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Phenotype Ontology
Like Gene Ontology (GO), phenotypy ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Phenotype ontologies we have incorporated are as follows:

• Disease Ontology (DO) Ontology (DO)
  DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
  
• Human Phenotype (HP) Ontology (HP)
  HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
  
• Mouse Phenotype (MP) Ontology (MP)
  MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
  
• Worm Phenotype (WP) Ontology (WP)
  WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
  
• Yeast Phenotype (YP) Ontology (YP)
  Based on YP which is the major contributor to the ‘Ascomycete phenotype ontology’, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
  
• Fly Phenotype (FP) Ontology (FP)
  FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
  
• Fly Anatomy (FA) Ontology (FA)
  FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
  
• Zebrafish Anatomy (ZA) Ontology (ZA)
  ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
  
• Xenopus Anatomy (XA) Ontology (XA)
  XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
  
• Arabidopsis Plant Ontology (AP) Ontology (AP)
  As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
  
• Enzyme Commission (EC) Ontology (EC)
  Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
  
• DrugBank ATC (DB) Ontology (DB)
  In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
  
• UniProtKB KeyWords (KW) Ontology (KW)
  Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
  
• UniProtKB UniPathway (UP) Ontology (UP)
  UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.
  

Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

• Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).
  

Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

• Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Human Phenotype (HP) Ontology (SPHP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).
  

Superfamily domains annotated to this AP term (Not in SDAP)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Tim10-like	0	DIRECT
RibA-like	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
BSD domain-like	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
SH3-domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Prokaryotic type KH domain (KH-domain type II)	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
YrdC/RibB	0	DIRECT
LuxS/MPP-like metallohydrolase	0	DIRECT
NHL repeat	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
Chelatase	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
Mog1p/PsbP-like	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
GlnB-like	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
HesB-like domain	0	DIRECT
Chalcone isomerase	0	DIRECT
S15/NS1 RNA-binding domain	0	DIRECT
Lipocalins	0	DIRECT
FKBP-like	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Folate-binding domain	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
XPC-binding domain	0	DIRECT
Ribosomal protein S6	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
Ribosomal protein L4	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
LigT-like	0	DIRECT
ADC-like	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
LysM domain	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
AMPKBI-like	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
eIF1-like	0	DIRECT
Oxygen-evolving enhancer protein 3,	0	DIRECT
RraA-like	0	DIRECT
Electron transport accessory proteins	0	DIRECT
Tautomerase/MIF	0	DIRECT
Ribosomal protein S2	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
Peptidyl-tRNA hydrolase II	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
SAM/Pointed domain	0	DIRECT
alpha-helical ferredoxin	0	DIRECT
S13-like H2TH domain	0	DIRECT
Rubredoxin-like	0	DIRECT
Peptidase/esterase 'gauge' domain	0	DIRECT
SIS domain	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
Signal peptide-binding domain	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Cytochrome c	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
AF1104-like	0	DIRECT
FAH	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Ribosomal protein L31e	0	DIRECT
CYTH-like phosphatases	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
LeuD/IlvD-like	0	DIRECT
Supernatant protein factor (SPF), C-terminal domain	0	DIRECT
Ribosomal protein L14	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
L28p-like	0	DIRECT
GroEL-intermediate domain like	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
tRNA-binding arm	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Ribosomal protein L1	0	DIRECT
Amine oxidase catalytic domain	0	DIRECT
Putative isomerase YbhE	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
BolA-like	0	DIRECT
Cryptochrome/photolyase, N-terminal domain	0	DIRECT
Alpha-L RNA-binding motif	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
GroEL apical domain-like	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
E2F-DP heterodimerization region	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
Flavoproteins	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
Ribosomal protein L39e	0	DIRECT
Ribosomal protein L13	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
RplX-like	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
Ribosomal protein L16p/L10e	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Release factor	0	DIRECT
Chorismate mutase II	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
GroEL equatorial domain-like	0	DIRECT
R3H domain	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
FF domain	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
RNA-binding domain, RBD	7.265e-05	DIRECT
ACT-like	0.0001672	DIRECT
Chaperone J-domain	0.000217	DIRECT
Mitochondrial carrier	0.0004198	DIRECT
Single hybrid motif	0.0006761	DIRECT

Family domains annotated to this AP term (SDAP level: Least Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
GAF domain	0	DIRECT
BolA-like	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
UBX domain	0	DIRECT
GAT domain	0	DIRECT
HspBP1 domain	0	DIRECT
HIT (HINT, histidine triad) family of protein kinase-interacting proteins	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Class-II DAHP synthetase	0	DIRECT
PhzC/PhzF-like	0	DIRECT
Methyl-CpG-binding domain, MBD	0	DIRECT
Spermidine synthase	0	DIRECT
Molybdenum cofactor biosynthesis protein MoeB	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
Plant stress-induced protein	0	DIRECT
AF1104-like	0	DIRECT
beta-sandwich domain of Sec23/24	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
HesB-like domain	0	DIRECT
Clp protease, ClpP subunit	0	DIRECT
Calnexin/calreticulin	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
CAT-like	0	DIRECT
Sigma4 domain	0	DIRECT
Ribosomal protein L14	0	DIRECT
Ribosomal protein S15	0	DIRECT
FAH	0	DIRECT
Enolase	0	DIRECT
NifU C-terminal domain-like	0	DIRECT
Ring hydroxylating alpha subunit ISP domain	0	DIRECT
Ribosomal protein L31e	0	DIRECT
Ribosomal protein S13	0	DIRECT
GroEL chaperone, ATPase domain	0	DIRECT
N-acetyl-l-glutamate kinase	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Ubiquitin carboxyl-terminal hydrolase UCH-L	0	DIRECT
DNase I-like	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
Ribosomal protein L3	0	DIRECT
PCI domain (PINT motif)	0	DIRECT
Reductases	0	DIRECT
Transcriptional coactivator PC4 C-terminal domain	0	DIRECT
Ribosomal protein L10e	0	DIRECT
2Fe-2S ferredoxin-related	0	DIRECT
HAT/Suf repeat	0	DIRECT
GroEL-like chaperone, apical domain	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
PNP-oxidase like	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
Receiver domain of the ethylene receptor	0	DIRECT
NHL repeat	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Ribosomal protein S6	0	DIRECT
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain	0	DIRECT
LeuD-like	0	DIRECT
5' nucleotidase-like	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
SAM (sterile alpha motif) domain	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
R3H domain	0	DIRECT
Glyoxalase II (hydroxyacylglutathione hydrolase)	0	DIRECT
Amine oxidase catalytic domain	0	DIRECT
Rubredoxin	0	DIRECT
Ribosomal protein L18 and S11	0	DIRECT
Myf domain	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
GroEL-like chaperone, intermediate domain	0	DIRECT
CoA-binding domain	0	DIRECT
LEA14-like	0	DIRECT
Leukotriene A4 hydrolase catalytic domain	0	DIRECT
HCDH C-domain-like	0	DIRECT
GroES	0	DIRECT
Sec63 C-terminal domain-like	0	DIRECT
Linker histone H1/H5	0	DIRECT
FF domain	0	DIRECT
Smc hinge domain	0	DIRECT
BSD domain	0	DIRECT
PDI-like	0	DIRECT
LplA-like	0	DIRECT
Ribosomal protein L1	0	DIRECT
3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
UDP-glucose pyrophosphorylase	0	DIRECT
GABARAP-like	0	DIRECT
LON domain-like	0	DIRECT
IPP isomerase-like	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
HD domain	0	DIRECT
PAPS reductase-like	0	DIRECT
YicI N-terminal domain-like	0	DIRECT
Eps15 homology domain (EH domain)	0	DIRECT
Branched-chain alpha-keto acid dehydrogenase Pyr module	0	DIRECT
RNB domain-like	0	DIRECT
HEAT repeat	0	DIRECT
PUA domain	0	DIRECT
RWD domain	0	DIRECT
RplX-like	0	DIRECT
SerA intervening domain-like	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
Aspartokinase allosteric domain-like	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Choline kinase	0	DIRECT
Tim10/DDP	0	DIRECT
Cryptochrome/photolyase, N-terminal domain	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Chromo domain	0	DIRECT
Ribosomal proteins L24p and L21e	0	DIRECT
Cytochrome p450 reductase N-terminal domain-like	0	DIRECT
NadC C-terminal domain-like	0	DIRECT
XPC-binding domain	0	DIRECT
RibA-like	0	DIRECT
Folylpolyglutamate synthetase	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Methionine aminopeptidase, insert domain	0	DIRECT
rRNA adenine dimethylase-like	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
Ribosomal protein L39e	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
Ribosomal protein L13	0	DIRECT
Plant transcriptional regulator PBF-2	0	DIRECT
Succinyl-CoA synthetase, beta-chain, N-terminal domain	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Prolyl oligopeptidase, N-terminal domain	0	DIRECT
RNA polymerase II subunit RBP4 (RpoF)	0	DIRECT
Tail specific protease, catalytic domain	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase dimerisation domain	0	DIRECT
gamma-carbonic anhydrase-like	0	DIRECT
Heme-dependent catalases	0	DIRECT
MIF-related	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
Release factor	0	DIRECT
ZZ domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
VHS domain	0	DIRECT
RuBisCo LSMT catalytic domain	0	DIRECT
eIF5a N-terminal domain-like	0	DIRECT
Pseudouridine synthase II TruB	0	DIRECT
CYTH domain	0	DIRECT
Acyl-ACP thioesterase-like	0	DIRECT
beta-Phosphoglucomutase-like	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Neurolysin-like	0	DIRECT
Sec63 N-terminal domain	0	DIRECT
Group II chaperonin (CCT, TRIC), ATPase domain	0	DIRECT
DJ-1/PfpI	0	DIRECT
Starch-binding domain	0	DIRECT
Trunk domain of Sec23/24	0	DIRECT
AMPK-beta glycogen binding domain-like	0	DIRECT
LysM domain	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Glyoxalase I (lactoylglutathione lyase)	0	DIRECT
PsbP-like	0	DIRECT
Phytochrome-specific domain	0	DIRECT
BAR domain	0	DIRECT
NADPH-cytochrome p450 reductase FAD-binding domain-like	0	DIRECT
Hypothetical protein HI1317	0	DIRECT
Dihydrodipicolinate reductase-like	0	DIRECT
Poly(ADP-ribose) polymerase, C-terminal domain	0	DIRECT
MPP-like	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Aminomethyltransferase folate-binding domain	0	DIRECT
Class I alpha-1;2-mannosidase, catalytic domain	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
SH3-domain	0	DIRECT
ATP sulfurylase catalytic domain	0	DIRECT
Sedlin (SEDL)	0	DIRECT
Ubiquitin activating enzymes (UBA)	0	DIRECT
NADPH-cytochrome p450 reductase-like	0	DIRECT
Cytidylyltransferase	0	DIRECT
AMPKBI-like	0	DIRECT
Prokaryotic type KH domain (KH-domain type II)	0	DIRECT
D-ribulose-5-phosphate 3-epimerase	0	DIRECT
Chalcone isomerase	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
Clathrin coat assembly domain	0	DIRECT
Molybdenum-containing oxidoreductases-like dimerisation domain	0	DIRECT
Ribosomal protein L19	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Allosteric chorismate mutase	0	DIRECT
Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	0	DIRECT
RraA-like	0	DIRECT
Class I aldolase	0	DIRECT
Oxygen-evolving enhancer protein 3,	0	DIRECT
monodomain cytochrome c	0	DIRECT
Ribosomal protein L37e	0	DIRECT
Diacylglycerol kinase-like	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
L23p	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
DNA polymerase III clamp loader subunits, C-terminal domain	0	DIRECT
RelA/SpoT domain	0	DIRECT
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0	DIRECT
NadC N-terminal domain-like	0	DIRECT
G domain-linked domain	0	DIRECT
IF2B-like	0	DIRECT
Ran-binding domain	0	DIRECT
Ribosomal protein L4	0	DIRECT
EDF1-like	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
alpha-Amylases, C-terminal beta-sheet domain	0	DIRECT
E2F dimerization segment	0	DIRECT
Peptidyl-tRNA hydrolase II	0	DIRECT
WrbA-like	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
FKBP immunophilin/proline isomerase	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Rps19E-like	0	DIRECT
eIF1-like	0	DIRECT
(Glycosyl)asparaginase	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Deoxycytidylate deaminase-like	0	DIRECT
ATP sulfurylase N-terminal domain	0	DIRECT
Pentapeptide repeats	0	DIRECT
6-phosphogluconate dehydrogenase-like, N-terminal domain	0	DIRECT
Ribosomal protein S27e	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
Prolyl oligopeptidase, C-terminal domain	0	DIRECT
Ribosomal protein S2	0	DIRECT
BphP N-terminal domain-like	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
RNase Z-like	0	DIRECT
Group II chaperonin (CCT, TRIC), apical domain	0	DIRECT
MYND zinc finger	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Cdc48 N-terminal domain-like	0	DIRECT
Signal peptide-binding domain	0	DIRECT
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains	0	DIRECT
Aminoacid dehydrogenases	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
Chaperone J-domain	0.0001641	DIRECT
Sm motif of small nuclear ribonucleoproteins, SNRNP	0.0003359	DIRECT
Mitochondrial carrier	0.000428	DIRECT
Biotinyl/lipoyl-carrier proteins and domains	0.0005116	DIRECT
WD40-repeat	0.0005917	DIRECT

Trees by TreeVector

A presence/absence matrix is generated using protein domain architecture data for all genomes in SUPERFAMILY. The PAUP software is used to produce a single, large tree topology using heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as if individual trees had been produced. However, this data is extracted from the single large tree. This produces a higher quality topology than if the trees had been produced on their own, and allows the trees to be displayed instantly.

Supra-domains annotated to this AP term (Not in SPAP)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
LigT-like	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
GroEL apical domain-like	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
Ribosomal protein L39e	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
SIS domain	0	DIRECT
SH3-domain	0	DIRECT
Ribosomal protein S2	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
SAM/Pointed domain	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Chalcone isomerase	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
HesB-like domain	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
Chorismate mutase II	0	DIRECT
FF domain	0	DIRECT
Rubredoxin-like	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
Supernatant protein factor (SPF), C-terminal domain	0	DIRECT
tRNA-binding arm	0	DIRECT
GroEL equatorial domain-like	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
L28p-like	0	DIRECT
YrdC/RibB	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
FAH	0	DIRECT
BolA-like	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
Prokaryotic type KH domain (KH-domain type II)	0	DIRECT
Folate-binding domain	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
Ribosomal protein L14	0	DIRECT
NHL repeat	0	DIRECT
LuxS/MPP-like metallohydrolase	0	DIRECT
ADC-like	0	DIRECT
AMPKBI-like	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
Chelatase	0	DIRECT
RplX-like	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
Signal peptide-binding domain	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
RibA-like	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
R3H domain	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
LeuD/IlvD-like	0	DIRECT
E2F-DP heterodimerization region	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Oxygen-evolving enhancer protein 3,	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
S13-like H2TH domain	0	DIRECT
Mog1p/PsbP-like	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Cryptochrome/photolyase, N-terminal domain	0	DIRECT
Tautomerase/MIF	0	DIRECT
Ribosomal protein L31e	0	DIRECT
CYTH-like phosphatases	0	DIRECT
Ribosomal protein L16p/L10e	0	DIRECT
Alpha-L RNA-binding motif	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Lipocalins	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
GroEL-intermediate domain like	0	DIRECT
eIF1-like	0	DIRECT
Peptidyl-tRNA hydrolase II	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Ribosomal protein L13	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Ribosomal protein L4	0	DIRECT
FKBP-like	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
S15/NS1 RNA-binding domain	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
RraA-like	0	DIRECT
XPC-binding domain	0	DIRECT
BSD domain-like	0	DIRECT
Putative isomerase YbhE	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
alpha-helical ferredoxin	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
LysM domain	0	DIRECT
Ribosomal protein L1	0	DIRECT
AF1104-like	0	DIRECT
GlnB-like	0	DIRECT
Peptidase/esterase 'gauge' domain	0	DIRECT
Ribosomal protein S6	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
Electron transport accessory proteins	0	DIRECT
Amine oxidase catalytic domain	0	DIRECT
Tim10-like	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Flavoproteins	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
Cytochrome c	0	DIRECT
Release factor	0	DIRECT
RNA-binding domain, RBD	5.84e-05	DIRECT
ACT-like	0.0001347	DIRECT
Chaperone J-domain	0.0001751	DIRECT
Mitochondrial carrier	0.0003401	DIRECT
Single hybrid motif	0.0005491	DIRECT

Supra-domains annotated to this AP term (Not in SPAP)
Highlighted in gray are those with FDR>0.001

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases	0	DIRECT
55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase	0	DIRECT
81698,81698 81698 - FF domain 81698 - FF domain	0	DIRECT
52402,52833 52402 - Adenine nucleotide alpha hydrolases-like 52833 - Thioredoxin-like	0	DIRECT
64356,49447 64356 - SNARE-like 49447 - Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like	0	DIRECT
101238,46934 101238 - XPC-binding domain 46934 - UBA-like	0	DIRECT
47473,103506 47473 - EF-hand 103506 - Mitochondrial carrier	0	DIRECT
53732,52016 53732 - Aconitase iron-sulfur domain 52016 - LeuD/IlvD-like	0	DIRECT
81995,81811 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24	0	DIRECT
53633,55021 53633 - Carbamate kinase-like 55021 - ACT-like	0	DIRECT
48371,50978 48371 - ARM repeat 50978 - WD40 repeat-like	0	DIRECT
48452,46565 48452 - TPR-like 46565 - Chaperone J-domain	0	DIRECT
109604,81301 109604 - HD-domain/PDEase-like 81301 - Nucleotidyltransferase	0	DIRECT
50156,52096 50156 - PDZ domain-like 52096 - ClpP/crotonase	0	DIRECT
51338,51556 51338 - Composite domain of metallo-dependent hydrolases 51556 - Metallo-dependent hydrolases	0	DIRECT
52172,52172 52172 - CheY-like 52172 - CheY-like	0	DIRECT
158702,81296 158702 - Sec63 N-terminal domain-like 81296 - E set domains	0	DIRECT
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0	DIRECT
50249,55681 50249 - Nucleic acid-binding proteins 55681 - Class II aaRS and biotin synthetases	0	DIRECT
48452,54277 48452 - TPR-like 54277 - CAD & PB1 domains	0	DIRECT
54160,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
49899,63887 49899 - Concanavalin A-like lectins/glucanases 63887 - P-domain of calnexin/calreticulin	0	DIRECT
54534,48452 54534 - FKBP-like 48452 - TPR-like	0	DIRECT
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like	0	DIRECT
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
63411,63411 63411 - LuxS/MPP-like metallohydrolase 63411 - LuxS/MPP-like metallohydrolase	0	DIRECT
50249,57756 50249 - Nucleic acid-binding proteins 57756 - Retrovirus zinc finger-like domains	0	DIRECT
50993,53474 50993 - Peptidase/esterase 'gauge' domain 53474 - alpha/beta-Hydrolases	0	DIRECT
143548,55021 143548 - Serine metabolism enzymes domain 55021 - ACT-like	0	DIRECT
50729,57863 50729 - PH domain-like 57863 - ArfGap/RecO-like zinc finger	0	DIRECT
81383,54518 81383 - F-box domain 54518 - Tubby C-terminal domain-like	0	DIRECT
53850,55021 53850 - Periplasmic binding protein-like II 55021 - ACT-like	0	DIRECT
82171,53474 82171 - DPP6 N-terminal domain-like 53474 - alpha/beta-Hydrolases	0	DIRECT
52425,48173 52425 - Cryptochrome/photolyase, N-terminal domain 48173 - Cryptochrome/photolyase FAD-binding domain	0	DIRECT
88697,52374 88697 - PUA domain-like 52374 - Nucleotidylyl transferase	0	DIRECT
81811,82754 81811 - Helical domain of Sec23/24 82754 - C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
117916,117916 117916 - Fe-S cluster assembly (FSCA) domain-like 117916 - Fe-S cluster assembly (FSCA) domain-like	0	DIRECT
55021,56112 55021 - ACT-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
54416,49998 54416 - Amine oxidase N-terminal region 49998 - Amine oxidase catalytic domain	0	DIRECT
54980,54980 54980 - EF-G C-terminal domain-like 54980 - EF-G C-terminal domain-like	0	DIRECT
52540,48403 52540 - P-loop containing nucleoside triphosphate hydrolases 48403 - Ankyrin repeat	0	DIRECT
53223,51735 53223 - Aminoacid dehydrogenase-like, N-terminal domain 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
82199,81822 82199 - SET domain 81822 - RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
88798,50249 88798 - N-terminal, heterodimerisation domain of RBP7 (RpoE) 50249 - Nucleic acid-binding proteins	0	DIRECT
56524,81296 56524 - Oxidoreductase molybdopterin-binding domain 81296 - E set domains	0	DIRECT
57863,48403 57863 - ArfGap/RecO-like zinc finger 48403 - Ankyrin repeat	0	DIRECT
101908,56219 101908 - Putative isomerase YbhE 56219 - DNase I-like	0	DIRECT
53383,53383 53383 - PLP-dependent transferases 53383 - PLP-dependent transferases	0	DIRECT
48403,52540 48403 - Ankyrin repeat 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
47661,58038 47661 - t-snare proteins 58038 - SNARE fusion complex	0	DIRECT
55785,55781 55785 - PYP-like sensor domain (PAS domain) 55781 - GAF domain-like	0	DIRECT
48179,52413 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 52413 - UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
55781,47384 55781 - GAF domain-like 47384 - Homodimeric domain of signal transducing histidine kinase	0	DIRECT
54747,46906 54747 - Ribosomal L11/L12e N-terminal domain 46906 - Ribosomal protein L11, C-terminal domain	0	DIRECT
51735,143548 51735 - NAD(P)-binding Rossmann-fold domains 143548 - Serine metabolism enzymes domain	0	DIRECT
52540,52058 52540 - P-loop containing nucleoside triphosphate hydrolases 52058 - L domain-like	0	DIRECT
55785,55785 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
63737,55486 63737 - Leukotriene A4 hydrolase N-terminal domain 55486 - Metalloproteases ("zincins"), catalytic domain	0	DIRECT
53300,81995 53300 - vWA-like 81995 - beta-sandwich domain of Sec23/24	0	DIRECT
55874,52172 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 52172 - CheY-like	0	DIRECT
50022,55961 50022 - ISP domain 55961 - Bet v1-like	0	DIRECT
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region	0	DIRECT
56112,48371 56112 - Protein kinase-like (PK-like) 48371 - ARM repeat	0	DIRECT
56059,52210 56059 - Glutathione synthetase ATP-binding domain-like 52210 - Succinyl-CoA synthetase domains	0	DIRECT
52540,47446 52540 - P-loop containing nucleoside triphosphate hydrolases 47446 - Signal peptide-binding domain	0	DIRECT
58014,51064 58014 - Coiled-coil domain of nucleotide exchange factor GrpE 51064 - Head domain of nucleotide exchange factor GrpE	0	DIRECT
47592,159042 47592 - SWIB/MDM2 domain 159042 - Plus3-like	0	DIRECT
101690,69065 101690 - PAZ domain 69065 - RNase III domain-like	0	DIRECT
88659,88659 88659 - Sigma3 and sigma4 domains of RNA polymerase sigma factors 88659 - Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
46785,158702 46785 - "Winged helix" DNA-binding domain 158702 - Sec63 N-terminal domain-like	0	DIRECT
52087,101576 52087 - CRAL/TRIO domain 101576 - Supernatant protein factor (SPF), C-terminal domain	0	DIRECT
88946,88659 88946 - Sigma2 domain of RNA polymerase sigma factors 88659 - Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
53738,53738 53738 - Phosphoglucomutase, first 3 domains 53738 - Phosphoglucomutase, first 3 domains	0	DIRECT
48403,57850 48403 - Ankyrin repeat 57850 - RING/U-box	0	DIRECT
50104,50249 50104 - Translation proteins SH3-like domain 50249 - Nucleic acid-binding proteins	0	DIRECT
81995,82919 81995 - beta-sandwich domain of Sec23/24 82919 - Zn-finger domain of Sec23/24	0	DIRECT
51045,51045 51045 - WW domain 51045 - WW domain	0	DIRECT
54160,54160 54160 - Chromo domain-like 54160 - Chromo domain-like	0	DIRECT
55781,55785 55781 - GAF domain-like 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
55821,142695 55821 - YrdC/RibB 142695 - RibA-like	0	DIRECT
81296,51445 81296 - E set domains 51445 - (Trans)glycosidases	0	DIRECT
52540,90002 52540 - P-loop containing nucleoside triphosphate hydrolases 90002 - Hypothetical protein YjiA, C-terminal domain	0	DIRECT
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54909,54909 54909 - Dimeric alpha+beta barrel 54909 - Dimeric alpha+beta barrel	0	DIRECT
53738,55957 53738 - Phosphoglucomutase, first 3 domains 55957 - Phosphoglucomutase, C-terminal domain	0	DIRECT
102848,54236 102848 - NSFL1 (p97 ATPase) cofactor p47, SEP domain 54236 - Ubiquitin-like	0	DIRECT
158702,52540 158702 - Sec63 N-terminal domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54416,54416 54416 - Amine oxidase N-terminal region 54416 - Amine oxidase N-terminal region	0	DIRECT
158639,63748 158639 - ENT-like 63748 - Tudor/PWWP/MBT	0	DIRECT
81296,52540 81296 - E set domains 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
103657,50729 103657 - BAR/IMD domain-like 50729 - PH domain-like	0	DIRECT
82919,53300 82919 - Zn-finger domain of Sec23/24 53300 - vWA-like	0	DIRECT
52317,52317 52317 - Class I glutamine amidotransferase-like 52317 - Class I glutamine amidotransferase-like	0	DIRECT
57850,54928 57850 - RING/U-box 54928 - RNA-binding domain, RBD	0	DIRECT
55781,55781 55781 - GAF domain-like 55781 - GAF domain-like	0	DIRECT
55920,46785 55920 - Creatinase/aminopeptidase 46785 - "Winged helix" DNA-binding domain	0	DIRECT