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  
d1vjfa-  (   2 )       ktradLfafFdahgV--dhtldhp----pvfrveegleikaa--pgg
d1wdva-  (   3 )          ekVeewikargl-tWrlli-qk---ptrtvaeAaallgvsese-
d2dxaa-  (   2 )          tpAvklLeknki-sfqihtyehdpaetnfgdeVvkklglnpdq-
d2z0xa-  (   2 )    slspsArrVQgaLetrgfghlkVvelpa---sTrtakeAaqavgaevGq-
d3op6a-  (   2 )         pvkLkqfLdshki-kylsiahs--payt---aeiavs------gq
                           aaaaaaaa        bb            aaaaaa       

                             60        70        80        90        100 
d1vjfa-  (  43 )    hTkNlfLkda--gqLWLISAlgettId--lLhhvIgS-gLsfGpqe--le
d1wdva-  (  42 )    iVkTlIvlDn-aggVyAVVIPGdkrLnins-kelagk-pVrlAranevve
d2dxaa-  (  44 )    VYkTlLVavngdkhLAVAVTpVagqLdlkkVAkalga-kkVeadp-vaqr
d2z0xa-  (  48 )    IVkSlVfvGe-k-gAyLFLVSGknrLdlgkAtrlvgg-pLrqAtpeeVre
d3op6a-  (  42 )    lAktviIkd---grl-aVVLPasdhIt-fkLkeaigtsdLelAtesefeg
                     bbbbbbb      bbbbbbb          aaaa     bb        

                             110       120       130       140       150 
d1vjfa-  (  92 )    tLg-VtpgSvTAFGLInDtekrVrFVLDkaLadsdpVnFhPLkndAtTaV
d1wdva-  (  90 )    lTg-ypvgGVPPVaLpp----nIvlVVDriLlsrkkVyGgGgrenAlLeF
d2dxaa-  (  95 )    sTg-YlvggiSPLgQkk----rlpTIIDapAqefatIyVsGGkrgldIeL
d2z0xa-  (  95 )    lTg-FaigGVPPvgHnt----pLpAYLDedLlgypeVwAaGGtprALFra
d3op6a-  (  90 )    kfaecdvg-ApPFgnly----glpvlVStkLsaqdnIlfnagshseL-qL
                                            bbbb        bbb      bbbbb

                             160       170   
d1vjfa-  ( 141 )    sqaGLrrFLaalgvepiVdFaaevv
d1wdva-  ( 135 )    sPreLveat---gA-vvadVse   
d2dxaa-  ( 140 )    aAgdLakil---dA-kfadIarr  
d2z0xa-  ( 140 )    tPkeLlaLT---gA-qvadLkeg  
d3op6a-  ( 136 )    sFgdFelV----kP-tlVtl     
                     aaaaaaaa      bbb

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d1vjfa- # 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 d1vjfa- # 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 CC0111	YbaK/ProRS associated domain	Caulobacter crescentus [TaxId: 155892]	view
d1wdva- # 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 d1wdva- # 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 APE2540	YbaK/ProRS associated domain	Aeropyrum pernix [TaxId: 56636]	view
d2dxaa- # 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 d2dxaa- # 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: 562]	view
d2z0xa- # 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 d2z0xa- # 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 [TaxId: 274]	view
d3op6a- # 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 d3op6a- # 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	Legionella pneumophila [TaxId: 272624]	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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S	L	S	P	S	A	R	R	V	Q	G	A	L	E	T	R	G	F	G	H	L	K	V	V	E	L	P	A	-	-	-	S	T	R	T	A	K	E	A	A	Q	A	V	G	A	E	V	G	Q	-	I	V	K	S	L	V	F	V	G	E	-	K	-	G	A	Y	L	F	L	V	S	G	K	N	R	L	D	L	G	K	A	T	R	L	V	G	G	-	P	L	R	Q	A	T	P	E	E	V	R	E	L	T	G	-	F	A	I	G	G	V	P	P	V	G	H	N	T	-	-	-	-	P	L	P	A	Y	L	D	E	D	L	L	G	Y	P	E	V	W	A	A	G	G	T	P	R	A	L	F	R	A	T	P	K	E	L	L	A	L	T	-	-	-	G	A	-	Q	V	A	D	L	K	E	G	-	-
-	-	-	-	-	P	V	K	L	K	Q	F	L	D	S	H	K	I	-	K	Y	L	S	I	A	H	S	-	-	P	A	Y	T	-	-	-	A	E	I	A	V	S	-	-	-	-	-	-	G	Q	L	A	K	T	V	I	I	K	D	-	-	-	G	R	L	-	A	V	V	L	P	A	S	D	H	I	T	-	F	K	L	K	E	A	I	G	T	S	D	L	E	L	A	T	E	S	E	F	E	G	K	F	A	E	C	D	V	G	-	A	P	P	F	G	N	L	Y	-	-	-	-	G	L	P	V	L	V	S	T	K	L	S	A	Q	D	N	I	L	F	N	A	G	S	H	S	E	L	-	Q	L	S	F	G	D	F	E	L	V	-	-	-	-	K	P	-	T	L	V	T	L	-	-	-	-	-

Member	Chain	UniProtKB	GO term
d1vjfa_	A	Q9ABV9	GO:0002161
d1vjfa_	A	Q9ABV9	GO:0003677
d1vjfa_	A	Q9ABV9	GO:0106074
d1wdva_	A	Q9Y8U3	GO:0002161
d1wdva_	A	Q9Y8U3	GO:0006399
d1wdva_	A	Q9Y8U3	GO:0016787
d1wdva_	A	Q9Y8U3	GO:0106074

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