Complet list of 1k8v hssp file
Complete list of 1k8v.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1K8V
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 2014-05-02
HEADER UNKNOWN FUNCTION 25-OCT-01 1K8V
COMPND MOL_ID: 1; MOLECULE: NEUROPEPTIDE F; CHAIN: A; ENGINEERED: YES
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THIS SEQUENCE OCCURS NATURAL
AUTHOR M.MISKOLZIE,G.KOTOVYCH
DBREF 1K8V A 1 39 UNP P41967 NPF_MONEX 1 39
SEQLENGTH 39
NCHAIN 1 chain(s) in 1K8V data set
NALIGN 6
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 : NPF_MONEX 1.00 1.00 1 39 1 39 39 0 0 39 P41967 Neuropeptide F OS=Moniezia expansa PE=1 SV=1
2 : Q9U0S8_MONEX 0.95 0.97 1 39 18 56 39 0 0 57 Q9U0S8 Neuropeptide F OS=Moniezia expansa GN=npf PE=3 SV=1
3 : U6I1X8_ECHMU 0.79 0.91 6 39 84 117 34 0 0 118 U6I1X8 Neuropeptide F OS=Echinococcus multilocularis GN=EmuJ_001070600 PE=3 SV=1
4 : U6J1J0_ECHGR 0.79 0.91 6 39 84 117 34 0 0 118 U6J1J0 Neuropeptide F OS=Echinococcus granulosus GN=EgrG_001070600 PE=3 SV=1
5 : W6UP81_ECHGR 0.78 0.91 6 37 84 115 32 0 0 124 W6UP81 Neuropeptide F OS=Echinococcus granulosus GN=EGR_05085 PE=4 SV=1
6 : G4LVY8_SCHMA 0.47 0.75 4 39 81 116 36 0 0 119 G4LVY8 Neuropeptide Y,putative OS=Schistosoma mansoni GN=Smp_159950 PE=3 SV=1
## ALIGNMENTS 1 - 6
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A P 0 0 172 3 0 PP
2 2 A D + 0 0 169 3 0 DD
3 3 A K - 0 0 141 3 73 KQ
4 4 A D S S+ 0 0 158 4 31 DD E
5 5 A F + 0 0 111 4 72 FA I
6 6 A I S S- 0 0 98 7 16 IIIIIV
7 7 A V S S+ 0 0 105 7 72 VVIIIP
8 8 A N + 0 0 131 7 60 NNNNNP
9 9 A P S > S- 0 0 43 7 56 PPPPPE
10 10 A S T 3 S- 0 0 95 7 80 SSPPPR
11 11 A D T 3 S+ 0 0 103 7 68 DDEEEP
12 12 A L < + 0 0 139 7 88 LLSSSF
13 13 A V S S- 0 0 72 7 16 VVVVVI
14 14 A L - 0 0 105 7 12 LLLLLF
15 15 A D S S+ 0 0 115 7 68 DDSSSE
16 16 A N S S+ 0 0 157 7 52 NNNNNT
17 17 A K + 0 0 111 7 64 KKPPPP
18 18 A A S >> S+ 0 0 56 7 48 AAAAAE
19 19 A A H 3> S+ 0 0 67 7 0 AAAAAA
20 20 A L H 3> S+ 0 0 125 7 0 LLLLLL
21 21 A R H X> S+ 0 0 132 7 0 RRRRRR
22 22 A D H 3X S+ 0 0 89 7 52 DDDDDT
23 23 A Y H 3X S+ 0 0 173 7 0 YYYYYY
24 24 A L H X S+ 0 0 65 7 38 IIVVVL
28 28 A N H 3X S+ 0 0 92 7 0 NNNNNN
29 29 A E H 34 S+ 0 0 117 7 0 EEEEEE
30 30 A Y H <> S+ 0 0 157 7 0 YYYYYY
31 31 A F H X S+ 0 0 95 7 0 FFFFFF
32 32 A A H X S+ 0 0 40 7 0 AAAAAA
33 33 A I H 4 S+ 0 0 140 7 0 IIIIII
34 34 A I H < S- 0 0 135 7 0 IIIIII
35 35 A G H < - 0 0 42 7 0 GGGGGG
36 36 A R < - 0 0 133 7 0 RRRRRR
37 37 A P S S+ 0 0 83 7 0 PPPPPP
38 38 A R 0 0 187 6 0 RRRR R
39 39 A F 0 0 250 6 0 FFFF F
## 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 0 100 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 3 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 67 33 0 0 0 3 0 0 0.637 21 0.27
4 4 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 75 4 0 0 0.562 18 0.69
5 5 A 0 0 25 0 50 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0 4 0 0 1.040 34 0.27
6 6 A 14 0 86 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.84
7 7 A 43 0 43 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 7 0 0 1.004 33 0.28
8 8 A 0 0 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 86 0 7 0 0 0.410 13 0.40
9 9 A 0 0 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 14 0 0 7 0 0 0.410 13 0.44
10 10 A 0 0 0 0 0 0 0 0 0 43 43 0 0 0 14 0 0 0 0 0 7 0 0 1.004 33 0.20
11 11 A 0 0 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 43 0 43 7 0 0 1.004 33 0.31
12 12 A 0 43 0 0 14 0 0 0 0 0 43 0 0 0 0 0 0 0 0 0 7 0 0 1.004 33 0.11
13 13 A 86 0 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.84
14 14 A 0 86 0 0 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.88
15 15 A 0 0 0 0 0 0 0 0 0 0 43 0 0 0 0 0 0 14 0 43 7 0 0 1.004 33 0.32
16 16 A 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 0 0 0 86 0 7 0 0 0.410 13 0.48
17 17 A 0 0 0 0 0 0 0 0 0 57 0 0 0 0 0 43 0 0 0 0 7 0 0 0.683 22 0.35
18 18 A 0 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 0 14 0 0 7 0 0 0.410 13 0.52
19 19 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
20 20 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 7 0 0 0.000 0 1.00
22 22 A 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 86 7 0 0 0.410 13 0.48
23 23 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
24 24 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
25 25 A 0 0 0 0 0 0 0 0 0 0 0 0 0 14 86 0 0 0 0 0 7 0 0 0.410 13 0.60
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 86 0 0 0 7 0 0 0.410 13 0.56
27 27 A 43 14 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 1.004 33 0.62
28 28 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 7 0 0 0.000 0 1.00
29 29 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 7 0 0 0.000 0 1.00
30 30 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
31 31 A 0 0 0 0 100 0 0 0 0 0 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 0 0 100 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
33 33 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
34 34 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
35 35 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
36 36 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 7 0 0 0.000 0 1.00
37 37 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
38 38 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 6 0 0 0.000 0 1.00
39 39 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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