Complet list of 1pjv hssp file
Complete list of 1pjv.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1PJV
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 2014-05-06
HEADER TOXIN 03-JUN-03 1PJV
COMPND MOL_ID: 1; MOLECULE: COBATOXIN 1; CHAIN: A; SYNONYM: COTX1, GTIX; ENGI
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THE PROTEIN WAS CHEMICALLY S
AUTHOR A.MOSBAH,B.JOUIROU,V.VISAN,S.GRISSMER,M.EL AYEB,H.ROCHAT, M.DE WAARD,K
DBREF 1PJV A 1 32 UNP O46028 SCK1_CENNO 29 60
SEQLENGTH 32
NCHAIN 1 chain(s) in 1PJV data set
NALIGN 10
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 : KA101_CENNO 1PJV 1.00 1.00 1 32 29 60 32 0 0 62 O46028 Potassium channel toxin alpha-KTx 10.1 OS=Centruroides noxius PE=1 SV=1
2 : KA102_CENNO 0.90 0.90 3 32 3 32 30 0 0 32 P58504 Potassium channel toxin alpha-KTx 10.2 OS=Centruroides noxius PE=1 SV=1
3 : D9IPD1_SPOEX 0.54 0.68 3 29 46 73 28 1 1 75 D9IPD1 Gallerimycin OS=Spodoptera exigua PE=4 SV=1
4 : KA232_VAEMS 0.52 0.69 3 30 6 34 29 1 1 35 P0DJ32 Potassium channel toxin alpha-KTx 23.2 OS=Vaejovis mexicanus smithi PE=1 SV=1
5 : B8XH28_BUTOS 0.50 0.57 3 31 30 59 30 1 1 59 B8XH28 Putative potassium channel toxin Tx1 (Precursor) OS=Buthus occitanus israelis PE=3 SV=1
6 : B8XH29_BUTOS 0.50 0.57 3 31 30 59 30 1 1 60 B8XH29 Putative potassium channel toxin Tx260 OS=Buthus occitanus israelis PE=3 SV=1
7 : KA191_MESMA 1R1G 0.50 0.57 1 30 1 30 30 0 0 31 P83407 Potassium channel toxin alpha-KTx 19.1 OS=Mesobuthus martensii PE=1 SV=1
8 : KAX3A_BUTOS 0.50 0.57 3 31 30 59 30 1 1 59 P0C908 Potassium channel toxin alpha-KTx 3.10 OS=Buthus occitanus israelis PE=1 SV=1
9 : SCKP2_TITSE 0.50 0.61 3 30 30 55 28 1 2 68 P0C175 Peptide TsPep2 OS=Tityus serrulatus PE=1 SV=1
10 : KTXA_LYCMC 0.48 0.61 1 31 29 59 31 0 0 61 D9U2B0 Putative neurotoxin-A OS=Lychas mucronatus PE=2 SV=1
## ALIGNMENTS 1 - 10
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A A 0 0 158 4 31 A A G
2 2 A V - 0 0 121 4 92 V A S
3 3 A a - 0 0 56 11 0 CCCCCCCCCC
4 4 A V > - 0 0 75 11 95 VVVVRRYRGS
5 5 A Y H > S+ 0 0 100 11 96 YYFgggSgGN
6 6 A R H > S+ 0 0 212 10 67 RRYkrrSr.K
7 7 A T H > S+ 0 0 82 10 60 TTEEDDDD.N
8 8 A b H X S+ 0 0 34 11 0 CCCCCCCCCC
9 9 A D H X S+ 0 0 38 11 101 DDSLLLRLNV
10 10 A K H X S+ 0 0 122 11 88 KKAPDDVDRS
11 11 A D H < S+ 0 0 84 11 79 DDSKPPKPKS
12 12 A c H ><>S+ 0 0 2 11 0 CCCCCCCCCC
13 13 A K H 3<5S+ 0 0 113 11 73 KTRKKKVKCQ
14 14 A R T 3<5S+ 0 0 206 11 80 RSRAKKAKAG
15 15 A R T < 5S- 0 0 170 11 91 RRRQAAMAGS
16 16 A G T 5S+ 0 0 72 11 19 GKGGGGGGGG
17 17 A Y S +A 26 0A 100 11 30 IITMIIIIII
24 24 A N T 3 S- 0 0 157 11 31 NNFNNNNNNN
25 25 A N T 3 S+ 0 0 155 11 61 NNNKSSSSGS
26 26 A A E < -A 23 0A 58 11 64 AAGKKKKKKK
27 27 A b E -A 22 0A 51 11 0 CCCCCCCCCC
28 28 A K E -A 21 0A 148 11 58 KKQKHHKHQK
29 29 A c E -A 20 0A 49 11 0 CCCCCCCCCC
30 30 A Y E -A 19 0A 91 10 65 YY YTTYTYY
31 31 A P 0 0 81 7 0 PP PP P P
32 32 A Y 0 0 244 3 0 YY
## 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 25 75 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.562 18 0.68
2 2 A 50 0 0 0 0 0 0 0 25 0 25 0 0 0 0 0 0 0 0 0 4 0 0 1.040 34 0.07
3 3 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
4 4 A 45 0 0 0 0 0 9 9 0 0 9 0 0 0 27 0 0 0 0 0 11 0 0 1.367 45 0.05
5 5 A 0 0 0 0 9 0 27 45 0 0 9 0 0 0 0 0 0 0 9 0 11 1 4 1.367 45 0.03
6 6 A 0 0 0 0 0 0 10 0 0 0 10 0 0 0 60 20 0 0 0 0 10 0 0 1.089 36 0.33
7 7 A 0 0 0 0 0 0 0 0 0 0 0 30 0 0 0 0 0 20 10 40 10 0 0 1.280 42 0.39
8 8 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
9 9 A 9 36 0 0 0 0 0 0 0 0 9 0 0 0 9 0 0 0 9 27 11 0 0 1.594 53 -0.01
10 10 A 9 0 0 0 0 0 0 0 9 9 9 0 0 0 9 27 0 0 0 27 11 0 0 1.799 60 0.12
11 11 A 0 0 0 0 0 0 0 0 0 27 18 0 0 0 0 27 0 0 0 27 11 0 0 1.373 45 0.21
12 12 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
13 13 A 9 0 0 0 0 0 0 0 0 0 0 9 9 0 9 55 9 0 0 0 11 0 0 1.421 47 0.26
14 14 A 0 0 0 0 0 0 0 9 27 0 9 0 0 0 27 27 0 0 0 0 11 0 0 1.499 50 0.19
15 15 A 0 0 0 9 0 0 0 9 27 0 9 0 0 0 36 0 9 0 0 0 11 0 0 1.594 53 0.09
16 16 A 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 9 0 0 0 0 11 0 0 0.305 10 0.81
17 17 A 0 0 0 27 9 0 36 0 0 0 0 0 18 0 0 0 0 0 9 0 11 0 0 1.468 49 0.19
18 18 A 0 0 0 0 0 0 0 0 0 0 18 0 0 0 73 9 0 0 0 0 11 0 0 0.760 25 0.59
19 19 A 0 0 0 0 27 0 0 0 0 0 73 0 0 0 0 0 0 0 0 0 11 0 0 0.586 19 0.40
20 20 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 91 0 0 0 0 11 0 1 0.305 10 0.75
22 22 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
23 23 A 0 0 82 9 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 11 0 0 0.600 20 0.69
24 24 A 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 91 0 11 0 0 0.305 10 0.69
25 25 A 0 0 0 0 0 0 0 9 0 0 45 0 0 0 0 9 0 0 36 0 11 0 0 1.162 38 0.38
26 26 A 0 0 0 0 0 0 0 9 27 0 0 0 0 0 0 64 0 0 0 0 11 0 0 0.860 28 0.36
27 27 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
28 28 A 0 0 0 0 0 0 0 0 0 0 0 0 0 27 0 55 18 0 0 0 11 0 0 0.995 33 0.42
29 29 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
30 30 A 0 0 0 0 0 0 70 0 0 0 0 30 0 0 0 0 0 0 0 0 10 0 0 0.611 20 0.35
31 31 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
32 32 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
3 20 65 1 gYc
4 4 9 1 gSk
5 4 33 1 gSr
6 4 33 1 gSr
8 4 33 1 gSr
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