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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/aging0.0003044Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.02732Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body region phenotype0.3718Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.3915Least InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.002839Moderately InformativeInherited
Mammalian Phenotype (MP)prenatal lethality0.003411Moderately InformativeInherited
Mammalian Phenotype (MP)neoplasm0.003745Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.004847Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.01118Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system physiology0.08228Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.172Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.242Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.7017Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.8161Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.9121Moderately InformativeInherited
Mammalian Phenotype (MP)chromosomal instability0InformativeDirect
Mammalian Phenotype (MP)embryonic lethality prior to organogenesis0.0003194InformativeDirect
Mammalian Phenotype (MP)abnormal DNA repair0.0009539InformativeDirect
Mammalian Phenotype (MP)abnormal sex determination0.001466InformativeInherited
Mammalian Phenotype (MP)abnormal prenatal growth/weight/body size0.001662InformativeInherited
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 morphology0.07785InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.2184InformativeInherited
Mammalian Phenotype (MP)abnormal oocyte number0.00002449Highly InformativeDirect
Mammalian Phenotype (MP)abnormal fibroblast proliferation0.00003408Highly InformativeDirect
Mammalian Phenotype (MP)abnormal ovary size0.00007125Highly InformativeDirect
Mammalian Phenotype (MP)decreased fetal size0.00007411Highly 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 number0.04416Highly InformativeInherited
Mammalian Phenotype (MP)abnormal reticulocyte morphology0.04775Highly 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 variant0.000000000001116Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.000001622Least InformativeDirect
Worm Phenotype (WP)cell development variant0.00000255Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0007798Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.004639Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.006941Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.01943Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.000000000000734Moderately InformativeDirect
Worm Phenotype (WP)germ cell development variant0.000000002111Moderately InformativeDirect
Worm Phenotype (WP)endocytic transport variant0.00001165Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00005117Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.0002128Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.002638Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.02593Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.02853Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.06067Moderately InformativeInherited
Worm Phenotype (WP)metabolic pathway variant0.09221Moderately InformativeInherited
Worm Phenotype (WP)germ cell differentiation variant0.1008Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.1045Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.2986Moderately InformativeInherited
Worm Phenotype (WP)drug response variant0.7926Moderately InformativeInherited
Worm Phenotype (WP)sick0.00000001551InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb0.00000002949InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.00000003136InformativeDirect
Worm Phenotype (WP)male gonad development variant0.0000002008InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.000001293InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.000004102InformativeDirect
Worm Phenotype (WP)cytokinesis variant emb0.000005175InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.000009538InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.0001271InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.0003948InformativeDirect
Worm Phenotype (WP)nuclear positioning variant0.01526InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.03526InformativeInherited
Worm Phenotype (WP)RNA expression variant0.0408InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.05142InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.06217InformativeInherited
Worm Phenotype (WP)oxygen response variant0.1511InformativeInherited
Worm Phenotype (WP)somatic gonad development variant0.2379InformativeInherited
Worm Phenotype (WP)no oocytes0.000000006153Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.00000004603Highly InformativeDirect
Worm Phenotype (WP)male somatic gonad development variant0.00000007435Highly InformativeDirect
Worm Phenotype (WP)gonad arm morphology variant0.0000002807Highly InformativeDirect
Worm Phenotype (WP)nuclear number variant0.00002543Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.00007744Highly InformativeDirect
Worm Phenotype (WP)hypoxia resistant0.0002008Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic streaming defective0.0002032Highly InformativeDirect
Worm Phenotype (WP)cell cycle variant0.0006652Highly InformativeDirect
Worm Phenotype (WP)cell differentiation variant0.0007846Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic appearance variant0.002012Highly InformativeInherited
Worm Phenotype (WP)RNA processing variant0.003503Highly InformativeInherited
Worm Phenotype (WP)cytokinesis defective early emb0.08304Highly InformativeInherited
Worm Phenotype (WP)nuclear morphology variation early emb0.08313Highly InformativeInherited
Worm Phenotype (WP)nuclear appearance number defective early emb0.141Highly InformativeInherited
Worm Phenotype (WP)nucleus defective early emb0.141Highly InformativeInherited
Worm Phenotype (WP)pronucleus centrosomes defective early emb0.141Highly InformativeInherited
Worm Phenotype (WP)pronuclear morphology defective early emb0.141Highly InformativeInherited
Worm Phenotype (WP)pronuclear nuclear appearance defective early emb0.1559Highly InformativeInherited
Worm Phenotype (WP)cleavage furrow defective0.6032Highly 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)embryo0.00000656Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.0003523Least InformativeDirect
Xenopus ANatomical entity (XAN)urogenital system0.0008931Least InformativeDirect
Xenopus ANatomical entity (XAN)germ cell0.04815Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0001379InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0.0005559InformativeDirect

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 groups0.01262Least 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-binding0.0000000001026InformativeDirect

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 ]