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

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

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

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

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

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

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

SCOP term	FDR (all)	Annotation (direct or inherited)
Tim10-like	0	DIRECT
RibA-like	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
BSD domain-like	0	DIRECT
SMR domain-like	0	DIRECT
Lipoxigenase	0	DIRECT
Rudiment single hybrid motif	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
SH3-domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Globin-like	0	DIRECT
TK C-terminal domain-like	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Prokaryotic type KH domain (KH-domain type II)	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
YrdC/RibB	0	DIRECT
LuxS/MPP-like metallohydrolase	0	DIRECT
Oxysterol-binding protein-like	0	DIRECT
NHL repeat	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
Chelatase	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
Carbohydrate phosphatase	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
Mog1p/PsbP-like	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
GlnB-like	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
AlbA-like	0	DIRECT
HesB-like domain	0	DIRECT
Chalcone isomerase	0	DIRECT
S15/NS1 RNA-binding domain	0	DIRECT
Protease propeptides/inhibitors	0	DIRECT
Lipocalins	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
FKBP-like	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
PABC (PABP) domain	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Preprotein translocase SecY subunit	0	DIRECT
Granulin repeat	0	DIRECT
HIT/MYND zinc finger-like	0	DIRECT
Folate-binding domain	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
beta-N-acetylhexosaminidase-like domain	0	DIRECT
XPC-binding domain	0	DIRECT
Ribosomal protein S6	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
Elongation factor TFIIS domain 2	0	DIRECT
Ribosomal protein L25-like	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
Ribosomal protein L4	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
LigT-like	0	DIRECT
ADC-like	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
AN1-like Zinc finger	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
LysM domain	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Single hybrid motif	0	DIRECT
Phospholipase C/P1 nuclease	0	DIRECT
AMPKBI-like	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
RBP11-like subunits of RNA polymerase	0	DIRECT
eIF1-like	0	DIRECT
Oxygen-evolving enhancer protein 3,	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
RraA-like	0	DIRECT
Electron transport accessory proteins	0	DIRECT
Tautomerase/MIF	0	DIRECT
Ribosomal protein S2	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
Peptidyl-tRNA hydrolase II	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
SAM/Pointed domain	0	DIRECT
alpha-helical ferredoxin	0	DIRECT
S13-like H2TH domain	0	DIRECT
Rubredoxin-like	0	DIRECT
Peptidase/esterase 'gauge' domain	0	DIRECT
SIS domain	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
BAG domain	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
Signal peptide-binding domain	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Cytochrome c	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
L9 N-domain-like	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
AF1104-like	0	DIRECT
FAH	0	DIRECT
Ribosomal protein S8	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Ribosomal protein L31e	0	DIRECT
CYTH-like phosphatases	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
LeuD/IlvD-like	0	DIRECT
WW domain	0	DIRECT
Supernatant protein factor (SPF), C-terminal domain	0	DIRECT
Ribosomal protein L14	0	DIRECT
HIT-like	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
Gamma-glutamyl cyclotransferase-like	0	DIRECT
L28p-like	0	DIRECT
GroEL-intermediate domain like	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
RuBisCO, small subunit	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
Acid phosphatase/Vanadium-dependent haloperoxidase	0	DIRECT
tRNA-binding arm	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
Ribosomal protein L1	0	DIRECT
ClpP/crotonase	0	DIRECT
Putative isomerase YbhE	0	DIRECT
Mitochondrial glycoprotein MAM33-like	0	DIRECT
Ferritin-like	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
BolA-like	0	DIRECT
Cryptochrome/photolyase, N-terminal domain	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
At5g01610-like	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
GroEL apical domain-like	0	DIRECT
Glutamine synthetase/guanido kinase	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
E2F-DP heterodimerization region	0	DIRECT
Smc hinge domain	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
Radical SAM enzymes	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
Flavoproteins	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
Pentein	0	DIRECT
DLC	0	DIRECT
Ribosomal protein L39e	0	DIRECT
Ribosomal protein L13	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
RplX-like	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
ADC synthase	0	DIRECT
Ribosomal protein L16p/L10e	0	DIRECT
Eukaryotic type KH-domain (KH-domain type I)	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Release factor	0	DIRECT
Chorismate mutase II	0	DIRECT
Probable bacterial effector-binding domain	0	DIRECT
Ricin B-like lectins	0	DIRECT
Poly A polymerase C-terminal region-like	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
GroEL equatorial domain-like	0	DIRECT
PGBD-like	0	DIRECT
PreATP-grasp domain	0	DIRECT
Lesion bypass DNA polymerase (Y-family), little finger domain	0	DIRECT
Cysteine alpha-hairpin motif	0	DIRECT
R3H domain	0	DIRECT
Metalloproteases ("zincins"), catalytic domain	0	DIRECT
Phosphofructokinase	0	DIRECT
alpha/beta knot	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
FF domain	0	DIRECT
Ribosomal L27 protein-like	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
RNA-binding domain, RBD	5.621e-06	DIRECT
Cupredoxins	0.7917	INHERITED FROM: sepal vascular system

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

SCOP term	FDR (all)	Annotation (direct or inherited)
GAF domain	0	DIRECT
BolA-like	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain	0	DIRECT
Gamma-glutamyl cyclotransferase-like	0	DIRECT
UBX domain	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), catalytic domain	0	DIRECT
GAT domain	0	DIRECT
Chromo barrel domain	0	DIRECT
HspBP1 domain	0	DIRECT
GDI-like N domain	0	DIRECT
Biotin dependent carboxylase carboxyltransferase domain	0	DIRECT
HIT (HINT, histidine triad) family of protein kinase-interacting proteins	0	DIRECT
Homoserine dehydrogenase-like	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Class-II DAHP synthetase	0	DIRECT
Cyclin A/CDK2-associated p19, Skp2	0	DIRECT
Methyl-CpG-binding domain, MBD	0	DIRECT
Spermidine synthase	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
Plant stress-induced protein	0	DIRECT
AF1104-like	0	DIRECT
beta-sandwich domain of Sec23/24	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
HesB-like domain	0	DIRECT
Clp protease, ClpP subunit	0	DIRECT
Calnexin/calreticulin	0	DIRECT
Glycosyl hydrolases family 32 N-terminal domain	0	DIRECT
DNA repair glycosylase, 2 C-terminal domains	0	DIRECT
Ribosomal protein S8	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
CAT-like	0	DIRECT
Sigma4 domain	0	DIRECT
B56-like	0	DIRECT
Ribosomal protein L14	0	DIRECT
Ribosomal protein S15	0	DIRECT
FAH	0	DIRECT
Enolase	0	DIRECT
Pyridoxal-dependent decarboxylase	0	DIRECT
NifU C-terminal domain-like	0	DIRECT
Ring hydroxylating alpha subunit ISP domain	0	DIRECT
Ribosomal protein L31e	0	DIRECT
Ribosomal protein S13	0	DIRECT
Ribonucleotide reductase-like	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
GroEL chaperone, ATPase domain	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
N-acetyl-l-glutamate kinase	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
Ubiquitin carboxyl-terminal hydrolase UCH-L	0	DIRECT
Subtilase propeptides/inhibitors	0	DIRECT
Shikimate kinase (AroK)	0	DIRECT
DNase I-like	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
Ribosomal protein L3	0	DIRECT
Band 7/SPFH domain	0	DIRECT
PCI domain (PINT motif)	0	DIRECT
Reductases	0	DIRECT
Transcriptional coactivator PC4 C-terminal domain	0	DIRECT
Ribosomal protein L10e	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
2Fe-2S ferredoxin-related	0	DIRECT
HAT/Suf repeat	0	DIRECT
GroEL-like chaperone, apical domain	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
PNP-oxidase like	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
Receiver domain of the ethylene receptor	0	DIRECT
NHL repeat	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Ribosomal protein S6	0	DIRECT
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain	0	DIRECT
SOUL heme-binding protein	0	DIRECT
LeuD-like	0	DIRECT
5' nucleotidase-like	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
SAM (sterile alpha motif) domain	0	DIRECT
Crotonase-like	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
R3H domain	0	DIRECT
Glyoxalase II (hydroxyacylglutathione hydrolase)	0	DIRECT
Rubredoxin	0	DIRECT
Ferritin	0	DIRECT
Ribosomal protein L18 and S11	0	DIRECT
Myf domain	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
GroEL-like chaperone, intermediate domain	0	DIRECT
CoA-binding domain	0	DIRECT
LEA14-like	0	DIRECT
AN1-like Zinc finger	0	DIRECT
Double-stranded RNA-binding domain (dsRBD)	0	DIRECT
Leukotriene A4 hydrolase catalytic domain	0	DIRECT
HCDH C-domain-like	0	DIRECT
GroES	0	DIRECT
Thiolase-related	0	DIRECT
Sec63 C-terminal domain-like	0	DIRECT
Linker histone H1/H5	0	DIRECT
FF domain	0	DIRECT
Smc hinge domain	0	DIRECT
BSD domain	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
PDI-like	0	DIRECT
LplA-like	0	DIRECT
Ribosomal protein L1	0	DIRECT
3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
UDP-glucose pyrophosphorylase	0	DIRECT
GABARAP-like	0	DIRECT
LON domain-like	0	DIRECT
IPP isomerase-like	0	DIRECT
YicI catalytic domain-like	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
Pseudouridine synthase I TruA	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
HD domain	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
PAPS reductase-like	0	DIRECT
YicI N-terminal domain-like	0	DIRECT
Eps15 homology domain (EH domain)	0	DIRECT
Branched-chain alpha-keto acid dehydrogenase Pyr module	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Macro domain	0	DIRECT
HAL/PAL-like	0	DIRECT
BC N-terminal domain-like	0	DIRECT
RNB domain-like	0	DIRECT
Poly A polymerase C-terminal region-like	0	DIRECT
C5 cytosine-specific DNA methylase, DCM	0	DIRECT
Hermes transposase-like	0	DIRECT
HEAT repeat	0	DIRECT
PUA domain	0	DIRECT
Phosphofructokinase	0	DIRECT
RWD domain	0	DIRECT
RplX-like	0	DIRECT
beta-N-acetylhexosaminidase catalytic domain	0	DIRECT
SerA intervening domain-like	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
Lipoxigenase N-terminal domain	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
DLC	0	DIRECT
Aspartokinase allosteric domain-like	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
SpoU-like RNA 2'-O ribose methyltransferase	0	DIRECT
Choline kinase	0	DIRECT
Anti-sigma factor antagonist SpoIIaa	0	DIRECT
Tim10/DDP	0	DIRECT
Cryptochrome/photolyase, N-terminal domain	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Chromo domain	0	DIRECT
Mitochondrial glycoprotein MAM33-like	0	DIRECT
Ribosomal proteins L24p and L21e	0	DIRECT
Mo25 protein	0	DIRECT
NOL1/NOP2/sun	0	DIRECT
Cytochrome p450 reductase N-terminal domain-like	0	DIRECT
NadC C-terminal domain-like	0	DIRECT
XPC-binding domain	0	DIRECT
RibA-like	0	DIRECT
Folylpolyglutamate synthetase	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
ADC synthase	0	DIRECT
Methionine aminopeptidase, insert domain	0	DIRECT
rRNA adenine dimethylase-like	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
Ribosomal protein L39e	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
Ribosomal protein L13	0	DIRECT
Oxysterol-binding protein	0	DIRECT
Plant transcriptional regulator PBF-2	0	DIRECT
Succinyl-CoA synthetase, beta-chain, N-terminal domain	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
PABC (PABP) domain	0	DIRECT
WW domain	0	DIRECT
Prolyl oligopeptidase, N-terminal domain	0	DIRECT
RNA polymerase II subunit RBP4 (RpoF)	0	DIRECT
Inositol monophosphatase/fructose-1,6-bisphosphatase-like	0	DIRECT
Tail specific protease, catalytic domain	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
1,3-glucuronyltransferase	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Protein prenyltransferases	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase dimerisation domain	0	DIRECT
gamma-carbonic anhydrase-like	0	DIRECT
Heme-dependent catalases	0	DIRECT
MIF-related	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
Release factor	0	DIRECT
ZZ domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
SufE-like	0	DIRECT
VHS domain	0	DIRECT
Class II glutamine amidotransferases	0	DIRECT
RuBisCo LSMT catalytic domain	0	DIRECT
eIF5a N-terminal domain-like	0	DIRECT
Pseudouridine synthase II TruB	0	DIRECT
CYTH domain	0	DIRECT
Preprotein translocase SecY subunit	0	DIRECT
Acyl-ACP thioesterase-like	0	DIRECT
beta-Phosphoglucomutase-like	0	DIRECT
Glycerol-3-phosphate dehydrogenase	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Neurolysin-like	0	DIRECT
Sec63 N-terminal domain	0	DIRECT
Group II chaperonin (CCT, TRIC), ATPase domain	0	DIRECT
DJ-1/PfpI	0	DIRECT
Starch-binding domain	0	DIRECT
Trunk domain of Sec23/24	0	DIRECT
AMPK-beta glycogen binding domain-like	0	DIRECT
LIM domain	0	DIRECT
Granulin repeat	0	DIRECT
LysM domain	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Glyoxalase I (lactoylglutathione lyase)	0	DIRECT
PsbP-like	0	DIRECT
Phytochrome-specific domain	0	DIRECT
BAR domain	0	DIRECT
NADPH-cytochrome p450 reductase FAD-binding domain-like	0	DIRECT
Hypothetical protein HI1317	0	DIRECT
Dihydrodipicolinate reductase-like	0	DIRECT
Poly(ADP-ribose) polymerase, C-terminal domain	0	DIRECT
MPP-like	0	DIRECT
MMP N-terminal domain	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Matrix metalloproteases, catalytic domain	0	DIRECT
Aminomethyltransferase folate-binding domain	0	DIRECT
Class I alpha-1;2-mannosidase, catalytic domain	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
Smr domain	0	DIRECT
SH3-domain	0	DIRECT
ATP sulfurylase catalytic domain	0	DIRECT
Sedlin (SEDL)	0	DIRECT
Ubiquitin activating enzymes (UBA)	0	DIRECT
NADPH-cytochrome p450 reductase-like	0	DIRECT
Cytidylyltransferase	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Plant lipoxigenases	0	DIRECT
AMPKBI-like	0	DIRECT
Prokaryotic type KH domain (KH-domain type II)	0	DIRECT
Poly A polymerase head domain-like	0	DIRECT
D-ribulose-5-phosphate 3-epimerase	0	DIRECT
Hypothetical protein At2g34160	0	DIRECT
Chalcone isomerase	0	DIRECT
SWIRM domain	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
Clathrin coat assembly domain	0	DIRECT
Molybdenum-containing oxidoreductases-like dimerisation domain	0	DIRECT
Thioredoxin-like 2Fe-2S ferredoxin	0	DIRECT
Ribosomal protein L19	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Allosteric chorismate mutase	0	DIRECT
28-residue LRR	0	DIRECT
BAG domain	0	DIRECT
Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	0	DIRECT
3-Methyladenine DNA glycosylase I (Tag)	0	DIRECT
Biotinyl/lipoyl-carrier proteins and domains	0	DIRECT
RraA-like	0	DIRECT
Class I aldolase	0	DIRECT
Oxygen-evolving enhancer protein 3,	0	DIRECT
Galactosyltransferase LgtC	0	DIRECT
Glutamine synthetase catalytic domain	0	DIRECT
monodomain cytochrome c	0	DIRECT
Ribosomal protein L37e	0	DIRECT
Diacylglycerol kinase-like	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
L23p	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
DNA polymerase III clamp loader subunits, C-terminal domain	0	DIRECT
AlkB-like	0	DIRECT
RelA/SpoT domain	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0	DIRECT
BC C-terminal domain-like	0	DIRECT
NadC N-terminal domain-like	0	DIRECT
G domain-linked domain	0	DIRECT
Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain	0	DIRECT
Lesion bypass DNA polymerase (Y-family), catalytic domain	0	DIRECT
IF2B-like	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
La domain	0	DIRECT
Carbon-carbon bond hydrolase	0	DIRECT
Ran-binding domain	0	DIRECT
Ribosomal protein L4	0	DIRECT
EDF1-like	0	DIRECT
TRM1-like	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
alpha-Amylases, C-terminal beta-sheet domain	0	DIRECT
E2F dimerization segment	0	DIRECT
Peptidyl-tRNA hydrolase II	0	DIRECT
WrbA-like	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
FKBP immunophilin/proline isomerase	0	DIRECT
Elongation factor TFIIS domain 2	0	DIRECT
Eukaryotic type KH-domain (KH-domain type I)	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Rps19E-like	0	DIRECT
eIF1-like	0	DIRECT
Adenosine-5'phosphosulfate kinase (APS kinase)	0	DIRECT
At5g01610-like	0	DIRECT
STAR domain	0	DIRECT
N-type ATP pyrophosphatases	0	DIRECT
(Glycosyl)asparaginase	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Deoxycytidylate deaminase-like	0	DIRECT
Putative glucosidase YicI, domain 3	0	DIRECT
Glycerophosphoryl diester phosphodiesterase	0	DIRECT
Glycosyl hydrolases family 32 C-terminal domain	0	DIRECT
RhoGDI-like	0	DIRECT
ATP sulfurylase N-terminal domain	0	DIRECT
Pentapeptide repeats	0	DIRECT
P1 nuclease	0	DIRECT
6-phosphogluconate dehydrogenase-like, N-terminal domain	0	DIRECT
Ribosomal protein S27e	0	DIRECT
PaaI/YdiI-like	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
Cystatins	0	DIRECT
RuBisCO, small subunit	0	DIRECT
Prolyl oligopeptidase, C-terminal domain	0	DIRECT
Ribosomal protein S2	0	DIRECT
BphP N-terminal domain-like	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
RNase Z-like	0	DIRECT
Group II chaperonin (CCT, TRIC), apical domain	0	DIRECT
MYND zinc finger	0	DIRECT
Gtf glycosyltransferase	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Cdc48 N-terminal domain-like	0	DIRECT
Signal peptide-binding domain	0	DIRECT
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains	0	DIRECT
Aminoacid dehydrogenases	0	DIRECT
Glucose 6-phosphate dehydrogenase-like	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
BC ATP-binding domain-like	0	DIRECT
HCP-like	0	DIRECT
Canonical RBD	1.129e-05	DIRECT
Multidomain cupredoxins	0.7702	INHERITED FROM: sepal vascular system

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)
LigT-like	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Ribosomal protein L25-like	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
GroEL apical domain-like	0	DIRECT
Radical SAM enzymes	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
Leukotriene A4 hydrolase N-terminal domain	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
Ribosomal protein L39e	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Lesion bypass DNA polymerase (Y-family), little finger domain	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
SIS domain	0	DIRECT
SH3-domain	0	DIRECT
MOSC N-terminal domain-like	0	DIRECT
Lipoxigenase	0	DIRECT
Ribosomal protein S2	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
Glutamine synthetase, N-terminal domain	0	DIRECT
SAM/Pointed domain	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Chalcone isomerase	0	DIRECT
PABC (PABP) domain	0	DIRECT
Smc hinge domain	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
TK C-terminal domain-like	0	DIRECT
Ribosomal L27 protein-like	0	DIRECT
Inorganic pyrophosphatase	0	DIRECT
AN1-like Zinc finger	0	DIRECT
HesB-like domain	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
PreATP-grasp domain	0	DIRECT
Chorismate mutase II	0	DIRECT
FF domain	0	DIRECT
Mitochondrial glycoprotein MAM33-like	0	DIRECT
Rubredoxin-like	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
Supernatant protein factor (SPF), C-terminal domain	0	DIRECT
tRNA-binding arm	0	DIRECT
GroEL equatorial domain-like	0	DIRECT
HIT/MYND zinc finger-like	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
C-terminal autoproteolytic domain of nucleoporin nup98	0	DIRECT
Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
L28p-like	0	DIRECT
YrdC/RibB	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
FAH	0	DIRECT
BolA-like	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
Probable bacterial effector-binding domain	0	DIRECT
Prokaryotic type KH domain (KH-domain type II)	0	DIRECT
Folate-binding domain	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
Ribosomal protein L14	0	DIRECT
Phosphofructokinase	0	DIRECT
SMR domain-like	0	DIRECT
WW domain	0	DIRECT
NHL repeat	0	DIRECT
LuxS/MPP-like metallohydrolase	0	DIRECT
ADC-like	0	DIRECT
AMPKBI-like	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
ClpP/crotonase	0	DIRECT
Granulin repeat	0	DIRECT
Ricin B-like lectins	0	DIRECT
Ferritin-like	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
Chelatase	0	DIRECT
Cysteine alpha-hairpin motif	0	DIRECT
RplX-like	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
L9 N-domain-like	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
Signal peptide-binding domain	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Glycerol-3-phosphate (1)-acyltransferase	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
RibA-like	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
R3H domain	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
LeuD/IlvD-like	0	DIRECT
RBP11-like subunits of RNA polymerase	0	DIRECT
alpha/beta knot	0	DIRECT
E2F-DP heterodimerization region	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Oxygen-evolving enhancer protein 3,	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
beta-N-acetylhexosaminidase-like domain	0	DIRECT
S13-like H2TH domain	0	DIRECT
Elongation factor TFIIS domain 2	0	DIRECT
Mog1p/PsbP-like	0	DIRECT
AlbA-like	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Cryptochrome/photolyase, N-terminal domain	0	DIRECT
Tautomerase/MIF	0	DIRECT
PGBD-like	0	DIRECT
Ribosomal protein L31e	0	DIRECT
CYTH-like phosphatases	0	DIRECT
HIT-like	0	DIRECT
Ribosomal protein L16p/L10e	0	DIRECT
Gamma-glutamyl cyclotransferase-like	0	DIRECT
Carbohydrate phosphatase	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
Pentein	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
Protease propeptides/inhibitors	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Eukaryotic type KH-domain (KH-domain type I)	0	DIRECT
Ribosomal protein S8	0	DIRECT
Lipocalins	0	DIRECT
At5g01610-like	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
GroEL-intermediate domain like	0	DIRECT
eIF1-like	0	DIRECT
Peptidyl-tRNA hydrolase II	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Ribosomal protein L13	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Ribosomal protein L4	0	DIRECT
Globin-like	0	DIRECT
RuBisCO, small subunit	0	DIRECT
FKBP-like	0	DIRECT
Preprotein translocase SecY subunit	0	DIRECT
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0	DIRECT
Rudiment single hybrid motif	0	DIRECT
Phospholipase C/P1 nuclease	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
S15/NS1 RNA-binding domain	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
Acid phosphatase/Vanadium-dependent haloperoxidase	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
RraA-like	0	DIRECT
XPC-binding domain	0	DIRECT
BSD domain-like	0	DIRECT
Putative isomerase YbhE	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
alpha-helical ferredoxin	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
Single hybrid motif	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
DLC	0	DIRECT
LysM domain	0	DIRECT
ADC synthase	0	DIRECT
Ribosomal protein L1	0	DIRECT
AF1104-like	0	DIRECT
Oxysterol-binding protein-like	0	DIRECT
GlnB-like	0	DIRECT
Peptidase/esterase 'gauge' domain	0	DIRECT
Ribosomal protein S6	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
Electron transport accessory proteins	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
Glutamine synthetase/guanido kinase	0	DIRECT
Tim10-like	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0	DIRECT
BAG domain	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Poly A polymerase C-terminal region-like	0	DIRECT
Flavoproteins	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
Cytochrome c	0	DIRECT
Release factor	0	DIRECT
Metalloproteases ("zincins"), catalytic domain	0	DIRECT
RNA-binding domain, RBD	4.488e-06	DIRECT
Cupredoxins	0.7707	INHERITED FROM: sepal vascular system