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  
d1doqa-  ( 247 )     eqeeeldlpleelglstrvlhslkeegiesvrallalnlkdlknipgig
d1z3eb1  ( 245 )       kevlemtIeeLdLsvrSyncLkragIntVqeLankteedMmkvrnLg
d3k4ga-  ( 247 )    pefdpillrpvddLeLtvrSancL-aeaIhyIGdLVqrteveLl-tpnLg
                                     aaaaaa        aaaaa   aaaa       

                             60        70        80  
d1doqa-  ( 296 )    erSleeikeAlekkgftlKe             
d1z3eb1  ( 293 )    rksleeVkakLeelglglr              
d3k4ga-  ( 299 )    --SLteI--vLasrglslgmrlenwppasiade

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d1doqa- # 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 d1doqa- # 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	C-terminal domain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	Thermus thermophilus [TaxId: 274]	view
d1z3eb1 # 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 d1z3eb1 # 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	C-terminal domain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	Bacillus subtilis [TaxId: 1423]	view
d3k4ga- # 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 d3k4ga- # 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	C-terminal domain of RNA polymerase alpha subunit	Escherichia coli K-12 [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

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

Member	Chain	UniProtKB	GO term
d1doqa_	A	Q9Z9H6	GO:0003677
d1doqa_	A	Q9Z9H6	GO:0003899
d1doqa_	A	Q9Z9H6	GO:0006351
d1z3eb1	B	O31602	GO:0003677
d1z3eb1	B	O31602	GO:0003899
d1z3eb1	B	O31602	GO:0006351
d1z3eb1	B	P20429	GO:0003677
d1z3eb1	B	P20429	GO:0003899
d1z3eb1	B	P20429	GO:0006351

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

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

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