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  
d1pj5a1  ( 743 )    arrlrCLtIddgrsiVlgkepVfyk---e-qavgyVtsAaygytvakPiA
d1v5va1  ( 313 )     rklvhFkMid-kgiPregykVyAn---g-emIgeVtsGtlSpllnvGig
d1vloa1  ( 278 )    teklVGLvte--kgvLrnelpVrftdaqgnqhegiItsGtfSptlgysiA
d1vlya1  ( 244 )    nralwlLagsA-srlPeagedLelkg---nwrtgtVlaAvkled-gqVvV
d1wosa1  ( 279 )     rklVALeLs-gkriArkgyeVlkn---g-ervgeItsGnfsptlgkSiA
                      bbbbbbb           bbbb      bbbbbbbbbbb      bbb

                             60        70        80        90     
d1pj5a1  ( 789 )    ySyLpgtV-svgdsVdIeyf-grritAtVtedplydpkmtrl---g
d1v5va1  ( 357 )    iAfVkeeyAkpgieIeVeIr-gqrkkAvTvtppfydpkkyglfret
d1vloa1  ( 327 )    lArVpgIg----etAiVqirn---epvkvtkpvfvr----ngkava
d1vlya1  ( 293 )    qvvnnd---epdsifrVr---dDantLhieplp-ysl         
d1wosa1  ( 323 )    lAlVsksV-kigdqLgVvFpggklveAlVvkkpfy---rgsv---r
                    bbbb         bbb          bbbb

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d1pj5a1 # 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 d1pj5a1 # 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	N,N-dimethylglycine oxidase, C-terminal domain	Aminomethyltransferase beta-barrel domain	Arthrobacter globiformis [TaxId: 1665]	view
d1v5va1 # 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 d1v5va1 # 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	Glycine cleavage system T protein, GcvT	Aminomethyltransferase beta-barrel domain	Pyrococcus horikoshii [TaxId: 53953]	view
d1vloa1 # 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 d1vloa1 # 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	Glycine cleavage system T protein, GcvT	Aminomethyltransferase beta-barrel domain	Escherichia coli [TaxId: 562]	view
d1vlya1 # 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 d1vlya1 # 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 YgfZ, C-terminal domain	Aminomethyltransferase beta-barrel domain	Escherichia coli [TaxId: 562]	view
d1wosa1 # 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 d1wosa1 # 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	Glycine cleavage system T protein, GcvT	Aminomethyltransferase beta-barrel domain	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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-	R	K	L	V	H	F	K	M	I	D	-	K	G	I	P	R	E	G	Y	K	V	Y	A	N	-	-	-	G	-	E	M	I	G	E	V	T	S	G	T	L	S	P	L	L	N	V	G	I	G	I	A	F	V	K	E	E	Y	A	K	P	G	I	E	I	E	V	E	I	R	-	G	Q	R	K	K	A	V	T	V	T	P	P	F	Y	D	P	K	K	Y	G	L	F	R	E	T
T	E	K	L	V	G	L	V	T	E	-	-	K	G	V	L	R	N	E	L	P	V	R	F	T	D	A	Q	G	N	Q	H	E	G	I	I	T	S	G	T	F	S	P	T	L	G	Y	S	I	A	L	A	R	V	P	G	I	G	-	-	-	-	E	T	A	I	V	Q	I	R	N	-	-	-	E	P	V	K	V	T	K	P	V	F	V	R	-	-	-	-	N	G	K	A	V	A
N	R	A	L	W	L	L	A	G	S	A	-	S	R	L	P	E	A	G	E	D	L	E	L	K	G	-	-	-	N	W	R	T	G	T	V	L	A	A	V	K	L	E	D	-	G	Q	V	V	V	Q	V	V	N	N	D	-	-	-	E	P	D	S	I	F	R	V	R	-	-	-	D	D	A	N	T	L	H	I	E	P	L	P	-	Y	S	L	-	-	-	-	-	-	-	-	-
-	R	K	L	V	A	L	E	L	S	-	G	K	R	I	A	R	K	G	Y	E	V	L	K	N	-	-	-	G	-	E	R	V	G	E	I	T	S	G	N	F	S	P	T	L	G	K	S	I	A	L	A	L	V	S	K	S	V	-	K	I	G	D	Q	L	G	V	V	F	P	G	G	K	L	V	E	A	L	V	V	K	K	P	F	Y	-	-	-	R	G	S	V	-	-	-	R

Member	Chain	UniProtKB	GO term
d1pj5a1	A	Q9AGP8	GO:0000166
d1pj5a1	A	Q9AGP8	GO:0016491
d1pj5a1	A	Q9AGP8	GO:0047866
d1pj5a1	A	Q9AGP8	GO:0000166
d1pj5a1	A	Q9AGP8	GO:0016491
d1pj5a1	A	Q9AGP8	GO:0047866
d1pj5a1	A	Q9AGP8	GO:0000166
d1pj5a1	A	Q9AGP8	GO:0016491
d1pj5a1	A	Q9AGP8	GO:0047866
d1pj5a1	A	Q9AGP8	GO:0000166
d1pj5a1	A	Q9AGP8	GO:0016491
d1pj5a1	A	Q9AGP8	GO:0047866
d1v5va1	A	O58888	GO:0004047
d1v5va1	A	O58888	GO:0005737
d1v5va1	A	O58888	GO:0005960
d1v5va1	A	O58888	GO:0006546
d1v5va1	A	O58888	GO:0008483
d1v5va1	A	O58888	GO:0019464
d1v5va1	A	O58888	GO:0004047
d1v5va1	A	O58888	GO:0005737
d1v5va1	A	O58888	GO:0005960
d1v5va1	A	O58888	GO:0006546
d1v5va1	A	O58888	GO:0008483
d1v5va1	A	O58888	GO:0019464
d1vloa1	A	P27248	GO:0004047
d1vloa1	A	P27248	GO:0005737
d1vloa1	A	P27248	GO:0005829
d1vloa1	A	P27248	GO:0005960
d1vloa1	A	P27248	GO:0006546
d1vloa1	A	P27248	GO:0006730
d1vloa1	A	P27248	GO:0008483
d1vloa1	A	P27248	GO:0019464
d1vloa1	A	P27248	GO:0004047
d1vloa1	A	P27248	GO:0005737
d1vloa1	A	P27248	GO:0005829
d1vloa1	A	P27248	GO:0005960
d1vloa1	A	P27248	GO:0006546
d1vloa1	A	P27248	GO:0006730
d1vloa1	A	P27248	GO:0008483
d1vloa1	A	P27248	GO:0019464
d1vlya1	A	P0ADE8	GO:0005542
d1vlya1	A	P0ADE8	GO:0005737
d1vlya1	A	P0ADE8	GO:0005829
d1vlya1	A	P0ADE8	GO:0008033
d1vlya1	A	P0ADE8	GO:0009451
d1vlya1	A	P0ADE8	GO:0016226
d1vlya1	A	P0ADE8	GO:0005542
d1vlya1	A	P0ADE8	GO:0005737
d1vlya1	A	P0ADE8	GO:0005829
d1vlya1	A	P0ADE8	GO:0008033
d1vlya1	A	P0ADE8	GO:0009451
d1vlya1	A	P0ADE8	GO:0016226
d1wosa1	A	Q9WY54	GO:0004047
d1wosa1	A	Q9WY54	GO:0005737
d1wosa1	A	Q9WY54	GO:0005829
d1wosa1	A	Q9WY54	GO:0005960
d1wosa1	A	Q9WY54	GO:0006546
d1wosa1	A	Q9WY54	GO:0008483
d1wosa1	A	Q9WY54	GO:0019464

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

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

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