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Nucleic acid-binding proteins superfamily

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)
Families:   Anticodon-binding domain [ 50250] (2)
  RecG "wedge" domain [ 69259]
  DNA helicase RuvA subunit, N-terminal domain [ 50259]
  Single strand DNA-binding domain, SSB [ 50263] (12)
  Myf domain [ 50277] (6)
  Cold shock DNA-binding domain-like [ 50282] (30)
  TRAM domain [ 101768] (3)
  Hypothetical protein MTH1 (MT0001), insert domain [ 74955]
  DNA ligase/mRNA capping enzyme postcatalytic domain [ 50307] (5)
  Phage ssDNA-binding proteins [ 50315] (3)
  DNA replication initiator (cdc21/cdc54) N-terminal domain [ 89332]
  RNA polymerase subunit RBP8 [ 50321]
  RecO N-terminal domain-like [ 117204]
  TIP49 domain [ 141315]
  SSO2064-like [ 159109]
  RNB domain-like [ 159112] (3)


Superfamily statistics
Genomes (3,263) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 147,633 0 241
Proteins 114,374 0 208


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters1Moderately InformativeInherited
Enzyme Commission (EC)Methyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Phenylalanine--tRNA ligase0InformativeDirect
Enzyme Commission (EC)Ligases that form phosphoric-ester bonds1InformativeInherited
Enzyme Commission (EC)Aminoacyltransferases0.1092InformativeInherited
Enzyme Commission (EC)Methionine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Aspartate--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Polyribonucleotide nucleotidyltransferase0Highly InformativeDirect
Enzyme Commission (EC)DNA ligase (NAD(+))0.0000000000006306Highly InformativeDirect
Enzyme Commission (EC)mRNA guanylyltransferase0.000000003114Highly InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.0003015Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.02766Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body region phenotype0.3717Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.3928Least InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.002835Moderately InformativeInherited
Mammalian Phenotype (MP)prenatal lethality0.003434Moderately InformativeInherited
Mammalian Phenotype (MP)neoplasm0.003778Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.004878Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.01123Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.2034Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.2411Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.7024Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.8162Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.9128Moderately InformativeInherited
Mammalian Phenotype (MP)chromosomal instability0InformativeDirect
Mammalian Phenotype (MP)embryonic lethality prior to organogenesis0.0003126InformativeDirect
Mammalian Phenotype (MP)abnormal DNA repair0.000956InformativeDirect
Mammalian Phenotype (MP)abnormal sex determination0.001499InformativeInherited
Mammalian Phenotype (MP)abnormal prenatal growth/weight/body size0.001646InformativeInherited
Mammalian Phenotype (MP)abnormal erythroid lineage cell morphology0.001945InformativeInherited
Mammalian Phenotype (MP)decreased cell proliferation0.006023InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.01352InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.07733InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.2192InformativeInherited
Mammalian Phenotype (MP)abnormal oocyte number0.00002461Highly InformativeDirect
Mammalian Phenotype (MP)abnormal fibroblast proliferation0.00003405Highly InformativeDirect
Mammalian Phenotype (MP)abnormal ovary size0.00007155Highly InformativeDirect
Mammalian Phenotype (MP)decreased fetal size0.00007438Highly InformativeDirect
Mammalian Phenotype (MP)decreased male germ cell number0.0001271Highly InformativeDirect
Mammalian Phenotype (MP)abnormal male reproductive system physiology0.0156Highly InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell number0.04411Highly InformativeInherited
Mammalian Phenotype (MP)abnormal reticulocyte morphology0.04772Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.0000000000003426Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0000001497Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0000003347Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0001135Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.002204Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.006076Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.0491Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.0000000001321Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00004049Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0002323Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.0003634Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.003274Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.06538Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.08103Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.09357Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.1494Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.6218Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.845Moderately InformativeInherited
Worm Phenotype (WP)pleiotropic defects severe early emb0.000000001448InformativeDirect
Worm Phenotype (WP)sick0.000000009457InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.00000002531InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.000001182InformativeDirect
Worm Phenotype (WP)cytokinesis variant emb0.000004078InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.000008969InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.0001104InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.000269InformativeDirect
Worm Phenotype (WP)gonad development variant0.001418InformativeInherited
Worm Phenotype (WP)RNA expression variant0.03939InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.04977InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.07681InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.08733InformativeInherited
Worm Phenotype (WP)oxygen response variant0.1215InformativeInherited
Worm Phenotype (WP)organelle organization biogenesis variant0.3402InformativeInherited
Worm Phenotype (WP)cell stress response variant0.8288InformativeInherited
Worm Phenotype (WP)no oocytes0.0000000006471Highly InformativeDirect
Worm Phenotype (WP)male somatic gonad development variant0.000000006259Highly InformativeDirect
Worm Phenotype (WP)gonad arm morphology variant0.00000002626Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.00000003726Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.000006363Highly InformativeDirect
Worm Phenotype (WP)nonsense mRNA accumulation0.00002982Highly InformativeDirect
Worm Phenotype (WP)multiple nuclei0.00005568Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.00007782Highly InformativeDirect
Worm Phenotype (WP)cell gamma ray response variant0.000093Highly InformativeDirect
Worm Phenotype (WP)hypoxia resistant0.0001532Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic streaming defective0.0001889Highly InformativeDirect
Worm Phenotype (WP)cell cycle variant0.000915Highly InformativeDirect
Worm Phenotype (WP)RNA processing variant0.003545Highly InformativeInherited
Worm Phenotype (WP)cytoplasmic appearance defective early emb0.02781Highly InformativeInherited
Worm Phenotype (WP)cytokinesis defective early emb0.09421Highly InformativeInherited
Worm Phenotype (WP)cleavage furrow defective0.6368Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)chromosome/plasmid maintenance0.000005328InformativeDirect
Yeast Phenotype (YP)heat sensitivity0.00001201InformativeDirect
Yeast Phenotype (YP)cell cycle progression0.0007942InformativeDirect

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)embryo0.000001932Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0.0000193Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.000161Least InformativeDirect
Xenopus ANatomical entity (XAN)egg0.000006687Moderately InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0001535InformativeDirect

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 cell0.0000549Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0.0003516Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0.02672Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Acyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)DNA helicase0InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compounds0InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups1InformativeInherited
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters1InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases1InformativeInherited
Enzyme Commission (EC)Phenylalanine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor1Highly InformativeInherited
Enzyme Commission (EC)Forming phosphoric ester bonds1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processTranscription regulation1Moderately InformativeInherited
Biological processDNA recombination0InformativeDirect
Biological processDNA repair0InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processProtein biosynthesis0InformativeDirect
Biological processTranscription termination0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentMitochondrion1Moderately InformativeInherited
Cellular componentChromosome1InformativeInherited
Cellular componentExosome0Highly InformativeDirect
Cellular componentPrimosome0Highly InformativeDirect
Cellular componentTelomere0.000000006872Highly InformativeDirect
Coding sequence diversityRNA editing0.0008993Moderately InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationNuclease0.1536Moderately InformativeInherited
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationHelicase0InformativeDirect
Post-translational modificationInitiation factor0InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationtRNA-binding0InformativeDirect
Post-translational modificationElongation factor0Highly InformativeDirect
Post-translational modificationMethylation0Moderately InformativeDirect
Post-translational modificationHydroxylation0InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · 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) · 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 131 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 Nucleic acid-binding proteins 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 131 hidden Markov models representing the Nucleic acid-binding proteins 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 · Enzyme Commission (EC) · 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) · UniProtKB KeyWords (KW) · Internal database links ]