Complet list of 1pfs hssp file
Complete list of 1pfs.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1PFS
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 2014-05-05
HEADER DNA-BINDING PROTEIN 03-AUG-96 1PFS
COMPND MOL_ID: 1; MOLECULE: PF3 SINGLE-STRANDED DNA BINDING PROTEIN; CHAIN: A
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: PSEUDOMONAS PHAGE PF3; ORGANISM_TAXID:
AUTHOR R.H.A.FOLMER,M.NILGES,R.N.H.KONINGS,C.W.HILBERS
DBREF 1PFS A 1 78 UNP P03672 VHED_BPPF3 1 78
DBREF 1PFS B 1 78 UNP P03672 VHED_BPPF3 1 78
SEQLENGTH 78
NCHAIN 2 chain(s) in 1PFS data set
KCHAIN 1 chain(s) used here ; chains(s) : A
NALIGN 6
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 : G5P_BPPF3 1PFS 0.99 0.99 1 78 1 78 78 0 0 78 P03672 DNA-Binding protein G5P OS=Pseudomonas phage Pf3 GN=V PE=1 SV=1
2 : S6ARR9_PSERE 0.32 0.62 1 77 6 85 80 1 3 103 S6ARR9 Uncharacterized protein OS=Pseudomonas resinovorans NBRC 106553 GN=PCA10_29060 PE=4 SV=1
3 : F3EBJ2_PSESL 0.31 0.58 1 77 3 83 81 2 4 98 F3EBJ2 Prophage PSPPH05, helix-destabilizing protein OS=Pseudomonas syringae pv. lachrymans str. M301315 GN=PLA107_10388 PE=4 SV=1
4 : Q48I04_PSE14 0.31 0.58 1 77 1 81 81 2 4 95 Q48I04 Prophage PSPPH05, helix-destabilizing protein OS=Pseudomonas syringae pv. phaseolicola (strain 1448A / Race 6) GN=PSPPH_2790 PE=4 SV=1
5 : B3G274_PSEAI 0.30 0.52 1 77 5 84 80 1 3 99 B3G274 Putative uncharacterized protein OS=Pseudomonas aeruginosa GN=PACL_0348 PE=4 SV=1
6 : B3G286_PSEAI 0.30 0.52 1 77 5 84 80 1 3 99 B3G286 Putative uncharacterized protein OS=Pseudomonas aeruginosa GN=PACL_0360 PE=4 SV=1
## ALIGNMENTS 1 - 6
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A M 0 0 87 7 23 MIMMLL
2 2 A N E -A 56 0A 77 7 68 NKTTTT
3 3 A I E -A 55 0A 7 7 30 IVLLII
4 4 A Q E -A 54 0A 74 7 102 QSLLRR
5 5 A I E -AB 53 29A 0 7 0 IIIIII
6 6 A T E -AB 52 28A 41 7 60 TTEEEE
7 7 A F E -AB 51 27A 4 7 98 FAVVTT
8 8 A T E - 0 0A 26 7 25 TSTTTT
9 9 A D E S+ 0 0A 143 7 59 DCGGGG
10 10 A S E + 0 0A 51 7 84 STIIVV
11 11 A V E - B 0 25A 36 7 86 VYQQVV
12 12 A R E - B 0 24A 135 7 0 RRRRRR
13 13 A Q E + B 0 23A 136 7 65 QSSSSS
14 14 A G E - B 0 22A 27 7 0 GGGGGG
15 15 A T E - B 0 21A 101 7 82 TTVVNN
16 16 A S > - 0 0 46 7 39 SSAASS
17 17 A A T 3 S+ 0 0 115 7 65 AGAAKK
18 18 A K T 3 S- 0 0 177 7 65 KAKKAA
19 19 A G S < S+ 0 0 53 7 31 GGssGG
20 20 A N - 0 0 97 7 47 NKkkNN
21 21 A P E -B 15 0A 105 7 49 PPPPEE
22 22 A Y E -B 14 0A 62 7 0 YYYYYY
23 23 A T E -B 13 0A 41 7 56 TTTTHH
24 24 A F E -BC 12 43A 60 7 40 FMMMMM
25 25 A Q E -BC 11 42A 0 7 123 QAFFCC
26 26 A E E + C 0 41A 28 7 28 EEQQEE
27 27 A G E -BC 7 40A 0 7 32 GAAAAA
28 28 A F E -BC 6 39A 67 7 2 FYFFFF
29 29 A L E -BC 5 38A 1 7 87 LAVVGG
30 30 A H - 0 0 58 7 0 HHHHHH
31 31 A L > - 0 0 12 7 0 LLLLLL
32 32 A E T 3 S+ 0 0 153 7 57 EPPPPP
33 33 A D T 3 S+ 0 0 59 7 62 DGNHGG
34 34 A K < - 0 0 76 7 89 KCIIII
35 35 A P S S+ 0 0 124 7 29 PDPPPP
36 36 A H S S- 0 0 146 7 29 FFYYYY
37 37 A P - 0 0 51 7 0 PPPPPP
38 38 A L E -C 29 0A 58 7 65 LQQQQQ
39 39 A Q E +C 28 0A 108 7 57 QKKKRR
40 40 A C E -C 27 0A 1 7 94 CFTTFF
41 41 A Q E -C 26 0A 55 7 62 QSDDEE
42 42 A F E -C 25 0A 9 7 4 FYFFYY
43 43 A F E +C 24 0A 131 7 4 FYYYYY
44 44 A V - 0 0 4 7 68 VCAAAA
45 45 A E S S+ 0 0 162 7 87 ERSSAA
46 46 A S S S- 0 0 83 7 73 Ssttkk
47 47 A V - 0 0 91 7 14 Vvvvii
48 48 A I - 0 0 13 7 79 ILPPLL
49 49 A P - 0 0 85 7 42 PPQQPP
50 50 A A S S+ 0 0 56 7 52 ATPPAA
51 51 A G E S-A 7 0A 12 7 0 GGGGGG
52 52 A S E -A 6 0A 34 7 93 SDTTHH
53 53 A Y E -AD 5 77A 27 7 0 YYYYYY
54 54 A Q E -AD 4 76A 89 7 32 QEEEEE
55 55 A V E -A 3 0A 0 7 60 VVCCCC
56 56 A P E -A 2 0A 34 7 64 PPDDDD
57 57 A Y E -E 70 0B 6 7 72 YLVVII
58 58 A R E -E 69 0B 107 7 97 RKIITT
59 59 A I E -E 68 0B 0 7 88 IGAACC
60 60 A N E -E 67 0B 68 7 75 NEDDRR
61 61 A V E -E 66 0B 30 7 0 VVVVVV
62 62 A N E > S-E 65 0B 108 7 63 NKRRKK
63 63 A N T 3 S- 0 0 128 7 32 NDDDDD
64 64 A G T 3 S+ 0 0 18 7 28 GGGGDD
65 65 A R E < -E 62 0B 108 7 0 RRRRRR
66 66 A P E +E 61 0B 26 7 79 PVLLLL
67 67 A E E -E 60 0B 67 7 115 EVEEWW
68 68 A L E -E 59 0B 24 7 12 LFFFFF
69 69 A A E -E 58 0B 36 7 75 ADTTEE
70 70 A F E -E 57 0B 36 7 86 FLCCVV
71 71 A D > + 0 0 38 7 0 DDDDDD
72 72 A F T 3 S+ 0 0 52 7 89 FPPPPP
73 73 A K T 3 S+ 0 0 169 7 28 KRRRRR
74 74 A A S < S+ 0 0 52 7 52 AQQQQQ
75 75 A M - 0 0 41 7 83 MGGGAA
76 76 A K E -D 54 0A 151 7 28 KRRRRR
77 77 A R E D 53 0A 172 7 0 RRRRRR
78 78 A A 0 0 74 2 0 A
## 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 29 14 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.956 31 0.76
2 2 A 0 0 0 0 0 0 0 0 0 0 0 57 0 0 0 14 0 0 29 0 7 0 0 0.956 31 0.31
3 3 A 14 29 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.956 31 0.69
4 4 A 0 29 0 0 0 0 0 0 0 0 14 0 0 0 29 0 29 0 0 0 7 0 0 1.352 45 -0.03
5 5 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 0 0 0 0 43 0 0 0 0 0 57 0 0 7 0 0 0.683 22 0.40
7 7 A 29 0 0 0 29 0 0 0 14 0 0 29 0 0 0 0 0 0 0 0 7 0 0 1.352 45 0.01
8 8 A 0 0 0 0 0 0 0 0 0 0 14 86 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.74
9 9 A 0 0 0 0 0 0 0 57 0 0 0 0 14 0 0 0 0 0 0 29 7 0 0 0.956 31 0.41
10 10 A 29 0 29 0 0 0 0 0 0 0 29 14 0 0 0 0 0 0 0 0 7 0 0 1.352 45 0.16
11 11 A 57 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 29 0 0 0 7 0 0 0.956 31 0.14
12 12 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 7 0 0 0.000 0 1.00
13 13 A 0 0 0 0 0 0 0 0 0 0 71 0 0 0 0 0 29 0 0 0 7 0 0 0.598 19 0.35
14 14 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
15 15 A 29 0 0 0 0 0 0 0 0 0 0 43 0 0 0 0 0 0 29 0 7 0 0 1.079 36 0.18
16 16 A 0 0 0 0 0 0 0 0 29 0 71 0 0 0 0 0 0 0 0 0 7 0 0 0.598 19 0.61
17 17 A 0 0 0 0 0 0 0 14 57 0 0 0 0 0 0 29 0 0 0 0 7 0 0 0.956 31 0.34
18 18 A 0 0 0 0 0 0 0 0 43 0 0 0 0 0 0 57 0 0 0 0 7 0 0 0.683 22 0.34
19 19 A 0 0 0 0 0 0 0 71 0 0 29 0 0 0 0 0 0 0 0 0 7 0 2 0.598 19 0.68
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 0 57 0 7 0 0 0.683 22 0.53
21 21 A 0 0 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 29 0 0 7 0 0 0.598 19 0.50
22 22 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
23 23 A 0 0 0 0 0 0 0 0 0 0 0 71 0 29 0 0 0 0 0 0 7 0 0 0.598 19 0.43
24 24 A 0 0 0 71 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.598 19 0.59
25 25 A 0 0 0 0 29 0 0 0 14 0 0 0 29 0 0 0 29 0 0 0 7 0 0 1.352 45 -0.24
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 71 0 0 7 0 0 0.598 19 0.72
27 27 A 0 0 0 0 0 0 0 29 71 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.598 19 0.67
28 28 A 0 0 0 0 86 0 14 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.98
29 29 A 29 29 0 0 0 0 0 29 14 0 0 0 0 0 0 0 0 0 0 0 7 0 0 1.352 45 0.13
30 30 A 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 7 0 0 0.000 0 1.00
31 31 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
32 32 A 0 0 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 29 0 0 7 0 0 0.598 19 0.43
33 33 A 0 0 0 0 0 0 0 43 0 0 0 0 0 14 0 0 0 0 14 29 7 0 0 1.277 42 0.38
34 34 A 0 0 57 0 0 0 0 0 0 0 0 0 14 0 0 29 0 0 0 0 7 0 0 0.956 31 0.10
35 35 A 0 0 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 0 0 14 7 0 0 0.410 13 0.70
36 36 A 0 0 0 0 29 0 57 0 0 0 0 0 0 14 0 0 0 0 0 0 7 0 0 0.956 31 0.71
37 37 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
38 38 A 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 71 0 0 0 7 0 0 0.598 19 0.35
39 39 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 43 29 0 0 0 7 0 0 1.079 36 0.42
40 40 A 0 0 0 0 43 0 0 0 0 0 0 29 29 0 0 0 0 0 0 0 7 0 0 1.079 36 0.05
41 41 A 0 0 0 0 0 0 0 0 0 0 14 0 0 0 0 0 29 29 0 29 7 0 0 1.352 45 0.38
42 42 A 0 0 0 0 57 0 43 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.683 22 0.96
43 43 A 0 0 0 0 29 0 71 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.598 19 0.96
44 44 A 29 0 0 0 0 0 0 0 57 0 0 0 14 0 0 0 0 0 0 0 7 0 0 0.956 31 0.31
45 45 A 0 0 0 0 0 0 0 0 29 0 29 0 0 0 14 0 0 29 0 0 7 0 0 1.352 45 0.12
46 46 A 0 0 0 0 0 0 0 0 0 0 43 29 0 0 0 29 0 0 0 0 7 0 5 1.079 36 0.26
47 47 A 71 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.598 19 0.86
48 48 A 0 43 29 0 0 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 7 0 0 1.079 36 0.21
49 49 A 0 0 0 0 0 0 0 0 0 71 0 0 0 0 0 0 29 0 0 0 7 0 0 0.598 19 0.57
50 50 A 0 0 0 0 0 0 0 0 57 29 0 14 0 0 0 0 0 0 0 0 7 0 0 0.956 31 0.47
51 51 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
52 52 A 0 0 0 0 0 0 0 0 0 0 29 29 0 29 0 0 0 0 0 14 7 0 0 1.352 45 0.06
53 53 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
54 54 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 71 0 0 7 0 0 0.598 19 0.67
55 55 A 43 0 0 0 0 0 0 0 0 0 0 0 57 0 0 0 0 0 0 0 7 0 0 0.683 22 0.40
56 56 A 0 0 0 0 0 0 0 0 0 43 0 0 0 0 0 0 0 0 0 57 7 0 0 0.683 22 0.35
57 57 A 29 14 29 0 0 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 1.352 45 0.27
58 58 A 0 0 29 0 0 0 0 0 0 0 0 29 0 0 29 14 0 0 0 0 7 0 0 1.352 45 0.02
59 59 A 0 0 29 0 0 0 0 14 29 0 0 0 29 0 0 0 0 0 0 0 7 0 0 1.352 45 0.11
60 60 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 0 0 14 29 29 7 0 0 1.352 45 0.24
61 61 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
62 62 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 43 0 0 29 0 7 0 0 1.079 36 0.37
63 63 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 71 7 0 0 0.598 19 0.67
64 64 A 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 0 0 0 0 29 7 0 0 0.598 19 0.72
65 65 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 7 0 0 0.000 0 1.00
66 66 A 14 57 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 7 0 0 0.956 31 0.20
67 67 A 14 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 0 57 0 0 7 0 0 0.956 31 -0.15
68 68 A 0 29 0 0 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.598 19 0.88
69 69 A 0 0 0 0 0 0 0 0 29 0 0 29 0 0 0 0 0 29 0 14 7 0 0 1.352 45 0.24
70 70 A 29 14 0 0 29 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 7 0 0 1.352 45 0.14
71 71 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 7 0 0 0.000 0 1.00
72 72 A 0 0 0 0 29 0 0 0 0 71 0 0 0 0 0 0 0 0 0 0 7 0 0 0.598 19 0.10
73 73 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 71 29 0 0 0 0 7 0 0 0.598 19 0.71
74 74 A 0 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 71 0 0 0 7 0 0 0.598 19 0.47
75 75 A 0 0 0 29 0 0 0 43 29 0 0 0 0 0 0 0 0 0 0 0 7 0 0 1.079 36 0.17
76 76 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 71 29 0 0 0 0 7 0 0 0.598 19 0.71
77 77 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 7 0 0 0.000 0 1.00
78 78 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
2 47 52 3 sEQEv
3 20 22 1 sQk
3 47 50 3 tPAEv
4 20 20 1 sQk
4 47 48 3 tPSEv
5 47 51 3 kQNEi
6 47 51 3 kQNEi
//