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  
d2odka1  (   2 )     hvWpvqdakarfseFldaCite-gpQivSrrgaeeavlvpigewrrlqa
d3d55a-  (   1 )     msisaseArqrlfplieqVntdhqpVritsra-gdavlmSaddydawqe
d7bwfb1  (   1 )    miiknysyArqnlkalmtkvnddsdmvtvtstddknvvimSesdynsmme
                      bbbaaaaaa aaaaaaaaaa    bbbb      bbb  aaaaaaaaa

                             60        70        80  
d2odka1  (  50 )    aa                               
d3d55a-  (  49 )    tvyllrspenarrlmeavar             
d7bwfb1  (  51 )    tlylqqnpnnaehlaqsiadlergktitkdidv
                    a

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d2odka1 # 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 d2odka1 # 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 NE2111	YefM-like	Nitrosomonas europaea [TaxId: 915]	view
d3d55a- # 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 d3d55a- # 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	Mycobacterium tuberculosis [TaxId: 1773]	view
d7bwfb1 # 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 d7bwfb1 # 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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-	H	V	W	P	V	Q	D	A	K	A	R	F	S	E	F	L	D	A	C	I	T	E	-	G	P	Q	I	V	S	R	R	G	A	E	E	A	V	L	V	P	I	G	E	W	R	R	L	Q	A	A	A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
-	M	S	I	S	A	S	E	A	R	Q	R	L	F	P	L	I	E	Q	V	N	T	D	H	Q	P	V	R	I	T	S	R	A	-	G	D	A	V	L	M	S	A	D	D	Y	D	A	W	Q	E	T	V	Y	L	L	R	S	P	E	N	A	R	R	L	M	E	A	V	A	R	-	-	-	-	-	-	-	-	-	-	-	-	-
M	I	I	K	N	Y	S	Y	A	R	Q	N	L	K	A	L	M	T	K	V	N	D	D	S	D	M	V	T	V	T	S	T	D	D	K	N	V	V	I	M	S	E	S	D	Y	N	S	M	M	E	T	L	Y	L	Q	Q	N	P	N	N	A	E	H	L	A	Q	S	I	A	D	L	E	R	G	K	T	I	T	K	D	I	D	V

Member	Chain	UniProtKB	GO term

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

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

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