Complet list of 1i8y hssp file
Complete list of 1i8y.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1I8Y
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 2014-04-30
HEADER CYTOKINE 16-MAR-01 1I8Y
COMPND MOL_ID: 1; MOLECULE: GRANULIN-1; CHAIN: A; FRAGMENT: N-TERMINUS (RESID
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY S
AUTHOR W.F.VRANKEN,S.JAMES,H.P.J.BENNETT,F.NI
DBREF 1I8Y A 1 28 UNP P81013 GRN1_CYPCA 3 30
SEQLENGTH 28
NCHAIN 1 chain(s) in 1I8Y data set
NALIGN 30
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 : GRN1_CYPCA 0.93 0.93 1 28 3 30 28 0 0 57 P81013 Granulin-1 OS=Cyprinus carpio PE=1 SV=1
2 : Q9PRN7_CARAU 0.86 0.93 1 28 3 30 28 0 0 57 Q9PRN7 GGRN=GRANULIN-like peptide OS=Carassius auratus PE=1 SV=1
3 : A8E5C4_DANRE 0.75 0.86 1 28 37 64 28 0 0 147 A8E5C4 Granulin 1 OS=Danio rerio GN=grn1 PE=2 SV=1
4 : Q90ZC8_DANRE 0.75 0.86 1 28 37 64 28 0 0 147 Q90ZC8 Hybrid granulin OS=Danio rerio PE=2 SV=1
5 : Q90ZD0_DANRE 0.75 0.86 1 28 37 64 28 0 0 147 Q90ZD0 Granulin 1 OS=Danio rerio GN=grn1 PE=2 SV=1
6 : Q1LWZ1_DANRE 0.74 0.85 2 28 38 64 27 0 0 147 Q1LWZ1 Uncharacterized protein OS=Danio rerio GN=grn1 PE=2 SV=1
7 : Q2EQQ4_CARAU 0.70 0.81 2 28 38 64 27 0 0 158 Q2EQQ4 Granulin OS=Carassius auratus PE=2 SV=1
8 : GRN3_CYPCA 0.69 0.77 2 27 4 29 26 0 0 57 P81015 Granulin-3 OS=Cyprinus carpio PE=1 SV=1
9 : GRN2_CYPCA 0.65 0.73 2 27 4 29 26 0 0 57 P81014 Granulin-2 OS=Cyprinus carpio PE=1 SV=1
10 : I3IT60_DANRE 0.64 0.75 1 28 37 64 28 0 0 152 I3IT60 Uncharacterized protein OS=Danio rerio GN=grn2 PE=4 SV=1
11 : Q502S6_DANRE 0.64 0.75 1 28 29 56 28 0 0 139 Q502S6 Grn2 protein OS=Danio rerio GN=grn2 PE=2 SV=1
12 : Q90ZC9_DANRE 0.64 0.75 1 28 37 64 28 0 0 147 Q90ZC9 Granulin 2 OS=Danio rerio GN=grn2 PE=2 SV=1
13 : I3JXP4_ORENI 0.61 0.71 1 28 477 504 28 0 0 542 I3JXP4 Uncharacterized protein (Fragment) OS=Oreochromis niloticus GN=LOC100692931 PE=4 SV=1
14 : C7E2T9_ORENI 0.59 0.67 2 28 124 150 27 0 0 206 C7E2T9 Progranulin OS=Oreochromis niloticus GN=LOC100692931 PE=2 SV=1
15 : K9JAE3_ORENI 0.59 0.67 2 28 124 150 27 0 0 206 K9JAE3 Granulin OS=Oreochromis niloticus PE=2 SV=1
16 : Q0GJR1_OREMO 0.59 0.67 2 28 124 150 27 0 0 170 Q0GJR1 Progranulin (Fragment) OS=Oreochromis mossambicus PE=2 SV=1
17 : Q102G1_OREMO 0.59 0.67 2 28 124 150 27 0 0 206 Q102G1 Progranulin OS=Oreochromis mossambicus PE=2 SV=1
18 : B9U2J5_PAROL 0.57 0.71 1 28 123 150 28 0 0 298 B9U2J5 Progranulin OS=Paralichthys olivaceus GN=pGRN PE=2 SV=1
19 : H3BZ49_TETNG 0.57 0.64 1 28 63 90 28 0 0 227 H3BZ49 Uncharacterized protein OS=Tetraodon nigroviridis PE=4 SV=1
20 : Q4RKF2_TETNG 0.57 0.64 1 28 118 145 28 0 0 282 Q4RKF2 Chromosome 21 SCAF15029, whole genome shotgun sequence OS=Tetraodon nigroviridis GN=GSTENG00032983001 PE=4 SV=1
21 : W5L481_ASTMX 0.57 0.75 1 28 111 138 28 0 0 290 W5L481 Uncharacterized protein OS=Astyanax mexicanus PE=4 SV=1
22 : M3ZEL3_XIPMA 0.56 0.63 2 28 124 150 27 0 0 341 M3ZEL3 Uncharacterized protein OS=Xiphophorus maculatus PE=4 SV=1
23 : F6QWT8_MONDO 0.54 0.61 1 28 286 313 28 0 0 581 F6QWT8 Uncharacterized protein OS=Monodelphis domestica GN=GRN PE=4 SV=2
24 : G3NST8_GASAC 0.54 0.64 1 28 119 146 28 0 0 295 G3NST8 Uncharacterized protein OS=Gasterosteus aculeatus PE=4 SV=1
25 : S4RVM2_PETMA 0.54 0.68 1 28 690 717 28 0 0 757 S4RVM2 Uncharacterized protein (Fragment) OS=Petromyzon marinus PE=4 SV=1
26 : W5MXK9_LEPOC 0.54 0.75 1 28 111 138 28 0 0 292 W5MXK9 Uncharacterized protein OS=Lepisosteus oculatus PE=4 SV=1
27 : H2L7S0_ORYLA 0.52 0.67 2 28 370 396 27 0 0 846 H2L7S0 Uncharacterized protein OS=Oryzias latipes PE=4 SV=1
28 : H2UNR5_TAKRU 0.52 0.63 2 28 121 147 27 0 0 203 H2UNR5 Uncharacterized protein OS=Takifugu rubripes GN=LOC101069841 PE=4 SV=1
29 : B5X266_SALSA 0.50 0.61 1 28 496 523 28 0 0 825 B5X266 Granulins OS=Salmo salar GN=GRN PE=2 SV=1
30 : G3HLK3_CRIGR 0.50 0.57 1 28 284 311 28 0 0 592 G3HLK3 Granulins OS=Cricetulus griseus GN=I79_011593 PE=4 SV=1
## ALIGNMENTS 1 - 30
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A H 0 0 204 20 40 HHHHH HHHH HHHH KHRQ KE
2 2 A a > + 0 0 9 31 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
3 3 A D T 5S+ 0 0 112 31 3 DDDDDDDDNDDDDDDDDDDDDDDDDDDDDD
4 4 A A T 5S+ 0 0 99 31 59 ASAAAAAAAAAASSSSSSNNSNGNSSGNES
5 5 A A T 5S+ 0 0 93 31 97 ASQQQQSGRRRRYYYYYYHHSFEYATSHQE
6 6 A T T 5S- 0 0 77 31 69 TTTTTTTITTTTTTTTTYYYYYMYYHTYTV
7 7 A I < - 0 0 125 31 85 IIVVVVTTTVVVYYYYYIMMTYSTAFSRIS
8 8 A b - 0 0 17 31 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
9 9 A P > - 0 0 80 31 0 PPPPPPPPPPPPPPPPPPPPPPPPPPPPPP
10 10 A D T 3 S+ 0 0 157 31 20 DDDDDDSSSDDDDDDDDDDDDDDDDDDDGD
11 11 A G T 3 S+ 0 0 72 31 41 GGGGGGGGRRRRGGGGGSGGGGGAGGQGGG
12 12 A T < - 0 0 29 31 32 TTTTTTTTTTTTTTTTTTNNTTNTTNTTTY
13 13 A T E -A 25 0A 61 31 0 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14 14 A a E -A 24 0A 15 31 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
15 15 A S E -A 23 0A 65 31 3 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
16 16 A L E -A 22 0A 91 31 65 LLLLLLRRRRRRRRRRRRRRRRLRQRKRRY
17 17 A S > - 0 0 29 31 86 SSSSSSSSSTTTHHHHHHSSTHLHLHTNQL
18 18 A P T 3 S+ 0 0 129 31 28 PPPPPPPPPPPPPPPPPPPPPPPPPPQLNT
19 19 A Y T 3 S- 0 0 217 31 95 YYYYYYFFFYYYKQQQQATTYKSAQYEASI
20 20 A G S < S+ 0 0 52 31 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
21 21 A V - 0 0 80 31 85 VVIIIIIVVKKKGGGGGAVVRARTQIGGQS
22 22 A W E +A 16 0A 153 31 0 WWWWWWWWWWWWWWWWWWWWWWWWWWWWWW
23 23 A Y E -A 15 0A 122 31 88 YYSSSSYYYTTTFTTTTFSSAFGFGKGFAG
24 24 A b E -A 14 0A 45 31 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
25 25 A S E > -A 13 0A 16 31 3 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
26 26 A P T 3 S+ 0 0 97 31 16 PPPPPPPPPPPPPPPPPPIIPPPPPPPPPP
27 27 A F T 3 0 0 159 31 14 FFYYYYFFFFFFYYYYYYYYYYFYLLFYLF
28 28 A S < 0 0 139 29 37 SSSSSSS PPPSSSSSSSSNSPSPSPSPS
## 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 0 0 0 0 75 5 10 5 5 0 0 20 0 0 0.895 29 0.60
2 2 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 31 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 0 0 0 3 97 31 0 0 0.143 4 0.96
4 4 A 0 0 0 0 0 0 0 6 39 0 35 0 0 0 0 0 0 3 16 0 31 0 0 1.317 43 0.41
5 5 A 0 0 0 0 3 0 23 3 10 0 13 3 0 10 13 0 16 6 0 0 31 0 0 2.120 70 0.02
6 6 A 3 0 3 3 0 0 26 0 0 0 0 61 0 3 0 0 0 0 0 0 31 0 0 1.093 36 0.31
7 7 A 23 0 16 6 3 0 19 0 3 0 10 16 0 0 3 0 0 0 0 0 31 0 0 1.978 66 0.14
8 8 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 31 0 0 0.000 0 1.00
9 9 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 31 0 0 0.000 0 1.00
10 10 A 0 0 0 0 0 0 0 3 0 0 10 0 0 0 0 0 0 0 0 87 31 0 0 0.457 15 0.79
11 11 A 0 0 0 0 0 0 0 77 3 0 3 0 0 0 13 0 3 0 0 0 31 0 0 0.795 26 0.58
12 12 A 0 0 0 0 0 0 3 0 0 0 0 84 0 0 0 0 0 0 13 0 31 0 0 0.523 17 0.68
13 13 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 31 0 0 0.000 0 1.00
14 14 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 31 0 0 0.000 0 1.00
15 15 A 0 0 0 0 0 0 0 0 0 0 3 0 97 0 0 0 0 0 0 0 31 0 0 0.143 4 0.96
16 16 A 0 26 0 0 0 0 3 0 0 0 0 0 0 0 65 3 3 0 0 0 31 0 0 0.965 32 0.35
17 17 A 0 10 0 0 0 0 0 0 0 0 39 16 0 29 0 0 3 0 3 0 31 0 0 1.468 49 0.14
18 18 A 0 3 0 0 0 0 0 0 0 87 0 3 0 0 0 0 3 0 3 0 31 0 0 0.563 18 0.72
19 19 A 0 0 3 0 10 0 39 0 10 0 6 6 0 0 0 6 16 3 0 0 31 0 0 1.866 62 0.05
20 20 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 31 0 0 0.000 0 1.00
21 21 A 23 0 19 0 0 0 0 23 6 0 3 3 0 0 6 10 6 0 0 0 31 0 0 1.968 65 0.15
22 22 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 0 0 0.000 0 1.00
23 23 A 0 0 0 0 16 0 19 13 6 0 19 23 0 0 0 3 0 0 0 0 31 0 0 1.818 60 0.11
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 31 0 0 0.000 0 1.00
25 25 A 0 0 0 0 0 0 0 0 0 0 3 0 97 0 0 0 0 0 0 0 31 0 0 0.143 4 0.96
26 26 A 0 0 6 0 0 0 0 0 0 94 0 0 0 0 0 0 0 0 0 0 31 0 0 0.239 7 0.84
27 27 A 0 10 0 0 39 0 52 0 0 0 0 0 0 0 0 0 0 0 0 0 31 0 0 0.935 31 0.86
28 28 A 0 0 0 0 0 0 0 0 0 24 72 0 0 0 0 0 0 0 3 0 29 0 0 0.693 23 0.63
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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