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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 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 (SPHO) 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:SPHO.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)
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
AlbA-like	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
Granulin repeat	0	DIRECT
Ribosomal protein L31e	0	DIRECT
Clc chloride channel	0	DIRECT
Tim10-like	0	DIRECT
GHMP Kinase, C-terminal domain	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
Cytochrome c	0	DIRECT
AMPKBI-like	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
FF domain	0	DIRECT
L9 N-domain-like	0	DIRECT
Globin-like	0	DIRECT
Folate-binding domain	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Peptidase/esterase 'gauge' domain	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
beta-N-acetylhexosaminidase-like domain	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
Ribosomal protein L39e	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
LDH C-terminal domain-like	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
SH3-domain	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Glutamine synthetase/guanido kinase	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
Tautomerase/MIF	0	DIRECT
Ribosomal protein L13	0	DIRECT
Electron transport accessory proteins	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
NHL repeat	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Ribosomal protein S2	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
RraA-like	0	DIRECT
Ribosomal protein L14	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
ADC-like	0	DIRECT
R3H domain	0	DIRECT
PABC (PABP) domain	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Flavoproteins	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
FKBP-like	0	DIRECT
eIF1-like	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
alpha-helical ferredoxin	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
Ribosomal protein L4	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
BolA-like	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
S13-like H2TH domain	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
GlnB-like	0	DIRECT
HesB-like domain	0	DIRECT
Acyl-CoA binding protein	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Putative isomerase YbhE	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
YrdC/RibB	0	DIRECT
tRNA-binding arm	0	DIRECT
Chelatase	0	DIRECT
CYTH-like phosphatases	0	DIRECT
Single hybrid motif	0	DIRECT
XPC-binding domain	0	DIRECT
E2F-DP heterodimerization region	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
RibA-like	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
Signal peptide-binding domain	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
Chorismate mutase II	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
LeuD/IlvD-like	0	DIRECT
Lipoxigenase	0	DIRECT
SMR domain-like	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
Phosphofructokinase	0	DIRECT
PAP/Archaeal CCA-adding enzyme, C-terminal domain	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
LysM domain	0	DIRECT
Lipocalins	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Ribosomal protein S6	0	DIRECT
ADC synthase	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Ribosomal protein L16p/L10e	0	DIRECT
RNA-binding domain, RBD	0.0001453	DIRECT
NAD(P)-binding Rossmann-fold domains	0.001539	INHERITED FROM: carpel
Mitochondrial carrier	0.01166	INHERITED FROM: carpel
Thioredoxin-like	0.01266	INHERITED FROM: carpel
ClpP/crotonase	0.02028	INHERITED FROM: carpel
GroEL apical domain-like	0.02839	INHERITED FROM: carpel
FtsH protease domain-like	0.04229	INHERITED FROM: carpel
Terpenoid synthases	1	INHERITED FROM: stigma
Subtilisin-like	1	INHERITED FROM: style
HLH, helix-loop-helix DNA-binding domain	1	INHERITED FROM: portion of transmitting tissue
Homeodomain-like	1	INHERITED FROM: ovary replum || style
Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin	1	INHERITED FROM: style
Terpenoid cyclases/Protein prenyltransferases	1	INHERITED FROM: stigma
DNA-binding pseudobarrel domain	1	INHERITED FROM: ovary placenta || plant ovary

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)
Ribosomal protein L31e	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
HEAT repeat	0	DIRECT
Choline kinase	0	DIRECT
LEA14-like	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
E2F dimerization segment	0	DIRECT
PCI domain (PINT motif)	0	DIRECT
Ribosomal protein S13	0	DIRECT
Allosteric chorismate mutase	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Spermidine synthase	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
MIF-related	0	DIRECT
Aminoacid dehydrogenases	0	DIRECT
Prolyl oligopeptidase, N-terminal domain	0	DIRECT
Cystatins	0	DIRECT
beta-sandwich domain of Sec23/24	0	DIRECT
La domain	0	DIRECT
RNB domain-like	0	DIRECT
RhoGDI-like	0	DIRECT
Poly(A) polymerase, PAP, middle domain	0	DIRECT
GHMP Kinase, N-terminal domain	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Phosphofructokinase	0	DIRECT
SerA intervening domain-like	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Methionine aminopeptidase, insert domain	0	DIRECT
LON domain-like	0	DIRECT
GDI-like N domain	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
gamma-carbonic anhydrase-like	0	DIRECT
Lipoxigenase N-terminal domain	0	DIRECT
Clc chloride channel	0	DIRECT
Ran-binding domain	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
RWD domain	0	DIRECT
DNA repair glycosylase, 2 C-terminal domains	0	DIRECT
ATP sulfurylase catalytic domain	0	DIRECT
Starch-binding domain	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Succinyl-CoA synthetase, beta-chain, N-terminal domain	0	DIRECT
Receiver domain of the ethylene receptor	0	DIRECT
Ubiquitin carboxyl-terminal hydrolase UCH-L	0	DIRECT
Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	0	DIRECT
L23p	0	DIRECT
Glyoxalase II (hydroxyacylglutathione hydrolase)	0	DIRECT
Thioredoxin-like 2Fe-2S ferredoxin	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Transcriptional coactivator PC4 C-terminal domain	0	DIRECT
Aminomethyltransferase folate-binding domain	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
RNase Z-like	0	DIRECT
Signal peptide-binding domain	0	DIRECT
IPP isomerase-like	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
MYND zinc finger	0	DIRECT
2Fe-2S ferredoxin-related	0	DIRECT
GAF domain	0	DIRECT
rRNA adenine dimethylase-like	0	DIRECT
Phosphoenolpyruvate carboxylase	0	DIRECT
PAPS reductase-like	0	DIRECT
STAR domain	0	DIRECT
Ribosomal protein L3	0	DIRECT
BolA-like	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
FKBP immunophilin/proline isomerase	0	DIRECT
WrbA-like	0	DIRECT
Ribosomal protein L39e	0	DIRECT
BphP N-terminal domain-like	0	DIRECT
Myf domain	0	DIRECT
Cytochrome p450 reductase N-terminal domain-like	0	DIRECT
eIF1-like	0	DIRECT
Ribosomal protein S27e	0	DIRECT
Granulin repeat	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
Hypothetical protein HI1317	0	DIRECT
GABARAP-like	0	DIRECT
Ribosomal protein L10e	0	DIRECT
Folylpolyglutamate synthetase	0	DIRECT
D-ribulose-5-phosphate 3-epimerase	0	DIRECT
LDH N-terminal domain-like	0	DIRECT
3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
Acyl-ACP thioesterase-like	0	DIRECT
Molybdenum-containing oxidoreductases-like dimerisation domain	0	DIRECT
Poly(A) polymerase, PAP, C-terminal domain	0	DIRECT
GroES	0	DIRECT
Cytidylyltransferase	0	DIRECT
PABC (PABP) domain	0	DIRECT
NHL repeat	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
Thiolase-related	0	DIRECT
AlkB-like	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
LysM domain	0	DIRECT
Group II chaperonin (CCT, TRIC), ATPase domain	0	DIRECT
PUA domain	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
HAT/Suf repeat	0	DIRECT
Pentapeptide repeats	0	DIRECT
ADC synthase	0	DIRECT
Cation efflux protein cytoplasmic domain-like	0	DIRECT
Ribosomal protein L37e	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
Pseudouridine synthase II TruB	0	DIRECT
CoA-binding domain	0	DIRECT
Rubredoxin	0	DIRECT
Ring hydroxylating alpha subunit ISP domain	0	DIRECT
DNase I-like	0	DIRECT
NADPH-cytochrome p450 reductase FAD-binding domain-like	0	DIRECT
Sedlin (SEDL)	0	DIRECT
Biotinyl/lipoyl-carrier proteins and domains	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
ZZ domain	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
Subtilase propeptides/inhibitors	0	DIRECT
Chromo barrel domain	0	DIRECT
Ribosomal protein L14	0	DIRECT
Branched-chain alpha-keto acid dehydrogenase Pyr module	0	DIRECT
5' nucleotidase-like	0	DIRECT
Gtf glycosyltransferase	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase dimerisation domain	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
Poly(ADP-ribose) polymerase, C-terminal domain	0	DIRECT
Prolyl oligopeptidase, C-terminal domain	0	DIRECT
R3H domain	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Class-II DAHP synthetase	0	DIRECT
Glycosyl hydrolases family 32 C-terminal domain	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
Calnexin/calreticulin	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
RelA/SpoT domain	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Universal stress protein-like	0	DIRECT
Cdc48 N-terminal domain-like	0	DIRECT
Ribosomal protein S6	0	DIRECT
Plant lipoxigenases	0	DIRECT
Ribosomal protein S15	0	DIRECT
Dihydrodipicolinate reductase-like	0	DIRECT
Biotin dependent carboxylase carboxyltransferase domain	0	DIRECT
Adenosine-5'phosphosulfate kinase (APS kinase)	0	DIRECT
N-type ATP pyrophosphatases	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
glucose-1-phosphate thymidylyltransferase	0	DIRECT
Trunk domain of Sec23/24	0	DIRECT
Sec63 N-terminal domain	0	DIRECT
Plant stress-induced protein	0	DIRECT
AMPK-beta glycogen binding domain-like	0	DIRECT
Ribosomal protein L4	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
(Glycosyl)asparaginase	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Plant transcriptional regulator PBF-2	0	DIRECT
Glycerol-3-phosphate dehydrogenase	0	DIRECT
HesB-like domain	0	DIRECT
Glyoxalase I (lactoylglutathione lyase)	0	DIRECT
LIM domain	0	DIRECT
Tim10/DDP	0	DIRECT
1,3-glucuronyltransferase	0	DIRECT
Clp protease, ClpP subunit	0	DIRECT
Acyl-CoA binding protein	0	DIRECT
Galactosyltransferase LgtC	0	DIRECT
YicI N-terminal domain-like	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
ATP sulfurylase N-terminal domain	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), catalytic domain	0	DIRECT
LeuD-like	0	DIRECT
Smr domain	0	DIRECT
PdxS-like	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
CAT-like	0	DIRECT
Ribosomal protein S2	0	DIRECT
Smc hinge domain	0	DIRECT
Glutamine synthetase catalytic domain	0	DIRECT
NADPH-cytochrome p450 reductase-like	0	DIRECT
EDF1-like	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
GlmU C-terminal domain-like	0	DIRECT
Ribosomal protein L13	0	DIRECT
Homoserine dehydrogenase-like	0	DIRECT
Phytochrome-specific domain	0	DIRECT
beta-Phosphoglucomutase-like	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Enolase	0	DIRECT
Rps19E-like	0	DIRECT
Heme-dependent catalases	0	DIRECT
6-phosphogluconate dehydrogenase-like, N-terminal domain	0	DIRECT
beta-N-acetylhexosaminidase catalytic domain	0	DIRECT
UDP-glucose pyrophosphorylase	0	DIRECT
XPC-binding domain	0	DIRECT
Shikimate kinase (AroK)	0	DIRECT
monodomain cytochrome c	0	DIRECT
Class I alpha-1;2-mannosidase, catalytic domain	0	DIRECT
FF domain	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
alpha-Amylases, C-terminal beta-sheet domain	0	DIRECT
Anti-sigma factor antagonist SpoIIaa	0	DIRECT
RibA-like	0	DIRECT
Hypothetical protein At2g34160	0	DIRECT
PDI-like	0	DIRECT
SH3-domain	0	DIRECT
RraA-like	0	DIRECT
G domain-linked domain	0	DIRECT
Sec63 C-terminal domain-like	0	DIRECT
Leukotriene A4 hydrolase catalytic domain	0	DIRECT
Eps15 homology domain (EH domain)	0	DIRECT
B56-like	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
BAR domain	0	DIRECT
Poly(A) polymerase, PAP, N-terminal domain	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
Tail specific protease, catalytic domain	0	DIRECT
Reductases	0	DIRECT
Lactate & malate dehydrogenases, C-terminal domain	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
AMPKBI-like	0	DIRECT
Group II chaperonin (CCT, TRIC), apical domain	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
NadC C-terminal domain-like	0	DIRECT
Sigma4 domain	0	DIRECT
NadC N-terminal domain-like	0	DIRECT
Canonical RBD	0.00005758	DIRECT
G proteins	0.0008379	DIRECT
Mitochondrial carrier	0.01058	INHERITED FROM: carpel
FtsH protease domain-like	0.04237	INHERITED FROM: carpel
Subtilases	1	INHERITED FROM: style
Homeodomain	1	INHERITED FROM: style
HLH, helix-loop-helix DNA-binding domain	1	INHERITED FROM: portion of transmitting tissue
Terpenoid cyclase N-terminal domain	1	INHERITED FROM: stigma
Plant lipid-transfer and hydrophobic proteins	1	INHERITED FROM: style
B3 DNA binding domain	1	INHERITED FROM: ovary placenta || plant ovary
Terpenoid cyclase C-terminal domain	1	INHERITED FROM: stigma

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 (SPAP level: Least Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Tim10-like	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Single hybrid motif	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
Glutamine synthetase/guanido kinase	0	DIRECT
Cytochrome c	0	DIRECT
Clc chloride channel	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Lipocalins	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
GHMP Kinase, C-terminal domain	0	DIRECT
Signal peptide-binding domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
SH3-domain	0	DIRECT
FKBP-like	0	DIRECT
FF domain	0	DIRECT
PABC (PABP) domain	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Ribosomal protein S6	0	DIRECT
Electron transport accessory proteins	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
Globin-like	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
Acyl-CoA binding protein	0	DIRECT
Ribosomal protein L4	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
NHL repeat	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
eIF1-like	0	DIRECT
Ribosomal protein L31e	0	DIRECT
RibA-like	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
alpha-helical ferredoxin	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
Chelatase	0	DIRECT
R3H domain	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
Putative isomerase YbhE	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
Phosphofructokinase	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Tautomerase/MIF	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Folate-binding domain	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
L9 N-domain-like	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
AMPKBI-like	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
PAP/Archaeal CCA-adding enzyme, C-terminal domain	0	DIRECT
ADC-like	0	DIRECT
XPC-binding domain	0	DIRECT
YrdC/RibB	0	DIRECT
LeuD/IlvD-like	0	DIRECT
S13-like H2TH domain	0	DIRECT
Ribosomal protein L16p/L10e	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
Ribosomal protein L39e	0	DIRECT
RraA-like	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
LDH C-terminal domain-like	0	DIRECT
E2F-DP heterodimerization region	0	DIRECT
Chorismate mutase II	0	DIRECT
beta-N-acetylhexosaminidase-like domain	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
BolA-like	0	DIRECT
HesB-like domain	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
ADC synthase	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
tRNA-binding arm	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
Ribosomal protein L14	0	DIRECT
Granulin repeat	0	DIRECT
SMR domain-like	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
GlnB-like	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
AlbA-like	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
LysM domain	0	DIRECT
CYTH-like phosphatases	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Flavoproteins	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
Ribosomal protein L13	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Lipoxigenase	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
Ribosomal protein S2	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
Peptidase/esterase 'gauge' domain	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
RNA-binding domain, RBD	0.000114	DIRECT
NAD(P)-binding Rossmann-fold domains	0.001223	INHERITED FROM: carpel
Nucleotidylyl transferase	0.002915	INHERITED FROM: carpel
Mitochondrial carrier	0.009466	INHERITED FROM: carpel
Thioredoxin-like	0.0103	INHERITED FROM: carpel
Metallo-hydrolase/oxidoreductase	0.01555	INHERITED FROM: carpel
ClpP/crotonase	0.01665	INHERITED FROM: carpel
GroEL apical domain-like	0.02351	INHERITED FROM: carpel
FtsH protease domain-like	0.03542	INHERITED FROM: carpel
Subtilisin-like	1	INHERITED FROM: style
Terpenoid synthases	1	INHERITED FROM: stigma
Homeodomain-like	1	INHERITED FROM: ovary replum || style
Terpenoid cyclases/Protein prenyltransferases	1	INHERITED FROM: stigma
DNA-binding pseudobarrel domain	1	INHERITED FROM: plant ovary || ovary placenta
HLH, helix-loop-helix DNA-binding domain	1	INHERITED FROM: portion of transmitting tissue || style
Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin	1	INHERITED FROM: style

Supra-domains annotated to this AP term (SPAP level: Least Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
50022,55961 50022 - ISP domain 55961 - Bet v1-like	0	DIRECT
46785,54928 46785 - "Winged helix" DNA-binding domain 54928 - RNA-binding domain, RBD	0	DIRECT
81995,82919 81995 - beta-sandwich domain of Sec23/24 82919 - Zn-finger domain of Sec23/24	0	DIRECT
56059,52210 56059 - Glutathione synthetase ATP-binding domain-like 52210 - Succinyl-CoA synthetase domains	0	DIRECT
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
81631,55003 81631 - PAP/OAS1 substrate-binding domain 55003 - PAP/Archaeal CCA-adding enzyme, C-terminal domain	0	DIRECT
55821,142695 55821 - YrdC/RibB 142695 - RibA-like	0	DIRECT
55781,55785 55781 - GAF domain-like 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
54368,55931 54368 - Glutamine synthetase, N-terminal domain 55931 - Glutamine synthetase/guanido kinase	0	DIRECT
57850,46689 57850 - RING/U-box 46689 - Homeodomain-like	0	DIRECT
82919,53300 82919 - Zn-finger domain of Sec23/24 53300 - vWA-like	0	DIRECT
81296,51445 81296 - E set domains 51445 - (Trans)glycosidases	0	DIRECT
48403,57850 48403 - Ankyrin repeat 57850 - RING/U-box	0	DIRECT
53732,52016 53732 - Aconitase iron-sulfur domain 52016 - LeuD/IlvD-like	0	DIRECT
48403,52540 48403 - Ankyrin repeat 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54747,46906 54747 - Ribosomal L11/L12e N-terminal domain 46906 - Ribosomal protein L11, C-terminal domain	0	DIRECT
101908,56219 101908 - Putative isomerase YbhE 56219 - DNase I-like	0	DIRECT
56524,81296 56524 - Oxidoreductase molybdopterin-binding domain 81296 - E set domains	0	DIRECT
53300,57850 53300 - vWA-like 57850 - RING/U-box	0	DIRECT
53738,55957 53738 - Phosphoglucomutase, first 3 domains 55957 - Phosphoglucomutase, C-terminal domain	0	DIRECT
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like	0	DIRECT
47661,58038 47661 - t-snare proteins 58038 - SNARE fusion complex	0	DIRECT
54001,57277 54001 - Cysteine proteinases 57277 - Granulin repeat	0	DIRECT
100950,75445 100950 - NagB/RpiA/CoA transferase-like 75445 - D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
158702,52540 158702 - Sec63 N-terminal domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
82199,81822 82199 - SET domain 81822 - RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
49899,63887 49899 - Concanavalin A-like lectins/glucanases 63887 - P-domain of calnexin/calreticulin	0	DIRECT
81383,54518 81383 - F-box domain 54518 - Tubby C-terminal domain-like	0	DIRECT
63737,55486 63737 - Leukotriene A4 hydrolase N-terminal domain 55486 - Metalloproteases ("zincins"), catalytic domain	0	DIRECT
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	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
51735,48179 51735 - NAD(P)-binding Rossmann-fold domains 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
58014,51064 58014 - Coiled-coil domain of nucleotide exchange factor GrpE 51064 - Head domain of nucleotide exchange factor GrpE	0	DIRECT
50729,57863 50729 - PH domain-like 57863 - ArfGap/RecO-like zinc finger	0	DIRECT
47473,103506 47473 - EF-hand 103506 - Mitochondrial carrier	0	DIRECT
55785,55781 55785 - PYP-like sensor domain (PAS domain) 55781 - GAF domain-like	0	DIRECT
46785,158702 46785 - "Winged helix" DNA-binding domain 158702 - Sec63 N-terminal domain-like	0	DIRECT
51045,51045 51045 - WW domain 51045 - WW domain	0	DIRECT
54160,54160 54160 - Chromo domain-like 54160 - Chromo domain-like	0	DIRECT
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases	0	DIRECT
53300,81995 53300 - vWA-like 81995 - beta-sandwich domain of Sec23/24	0	DIRECT
50249,57756 50249 - Nucleic acid-binding proteins 57756 - Retrovirus zinc finger-like domains	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
143548,55021 143548 - Serine metabolism enzymes domain 55021 - ACT-like	0	DIRECT
109604,81301 109604 - HD-domain/PDEase-like 81301 - Nucleotidyltransferase	0	DIRECT
53448,51161 53448 - Nucleotide-diphospho-sugar transferases 51161 - Trimeric LpxA-like enzymes	0	DIRECT
54909,54909 54909 - Dimeric alpha+beta barrel 54909 - Dimeric alpha+beta barrel	0	DIRECT
117916,117916 117916 - Fe-S cluster assembly (FSCA) domain-like 117916 - Fe-S cluster assembly (FSCA) domain-like	0	DIRECT
46689,51905 46689 - Homeodomain-like 51905 - FAD/NAD(P)-binding domain	0	DIRECT
52374,47323 52374 - Nucleotidylyl transferase 47323 - Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0	DIRECT
50249,55681 50249 - Nucleic acid-binding proteins 55681 - Class II aaRS and biotin synthetases	0	DIRECT
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region	0	DIRECT
51735,143548 51735 - NAD(P)-binding Rossmann-fold domains 143548 - Serine metabolism enzymes domain	0	DIRECT
52540,90002 52540 - P-loop containing nucleoside triphosphate hydrolases 90002 - Hypothetical protein YjiA, C-terminal domain	0	DIRECT
52540,52317 52540 - P-loop containing nucleoside triphosphate hydrolases 52317 - Class I glutamine amidotransferase-like	0	DIRECT
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0	DIRECT
57850,54928 57850 - RING/U-box 54928 - RNA-binding domain, RBD	0	DIRECT
88798,50249 88798 - N-terminal, heterodimerisation domain of RBP7 (RpoE) 50249 - Nucleic acid-binding proteins	0	DIRECT
55021,56112 55021 - ACT-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
52833,52833 52833 - Thioredoxin-like 52833 - Thioredoxin-like	0	DIRECT
49723,48484 49723 - Lipase/lipooxygenase domain (PLAT/LH2 domain) 48484 - Lipoxigenase	0	DIRECT
57863,48403 57863 - ArfGap/RecO-like zinc finger 48403 - Ankyrin repeat	0	DIRECT
102848,54236 102848 - NSFL1 (p97 ATPase) cofactor p47, SEP domain 54236 - Ubiquitin-like	0	DIRECT
101238,46934 101238 - XPC-binding domain 46934 - UBA-like	0	DIRECT
52540,47446 52540 - P-loop containing nucleoside triphosphate hydrolases 47446 - Signal peptide-binding domain	0	DIRECT
54980,54980 54980 - EF-G C-terminal domain-like 54980 - EF-G C-terminal domain-like	0	DIRECT
158639,63748 158639 - ENT-like 63748 - Tudor/PWWP/MBT	0	DIRECT
54534,48452 54534 - FKBP-like 48452 - TPR-like	0	DIRECT
55920,46785 55920 - Creatinase/aminopeptidase 46785 - "Winged helix" DNA-binding domain	0	DIRECT
55545,51445 55545 - beta-N-acetylhexosaminidase-like domain 51445 - (Trans)glycosidases	0	DIRECT
88697,52374 88697 - PUA domain-like 52374 - Nucleotidylyl transferase	0	DIRECT
158702,81296 158702 - Sec63 N-terminal domain-like 81296 - E set domains	0	DIRECT
81698,81698 81698 - FF domain 81698 - FF domain	0	DIRECT
52540,48340 52540 - P-loop containing nucleoside triphosphate hydrolases 48340 - Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
56219,56219 56219 - DNase I-like 56219 - DNase I-like	0	DIRECT
55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase	0	DIRECT
48179,52413 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 52413 - UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
52540,48403 52540 - P-loop containing nucleoside triphosphate hydrolases 48403 - Ankyrin repeat	0	DIRECT
81296,52540 81296 - E set domains 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
53850,55021 53850 - Periplasmic binding protein-like II 55021 - ACT-like	0	DIRECT
56112,48371 56112 - Protein kinase-like (PK-like) 48371 - ARM repeat	0	DIRECT
88946,88659 88946 - Sigma2 domain of RNA polymerase sigma factors 88659 - Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
81811,82754 81811 - Helical domain of Sec23/24 82754 - C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
54211,55060 54211 - Ribosomal protein S5 domain 2-like 55060 - GHMP Kinase, C-terminal domain	0	DIRECT
52743,52025 52743 - Subtilisin-like 52025 - PA domain	0	DIRECT
55874,52172 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 52172 - CheY-like	0	DIRECT
52025,57850 52025 - PA domain 57850 - RING/U-box	0	DIRECT
53383,53383 53383 - PLP-dependent transferases 53383 - PLP-dependent transferases	0	DIRECT
81923,52540 81923 - Double Clp-N motif 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54160,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54236,63491 54236 - Ubiquitin-like 63491 - BAG domain	0	DIRECT
101690,69065 101690 - PAZ domain 69065 - RNase III domain-like	0	DIRECT
52425,48173 52425 - Cryptochrome/photolyase, N-terminal domain 48173 - Cryptochrome/photolyase FAD-binding domain	0	DIRECT
50729,55961 50729 - PH domain-like 55961 - Bet v1-like	0	DIRECT
141673,50800 141673 - MOSC N-terminal domain-like 50800 - PK beta-barrel domain-like	0	DIRECT
55785,55785 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
55781,47384 55781 - GAF domain-like 47384 - Homodimeric domain of signal transducing histidine kinase	0	DIRECT
50993,53474 50993 - Peptidase/esterase 'gauge' domain 53474 - alpha/beta-Hydrolases	0	DIRECT
51735,56327 51735 - NAD(P)-binding Rossmann-fold domains 56327 - LDH C-terminal domain-like	0	DIRECT
53738,53738 53738 - Phosphoglucomutase, first 3 domains 53738 - Phosphoglucomutase, first 3 domains	0	DIRECT
103657,50729 103657 - BAR/IMD domain-like 50729 - PH domain-like	0	DIRECT
55781,55781 55781 - GAF domain-like 55781 - GAF domain-like	0	DIRECT
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
82171,53474 82171 - DPP6 N-terminal domain-like 53474 - alpha/beta-Hydrolases	0	DIRECT
81995,81811 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24	0	DIRECT
52172,52172 52172 - CheY-like 52172 - CheY-like	0	DIRECT
50156,52096 50156 - PDZ domain-like 52096 - ClpP/crotonase	0	DIRECT
52540,52058 52540 - P-loop containing nucleoside triphosphate hydrolases 52058 - L domain-like	0	DIRECT
48239,48576 48239 - Terpenoid cyclases/Protein prenyltransferases 48576 - Terpenoid synthases	1	INHERITED FROM: stigma