SUPERFAMILY 1.75 HMM library and genome assignments server


Cytidine deaminase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Cytidine deaminase-like [ 53926] (2)
Superfamily:   Cytidine deaminase-like [ 53927] (5)
Families:   Cytidine deaminase [ 53928] (3)
  Deoxycytidylate deaminase-like [ 89800] (7)
  Hypothetical protein TM1506 [ 110651]
  AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC [ 64198]
  FdhD/NarQ [ 159821]


Superfamily statistics
Genomes (2,466) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 14,040 40,592 31
Proteins 13,516 38,586 30


Functional annotation
General category Metabolism
Detailed category Other enzymes

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 process3.099e-150Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process6.09e-150Least InformativeDirect
Biological Process (BP)single-organism metabolic process2.492e-067.835e-15Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)regulation of metabolic process9.43e-060.7783Least InformativeInherited
Biological Process (BP)regulation of cellular process0.67980.5585Least InformativeInherited
Biological Process (BP)response to stimulus10.8803Least InformativeInherited
Biological Process (BP)biosynthetic process10.8903Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.00022260.3225Least InformativeInherited
Biological Process (BP)cellular catabolic process1.388e-053.676e-08Moderately InformativeDirect
Biological Process (BP)negative regulation of cellular process2.171e-078.652e-09Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process2.097e-080Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process3.203e-100Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process8.86e-052.879e-07Moderately InformativeDirect
Biological Process (BP)positive regulation of metabolic process0.016210.387Moderately InformativeInherited
Biological Process (BP)regulation of cellular metabolic process0.12011Moderately InformativeInherited
Biological Process (BP)regulation of cellular component organization7.964e-060.02172Moderately InformativeInherited
Biological Process (BP)regulation of gene expression1.455e-110.0741Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.11051Moderately InformativeInherited
Biological Process (BP)regulation of biosynthetic process0.52351Moderately InformativeInherited
Biological Process (BP)regulation of nitrogen compound metabolic process0.25731Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.049110.05846Moderately InformativeInherited
Biological Process (BP)multi-organism process0.082552.104e-06Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.78970.08579Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.74780.6154Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.81210.105Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.86310.2248Moderately InformativeInherited
Biological Process (BP)gene expression0.95221Moderately InformativeInherited
Biological Process (BP)immune system process0.012783.401e-07Moderately InformativeInherited
Biological Process (BP)immune effector process0.00087855.264e-14InformativeDirect
Biological Process (BP)DNA metabolic process1.201e-120InformativeDirect
Biological Process (BP)tRNA metabolic process0.00085881.284e-06InformativeDirect
Biological Process (BP)RNA modification0.00034015.632e-11InformativeDirect
Biological Process (BP)nucleobase-containing compound catabolic process4.988e-052.911e-10InformativeDirect
Biological Process (BP)cellular metabolic compound salvage8.227e-065.003e-06InformativeDirect
Biological Process (BP)negative regulation of cellular component organization3.084e-112.271e-06InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process00InformativeDirect
Biological Process (BP)carbohydrate derivative catabolic process3.099e-150InformativeDirect
Biological Process (BP)organonitrogen compound catabolic process1.694e-103.881e-12InformativeDirect
Biological Process (BP)regulation of organelle organization0.0012870.001181InformativeInherited
Biological Process (BP)regulation of reproductive process0.0018319.202e-08InformativeInherited
Biological Process (BP)defense response0.033661.315e-08InformativeInherited
Biological Process (BP)ribonucleoside metabolic process11InformativeInherited
Biological Process (BP)positive regulation of macromolecule biosynthetic process1.834e-080.05761InformativeInherited
Biological Process (BP)positive regulation of cellular biosynthetic process5.923e-080.08551InformativeInherited
Biological Process (BP)positive regulation of nitrogen compound metabolic process4.416e-050.06796InformativeInherited
Biological Process (BP)positive regulation of gene expression0.016510.09506InformativeInherited
Biological Process (BP)response to other organism0.034727.451e-06InformativeInherited
Biological Process (BP)ncRNA processing0.11660.0005277InformativeInherited
Biological Process (BP)pyrimidine nucleoside metabolic process00Highly InformativeDirect
Biological Process (BP)response to virus6.154e-054.008e-15Highly InformativeDirect
Biological Process (BP)regulation of gene expression, epigenetic02.076e-15Highly InformativeDirect
Biological Process (BP)regulation of multi-organism process0.00011083.296e-10Highly InformativeDirect
Biological Process (BP)pyrimidine-containing compound catabolic process00Highly InformativeDirect
Biological Process (BP)negative regulation of reproductive process0.00036043.232e-10Highly InformativeDirect
Biological Process (BP)DNA methylation or demethylation0.63461Highly InformativeInherited
Molecular Function (MF)hydrolase activity2.589e-090Least InformativeDirect
Molecular Function (MF)binding0.11050.8281Least InformativeInherited
Molecular Function (MF)cation binding0.0038630.0001827Moderately InformativeInherited
Molecular Function (MF)organic cyclic compound binding0.010170.3201Moderately InformativeInherited
Molecular Function (MF)heterocyclic compound binding0.006950.2952Moderately InformativeInherited
Molecular Function (MF)RNA binding2.928e-060.0006859InformativeDirect
Molecular Function (MF)transition metal ion binding7.491e-054.719e-07InformativeDirect
Molecular Function (MF)zinc ion binding8.599e-076.467e-10Highly InformativeDirect
Molecular Function (MF)hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines00Highly InformativeDirect
Molecular Function (MF)deaminase activity00Highly InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle0.82050.1488Least InformativeInherited
Cellular Component (CC)cytoplasmic part10.2248Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex0.084881.084e-08Moderately InformativeInherited
Cellular Component (CC)cytoplasmic mRNA processing body2.366e-060Highly 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 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 7.835e-15 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.7783 Least Informative Inherited
Biological Process (BP) response to stimulus 0.8803 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.5585 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.8903 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.3225 Least Informative Inherited
Biological Process (BP) immune system process 3.401e-07 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 3.676e-08 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 8.652e-09 Moderately Informative Direct
Biological Process (BP) multi-organism process 2.104e-06 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 2.879e-07 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.387 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.02172 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.2255 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.2178 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.0741 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.05846 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.6154 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.08579 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.105 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.2248 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.1227 Moderately Informative Inherited
Biological Process (BP) immune effector process 5.264e-14 Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) tRNA metabolic process 1.284e-06 Informative Direct
Biological Process (BP) defense response 1.315e-08 Informative Direct
Biological Process (BP) RNA modification 5.632e-11 Informative Direct
Biological Process (BP) ncRNA processing 0.0005277 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 2.911e-10 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 5.003e-06 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 2.271e-06 Informative Direct
Biological Process (BP) response to other organism 7.451e-06 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.0006171 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0 Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 3.881e-12 Informative Direct
Biological Process (BP) regulation of reproductive process 9.202e-08 Informative Direct
Biological Process (BP) regulation of organelle organization 0.001181 Informative Inherited
Biological Process (BP) ribonucleoside metabolic process 1 Informative Inherited
Biological Process (BP) ribose phosphate metabolic process 0.6317 Informative Inherited
Biological Process (BP) purine nucleotide metabolic process 0.6053 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.05761 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.08551 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.06796 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.09506 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.002509 Informative Inherited
Biological Process (BP) vitamin metabolic process 0.007951 Informative Inherited
Biological Process (BP) pyrimidine nucleoside metabolic process 0 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 1.917e-08 Highly Informative Direct
Biological Process (BP) response to virus 4.008e-15 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 2.076e-15 Highly Informative Direct
Biological Process (BP) regulation of multi-organism process 3.296e-10 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) negative regulation of reproductive process 3.232e-10 Highly Informative Direct
Biological Process (BP) DNA methylation or demethylation 1 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.8281 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) cation binding 0.0001827 Moderately Informative Direct
Molecular Function (MF) protein binding 0.7686 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.3201 Moderately Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0.2952 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0006859 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 5.98e-07 Informative Direct
Molecular Function (MF) transition metal ion binding 4.719e-07 Informative Direct
Molecular Function (MF) protein dimerization activity 5.474e-05 Informative Direct
Molecular Function (MF) zinc ion binding 6.467e-10 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0 Highly Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines 0 Highly Informative Direct
Molecular Function (MF) deaminase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.1488 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.2248 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 1.084e-08 Moderately Informative Direct
Cellular Component (CC) cytoplasmic mRNA processing body 0 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)Transferring one-carbon groups0Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1Moderately InformativeInherited
Enzyme Commission (EC)In cyclic amidines0InformativeDirect
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)IMP cyclohydrolase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)no abnormal phenotype detected0Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)head0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) 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)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0Moderately InformativeDirect
Enzyme Commission (EC)Acting on the CH-OH group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)In cyclic amidines0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processInnate immunity0InformativeDirect
Biological processPurine biosynthesis0InformativeDirect
Biological processAntiviral defense0Highly InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding1.66e-05Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)cofactor metabolism1Least InformativeInherited
UniPathway (UP)nucleotide metabolism0Moderately InformativeDirect
UniPathway (UP)purine metabolism0Moderately InformativeDirect
UniPathway (UP)IMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)riboflavin biosynthesis6.758e-08Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 23 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 Cytidine deaminase-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 23 hidden Markov models representing the Cytidine deaminase-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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 ]