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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

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)mortality/aging0.0003027Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.02741Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body region phenotype0.3719Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.3915Least InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.002835Moderately InformativeInherited
Mammalian Phenotype (MP)prenatal lethality0.003409Moderately InformativeInherited
Mammalian Phenotype (MP)neoplasm0.003759Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.004888Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.01119Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.2032Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.2411Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.7024Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.8163Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.913Moderately InformativeInherited
Mammalian Phenotype (MP)chromosomal instability0InformativeDirect
Mammalian Phenotype (MP)embryonic lethality prior to organogenesis0.0003153InformativeDirect
Mammalian Phenotype (MP)abnormal DNA repair0.0009572InformativeDirect
Mammalian Phenotype (MP)abnormal sex determination0.001491InformativeInherited
Mammalian Phenotype (MP)abnormal prenatal growth/weight/body size0.001652InformativeInherited
Mammalian Phenotype (MP)abnormal erythroid lineage cell morphology0.001936InformativeInherited
Mammalian Phenotype (MP)decreased cell proliferation0.006028InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.01349InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.07741InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.2193InformativeInherited
Mammalian Phenotype (MP)abnormal oocyte number0.00002453Highly InformativeDirect
Mammalian Phenotype (MP)abnormal fibroblast proliferation0.00003409Highly InformativeDirect
Mammalian Phenotype (MP)abnormal ovary size0.00007121Highly InformativeDirect
Mammalian Phenotype (MP)decreased fetal size0.00007413Highly InformativeDirect
Mammalian Phenotype (MP)decreased male germ cell number0.0001264Highly InformativeDirect
Mammalian Phenotype (MP)abnormal male reproductive system physiology0.0157Highly InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell number0.04416Highly 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 variant0.0000000000003476Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0000007241Least InformativeDirect
Worm Phenotype (WP)cell development variant0.000001513Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0001379Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.00226Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.00429Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.04952Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.0000000007491Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00003726Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0002779Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.0003175Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.00325Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.07639Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.1136Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.1188Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.185Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.7645Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.8055Moderately InformativeInherited
Worm Phenotype (WP)sick0.00000001017InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb0.00000002153InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.00000002375InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.000001128InformativeDirect
Worm Phenotype (WP)cytokinesis variant emb0.000004038InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.000007554InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.0002368InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.0004868InformativeDirect
Worm Phenotype (WP)RNA expression variant0.03692InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.05219InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.06926InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.08106InformativeInherited
Worm Phenotype (WP)oxygen response variant0.1159InformativeInherited
Worm Phenotype (WP)somatic gonad development variant0.2433InformativeInherited
Worm Phenotype (WP)organelle organization biogenesis variant0.3604InformativeInherited
Worm Phenotype (WP)cell stress response variant0.845InformativeInherited
Worm Phenotype (WP)no oocytes0.000000005324Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.00000003504Highly InformativeDirect
Worm Phenotype (WP)male somatic gonad development variant0.00000007252Highly InformativeDirect
Worm Phenotype (WP)gonad arm morphology variant0.0000002691Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.000005815Highly InformativeDirect
Worm Phenotype (WP)multiple nuclei0.00005521Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.00006707Highly InformativeDirect
Worm Phenotype (WP)cell gamma ray response variant0.00007284Highly InformativeDirect
Worm Phenotype (WP)hypoxia resistant0.0001525Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic streaming defective0.0001879Highly InformativeDirect
Worm Phenotype (WP)cell cycle variant0.0008591Highly InformativeDirect
Worm Phenotype (WP)RNA processing variant0.003697Highly InformativeInherited
Worm Phenotype (WP)cytoplasmic appearance defective early emb0.02344Highly InformativeInherited
Worm Phenotype (WP)cytokinesis defective early emb0.07932Highly InformativeInherited
Worm Phenotype (WP)cleavage furrow defective0.6315Highly 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)embryo0.000004939Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.000307Least InformativeDirect
Xenopus ANatomical entity (XAN)germ cell0.05089Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0001522InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0.0007715InformativeDirect

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 groups0.01612Least 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-binding0.0000000001037InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · 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) · 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]