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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 (SDAP level: Least Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
FAH	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
EF-G C-terminal domain-like	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
Enolase C-terminal domain-like	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
Ribosomal protein L31e	0	DIRECT
Clc chloride channel	0	DIRECT
Tim10-like	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
Cytochrome c	0	DIRECT
AMPKBI-like	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
Amine oxidase catalytic domain	0	DIRECT
SIS domain	0	DIRECT
Formyltransferase	0	DIRECT
NagB/RpiA/CoA transferase-like	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
beta-sandwich domain of Sec23/24	0	DIRECT
PapD-like	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Mog1p/PsbP-like	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Release factor	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
LuxS/MPP-like metallohydrolase	0	DIRECT
Folate-binding domain	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Endosomal sorting complex assembly domain	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Formate/glycerate dehydrogenase catalytic domain-like	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
LigT-like	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
Ribosomal protein L39e	0	DIRECT
S15/NS1 RNA-binding domain	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
Ribosomal proteins L15p and L18e	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
SH3-domain	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
EGF/Laminin	0	DIRECT
Enolase N-terminal domain-like	0	DIRECT
Tautomerase/MIF	0	DIRECT
Ribosomal protein L13	0	DIRECT
Electron transport accessory proteins	0	DIRECT
Carbon-nitrogen hydrolase	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
NHL repeat	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Ribosomal protein S2	0	DIRECT
Mss4-like	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
RraA-like	0	DIRECT
R3H domain	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
RNase III domain-like	0	DIRECT
CO dehydrogenase flavoprotein C-terminal domain-like	0	DIRECT
Peptidyl-tRNA hydrolase II	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
FKBP-like	0	DIRECT
eIF1-like	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
Gamma-glutamyl cyclotransferase-like	0	DIRECT
L28p-like	0	DIRECT
TAZ domain	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
Ribosomal protein L25-like	0	DIRECT
Ribosomal protein L4	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
Oxygen-evolving enhancer protein 3,	0	DIRECT
BolA-like	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
Ribosomal protein L1	0	DIRECT
S13-like H2TH domain	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
GlnB-like	0	DIRECT
HesB-like domain	0	DIRECT
Acyl-CoA binding protein	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
PLP-binding barrel	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
YrdC/RibB	0	DIRECT
Rubredoxin-like	0	DIRECT
Amidase signature (AS) enzymes	0	DIRECT
tRNA-binding arm	0	DIRECT
Chelatase	0	DIRECT
CYTH-like phosphatases	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
AF1104-like	0	DIRECT
XPC-binding domain	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Ribosomal protein S10	0	DIRECT
RplX-like	0	DIRECT
RibA-like	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
Chorismate mutase II	0	DIRECT
BSD domain-like	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
LeuD/IlvD-like	0	DIRECT
Lipoxigenase	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
GINS helical bundle-like	0	DIRECT
Cyclophilin-like	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
LysM domain	0	DIRECT
Lipocalins	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Quinoprotein alcohol dehydrogenase-like	0	DIRECT
Ribosomal protein S6	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Probable bacterial effector-binding domain	0	DIRECT
Supernatant protein factor (SPF), C-terminal domain	0	DIRECT
PX domain	0	DIRECT
RL5-like	0	DIRECT
ACT-like	0.000167	DIRECT
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	0.000326	DIRECT
NAD(P)-binding Rossmann-fold domains	0.0005295	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0.000636	DIRECT

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

SCOP term	FDR (all)	Annotation (direct or inherited)
Ribosomal protein L31e	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
HEAT repeat	0	DIRECT
Choline kinase	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain	0	DIRECT
LEA14-like	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
PCI domain (PINT motif)	0	DIRECT
Ribosomal protein S10	0	DIRECT
Ribosomal protein S13	0	DIRECT
Enolase N-terminal domain-like	0	DIRECT
Allosteric chorismate mutase	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Spermidine synthase	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0	DIRECT
MIF-related	0	DIRECT
Ribosomal proteins L15p and L18e	0	DIRECT
Aminoacid dehydrogenases	0	DIRECT
Plus3	0	DIRECT
beta-sandwich domain of Sec23/24	0	DIRECT
Formate/glycerate dehydrogenases, substrate-binding domain	0	DIRECT
RNB domain-like	0	DIRECT
RNA-polymerase beta	0	DIRECT
SOUL heme-binding protein	0	DIRECT
Aspartokinase allosteric domain-like	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
SerA intervening domain-like	0	DIRECT
MSP-like	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Methionine aminopeptidase, insert domain	0	DIRECT
LON domain-like	0	DIRECT
Kunitz (STI) inhibitors	0	DIRECT
GDI-like N domain	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
NifU C-terminal domain-like	0	DIRECT
gamma-carbonic anhydrase-like	0	DIRECT
Deoxycytidylate deaminase-like	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
CAF1-like ribonuclease	0	DIRECT
Lipoxigenase N-terminal domain	0	DIRECT
Clc chloride channel	0	DIRECT
Ran-binding domain	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
RWD domain	0	DIRECT
DNA repair glycosylase, 2 C-terminal domains	0	DIRECT
ATP sulfurylase catalytic domain	0	DIRECT
Starch-binding domain	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Succinyl-CoA synthetase, beta-chain, N-terminal domain	0	DIRECT
Ubiquitin carboxyl-terminal hydrolase UCH-L	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	0	DIRECT
Formyltransferase	0	DIRECT
Chromo domain	0	DIRECT
GAPDH-like	0	DIRECT
L23p	0	DIRECT
Glyoxalase II (hydroxyacylglutathione hydrolase)	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
C5 cytosine-specific DNA methylase, DCM	0	DIRECT
Ribosomal proteins L24p and L21e	0	DIRECT
Transcriptional coactivator PC4 C-terminal domain	0	DIRECT
Aminomethyltransferase folate-binding domain	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
HD domain	0	DIRECT
RNase Z-like	0	DIRECT
Translational machinery components	0	DIRECT
IPP isomerase-like	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
MYND zinc finger	0	DIRECT
2Fe-2S ferredoxin-related	0	DIRECT
PAPS reductase-like	0	DIRECT
CO dehydrogenase flavoprotein C-terminal domain-like	0	DIRECT
Ribosomal protein L3	0	DIRECT
BolA-like	0	DIRECT
PNP-oxidase like	0	DIRECT
VHS domain	0	DIRECT
LplA-like	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
FKBP immunophilin/proline isomerase	0	DIRECT
BSD domain	0	DIRECT
WrbA-like	0	DIRECT
Ribosomal protein L39e	0	DIRECT
BphP N-terminal domain-like	0	DIRECT
Myf domain	0	DIRECT
eIF1-like	0	DIRECT
Ribosomal protein S27e	0	DIRECT
RNA polymerase II subunit RBP4 (RpoF)	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
GABARAP-like	0	DIRECT
Ribosomal protein L10e	0	DIRECT
Folylpolyglutamate synthetase	0	DIRECT
D-ribulose-5-phosphate 3-epimerase	0	DIRECT
3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Cytochrome b5	0	DIRECT
Serine acetyltransferase	0	DIRECT
Amine oxidase catalytic domain	0	DIRECT
Methyl-CpG-binding domain, MBD	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
Acyl-ACP thioesterase-like	0	DIRECT
Molybdenum-containing oxidoreductases-like dimerisation domain	0	DIRECT
Amidase signature (AS) enzymes	0	DIRECT
Ribosomal S5 protein, N-terminal domain	0	DIRECT
Cytidylyltransferase	0	DIRECT
AF1104-like	0	DIRECT
NHL repeat	0	DIRECT
Thiolase-related	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
LysM domain	0	DIRECT
Group II chaperonin (CCT, TRIC), ATPase domain	0	DIRECT
PUA domain	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
HAT/Suf repeat	0	DIRECT
CO dehydrogenase flavoprotein N-terminal domain-like	0	DIRECT
Pentapeptide repeats	0	DIRECT
Linker histone H1/H5	0	DIRECT
Ribosomal protein L37e	0	DIRECT
TAZ domain	0	DIRECT
HspBP1 domain	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
MPP-like	0	DIRECT
Pseudouridine synthase II TruB	0	DIRECT
CoA-binding domain	0	DIRECT
Rubredoxin	0	DIRECT
Ring hydroxylating alpha subunit ISP domain	0	DIRECT
EF-G/eEF-2 domains III and V	0	DIRECT
Sedlin (SEDL)	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
ZZ domain	0	DIRECT
Class I aldolase	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
PX domain	0	DIRECT
Branched-chain alpha-keto acid dehydrogenase Pyr module	0	DIRECT
5' nucleotidase-like	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase dimerisation domain	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
DJ-1/PfpI	0	DIRECT
Poly(ADP-ribose) polymerase, C-terminal domain	0	DIRECT
Trehalose-6-phosphate synthase, OtsA	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
Ribosomal protein L5	0	DIRECT
R3H domain	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Peptidyl-tRNA hydrolase II	0	DIRECT
Class-II DAHP synthetase	0	DIRECT
PsbP-like	0	DIRECT
IF2B-like	0	DIRECT
Calnexin/calreticulin	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
RelA/SpoT domain	0	DIRECT
SelR domain	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Cdc48 N-terminal domain-like	0	DIRECT
Ribosomal protein S6	0	DIRECT
Plant lipoxigenases	0	DIRECT
Formate/glycerate dehydrogenases, NAD-domain	0	DIRECT
Ribosomal protein S15	0	DIRECT
Dihydrodipicolinate reductase-like	0	DIRECT
Histidine kinase	0	DIRECT
DNA polymerase III clamp loader subunits, C-terminal domain	0	DIRECT
RplX-like	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
N-type ATP pyrophosphatases	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
FAH	0	DIRECT
Trunk domain of Sec23/24	0	DIRECT
Sec63 N-terminal domain	0	DIRECT
Plant stress-induced protein	0	DIRECT
Gamma-glutamyl cyclotransferase-like	0	DIRECT
AMPK-beta glycogen binding domain-like	0	DIRECT
Ribosomal protein L4	0	DIRECT
N-acetyl-l-glutamate kinase	0	DIRECT
(Glycosyl)asparaginase	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Plant transcriptional regulator PBF-2	0	DIRECT
HesB-like domain	0	DIRECT
Glyoxalase I (lactoylglutathione lyase)	0	DIRECT
Release factor	0	DIRECT
Tim10/DDP	0	DIRECT
Clp protease, ClpP subunit	0	DIRECT
Acyl-CoA binding protein	0	DIRECT
eIF5a N-terminal domain-like	0	DIRECT
YicI N-terminal domain-like	0	DIRECT
ATP sulfurylase N-terminal domain	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), catalytic domain	0	DIRECT
Diacylglycerol kinase-like	0	DIRECT
RNase III catalytic domain-like	0	DIRECT
LeuD-like	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
SufE-like	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
CAT-like	0	DIRECT
Ribosomal protein S2	0	DIRECT
Smc hinge domain	0	DIRECT
Ribosomal protein L1	0	DIRECT
EDF1-like	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
Ribosomal protein L13	0	DIRECT
RuBisCo LSMT catalytic domain	0	DIRECT
Homoserine dehydrogenase-like	0	DIRECT
HMGL-like	0	DIRECT
Phytochrome-specific domain	0	DIRECT
beta-Phosphoglucomutase-like	0	DIRECT
Enolase	0	DIRECT
Rps19E-like	0	DIRECT
Heme-dependent catalases	0	DIRECT
6-phosphogluconate dehydrogenase-like, N-terminal domain	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
UDP-glucose pyrophosphorylase	0	DIRECT
XPC-binding domain	0	DIRECT
Shikimate kinase (AroK)	0	DIRECT
monodomain cytochrome c	0	DIRECT
Class I alpha-1;2-mannosidase, catalytic domain	0	DIRECT
Neurolysin-like	0	DIRECT
Single-domain sulfurtransferase	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
alpha-Amylases, C-terminal beta-sheet domain	0	DIRECT
RibA-like	0	DIRECT
PDI-like	0	DIRECT
SH3-domain	0	DIRECT
RraA-like	0	DIRECT
G domain-linked domain	0	DIRECT
Sec63 C-terminal domain-like	0	DIRECT
Cyclophilin (peptidylprolyl isomerase)	0	DIRECT
Eps15 homology domain (EH domain)	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Tryptophan biosynthesis enzymes	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
Oxygen-evolving enhancer protein 3,	0	DIRECT
Band 7/SPFH domain	0	DIRECT
Tail specific protease, catalytic domain	0	DIRECT
Reductases	0	DIRECT
NagB-like	0	DIRECT
AMPKBI-like	0	DIRECT
Ribosomal protein L19	0	DIRECT
GAT domain	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
HIT (HINT, histidine triad) family of protein kinase-interacting proteins	0	DIRECT
Group II chaperonin (CCT, TRIC), apical domain	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
NadC C-terminal domain-like	0	DIRECT
Clathrin coat assembly domain	0	DIRECT
Sigma4 domain	0	DIRECT
UBX domain	0	DIRECT
NadC N-terminal domain-like	0	DIRECT

Trees by TreeVector

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

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

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Tim10-like	0	DIRECT
AF1104-like	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Endosomal sorting complex assembly domain	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
Cytochrome c	0	DIRECT
Clc chloride channel	0	DIRECT
GINS helical bundle-like	0	DIRECT
Enolase C-terminal domain-like	0	DIRECT
Carbon-nitrogen hydrolase	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Lipocalins	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
Phosphoglucomutase, C-terminal domain	0	DIRECT
Ribosomal protein L1	0	DIRECT
SH3-domain	0	DIRECT
Release factor	0	DIRECT
FKBP-like	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Ribosomal protein S6	0	DIRECT
Electron transport accessory proteins	0	DIRECT
Amine oxidase catalytic domain	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
Hypothetical protein YjiA, C-terminal domain	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
Enolase N-terminal domain-like	0	DIRECT
Acyl-CoA binding protein	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
Ribosomal protein L4	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
NHL repeat	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
NagB/RpiA/CoA transferase-like	0	DIRECT
EF-G C-terminal domain-like	0	DIRECT
L28p-like	0	DIRECT
CO dehydrogenase flavoprotein C-terminal domain-like	0	DIRECT
Ribosomal protein S10	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
Gamma-glutamyl cyclotransferase-like	0	DIRECT
Supernatant protein factor (SPF), C-terminal domain	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
eIF1-like	0	DIRECT
Ribosomal protein L31e	0	DIRECT
RibA-like	0	DIRECT
Pentapeptide repeat-like	0	DIRECT
PX domain	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
Chelatase	0	DIRECT
R3H domain	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
RplX-like	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
BSD domain-like	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
RNase III domain-like	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Tautomerase/MIF	0	DIRECT
Folate-binding domain	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
FAH	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
AMPKBI-like	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
XPC-binding domain	0	DIRECT
YrdC/RibB	0	DIRECT
LeuD/IlvD-like	0	DIRECT
Mog1p/PsbP-like	0	DIRECT
TAZ domain	0	DIRECT
S13-like H2TH domain	0	DIRECT
Formate/glycerate dehydrogenase catalytic domain-like	0	DIRECT
Quinoprotein alcohol dehydrogenase-like	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
Ribosomal protein L39e	0	DIRECT
RraA-like	0	DIRECT
N-terminal domain of the delta subunit of the F1F0-ATP synthase	0	DIRECT
beta-sandwich domain of Sec23/24	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
Ribosomal proteins L15p and L18e	0	DIRECT
Chorismate mutase II	0	DIRECT
PLP-binding barrel	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
Expressed protein At2g23090/F21P24.15	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
Probable bacterial effector-binding domain	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
Ribosomal protein L25-like	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
BolA-like	0	DIRECT
HesB-like domain	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
Phosphoglycerate kinase	0	DIRECT
Amidase signature (AS) enzymes	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
tRNA-binding arm	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
Formyltransferase	0	DIRECT
Mss4-like	0	DIRECT
RL5-like	0	DIRECT
Oxygen-evolving enhancer protein 3,	0	DIRECT
Glycolipid transfer protein, GLTP	0	DIRECT
Peptidyl-tRNA hydrolase II	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
PapD-like	0	DIRECT
EGF/Laminin	0	DIRECT
GlnB-like	0	DIRECT
LuxS/MPP-like metallohydrolase	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
NSFL1 (p97 ATPase) cofactor p47, SEP domain	0	DIRECT
Cyclophilin-like	0	DIRECT
LysM domain	0	DIRECT
CYTH-like phosphatases	0	DIRECT
Heme-dependent catalase-like	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
S15/NS1 RNA-binding domain	0	DIRECT
Ribosomal protein L13	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
LigT-like	0	DIRECT
Rubredoxin-like	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
Lipoxigenase	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
Ribosomal protein S2	0	DIRECT
SIS domain	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
ACT-like	0.0001409	DIRECT
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	0.0002755	DIRECT
NAD(P)-binding Rossmann-fold domains	0.0004478	DIRECT
6-phosphogluconate dehydrogenase C-terminal domain-like	0.0005382	DIRECT

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)
51338,51556 51338 - Composite domain of metallo-dependent hydrolases 51556 - Metallo-dependent hydrolases	0	DIRECT
50022,55961 50022 - ISP domain 55961 - Bet v1-like	0	DIRECT
52317,52317 52317 - Class I glutamine amidotransferase-like 52317 - Class I glutamine amidotransferase-like	0	DIRECT
81995,82919 81995 - beta-sandwich domain of Sec23/24 82919 - Zn-finger domain of Sec23/24	0	DIRECT
56059,52210 56059 - Glutathione synthetase ATP-binding domain-like 52210 - Succinyl-CoA synthetase domains	0	DIRECT
54416,49998 54416 - Amine oxidase N-terminal region 49998 - Amine oxidase catalytic domain	0	DIRECT
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
55821,142695 55821 - YrdC/RibB 142695 - RibA-like	0	DIRECT
55781,55785 55781 - GAF domain-like 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
52087,101576 52087 - CRAL/TRIO domain 101576 - Supernatant protein factor (SPF), C-terminal domain	0	DIRECT
82919,53300 82919 - Zn-finger domain of Sec23/24 53300 - vWA-like	0	DIRECT
81296,51445 81296 - E set domains 51445 - (Trans)glycosidases	0	DIRECT
48403,57850 48403 - Ankyrin repeat 57850 - RING/U-box	0	DIRECT
47473,52540 47473 - EF-hand 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
47741,56176 47741 - CO dehydrogenase ISP C-domain like 56176 - FAD-binding/transporter-associated domain-like	0	DIRECT
53732,52016 53732 - Aconitase iron-sulfur domain 52016 - LeuD/IlvD-like	0	DIRECT
48403,52540 48403 - Ankyrin repeat 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54747,46906 54747 - Ribosomal L11/L12e N-terminal domain 46906 - Ribosomal protein L11, C-terminal domain	0	DIRECT
55447,54665 55447 - CO dehydrogenase flavoprotein C-terminal domain-like 54665 - CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
56524,81296 56524 - Oxidoreductase molybdopterin-binding domain 81296 - E set domains	0	DIRECT
53300,57850 53300 - vWA-like 57850 - RING/U-box	0	DIRECT
81324,81324 81324 - Voltage-gated potassium channels 81324 - Voltage-gated potassium channels	0	DIRECT
53738,55957 53738 - Phosphoglucomutase, first 3 domains 55957 - Phosphoglucomutase, C-terminal domain	0	DIRECT
100950,75445 100950 - NagB/RpiA/CoA transferase-like 75445 - D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
158702,52540 158702 - Sec63 N-terminal domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
47384,55874 47384 - Homodimeric domain of signal transducing histidine kinase 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	0	DIRECT
54292,47741 54292 - 2Fe-2S ferredoxin-like 47741 - CO dehydrogenase ISP C-domain like	0	DIRECT
56235,52402 56235 - N-terminal nucleophile aminohydrolases (Ntn hydrolases) 52402 - Adenine nucleotide alpha hydrolases-like	0	DIRECT
82199,81822 82199 - SET domain 81822 - RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
49899,63887 49899 - Concanavalin A-like lectins/glucanases 63887 - P-domain of calnexin/calreticulin	0	DIRECT
81383,54518 81383 - F-box domain 54518 - Tubby C-terminal domain-like	0	DIRECT
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
52402,52833 52402 - Adenine nucleotide alpha hydrolases-like 52833 - Thioredoxin-like	0	DIRECT
53223,51735 53223 - Aminoacid dehydrogenase-like, N-terminal domain 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
64356,49447 64356 - SNARE-like 49447 - Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
58014,51064 58014 - Coiled-coil domain of nucleotide exchange factor GrpE 51064 - Head domain of nucleotide exchange factor GrpE	0	DIRECT
47473,103506 47473 - EF-hand 103506 - Mitochondrial carrier	0	DIRECT
55785,55781 55785 - PYP-like sensor domain (PAS domain) 55781 - GAF domain-like	0	DIRECT
46785,158702 46785 - "Winged helix" DNA-binding domain 158702 - Sec63 N-terminal domain-like	0	DIRECT
54160,54160 54160 - Chromo domain-like 54160 - Chromo domain-like	0	DIRECT
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases	0	DIRECT
53300,81995 53300 - vWA-like 81995 - beta-sandwich domain of Sec23/24	0	DIRECT
50249,57756 50249 - Nucleic acid-binding proteins 57756 - Retrovirus zinc finger-like domains	0	DIRECT
88659,88659 88659 - Sigma3 and sigma4 domains of RNA polymerase sigma factors 88659 - Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
143548,55021 143548 - Serine metabolism enzymes domain 55021 - ACT-like	0	DIRECT
109604,81301 109604 - HD-domain/PDEase-like 81301 - Nucleotidyltransferase	0	DIRECT
54909,54909 54909 - Dimeric alpha+beta barrel 54909 - Dimeric alpha+beta barrel	0	DIRECT
117916,117916 117916 - Fe-S cluster assembly (FSCA) domain-like 117916 - Fe-S cluster assembly (FSCA) domain-like	0	DIRECT
48371,50978 48371 - ARM repeat 50978 - WD40 repeat-like	0	DIRECT
50249,55681 50249 - Nucleic acid-binding proteins 55681 - Class II aaRS and biotin synthetases	0	DIRECT
54416,54416 54416 - Amine oxidase N-terminal region 54416 - Amine oxidase N-terminal region	0	DIRECT
51735,143548 51735 - NAD(P)-binding Rossmann-fold domains 143548 - Serine metabolism enzymes domain	0	DIRECT
52540,90002 52540 - P-loop containing nucleoside triphosphate hydrolases 90002 - Hypothetical protein YjiA, C-terminal domain	0	DIRECT
50447,54980 50447 - Translation proteins 54980 - EF-G C-terminal domain-like	0	DIRECT
103481,103481 103481 - Multidrug resistance efflux transporter EmrE 103481 - Multidrug resistance efflux transporter EmrE	0	DIRECT
57850,54928 57850 - RING/U-box 54928 - RNA-binding domain, RBD	0	DIRECT
49599,49599 49599 - TRAF domain-like 49599 - TRAF domain-like	0	DIRECT
55021,56112 55021 - ACT-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
49723,48484 49723 - Lipase/lipooxygenase domain (PLAT/LH2 domain) 48484 - Lipoxigenase	0	DIRECT
102848,54236 102848 - NSFL1 (p97 ATPase) cofactor p47, SEP domain 54236 - Ubiquitin-like	0	DIRECT
101238,46934 101238 - XPC-binding domain 46934 - UBA-like	0	DIRECT
53756,56784 53756 - UDP-Glycosyltransferase/glycogen phosphorylase 56784 - HAD-like	0	DIRECT
54980,54980 54980 - EF-G C-terminal domain-like 54980 - EF-G C-terminal domain-like	0	DIRECT
158639,63748 158639 - ENT-like 63748 - Tudor/PWWP/MBT	0	DIRECT
54534,48452 54534 - FKBP-like 48452 - TPR-like	0	DIRECT
55920,46785 55920 - Creatinase/aminopeptidase 46785 - "Winged helix" DNA-binding domain	0	DIRECT
88697,52374 88697 - PUA domain-like 52374 - Nucleotidylyl transferase	0	DIRECT
54768,54211 54768 - dsRNA-binding domain-like 54211 - Ribosomal protein S5 domain 2-like	0	DIRECT
158702,81296 158702 - Sec63 N-terminal domain-like 81296 - E set domains	0	DIRECT
55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase	0	DIRECT
48179,52413 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like 52413 - UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	0	DIRECT
52540,48403 52540 - P-loop containing nucleoside triphosphate hydrolases 48403 - Ankyrin repeat	0	DIRECT
81296,52540 81296 - E set domains 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
63411,63411 63411 - LuxS/MPP-like metallohydrolase 63411 - LuxS/MPP-like metallohydrolase	0	DIRECT
53850,55021 53850 - Periplasmic binding protein-like II 55021 - ACT-like	0	DIRECT
54826,51604 54826 - Enolase N-terminal domain-like 51604 - Enolase C-terminal domain-like	0	DIRECT
56112,48371 56112 - Protein kinase-like (PK-like) 48371 - ARM repeat	0	DIRECT
54637,54637 54637 - Thioesterase/thiol ester dehydrase-isomerase 54637 - Thioesterase/thiol ester dehydrase-isomerase	0	DIRECT
88946,88659 88946 - Sigma2 domain of RNA polymerase sigma factors 88659 - Sigma3 and sigma4 domains of RNA polymerase sigma factors	0	DIRECT
81811,82754 81811 - Helical domain of Sec23/24 82754 - C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
48452,54277 48452 - TPR-like 54277 - CAD & PB1 domains	0	DIRECT
55874,52172 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 52172 - CheY-like	0	DIRECT
53383,53383 53383 - PLP-dependent transferases 53383 - PLP-dependent transferases	0	DIRECT
54160,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
53633,55021 53633 - Carbamate kinase-like 55021 - ACT-like	0	DIRECT
52283,51735 52283 - Formate/glycerate dehydrogenase catalytic domain-like 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
57850,57933 57850 - RING/U-box 57933 - TAZ domain	0	DIRECT
101690,69065 101690 - PAZ domain 69065 - RNase III domain-like	0	DIRECT
55785,55785 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
51905,55424 51905 - FAD/NAD(P)-binding domain 55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	DIRECT
53738,53738 53738 - Phosphoglucomutase, first 3 domains 53738 - Phosphoglucomutase, first 3 domains	0	DIRECT
69065,54768 69065 - RNase III domain-like 54768 - dsRNA-binding domain-like	0	DIRECT
55781,55781 55781 - GAF domain-like 55781 - GAF domain-like	0	DIRECT
54665,56003 54665 - CO dehydrogenase molybdoprotein N-domain-like 56003 - Molybdenum cofactor-binding domain	0	DIRECT
53187,55031 53187 - Zn-dependent exopeptidases 55031 - Bacterial exopeptidase dimerisation domain	0	DIRECT
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
82171,53474 82171 - DPP6 N-terminal domain-like 53474 - alpha/beta-Hydrolases	0	DIRECT
81995,81811 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24	0	DIRECT
56176,55447 56176 - FAD-binding/transporter-associated domain-like 55447 - CO dehydrogenase flavoprotein C-terminal domain-like	0	DIRECT
50104,50249 50104 - Translation proteins SH3-like domain 50249 - Nucleic acid-binding proteins	0	DIRECT
52172,52172 52172 - CheY-like 52172 - CheY-like	0	DIRECT
50156,52096 50156 - PDZ domain-like 52096 - ClpP/crotonase	0	DIRECT
52540,52058 52540 - P-loop containing nucleoside triphosphate hydrolases 52058 - L domain-like	0	DIRECT
51735,55347 51735 - NAD(P)-binding Rossmann-fold domains 55347 - Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	0.0002755	DIRECT
51735,48179 51735 - NAD(P)-binding Rossmann-fold domains 48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like	0.0007521	DIRECT