Complet list of 1vtp hssp file
Complete list of 1vtp.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1VTP
THRESHOLD according to: t(L)=(290.15 * L ** -0.562) + 5
REFERENCE Sander C., Schneider R. : Database of homology-derived protein structures. Proteins, 9:56-68 (1991).
CONTACT Maintained at http://www.cmbi.ru.nl/ by Maarten L. Hekkelman
DATE file generated on 2014-05-11
HEADER TARGETING PEPTIDE 14-NOV-95 1VTP
COMPND MOL_ID: 1; MOLECULE: VACUOLAR TARGETING PEPTIDE; CHAIN: A; FRAGMENT: C
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: NICOTIANA ALATA; ORGANISM_COMMON: PERS
AUTHOR K.J.NIELSEN,J.M.HILL,M.A.ANDERSON,D.J.CRAIK
DBREF 1VTP A 1 26 UNP Q40378 Q40378_NICAL 256 281
SEQLENGTH 26
NCHAIN 1 chain(s) in 1VTP data set
NALIGN 17
NOTATION : ID: EMBL/SWISSPROT identifier of the aligned (homologous) protein
NOTATION : STRID: if the 3-D structure of the aligned protein is known, then STRID is the Protein Data Bank identifier as taken
NOTATION : from the database reference or DR-line of the EMBL/SWISSPROT entry
NOTATION : %IDE: percentage of residue identity of the alignment
NOTATION : %SIM (%WSIM): (weighted) similarity of the alignment
NOTATION : IFIR/ILAS: first and last residue of the alignment in the test sequence
NOTATION : JFIR/JLAS: first and last residue of the alignment in the alignend protein
NOTATION : LALI: length of the alignment excluding insertions and deletions
NOTATION : NGAP: number of insertions and deletions in the alignment
NOTATION : LGAP: total length of all insertions and deletions
NOTATION : LSEQ2: length of the entire sequence of the aligned protein
NOTATION : ACCNUM: SwissProt accession number
NOTATION : PROTEIN: one-line description of aligned protein
NOTATION : SeqNo,PDBNo,AA,STRUCTURE,BP1,BP2,ACC: sequential and PDB residue numbers, amino acid (lower case = Cys), secondary
NOTATION : structure, bridge partners, solvent exposure as in DSSP (Kabsch and Sander, Biopolymers 22, 2577-2637(1983)
NOTATION : VAR: sequence variability on a scale of 0-100 as derived from the NALIGN alignments
NOTATION : pair of lower case characters (AvaK) in the alignend sequence bracket a point of insertion in this sequence
NOTATION : dots (....) in the alignend sequence indicate points of deletion in this sequence
NOTATION : SEQUENCE PROFILE: relative frequency of an amino acid type at each position. Asx and Glx are in their
NOTATION : acid/amide form in proportion to their database frequencies
NOTATION : NOCC: number of aligned sequences spanning this position (including the test sequence)
NOTATION : NDEL: number of sequences with a deletion in the test protein at this position
NOTATION : NINS: number of sequences with an insertion in the test protein at this position
NOTATION : ENTROPY: entropy measure of sequence variability at this position
NOTATION : RELENT: relative entropy, i.e. entropy normalized to the range 0-100
NOTATION : WEIGHT: conservation weight
## PROTEINS : identifier and alignment statistics
NR. ID STRID %IDE %WSIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCNUM PROTEIN
1 : Q40378_NICAL2JZM 1.00 1.00 1 26 372 397 26 0 0 397 Q40378 Proteinase inhibitor OS=Nicotiana alata PE=1 SV=1
2 : Q9SQ77_NICAL2JZM 1.00 1.00 1 26 256 281 26 0 0 281 Q9SQ77 Proteinase inhibitor OS=Nicotiana alata PE=2 SV=1
3 : Q1WL43_TOBAC 0.96 0.96 1 26 372 397 26 0 0 397 Q1WL43 Trypsin proteinase inhibitor OS=Nicotiana tabacum GN=PI PE=2 SV=1
4 : Q1WL44_NICSY 0.96 0.96 1 26 372 397 26 0 0 397 Q1WL44 Trypsin proteinase inhibitor OS=Nicotiana sylvestris GN=PI PE=2 SV=1
5 : Q3SBE6_TOBAC 0.96 0.96 1 26 256 281 26 0 0 281 Q3SBE6 Insect injury-induced proteinase inhibitor OS=Nicotiana tabacum PE=2 SV=1
6 : B3F0C1_TOBAC 0.92 0.92 1 26 371 396 26 0 0 396 B3F0C1 Proteinase inhibitor II OS=Nicotiana tabacum PE=2 SV=1
7 : Q1WL49_9SOLA 0.92 0.96 1 26 370 395 26 0 0 395 Q1WL49 Trypsin proteinase inhibitor OS=Nicotiana occidentalis subsp. hesperis GN=PI PE=2 SV=1
8 : Q2XVY5_TOBAC 0.92 0.92 1 26 372 397 26 0 0 397 Q2XVY5 Six domain proteinase inhibitor OS=Nicotiana tabacum PE=2 SV=1
9 : Q1WL39_9SOLA 0.88 0.92 1 26 372 397 26 0 0 397 Q1WL39 Trypsin proteinase inhibitor OS=Nicotiana pauciflora GN=PI PE=2 SV=1
10 : Q1WL41_9SOLA 0.88 0.92 1 26 313 338 26 0 0 338 Q1WL41 Trypsin proteinase inhibitor OS=Nicotiana spegazzinii GN=PI PE=2 SV=1
11 : Q1WL42_9SOLA 0.88 0.92 1 26 313 338 26 0 0 338 Q1WL42 Trypsin proteinase inhibitor OS=Nicotiana linearis GN=PI PE=2 SV=1
12 : Q1WL46_9SOLA 0.88 0.88 1 26 314 339 26 0 0 339 Q1WL46 Trypsin proteinase inhibitor OS=Nicotiana umbratica GN=PI PE=2 SV=1
13 : Q1WL50_NICBE 0.88 0.96 1 26 254 279 26 0 0 279 Q1WL50 Trypsin proteinase inhibitor OS=Nicotiana benthamiana GN=PI PE=2 SV=1
14 : Q1WL51_9SOLA 0.88 0.92 1 26 138 163 26 0 0 163 Q1WL51 Trypsin proteinase inhibitor OS=Nicotiana cavicola GN=PI PE=2 SV=1
15 : Q5YLI5_NICAT 0.88 0.92 1 26 370 395 26 0 0 395 Q5YLI5 6-domain trypsin inhibitor (Fragment) OS=Nicotiana attenuata PE=2 SV=1
16 : Q84LJ9_NICAT 0.88 0.92 1 26 430 455 26 0 0 455 Q84LJ9 7-domain trypsin inhibitor OS=Nicotiana attenuata GN=7-domain TI PE=2 SV=1
17 : Q1WL40_9SOLA 0.85 0.92 1 26 372 397 26 0 0 397 Q1WL40 Trypsin proteinase inhibitor OS=Nicotiana miersii GN=PI PE=2 SV=1
## ALIGNMENTS 1 - 17
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A S >> 0 0 139 18 0 SSSSSSSSSSSSSSSSS
2 2 A E T 34 + 0 0 133 18 0 EEEEEEEEEEEEEEEEE
3 3 A Y T 34 S- 0 0 210 18 0 YYYYYYYYYYYYYYYYY
4 4 A A T <4 S+ 0 0 79 18 61 AAAAAVAAVVVAGAVVV
5 5 A S S >X S+ 0 0 74 18 0 SSSSSSSSSSSSSSSSS
6 6 A K H 3> S+ 0 0 115 18 0 KKKKKKKKKKKKKKKKK
7 7 A V H 34 S+ 0 0 73 18 20 VVVVVVVVVVVVVAVVL
8 8 A D H <4 S+ 0 0 116 18 62 DDDDDDVDDDDVVVDDD
9 9 A E H < S+ 0 0 165 18 0 EEEEEEEEEEEEEEEEE
10 10 A Y S >X S+ 0 0 111 18 0 YYYYYYYYYYYYYYYYY
11 11 A V H 3> S+ 0 0 78 18 0 VVVVVVVVVVVVVVVVV
12 12 A G H 3> S+ 0 0 42 18 97 GGRRRRGRHLLGGGHHH
13 13 A E H <> S+ 0 0 113 18 0 EEEEEEEEEEEEEEEEE
14 14 A V H X S+ 0 0 70 18 0 VVVVVVVVVVVVVVVVV
15 15 A E H X S+ 0 0 105 18 0 EEEEEEEEEEEEEEEEE
16 16 A N H X S+ 0 0 83 18 41 NNNNNNDNNNNIDDNNN
17 17 A D H X S+ 0 0 97 18 0 DDDDDDDDDDDDDDDDD
18 18 A L H X S+ 0 0 105 18 0 LLLLLLLLLLLLLLLLL
19 19 A Q H < S+ 0 0 116 18 13 QQQQQQQQQQQPQQQQQ
20 20 A K H >< S+ 0 0 151 18 0 KKKKKKKKKKKKKKKKK
21 21 A S H 3< S+ 0 0 95 18 14 SSSSSSSFSSSSSSSSS
22 22 A K T 3< S+ 0 0 162 18 29 KKKKKKKKRRRKKKRRR
23 23 A V S < S- 0 0 99 18 0 VVVVVVVVVVVVVVVVV
24 24 A A S S- 0 0 93 18 0 AAAAAAAAAAAAAAAAA
25 25 A V 0 0 112 18 0 VVVVVVVVVVVVVVVVV
26 26 A S 0 0 183 18 0 SSSSSSSSSSSSSSSSS
## SEQUENCE PROFILE AND ENTROPY
SeqNo PDBNo V L I M F W Y G A P S T C H R K Q E N D NOCC NDEL NINS ENTROPY RELENT WEIGHT
1 1 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 18 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 18 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0.000 0 1.00
4 4 A 39 0 0 0 0 0 0 6 56 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0.854 28 0.39
5 5 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 18 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 18 0 0 0.000 0 1.00
7 7 A 89 6 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0.426 14 0.80
8 8 A 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 78 18 0 0 0.530 17 0.38
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 18 0 0 0.000 0 1.00
10 10 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0.000 0 1.00
11 11 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0.000 0 1.00
12 12 A 0 11 0 0 0 0 0 39 0 0 0 0 0 22 28 0 0 0 0 0 18 0 0 1.301 43 0.02
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 18 0 0 0.000 0 1.00
14 14 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0.000 0 1.00
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 18 0 0 0.000 0 1.00
16 16 A 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 78 17 18 0 0 0.655 21 0.59
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 18 0 0 0.000 0 1.00
18 18 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0.000 0 1.00
19 19 A 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 94 0 0 0 18 0 0 0.215 7 0.87
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 18 0 0 0.000 0 1.00
21 21 A 0 0 0 0 6 0 0 0 0 0 94 0 0 0 0 0 0 0 0 0 18 0 0 0.215 7 0.86
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 67 0 0 0 0 18 0 0 0.637 21 0.71
23 23 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0.000 0 1.00
24 24 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0.000 0 1.00
25 25 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0.000 0 1.00
26 26 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 18 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
//