SUPERFAMILY 1.75 HMM library and genome assignments server


ABC transporter transmembrane region superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Membrane and cell surface proteins and peptides [ 56835] (58)
Fold:   ABC transporter transmembrane region [ 90122]
Superfamily:   ABC transporter transmembrane region [ 90123]
Families:   ABC transporter transmembrane region [ 90124] (2)


Superfamily statistics
Genomes (2,378) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 38,568 87,372 4
Proteins 30,023 79,814 4


Functional annotation
General category Processes_IC
Detailed category Transport

Document:
Function annotation of SCOP domain superfamilies

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) response to stimulus 7.282e-12 Least Informative Direct
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.0009839 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.703 Moderately Informative Inherited
Biological Process (BP) ion transport 0.001117 Moderately Informative Inherited
Biological Process (BP) reproduction 0.4639 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.6383 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.7503 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.9472 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.3483 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.8198 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.7778 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.163 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.7711 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.1431 Moderately Informative Inherited
Biological Process (BP) immune system process 0.3491 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.001115 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) transmembrane transport 0 Informative Direct
Biological Process (BP) response to organic cyclic compound 2.246e-08 Informative Direct
Biological Process (BP) organic acid transport 3.356e-08 Informative Direct
Biological Process (BP) response to organic nitrogen 2.708e-07 Informative Direct
Biological Process (BP) regulation of immune effector process 4.412e-06 Informative Direct
Biological Process (BP) lipid transport 2.575e-05 Informative Direct
Biological Process (BP) anion transport 0.0001621 Informative Direct
Biological Process (BP) nitrogen compound transport 0.01189 Informative Inherited
Biological Process (BP) metal ion transport 0.1755 Informative Inherited
Biological Process (BP) reproductive system development 0.004063 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.1997 Informative Inherited
Biological Process (BP) response to external stimulus 0.5013 Informative Inherited
Biological Process (BP) response to inorganic substance 0.04142 Informative Inherited
Biological Process (BP) response to light stimulus 0.1256 Informative Inherited
Biological Process (BP) lipid catabolic process 0.01126 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.1033 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.05223 Informative Inherited
Biological Process (BP) metal ion homeostasis 0.0231 Informative Inherited
Biological Process (BP) cellular cation homeostasis 0.02947 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.02735 Informative Inherited
Biological Process (BP) purine nucleoside metabolic process 0.06063 Informative Inherited
Biological Process (BP) ribonucleoside metabolic process 0.0838 Informative Inherited
Biological Process (BP) purine nucleotide metabolic process 0.1341 Informative Inherited
Biological Process (BP) ribose phosphate metabolic process 0.1422 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.0499 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.09362 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.2949 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.3637 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.01438 Informative Inherited
Biological Process (BP) regulation of immune response 0.02224 Informative Inherited
Biological Process (BP) response to other organism 0.09657 Informative Inherited
Biological Process (BP) amide transport 2.86e-12 Highly Informative Direct
Biological Process (BP) regulation of cell killing 8.024e-12 Highly Informative Direct
Biological Process (BP) response to drug 6.721e-11 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response 6.817e-11 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte mediated immunity 1.11e-09 Highly Informative Direct
Biological Process (BP) antigen processing and presentation 1.125e-09 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 7.812e-09 Highly Informative Direct
Biological Process (BP) positive regulation of immune effector process 4.904e-08 Highly Informative Direct
Biological Process (BP) response to UV 8.366e-08 Highly Informative Direct
Biological Process (BP) cellular iron ion homeostasis 1.495e-06 Highly Informative Direct
Biological Process (BP) response to cold 7.775e-06 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 0.0004351 Highly Informative Direct
Biological Process (BP) ion transmembrane transport 0.03864 Highly Informative Inherited
Biological Process (BP) monovalent inorganic cation transport 0.09518 Highly Informative Inherited
Biological Process (BP) purine ribonucleoside triphosphate metabolic process 0.02007 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.004058 Highly Informative Inherited
Biological Process (BP) amino acid transport 0.4818 Highly Informative Inherited
Biological Process (BP) lipid modification 0.001207 Highly Informative Inherited
Biological Process (BP) monocarboxylic acid transport 0.008826 Highly Informative Inherited
Biological Process (BP) monocarboxylic acid catabolic process 0.00173 Highly Informative Inherited
Biological Process (BP) nucleoside triphosphate catabolic process 0.01278 Highly Informative Inherited
Biological Process (BP) purine ribonucleoside catabolic process 0.01557 Highly Informative Inherited
Biological Process (BP) nucleotide catabolic process 0.0253 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 4.888e-13 Moderately Informative Direct
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0.0194 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.02509 Moderately Informative Inherited
Molecular Function (MF) nucleoside-triphosphatase activity 0 Informative Direct
Molecular Function (MF) anion transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) nucleotide binding 0 Informative Direct
Molecular Function (MF) active transmembrane transporter activity 6.09e-14 Informative Direct
Molecular Function (MF) receptor binding 0.05737 Informative Inherited
Molecular Function (MF) molecular transducer activity 1 Informative Inherited
Molecular Function (MF) receptor activity 1 Informative Inherited
Molecular Function (MF) metal ion transmembrane transporter activity 0.004136 Informative Inherited
Molecular Function (MF) inorganic cation transmembrane transporter activity 0.05857 Informative Inherited
Molecular Function (MF) channel regulator activity 0 Highly Informative Direct
Molecular Function (MF) ATP binding 0 Highly Informative Direct
Molecular Function (MF) ion channel activity 0.0007886 Highly Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0003371 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.06074 Least Informative Inherited
Cellular Component (CC) plasma membrane 0 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 8.39e-05 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.003534 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.02053 Moderately Informative Inherited
Cellular Component (CC) endosome 0 Informative Direct
Cellular Component (CC) integral to membrane 0 Informative Direct
Cellular Component (CC) microbody 1.572e-11 Informative Direct
Cellular Component (CC) vacuole 2.459e-09 Informative Direct
Cellular Component (CC) cell junction 0.0002105 Informative Direct
Cellular Component (CC) microbody part 0 Highly Informative Direct
Cellular Component (CC) ATP-binding cassette (ABC) transporter complex 0 Highly Informative Direct
Cellular Component (CC) microbody membrane 1.905e-12 Highly Informative Direct
Cellular Component (CC) cell-cell junction 2.688e-06 Highly Informative Direct
Cellular Component (CC) vacuolar membrane 2.324e-05 Highly Informative Direct
Cellular Component (CC) symplast 4.919e-05 Highly Informative Direct
Cellular Component (CC) apical plasma membrane 0.0006536 Highly Informative Direct
Cellular Component (CC) integral to organelle membrane 0.001694 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; catalyzing transmembran0InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)immune system disease0.006265Least InformativeInherited
Disease Ontology (DO)organ system cancer0.03528Least InformativeInherited
Disease Ontology (DO)nervous system disease0.167Least InformativeInherited
Disease Ontology (DO)genetic disease0.001165Moderately InformativeInherited
Disease Ontology (DO)brain disease0.01729Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.02356Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.1035Moderately InformativeInherited
Disease Ontology (DO)lung disease0.1471Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.2507Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.4639Moderately InformativeInherited
Disease Ontology (DO)autosomal recessive disease2.838e-05InformativeDirect
Disease Ontology (DO)myeloid leukemia5.229e-05InformativeDirect
Disease Ontology (DO)leukodystrophy0.001182InformativeInherited
Disease Ontology (DO)primary bacterial infectious disease0.006055InformativeInherited
Disease Ontology (DO)liver disease0.9108InformativeInherited
Disease Ontology (DO)bronchiectasis3.651e-06Highly InformativeDirect
Disease Ontology (DO)intrahepatic cholestasis0.000521Highly InformativeDirect
Disease Ontology (DO)liver cirrhosis0.2513Highly InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the abdomen0.1161Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.2162Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.2354Moderately InformativeInherited
Phenotypic Abnormality (PA)Generalized abnormality of skin0.6662Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.6777Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the biliary system0.002449InformativeInherited
Phenotypic Abnormality (PA)Dermatological manifestations of systemic disorders0.009336InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.1668InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the tracheobronchial system0.02349Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.8019Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.8107Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid level6.122e-05Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.06267Moderately InformativeInherited
Mammalian Phenotype (MP)other phenotype0.001747InformativeInherited
Mammalian Phenotype (MP)abnormal hepatobiliary system physiology0.1181InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.185InformativeInherited
Mammalian Phenotype (MP)abnormal xenobiotic pharmacokinetics3.574e-05Highly InformativeDirect
Mammalian Phenotype (MP)other aberrant phenotype0.0005723Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.02182Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.691Least InformativeInherited
Worm Phenotype (WP)organ system development variant0.408Moderately InformativeInherited
Worm Phenotype (WP)metal response variant3.133e-07InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.001104InformativeInherited
Worm Phenotype (WP)gut granule biogenesis reduced1.49e-08Highly InformativeDirect
Worm Phenotype (WP)RNAi response variant2.428e-05Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least 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)portion of ground tissue0.0002029InformativeDirect
Plant ANatomical entity (PAN)portion of vascular tissue0.02776InformativeInherited
Plant ANatomical entity (PAN)vascular bundle0.0003367Highly InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; catalyzing transmembrane movement of substances0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport1Moderately InformativeInherited
Biological processLipid transport0InformativeDirect
Biological processAntibiotic resistance0.000133InformativeDirect
Biological processCytolysis0.0006427InformativeDirect
Biological processAdaptive immunity1.392e-08Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentMitochondrion0.0006757Moderately InformativeDirect
Cellular componentCell membrane0.000807Moderately InformativeDirect
Cellular componentMitochondrion inner membrane2.187e-10InformativeDirect
Cellular componentCell inner membrane3.432e-08InformativeDirect
Cellular componentPeroxisome4.346e-08InformativeDirect
Cellular componentVacuole7.397e-08InformativeDirect
DiseaseDisease mutation1.173e-05Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionIron1Moderately InformativeInherited
Molecular functionIron transport0Highly InformativeDirect
Molecular functionChloride0Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationProtease1Moderately InformativeInherited
Post-translational modificationIon channel0InformativeDirect
Post-translational modificationThiol protease6.175e-10InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationPhosphoprotein4.302e-05Least InformativeDirect
Post-translational modificationPalmitate0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationUbl conjugation1.364e-14Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011527 SSF90123 Protein matches
Abstract

ABC transporters minimally contain two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). In certain bacterial transporters, these regions are found on different polypeptides. The function of the integral inner-membrane protein is to translocate the substrate across the membrane, as well as in substrate recognition [PubMed9873074, PubMed10529352].


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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · 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 3 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 ABC transporter transmembrane region 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 3 hidden Markov models representing the ABC transporter transmembrane region 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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]