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  
d1wn2a-  (   4 )    mfkykQVIVAradlkLskgklaaQvahGavtAafeAykkkrewfeaWfre
d2gaxa1  (   2 )     fdtkIAViLrdd--LavwqklnVtafL-sgivaqt--------geIige
                       bbbb          aaaaaaaaaa   aaaaa               

                             60        70        80        90        100 
d1wn2a-  (  54 )    --------------gqkkvvVkVeseeeLfklkaeAeklgLpnalirdag
d2gaxa1  (  41 )    pyrdgagnvynplsiQpivvat--dqeaLrkIhqrSlerdittslyIeef
                                     bb      aaaaaaaaaaaaa       bb   

                             110       120       130       140  
d1wn2a-  (  90 )    Lt----eip-------pgtvTVLAVGPAPeeiVdkVTgnlkll 
d2gaxa1  (  91 )    atghdaanrqvfshfspdtAkVVGALradrkiVdkItkgaklha
                                         bbb bbbbaaaaaaa

Domains
Outliers

Domain ID	Name	Family	Source	Domain	STRING-DB
d1wn2a- # 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 d1wn2a- # 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	Pyrococcus horikoshii OT3 [TaxId: 70601]		view
d2gaxa1 # 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 d2gaxa1 # 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	Hypothetical protein Atu0240	Peptidyl-tRNA hydrolase II	Agrobacterium tumefaciens [TaxId: 358]		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

									10										20										30										40										50										60										70										80										90										100										110										120										130										140
M	F	K	Y	K	Q	V	I	V	A	R	A	D	L	K	L	S	K	G	K	L	A	A	Q	V	A	H	G	A	V	T	A	A	F	E	A	Y	K	K	K	R	E	W	F	E	A	W	F	R	E	-	-	-	-	-	-	-	-	-	-	-	-	-	-	G	Q	K	K	V	V	V	K	V	E	S	E	E	E	L	F	K	L	K	A	E	A	E	K	L	G	L	P	N	A	L	I	R	D	A	G	L	T	-	-	-	-	E	I	P	-	-	-	-	-	-	-	P	G	T	V	T	V	L	A	V	G	P	A	P	E	E	I	V	D	K	V	T	G	N	L	K	L	L	-
-	F	D	T	K	I	A	V	I	L	R	D	D	-	-	L	A	V	W	Q	K	L	N	V	T	A	F	L	-	S	G	I	V	A	Q	T	-	-	-	-	-	-	-	-	G	E	I	I	G	E	P	Y	R	D	G	A	G	N	V	Y	N	P	L	S	I	Q	P	I	V	V	A	T	-	-	D	Q	E	A	L	R	K	I	H	Q	R	S	L	E	R	D	I	T	T	S	L	Y	I	E	E	F	A	T	G	H	D	A	A	N	R	Q	V	F	S	H	F	S	P	D	T	A	K	V	V	G	A	L	R	A	D	R	K	I	V	D	K	I	T	K	G	A	K	L	H	A

Member	Chain	UniProtKB	GO term

									10										20										30										40										50										60										70										80										90										100										110										120										130										140
M	F	K	Y	K	Q	V	I	V	A	R	A	D	L	K	L	S	K	G	K	L	A	A	Q	V	A	H	G	A	V	T	A	A	F	E	A	Y	K	K	K	R	E	W	F	E	A	W	F	R	E	-	-	-	-	-	-	-	-	-	-	-	-	-	-	G	Q	K	K	V	V	V	K	V	E	S	E	E	E	L	F	K	L	K	A	E	A	E	K	L	G	L	P	N	A	L	I	R	D	A	G	L	T	-	-	-	-	E	I	P	-	-	-	-	-	-	-	P	G	T	V	T	V	L	A	V	G	P	A	P	E	E	I	V	D	K	V	T	G	N	L	K	L	L	-
-	F	D	T	K	I	A	V	I	L	R	D	D	-	-	L	A	V	W	Q	K	L	N	V	T	A	F	L	-	S	G	I	V	A	Q	T	-	-	-	-	-	-	-	-	G	E	I	I	G	E	P	Y	R	D	G	A	G	N	V	Y	N	P	L	S	I	Q	P	I	V	V	A	T	-	-	D	Q	E	A	L	R	K	I	H	Q	R	S	L	E	R	D	I	T	T	S	L	Y	I	E	E	F	A	T	G	H	D	A	A	N	R	Q	V	F	S	H	F	S	P	D	T	A	K	V	V	G	A	L	R	A	D	R	K	I	V	D	K	I	T	K	G	A	K	L	H	A

									10										20										30										40										50										60										70										80										90										100										110										120										130										140
M	F	K	Y	K	Q	V	I	V	A	R	A	D	L	K	L	S	K	G	K	L	A	A	Q	V	A	H	G	A	V	T	A	A	F	E	A	Y	K	K	K	R	E	W	F	E	A	W	F	R	E	-	-	-	-	-	-	-	-	-	-	-	-	-	-	G	Q	K	K	V	V	V	K	V	E	S	E	E	E	L	F	K	L	K	A	E	A	E	K	L	G	L	P	N	A	L	I	R	D	A	G	L	T	-	-	-	-	E	I	P	-	-	-	-	-	-	-	P	G	T	V	T	V	L	A	V	G	P	A	P	E	E	I	V	D	K	V	T	G	N	L	K	L	L	-
-	F	D	T	K	I	A	V	I	L	R	D	D	-	-	L	A	V	W	Q	K	L	N	V	T	A	F	L	-	S	G	I	V	A	Q	T	-	-	-	-	-	-	-	-	G	E	I	I	G	E	P	Y	R	D	G	A	G	N	V	Y	N	P	L	S	I	Q	P	I	V	V	A	T	-	-	D	Q	E	A	L	R	K	I	H	Q	R	S	L	E	R	D	I	T	T	S	L	Y	I	E	E	F	A	T	G	H	D	A	A	N	R	Q	V	F	S	H	F	S	P	D	T	A	K	V	V	G	A	L	R	A	D	R	K	I	V	D	K	I	T	K	G	A	K	L	H	A

									10										20										30										40										50										60										70										80										90										100										110										120										130										140
M	F	K	Y	K	Q	V	I	V	A	R	A	D	L	K	L	S	K	G	K	L	A	A	Q	V	A	H	G	A	V	T	A	A	F	E	A	Y	K	K	K	R	E	W	F	E	A	W	F	R	E	-	-	-	-	-	-	-	-	-	-	-	-	-	-	G	Q	K	K	V	V	V	K	V	E	S	E	E	E	L	F	K	L	K	A	E	A	E	K	L	G	L	P	N	A	L	I	R	D	A	G	L	T	-	-	-	-	E	I	P	-	-	-	-	-	-	-	P	G	T	V	T	V	L	A	V	G	P	A	P	E	E	I	V	D	K	V	T	G	N	L	K	L	L	-
-	F	D	T	K	I	A	V	I	L	R	D	D	-	-	L	A	V	W	Q	K	L	N	V	T	A	F	L	-	S	G	I	V	A	Q	T	-	-	-	-	-	-	-	-	G	E	I	I	G	E	P	Y	R	D	G	A	G	N	V	Y	N	P	L	S	I	Q	P	I	V	V	A	T	-	-	D	Q	E	A	L	R	K	I	H	Q	R	S	L	E	R	D	I	T	T	S	L	Y	I	E	E	F	A	T	G	H	D	A	A	N	R	Q	V	F	S	H	F	S	P	D	T	A	K	V	V	G	A	L	R	A	D	R	K	I	V	D	K	I	T	K	G	A	K	L	H	A