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  
d1josa-  (   7 )          rsdrvaqeIqkeIavILqrevkdprIg--mVtvsdVeVssdlsy
d1pa4a-  (   6 )           kerlendiirlinrtviheiy--netvktGhvthvklsddllh
d2dyja1  (   4 )          gkahleaqLkrALaeeIqa-ledprLf--lLtVeaVrLskdgsv
d2e7ga1  (  86 )    rkedharlralngllykaltdllctpevSqelydlnvelskvsltpdfsa
d2kzfa1  (   2 )    mn-payrkamleseiqkllmeAlqq-lrdprlkkdfvtFsrvelskdkry
                            aaaaaaaaaaaaaaaa              bbbbbb     b

                             60        70        80        90        100 
d1josa-  (  49 )    AkIfVtFlfdhdemAieqgmkgLekaspyIrslLgkamrlrivPeIrFiy
d1pa4a-  (  47 )    vtvyldCynr---eqidrvvgaFnqAkgvFsrvlahnlylakavqihfvk
d2dyja1  (  45 )    LsVYVeAfr-----eeeGAlrALsrAerrLvaaLarrVrmrrlPrLeFlp
d2e7ga1  ( 136 )    CrAyWktt--lsaeqnahmeavlqrsaahMrhllmsqqtlrnvPpivFvq
d2kzfa1  (  50 )    AdvyvsFlg--tpeeRketveilnrakgfFrtfiaknlrlyvAPeirFye
                    bbbbb          aaaaaaaaaa aaaaaaaaa          bbbb 

                             110       120 
d1josa-  (  99 )    dqs-lvegm            
d1pa4a-  (  94 )    dkaidnam             
d2dyja1  (  90 )    wra-sp               
d2e7ga1  ( 184 )    dkgn---aalaeldqllavad
d2kzfa1  (  98 )    dkgieasvk

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d1josa- # 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 d1josa- # 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	Ribosome-binding factor A, RbfA	Ribosome-binding factor A, RbfA	Haemophilus influenzae [TaxId: 727]	view
d1pa4a- # 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 d1pa4a- # 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	Ribosome-binding factor A, RbfA	Ribosome-binding factor A, RbfA	Mycoplasma pneumoniae [TaxId: 2104]	view
d2dyja1 # 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 d2dyja1 # 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	Ribosome-binding factor A, RbfA	Ribosome-binding factor A, RbfA	Thermus thermophilus [TaxId: 274]	view
d2e7ga1 # 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 d2e7ga1 # 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	Ribosome-binding factor A, RbfA	Ribosome-binding factor A, RbfA	Human (Homo sapiens) [TaxId: 9606]	view
d2kzfa1 # 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 d2kzfa1 # 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	Thermotoga maritima [TaxId: 2336]	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	N	-	P	A	Y	R	K	A	M	L	E	S	E	I	Q	K	L	L	M	E	A	L	Q	Q	-	L	R	D	P	R	L	K	K	D	F	V	T	F	S	R	V	E	L	S	K	D	K	R	Y	A	D	V	Y	V	S	F	L	G	-	-	T	P	E	E	R	K	E	T	V	E	I	L	N	R	A	K	G	F	F	R	T	F	I	A	K	N	L	R	L	Y	V	A	P	E	I	R	F	Y	E	D	K	G	I	E	A	S	V	K	-	-	-	-	-	-	-	-	-	-	-	-

Member	Chain	UniProtKB	GO term
d1josa_	A	P45141	GO:0005737
d1josa_	A	P45141	GO:0005829
d1josa_	A	P45141	GO:0006364
d1josa_	A	P45141	GO:0030490
d1josa_	A	P45141	GO:0042254
d1josa_	A	P45141	GO:0043024
d1josa_	A	P45141	GO:0005737
d1josa_	A	P45141	GO:0005829
d1josa_	A	P45141	GO:0006364
d1josa_	A	P45141	GO:0030490
d1josa_	A	P45141	GO:0042254
d1josa_	A	P45141	GO:0043024
d1pa4a_	A	P75589	GO:0005737
d1pa4a_	A	P75589	GO:0005829
d1pa4a_	A	P75589	GO:0006364
d1pa4a_	A	P75589	GO:0030490
d1pa4a_	A	P75589	GO:0042254
d1pa4a_	A	P75589	GO:0043024
d1pa4a_	A	P75589	GO:0005737
d1pa4a_	A	P75589	GO:0005829
d1pa4a_	A	P75589	GO:0006364
d1pa4a_	A	P75589	GO:0030490
d1pa4a_	A	P75589	GO:0042254
d1pa4a_	A	P75589	GO:0043024
d2dyja1	A	Q5SJV1	GO:0005737
d2dyja1	A	Q5SJV1	GO:0006364
d2dyja1	A	Q5SJV1	GO:0019843
d2dyja1	A	Q5SJV1	GO:0030490
d2dyja1	A	Q5SJV1	GO:0042254
d2dyja1	A	Q5SJV1	GO:0005737
d2dyja1	A	Q5SJV1	GO:0006364
d2dyja1	A	Q5SJV1	GO:0019843
d2dyja1	A	Q5SJV1	GO:0030490
d2dyja1	A	Q5SJV1	GO:0042254
d2e7ga1	A	Q8N0V3	GO:0006364
d2e7ga1	A	Q8N0V3	GO:0006364

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