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

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

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)
Homocysteine S-methyltransferase	0	DIRECT
Ribosomal protein L31e	0	DIRECT
Ribosomal protein L13	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
FKBP-like	0	DIRECT
Ribosomal protein L14	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Ribosomal protein L39e	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Acyl-CoA binding protein	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
ADC synthase	0	DIRECT
AMPKBI-like	0	DIRECT
FF domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
L9 N-domain-like	0	DIRECT
Signal peptide-binding domain	0	DIRECT
eIF1-like	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
LDH C-terminal domain-like	0	DIRECT
S13-like H2TH domain	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
Electron transport accessory proteins	0	DIRECT
Peptidase/esterase 'gauge' domain	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
NHL repeat	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
E2F-DP heterodimerization region	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
Lipocalins	0	DIRECT
Ribosomal protein S6	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
Phosphofructokinase	0	DIRECT
Folate-binding domain	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
Chorismate mutase II	0	DIRECT
BolA-like	0	DIRECT
CYTH-like phosphatases	0	DIRECT
AlbA-like	0	DIRECT
GHMP Kinase, C-terminal domain	0	DIRECT
Ribosomal protein L16p/L10e	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
LysM domain	0	DIRECT
LeuD/IlvD-like	0	DIRECT
PAP/Archaeal CCA-adding enzyme, C-terminal domain	0	DIRECT
tRNA-binding arm	0	DIRECT
Cytochrome c	0	DIRECT
Glutamine synthetase/guanido kinase	0	DIRECT
Putative isomerase YbhE	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
Globin-like	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
Flavoproteins	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
Tim10-like	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
SH3-domain	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
Tautomerase/MIF	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
Ribosomal protein L4	0	DIRECT
YrdC/RibB	0	DIRECT
GlnB-like	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
R3H domain	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
alpha-helical ferredoxin	0	DIRECT
SMR domain-like	0	DIRECT
XPC-binding domain	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Ribosomal protein S2	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Lipoxigenase	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
beta-N-acetylhexosaminidase-like domain	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
Clc chloride channel	0	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
Single hybrid motif	0	DIRECT
RraA-like	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
PABC (PABP) domain	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
RibA-like	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Chelatase	0	DIRECT
Granulin repeat	0	DIRECT
HesB-like domain	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
ADC-like	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
Transducin (alpha subunit), insertion domain	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
Homeodomain-like	1	INHERITED FROM: style || ovary replum
Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin	1	INHERITED FROM: style
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
Terpenoid synthases	1	INHERITED FROM: stigma
Terpenoid cyclases/Protein prenyltransferases	1	INHERITED FROM: stigma
Subtilisin-like	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)
55821,142695 55821 - YrdC/RibB 142695 - RibA-like	0	DIRECT
55781,55781 55781 - GAF domain-like 55781 - GAF domain-like	0	DIRECT
158702,52540 158702 - Sec63 N-terminal domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
50022,55961 50022 - ISP domain 55961 - Bet v1-like	0	DIRECT
54001,57277 54001 - Cysteine proteinases 57277 - Granulin repeat	0	DIRECT
48403,52540 48403 - Ankyrin repeat 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
100950,75445 100950 - NagB/RpiA/CoA transferase-like 75445 - D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
53738,53738 53738 - Phosphoglucomutase, first 3 domains 53738 - Phosphoglucomutase, first 3 domains	0	DIRECT
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases	0	DIRECT
52540,52058 52540 - P-loop containing nucleoside triphosphate hydrolases 52058 - L domain-like	0	DIRECT
81631,55003 81631 - PAP/OAS1 substrate-binding domain 55003 - PAP/Archaeal CCA-adding enzyme, C-terminal domain	0	DIRECT
117916,117916 117916 - Fe-S cluster assembly (FSCA) domain-like 117916 - Fe-S cluster assembly (FSCA) domain-like	0	DIRECT
55920,46785 55920 - Creatinase/aminopeptidase 46785 - "Winged helix" DNA-binding domain	0	DIRECT
57863,48403 57863 - ArfGap/RecO-like zinc finger 48403 - Ankyrin repeat	0	DIRECT
49899,63887 49899 - Concanavalin A-like lectins/glucanases 63887 - P-domain of calnexin/calreticulin	0	DIRECT
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like	0	DIRECT
101908,56219 101908 - Putative isomerase YbhE 56219 - DNase I-like	0	DIRECT
88798,50249 88798 - N-terminal, heterodimerisation domain of RBP7 (RpoE) 50249 - Nucleic acid-binding proteins	0	DIRECT
50249,55681 50249 - Nucleic acid-binding proteins 55681 - Class II aaRS and biotin synthetases	0	DIRECT
51735,56327 51735 - NAD(P)-binding Rossmann-fold domains 56327 - LDH C-terminal domain-like	0	DIRECT
54368,55931 54368 - Glutamine synthetase, N-terminal domain 55931 - Glutamine synthetase/guanido kinase	0	DIRECT
54980,54980 54980 - EF-G C-terminal domain-like 54980 - EF-G C-terminal domain-like	0	DIRECT
53732,52016 53732 - Aconitase iron-sulfur domain 52016 - LeuD/IlvD-like	0	DIRECT
54585,52540 54585 - Cdc48 domain 2-like 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
82171,53474 82171 - DPP6 N-terminal domain-like 53474 - alpha/beta-Hydrolases	0	DIRECT
56059,52210 56059 - Glutathione synthetase ATP-binding domain-like 52210 - Succinyl-CoA synthetase domains	0	DIRECT
55785,55781 55785 - PYP-like sensor domain (PAS domain) 55781 - GAF domain-like	0	DIRECT
55781,55785 55781 - GAF domain-like 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
54236,63491 54236 - Ubiquitin-like 63491 - BAG domain	0	DIRECT
81698,81698 81698 - FF domain 81698 - FF domain	0	DIRECT
56524,81296 56524 - Oxidoreductase molybdopterin-binding domain 81296 - E set domains	0	DIRECT
55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase	0	DIRECT
57850,54928 57850 - RING/U-box 54928 - RNA-binding domain, RBD	0	DIRECT
51045,51045 51045 - WW domain 51045 - WW domain	0	DIRECT
63737,55486 63737 - Leukotriene A4 hydrolase N-terminal domain 55486 - Metalloproteases ("zincins"), catalytic domain	0	DIRECT
52540,52317 52540 - P-loop containing nucleoside triphosphate hydrolases 52317 - Class I glutamine amidotransferase-like	0	DIRECT
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region	0	DIRECT
53300,81995 53300 - vWA-like 81995 - beta-sandwich domain of Sec23/24	0	DIRECT
51735,48179 51735 - NAD(P)-binding Rossmann-fold domains 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
55874,52172 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 52172 - CheY-like	0	DIRECT
56219,56219 56219 - DNase I-like 56219 - DNase I-like	0	DIRECT
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
52540,90002 52540 - P-loop containing nucleoside triphosphate hydrolases 90002 - Hypothetical protein YjiA, C-terminal domain	0	DIRECT
81383,54518 81383 - F-box domain 54518 - Tubby C-terminal domain-like	0	DIRECT
52540,47446 52540 - P-loop containing nucleoside triphosphate hydrolases 47446 - Signal peptide-binding domain	0	DIRECT
103657,50729 103657 - BAR/IMD domain-like 50729 - PH domain-like	0	DIRECT
81995,81811 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24	0	DIRECT
52402,52833 52402 - Adenine nucleotide alpha hydrolases-like 52833 - Thioredoxin-like	0	DIRECT
81923,52540 81923 - Double Clp-N motif 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
82919,53300 82919 - Zn-finger domain of Sec23/24 53300 - vWA-like	0	DIRECT
81995,82919 81995 - beta-sandwich domain of Sec23/24 82919 - Zn-finger domain of Sec23/24	0	DIRECT
81811,82754 81811 - Helical domain of Sec23/24 82754 - C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
50156,52096 50156 - PDZ domain-like 52096 - ClpP/crotonase	0	DIRECT
52374,47323 52374 - Nucleotidylyl transferase 47323 - Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0	DIRECT
64356,49447 64356 - SNARE-like 49447 - Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0	DIRECT
46785,158702 46785 - "Winged helix" DNA-binding domain 158702 - Sec63 N-terminal domain-like	0	DIRECT
53738,55957 53738 - Phosphoglucomutase, first 3 domains 55957 - Phosphoglucomutase, C-terminal domain	0	DIRECT
50993,53474 50993 - Peptidase/esterase 'gauge' domain 53474 - alpha/beta-Hydrolases	0	DIRECT
102848,54236 102848 - NSFL1 (p97 ATPase) cofactor p47, SEP domain 54236 - Ubiquitin-like	0	DIRECT
50729,55961 50729 - PH domain-like 55961 - Bet v1-like	0	DIRECT
101238,46934 101238 - XPC-binding domain 46934 - UBA-like	0	DIRECT
53850,55021 53850 - Periplasmic binding protein-like II 55021 - ACT-like	0	DIRECT
52425,48173 52425 - Cryptochrome/photolyase, N-terminal domain 48173 - Cryptochrome/photolyase FAD-binding domain	0	DIRECT
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
52540,48340 52540 - P-loop containing nucleoside triphosphate hydrolases 48340 - Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
52743,52025 52743 - Subtilisin-like 52025 - PA domain	0	DIRECT
50249,57756 50249 - Nucleic acid-binding proteins 57756 - Retrovirus zinc finger-like domains	0	DIRECT
58014,51064 58014 - Coiled-coil domain of nucleotide exchange factor GrpE 51064 - Head domain of nucleotide exchange factor GrpE	0	DIRECT
53383,53383 53383 - PLP-dependent transferases 53383 - PLP-dependent transferases	0	DIRECT
53300,57850 53300 - vWA-like 57850 - RING/U-box	0	DIRECT
46689,51905 46689 - Homeodomain-like 51905 - FAD/NAD(P)-binding domain	0	DIRECT
55021,56112 55021 - ACT-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
158702,81296 158702 - Sec63 N-terminal domain-like 81296 - E set domains	0	DIRECT
57850,46689 57850 - RING/U-box 46689 - Homeodomain-like	0	DIRECT
141673,50800 141673 - MOSC N-terminal domain-like 50800 - PK beta-barrel domain-like	0	DIRECT
158639,63748 158639 - ENT-like 63748 - Tudor/PWWP/MBT	0	DIRECT
53448,51161 53448 - Nucleotide-diphospho-sugar transferases 51161 - Trimeric LpxA-like enzymes	0	DIRECT
101690,69065 101690 - PAZ domain 69065 - RNase III domain-like	0	DIRECT
109604,81301 109604 - HD-domain/PDEase-like 81301 - Nucleotidyltransferase	0	DIRECT
51735,143548 51735 - NAD(P)-binding Rossmann-fold domains 143548 - Serine metabolism enzymes domain	0	DIRECT
54909,54909 54909 - Dimeric alpha+beta barrel 54909 - Dimeric alpha+beta barrel	0	DIRECT
52833,52833 52833 - Thioredoxin-like 52833 - Thioredoxin-like	0	DIRECT
47473,103506 47473 - EF-hand 103506 - Mitochondrial carrier	0	DIRECT
54211,55060 54211 - Ribosomal protein S5 domain 2-like 55060 - GHMP Kinase, C-terminal domain	0	DIRECT
88697,52374 88697 - PUA domain-like 52374 - Nucleotidylyl transferase	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
49723,48484 49723 - Lipase/lipooxygenase domain (PLAT/LH2 domain) 48484 - Lipoxigenase	0	DIRECT
55545,51445 55545 - beta-N-acetylhexosaminidase-like domain 51445 - (Trans)glycosidases	0	DIRECT
56112,48371 56112 - Protein kinase-like (PK-like) 48371 - ARM repeat	0	DIRECT
50729,57863 50729 - PH domain-like 57863 - ArfGap/RecO-like zinc finger	0	DIRECT
54534,48452 54534 - FKBP-like 48452 - TPR-like	0	DIRECT
54160,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
48403,57850 48403 - Ankyrin repeat 57850 - RING/U-box	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
81296,51445 81296 - E set domains 51445 - (Trans)glycosidases	0	DIRECT
88946,88659 88946 - Sigma2 domain of RNA polymerase sigma factors 88659 - Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
55781,47384 55781 - GAF domain-like 47384 - Homodimeric domain of signal transducing histidine kinase	0	DIRECT
82199,81822 82199 - SET domain 81822 - RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
47661,58038 47661 - t-snare proteins 58038 - SNARE fusion complex	0	DIRECT
46785,54928 46785 - "Winged helix" DNA-binding domain 54928 - RNA-binding domain, RBD	0	DIRECT
52172,52172 52172 - CheY-like 52172 - CheY-like	0	DIRECT
55785,55785 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
54160,54160 54160 - Chromo domain-like 54160 - Chromo domain-like	0	DIRECT
81296,52540 81296 - E set domains 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
143548,55021 143548 - Serine metabolism enzymes domain 55021 - ACT-like	0	DIRECT
52025,57850 52025 - PA domain 57850 - RING/U-box	0	DIRECT
48239,48576 48239 - Terpenoid cyclases/Protein prenyltransferases 48576 - Terpenoid synthases	1	INHERITED FROM: stigma