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 (3,070) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 44,757 87,372 4
Proteins 36,102 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 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.6682 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.7782 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.5805 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.8281 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.01089 Least Informative Inherited
Biological Process (BP) developmental process 0.001755 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.01061 Least Informative Inherited
Biological Process (BP) reproduction 0 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 3.773e-14 Moderately Informative Direct
Biological Process (BP) homeostatic process 1.796e-11 Moderately Informative Direct
Biological Process (BP) ion transport 9.45e-10 Moderately Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 1.114e-08 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 5.464e-08 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 1.231e-06 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 1.44e-06 Moderately Informative Direct
Biological Process (BP) tissue development 7.749e-06 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 3.351e-05 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 8.23e-05 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0001987 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.000745 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.1135 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.009877 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.3882 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.7014 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.169 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.1157 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.002295 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.3775 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.7921 Moderately Informative Inherited
Biological Process (BP) immune system process 0.133 Moderately Informative Inherited
Biological Process (BP) transmembrane transport 0 Informative Direct
Biological Process (BP) response to organonitrogen compound 0 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0 Informative Direct
Biological Process (BP) response to organic cyclic compound 0 Informative Direct
Biological Process (BP) cellular process involved in reproduction 0 Informative Direct
Biological Process (BP) epithelium development 0 Informative Direct
Biological Process (BP) anion transport 5.586e-15 Informative Direct
Biological Process (BP) lipid localization 8.593e-14 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 2.127e-13 Informative Direct
Biological Process (BP) glycosyl compound catabolic process 2.518e-13 Informative Direct
Biological Process (BP) organophosphate catabolic process 1.074e-12 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 2.57e-12 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 1.196e-11 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 2.449e-11 Informative Direct
Biological Process (BP) cellular chemical homeostasis 2.179e-10 Informative Direct
Biological Process (BP) single organism reproductive process 3.63e-10 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 5.401e-10 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 2.716e-09 Informative Direct
Biological Process (BP) reproductive structure development 1.245e-06 Informative Direct
Biological Process (BP) regulation of immune effector process 1.258e-05 Informative Direct
Biological Process (BP) response to nutrient levels 2.706e-05 Informative Direct
Biological Process (BP) organic acid transport 3.252e-05 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 8.934e-05 Informative Direct
Biological Process (BP) nitrogen compound transport 0.1049 Informative Inherited
Biological Process (BP) metal ion transport 0.2524 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.8839 Informative Inherited
Biological Process (BP) cation homeostasis 0.03325 Informative Inherited
Biological Process (BP) response to inorganic substance 0.4166 Informative Inherited
Biological Process (BP) response to light stimulus 0.1175 Informative Inherited
Biological Process (BP) lipid catabolic process 0.03144 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.07845 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.03117 Informative Inherited
Biological Process (BP) sexual reproduction 0.001246 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.03105 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.01182 Informative Inherited
Biological Process (BP) regulation of immune response 0.02781 Informative Inherited
Biological Process (BP) spermatogenesis 0 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 0 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) developmental maturation 0 Highly Informative Direct
Biological Process (BP) epithelial cell development 0 Highly Informative Direct
Biological Process (BP) ATP metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of intracellular pH 0 Highly Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 1.086e-14 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 3.281e-14 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 4.755e-14 Highly Informative Direct
Biological Process (BP) regulation of cell killing 1.702e-11 Highly Informative Direct
Biological Process (BP) fruiting body development 2.309e-11 Highly Informative Direct
Biological Process (BP) antigen processing and presentation 3.255e-11 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response 6.467e-11 Highly Informative Direct
Biological Process (BP) amide transport 9.627e-11 Highly Informative Direct
Biological Process (BP) response to drug 5.509e-10 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte mediated immunity 1.64e-09 Highly Informative Direct
Biological Process (BP) cellular response to organic cyclic compound 2.024e-09 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 1.016e-08 Highly Informative Direct
Biological Process (BP) response to UV 2.309e-08 Highly Informative Direct
Biological Process (BP) response to cold 3.933e-05 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0.0002156 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.0002585 Highly Informative Direct
Biological Process (BP) positive regulation of leukocyte mediated immunity 0.0008366 Highly Informative Direct
Biological Process (BP) ion transmembrane transport 1 Highly Informative Inherited
Biological Process (BP) monovalent inorganic cation transport 0.0423 Highly Informative Inherited
Biological Process (BP) post-embryonic organ development 0.004691 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.01851 Highly Informative Inherited
Biological Process (BP) amino acid transport 0.7921 Highly Informative Inherited
Biological Process (BP) lipid modification 0.001246 Highly Informative Inherited
Biological Process (BP) monocarboxylic acid transport 0.003358 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 3.141e-10 Moderately Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0 Informative Direct
Molecular Function (MF) anion transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) active transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) nucleotide binding 0 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0 Informative Direct
Molecular Function (MF) metal ion transmembrane transporter activity 0.0009259 Informative Direct
Molecular Function (MF) receptor binding 0.005631 Informative Inherited
Molecular Function (MF) molecular transducer activity 1 Informative Inherited
Molecular Function (MF) receptor activity 1 Informative Inherited
Molecular Function (MF) inorganic cation transmembrane transporter activity 0.08042 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 0.000129 Highly Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.01177 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.005571 Least Informative Inherited
Cellular Component (CC) organelle membrane 0 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 1.335e-05 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 4.466e-05 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.001796 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.01745 Moderately Informative Inherited
Cellular Component (CC) endosome 0 Informative Direct
Cellular Component (CC) integral to membrane 0 Informative Direct
Cellular Component (CC) vacuolar part 2.972e-15 Informative Direct
Cellular Component (CC) microbody 4.75e-12 Informative Direct
Cellular Component (CC) cell-cell junction 7.065e-07 Informative Direct
Cellular Component (CC) lytic vacuole 0.8169 Informative Inherited
Cellular Component (CC) microbody part 0 Highly Informative Direct
Cellular Component (CC) ATP-binding cassette (ABC) transporter complex 2.972e-15 Highly Informative Direct
Cellular Component (CC) early endosome 5.839e-15 Highly Informative Direct
Cellular Component (CC) microbody membrane 9.546e-14 Highly Informative Direct
Cellular Component (CC) intrinsic to organelle membrane 2.918e-08 Highly Informative Direct
Cellular Component (CC) symplast 1.204e-05 Highly Informative Direct
Cellular Component (CC) vacuolar membrane 3.46e-05 Highly Informative Direct
Cellular Component (CC) apical plasma membrane 0.0006102 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)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 disease0.00579Least InformativeInherited
Disease Ontology (DO)organ system cancer0.03741Least InformativeInherited
Disease Ontology (DO)nervous system disease0.2149Least InformativeInherited
Disease Ontology (DO)genetic disease0.001065Moderately InformativeInherited
Disease Ontology (DO)brain disease0.001667Moderately InformativeInherited
Disease Ontology (DO)bacterial infectious disease0.0104Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.0246Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.1002Moderately InformativeInherited
Disease Ontology (DO)lung disease0.1415Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.4362Moderately InformativeInherited
Disease Ontology (DO)autosomal recessive disease2.318e-05InformativeDirect
Disease Ontology (DO)myeloid leukemia5.172e-05InformativeDirect
Disease Ontology (DO)leukodystrophy0.001146InformativeInherited
Disease Ontology (DO)primary bacterial infectious disease0.005851InformativeInherited
Disease Ontology (DO)autoimmune disease of urogenital tract0.02721InformativeInherited
Disease Ontology (DO)liver disease0.8955InformativeInherited
Disease Ontology (DO)bronchiectasis3.165e-06Highly InformativeDirect
Disease Ontology (DO)intrahepatic cholestasis0.0004843Highly InformativeDirect

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 abdomen0.1242Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.2312Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.5106Moderately InformativeInherited
Phenotypic Abnormality (PA)Generalized abnormality of skin0.6359Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the biliary system0.002621InformativeInherited
Phenotypic Abnormality (PA)Dermatological manifestations of systemic disorders0.01153InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.1692InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the tracheobronchial system0.02445Highly 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 phenotype0.8116Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.8718Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.00707Moderately InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.06216Moderately InformativeInherited
Mammalian Phenotype (MP)other phenotype0.0009563InformativeDirect
Mammalian Phenotype (MP)abnormal metabolism0.07227InformativeInherited
Mammalian Phenotype (MP)abnormal hepatobiliary system physiology0.1187InformativeInherited
Mammalian Phenotype (MP)abnormal xenobiotic pharmacokinetics0.0001373Highly InformativeDirect
Mammalian Phenotype (MP)other aberrant phenotype0.112Highly InformativeInherited

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

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least 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)whole plant0.9025Least InformativeInherited
Plant ANatomical entity (PAN)portion of ground tissue0.0002655InformativeDirect
Plant ANatomical entity (PAN)vascular system0.1629InformativeInherited
Plant ANatomical entity (PAN)vascular bundle0.0004196Highly InformativeDirect
Plant structure DEvelopment stage (PDE)seedling development stage0.0008931InformativeDirect

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 resistance0.0001307InformativeDirect
Biological processCytolysis0.0006631InformativeDirect
Biological processAdaptive immunity1.483e-08Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCell membrane2.205e-06Moderately InformativeDirect
Cellular componentMitochondrion0.0006958Moderately InformativeDirect
Cellular componentMitochondrion inner membrane1.321e-10InformativeDirect
Cellular componentPeroxisome4.306e-08InformativeDirect
Cellular componentVacuole7.941e-08InformativeDirect
Cellular componentCell inner membrane1.325e-06InformativeDirect
DiseaseDisease mutation2.156e-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 protease7.095e-10InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationPhosphoprotein0.0002524Least InformativeDirect
Post-translational modificationPalmitate0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationUbl conjugation3.949e-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) · 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]