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 (2,315) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,180 19,564 5
Proteins 5,116 19,475 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)single-organism cellular process0.46180.856Least InformativeInherited
Biological Process (BP)response to stimulus11Least InformativeInherited
Biological Process (BP)multicellular organismal process0.14161Least InformativeInherited
Biological Process (BP)developmental process0.065591Least InformativeInherited
Biological Process (BP)ion transport00Moderately InformativeDirect
Biological Process (BP)regulation of biological quality0.000000000024630.00000000002767Moderately InformativeDirect
Biological Process (BP)organ development0.0029110.2121Moderately InformativeInherited
Biological Process (BP)response to external stimulus0.011810.01046Moderately InformativeInherited
Biological Process (BP)immune system process0.0017560.03671Moderately InformativeInherited
Biological Process (BP)cell differentiation0.013920.6917Moderately InformativeInherited
Biological Process (BP)organic substance transport11Moderately InformativeInherited
Biological Process (BP)anion transport00InformativeDirect
Biological Process (BP)monovalent inorganic cation transport00InformativeDirect
Biological Process (BP)nitrogen compound transport00InformativeDirect
Biological Process (BP)hematopoietic or lymphoid organ development0.000028020.0005672InformativeDirect
Biological Process (BP)multicellular organismal homeostasis0.000085120.00001639InformativeDirect
Biological Process (BP)response to nutrient levels0.00024550.000002272InformativeDirect
Biological Process (BP)ion transmembrane transport0.00046180.008796InformativeInherited
Biological Process (BP)cation homeostasis11InformativeInherited
Biological Process (BP)inorganic anion transport00Highly InformativeDirect
Biological Process (BP)myeloid cell development0.000000000001990.0000000001807Highly InformativeDirect
Biological Process (BP)erythrocyte differentiation0.000000000052770.000000003118Highly InformativeDirect
Biological Process (BP)transition metal ion homeostasis0.000000011650.0000001444Highly InformativeDirect
Biological Process (BP)anion transmembrane transport0.000000085630.0000000000002449Highly InformativeDirect
Biological Process (BP)one-carbon compound transport0.00038350.00000001453Highly InformativeDirect
Molecular Function (MF)binding0.82281Least InformativeInherited
Molecular Function (MF)transporter activity00Moderately InformativeDirect
Molecular Function (MF)monovalent inorganic cation transmembrane transporter activity00InformativeDirect
Molecular Function (MF)anion transmembrane transporter activity00InformativeDirect
Molecular Function (MF)cytoskeletal protein binding0.00000000000031150.0000000001518InformativeDirect
Molecular Function (MF)inorganic anion transmembrane transporter activity00Highly InformativeDirect
Molecular Function (MF)organic cation transmembrane transporter activity00Highly InformativeDirect
Cellular Component (CC)membrane00Least InformativeDirect
Cellular Component (CC)cytoplasmic part10.8667Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.0060330.08486Least InformativeInherited
Cellular Component (CC)plasma membrane part00Moderately InformativeDirect
Cellular Component (CC)cytoskeleton0.000000029530.00004195Moderately InformativeDirect
Cellular Component (CC)membrane region0.000000044040.000001153Moderately InformativeDirect
Cellular Component (CC)vesicle0.0002220.000004585Moderately InformativeDirect
Cellular Component (CC)plasma membrane region0.0000000000000055070.0000000000006419InformativeDirect
Cellular Component (CC)basolateral plasma membrane00.00000000000002857Highly InformativeDirect
Cellular Component (CC)apical plasma membrane0.00000022170.0000005201Highly 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) single-organism cellular process 0.856 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) ion transport 0 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.00000000002767 Moderately Informative Direct
Biological Process (BP) organ development 0.2121 Moderately Informative Inherited
Biological Process (BP) immune system process 0.03671 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.6917 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.01046 Moderately Informative Inherited
Biological Process (BP) anion transport 0 Informative Direct
Biological Process (BP) monovalent inorganic cation transport 0 Informative Direct
Biological Process (BP) nitrogen compound transport 0 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0005672 Informative Direct
Biological Process (BP) multicellular organismal homeostasis 0.00001639 Informative Direct
Biological Process (BP) response to nutrient levels 0.000002272 Informative Direct
Biological Process (BP) cellular response to external stimulus 0.0001975 Informative Direct
Biological Process (BP) ion transmembrane transport 0.008796 Informative Inherited
Biological Process (BP) cation homeostasis 1 Informative Inherited
Biological Process (BP) inorganic anion transport 0 Highly Informative Direct
Biological Process (BP) myeloid cell development 0.0000000001807 Highly Informative Direct
Biological Process (BP) erythrocyte differentiation 0.000000003118 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0.0000001444 Highly Informative Direct
Biological Process (BP) anion transmembrane transport 0.0000000000002449 Highly Informative Direct
Biological Process (BP) one-carbon compound transport 0.00000001453 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0 Moderately Informative Direct
Molecular Function (MF) monovalent inorganic cation transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) anion transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0.0000000001518 Informative Direct
Molecular Function (MF) inorganic anion transmembrane transporter activity 0 Highly 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 0.8667 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.08486 Least Informative Inherited
Cellular Component (CC) plasma membrane part 0 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.00004195 Moderately Informative Direct
Cellular Component (CC) membrane region 0.000001153 Moderately Informative Direct
Cellular Component (CC) vesicle 0.000004585 Moderately Informative Direct
Cellular Component (CC) plasma membrane region 0.0000000000006419 Informative Direct
Cellular Component (CC) basolateral plasma membrane 0.00000000000002857 Highly Informative Direct
Cellular Component (CC) apical plasma membrane 0.0000005201 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 homeostasis0.0009809InformativeDirect
Mammalian Phenotype (MP)abnormal circulating mineral level0.00001742Highly 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 epidermis0.000004674InformativeDirect
Plant ANatomical entity (PAN)root tip0.000006885InformativeDirect
Plant ANatomical entity (PAN)root hair cell0.0000005284Highly 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 ]