Complet list of 2b68 hssp file
Complete list of 2b68.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 2B68
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 2014-05-16
HEADER ANTIMICROBIAL PROTEIN 30-SEP-05 2B68
COMPND MOL_ID: 1; MOLECULE: DEFENSIN; CHAIN: A; FRAGMENT: RESIDUES 1-43; ENGI
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: CRASSOSTREA GIGAS; ORGANISM_COMMON: PA
AUTHOR Y.GUEGUEN,H.AMAURY,A.AUMELAS,J.GARNIER,J.FIEVET, J.M.ESCOUBAS,P.BULET,
DBREF 2B68 A 1 43 UNP Q4GWV4 Q4GWV4_CRAGI 23 65
SEQLENGTH 43
NCHAIN 1 chain(s) in 2B68 data set
NALIGN 59
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 : C4NY99_CRAGI 1.00 1.00 1 42 23 64 42 0 0 65 C4NY99 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
2 : G3FZK5_CRAGI 1.00 1.00 1 43 23 65 43 0 0 65 G3FZK5 Mantle defensin OS=Crassostrea gigas PE=4 SV=1
3 : G3FZK6_CRAGI 1.00 1.00 1 43 23 65 43 0 0 65 G3FZK6 Mantle defensin OS=Crassostrea gigas PE=4 SV=1
4 : Q4GWV4_CRAGI2B68 1.00 1.00 1 43 23 65 43 0 0 65 Q4GWV4 Defensin OS=Crassostrea gigas GN=def PE=1 SV=1
5 : C4NY93_CRAGI 0.98 1.00 1 42 23 64 42 0 0 73 C4NY93 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
6 : C4NY97_CRAGI 0.98 0.98 1 43 23 65 43 0 0 65 C4NY97 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
7 : C4NYA0_CRAGI 0.98 1.00 1 43 23 65 43 0 0 65 C4NYA0 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
8 : C4NYA1_CRAGI 0.98 1.00 1 43 23 65 43 0 0 65 C4NYA1 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
9 : C4NYA3_CRAGI 0.98 1.00 1 43 23 65 43 0 0 65 C4NYA3 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
10 : C4NYA4_CRAGI 0.98 1.00 1 43 23 65 43 0 0 65 C4NYA4 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
11 : C4NYH5_CRAGI 0.98 1.00 1 43 23 65 43 0 0 65 C4NYH5 Defs OS=Crassostrea gigas GN=defs PE=4 SV=1
12 : G3FZJ2_CRAGI 0.98 0.98 1 43 23 65 43 0 0 65 G3FZJ2 Mantle defensin OS=Crassostrea gigas PE=4 SV=1
13 : G3FZJ6_CRAGI 0.98 1.00 1 43 23 65 43 0 0 65 G3FZJ6 Mantle defensin OS=Crassostrea gigas PE=4 SV=1
14 : G3FZK8_CRAGI 0.98 1.00 1 43 23 65 43 0 0 65 G3FZK8 Mantle defensin OS=Crassostrea gigas PE=4 SV=1
15 : C4NYA6_CRAGI 0.95 0.98 1 43 23 65 43 0 0 65 C4NYA6 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
16 : G3FZJ1_CRAGI 0.95 0.98 1 43 23 65 43 0 0 65 G3FZJ1 Mantle defensin OS=Crassostrea gigas PE=4 SV=1
17 : C6KEN0_CRAGI 0.86 0.94 9 43 31 65 35 0 0 65 C6KEN0 Defensin h1 OS=Crassostrea gigas PE=4 SV=1
18 : C4NYB2_CRAGI 0.84 0.93 1 43 23 65 43 0 0 65 C4NYB2 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
19 : C4NYB5_CRAGI 0.84 0.93 1 43 23 65 43 0 0 65 C4NYB5 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
20 : C4NYB7_CRAGI 0.84 0.93 1 43 23 65 43 0 0 65 C4NYB7 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
21 : Q20A06_CRAGI 0.84 0.93 1 43 18 60 43 0 0 60 Q20A06 Hemocyte defensin Defh1 (Fragment) OS=Crassostrea gigas PE=2 SV=1
22 : C4NYB1_CRAGI 0.81 0.93 1 43 23 65 43 0 0 65 C4NYB1 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
23 : C4NYB6_CRAGI 0.81 0.93 1 43 23 65 43 0 0 65 C4NYB6 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
24 : C4NYB8_CRAGI 0.81 0.93 1 43 23 65 43 0 0 65 C4NYB8 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
25 : K1PTY8_CRAGI 0.81 0.93 1 42 23 64 42 0 0 70 K1PTY8 Uncharacterized protein OS=Crassostrea gigas GN=CGI_10009486 PE=4 SV=1
26 : C4NYB9_CRAGI 0.79 0.91 1 43 23 65 43 0 0 65 C4NYB9 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
27 : C4NYC0_CRAGI 0.79 0.91 1 43 23 65 43 0 0 65 C4NYC0 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
28 : C4NYC1_CRAGI 0.79 0.91 1 43 23 65 43 0 0 65 C4NYC1 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
29 : C4NYC2_CRAGI 0.79 0.91 1 43 23 65 43 0 0 65 C4NYC2 Defensin OS=Crassostrea gigas GN=defs PE=4 SV=1
30 : C4NYI1_CRAGI 0.79 0.91 1 43 23 65 43 0 0 65 C4NYI1 Defs OS=Crassostrea gigas GN=defs PE=4 SV=1
31 : C4NYI4_CRAGI 0.79 0.91 1 43 23 65 43 0 0 65 C4NYI4 Defs OS=Crassostrea gigas GN=defs PE=4 SV=1
32 : G3FZL7_CRAGI 0.79 0.91 1 43 23 65 43 0 0 65 G3FZL7 Defensin OS=Crassostrea gigas PE=4 SV=1
33 : G3FZM7_CRAGI 0.79 0.91 1 43 23 65 43 0 0 65 G3FZM7 Defensin OS=Crassostrea gigas PE=4 SV=1
34 : Q20A05_CRAGI 0.79 0.91 1 43 18 60 43 0 0 60 Q20A05 Hemocyte defensin Defh2 (Fragment) OS=Crassostrea gigas PE=2 SV=1
35 : C6KEN1_CRAGI 0.78 0.89 8 43 30 65 36 0 0 65 C6KEN1 Defensin h2 OS=Crassostrea gigas PE=4 SV=1
36 : C4NYJ0_CRAGI 0.77 0.88 1 43 23 65 43 0 0 65 C4NYJ0 Defs OS=Crassostrea gigas GN=defs PE=4 SV=1
37 : G3FZM3_CRAGI 0.77 0.88 1 43 23 65 43 0 0 65 G3FZM3 Defensin OS=Crassostrea gigas PE=4 SV=1
38 : G3FZM4_CRAGI 0.77 0.91 1 43 23 65 43 0 0 65 G3FZM4 Defensin OS=Crassostrea gigas PE=4 SV=1
39 : G3FZM6_CRAGI 0.77 0.88 1 43 23 65 43 0 0 65 G3FZM6 Defensin OS=Crassostrea gigas PE=4 SV=1
40 : E3VXC1_VENPH 0.60 0.84 1 42 24 66 43 1 1 72 E3VXC1 Defensin OS=Venerupis philippinarum GN=Def PE=4 SV=1
41 : J7FS06_VENPH 0.60 0.84 1 42 24 66 43 1 1 72 J7FS06 Defensin OS=Venerupis philippinarum GN=Def PE=4 SV=1
42 : J7FU14_VENPH 0.60 0.84 1 42 24 66 43 1 1 72 J7FU14 Defensin OS=Venerupis philippinarum GN=Def PE=4 SV=1
43 : J7FYT9_VENPH 0.60 0.86 1 42 24 66 43 1 1 72 J7FYT9 Defensin OS=Venerupis philippinarum GN=Def PE=4 SV=1
44 : J7FYY5_VENPH 0.59 0.82 1 43 24 67 44 1 1 72 J7FYY5 Defensin OS=Venerupis philippinarum GN=Def PE=4 SV=1
45 : DEFI_ORNCO 0.58 0.69 1 36 7 41 36 1 1 44 B2D2C0 Defensin OS=Ornithodoros coriaceus PE=3 SV=1
46 : J7FRX3_VENPH 0.57 0.80 1 43 24 67 44 1 1 72 J7FRX3 Defensin OS=Venerupis philippinarum GN=Def PE=4 SV=1
47 : DEF1_CRAVI 0.56 0.83 1 36 1 35 36 1 1 38 P85008 Defensin-1 OS=Crassostrea virginica PE=1 SV=1
48 : J7FS28_VENPH 0.55 0.80 1 43 23 66 44 1 1 70 J7FS28 Defensin OS=Venerupis philippinarum GN=Def PE=4 SV=1
49 : DEFB_MYTED 0.53 0.69 1 36 1 35 36 1 1 35 P81611 Defensin-B (Fragment) OS=Mytilus edulis PE=1 SV=1
50 : J7FYT5_VENPH 0.52 0.80 1 43 23 66 44 1 1 70 J7FYT5 Defensin OS=Venerupis philippinarum GN=Def PE=4 SV=1
51 : DEFA_MYTED 0.50 0.67 1 36 1 35 36 1 1 37 P81610 Defensin-A OS=Mytilus edulis PE=1 SV=1
52 : M4NCH1_CRIPL 0.50 0.65 1 39 25 63 40 2 2 63 M4NCH1 Defensin OS=Cristaria plicata PE=4 SV=1
53 : DEFI_MYTGA 1FJN 0.49 0.70 1 43 1 42 43 1 1 60 P80571 Defensin MGD-1 (Fragment) OS=Mytilus galloprovincialis GN=FH3 PE=1 SV=2
54 : H2DH26_9BIVA 0.48 0.60 1 36 24 63 40 1 4 65 H2DH26 Defensin OS=Hyriopsis cumingii PE=4 SV=1
55 : DEFI_AESCY 0.47 0.75 1 36 1 36 36 0 0 38 P80154 Defensin OS=Aeshna cyanea PE=1 SV=1
56 : G1E712_9BIVA 0.45 0.60 1 36 24 63 40 1 4 65 G1E712 Defensin OS=Hyriopsis schlegelii PE=4 SV=1
57 : H9AXM9_MYTGA 0.45 0.76 2 39 25 61 38 1 1 61 H9AXM9 Defensin OS=Mytilus galloprovincialis PE=4 SV=1
58 : U4LUG1_PYROM 0.44 0.67 1 34 56 94 39 2 5 95 U4LUG1 Similar to Plectasin acc. no. Q53I06 OS=Pyronema omphalodes (strain CBS 100304) GN=PCON_01609 PE=4 SV=1
59 : U4LWE8_PYROM 0.44 0.69 1 34 53 91 39 2 5 92 U4LWE8 Similar to Plectasin acc. no. Q53I06 OS=Pyronema omphalodes (strain CBS 100304) GN=PCON_01610 PE=4 SV=1
## ALIGNMENTS 1 - 59
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A G 0 0 57 57 3 GGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGSGGGG GG
2 2 A F - 0 0 124 58 9 FFFFFFFFFFFCFFFF FFFFFLFFFFFFFFFFF FFFFFFFFFCFFFFFFWFFFFFFF
3 3 A G S S+ 0 0 27 58 0 GGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGGGGGGGG
4 4 A a + 0 0 16 58 0 CCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCCCCCC
5 5 A P S S+ 0 0 86 58 21 PPPPPPPPPPPPPPPP PPPPPPPPPPPPPPPPP PPPPPPPPPPPPPPPPPPNPNPNN
6 6 A G S S+ 0 0 70 56 76 GGGGGGGGGGDGGGGG RRRRRRRLGGGGGGGGG GGGGEEEDDLDWD.KNF.gLgLgg
7 7 A N + 0 0 54 58 33 NNNNNNNDNNNNDNDN DDDDDDDNDDDDDDDDD DDDDDDDDDNDNKNSDNNnDdNdd
8 8 A Q S > S+ 0 0 94 58 37 QQQQQQQQQRQQQQQQ QQQQQQQQQQQQQQQQQQQQQQEEEEEQERQDE.QNPQPQDD
9 9 A L H > S+ 0 0 114 60 59 LLLLLSLLLLLLLLLLYYYYYYYYYYYYYYYYYYYYYYYYYYYYGYYYYYYKYYMYHMM
10 10 A K H > S+ 0 0 110 60 66 KKKKKKKKKKKKKKKKKKKKKKKKQEEEEEEEEEEEEEEEEEEEAEQEPVPLQQQQRKK
11 11 A b H > S+ 0 0 0 60 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
12 12 A N H X S+ 0 0 53 60 42 NNNNNNNNNNNNNDNNNNNNNNNNNNNNNNNNNNNNNSNHHHHHHHHHHHHNHNHNHHH
13 13 A N H X S+ 0 0 56 60 68 NNNNNNNNNNNNNNNNSSSSSSSSSRRRRRRRRRRRRRRNNNNNRNSNRNRNRARAVNN
14 14 A H H X S+ 0 0 49 60 3 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHNHHHHHHH
15 15 A c H X>S+ 0 0 0 60 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCYCCCCCCCCCCCCCCCCCCCC
16 16 A K H <5S+ 0 0 140 60 46 KKKKKKRKKKKKKKKKQQQQQQQQKRRRRRRRRRRRRRRKKKKKKKRKKKKIKRQRLKK
17 17 A S H <5S+ 0 0 108 60 48 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSnnnndSdSySnSvSRTRAss
18 18 A I H <5S- 0 0 77 60 42 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIvvvvvIvIvIvIrININAkk
19 19 A S T <5S+ 0 0 95 60 47 SSSSSSSSSSSSSSSSGGGGGGGGRGGGGGGGGGGGGGGGGGGGGGGGPGPKPGTGNGG
20 20 A d < - 0 0 26 60 41 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCRCRCGCGCGFGFCYY
21 21 A R S S- 0 0 141 60 23 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRLRRRRRRTRTKKK
22 22 A A E -A 37 0A 39 59 43 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGYGXGCGSGGGG
23 23 A G E -A 36 0A 14 60 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
24 24 A Y E -A 35 0A 100 60 30 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYCYYGYGYGYGYYYY
25 25 A a - 0 0 0 60 6 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCYCYCYCYCCCC
26 26 A D > > - 0 0 57 57 50 DDDDDDDDDDDDDDDDDDDDDGDGDDDDDDDDDDDDDDDDDDDD.D.DCDCKCNCN.AA
27 27 A A T 3 5S+ 0 0 50 60 30 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAVGAGPGASAGKS
28 28 A A T 3 5S+ 0 0 91 60 83 AAAAAAAAAAAAAAAAVVVVVVVVAVVVVVVAVVVVVVVGGGGWGWGLGWGSGWGWGAA
29 29 A T T < 5S- 0 0 51 58 51 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTSTXTXSWLPLWGG
30 30 A L T 5S- 0 0 144 60 25 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHAHLHLLLFFF
31 31 A W S