SUPERFAMILY 1.75 HMM library and genome assignments server


Ammonium transporter superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Membrane and cell surface proteins and peptides [ 56835] (58)
Fold:   Ammonium transporter [ 111351]
Superfamily:   Ammonium transporter [ 111352]
Families:   Ammonium transporter [ 111353]


Superfamily statistics
Genomes (2,305) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,042 0 5
Proteins 4,990 0 5


Functional annotation
General category Processes_IC
Detailed category Transport

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)localization00Least InformativeDirect
Biological Process (BP)developmental process0.056650.9965Least InformativeInherited
Biological Process (BP)single-organism cellular process0.25961Least InformativeInherited
Biological Process (BP)multicellular organismal process0.14821Least InformativeInherited
Biological Process (BP)response to stimulus11Least InformativeInherited
Biological Process (BP)ion transport00Moderately InformativeDirect
Biological Process (BP)homeostatic process1.714e-093.056e-10Moderately InformativeDirect
Biological Process (BP)organ development0.0031150.2086Moderately InformativeInherited
Biological Process (BP)single-organism developmental process11Moderately InformativeInherited
Biological Process (BP)immune system process0.001650.03125Moderately InformativeInherited
Biological Process (BP)cell differentiation0.010970.6571Moderately InformativeInherited
Biological Process (BP)organic substance transport11Moderately InformativeInherited
Biological Process (BP)anion transport00InformativeDirect
Biological Process (BP)nitrogen compound transport00InformativeDirect
Biological Process (BP)transmembrane transport1.099e-120InformativeDirect
Biological Process (BP)hematopoietic or lymphoid organ development3.428e-050.000517InformativeDirect
Biological Process (BP)response to nutrient levels0.00016651.189e-06InformativeDirect
Biological Process (BP)metal ion homeostasis0.50160.9939InformativeInherited
Biological Process (BP)monovalent inorganic cation transport00Highly InformativeDirect
Biological Process (BP)inorganic anion transport00Highly InformativeDirect
Biological Process (BP)myeloid cell development7.341e-134.074e-11Highly InformativeDirect
Biological Process (BP)erythrocyte differentiation3.275e-112.413e-09Highly InformativeDirect
Biological Process (BP)iron ion homeostasis2.623e-099.29e-09Highly InformativeDirect
Biological Process (BP)one-carbon compound transport0.00022748.418e-09Highly InformativeDirect
Biological Process (BP)ion transmembrane transport0.0022750.02702Highly InformativeInherited
Molecular Function (MF)binding0.74181Least InformativeInherited
Molecular Function (MF)transporter activity00Moderately InformativeDirect
Molecular Function (MF)inorganic cation transmembrane transporter activity00InformativeDirect
Molecular Function (MF)anion transmembrane transporter activity00InformativeDirect
Molecular Function (MF)cytoskeletal protein binding1.909e-131.223e-10InformativeDirect
Molecular Function (MF)organic cation transmembrane transporter activity00Highly InformativeDirect
Cellular Component (CC)membrane00Least InformativeDirect
Cellular Component (CC)cytoplasmic part10.832Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.0057190.08164Least InformativeInherited
Cellular Component (CC)plasma membrane00Moderately InformativeDirect
Cellular Component (CC)cytoskeleton2.117e-082.713e-05Moderately InformativeDirect
Cellular Component (CC)vesicle0.00016072.337e-06Moderately InformativeDirect
Cellular Component (CC)intrinsic to membrane0.13950.4112Moderately InformativeInherited
Cellular Component (CC)integral to membrane2.557e-131.171e-11InformativeDirect
Cellular Component (CC)basolateral plasma membrane5.351e-111.62e-11Highly InformativeDirect
Cellular Component (CC)apical plasma membrane0.00056765.283e-05Highly InformativeDirect

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) localization 0 Least Informative Direct
Biological Process (BP) developmental process 0.9965 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) ion transport 0 Moderately Informative Direct
Biological Process (BP) homeostatic process 3.056e-10 Moderately Informative Direct
Biological Process (BP) organ development 0.2086 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.03125 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.6571 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) anion transport 0 Informative Direct
Biological Process (BP) nitrogen compound transport 0 Informative Direct
Biological Process (BP) transmembrane transport 0 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.000517 Informative Direct
Biological Process (BP) response to nutrient levels 1.189e-06 Informative Direct
Biological Process (BP) metal ion homeostasis 0.9939 Informative Inherited
Biological Process (BP) monovalent inorganic cation transport 0 Highly Informative Direct
Biological Process (BP) inorganic anion transport 0 Highly Informative Direct
Biological Process (BP) myeloid cell development 4.074e-11 Highly Informative Direct
Biological Process (BP) erythrocyte differentiation 2.413e-09 Highly Informative Direct
Biological Process (BP) iron ion homeostasis 9.29e-09 Highly Informative Direct
Biological Process (BP) one-carbon compound transport 8.418e-09 Highly Informative Direct
Biological Process (BP) ion transmembrane transport 0.02702 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0 Moderately Informative Direct
Molecular Function (MF) inorganic cation transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) anion transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) cytoskeletal protein binding 1.223e-10 Informative Direct
Molecular Function (MF) organic cation transmembrane transporter activity 0 Highly Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.832 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.08164 Least Informative Inherited
Cellular Component (CC) plasma membrane 0 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 2.713e-05 Moderately Informative Direct
Cellular Component (CC) vesicle 2.337e-06 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.4112 Moderately Informative Inherited
Cellular Component (CC) integral to membrane 1.171e-11 Informative Direct
Cellular Component (CC) basolateral plasma membrane 1.62e-11 Highly Informative Direct
Cellular Component (CC) apical plasma membrane 5.283e-05 Highly Informative Direct

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0Least InformativeDirect
Mammalian Phenotype (MP)abnormal mineral homeostasis0.001008InformativeInherited
Mammalian Phenotype (MP)abnormal circulating mineral level1.938e-05Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect
Yeast Phenotype (YP)chemical compound accumulation0InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.2786Least InformativeInherited
Plant ANatomical entity (PAN)root system0.3029Least InformativeInherited
Plant ANatomical entity (PAN)root epidermis4.674e-06InformativeDirect
Plant ANatomical entity (PAN)root tip6.885e-06InformativeDirect
Plant ANatomical entity (PAN)root hair cell5.284e-07Highly InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010256 SSF111352 Protein matches
Abstract

A number of evolutionarily-related proteins have been found to be involved in the transport of ammonium ions across membranes [PubMed8062823, PubMed8621394].

Members of this family include:

  • Saccharomyces cerevisiae ammonium transporters MEP1, MEP2 and MEP3.
  • Arabidopsis thaliana high affinity ammonium transporter (gene AMT1).
  • Corynebacterium glutamicum ammonium and methylammonium transport system.
  • Escherichia coli putative ammonium transporter amtB.
  • Bacillus subtilis nrgA.
  • Mycobacterium tuberculosis hypothetical protein MtCY338.09c.
  • Synechocystis sp. (strain PCC 6803) hypothetical proteins sll0108, sll0537 and sll1017.
  • Methanococcus jannaschii hypothetical proteins MJ0058 and MJ1343.
  • Caenorhabditis elegans hypothetical proteins C05E11.4, F49E11.3 and M195.3.

As expected by their transport function, these proteins are highly hydrophobic and seem to contain from 10 to 12 transmembrane domains.


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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 1 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 Ammonium transporter 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 1 hidden Markov models representing the Ammonium transporter 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]