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  
d2ywqa1  (   2 )     niykLiGrnleitdairdyVekklarLdryqdg-eLakVVLslag----
d3tqma-  (   2 )     hi-q-tGqgvdispalreltekklhriqpcrdeIsnIhIifhink---l
d3v2cy-  (   2 )     tm-nitSkqMeitpairqhVadrLakLekwqthlinPhIiLskep---q
d4fyla1  (   2 )     qi-nIqghhidltdsmqdyVhskFdkLerffdhinhVqViLrvek---l
d6qbza-  (   1 )    mirfeihGdnltitdairnyieekigkleryFndvpnAvAhvkvktysns
                        b bbb     aaaaaaaaaaa             bbbbbb      

                             60        70        80        90        100 
d2ywqa1  (  53 )    kArAeIqVdLpgglvrVeeedadlyaAIdrAVdrLetqVkrfr       
d3tqma-  (  47 )    kkIvdAnVkLpgstinaqaesdd-ykTvdlL-hkLetqLskykak     
d3v2cy-  (  47 )    gfvAdAtInTpngvLvasGkh-dmytAIneLInkLerqLnklqhkgearr
d4fyla1  (  47 )    rqIAeAtLhVnqaeihahaddenMyaAIdsLvdkLvrqLnkh        
d6qbza-  (  51 )    atkievtiplknvtlraeernddlyaGidlinnklerqvrkyktrinrks
                     bbbbbbbbb  bbbbbbb    aaaaaaaaaaaaaaaaaa         

                             110 
d2ywqa1                       
d3tqma-                       
d3v2cy-                       
d4fyla1                       
d6qbza-  ( 101 )    rdrgdqevfv

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d2ywqa1 # 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 d2ywqa1 # 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	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	Thermus thermophilus [TaxId: 274]	view
d3tqma- # 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 d3tqma- # 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	Coxiella burnetii [TaxId: 777]	view
d3v2cy- # 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 d3v2cy- # 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	Ribosome binding protein Y (YfiA homologue)	Escherichia coli K-12 [TaxId: 83333]	view
d4fyla1 # 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 d4fyla1 # 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	Vibrio cholerae [TaxId: 666]	view
d6qbza- # 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 d6qbza- # 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	Staphylococcus aureus [TaxId: 1280]	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	I	R	F	E	I	H	G	D	N	L	T	I	T	D	A	I	R	N	Y	I	E	E	K	I	G	K	L	E	R	Y	F	N	D	V	P	N	A	V	A	H	V	K	V	K	T	Y	S	N	S	A	T	K	I	E	V	T	I	P	L	K	N	V	T	L	R	A	E	E	R	N	D	D	L	Y	A	G	I	D	L	I	N	N	K	L	E	R	Q	V	R	K	Y	K	T	R	I	N	R	K	S	R	D	R	G	D	Q	E	V	F	V

Member	Chain	UniProtKB	GO term
d2ywqa1	A	Q5SIS0	GO:0044238
d2ywqa1	A	Q5SIS0	GO:0044238

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

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

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