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  
d1iiba-  (   3 )       kkhIyLFSsagm-sTslLVskMraqaekyev-pViIeafpet-----
d1vkra-  ( 375 )     shvrkiivAcdaGmgsSamGagvlrkkiqdaglsqisvtnsain-----
d2kyra-  (   1 )    mskkliAlCACpmglahtfmAaqaleeAAveagY-evkiEtqgadgiqnr
d2r48a1  (   2 )       kLLAITScpngiahTy-AaenLqkAAdrlgv-sIkVEtqGgigvenk
d4tn5a-  (   2 )      ayLVAVTACvsgvahTy-AaerLeklCllekw-gvsIETqgalgtenr
                        bbbbbb           aaaaaaaaaa     bbbbbb        

                             60        70        80        90        100 
d1iiba-  (  43 )    lAgekGqnAdVVLL-GpqIaymlpeIqrlLpnkpVevIdsllYgkvdGl-
d1vkra-  ( 419 )    ---nlppdvdlvit-hrd---lterAmrqvpqaqHisltnfldsg-lYt-
d2kyra-  (  50 )    ltaqdiaeAtiiiHSvavtPe----dnerFesrdvyeitlqdAik-naa-
d2r48a1  (  48 )    LteeeireAdAIIIAAdrsVn-----kdrFigkkLlsvgVqdGir-kpe-
d4tn5a-  (  49 )    LadedIrrAdVALLITdieLa----gaerFehcryVqCsIyAFlr-epqr
                      aaaa    bbbb b                  bbbb   aaaa  aa 

                             110       120 
d1iiba-  (  91 )    -gVLkaAvaaikkaaa       
d1vkra-  ( 460 )    -slterlvaaqr---h       
d2kyra-  (  94 )    -giikeieemiaseq-------q
d2r48a1  (  91 )    -eLIqkAlngd----Ipvy    
d4tn5a-  (  94 )    VsaVrkVlsap----qqthlile
                     aaaaaaaa

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d1iiba- # 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 d1iiba- # 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	Enzyme IIB-cellobiose	PTS system, Lactose/Cellobiose specific IIB subunit	Escherichia coli [TaxId: 562]	view
d1vkra- # 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 d1vkra- # 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	PTS system mannitol-specific EIICBA component	PTS system, Lactose/Cellobiose specific IIB subunit	Escherichia coli [TaxId: 562]	view
d2kyra- # 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 d2kyra- # 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	Escherichia coli K-12 [TaxId: 83333]	view
d2r48a1 # 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 d2r48a1 # 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	Mannose-specific enzyme IIBCA component ManP, N-terminal domain	PTS system, Fructose specific IIB subunit-like	Bacillus subtilis [TaxId: 1423]	view
d4tn5a- # 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 d4tn5a- # 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	Escherichia coli [TaxId: 83333]	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	S	K	K	L	I	A	L	C	A	C	P	M	G	L	A	H	T	F	M	A	A	Q	A	L	E	E	A	A	V	E	A	G	Y	-	E	V	K	I	E	T	Q	G	A	D	G	I	Q	N	R	L	T	A	Q	D	I	A	E	A	T	I	I	I	H	S	V	A	V	T	P	E	-	-	-	-	D	N	E	R	F	E	S	R	D	V	Y	E	I	T	L	Q	D	A	I	K	-	N	A	A	-	-	G	I	I	K	E	I	E	E	M	I	A	S	E	Q	-	-	-	-	-	-	-	Q
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Member	Chain	UniProtKB	GO term
d1iiba_	A	P69795	GO:0005515
d1iiba_	A	P69795	GO:0005737
d1iiba_	A	P69795	GO:0005829
d1iiba_	A	P69795	GO:0008982
d1iiba_	A	P69795	GO:0009401
d1iiba_	A	P69795	GO:0016301
d1iiba_	A	P69795	GO:0016310
d1iiba_	A	P69795	GO:0090566
d1iiba_	A	P69795	GO:1902495
d1iiba_	A	P69795	GO:1902815
d1vkra_	A	P00550	GO:0008982
d1vkra_	A	P00550	GO:0009401
d1vkra_	A	P00550	GO:0022872
d2r48a1	A	O31645	GO:0008982
d2r48a1	A	O31645	GO:0009401
d2r48a1	A	O31645	GO:0022877

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