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  
d1vmha-  (   5 )        ieysl-TsnddqFidItnlVkkAVdesgvsdgmAvVfCphttAGIt
d1vmja-  (   1 )    msyrkelwfhTkrrrefinITplLeeCVreSgikeglLlCNAmhiTASVf
d2cu5a-  (   1 )    megvvrleVpTp-eegFvnItrkVeaaLs--gh-tglVyLfVphtTCGLt
d2p6ha-  (   1 )     metgsftVkTerrLqVldvtgkVeewlstvggvnglLvVyVphttAAVa
                        bbbbb      bbbb aaaaaaaaa      bbbbbb     bbbb

                             60        70        80        90        100 
d1vmha-  (  51 )    inenadpdvtrdilvnldkvfpvg--dykh---vegnshAhiKaslmgss
d1vmja-  (  52 )    indd-epglhhdfevwLeklApepysqykhNdtgednaDAhlKrtiMgre
d2cu5a-  (  47 )    vqegadptvaqdllgrlaelAprhrpqdrh---legnsHAhlKSlltgvh
d2p6ha-  (  50 )    Vnea-eprlmedivefIrelTkpgg-pwkhnl-vdvnaHAhlGntiigds
                    bb    aaaaaaaaaaaaaa                 aaaaaaaaaa  b

                             110       120       130      
d1vmha-  (  97 )    qqIiIengkLklgtwqGIyFTEFdGprdRkVfVkIi  
d1vmja-  ( 102 )    vvIaItdrkMdlgpweqVFYGEFdGmrpKrVlVkIig 
d2cu5a-  (  94 )    llllAekgrLrlgrwqqVFLAEFdGprvReVwVrll  
d2p6ha-  (  97 )    rvIpVvggrLslgtwqrILFVEMdGpreRtVnLlYlge
                    bbbbbb  bb      bbbbbb      bbbbbbbb

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d1vmha- # 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 d1vmha- # 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	B.subtilis YugU ortolog CAC0907	YjbQ-like	Clostridium acetobutylicum [TaxId: 1488]	view
d1vmja- # 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 d1vmja- # 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 TM0723	YjbQ-like	Thermotoga maritima [TaxId: 2336]	view
d2cu5a- # 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 d2cu5a- # 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
d2p6ha- # 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 d2p6ha- # 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	Aeropyrum pernix [TaxId: 56636]	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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-	-	-	-	I	E	Y	S	L	-	T	S	N	D	D	Q	F	I	D	I	T	N	L	V	K	K	A	V	D	E	S	G	V	S	D	G	M	A	V	V	F	C	P	H	T	T	A	G	I	T	I	N	E	N	A	D	P	D	V	T	R	D	I	L	V	N	L	D	K	V	F	P	V	G	-	-	D	Y	K	H	-	-	-	V	E	G	N	S	H	A	H	I	K	A	S	L	M	G	S	S	Q	Q	I	I	I	E	N	G	K	L	K	L	G	T	W	Q	G	I	Y	F	T	E	F	D	G	P	R	D	R	K	V	F	V	K	I	I	-	-
M	S	Y	R	K	E	L	W	F	H	T	K	R	R	R	E	F	I	N	I	T	P	L	L	E	E	C	V	R	E	S	G	I	K	E	G	L	L	L	C	N	A	M	H	I	T	A	S	V	F	I	N	D	D	-	E	P	G	L	H	H	D	F	E	V	W	L	E	K	L	A	P	E	P	Y	S	Q	Y	K	H	N	D	T	G	E	D	N	A	D	A	H	L	K	R	T	I	M	G	R	E	V	V	I	A	I	T	D	R	K	M	D	L	G	P	W	E	Q	V	F	Y	G	E	F	D	G	M	R	P	K	R	V	L	V	K	I	I	G	-
M	E	G	V	V	R	L	E	V	P	T	P	-	E	E	G	F	V	N	I	T	R	K	V	E	A	A	L	S	-	-	G	H	-	T	G	L	V	Y	L	F	V	P	H	T	T	C	G	L	T	V	Q	E	G	A	D	P	T	V	A	Q	D	L	L	G	R	L	A	E	L	A	P	R	H	R	P	Q	D	R	H	-	-	-	L	E	G	N	S	H	A	H	L	K	S	L	L	T	G	V	H	L	L	L	L	A	E	K	G	R	L	R	L	G	R	W	Q	Q	V	F	L	A	E	F	D	G	P	R	V	R	E	V	W	V	R	L	L	-	-
-	M	E	T	G	S	F	T	V	K	T	E	R	R	L	Q	V	L	D	V	T	G	K	V	E	E	W	L	S	T	V	G	G	V	N	G	L	L	V	V	Y	V	P	H	T	T	A	A	V	A	V	N	E	A	-	E	P	R	L	M	E	D	I	V	E	F	I	R	E	L	T	K	P	G	G	-	P	W	K	H	N	L	-	V	D	V	N	A	H	A	H	L	G	N	T	I	I	G	D	S	R	V	I	P	V	V	G	G	R	L	S	L	G	T	W	Q	R	I	L	F	V	E	M	D	G	P	R	E	R	T	V	N	L	L	Y	L	G	E

Member	Chain	UniProtKB	GO term

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

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

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