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 (3,106) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 47,281 177,294 4
Proteins 37,703 165,477 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 0.7038 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.8139 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.6201 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.8611 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.01409 Least Informative Inherited
Biological Process (BP) developmental process 0.004228 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.02356 Least Informative Inherited
Biological Process (BP) reproduction 0 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0.000000000000009067 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.00000000002145 Moderately Informative Direct
Biological Process (BP) ion transport 0.0000000001509 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.000001908 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.000002091 Moderately Informative Direct
Biological Process (BP) tissue development 0.000009026 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.00004548 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0001048 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0002939 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.1438 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.01559 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.5032 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.6408 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.713 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 0.1916 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.003642 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.1219 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.003341 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.3945 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.6944 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1924 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) developmental process involved in reproduction 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 0.00000000000004724 Informative Direct
Biological Process (BP) lipid localization 0.0000000000001152 Informative Direct
Biological Process (BP) glycosyl compound catabolic process 0.0000000000002975 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0.0000000000004171 Informative Direct
Biological Process (BP) organophosphate catabolic process 0.000000000001774 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.000000000004978 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.00000000002383 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.00000000002696 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 0.0000000003925 Informative Direct
Biological Process (BP) single organism reproductive process 0.0000000004759 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.000000003659 Informative Direct
Biological Process (BP) reproductive system development 0.00000001775 Informative Direct
Biological Process (BP) regulation of immune effector process 0.00001597 Informative Direct
Biological Process (BP) organic acid transport 0.00002546 Informative Direct
Biological Process (BP) response to nutrient levels 0.00003391 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.00005502 Informative Direct
Biological Process (BP) nitrogen compound transport 0.08789 Informative Inherited
Biological Process (BP) metal ion transport 0.3681 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.9164 Informative Inherited
Biological Process (BP) metal ion homeostasis 1 Informative Inherited
Biological Process (BP) cellular cation homeostasis 0.001402 Informative Inherited
Biological Process (BP) response to inorganic substance 0.248 Informative Inherited
Biological Process (BP) response to light stimulus 0.1155 Informative Inherited
Biological Process (BP) lipid catabolic process 0.03129 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.07873 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.03297 Informative Inherited
Biological Process (BP) sexual reproduction 0.001411 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.03468 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.01278 Informative Inherited
Biological Process (BP) regulation of immune response 0.0292 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 0.00000000000002099 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0.00000000000006012 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0.00000000000008708 Highly Informative Direct
Biological Process (BP) regulation of cell killing 0.00000000002429 Highly Informative Direct
Biological Process (BP) fruiting body development 0.00000000002637 Highly Informative Direct
Biological Process (BP) antigen processing and presentation 0.00000000002985 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response 0.00000000007968 Highly Informative Direct
Biological Process (BP) response to drug 0.0000000001669 Highly Informative Direct
Biological Process (BP) amide transport 0.0000000002263 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte mediated immunity 0.000000002176 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 0.00000001176 Highly Informative Direct
Biological Process (BP) response to UV 0.00000002145 Highly Informative Direct
Biological Process (BP) iron ion homeostasis 0.00000008437 Highly Informative Direct
Biological Process (BP) response to cold 0.00004181 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.000255 Highly Informative Direct
Biological Process (BP) cellular transition metal ion homeostasis 0.0006744 Highly Informative Direct
Biological Process (BP) positive regulation of leukocyte mediated immunity 0.0006998 Highly Informative Direct
Biological Process (BP) response to cadmium ion 0.1243 Highly Informative Inherited
Biological Process (BP) ion transmembrane transport 1 Highly Informative Inherited
Biological Process (BP) monovalent inorganic cation transport 0.09751 Highly Informative Inherited
Biological Process (BP) post-embryonic organ development 0.00739 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.02111 Highly Informative Inherited
Biological Process (BP) amino acid transport 0.7966 Highly Informative Inherited
Biological Process (BP) lipid modification 0.001271 Highly Informative Inherited
Biological Process (BP) monocarboxylic acid transport 0.003776 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 0.00000001826 Moderately Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0 Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances 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 0.0006119 Informative Direct
Molecular Function (MF) receptor binding 0.006674 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 0.2733 Informative Inherited
Molecular Function (MF) channel regulator activity 0 Highly Informative Direct
Molecular Function (MF) ATP binding 0 Highly Informative Direct
Molecular Function (MF) cation channel activity 1 Highly Informative Inherited
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 membrane-bounded organelle 0.002544 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.0386 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 0.000002907 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.002345 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.01443 Moderately Informative Inherited
Cellular Component (CC) endosome 0 Informative Direct
Cellular Component (CC) integral to membrane 0 Informative Direct
Cellular Component (CC) vacuolar part 0.000000000000001608 Informative Direct
Cellular Component (CC) microbody 0.000000000005184 Informative Direct
Cellular Component (CC) cell-cell junction 0.0000008367 Informative Direct
Cellular Component (CC) lytic vacuole 0.8825 Informative Inherited
Cellular Component (CC) microbody part 0 Highly Informative Direct
Cellular Component (CC) early endosome 0.000000000000009113 Highly Informative Direct
Cellular Component (CC) ATP-binding cassette (ABC) transporter complex 0.000000000000009113 Highly Informative Direct
Cellular Component (CC) microbody membrane 0.00000000000006238 Highly Informative Direct
Cellular Component (CC) intrinsic to organelle membrane 0.0000000289 Highly Informative Direct
Cellular Component (CC) symplast 0.00001146 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 disease0.005852Least InformativeInherited
Disease Ontology (DO)organ system cancer0.03711Least InformativeInherited
Disease Ontology (DO)nervous system disease0.2082Least InformativeInherited
Disease Ontology (DO)genetic disease0.001064Moderately InformativeInherited
Disease Ontology (DO)brain disease0.001429Moderately InformativeInherited
Disease Ontology (DO)bacterial infectious disease0.01035Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.02443Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.1Moderately InformativeInherited
Disease Ontology (DO)lung disease0.1404Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.4331Moderately InformativeInherited
Disease Ontology (DO)autosomal recessive disease0.0000232InformativeDirect
Disease Ontology (DO)myeloid leukemia0.00005169InformativeDirect
Disease Ontology (DO)leukodystrophy0.001145InformativeInherited
Disease Ontology (DO)primary bacterial infectious disease0.005828InformativeInherited
Disease Ontology (DO)autoimmune disease of urogenital tract0.02704InformativeInherited
Disease Ontology (DO)liver disease0.8894InformativeInherited
Disease Ontology (DO)bronchiectasis0.000003167Highly InformativeDirect
Disease Ontology (DO)intrahepatic cholestasis0.0004834Highly 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 abdomen0.124Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.2312Moderately InformativeInherited
Phenotypic Abnormality (PA)Generalized abnormality of skin0.6359Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.7022Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the biliary system0.00262InformativeInherited
Phenotypic Abnormality (PA)Dermatological manifestations of systemic disorders0.01148InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.05895InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the tracheobronchial system0.02429Highly 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 phenotype0.8167Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.8418Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.006994Moderately InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.06418Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.09316Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hepatobiliary system physiology0.1196InformativeInherited
Mammalian Phenotype (MP)abnormal xenobiotic pharmacokinetics0.00009057Highly 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 variant0.0000003133InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.001104InformativeInherited
Worm Phenotype (WP)gut granule biogenesis reduced0.0000000149Highly InformativeDirect
Worm Phenotype (WP)RNAi response variant0.00002428Highly 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 resistance0.0001202InformativeDirect
Biological processCytolysis0.0007198InformativeDirect
Biological processAdaptive immunity0.00000001768Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCell membrane0.000001039Moderately InformativeDirect
Cellular componentMitochondrion0.0006827Moderately InformativeDirect
Cellular componentMitochondrion inner membrane0.0000000001244InformativeDirect
Cellular componentPeroxisome0.00000003798InformativeDirect
Cellular componentVacuole0.00000007649InformativeDirect
Cellular componentCell inner membrane0.00000109InformativeDirect
DiseaseDisease mutation0.00002617Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately 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 protease0.0000000006472InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationPhosphoprotein0.000253Least InformativeDirect
Post-translational modificationPalmitate0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0000000000000462Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details) Document: UP 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) · UniProtKB UniPathway (UP) ]

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) · UniProtKB UniPathway (UP) · Internal database links ]