Complet list of 1q3j hssp file
Complete list of 1q3j.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1Q3J
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 2013-09-25
HEADER knottin, cystine-knot, ANTIFUNGAL PROTE 2003-12-23 1Q3J
COMPND ALO3
SOURCE ?
AUTHOR Barbault, F.; Landon, C.; Guenneugues, M.; Meyer, J.P.; Schott, V.; Di
SEQLENGTH 36
NCHAIN 1 chain(s) in 1Q3J data set
NALIGN 11
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 : ALO3_ACRLO 1Q3J 1.00 1.00 1 36 1 36 36 0 0 36 P83653 Antimicrobial peptide Alo-3 OS=Acrocinus longimanus PE=1 SV=1
2 : ALO1_ACRLO 0.91 0.97 1 34 1 34 34 0 0 34 P83651 Antimicrobial peptide Alo-1 OS=Acrocinus longimanus PE=1 SV=1
3 : ALO2_ACRLO 0.88 0.94 1 34 1 34 34 0 0 34 P83652 Antimicrobial peptide Alo-2 OS=Acrocinus longimanus PE=1 SV=1
4 : G3J3B5_CORMM 0.53 0.72 1 36 32 66 36 1 1 66 G3J3B5 Gurmarin-like inhibitors/Antifungal toxin OS=Cordyceps militaris (strain CM01) GN=CCM_00299 PE=4 SV=1
5 : Q2PQC7_BEMTA 0.51 0.70 1 36 26 62 37 1 1 62 Q2PQC7 Putative antimicrobial knottin protein Btk-4 OS=Bemisia tabaci GN=btk-4 PE=4 SV=1
6 : AMP1_MESCR 0.50 0.72 1 36 29 64 36 0 0 64 O81338 Antimicrobial peptide 1 OS=Mesembryanthemum crystallinum PE=3 SV=1
7 : J4KLB7_BEAB2 0.50 0.76 1 34 28 61 34 0 0 61 J4KLB7 Uncharacterized protein OS=Beauveria bassiana (strain ARSEF 2860) GN=BBA_09080 PE=4 SV=1
8 : AMP1_MIRJA 0.47 0.64 1 36 26 61 36 0 0 61 P25403 Antimicrobial peptide 1 (Fragment) OS=Mirabilis jalapa GN=AMP1 PE=1 SV=4
9 : C0SFU5_PARBP 0.47 0.59 2 33 120 151 32 0 0 155 C0SFU5 Uncharacterized protein OS=Paracoccidioides brasiliensis (strain Pb03) GN=PABG_06550 PE=4 SV=1
10 : J5K012_BEAB2 0.47 0.67 1 36 83 117 36 1 1 117 J5K012 Uncharacterized protein OS=Beauveria bassiana (strain ARSEF 2860) GN=BBA_03436 PE=4 SV=1
11 : AMP2_MIRJA 0.44 0.58 1 36 28 63 36 0 0 63 P25404 Antimicrobial peptide 2 OS=Mirabilis jalapa GN=AMP2 PE=1 SV=2
## ALIGNMENTS 1 - 11
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A a 0 0 76 11 0 CCCCCCCC CC
2 2 A I + 0 0 64 12 15 IIILIIIIILI
3 3 A K S S- 0 0 128 12 75 KKAASKNGPGG
4 4 A N S S+ 0 0 84 12 0 NNNNNNNNNNN
5 5 A G S S+ 0 0 56 12 44 GGRGWGGGGGG
6 6 A N S S- 0 0 72 12 76 NNNKTKSGRKG
7 7 A G E +A 32 0A 56 12 77 GGGRKGGRPKR
8 8 A b E S+ 0 0A 11 12 0 CCCCCCCCCCC
9 9 A Q E +A 31 0A 53 12 61 QQQRKRKNKKN
10 10 A P S S- 0 0 66 12 71 PPPAPEAEKAE
11 11 A N S S- 0 0 115 12 29 NDDNDDDNDNN
12 12 A G + 0 0 47 12 44 GGGGGQGVGGV
13 13 A S S S- 0 0 77 12 28 SSSSSGSGSSG
14 14 A Q S S- 0 0 188 12 95 QQQMIPWPMMP
15 15 A G + 0 0 26 12 38 GGGGGPGPGGP
16 16 A N - 0 0 133 12 87 NNNINFVYNTY
17 17 A c > - 0 0 2 12 0 CCCCCCCCCCC
18 18 A a T 3 S+ 0 0 96 12 14 CCCCCCCCACC
19 19 A S T 3 S- 0 0 50 12 0 SSSSSSSSSSS
20 20 A G S < S+ 0 0 59 12 17 GRGGGGGGGGG
21 21 A Y + 0 0 101 12 4 YYYFYFFFFFF
22 22 A b E -B 33 0A 18 12 0 CCCCcCCCCCC
23 23 A H E +B 32 0A 42 11 79 HHHLqYLLL.L
24 24 A K - 0 0 78 12 77 KKKAERQRQLR
25 25 A Q - 0 0 95 12 74 QEEQKQYQIAQ
26 26 A P S S+ 0 0 147 12 59 PPPGPVQPQQP
27 27 A G S S+ 0 0 68 12 31 GGGNDGGGGGN
28 28 A W S S- 0 0 75 12 91 WWWRWWAQENQ
29 29 A V S S+ 0 0 120 12 82 VVVVEASGSKG
30 30 A A S S- 0 0 52 11 102 AAA.YRSYQVY
31 31 A G E -A 9 0A 1 12 0 GGGGGGGGGGG
32 32 A Y E -AB 7 23A 71 12 76 YYYVIYVYKVV
33 33 A c E - B 0 22A 0 12 0 CCCCCCCCCCC
34 34 A R - 0 0 61 11 27 RRRRKKKK KR
35 35 A R 0 0 167 8 63 R QNN N KN
36 36 A K 0 0 184 8 29 K KRR R KR
## 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 0 100 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
2 2 A 0 17 83 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.451 15 0.84
3 3 A 0 0 0 0 0 0 0 25 17 8 8 0 0 0 0 33 0 0 8 0 12 0 0 1.633 54 0.25
4 4 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 12 0 0 0.000 0 1.00
5 5 A 0 0 0 0 0 8 0 83 0 0 0 0 0 0 8 0 0 0 0 0 12 0 0 0.566 18 0.55
6 6 A 0 0 0 0 0 0 0 17 0 0 8 8 0 0 8 25 0 0 33 0 12 0 0 1.633 54 0.24
7 7 A 0 0 0 0 0 0 0 50 0 8 0 0 0 0 25 17 0 0 0 0 12 0 0 1.199 40 0.23
8 8 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 33 33 0 17 0 12 0 0 1.330 44 0.38
10 10 A 0 0 0 0 0 0 0 0 25 42 0 0 0 0 0 8 0 25 0 0 12 0 0 1.265 42 0.29
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 50 12 0 0 0.693 23 0.70
12 12 A 17 0 0 0 0 0 0 75 0 0 0 0 0 0 0 0 8 0 0 0 12 0 0 0.721 24 0.56
13 13 A 0 0 0 0 0 0 0 25 0 0 75 0 0 0 0 0 0 0 0 0 12 0 0 0.562 18 0.71
14 14 A 0 0 8 25 0 8 0 0 0 25 0 0 0 0 0 0 33 0 0 0 12 0 0 1.474 49 0.05
15 15 A 0 0 0 0 0 0 0 75 0 25 0 0 0 0 0 0 0 0 0 0 12 0 0 0.562 18 0.61
16 16 A 8 0 8 0 8 0 17 0 0 0 0 8 0 0 0 0 0 0 50 0 12 0 0 1.474 49 0.12
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
18 18 A 0 0 0 0 0 0 0 0 8 0 0 0 92 0 0 0 0 0 0 0 12 0 0 0.287 9 0.85
19 19 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 0 0 92 0 0 0 0 0 0 8 0 0 0 0 0 12 0 0 0.287 9 0.82
21 21 A 0 0 0 0 58 0 42 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.679 22 0.96
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 12 1 1 0.000 0 1.00
23 23 A 0 45 0 0 0 0 9 0 0 0 0 0 0 36 0 0 9 0 0 0 11 0 0 1.162 38 0.20
24 24 A 0 8 0 0 0 0 0 0 8 0 0 0 0 0 25 33 17 8 0 0 12 0 0 1.633 54 0.22
25 25 A 0 0 8 0 0 0 8 0 8 0 0 0 0 0 0 8 50 17 0 0 12 0 0 1.474 49 0.25
26 26 A 8 0 0 0 0 0 0 8 0 58 0 0 0 0 0 0 25 0 0 0 12 0 0 1.075 35 0.40
27 27 A 0 0 0 0 0 0 0 75 0 0 0 0 0 0 0 0 0 0 17 8 12 0 0 0.721 24 0.69
28 28 A 0 0 0 0 0 50 0 0 8 0 0 0 0 0 8 0 17 8 8 0 12 0 0 1.474 49 0.08
29 29 A 42 0 0 0 0 0 0 17 8 0 17 0 0 0 0 8 0 8 0 0 12 1 0 1.583 52 0.17
30 30 A 9 0 0 0 0 0 27 0 36 0 9 0 0 0 9 0 9 0 0 0 11 0 0 1.594 53 -0.02
31 31 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
32 32 A 33 0 8 0 0 0 50 0 0 0 0 0 0 0 0 8 0 0 0 0 12 0 0 1.127 37 0.23
33 33 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
34 34 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 45 0 0 0 0 11 0 0 0.689 22 0.72
35 35 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 13 13 0 50 0 8 0 0 1.213 40 0.36
36 36 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 50 0 0 0 0 8 0 0 0.693 23 0.70
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
5 23 48 1 cFq
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