SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


GlnB-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   GlnB-like [ 54913] (5)
Families:   Prokaryotic signal transducing protein [ 54914] (3)
  Divalent ion tolerance proteins CutA (CutA1) [ 75434] (3)
  DUF190/COG1993 [ 89934]
  ATP phosphoribosyltransferase (ATP-PRTase, HisG), regulatory C-terminal domain [ 88851]
  RPA1041-like [ 160310]


Superfamily statistics
Genomes (2,678) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 7,541 41,827 24
Proteins 7,378 41,001 24


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)biological regulation0.24691Least InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) organonitrogen compound metabolic process 0.2427 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.8309 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.02197 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.02342 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.05194 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.03806 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.04699 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.02169 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.0000001041 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.00004214 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.00002956 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.0000668 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0001168 Moderately Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.00101 Informative Inherited
Biological Process (BP) imidazole-containing compound metabolic process 0 Highly Informative Direct
Molecular Function (MF) transferase activity 0.02222 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring glycosyl groups 0.000000006045 Informative Direct
Molecular Function (MF) transferase activity, transferring pentosyl groups 0.000000000000007771 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processTranscription regulation0.0000000000001607Moderately InformativeDirect
Biological processNitrogen fixation0InformativeDirect
Biological processHistidine biosynthesis0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionCopper0.000006291InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationGlycosyltransferase0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011322 SSF54913 Protein matches
Abstract

This entry represents a structural domain found in the nitrogen regulatory protein PII, in ATP phosphribosyltransferases (C-terminal domain), in the divalent ion tolerance protein CutA1, and in some bacterial hypothetical proteins. This domain consists of a ferredoxin-like alpha/beta sandwich, which forms trimeric structures with orthogonally packed beta-sheets around a three-fold axis.

PII is a tetrameric protein encoded by glnB that functions as a component of the adenylation cascade involved in the regulation of GS activity [PubMed1702507]. PII helps regulate the level of glutamine synthetase in response to nitrogen source availability. In nitrogen-limiting conditions, PII is uridylylated to form PII-UMP, which allows the deadenylation of glutamine synthetase, thus activating the enzyme. Conversely, in nitrogen excess, PI-UMP is deuridylated to PII, promoting the adenylation and deactivation of glutamine synthetase [PubMed16860774].

ATP phosphoribosyltransferase is the first enzyme of the histidine pathway. It is allosterically regulated, controlling the flow of intermediates through the pathway. The C-terminal domain is the regulatory region of the protein, which binds the allosteric inhibitor histidine [PubMed14741209].

CutA1 functions in divalent ion tolerance in bacteria, plants and animals [PubMed12949080, PubMed7623666]. Divalent metal ions play key roles in all living organisms, serving as cofactors for many proteins involved in a variety of electron-transfer activities. In Escherichia coli it is thought to be involved in copper ion tolerance, excessive copper ions being toxic [PubMed17077491].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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 17 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 GlnB-like 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 17 hidden Markov models representing the GlnB-like 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]