Complet list of 1bom hssp file
Complete list of 1bom.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1BOM
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 2014-04-27
HEADER INSULIN-LIKE BRAIN-SECRETORY PEPTIDE 21-JUL-94 1BOM
COMPND MOL_ID: 1; MOLECULE: BOMBYXIN-II,BOMBYXIN A-2; CHAIN: A; ENGINEERED: Y
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: BOMBYX MORI; ORGANISM_COMMON: DOMESTIC
AUTHOR K.NAGATA,H.HATANAKA,D.KOHDA,F.INAGAKI
DBREF 1BOM A 1 20 UNP P15411 BXA2_BOMMO 70 89
DBREF 1BOM B -1 25 UNP P26729 BXA6_BOMMO 20 47
SEQLENGTH 28
NCHAIN 1 chain(s) in 1BOM data set
NALIGN 19
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 : BXA6_BOMMO 1BOM 1.00 1.00 2 28 21 47 27 0 0 92 P26729 Bombyxin A-6 OS=Bombyx mori GN=BBXA6 PE=1 SV=1
2 : BXA7_BOMMO 1.00 1.00 2 28 21 47 27 0 0 92 P26730 Bombyxin A-7 OS=Bombyx mori GN=BBXA7 PE=1 SV=1
3 : BXA9_BOMMO 1.00 1.00 2 28 21 47 27 0 0 92 P26732 Bombyxin A-9 OS=Bombyx mori GN=BBXA9 PE=1 SV=1
4 : H9JQX3_BOMMO 1.00 1.00 2 28 21 47 27 0 0 92 H9JQX3 Uncharacterized protein OS=Bombyx mori GN=Bbx-a4 PE=3 SV=1
5 : Q17193_BOMMO 1.00 1.00 2 28 21 47 27 0 0 82 Q17193 Bombyxin A-10 (Precursor) OS=Bombyx mori GN=bbxA10 PE=4 SV=1
6 : BXA1_BOMMO 0.96 0.96 2 28 21 47 27 0 0 92 Q17192 Bombyxin A-1 OS=Bombyx mori GN=BBXA1 PE=3 SV=1
7 : BXA4_BOMMO 0.96 1.00 2 28 21 47 27 0 0 92 P26727 Bombyxin A-4 OS=Bombyx mori GN=BBXA4 PE=3 SV=1
8 : H9JY76_BOMMO 0.96 1.00 2 28 7 33 27 0 0 78 H9JY76 Uncharacterized protein OS=Bombyx mori PE=3 SV=1
9 : BXA3_BOMMO 0.93 1.00 2 28 21 47 27 0 0 92 P26726 Bombyxin A-3 OS=Bombyx mori GN=BBXA3 PE=3 SV=1
10 : BXA5_BOMMO 0.93 1.00 2 28 21 47 27 0 0 92 P26728 Bombyxin A-5 OS=Bombyx mori GN=BBXA5 PE=3 SV=1
11 : BXA8_BOMMO 0.93 0.96 2 28 21 47 27 0 0 89 P26731 Bombyxin A-8 OS=Bombyx mori GN=BBXA8 PE=3 SV=1
12 : H9JQX2_BOMMO 0.93 0.96 2 28 7 33 27 0 0 75 H9JQX2 Uncharacterized protein OS=Bombyx mori PE=3 SV=1
13 : BXA2_BOMMO 1BOM 0.89 0.93 2 28 21 47 27 0 0 89 P15411 Bombyxin A-2 OS=Bombyx mori GN=BBXA2 PE=1 SV=1
14 : B9A0V1_BOMMO 0.68 0.86 7 28 25 46 22 0 0 88 B9A0V1 IGF-like peptide OS=Bombyx mori GN=IGFLP PE=3 SV=1
15 : H9JRY3_BOMMO 0.65 0.74 2 24 20 42 23 0 0 94 H9JRY3 Uncharacterized protein OS=Bombyx mori PE=3 SV=1
16 : BXE1_BOMMO 0.59 0.85 2 28 21 47 27 0 0 98 P21808 Bombyxin E-1 OS=Bombyx mori GN=BBXE1 PE=1 SV=4
17 : Q4JJX8_MANSE 0.58 0.81 3 28 19 44 26 0 0 94 Q4JJX8 Bombyxin OS=Manduca sexta GN=bbx PE=3 SV=1
18 : H9JRY4_BOMMO 0.56 0.81 2 28 21 47 27 0 0 98 H9JRY4 Uncharacterized protein OS=Bombyx mori GN=Bbx-e1 PE=3 SV=1
19 : BXD1_BOMMO 0.54 0.69 3 28 20 45 26 0 0 90 P26736 Bombyxin D-1 OS=Bombyx mori GN=BBXD1 PE=3 SV=1
## ALIGNMENTS 1 - 19
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 -2 B X 0 0 172 0 0
2 -1 B Q - 0 0 164 17 29 QQQQQQQQQQQQQ QE E
3 0 B P - 0 0 60 19 60 PPPPPPPPPPPPP QAAAS
4 1 B Q S S- 0 0 177 19 48 QQQQQQQQQQQQQ KNQNE
5 2 B A S S+ 0 0 47 19 78 AAAAARGGGTEEE QVGVE
6 3 B V + 0 0 75 19 69 VVVVVVVVVVVVV AAGAG
7 4 B H + 0 0 116 20 27 HHHHHHHHHHHHHRRHQHH
8 5 B T - 0 0 24 20 78 TTTTTTTTTTTTTTHHRHI
9 6 B Y - 0 0 102 20 1 YYYYYYYYYYYYYYYYFYY
10 7 B b - 0 0 68 20 0 CCCCCCCCCCCCCCCCCCC
11 8 B G S S+ 0 0 33 20 0 GGGGGGGGGGGGGGGGGGG
12 9 B R S >> S+ 0 0 189 20 5 RRRRRRRRRHRRRRRRRRR
13 10 B H T 34 S+ 0 0 98 20 38 HHHHHHHHHHHHHYFHHHY
14 11 B L T 3> S+ 0 0 4 20 0 LLLLLLLLLLLLLLLLLLL
15 12 B A T <4 S+ 0 0 80 20 0 AAAAAAAAAAAAAAAAAAA
16 13 B R T >< S+ 0 0 169 20 72 RRRRRRRRRRRRRRLNRNY
17 14 B T G >> S+ 0 0 25 20 16 TTTTTTTTTTTTTTTTTTK
18 15 B L G 3< S+ 0 0 43 20 5 LLLLLLLLLLMMMLLLLLM
19 16 B A G <4 S+ 0 0 41 20 0 AAAAAAAAAAAAAAAAAAA
20 17 B D T <> S+ 0 0 82 20 11 DDDDDDDDNDDDDNDDDDD
21 18 B L H X S+ 0 0 24 20 0 LLLLLLLLLLLLLLLLLLL
22 19 B c H 4 S+ 0 0 61 20 0 CCCCCCCCCCCCCCCCCCC
23 20 B W H > S+ 0 0 148 20 16 WWWWWWWWWWWWWSWWYWW
24 21 B E H < S+ 0 0 161 20 33 EEEEEEEEEEEEEDEDEDR
25 22 B A T < S- 0 0 72 19 49 AAAAAAAAAAAAEA TVTA
26 23 B G T 4 - 0 0 26 19 33 GGGGGGGGGGGGGG SDSG
27 24 B V < 0 0 82 19 69 VVVVVVVVVVVVVQ VYAF
28 25 B D 0 0 212 19 25 DDDDDDDDDDDDDE EEEE
## 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
165534 B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.000 0 1.00
265535 B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 88 12 0 0 17 0 0 0.362 12 0.70
3 0 B 0 0 0 0 0 0 0 0 16 74 5 0 0 0 0 0 5 0 0 0 19 0 0 0.826 27 0.40
4 1 B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 79 5 11 0 19 0 0 0.734 24 0.51
5 2 B 11 0 0 0 0 0 0 21 32 0 0 5 0 0 5 0 5 21 0 0 19 0 0 1.722 57 0.22
6 3 B 74 0 0 0 0 0 0 11 16 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0.753 25 0.30
7 4 B 0 0 0 0 0 0 0 0 0 0 0 0 0 85 10 0 5 0 0 0 20 0 0 0.518 17 0.72
8 5 B 0 0 5 0 0 0 0 0 0 0 0 75 0 15 5 0 0 0 0 0 20 0 0 0.800 26 0.22
9 6 B 0 0 0 0 5 0 95 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.199 6 0.99
10 7 B 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
11 8 B 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
12 9 B 0 0 0 0 0 0 0 0 0 0 0 0 0 5 95 0 0 0 0 0 20 0 0 0.199 6 0.94
13 10 B 0 0 0 0 5 0 10 0 0 0 0 0 0 85 0 0 0 0 0 0 20 0 0 0.518 17 0.61
14 11 B 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
15 12 B 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
16 13 B 0 5 0 0 0 0 5 0 0 0 0 0 0 0 80 0 0 0 10 0 20 0 0 0.708 23 0.28
17 14 B 0 0 0 0 0 0 0 0 0 0 0 95 0 0 0 5 0 0 0 0 20 0 0 0.199 6 0.83
18 15 B 0 80 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.500 16 0.95
19 16 B 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
20 17 B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 90 20 0 0 0.325 10 0.89
21 18 B 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
22 19 B 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
23 20 B 0 0 0 0 0 90 5 0 0 0 5 0 0 0 0 0 0 0 0 0 20 0 0 0.394 13 0.83
24 21 B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 80 0 15 20 0 0 0.613 20 0.67
25 22 B 5 0 0 0 0 0 0 0 79 0 0 11 0 0 0 0 0 5 0 0 19 0 0 0.734 24 0.50
26 23 B 0 0 0 0 0 0 0 84 0 0 11 0 0 0 0 0 0 0 0 5 19 0 0 0.537 17 0.66
27 24 B 79 0 0 0 5 0 5 0 5 0 0 0 0 0 0 0 5 0 0 0 19 0 0 0.807 26 0.30
28 25 B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 0 74 19 0 0 0.576 19 0.75
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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