PASS2.8 - Home

solvent inaccessible: UPPER CASE X
solvent accesible: lower case x
alpha helix: red x

beta strand: blue x
3 - 10 helix: maroon x
hydrogen bond to main chain amide: bold x

hydrogen bond to mainchain carbonyl: underline x
disulphide bond: cedilla
positive phi: italic x

                             10        20        30        40        50  
d1ni3a2  ( 307 )    linYftcg--edevrswtir-kgtkApqaAgvihtdfekaFvvgeIh-yq
d1nyra2  (   4 )     inIqfpdgn-----kkafd-kgttTedIAqsispglrkkAvaGkfng--
d1tkea1  (   1 )    mPvItlpdgs-----qrhyd-haVsPmdVAldigpglakaCiaGrvng--
d1wxqa2  ( 320 )    IpVypvhdeqfgnvlphvflkkgstPrdLAfkvhtdlGkgFlyAinArtk
d2dbya2  ( 284 )    lLtFftag--ekevrawtvr-rgTkAprAAgeihsd-ergFirAeVIpwd
                      bbb                    aaaaaaaa aaaaa   bbbb    

                             60        70        80      
d1ni3a2  ( 354 )    dlfdyktenaCraagkyltkgkeyv-esgDiAhWk  
d1nyra2  (  45 )    -----------------qlvdltkpLetdgsIeiv  
d1tkea1  (  43 )    -----------------elvdacdlIendAqLsIita
d1wxqa2  ( 376 )    -----------------rrvgedyeLqfndiVkIvSv
d2dbya2  ( 331 )    klveAggwarAkergwVrlegkdyeVqdgDVIyvl-f
                                      bb             bb

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d1ni3a2 # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d1ni3a2 # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	YchF GTP-binding protein, C-terminal domain	G domain-linked domain	Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]	view
d1nyra2 # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d1nyra2 # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	Threonyl-tRNA synthetase (ThrRS), N-terminal 'additional' domain	TGS domain	Staphylococcus aureus [TaxId: 1280]	view
d1tkea1 # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d1tkea1 # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	Threonyl-tRNA synthetase (ThrRS), N-terminal 'additional' domain	TGS domain	Escherichia coli [TaxId: 562]	view
d1wxqa2 # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d1wxqa2 # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	GTP-binding protein PH0525	G domain-linked domain	Pyrococcus horikoshii [TaxId: 53953]	view
d2dbya2 # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d2dbya2 # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	automated matches	automated matches	Thermus thermophilus HB8 [TaxId: 300852]	view

No outliers

Feature	Download
Superfamily
Distance Matrix
Conserved Interactions
Cusp Results
Alistat - Alignment Statistics
SMotif - Conserved Structural Motifs
MeanRMS
PCSSE Details
Absolutely Conserved Residues
Highly Conserved Residues

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M	P	V	I	T	L	P	D	G	S	-	-	-	-	-	Q	R	H	Y	D	-	H	A	V	S	P	M	D	V	A	L	D	I	G	P	G	L	A	K	A	C	I	A	G	R	V	N	G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	E	L	V	D	A	C	D	L	I	E	N	D	A	Q	L	S	I	I	T	A
I	P	V	Y	P	V	H	D	E	Q	F	G	N	V	L	P	H	V	F	L	K	K	G	S	T	P	R	D	L	A	F	K	V	H	T	D	L	G	K	G	F	L	Y	A	I	N	A	R	T	K	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	R	R	V	G	E	D	Y	E	L	Q	F	N	D	I	V	K	I	V	S	V
L	L	T	F	F	T	A	G	-	-	E	K	E	V	R	A	W	T	V	R	-	R	G	T	K	A	P	R	A	A	G	E	I	H	S	D	-	E	R	G	F	I	R	A	E	V	I	P	W	D	K	L	V	E	A	G	G	W	A	R	A	K	E	R	G	W	V	R	L	E	G	K	D	Y	E	V	Q	D	G	D	V	I	Y	V	L	-	F

Member	Chain	UniProtKB	GO term
d1ni3a2	A	O13998	GO:0005524
d1ni3a2	A	O13998	GO:0005525
d1ni3a2	A	O13998	GO:0005634
d1ni3a2	A	O13998	GO:0005737
d1ni3a2	A	O13998	GO:0005829
d1ni3a2	A	O13998	GO:0008150
d1ni3a2	A	O13998	GO:0016787
d1ni3a2	A	O13998	GO:0016887
d1ni3a2	A	O13998	GO:0043023
d1ni3a2	A	O13998	GO:0046872
d1nyra2	A	Q8NW68	GO:0000049
d1nyra2	A	Q8NW68	GO:0000166
d1nyra2	A	Q8NW68	GO:0004812
d1nyra2	A	Q8NW68	GO:0004829
d1nyra2	A	Q8NW68	GO:0005524
d1nyra2	A	Q8NW68	GO:0005737
d1nyra2	A	Q8NW68	GO:0006412
d1nyra2	A	Q8NW68	GO:0006418
d1nyra2	A	Q8NW68	GO:0006435
d1nyra2	A	Q8NW68	GO:0016740
d1nyra2	A	Q8NW68	GO:0043039
d1nyra2	A	Q8NW68	GO:0046872
d1tkea1	A	P0A8M3	GO:0000166
d1tkea1	A	P0A8M3	GO:0004812
d1tkea1	A	P0A8M3	GO:0005524
d1tkea1	A	P0A8M3	GO:0043039
d1tkea1	A	P0A8M3	GO:0000166
d1tkea1	A	P0A8M3	GO:0004812
d1tkea1	A	P0A8M3	GO:0005524
d1tkea1	A	P0A8M3	GO:0043039
d1wxqa2	A	O58261	GO:0000166
d1wxqa2	A	O58261	GO:0005525
d1wxqa2	A	O58261	GO:0005737
d1wxqa2	A	O58261	GO:0016887

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-	I	N	I	Q	F	P	D	G	N	-	-	-	-	-	K	K	A	F	D	-	K	G	T	T	T	E	D	I	A	Q	S	I	S	P	G	L	R	K	K	A	V	A	G	K	F	N	G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	Q	L	V	D	L	T	K	P	L	E	T	D	G	S	I	E	I	V	-	-
M	P	V	I	T	L	P	D	G	S	-	-	-	-	-	Q	R	H	Y	D	-	H	A	V	S	P	M	D	V	A	L	D	I	G	P	G	L	A	K	A	C	I	A	G	R	V	N	G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	E	L	V	D	A	C	D	L	I	E	N	D	A	Q	L	S	I	I	T	A
I	P	V	Y	P	V	H	D	E	Q	F	G	N	V	L	P	H	V	F	L	K	K	G	S	T	P	R	D	L	A	F	K	V	H	T	D	L	G	K	G	F	L	Y	A	I	N	A	R	T	K	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	R	R	V	G	E	D	Y	E	L	Q	F	N	D	I	V	K	I	V	S	V
L	L	T	F	F	T	A	G	-	-	E	K	E	V	R	A	W	T	V	R	-	R	G	T	K	A	P	R	A	A	G	E	I	H	S	D	-	E	R	G	F	I	R	A	E	V	I	P	W	D	K	L	V	E	A	G	G	W	A	R	A	K	E	R	G	W	V	R	L	E	G	K	D	Y	E	V	Q	D	G	D	V	I	Y	V	L	-	F

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L	I	N	Y	F	T	C	G	-	-	E	D	E	V	R	S	W	T	I	R	-	K	G	T	K	A	P	Q	A	A	G	V	I	H	T	D	F	E	K	A	F	V	V	G	E	I	H	-	Y	Q	D	L	F	D	Y	K	T	E	N	A	C	R	A	A	G	K	Y	L	T	K	G	K	E	Y	V	-	E	S	G	D	I	A	H	W	K	-	-
-	I	N	I	Q	F	P	D	G	N	-	-	-	-	-	K	K	A	F	D	-	K	G	T	T	T	E	D	I	A	Q	S	I	S	P	G	L	R	K	K	A	V	A	G	K	F	N	G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	Q	L	V	D	L	T	K	P	L	E	T	D	G	S	I	E	I	V	-	-
M	P	V	I	T	L	P	D	G	S	-	-	-	-	-	Q	R	H	Y	D	-	H	A	V	S	P	M	D	V	A	L	D	I	G	P	G	L	A	K	A	C	I	A	G	R	V	N	G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	E	L	V	D	A	C	D	L	I	E	N	D	A	Q	L	S	I	I	T	A
I	P	V	Y	P	V	H	D	E	Q	F	G	N	V	L	P	H	V	F	L	K	K	G	S	T	P	R	D	L	A	F	K	V	H	T	D	L	G	K	G	F	L	Y	A	I	N	A	R	T	K	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	R	R	V	G	E	D	Y	E	L	Q	F	N	D	I	V	K	I	V	S	V
L	L	T	F	F	T	A	G	-	-	E	K	E	V	R	A	W	T	V	R	-	R	G	T	K	A	P	R	A	A	G	E	I	H	S	D	-	E	R	G	F	I	R	A	E	V	I	P	W	D	K	L	V	E	A	G	G	W	A	R	A	K	E	R	G	W	V	R	L	E	G	K	D	Y	E	V	Q	D	G	D	V	I	Y	V	L	-	F

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-	I	N	I	Q	F	P	D	G	N	-	-	-	-	-	K	K	A	F	D	-	K	G	T	T	T	E	D	I	A	Q	S	I	S	P	G	L	R	K	K	A	V	A	G	K	F	N	G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	Q	L	V	D	L	T	K	P	L	E	T	D	G	S	I	E	I	V	-	-
M	P	V	I	T	L	P	D	G	S	-	-	-	-	-	Q	R	H	Y	D	-	H	A	V	S	P	M	D	V	A	L	D	I	G	P	G	L	A	K	A	C	I	A	G	R	V	N	G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	E	L	V	D	A	C	D	L	I	E	N	D	A	Q	L	S	I	I	T	A
I	P	V	Y	P	V	H	D	E	Q	F	G	N	V	L	P	H	V	F	L	K	K	G	S	T	P	R	D	L	A	F	K	V	H	T	D	L	G	K	G	F	L	Y	A	I	N	A	R	T	K	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	R	R	V	G	E	D	Y	E	L	Q	F	N	D	I	V	K	I	V	S	V
L	L	T	F	F	T	A	G	-	-	E	K	E	V	R	A	W	T	V	R	-	R	G	T	K	A	P	R	A	A	G	E	I	H	S	D	-	E	R	G	F	I	R	A	E	V	I	P	W	D	K	L	V	E	A	G	G	W	A	R	A	K	E	R	G	W	V	R	L	E	G	K	D	Y	E	V	Q	D	G	D	V	I	Y	V	L	-	F