Complet list of 2bic hssp file
Complete list of 2bic.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 2BIC
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 2014-02-05
HEADER PLANT PATHOGEN, PHYTOPHTHORA CACTORUM F 2006-06-28 2BIC
COMPND PHYTOTOXIC PROTEIN PCF
SOURCE PHYTOPHTHORA CACTORUM
AUTHOR Nicastro, G.; Orsomando, G.; Desario, F.; Ferrari, E.; Manconi, L.; Sp
SEQLENGTH 52
NCHAIN 1 chain(s) in 2BIC data set
NALIGN 7
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 : Q94FS7_9STRA2BIC 1.00 1.00 1 52 22 73 52 0 0 73 Q94FS7 Phytotoxic protein PcF (Precursor) OS=Phytophthora cactorum PE=1 SV=1
2 : D0MV82_PHYIT 0.69 0.90 1 49 22 70 49 0 0 70 D0MV82 PcF and SCR74-like cys-rich secreted peptide, putative OS=Phytophthora infestans (strain T30-4) GN=PITG_22677 PE=4 SV=1
3 : Q2M413_PHYIN 0.67 0.86 3 50 29 77 49 1 1 91 Q2M413 Small cysteine-rich protein SCR91 OS=Phytophthora infestans PE=4 SV=1
4 : Q2M443_PHYIN 0.67 0.86 3 50 29 77 49 1 1 91 Q2M443 Small cysteine-rich protein SCR91 OS=Phytophthora infestans PE=4 SV=1
5 : D0NTX2_PHYIT 0.63 0.80 1 50 27 77 51 1 1 91 D0NTX2 Small cysteine-rich protein SCR91 OS=Phytophthora infestans (strain T30-4) GN=PITG_23077 PE=4 SV=1
6 : G4ZGN4_PHYSP 0.61 0.88 3 51 28 76 49 0 0 1271 G4ZGN4 Putative uncharacterized protein OS=Phytophthora sojae (strain P6497) GN=PHYSODRAFT_346079 PE=4 SV=1
7 : H3G5T2_PHYRM 0.48 0.62 1 48 22 73 52 2 4 73 H3G5T2 Uncharacterized protein OS=Phytophthora ramorum GN=gwEuk.18.204.1 PE=4 SV=1
## ALIGNMENTS 1 - 7
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A E 0 0 238 5 55 EE K Q
2 2 A D - 0 0 147 5 65 DD P P
3 3 A P - 0 0 84 8 0 PPPPPPP
4 4 A L + 0 0 73 8 88 LLPPPLQ
5 5 A Y - 0 0 49 8 0 YYYYYYY
6 6 A a + 0 0 16 8 0 CCCCCCC
7 7 A Q + 0 0 136 8 75 QQnnnQv
8 8 A A - 0 0 30 8 63 AAsssAe
9 9 A I S S+ 0 0 165 8 74 ITTTTIN
10 10 A G S S+ 0 0 65 8 0 GGGGGGG
11 11 A b S S- 0 0 8 8 0 CCCCCCC
12 12 A P - 0 0 34 8 48 PPQQQPP
13 13 A T > - 0 0 93 8 43 TSTTTTS
14 14 A L T 3 S+ 0 0 35 8 0 LLLLLLL
15 15 A Y T 3 S+ 0 0 200 8 0 YYYYYYY
16 16 A S S <> S- 0 0 25 8 46 SPSSSST
17 17 A E H > S+ 0 0 171 8 0 EEEEEEE
18 18 A A H > S+ 0 0 61 8 21 AAAAASA
19 19 A N H > S+ 0 0 0 8 30 NNNNNNS
20 20 A L H X S+ 0 0 68 8 25 LLLLLII
21 21 A A H X S+ 0 0 70 8 30 AAAAAAD
22 22 A V H X S+ 0 0 15 8 19 VLVVVIV
23 23 A S H X S+ 0 0 2 8 0 SSSSSSS
24 24 A K H X S+ 0 0 112 8 32 KRKKKQK
25 25 A E H X S+ 0 0 109 8 62 EEEEVQT
26 26 A c H < S+ 0 0 2 8 0 CCCCCCC
27 27 A R H < S+ 0 0 102 8 0 RRRRRRR
28 28 A D H < S+ 0 0 128 8 26 DNDDDND
29 29 A Q S < S- 0 0 110 8 66 QQEEEEI
30 30 A G S S- 0 0 67 8 45 GGGGGGI
31 31 A K S S- 0 0 180 8 77 KKNNNHA
32 32 A L S S+ 0 0 138 8 79 LVSSSVV
33 33 A G S S- 0 0 60 8 40 GGGGGGK
34 34 A D S > S+ 0 0 131 8 20 DDDDDDg
35 35 A D T >> S+ 0 0 39 8 23 DDDDDAd
36 36 A F H 3> S+ 0 0 39 8 0 FFFFFFF
37 37 A H H <> S+ 0 0 138 8 42 HHHHHHL
38 38 A R H <> S+ 0 0 187 8 76 RTTTTSR
39 39 A c H X S+ 0 0 21 8 0 CCCCCCC
40 40 A a H < S+ 0 0 3 8 0 CCCCCCC
41 41 A E H < S+ 0 0 88 8 89 ETIIISE
42 42 A E H < S+ 0 0 156 8 73 EDNNNTS
43 43 A Q S < S+ 0 0 97 8 59 QKKKKKT
44 44 A b - 0 0 35 8 0 CCCCCCC
45 45 A G S S+ 0 0 51 8 0 GGGGGGG
46 46 A S S S- 0 0 129 8 66 SESSSAK
47 47 A T - 0 0 128 8 53 TKTTTTV
48 48 A T - 0 0 113 8 57 TSAAAAT
49 49 A P + 0 0 126 7 77 PSAAAV
50 50 A A - 0 0 84 6 63 A SPSP
51 51 A S 0 0 134 3 59 S G
52 52 A A 0 0 176 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 20 60 0 0 5 0 0 0.950 31 0.44
2 2 A 0 0 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 0 0 60 5 0 0 0.673 22 0.35
3 3 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
4 4 A 0 50 0 0 0 0 0 0 0 38 0 0 0 0 0 0 13 0 0 0 8 0 0 0.974 32 0.12
5 5 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
6 6 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
7 7 A 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 38 0 8 0 4 0.974 32 0.24
8 8 A 0 0 0 0 0 0 0 0 50 0 38 0 0 0 0 0 0 13 0 0 8 0 0 0.974 32 0.37
9 9 A 0 0 38 0 0 0 0 0 0 0 0 50 0 0 0 0 0 0 13 0 8 0 0 0.974 32 0.26
10 10 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 0 0 63 0 0 0 0 0 0 38 0 0 0 8 0 0 0.662 22 0.52
13 13 A 0 0 0 0 0 0 0 0 0 0 25 75 0 0 0 0 0 0 0 0 8 0 0 0.562 18 0.57
14 14 A 0 100 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
15 15 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
16 16 A 0 0 0 0 0 0 0 0 0 13 75 13 0 0 0 0 0 0 0 0 8 0 0 0.736 24 0.54
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 8 0 0 0.000 0 1.00
18 18 A 0 0 0 0 0 0 0 0 88 0 13 0 0 0 0 0 0 0 0 0 8 0 0 0.377 12 0.78
19 19 A 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 88 0 8 0 0 0.377 12 0.70
20 20 A 0 75 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.562 18 0.74
21 21 A 0 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 0 0 0 13 8 0 0 0.377 12 0.70
22 22 A 75 13 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.736 24 0.80
23 23 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 75 13 0 0 0 8 0 0 0.736 24 0.67
25 25 A 13 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 13 63 0 0 8 0 0 1.074 35 0.37
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
27 27 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 8 0 0 0.000 0 1.00
28 28 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 75 8 0 0 0.562 18 0.74
29 29 A 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 38 50 0 0 8 0 0 0.974 32 0.33
30 30 A 0 0 13 0 0 0 0 88 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.377 12 0.55
31 31 A 0 0 0 0 0 0 0 0 13 0 0 0 0 13 0 38 0 0 38 0 8 0 0 1.255 41 0.22
32 32 A 38 25 0 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 0 0 8 0 0 1.082 36 0.21
33 33 A 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 13 0 0 0 0 8 0 0 0.377 12 0.60
34 34 A 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 88 8 0 1 0.377 12 0.80
35 35 A 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 88 8 0 0 0.377 12 0.76
36 36 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
37 37 A 0 13 0 0 0 0 0 0 0 0 0 0 0 88 0 0 0 0 0 0 8 0 0 0.377 12 0.57
38 38 A 0 0 0 0 0 0 0 0 0 0 13 50 0 0 38 0 0 0 0 0 8 0 0 0.974 32 0.23
39 39 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
40 40 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
41 41 A 0 0 38 0 0 0 0 0 0 0 13 13 0 0 0 0 0 38 0 0 8 0 0 1.255 41 0.10
42 42 A 0 0 0 0 0 0 0 0 0 0 13 13 0 0 0 0 0 25 38 13 8 0 0 1.494 49 0.27
43 43 A 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 63 25 0 0 0 8 0 0 0.900 30 0.41
44 44 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
45 45 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
46 46 A 0 0 0 0 0 0 0 0 13 0 63 0 0 0 0 13 0 13 0 0 8 0 0 1.074 35 0.34
47 47 A 13 0 0 0 0 0 0 0 0 0 0 75 0 0 0 13 0 0 0 0 8 0 0 0.736 24 0.47
48 48 A 0 0 0 0 0 0 0 0 50 0 13 38 0 0 0 0 0 0 0 0 8 0 0 0.974 32 0.43
49 49 A 14 0 0 0 0 0 0 0 43 29 14 0 0 0 0 0 0 0 0 0 7 0 0 1.277 42 0.23
50 50 A 0 0 0 0 0 0 0 0 33 33 33 0 0 0 0 0 0 0 0 0 6 0 0 1.099 36 0.36
51 51 A 0 0 0 0 0 0 0 33 0 0 67 0 0 0 0 0 0 0 0 0 3 0 0 0.637 21 0.40
52 52 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
3 6 34 1 nFs
4 6 34 1 nFs
5 8 34 1 nFs
7 8 29 3 vPTEe
7 35 59 1 gGd
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