SUPERFAMILY 1.75 HMM library and genome assignments server

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Cold shock DNA-binding domain-like family

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   OB-fold [ 50198] (16)
Superfamily:   Nucleic acid-binding proteins [ 50249] (16)
Family:   Cold shock DNA-binding domain-like [ 50282] (30)


Family statistics
Genomes (3,249) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 17,195 116,850 106
Proteins 16,680 114,557 97


Enzyme Commission (EC)

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show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0.000000000001445Least InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters1InformativeInherited
Enzyme Commission (EC)Polyribonucleotide nucleotidyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details) Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body region phenotype0.5762Least InformativeInherited
Mammalian Phenotype (MP)abnormal prenatal body size0.003592InformativeInherited
Mammalian Phenotype (MP)decreased fetal size0.00008233Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.001592Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.03672Least InformativeInherited
Worm Phenotype (WP)cell development variant0.1314Least InformativeInherited
Worm Phenotype (WP)germ cell differentiation variant0.0005601Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.006462Moderately InformativeInherited
Worm Phenotype (WP)germ cell development variant0.008349Moderately InformativeInherited
Worm Phenotype (WP)cell death variant0.01998Moderately InformativeInherited
Worm Phenotype (WP)cell type morphology variant0.0254Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.06056Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.1532Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.1536Moderately InformativeInherited
Worm Phenotype (WP)pachytene progression during oogenesis variant0.000006038InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.000006038InformativeDirect
Worm Phenotype (WP)sick0.00001344InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.00004595InformativeDirect
Worm Phenotype (WP)germ cell physiology variant0.0004738InformativeDirect
Worm Phenotype (WP)hermaphrodite physiology variant0.0009959InformativeDirect
Worm Phenotype (WP)RNA expression variant0.01486InformativeInherited
Worm Phenotype (WP)rachis morphology variant0.02493InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.1389InformativeInherited
Worm Phenotype (WP)pleiotropic defects severe early emb0.00000002846Highly InformativeDirect
Worm Phenotype (WP)rachis narrow0.000003724Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.000005839Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.00002656Highly InformativeDirect
Worm Phenotype (WP)no oocytes0.0001013Highly InformativeDirect
Worm Phenotype (WP)gonad vesiculated0.0003108Highly InformativeDirect
Worm Phenotype (WP)molt variant0.0005405Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)heat sensitivity0.00000009844InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.0001699Least InformativeDirect
Xenopus ANatomical entity (XAN)urogenital system0.03987Least InformativeInherited
Xenopus ANatomical entity (XAN)germ cell0.001021Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.000002898InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)branch0.0009432Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0.002884Least InformativeInherited
Plant structure DEvelopment stage (PDE)F mature embryo stage0.0001382Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0.0004864Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0.0006411Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferases0Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0.00000000002194Moderately InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0Highly InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups0.7343Highly InformativeInherited

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

Internal database links

   
Superfamily level     Family level

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.


   
Superfamily level     Family level

Alignments of sequences to 186 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.


Superfamily level

Browse and view proteins in genomes which have different domain combinations including a Nucleic acid-binding proteins domain.


   
Superfamily level     Family level

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.


Jump to [ Top of page · SCOP classification · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]