Complet list of 1pyv hssp file
Complete list of 1pyv.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1PYV
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 2014-05-06
HEADER HYDROLASE 09-JUL-03 1PYV
COMPND MOL_ID: 1; MOLECULE: ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR;
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: NICOTIANA PLUMBAGINIFOLIA; ORGANISM_CO
AUTHOR P.MOBERG,S.NILSSON,A.STAHL,A.C.ERIKSSON,E.GLASER,L.MALER
DBREF 1PYV A 0 53 UNP P17614 ATPBM_NICPL 1 54
SEQLENGTH 53
NCHAIN 1 chain(s) in 1PYV data set
NALIGN 8
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 : ATPBM_NICPL 1PYV 1.00 1.00 1 53 2 54 53 0 0 560 P17614 ATP synthase subunit beta, mitochondrial OS=Nicotiana plumbaginifolia GN=ATPB PE=1 SV=1
2 : O82721_NICSY 0.92 0.98 1 50 2 51 50 0 0 561 O82721 ATP synthase subunit beta OS=Nicotiana sylvestris GN=nsatp2.1.1 PE=2 SV=1
3 : M1A5X1_SOLTU 0.67 0.87 1 53 2 55 54 1 1 562 M1A5X1 ATP synthase subunit beta OS=Solanum tuberosum GN=PGSC0003DMG400005994 PE=3 SV=1
4 : K4BNR2_SOLLC 0.65 0.87 1 53 2 55 54 1 1 562 K4BNR2 ATP synthase subunit beta OS=Solanum lycopersicum GN=Solyc04g007550.2 PE=3 SV=1
5 : O82722_NICSY 0.64 0.83 1 53 2 50 53 1 4 556 O82722 ATP synthase subunit beta OS=Nicotiana sylvestris GN=nsatp2.2.1 PE=1 SV=1
6 : Q9SAQ0_NICSY 0.64 0.83 1 53 2 50 53 1 4 555 Q9SAQ0 ATP synthase subunit beta OS=Nicotiana sylvestris GN=nsatp2.2.1 PE=3 SV=1
7 : K4BX20_SOLLC 0.62 0.81 1 53 2 50 53 1 4 557 K4BX20 ATP synthase subunit beta OS=Solanum lycopersicum GN=Solyc05g008460.2 PE=3 SV=1
8 : M1D096_SOLTU 0.60 0.81 1 53 2 50 53 1 4 556 M1D096 ATP synthase subunit beta OS=Solanum tuberosum GN=PGSC0003DMG400030560 PE=3 SV=1
## ALIGNMENTS 1 - 8
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A A 0 0 119 9 14 AAAAASAA
2 2 A S - 0 0 86 9 29 STSSTSSS
3 3 A R S >> S+ 0 0 175 9 0 RRRRRRRR
4 4 A R H 3> S+ 0 0 190 9 0 RRRRRRRR
5 5 A L H 3> S+ 0 0 75 9 0 LLLLLLLL
6 6 A L H <> S+ 0 0 37 9 29 LLIILLMM
7 7 A A H >X S+ 0 0 18 9 18 ATAAAAAA
8 8 A S H 3X S+ 0 0 61 9 0 SSSSSSSS
9 9 A L H 3X S+ 0 0 12 9 0 LLLLLLLL
10 10 A L H < S+ 0 0 53 9 0 AAAAAAAA
15 15 A Q T 3< S+ 0 0 117 9 0 QQQQQQQQ
16 16 A R T 3 S- 0 0 174 9 0 RRRRRRRR
17 17 A G S < S- 0 0 73 9 0 GGGGGGGG
18 18 A G S S+ 0 0 40 9 27 GGAAGGGG
19 19 A G + 0 0 19 9 38 GGGGAAAA
20 20 A L S S+ 0 0 118 9 86 LPSSIIII
21 21 A I S S+ 0 0 25 9 89 IIGGSSSS
22 22 A S S S- 0 0 77 9 87 SSGGRRRR
23 23 A R S > S+ 0 0 185 9 83 RRGGSSSS
24 24 A S T >4 S+ 0 0 64 9 47 SSPPPPPP
25 25 A L G >4 S+ 0 0 24 9 23 LLIILLLL
26 26 A G G >4 S+ 0 0 16 9 57 GGSSAAAA
27 27 A N G << S+ 0 0 102 9 47 NNrrNNNN
28 28 A S G < >S+ 0 0 6 5 0 SSss....
29 29 A I T X 5S+ 0 0 44 5 12 IIIV....
30 30 A P T 3 5S+ 0 0 109 5 61 PPAA....
31 31 A K T 3 5S- 0 0 143 5 67 KKNN....
32 32 A S T < 5S- 0 0 110 9 0 SSSSSSSS
33 33 A A S >< S+ 0 0 93 9 71 SSAATTTT
38 38 A S T 3 S+ 0 0 123 9 0 SSSSSSSS
39 39 A R T 3 S+ 0 0 167 9 0 RRRRRRRR
40 40 A A < + 0 0 21 9 0 AAAAAAAA
41 41 A S S > S+ 0 0 113 9 0 SSSSSSSS
42 42 A P H > S+ 0 0 39 9 0 PPPPPPPP
43 43 A K H > S+ 0 0 51 9 41 KKKKKKAA
44 44 A G H > S+ 0 0 19 9 0 GGGGGGGG
45 45 A F H X S+ 0 0 93 9 0 FFFFFFFF
46 46 A L H X S+ 0 0 26 9 0 LLLLLLLL
47 47 A L H X S+ 0 0 6 9 0 LLLLLLLL
48 48 A N H X S+ 0 0 114 9 0 NNNNNNNN
49 49 A R H X S+ 0 0 119 9 0 RRRRRRRR
50 50 A A H < S+ 0 0 61 9 0 AAAAAAAA
51 51 A V H < S+ 0 0 92 8 0 V VVVVVV
52 52 A Q H < 0 0 131 8 54 Q QQKKKK
53 53 A Y < 0 0 230 8 0 Y YYYYYY
## 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 89 0 11 0 0 0 0 0 0 0 0 0 9 0 0 0.349 11 0.86
2 2 A 0 0 0 0 0 0 0 0 0 0 78 22 0 0 0 0 0 0 0 0 9 0 0 0.530 17 0.70
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 9 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 9 0 0 0.000 0 1.00
5 5 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
6 6 A 0 56 22 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.995 33 0.71
7 7 A 0 0 0 0 0 0 0 0 89 0 0 11 0 0 0 0 0 0 0 0 9 0 0 0.349 11 0.82
8 8 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
9 9 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
10 10 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 9 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 0 0 0 67 0 0 0 0 0 33 0 0 0 9 0 0 0.637 21 0.31
13 13 A 0 0 0 0 0 0 0 0 0 0 56 44 0 0 0 0 0 0 0 0 9 0 0 0.687 22 0.43
14 14 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 9 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 0 100 0 0 0 9 0 0 0.000 0 1.00
16 16 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 9 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
18 18 A 0 0 0 0 0 0 0 78 22 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.530 17 0.73
19 19 A 0 0 0 0 0 0 0 56 44 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.687 22 0.62
20 20 A 0 22 44 0 0 0 0 0 0 11 22 0 0 0 0 0 0 0 0 0 9 0 0 1.273 42 0.14
21 21 A 0 0 33 0 0 0 0 22 0 0 44 0 0 0 0 0 0 0 0 0 9 0 0 1.061 35 0.11
22 22 A 0 0 0 0 0 0 0 22 0 0 33 0 0 0 44 0 0 0 0 0 9 0 0 1.061 35 0.12
23 23 A 0 0 0 0 0 0 0 22 0 0 44 0 0 0 33 0 0 0 0 0 9 0 0 1.061 35 0.16
24 24 A 0 0 0 0 0 0 0 0 0 67 33 0 0 0 0 0 0 0 0 0 9 0 0 0.637 21 0.53
25 25 A 0 78 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.530 17 0.76
26 26 A 0 0 0 0 0 0 0 33 44 0 22 0 0 0 0 0 0 0 0 0 9 0 0 1.061 35 0.43
27 27 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 0 0 0 78 0 9 4 2 0.530 17 0.53
28 28 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 5 0 0 0.000 0 1.00
29 29 A 20 0 80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0.500 16 0.87
30 30 A 0 0 0 0 0 0 0 0 40 60 0 0 0 0 0 0 0 0 0 0 5 0 0 0.673 22 0.39
31 31 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 60 0 0 40 0 5 0 0 0.673 22 0.33
32 32 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
33 33 A 0 0 67 0 0 0 0 0 33 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.637 21 0.35
34 34 A 0 0 0 0 0 0 0 0 33 44 22 0 0 0 0 0 0 0 0 0 9 0 0 1.061 35 0.39
35 35 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 78 22 0 0 0 0 9 0 0 0.530 17 0.81
36 36 A 0 0 0 0 0 0 0 0 44 22 0 33 0 0 0 0 0 0 0 0 9 0 0 1.061 35 0.38
37 37 A 0 0 0 0 0 0 0 0 22 0 33 44 0 0 0 0 0 0 0 0 9 0 0 1.061 35 0.29
38 38 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
39 39 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 9 0 0 0.000 0 1.00
40 40 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
41 41 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
42 42 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
43 43 A 0 0 0 0 0 0 0 0 22 0 0 0 0 0 0 78 0 0 0 0 9 0 0 0.530 17 0.59
44 44 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
45 45 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
46 46 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
47 47 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
48 48 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 9 0 0 0.000 0 1.00
49 49 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 9 0 0 0.000 0 1.00
50 50 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
51 51 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
52 52 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 50 0 0 0 8 0 0 0.693 23 0.45
53 53 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
3 28 29 1 rSs
4 28 29 1 rSs
//