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  
d1ucsa-  (   1 )           nkaSvvAnqlipintaltlimMkaevvt--pmGipaeeipklv
d1vlia1  ( 297 )      eirnfayrGIFTtapIqkgeaFsednIavlrPgqkpqGlhprffelLt
d2wqpa2  ( 282 )    ekptkdfafaSVVAdkdIkkgelLsgdnLwvkrpgn--GdfsvneyetLf
                              bbbb              bbbb          333     

                             60        70   
d1ucsa-  (  42 )    -gmqvnravplgttlmpdmvknye
d1vlia1  ( 345 )    sgvrAvrdIpadtGIvwdDIllkd
d2wqpa2  ( 330 )    -gkvAacnIrkgaqIkktDie   
                                    333

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d1ucsa- # 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 d1ucsa- # 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	Type III antifreeze protein, AFP III	AFP III-like domain	Antarctic eel pout (Lycodichthys dearborni), RD1 isoform [TaxId: 8201]	view
d1vlia1 # 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 d1vlia1 # 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	Spore coat polysaccharide biosynthesis protein SpsE, C-terminal domain	AFP III-like domain	Bacillus subtilis [TaxId: 1423]	view
d2wqpa2 # 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 d2wqpa2 # 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	Neisseria meningitidis [TaxId: 491]	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
-	-	-	-	-	-	-	N	K	A	S	V	V	A	N	Q	L	I	P	I	N	T	A	L	T	L	I	M	M	K	A	E	V	V	T	-	-	P	M	G	I	P	A	E	E	I	P	K	L	V	-	G	M	Q	V	N	R	A	V	P	L	G	T	T	L	M	P	D	M	V	K	N	Y	E
-	-	E	I	R	N	F	A	Y	R	G	I	F	T	T	A	P	I	Q	K	G	E	A	F	S	E	D	N	I	A	V	L	R	P	G	Q	K	P	Q	G	L	H	P	R	F	F	E	L	L	T	S	G	V	R	A	V	R	D	I	P	A	D	T	G	I	V	W	D	D	I	L	L	K	D
E	K	P	T	K	D	F	A	F	A	S	V	V	A	D	K	D	I	K	K	G	E	L	L	S	G	D	N	L	W	V	K	R	P	G	N	-	-	G	D	F	S	V	N	E	Y	E	T	L	F	-	G	K	V	A	A	C	N	I	R	K	G	A	Q	I	K	K	T	D	I	E	-	-	-

Member	Chain	UniProtKB	GO term
d1ucsa_	A	P35751	GO:0005576
d1vlia1	A	P39625	GO:0016051
d1vlia1	A	P39625	GO:0047444
d1vlia1	A	P39625	GO:0070085
d1vlia1	A	P39625	GO:0016051
d1vlia1	A	P39625	GO:0047444
d1vlia1	A	P39625	GO:0070085
d1vlia1	A	P39625	GO:0016051
d1vlia1	A	P39625	GO:0047444
d1vlia1	A	P39625	GO:0070085

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

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

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