Complet list of 2fqa hssp file
Complete list of 2fqa.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 2FQA
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 2014-05-19
HEADER PLANT PROTEIN 17-JAN-06 2FQA
COMPND MOL_ID: 1; MOLECULE: VIOLACIN 1; CHAIN: A; FRAGMENT: RESIDUES 1-27; SY
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: VIOLA ODORATA; ORGANISM_TAXID: 97441
AUTHOR D.C.IRELAND,D.J.CRAIK,N.L.DALY
DBREF 2FQA A 1 27 GB 86285728 ABC94585 80 106
SEQLENGTH 27
NCHAIN 1 chain(s) in 2FQA data set
NALIGN 44
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 : VIOLA_VIOOD 2FQA 1.00 1.00 1 27 80 106 27 0 0 106 Q2HY54 Violacin-A OS=Viola odorata PE=1 SV=1
2 : CYO14_VIOOD 2GJ0 0.78 0.87 5 26 6 28 23 1 1 31 P85177 Cycloviolacin-O14 OS=Viola odorata PE=1 SV=1
3 : CYO15_VIOOD 0.76 0.88 3 27 3 27 25 0 0 29 P85178 Cycloviolacin-O15 OS=Viola odorata PE=1 SV=1
4 : CYO16_VIOOD 0.73 0.88 2 27 1 26 26 0 0 29 P85179 Cycloviolacin-O16 OS=Viola odorata PE=1 SV=1
5 : CYVA_VIOBI 0.73 0.77 5 26 5 26 22 0 0 29 P85239 Cyclotide vibi-A OS=Viola biflora PE=1 SV=1
6 : CYVC_VIOBI 0.73 0.73 5 26 5 26 22 0 0 29 P85241 Cyclotide vibi-C OS=Viola biflora PE=1 SV=1
7 : VODM_VIOOD 0.73 0.82 5 26 5 26 22 0 0 29 P83839 Vodo peptide M OS=Viola odorata PE=1 SV=1
8 : VODN_VIOOD 0.73 0.77 5 26 5 26 22 0 0 29 P83838 Vodo peptide N OS=Viola odorata PE=1 SV=1
9 : D2WPK8_9ROSI 0.70 0.78 1 27 70 96 27 0 0 102 D2WPK8 Cyclotide E (Fragment) OS=Gloeospermum blakeanum PE=2 SV=1
10 : CYO12_VIOAR 0.68 0.68 5 26 5 26 22 0 0 29 P83835 Varv peptide E OS=Viola arvensis PE=1 SV=1
11 : CYO12_VIOOD 0.68 0.68 5 26 5 26 22 0 0 29 P83836 Cycloviolacin-O12 OS=Viola odorata PE=1 SV=1
12 : CYO21_VIOOD 0.68 0.73 5 26 5 26 22 0 0 29 P85184 Cycloviolacin-O21 OS=Viola odorata PE=1 SV=1
13 : CYVB_VIOBI 0.68 0.77 5 26 5 26 22 0 0 29 P85240 Cyclotide vibi-B OS=Viola biflora PE=1 SV=1
14 : CYVD_VIOBI 0.68 0.82 5 26 5 26 22 0 0 29 P85242 Cyclotide vibi-D OS=Viola biflora PE=1 SV=1
15 : KABS_OLDAF 0.68 0.68 5 26 5 26 22 0 0 29 P58458 Kalata-S OS=Oldenlandia affinis PE=1 SV=1
16 : VARA_VIOAR 0.68 0.68 5 26 5 26 22 0 0 29 P58446 Varv peptide A OS=Viola arvensis PE=1 SV=1
17 : VARA_VIOBI 0.68 0.68 5 26 5 26 22 0 0 29 P85525 Cyclotide varv-A OS=Viola biflora PE=1 SV=1
18 : VARC_VIOAR 0.68 0.68 5 26 5 26 22 0 0 29 P58448 Varv peptide C OS=Viola arvensis PE=1 SV=1
19 : VARD_VIOAR 0.68 0.68 5 26 5 26 22 0 0 29 P58449 Varv peptide D OS=Viola arvensis PE=1 SV=1
20 : VARF_VIOAR 3E4H 0.68 0.73 5 26 5 26 22 0 0 29 P58451 Varv peptide F OS=Viola arvensis PE=1 SV=1
21 : B6E620_OLDAF 0.65 0.70 5 26 71 93 23 1 1 155 B6E620 Kalata B6 and kalata B3 protein (Fragment) OS=Oldenlandia affinis PE=4 SV=1
22 : KAB10_OLDAF 0.65 0.70 5 26 5 27 23 1 1 30 P85128 Kalata-B10 OS=Oldenlandia affinis PE=1 SV=1
23 : KAB3_OLDAF 1WN8 0.65 0.70 5 26 71 93 23 1 1 158 P58455 Kalata-B3/B6 OS=Oldenlandia affinis GN=OAK2 PE=1 SV=1
24 : Q30CA6_9ROSI 0.65 0.70 5 27 1 23 23 0 0 35 Q30CA6 Cyclotide B (Fragment) OS=Hybanthus monopetalus PE=2 SV=1
25 : VARG_VIOAR 0.65 0.65 5 26 5 27 23 1 1 30 P58452 Varv peptide G OS=Viola arvensis PE=1 SV=1
26 : VARH_VIOAR 0.65 0.65 5 26 5 27 23 1 1 30 P58453 Varv peptide H OS=Viola arvensis PE=1 SV=1
27 : CYCN_CLITE 0.64 0.68 5 26 5 26 22 0 0 29 P86900 Cyclotide cter-N OS=Clitoria ternatea PE=1 SV=1
28 : CYO22_VIOOD 0.64 0.68 5 26 5 26 22 0 0 29 P85185 Cycloviolacin-O22 OS=Viola odorata PE=1 SV=1
29 : F8W671_CLITE2LAM 0.64 0.68 5 26 5 26 22 0 0 29 F8W671 Cyclotide Cter M OS=Clitoria ternatea PE=1 SV=1
30 : KAB11_OLDAF 0.64 0.73 5 26 5 26 22 0 0 29 P85129 Kalata-B11 OS=Oldenlandia affinis PE=1 SV=1
31 : KAB15_OLDAF 0.64 0.77 5 26 5 26 22 0 0 29 P85133 Kalata-B15 OS=Oldenlandia affinis PE=1 SV=1
32 : KAB4_OLDAF 1ZNU 0.64 0.68 5 26 5 26 22 0 0 29 P83938 Kalata-B4 OS=Oldenlandia affinis PE=1 SV=2
33 : A9P3R3_9ROSI 0.62 0.73 1 26 62 87 26 0 0 94 A9P3R3 Cyclotide protein Mra25 (Fragment) OS=Melicytus ramiflorus PE=2 SV=1
34 : B6E619_OLDAF 0.61 0.70 5 27 80 102 23 0 0 107 B6E619 Kalata B7 protein (Fragment) OS=Oldenlandia affinis PE=4 SV=1
35 : CYO24_VIOOD 0.61 0.65 5 26 5 27 23 1 1 30 P85187 Cycloviolacin-O24 OS=Viola odorata PE=1 SV=1
36 : KAB7_OLDAF 2M9O 0.61 0.70 5 27 80 102 23 0 0 111 P58457 Kalata-B7 OS=Oldenlandia affinis GN=OAK3 PE=1 SV=1
37 : Q30CA3_9ROSI 0.61 0.70 5 26 1 23 23 1 1 30 Q30CA3 Cyclotide A (Fragment) OS=Hybanthus calycinus PE=2 SV=1
38 : VHL2_VIOHE 2KUK 0.61 0.65 5 26 5 27 23 1 1 30 P85231 Leaf cyclotide 2 OS=Viola hederacea PE=1 SV=1
39 : G1CWH1_CLITE 0.56 0.72 3 27 32 56 25 0 0 132 G1CWH1 Cyclotide cliotide T2 OS=Clitoria ternatea PE=2 SV=1
40 : KAB9_OLDAF 0.56 0.70 1 26 2 28 27 1 1 31 P85127 Kalata-B9 OS=Oldenlandia affinis PE=1 SV=1
41 : CYH2_VIOHE 0.54 0.69 1 26 1 26 26 0 0 29 P85233 Cycloviolacin-H2 OS=Viola hederacea PE=1 SV=1
42 : CYO23_VIOOD 0.54 0.62 5 26 5 28 24 1 2 31 P85186 Cycloviolacin-O23 OS=Viola odorata PE=1 SV=1
43 : D8WS38_OLDAF 0.52 0.59 1 26 55 81 27 1 1 93 D8WS38 Cyclotide Oak7 (Fragment) OS=Oldenlandia affinis GN=oak7 PE=2 SV=1
44 : Q30C63_HYBFL 0.52 0.63 2 26 1 27 27 1 2 35 Q30C63 Cyclotide F (Fragment) OS=Hybanthus floribundus subsp. floribundus PE=2 SV=1
## ALIGNMENTS 1 - 44
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A S 0 0 80 7 28 S S S SS T
2 2 A A - 0 0 41 9 51 A G A A VA GS
3 3 A I S S+ 0 0 165 11 50 I VL F I LFI SI
4 4 A S S S+ 0 0 62 11 87 S PP G L KNA HS
5 5 A a + 0 0 13 45 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
6 6 A G S S+ 0 0 87 45 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
7 7 A E S S- 0 0 102 45 0 EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
8 8 A T B -A 25 0A 85 45 23 TSTTTTSTTTTTTTTTTTTTTTTTTTTTTTSTSTTTTTSTSTTT
9 9 A b - 0 0 1 45 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
10 10 A F - 0 0 137 45 67 FFFFFAFTVVVVFFVVVVVTFFFVFFVVTFFVTTFTVFVVVFFT
11 11 A K S S- 0 0 163 45 89 KKTTGFTLKGGTGGGGGGGLGGGTGGLGLGGGLLGLVTQLYGFT
12 12 A F S S+ 0 0 120 45 45 FGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGIGFF
13 13 A K + 0 0 90 45 60 KKKKTSKKKTTSTRTTTTSTTTTTTTTTTTSTETTTtTETPTGN
14 14 A c + 0 0 2 45 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCC
15 15 A Y E +C 20 0B 171 45 63 YYYYNYYYNNNYNNNNNNNYNNNYNNYNYNYNYYNYYYYYFNYW
16 16 A T E > S-C 19 0B 46 45 23 TTTTTTTTTTTTTTTTTTTTTTTTTTTTVTTTTTTTTTTTITKI
17 17 A P T 3 S+ 0 0 108 45 26 PPPPPPVAPPPPPPPPPPPAPPPPPPPPPPPPPQPQKNPPPPPP
18 18 A R T 3 S+ 0 0 153 45 32 RGGGGGQGGGGGGGGGGGGGGGGGGGDGDGGGGGGGKGGGGGGN
19 19 A a E < +C 16 0B 1 45 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
20 20 A S E -C 15 0B 54 45 43 SSSSSSSSVSSTTTSSSSSSSSSASSSTSSSTTTTTSTSTSTSK
21 21 A b E +B 26 0A 12 45 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
22 22 A S E > -B 25 0A 82 45 51 SsSSSSSSSSSSSSSSSSSSsssDdeTSSTTSSSdSAdDnRddn
23 23 A Y T 3 S+ 0 0 157 45 47 YyYYYWWWWWWWYYWWWWWWwwwWwwAWWDWWWWwWWwWyNwld
24 24 A P T 3 S+ 0 0 62 45 28 PPPPPPPPPPPPPPPPPPPPPPPPPPLPPPPPPPPPPPPRRPRK
25 25 A V E < -AB 8 22A 64 45 22 VLIIIVVVVVVVIIVVVVVVIIIVVVVVIIIVIIVIVVIVVIQV
26 26 A c E B 0 21A 1 45 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
27 27 A K 0 0 119 9 0 K KK K K K K K
## 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 86 14 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.71
2 2 A 11 0 0 0 0 0 0 22 56 0 11 0 0 0 0 0 0 0 0 0 9 0 0 1.149 38 0.48
3 3 A 9 18 45 0 18 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 11 0 0 1.414 47 0.50
4 4 A 0 9 0 0 0 0 0 9 9 18 27 0 0 9 0 9 0 0 9 0 11 0 0 1.972 65 0.13
5 5 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 45 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 45 0 0 0.000 0 1.00
7 7 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 45 0 0 0.000 0 1.00
8 8 A 0 0 0 0 0 0 0 0 0 0 13 87 0 0 0 0 0 0 0 0 45 0 0 0.393 13 0.76
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 45 0 0 0.000 0 1.00
10 10 A 38 0 0 0 44 0 0 0 2 0 0 16 0 0 0 0 0 0 0 0 45 0 0 1.102 36 0.32
11 11 A 2 18 0 0 4 0 2 47 0 0 0 16 0 0 0 9 2 0 0 0 45 0 0 1.559 52 0.10
12 12 A 0 0 2 0 9 0 0 87 0 0 0 0 0 0 0 0 0 0 0 2 45 0 0 0.508 16 0.55
13 13 A 0 0 0 0 0 0 0 2 0 2 9 60 0 0 2 18 0 4 2 0 45 0 1 1.305 43 0.40
14 14 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 45 0 0 0.000 0 1.00
15 15 A 0 0 0 0 2 2 49 0 0 0 0 0 0 0 0 0 0 0 47 0 45 0 0 0.875 29 0.37
16 16 A 2 0 4 0 0 0 0 0 0 0 0 91 0 0 0 2 0 0 0 0 45 0 0 0.392 13 0.77
17 17 A 2 0 0 0 0 0 0 0 4 84 0 0 0 0 0 2 4 0 2 0 45 0 0 0.673 22 0.73
18 18 A 0 0 0 0 0 0 0 84 0 0 0 0 0 0 4 2 2 0 2 4 45 0 0 0.673 22 0.67
19 19 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 45 0 0 0.000 0 1.00
20 20 A 2 0 0 0 0 0 0 0 2 0 67 27 0 0 0 2 0 0 0 0 45 0 0 0.877 29 0.56
21 21 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 45 0 0 0.000 0 1.00
22 22 A 0 0 0 0 0 0 0 0 2 0 67 7 0 0 2 0 0 2 4 16 45 0 12 1.132 37 0.48
23 23 A 0 2 0 0 0 69 20 0 2 0 0 0 0 0 0 0 0 0 2 4 45 0 0 0.971 32 0.52
24 24 A 0 2 0 0 0 0 0 0 0 89 0 0 0 0 7 2 0 0 0 0 45 0 0 0.454 15 0.71
25 25 A 60 2 36 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 45 0 0 0.843 28 0.77
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 45 0 0 0.000 0 1.00
27 27 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 9 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
2 19 24 1 sKy
21 19 89 1 sSw
22 19 23 1 sSw
23 19 89 1 sSw
25 19 23 1 dPw
26 19 23 1 eTw
35 19 23 1 dPw
37 10 10 1 tRc
38 19 23 1 dPw
40 23 24 1 nTy
42 19 23 2 dSSw
43 23 77 1 dEl
44 22 22 2 nHHd
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