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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 147,633 967,813 241
Proteins 114,374 766,565 208


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/aging0.0003038Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.02729Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body region phenotype0.3716Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.3919Least InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.002841Moderately InformativeInherited
Mammalian Phenotype (MP)prenatal lethality0.003415Moderately InformativeInherited
Mammalian Phenotype (MP)neoplasm0.003743Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.004847Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.01118Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system physiology0.08221Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.1721Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.2415Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.7018Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.8162Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.9123Moderately InformativeInherited
Mammalian Phenotype (MP)chromosomal instability0InformativeDirect
Mammalian Phenotype (MP)embryonic lethality prior to organogenesis0.0003198InformativeDirect
Mammalian Phenotype (MP)abnormal DNA repair0.0009537InformativeDirect
Mammalian Phenotype (MP)abnormal sex determination0.001465InformativeInherited
Mammalian Phenotype (MP)abnormal prenatal growth/weight/body size0.001661InformativeInherited
Mammalian Phenotype (MP)abnormal erythroid lineage cell morphology0.001926InformativeInherited
Mammalian Phenotype (MP)decreased cell proliferation0.006027InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.01348InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.07788InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.2184InformativeInherited
Mammalian Phenotype (MP)abnormal oocyte number0.00002445Highly InformativeDirect
Mammalian Phenotype (MP)abnormal fibroblast proliferation0.00003404Highly InformativeDirect
Mammalian Phenotype (MP)abnormal ovary size0.00007112Highly InformativeDirect
Mammalian Phenotype (MP)decreased fetal size0.00007399Highly InformativeDirect
Mammalian Phenotype (MP)decreased male germ cell number0.0001235Highly InformativeDirect
Mammalian Phenotype (MP)abnormal male reproductive system physiology0.01554Highly InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell number0.04407Highly InformativeInherited
Mammalian Phenotype (MP)abnormal reticulocyte morphology0.04776Highly 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 variant0.0000000000002374Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0000008395Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.000001708Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0008259Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.0008371Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.002737Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.00316Least InformativeInherited
Worm Phenotype (WP)germ cell development variant0.000000002193Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.00000001027Moderately InformativeDirect
Worm Phenotype (WP)cell cycle variant0.000006681Moderately InformativeDirect
Worm Phenotype (WP)endocytic transport variant0.00003034Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00005179Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.0005056Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.002498Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.01179Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.0253Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.08812Moderately InformativeInherited
Worm Phenotype (WP)germ cell differentiation variant0.09891Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.1038Moderately InformativeInherited
Worm Phenotype (WP)metabolic pathway variant0.1054Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.3098Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.3296Moderately InformativeInherited
Worm Phenotype (WP)drug response variant0.8711Moderately InformativeInherited
Worm Phenotype (WP)sick0.0000000153InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb0.00000002988InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.00000003028InformativeDirect
Worm Phenotype (WP)male gonad development variant0.0000002041InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.000001268InformativeDirect
Worm Phenotype (WP)cytokinesis variant emb0.000005286InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.0000242InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.0001283InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.0003103InformativeDirect
Worm Phenotype (WP)nuclear positioning variant0.01933InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.03488InformativeInherited
Worm Phenotype (WP)drug hypersensitive0.03611InformativeInherited
Worm Phenotype (WP)RNA expression variant0.04563InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.05153InformativeInherited
Worm Phenotype (WP)chemical hypersensitive0.07185InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.1229InformativeInherited
Worm Phenotype (WP)hypoxia response variant0.1788InformativeInherited
Worm Phenotype (WP)somatic gonad development variant0.237InformativeInherited
Worm Phenotype (WP)no oocytes0.000000006241Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.00000004453Highly InformativeDirect
Worm Phenotype (WP)male somatic gonad development variant0.00000007539Highly InformativeDirect
Worm Phenotype (WP)gonad arm morphology variant0.0000002844Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.000008635Highly InformativeDirect
Worm Phenotype (WP)nuclear number variant0.00002569Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.00007809Highly InformativeDirect
Worm Phenotype (WP)embryonic cell morphology variant0.0001312Highly InformativeDirect
Worm Phenotype (WP)hypoxia resistant0.0002023Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic streaming defective0.0002196Highly InformativeDirect
Worm Phenotype (WP)cell differentiation variant0.0009776Highly InformativeDirect
Worm Phenotype (WP)RNA processing variant0.003403Highly InformativeInherited
Worm Phenotype (WP)cytoplasmic appearance defective early emb0.01639Highly InformativeInherited
Worm Phenotype (WP)cytokinesis defective early emb0.04909Highly InformativeInherited
Worm Phenotype (WP)cleavage furrow defective0.599Highly 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 maintenance0.000005488InformativeDirect
Yeast Phenotype (YP)heat sensitivity0.0000123InformativeDirect
Yeast Phenotype (YP)cell cycle progression0.0007684InformativeDirect

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)embryo0.000004193Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.0002581Least InformativeDirect
Xenopus ANatomical entity (XAN)urogenital system0.0006801Least InformativeDirect
Xenopus ANatomical entity (XAN)germ cell0.04494Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.00007493InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0.0004076InformativeDirect

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 cell0.00005535Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0.0003519Least 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 groups0.01358Least 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)Aminoacyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)DNA helicase0InformativeDirect
Enzyme Commission (EC)Forming carbon-oxygen bonds0InformativeDirect
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)
Post-translational modificationDNA-binding0Moderately InformativeDirect

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 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.


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 186 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 ]