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  
d1ku3a-  ( 372 )                  alskLserEamVlkMrkglid--grehtleeVGayf
d1l0oc-  ( 103 )              gtvkvsrslkemGnkirkAkdelsktrgraPtvteiAdhl
d1or7a1  ( 120 )    nlmlseelrqivfrtiesLpedlrmAitlre--ld--g--lsyeeIaaim
d1rp3a1  (  87 )                           gsvkeikevvleklgrePtdeevAe-l
d4g7hf2  ( 258 )                iripvhmvetinkLsrtarqlqqelgrePtyeeiAeaM
                                        aaaaaaaaaa            aaaaaaa 

                             60        70        80       
d1ku3a-  ( 406 )    g--vtrerIrqiEnkAlrklkyh               
d1l0oc-  ( 143 )    g--ispedVvlAqeavr                     
d1or7a1  ( 164 )    d--cpvgtVrsrIfrAreaidnkvqp            
d1rp3a1  ( 123 )    gisteLftldkinfsyilsleevfrdfardyslipsst
d4g7hf2  ( 296 )    gpgwdakrVeetlkiaq---epvsle            
                         aaaaaaaaaaa

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d1ku3a- # 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 d1ku3a- # 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	Sigma70 (SigA, RpoD)	Sigma4 domain	Thermus aquaticus [TaxId: 271]	view
d1l0oc- # 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 d1l0oc- # 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	SigmaF	Sigma4 domain	Bacillus stearothermophilus [TaxId: 1422]	view
d1or7a1 # 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 d1or7a1 # 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	SigmaE factor (RpoE)	Sigma4 domain	Escherichia coli [TaxId: 562]	view
d1rp3a1 # 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 d1rp3a1 # 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	Sigma factor sigma-28 (FliA)	Sigma3 domain	Aquifex aeolicus [TaxId: 63363]	view
d4g7hf2 # 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 d4g7hf2 # 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

Domain ID	Name
d1xsva-	1xsv A:
d1rp3a2	1rp3 A:164-234
d2k6xa1	2k6x A:29-96

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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-	-	-	-	-	-	-	-	-	-	G	T	V	K	V	S	R	S	L	K	E	M	G	N	K	I	R	K	A	K	D	E	L	S	K	T	R	G	R	A	P	T	V	T	E	I	A	D	H	L	G	-	-	I	S	P	E	D	V	V	L	A	Q	E	A	V	R	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
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Member	Chain	UniProtKB	GO term
d1ku3a_	A	Q9EZJ8	GO:0003700
d1ku3a_	A	Q9EZJ8	GO:0006352
d1ku3a_	A	Q9EZJ8	GO:0006355
d1l0oc_	C	O32727	GO:0005515
d1l0oc_	C	O32727	GO:0030435
d1l0oc_	C	O32727	GO:0003677
d1l0oc_	C	O32727	GO:0003700
d1l0oc_	C	O32727	GO:0006352
d1l0oc_	C	O32727	GO:0006355
d1l0oc_	C	O32727	GO:0016987
d1l0oc_	C	O32727	GO:2000142
d1l0oc_	C	O32728	GO:0005515
d1l0oc_	C	O32728	GO:0030435
d1l0oc_	C	O32728	GO:0003677
d1l0oc_	C	O32728	GO:0003700
d1l0oc_	C	O32728	GO:0006352
d1l0oc_	C	O32728	GO:0006355
d1l0oc_	C	O32728	GO:0016987
d1l0oc_	C	O32728	GO:2000142
d1or7a1	A	P0AGB6	GO:0000345
d1or7a1	A	P0AGB6	GO:0003677
d1or7a1	A	P0AGB6	GO:0003700
d1or7a1	A	P0AGB6	GO:0005515
d1or7a1	A	P0AGB6	GO:0005737
d1or7a1	A	P0AGB6	GO:0005886
d1or7a1	A	P0AGB6	GO:0006351
d1or7a1	A	P0AGB6	GO:0006352
d1or7a1	A	P0AGB6	GO:0006355
d1or7a1	A	P0AGB6	GO:0006970
d1or7a1	A	P0AGB6	GO:0009266
d1or7a1	A	P0AGB6	GO:0016987
d1or7a1	A	P0AGB6	GO:0036460
d1or7a1	A	P0AGB6	GO:0045892
d1or7a1	A	P0AGB6	GO:0090605
d1or7a1	A	P0AGB6	GO:1903865
d1or7a1	A	P0AGB6	GO:2000142
d1or7a1	A	P0AFX7	GO:0000345
d1or7a1	A	P0AFX7	GO:0003677
d1or7a1	A	P0AFX7	GO:0003700
d1or7a1	A	P0AFX7	GO:0005515
d1or7a1	A	P0AFX7	GO:0005737
d1or7a1	A	P0AFX7	GO:0005886
d1or7a1	A	P0AFX7	GO:0006351
d1or7a1	A	P0AFX7	GO:0006352
d1or7a1	A	P0AFX7	GO:0006355
d1or7a1	A	P0AFX7	GO:0006970
d1or7a1	A	P0AFX7	GO:0009266
d1or7a1	A	P0AFX7	GO:0016987
d1or7a1	A	P0AFX7	GO:0036460
d1or7a1	A	P0AFX7	GO:0045892
d1or7a1	A	P0AFX7	GO:0090605
d1or7a1	A	P0AFX7	GO:1903865
d1or7a1	A	P0AFX7	GO:2000142
d1or7a1	A	P0AGB6	GO:0000345
d1or7a1	A	P0AGB6	GO:0003677
d1or7a1	A	P0AGB6	GO:0003700
d1or7a1	A	P0AGB6	GO:0005515
d1or7a1	A	P0AGB6	GO:0005737
d1or7a1	A	P0AGB6	GO:0005886
d1or7a1	A	P0AGB6	GO:0006351
d1or7a1	A	P0AGB6	GO:0006352
d1or7a1	A	P0AGB6	GO:0006355
d1or7a1	A	P0AGB6	GO:0006970
d1or7a1	A	P0AGB6	GO:0009266
d1or7a1	A	P0AGB6	GO:0016987
d1or7a1	A	P0AGB6	GO:0036460
d1or7a1	A	P0AGB6	GO:0045892
d1or7a1	A	P0AGB6	GO:0090605
d1or7a1	A	P0AGB6	GO:1903865
d1or7a1	A	P0AGB6	GO:2000142
d1or7a1	A	P0AFX7	GO:0000345
d1or7a1	A	P0AFX7	GO:0003677
d1or7a1	A	P0AFX7	GO:0003700
d1or7a1	A	P0AFX7	GO:0005515
d1or7a1	A	P0AFX7	GO:0005737
d1or7a1	A	P0AFX7	GO:0005886
d1or7a1	A	P0AFX7	GO:0006351
d1or7a1	A	P0AFX7	GO:0006352
d1or7a1	A	P0AFX7	GO:0006355
d1or7a1	A	P0AFX7	GO:0006970
d1or7a1	A	P0AFX7	GO:0009266
d1or7a1	A	P0AFX7	GO:0016987
d1or7a1	A	P0AFX7	GO:0036460
d1or7a1	A	P0AFX7	GO:0045892
d1or7a1	A	P0AFX7	GO:0090605
d1or7a1	A	P0AFX7	GO:1903865
d1or7a1	A	P0AFX7	GO:2000142
d1rp3a1	A	O67268	GO:0003677
d1rp3a1	A	O67268	GO:0003700
d1rp3a1	A	O67268	GO:0003899
d1rp3a1	A	O67268	GO:0006352
d1rp3a1	A	O67268	GO:0006355
d1rp3a1	A	O67268	GO:0016987
d1rp3a1	A	O67268	GO:0045152
d1rp3a1	A	O67268	GO:0097718
d1rp3a1	A	O67268	GO:1903865
d1rp3a1	A	O67268	GO:2000142
d1rp3a1	A	O66683	GO:0003677
d1rp3a1	A	O66683	GO:0003700
d1rp3a1	A	O66683	GO:0003899
d1rp3a1	A	O66683	GO:0006352
d1rp3a1	A	O66683	GO:0006355
d1rp3a1	A	O66683	GO:0016987
d1rp3a1	A	O66683	GO:0045152
d1rp3a1	A	O66683	GO:0097718
d1rp3a1	A	O66683	GO:1903865
d1rp3a1	A	O66683	GO:2000142
d1rp3a1	A	O67268	GO:0003677
d1rp3a1	A	O67268	GO:0003700
d1rp3a1	A	O67268	GO:0003899
d1rp3a1	A	O67268	GO:0006352
d1rp3a1	A	O67268	GO:0006355
d1rp3a1	A	O67268	GO:0016987
d1rp3a1	A	O67268	GO:0045152
d1rp3a1	A	O67268	GO:0097718
d1rp3a1	A	O67268	GO:1903865
d1rp3a1	A	O67268	GO:2000142
d1rp3a1	A	O66683	GO:0003677
d1rp3a1	A	O66683	GO:0003700
d1rp3a1	A	O66683	GO:0003899
d1rp3a1	A	O66683	GO:0006352
d1rp3a1	A	O66683	GO:0006355
d1rp3a1	A	O66683	GO:0016987
d1rp3a1	A	O66683	GO:0045152
d1rp3a1	A	O66683	GO:0097718
d1rp3a1	A	O66683	GO:1903865
d1rp3a1	A	O66683	GO:2000142

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