Complet list of 1rmk hssp file
Complete list of 1rmk.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1RMK
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 2014-05-07
HEADER TOXIN 28-NOV-03 1RMK
COMPND MOL_ID: 1; MOLECULE: MU-O-CONOTOXIN MRVIB; CHAIN: A
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: CONUS MARMOREUS; ORGANISM_TAXID: 42752
AUTHOR N.L.DALY,J.A.EKBERG,L.THOMAS,D.J.ADAMS,R.J.LEWIS,D.J.CRAIK
DBREF 1RMK A 1 31 UNP Q26443 CXMB_CONMR 52 82
SEQLENGTH 31
NCHAIN 1 chain(s) in 1RMK data set
NALIGN 12
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 : CO16B_CONMR 1RMK 1.00 1.00 1 31 52 82 31 0 0 82 Q26443 Mu-conotoxin MrVIB OS=Conus marmoreus PE=1 SV=1
2 : U6BZL1_CONMR 1.00 1.00 1 31 64 94 31 0 0 94 U6BZL1 Mr_precursor_150 OS=Conus marmoreus PE=3 SV=1
3 : U6C1V9_CONMR 1.00 1.00 1 31 47 77 31 0 0 77 U6C1V9 Mr_precursor_142 OS=Conus marmoreus PE=3 SV=1
4 : U6C253_CONMR 1.00 1.00 1 31 52 82 31 0 0 82 U6C253 Mr_precursor_028 OS=Conus marmoreus PE=3 SV=1
5 : U6C2B9_CONMR 0.97 0.97 1 31 52 82 31 0 0 82 U6C2B9 Mr_precursor_108 OS=Conus marmoreus PE=3 SV=1
6 : CO6A_CONMR 0.90 0.97 1 31 52 82 31 0 0 82 P56708 Mu-conotoxin MrVIA OS=Conus marmoreus PE=1 SV=2
7 : U6BZX5_CONMR 0.90 0.97 1 31 46 76 31 0 0 76 U6BZX5 Mr_precursor_134 OS=Conus marmoreus PE=3 SV=1
8 : U6BZY0_CONMR 0.90 0.97 1 31 47 77 31 0 0 77 U6BZY0 Mr_precursor_144 OS=Conus marmoreus PE=3 SV=1
9 : U6C2E4_CONMR 0.90 0.97 1 31 47 77 31 0 0 77 U6C2E4 Mr_precursor_143 OS=Conus marmoreus PE=3 SV=1
10 : W4VSF9_CONVC 0.90 0.93 2 31 53 82 30 0 0 82 W4VSF9 O1_Vc6.31 prepropeptide OS=Conus victoriae PE=3 SV=1
11 : CO16_CONTE 0.59 0.69 2 30 53 81 29 0 0 82 Q9XZL3 Omega-conotoxin-like TxO6 OS=Conus textile GN=TXO6 PE=2 SV=1
12 : W4VSL3_CONVC 0.57 0.73 2 31 53 82 30 0 0 84 W4VSL3 O1_Vc6.30 prepropeptide OS=Conus victoriae PE=3 SV=1
## ALIGNMENTS 1 - 12
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A A 0 0 106 10 0 AAAAAAAAA
2 2 A a E -a 18 0A 48 13 0 CCCCCCCCCCCC
3 3 A S E -a 19 0A 11 13 80 SSSSRRRRRQQQ
4 4 A K > - 0 0 116 13 71 KKKKKKKKKDEA
5 5 A K T 3 S+ 0 0 57 13 46 KKKKKKKKKKKL
6 6 A W T 3 S+ 0 0 221 13 0 WWWWWWWWWWWW
7 7 A E S < S- 0 0 80 13 23 EEEEEEEEEEDD
8 8 A Y + 0 0 136 13 1 YYYYYYYYYFYY
9 9 A b - 0 0 1 13 0 CCCCCCCCCCCC
10 10 A I - 0 0 59 13 80 IIIIIIIIIIPP
11 11 A V + 0 0 66 13 0 VVVVVVVVVVVV
12 12 A P > - 0 0 53 13 0 PPPPPPPPPPPP
13 13 A I T 3 S+ 0 0 175 13 37 IIIIIIIIIIFF
14 14 A L T 3 S- 0 0 169 13 22 LLLLLIIIILLL
15 15 A G < + 0 0 44 13 23 GGGGGGGGGGGS
16 16 A F - 0 0 141 13 84 FFFFFFFFFFSS
17 17 A V - 0 0 63 13 86 VVVVVIIIIVRG
18 18 A Y E -a 2 0A 142 13 51 YYYYYYYYYYYD
19 19 A c E -a 3 0A 15 13 0 CCCCCCCCCCCC
20 20 A a S > S- 0 0 35 13 0 CCCCCCCCCCCC
21 21 A P T 3 S+ 0 0 138 13 76 PPPPPPPPPPDI
22 22 A G T 3 S+ 0 0 72 13 0 GGGGGGGGGGGG
23 23 A L < - 0 0 54 13 0 LLLLLLLLLLLL
24 24 A I - 0 0 104 13 19 IIIIIIIIIIFI
25 25 A b B +B 30 0B 27 13 0 CCCCCCCCCCCC
26 26 A G + 0 0 22 13 27 GGGGGGGGGGTG
27 27 A P S S- 0 0 104 13 44 PPPPPPPPPPLP
28 28 A F S S+ 0 0 117 13 0 FFFFFFFFFFFF
29 29 A V S S- 0 0 46 13 40 VVVVVVVVVVFI
30 30 A c B B 25 0B 0 13 0 CCCCCCCCCCCC
31 31 A V 0 0 79 12 15 VVVVVVVVVV I
## 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 0 100 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 0 0 0 0 38 0 0 0 38 0 23 0 0 0 13 0 0 1.073 35 0.20
4 4 A 0 0 0 0 0 0 0 0 8 0 0 0 0 0 0 77 0 8 0 8 13 0 0 0.794 26 0.29
5 5 A 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 92 0 0 0 0 13 0 0 0.271 9 0.54
6 6 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
7 7 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 0 15 13 0 0 0.429 14 0.76
8 8 A 0 0 0 0 8 0 92 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.271 9 0.99
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
10 10 A 0 0 85 0 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0 13 0 0 0.429 14 0.20
11 11 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
13 13 A 0 0 85 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.429 14 0.62
14 14 A 0 69 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.617 20 0.78
15 15 A 0 0 0 0 0 0 0 92 0 0 8 0 0 0 0 0 0 0 0 0 13 0 0 0.271 9 0.77
16 16 A 0 0 0 0 85 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 13 0 0 0.429 14 0.15
17 17 A 54 0 31 0 0 0 0 8 0 0 0 0 0 0 8 0 0 0 0 0 13 0 0 1.091 36 0.14
18 18 A 0 0 0 0 0 0 92 0 0 0 0 0 0 0 0 0 0 0 0 8 13 0 0 0.271 9 0.48
19 19 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
21 21 A 0 0 8 0 0 0 0 0 0 85 0 0 0 0 0 0 0 0 0 8 13 0 0 0.536 17 0.24
22 22 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
23 23 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
24 24 A 0 0 92 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.271 9 0.80
25 25 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
26 26 A 0 0 0 0 0 0 0 92 0 0 0 8 0 0 0 0 0 0 0 0 13 0 0 0.271 9 0.73
27 27 A 0 8 0 0 0 0 0 0 0 92 0 0 0 0 0 0 0 0 0 0 13 0 0 0.271 9 0.55
28 28 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
29 29 A 85 0 8 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.536 17 0.59
30 30 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
31 31 A 92 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.287 9 0.85
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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