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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
Lipoxigenase	0	DIRECT
RNase III domain-like	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
TATA-box binding protein-like	0	DIRECT
Domain of the SRP/SRP receptor G-proteins	0	DIRECT
Prokaryotic type KH domain (KH-domain type II)	0	DIRECT
EF-G C-terminal domain-like	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
YrdC/RibB	0	DIRECT
EGF/Laminin	0	DIRECT
CO dehydrogenase flavoprotein C-terminal domain-like	0	DIRECT
ATP-dependent DNA ligase DNA-binding domain	0	DIRECT
NHL repeat	0	DIRECT
Prokaryotic type I DNA topoisomerase	0	DIRECT
Chelatase	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	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
Prefoldin	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
PLP-binding barrel	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
HesB-like domain	0	DIRECT
DNA ligase/mRNA capping enzyme, catalytic domain	0	DIRECT
S15/NS1 RNA-binding domain	0	DIRECT
TAZ domain	0	DIRECT
Lipocalins	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
FKBP-like	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	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
Formyltransferase	0	DIRECT
Folate-binding domain	0	DIRECT
PapD-like	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
XPC-binding domain	0	DIRECT
Crambin-like	0	DIRECT
Ribosomal protein S6	0	DIRECT
Heme oxygenase-like	0	DIRECT
Peptidyl-tRNA hydrolase-like	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
Ribosomal protein L4	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
Ribonuclease PH domain 2-like	0	DIRECT
LigT-like	0	DIRECT
Enolase C-terminal domain-like	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
LysM domain	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
Single hybrid motif	0	DIRECT
AMPKBI-like	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
eIF1-like	0	DIRECT
Oxygen-evolving enhancer protein 3,	0	DIRECT
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
CO dehydrogenase ISP C-domain like	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
S13-like H2TH domain	0	DIRECT
Rubredoxin-like	0	DIRECT
SIS domain	0	DIRECT
Cryptochrome/photolyase FAD-binding domain	0	DIRECT
GINS helical bundle-like	0	DIRECT
MurD-like peptide ligases, catalytic domain	0	DIRECT
NAD(P)-linked oxidoreductase	0	DIRECT
Signal peptide-binding domain	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Aldolase	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 S10	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
Acyl-CoA binding protein	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
Enolase N-terminal domain-like	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Ribosomal protein L31e	0	DIRECT
Isochorismatase-like hydrolases	0	DIRECT
CYTH-like phosphatases	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
Supernatant protein factor (SPF), C-terminal domain	0	DIRECT
PAH2 domain	0	DIRECT
Ribosomal protein L14	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
Formate/glycerate dehydrogenase catalytic domain-like	0	DIRECT
Activating enzymes of the ubiquitin-like proteins	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
tRNA-binding arm	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
Ribosomal protein L1	0	DIRECT
Amine oxidase catalytic domain	0	DIRECT
Putative isomerase YbhE	0	DIRECT
Mitochondrial glycoprotein MAM33-like	0	DIRECT
Endosomal sorting complex assembly domain	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
RL5-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
Preprotein translocase SecE subunit	0	DIRECT
GroEL apical domain-like	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
E2F-DP heterodimerization region	0	DIRECT
Quinoprotein alcohol dehydrogenase-like	0	DIRECT
Ribulose-phoshate binding barrel	0	DIRECT
PX domain	0	DIRECT
beta-sandwich domain of Sec23/24	0	DIRECT
Radical SAM enzymes	0	DIRECT
ssDNA-binding transcriptional regulator domain	0	DIRECT
Flavoproteins	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
Ribosomal protein L39e	0	DIRECT
Ribosomal protein L13	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
Zn-finger domain of Sec23/24	0	DIRECT
Nicotinate/Quinolinate PRTase N-terminal domain-like	0	DIRECT
Clc chloride channel	0	DIRECT
RplX-like	0	DIRECT
Ribosomal protein L30p/L7e	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
Ribosomal proteins S24e, L23 and L15e	0	DIRECT
Ribosomal protein L16p/L10e	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Release factor	0	DIRECT
Chorismate mutase II	0	DIRECT
NagB/RpiA/CoA transferase-like	0	DIRECT
Probable bacterial effector-binding domain	0	DIRECT
Poly A polymerase C-terminal region-like	0	DIRECT
Nicotinate/Quinolinate PRTase C-terminal domain-like	0	DIRECT
Ribosomal proteins L15p and L18e	0	DIRECT
Amidase signature (AS) enzymes	0	DIRECT
PreATP-grasp domain	0	DIRECT
Cysteine alpha-hairpin motif	0	DIRECT
Cyclophilin-like	0	DIRECT
Plus3-like	0	DIRECT
R3H domain	0	DIRECT
alpha/beta knot	0	DIRECT
Head domain of nucleotide exchange factor GrpE	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
Mss4-like	0	DIRECT
Phosphoglycerate kinase	0	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 L5	0	DIRECT
Crambin-like	0	DIRECT
BolA-like	0	DIRECT
Ribosomal protein L19 (L19e)	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
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
GAPDH-like	0	DIRECT
Class-II DAHP synthetase	0	DIRECT
Cyclin A/CDK2-associated p19, Skp2	0	DIRECT
PhzC/PhzF-like	0	DIRECT
Methyl-CpG-binding domain, MBD	0	DIRECT
Spermidine synthase	0	DIRECT
Molybdenum cofactor biosynthesis protein MoeB	0	DIRECT
MutT-like	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
HMGL-like	0	DIRECT
DNA repair glycosylase, 2 C-terminal domains	0	DIRECT
SelR domain	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
CAT-like	0	DIRECT
Sigma4 domain	0	DIRECT
Ribosomal protein L14	0	DIRECT
Ribosomal protein S15	0	DIRECT
FAH	0	DIRECT
Enolase	0	DIRECT
Enolase N-terminal domain-like	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
Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
GroEL chaperone, ATPase domain	0	DIRECT
N-acetyl-l-glutamate kinase	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
D-ribose-5-phosphate isomerase (RpiA), lid domain	0	DIRECT
Ubiquitin carboxyl-terminal hydrolase UCH-L	0	DIRECT
Shikimate kinase (AroK)	0	DIRECT
DNase I-like	0	DIRECT
Cyclophilin (peptidylprolyl isomerase)	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
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
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
Clc chloride channel	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Trehalose-6-phosphate synthase, OtsA	0	DIRECT
Domain of the SRP/SRP receptor G-proteins	0	DIRECT
Isochorismatase-like hydrolases	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
R3H domain	0	DIRECT
Serine acetyltransferase	0	DIRECT
Glyoxalase II (hydroxyacylglutathione hydrolase)	0	DIRECT
Cytochrome b5	0	DIRECT
Amine oxidase catalytic domain	0	DIRECT
Rubredoxin	0	DIRECT
Ribosomal protein L18 and S11	0	DIRECT
Myf domain	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Translational machinery components	0	DIRECT
GroEL-like chaperone, intermediate domain	0	DIRECT
CoA-binding domain	0	DIRECT
LEA14-like	0	DIRECT
Amidase signature (AS) enzymes	0	DIRECT
HCDH C-domain-like	0	DIRECT
Phosphoenolpyruvate mutase/Isocitrate lyase-like	0	DIRECT
GroES	0	DIRECT
Thiolase-related	0	DIRECT
Sec63 C-terminal domain-like	0	DIRECT
Linker histone H1/H5	0	DIRECT
Smc hinge domain	0	DIRECT
BSD domain	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
Formyltransferase	0	DIRECT
CO dehydrogenase flavoprotein N-terminal domain-like	0	DIRECT
GABARAP-like	0	DIRECT
LON domain-like	0	DIRECT
IPP isomerase-like	0	DIRECT
Ribosomal protein L10-like	0	DIRECT
Pseudouridine synthase I TruA	0	DIRECT
HD domain	0	DIRECT
PAPS reductase-like	0	DIRECT
YicI N-terminal domain-like	0	DIRECT
Eps15 homology domain (EH domain)	0	DIRECT
Branched-chain alpha-keto acid dehydrogenase Pyr module	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
BC N-terminal domain-like	0	DIRECT
RNB domain-like	0	DIRECT
Poly A polymerase C-terminal region-like	0	DIRECT
CAF1-like ribonuclease	0	DIRECT
C5 cytosine-specific DNA methylase, DCM	0	DIRECT
HEAT repeat	0	DIRECT
PUA domain	0	DIRECT
RWD domain	0	DIRECT
RplX-like	0	DIRECT
SerA intervening domain-like	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
Lipoxigenase N-terminal domain	0	DIRECT
beta-carbonic anhydrase, cab	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
Plus3	0	DIRECT
MSP-like	0	DIRECT
Choline kinase	0	DIRECT
Type II chitinase	0	DIRECT
Tryptophan biosynthesis enzymes	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
NagB-like	0	DIRECT
Ribosomal proteins L24p and L21e	0	DIRECT
PX domain	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
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
Plant transcriptional regulator PBF-2	0	DIRECT
Succinyl-CoA synthetase, beta-chain, N-terminal domain	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Prolyl oligopeptidase, N-terminal domain	0	DIRECT
Ribosomal proteins L15p and L18e	0	DIRECT
RNA polymerase II subunit RBP4 (RpoF)	0	DIRECT
RNase III catalytic domain-like	0	DIRECT
Tail specific protease, catalytic domain	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
UDP-glucose/GDP-mannose dehydrogenase dimerisation domain	0	DIRECT
gamma-carbonic anhydrase-like	0	DIRECT
Heme-dependent catalases	0	DIRECT
MIF-related	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	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
RuBisCo LSMT catalytic domain	0	DIRECT
eIF5a N-terminal domain-like	0	DIRECT
Pseudouridine synthase II TruB	0	DIRECT
CYTH domain	0	DIRECT
CO dehydrogenase flavoprotein C-terminal domain-like	0	DIRECT
Acyl-ACP thioesterase-like	0	DIRECT
beta-Phosphoglucomutase-like	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Neurolysin-like	0	DIRECT
Molybdenum cofactor-binding domain	0	DIRECT
Sec63 N-terminal domain	0	DIRECT
Group II chaperonin (CCT, TRIC), ATPase domain	0	DIRECT
DJ-1/PfpI	0	DIRECT
Starch-binding domain	0	DIRECT
Trunk domain of Sec23/24	0	DIRECT
AMPK-beta glycogen binding domain-like	0	DIRECT
LysM domain	0	DIRECT
Transducin (alpha subunit), insertion domain	0	DIRECT
Glyoxalase I (lactoylglutathione lyase)	0	DIRECT
PsbP-like	0	DIRECT
Phytochrome-specific domain	0	DIRECT
TAZ domain	0	DIRECT
NADPH-cytochrome p450 reductase FAD-binding domain-like	0	DIRECT
DNA ligase/mRNA capping enzyme postcatalytic domain	0	DIRECT
Hypothetical protein HI1317	0	DIRECT
Dihydrodipicolinate reductase-like	0	DIRECT
Poly(ADP-ribose) polymerase, C-terminal domain	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Aminomethyltransferase folate-binding domain	0	DIRECT
Class I alpha-1;2-mannosidase, catalytic domain	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
SH3-domain	0	DIRECT
ATP sulfurylase catalytic domain	0	DIRECT
Amylase, 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
ATP-dependent DNA ligase catalytic domain	0	DIRECT
NLI interacting factor-like phosphatase	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
Formate/glycerate dehydrogenases, substrate-binding domain	0	DIRECT
Clathrin coat assembly domain	0	DIRECT
Molybdenum-containing oxidoreductases-like dimerisation domain	0	DIRECT
Prefoldin	0	DIRECT
Ribosomal protein L19	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Ribosomal S5 protein, N-terminal domain	0	DIRECT
ATP-dependent DNA ligase DNA-binding domain	0	DIRECT
Allosteric chorismate mutase	0	DIRECT
Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	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
Histidine kinase	0	DIRECT
monodomain cytochrome c	0	DIRECT
Ribosomal protein L37e	0	DIRECT
Nitrogenase iron protein-like	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
Formate/glycerate dehydrogenases, NAD-domain	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 PP module	0	DIRECT
IF2B-like	0	DIRECT
Homocysteine S-methyltransferase	0	DIRECT
Ran-binding domain	0	DIRECT
Ribosomal protein L4	0	DIRECT
EDF1-like	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
alpha-Amylases, C-terminal beta-sheet domain	0	DIRECT
E2F dimerization segment	0	DIRECT
Peptidyl-tRNA hydrolase II	0	DIRECT
WrbA-like	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
FKBP immunophilin/proline isomerase	0	DIRECT
Ribonuclease PH domain 2-like	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
Rps19E-like	0	DIRECT
EF-G/eEF-2 domains III and V	0	DIRECT
PAH2 domain	0	DIRECT
eIF1-like	0	DIRECT
Acyl-CoA binding protein	0	DIRECT
STAR domain	0	DIRECT
N-type ATP pyrophosphatases	0	DIRECT
Alpha subunit of glutamate synthase, C-terminal domain	0	DIRECT
Deoxycytidylate deaminase-like	0	DIRECT
Kunitz (STI) inhibitors	0	DIRECT
ATP sulfurylase N-terminal domain	0	DIRECT
Pentapeptide repeats	0	DIRECT
Ribosomal protein S10	0	DIRECT
6-phosphogluconate dehydrogenase-like, N-terminal domain	0	DIRECT
Ribosomal protein S27e	0	DIRECT
Cystatins	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
RNA-polymerase beta	0	DIRECT
Group II chaperonin (CCT, TRIC), apical domain	0	DIRECT
MYND zinc finger	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
Ribosomal protein L29 (L29p)	0	DIRECT
Cdc48 N-terminal domain-like	0	DIRECT
Aldo-keto reductases (NADP)	0	DIRECT
Signal peptide-binding domain	0	DIRECT
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains	0	DIRECT
Aminoacid dehydrogenases	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
BC ATP-binding 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)
LigT-like	0	DIRECT
N-terminal, heterodimerisation domain of RBP7 (RpoE)	0	DIRECT
Heme oxygenase-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
Molybdenum cofactor-binding domain	0	DIRECT
Acyl-CoA binding protein	0	DIRECT
MurD-like peptide ligases, peptide-binding domain	0	DIRECT
Ribosomal protein L39e	0	DIRECT
Ribosomal protein L19 (L19e)	0	DIRECT
Cu,Zn superoxide dismutase-like	0	DIRECT
DNA repair protein MutS, domain I	0	DIRECT
Ligand-binding domain in the NO signalling and Golgi transport	0	DIRECT
Dimeric alpha+beta barrel	0	DIRECT
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
Lipoxigenase	0	DIRECT
Ribosomal protein S2	0	DIRECT
ATP-dependent DNA ligase DNA-binding domain	0	DIRECT
Succinyl-CoA synthetase domains	0	DIRECT
Creatinase/prolidase N-terminal domain	0	DIRECT
NAD(P)-linked oxidoreductase	0	DIRECT
Crambin-like	0	DIRECT
CO dehydrogenase ISP C-domain like	0	DIRECT
Prokaryotic ribosomal protein L17	0	DIRECT
Ribosomal protein S10	0	DIRECT
Peptide methionine sulfoxide reductase	0	DIRECT
RNase III domain-like	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
Ribonuclease PH domain 2-like	0	DIRECT
Mitochondrial glycoprotein MAM33-like	0	DIRECT
Rubredoxin-like	0	DIRECT
Ribosomal proteins L15p and L18e	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
Supernatant protein factor (SPF), C-terminal domain	0	DIRECT
tRNA-binding arm	0	DIRECT
CO dehydrogenase flavoprotein C-terminal domain-like	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	DIRECT
Diaminopimelate epimerase-like	0	DIRECT
Inosine monophosphate dehydrogenase (IMPDH)	0	DIRECT
L28p-like	0	DIRECT
YrdC/RibB	0	DIRECT
Enolase C-terminal domain-like	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
Formyltransferase	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
Mss4-like	0	DIRECT
NHL repeat	0	DIRECT
AMPKBI-like	0	DIRECT
FAD-dependent thiol oxidase	0	DIRECT
DNA ligase/mRNA capping enzyme, catalytic domain	0	DIRECT
Endosomal sorting complex assembly domain	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
Prefoldin	0	DIRECT
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	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
Aldolase	0	DIRECT
Preprotein translocase SecE subunit	0	DIRECT
RibA-like	0	DIRECT
Casein kinase II beta subunit	0	DIRECT
R3H domain	0	DIRECT
LeuD/IlvD-like	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
S13-like H2TH domain	0	DIRECT
NagB/RpiA/CoA transferase-like	0	DIRECT
RL5-like	0	DIRECT
Mog1p/PsbP-like	0	DIRECT
Seven-hairpin glycosidases	0	DIRECT
Cryptochrome/photolyase, N-terminal domain	0	DIRECT
Tautomerase/MIF	0	DIRECT
Amidase signature (AS) enzymes	0	DIRECT
PapD-like	0	DIRECT
Ribosomal protein L31e	0	DIRECT
CYTH-like phosphatases	0	DIRECT
Bacterial exopeptidase dimerisation domain	0	DIRECT
Ribosomal protein L16p/L10e	0	DIRECT
Gamma-glutamyl cyclotransferase-like	0	DIRECT
Domain of the SRP/SRP receptor G-proteins	0	DIRECT
Quinoprotein alcohol dehydrogenase-like	0	DIRECT
Serine metabolism enzymes domain	0	DIRECT
Nitrite and sulphite reductase 4Fe-4S domain-like	0	DIRECT
CO dehydrogenase molybdoprotein N-domain-like	0	DIRECT
Coiled-coil domain of nucleotide exchange factor GrpE	0	DIRECT
Phosphoglucomutase, first 3 domains	0	DIRECT
Plus3-like	0	DIRECT
PAH2 domain	0	DIRECT
Lipocalins	0	DIRECT
ATP synthase (F1-ATPase), gamma subunit	0	DIRECT
Activating enzymes of the ubiquitin-like proteins	0	DIRECT
GroEL-intermediate domain like	0	DIRECT
eIF1-like	0	DIRECT
Peptidyl-tRNA hydrolase II	0	DIRECT
Oxidoreductase molybdopterin-binding domain	0	DIRECT
PX domain	0	DIRECT
Helical domain of Sec23/24	0	DIRECT
RuBisCo LSMT C-terminal, substrate-binding domain	0	DIRECT
GINS helical bundle-like	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
PLP-binding barrel	0	DIRECT
FKBP-like	0	DIRECT
Rudiment single hybrid motif	0	DIRECT
Ribosomal L11/L12e N-terminal domain	0	DIRECT
Tetrapyrrole methylase	0	DIRECT
S15/NS1 RNA-binding domain	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
Tetrahydrobiopterin biosynthesis enzymes-like	0	DIRECT
DNA repair protein MutS, domain II	0	DIRECT
C-terminal, gelsolin-like domain of Sec23/24	0	DIRECT
TAZ domain	0	DIRECT
RraA-like	0	DIRECT
XPC-binding domain	0	DIRECT
Clc chloride channel	0	DIRECT
BSD domain-like	0	DIRECT
Putative isomerase YbhE	0	DIRECT
Heme-dependent catalase-like	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
LysM domain	0	DIRECT
Ribosomal protein L1	0	DIRECT
AF1104-like	0	DIRECT
GlnB-like	0	DIRECT
beta-sandwich domain of Sec23/24	0	DIRECT
Cyclophilin-like	0	DIRECT
Formate/glycerate dehydrogenase catalytic domain-like	0	DIRECT
Ribosomal protein S6	0	DIRECT
Isochorismatase-like hydrolases	0	DIRECT
Sigma2 domain of RNA polymerase sigma factors	0	DIRECT
Electron transport accessory proteins	0	DIRECT
beta-carbonic anhydrase, cab	0	DIRECT
EF-G C-terminal domain-like	0	DIRECT
Amine oxidase catalytic domain	0	DIRECT
Magnesium transport protein CorA, transmembrane region	0	DIRECT
Enolase N-terminal domain-like	0	DIRECT
Creatinase/aminopeptidase	0	DIRECT
Tim10-like	0	DIRECT
Aconitase iron-sulfur domain	0	DIRECT
P-domain of calnexin/calreticulin	0	DIRECT
Poly A polymerase C-terminal region-like	0	DIRECT
Flavoproteins	0	DIRECT
Ribulose-phoshate binding barrel	0	DIRECT
EGF/Laminin	0	DIRECT
S-adenosylmethionine synthetase	0	DIRECT
Nucleoside diphosphate kinase, NDK	0	DIRECT
Cytochrome c	0	DIRECT
Release factor	0	DIRECT