecular Function (MF)manganese ion binding0.00000001360.000000004508Highly 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) single-organism metabolic process 0.2041 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.5619 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.3615 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.4946 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.3486 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.7399 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.00001391 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.007643 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.03979 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.008862 Moderately Informative Inherited
Biological Process (BP) monosaccharide metabolic process 0.00000002329 Informative Direct
Biological Process (BP) DNA metabolic process 0.0007428 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.00006786 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.000773 Informative Direct
Biological Process (BP) monosaccharide catabolic process 0.00000452 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.7615 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.000449 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.009579 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0.00000002429 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.0591 Informative Inherited
Molecular Function (MF) racemase and epimerase activity 0.01626 Informative Inherited
Molecular Function (MF) racemase and epimerase activity, acting on carbohydrates and derivatives 0.0000000000002843 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, interconverting aldoses and ketoses 0.000000000000003188 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.000000004508 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases0.0000000000001863Moderately InformativeDirect
Enzyme Commission (EC)Racemases and epimerases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on carbohydrates and derivatives0InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses, and related c0.0000000000491InformativeDirect
Enzyme Commission (EC)Endodeoxyribonucleases producing 5'-phosphomonoest0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCarbohydrate metabolism0Moderately InformativeDirect
Biological processDNA damage0Moderately InformativeDirect
Biological processDNA repair0InformativeDirect
Biological processDNA excision0.00000000000002275Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMagnesium0.00000001431Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionIron0.000235Moderately InformativeDirect
Molecular functionCobalt0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR013022 SSF51658 Protein matches
Abstract

This entry represents a structural motif with a beta/alpha TIM barrel found in several proteins families:

  • Endonuclease IV , an AP (apurinic/apyrimidinic) endonuclease that primes DNA repair synthesis by cleaving the DNA backbone 5' of AP sites [PubMed10458614].
  • L-rhamnose isomerase , a tetramer of four TIM barrels that catalyses the isomerisation between aldoses and ketoses, such as between L-rhamnose and L-rhamnulose [PubMed17141803].
  • Xylose isomerase , which catalyses the first reaction in the catabolism of D-xylose by converting D-xylose to D-xylulose [PubMed16673077].
  • Mannonate dehydratase UxuA, which along with mannonate oxidoreductase converts D-fructuronate to 2-keto-3-deoxy-D-gluconate [PubMed7007313].

These proteins share similar, but not identical, metal-binding sites. In addition, xylose isomerase and L-rhamnose isomerase each have additional alpha-helical domains involved in tetramer formation. This entry differs from IPR012307 in having a wider coverage of TIM-barrel protein families.


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) · 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 19 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 Xylose isomerase-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 19 hidden Markov models representing the Xylose isomerase-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) · UniProtKB KeyWords (KW) · Internal database links ]