Complet list of 1qgm hssp file
Complete list of 1qgm.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1QGM
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 CYTOKINE 01-MAY-99 1QGM
COMPND MOL_ID: 1; MOLECULE: PROTEIN (AMINO-TERMINAL CARP GRANULIN-1); CHAIN:
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY S
AUTHOR W.F.VRANKEN,P.XU,F.NI
DBREF 1QGM A 1 30 UNP P81013 GRN1_CYPCA 1 30
SEQLENGTH 30
NCHAIN 1 chain(s) in 1QGM data set
NALIGN 27
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 30 1 30 30 0 0 57 P81013 Granulin-1 OS=Cyprinus carpio PE=1 SV=1
2 : Q9PRN7_CARAU 0.87 0.93 1 30 1 30 30 0 0 57 Q9PRN7 GGRN=GRANULIN-like peptide OS=Carassius auratus PE=1 SV=1
3 : A8E5C4_DANRE 0.77 0.87 1 30 35 64 30 0 0 147 A8E5C4 Granulin 1 OS=Danio rerio GN=grn1 PE=2 SV=1
4 : Q90ZC8_DANRE 0.77 0.87 1 30 35 64 30 0 0 147 Q90ZC8 Hybrid granulin OS=Danio rerio PE=2 SV=1
5 : Q90ZD0_DANRE 0.77 0.87 1 30 35 64 30 0 0 147 Q90ZD0 Granulin 1 OS=Danio rerio GN=grn1 PE=2 SV=1
6 : Q1LWZ1_DANRE 0.73 0.83 1 30 35 64 30 0 0 147 Q1LWZ1 Uncharacterized protein OS=Danio rerio GN=grn1 PE=2 SV=1
7 : I3IT60_DANRE 0.67 0.77 1 30 35 64 30 0 0 152 I3IT60 Uncharacterized protein OS=Danio rerio GN=grn2 PE=4 SV=1
8 : Q2EQQ4_CARAU 0.67 0.80 1 30 35 64 30 0 0 158 Q2EQQ4 Granulin OS=Carassius auratus PE=2 SV=1
9 : Q502S6_DANRE 0.67 0.77 1 30 27 56 30 0 0 139 Q502S6 Grn2 protein OS=Danio rerio GN=grn2 PE=2 SV=1
10 : Q90ZC9_DANRE 0.67 0.77 1 30 35 64 30 0 0 147 Q90ZC9 Granulin 2 OS=Danio rerio GN=grn2 PE=2 SV=1
11 : GRN3_CYPCA 0.66 0.76 1 29 1 29 29 0 0 57 P81015 Granulin-3 OS=Cyprinus carpio PE=1 SV=1
12 : GRN2_CYPCA 0.62 0.72 1 29 1 29 29 0 0 57 P81014 Granulin-2 OS=Cyprinus carpio PE=1 SV=1
13 : I3JXP4_ORENI 0.60 0.73 1 30 475 504 30 0 0 542 I3JXP4 Uncharacterized protein (Fragment) OS=Oreochromis niloticus GN=LOC100692931 PE=4 SV=1
14 : B9U2J5_PAROL 0.57 0.73 1 30 121 150 30 0 0 298 B9U2J5 Progranulin OS=Paralichthys olivaceus GN=pGRN PE=2 SV=1
15 : C7E2T9_ORENI 0.57 0.67 1 30 121 150 30 0 0 206 C7E2T9 Progranulin OS=Oreochromis niloticus GN=LOC100692931 PE=2 SV=1
16 : H3BZ49_TETNG 0.57 0.67 1 30 61 90 30 0 0 227 H3BZ49 Uncharacterized protein OS=Tetraodon nigroviridis PE=4 SV=1
17 : K9JAE3_ORENI 0.57 0.67 1 30 121 150 30 0 0 206 K9JAE3 Granulin OS=Oreochromis niloticus PE=2 SV=1
18 : Q0GJR1_OREMO 0.57 0.67 1 30 121 150 30 0 0 170 Q0GJR1 Progranulin (Fragment) OS=Oreochromis mossambicus PE=2 SV=1
19 : Q102G1_OREMO 0.57 0.67 1 30 121 150 30 0 0 206 Q102G1 Progranulin OS=Oreochromis mossambicus PE=2 SV=1
20 : Q4RKF2_TETNG 0.57 0.67 1 30 116 145 30 0 0 282 Q4RKF2 Chromosome 21 SCAF15029, whole genome shotgun sequence OS=Tetraodon nigroviridis GN=GSTENG00032983001 PE=4 SV=1
21 : G3NST8_GASAC 0.53 0.67 1 30 117 146 30 0 0 295 G3NST8 Uncharacterized protein OS=Gasterosteus aculeatus PE=4 SV=1
22 : M3ZEL3_XIPMA 0.53 0.63 1 30 121 150 30 0 0 341 M3ZEL3 Uncharacterized protein OS=Xiphophorus maculatus PE=4 SV=1
23 : W5L481_ASTMX 0.53 0.77 1 30 109 138 30 0 0 290 W5L481 Uncharacterized protein OS=Astyanax mexicanus PE=4 SV=1
24 : B5X266_SALSA 0.52 0.63 4 30 497 523 27 0 0 825 B5X266 Granulins OS=Salmo salar GN=GRN PE=2 SV=1
25 : F6QWT8_MONDO 0.52 0.62 2 30 285 313 29 0 0 581 F6QWT8 Uncharacterized protein OS=Monodelphis domestica GN=GRN PE=4 SV=2
26 : W5MXK9_LEPOC 0.52 0.76 2 30 110 138 29 0 0 292 W5MXK9 Uncharacterized protein OS=Lepisosteus oculatus PE=4 SV=1
27 : H0ZU79_TAEGU 0.50 0.61 1 28 281 308 28 0 0 308 H0ZU79 Uncharacterized protein (Fragment) OS=Taeniopygia guttata GN=GRN PE=4 SV=1
## ALIGNMENTS 1 - 27
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A V 0 0 115 25 7 VVVVVVVIVVVVVVVVVVVVVVM V
2 2 A I B -A 10 0A 75 27 15 IIIIIIIIIIVVVVVVVVVVVVV VVV
3 3 A H + 0 0 105 27 60 HHHHHYHFHHFYHHYHYYYHHYH KQI
4 4 A a S S+ 0 0 69 28 0 CCCCCCCCCCCCCCCCCCCCCCCCCCC
5 5 A D S S- 0 0 59 28 4 DDDDDDDDDDDNDDDDDDDDDDDDDDD
6 6 A A S S+ 0 0 91 28 60 ASAAAAAAAAAASSSNSSSNNNSEGSE
7 7 A A S S+ 0 0 83 28 100 ASQQQQRSRRGRYYYHYYYHYFSQETE
8 8 A T S S- 0 0 46 28 62 TTTTTTTTTTITTYTYTTTYYYYTMHT
9 9 A I - 0 0 94 28 80 IIVVVVVTVVTTYIYMYYYMTYTISFS
10 10 A b B -A 2 0A 2 28 0 CCCCCCCCCCCCCCCCCCCCCCCCCCC
11 11 A P - 0 0 69 28 0 PPPPPPPPPPPPPPPPPPPPPPPPPPP
12 12 A D S S+ 0 0 132 28 23 DDDDDDDSDDSSDDDDDDDDDDDGDDD
13 13 A G S S+ 0 0 55 28 39 GGGGGGRGRRGRGSGGGGGGAGGGGGG
14 14 A T - 0 0 19 28 31 TTTTTTTTTTTTTTTNTTTNTTTTNNS
15 15 A T E -B 27 0B 70 28 0 TTTTTTTTTTTTTTTTTTTTTTTTTTT
16 16 A a E +B 26 0B 32 28 0 CCCCCCCCCCCCCCCCCCCCCCCCCCC
17 17 A S E -B 25 0B 32 28 4 CCCCCCCCCCCCCCCCCCCCCCCCCCC
18 18 A L E -B 24 0B 82 28 61 LLLLLLRRRRRRRRRRRRRRRRRRLRQ
19 19 A S > - 0 0 14 28 84 SSSSSSTSTTSSHHHSHHHSHHTQLHL
20 20 A P T 3 S+ 0 0 107 28 15 PPPPPPPPPPPPPPPPPPPPPPPNPPS
21 21 A Y T 3 S- 0 0 195 28 90 YYYYYYYFYYFFKAQTQQQTAKYSSYL
22 22 A G S < S+ 0 0 54 28 0 GGGGGGGGGGGGGGGGGGGGGGGGGGG
23 23 A V - 0 0 77 28 83 VVIIIIKIKKVVGAGVGGGVTARQRIT
24 24 A W E +B 18 0B 99 28 0 WWWWWWWWWWWWWWWWWWWWWWWWWWW
25 25 A Y E -B 17 0B 84 28 88 YYSSSSTYTTYYFFTSTTTSFFAAGKG
26 26 A b E -B 16 0B 19 28 0 CCCCCCCCCCCCCCCCCCCCCCCCCCC
27 27 A S E -B 15 0B 42 28 4 CCCCCCCCCCCCCCCCCCCCCCCCCCC
28 28 A P - 0 0 104 28 17 PPPPPPPPPPPPPPPIPPPIPPPPPPP
29 29 A F 0 0 122 27 12 FFYYYYFFFFFFYYYYYYYYYYYLFL
30 30 A S 0 0 186 25 34 SSSSSSPSPP SSSSSSSSSSNPPS
## 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 92 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.334 11 0.92
2 2 A 59 0 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 0 0 0.676 22 0.85
3 3 A 0 0 4 0 7 0 26 0 0 0 0 0 0 56 0 4 4 0 0 0 27 0 0 1.236 41 0.39
4 4 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 28 0 0 0.000 0 1.00
5 5 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 96 28 0 0 0.154 5 0.96
6 6 A 0 0 0 0 0 0 0 4 43 0 32 0 0 0 0 0 0 7 14 0 28 0 0 1.313 43 0.39
7 7 A 0 0 0 0 4 0 25 4 7 0 11 4 0 7 14 0 18 7 0 0 28 0 0 2.094 69 -0.00
8 8 A 0 0 4 4 0 0 21 0 0 0 0 68 0 4 0 0 0 0 0 0 28 0 0 0.950 31 0.37
9 9 A 25 0 18 7 4 0 21 0 0 0 7 18 0 0 0 0 0 0 0 0 28 0 0 1.788 59 0.19
10 10 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 28 0 0 0.000 0 1.00
11 11 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 28 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 4 0 0 11 0 0 0 0 0 0 0 0 86 28 0 0 0.490 16 0.77
13 13 A 0 0 0 0 0 0 0 79 4 0 4 0 0 0 14 0 0 0 0 0 28 0 0 0.705 23 0.60
14 14 A 0 0 0 0 0 0 0 0 0 0 4 82 0 0 0 0 0 0 14 0 28 0 0 0.559 18 0.68
15 15 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 28 0 0 0.000 0 1.00
16 16 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 28 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 0 0 0 4 0 96 0 0 0 0 0 0 0 28 0 0 0.154 5 0.96
18 18 A 0 29 0 0 0 0 0 0 0 0 0 0 0 0 68 0 4 0 0 0 28 0 0 0.740 24 0.39
19 19 A 0 7 0 0 0 0 0 0 0 0 43 14 0 32 0 0 4 0 0 0 28 0 0 1.313 43 0.16
20 20 A 0 0 0 0 0 0 0 0 0 93 4 0 0 0 0 0 0 0 4 0 28 0 0 0.307 10 0.85
21 21 A 0 4 0 0 11 0 43 0 7 0 7 7 0 0 0 7 14 0 0 0 28 0 0 1.753 58 0.09
22 22 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 28 0 0 0.000 0 1.00
23 23 A 25 0 21 0 0 0 0 18 7 0 0 7 0 0 7 11 4 0 0 0 28 0 0 1.908 63 0.16
24 24 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 0 0 0.000 0 1.00
25 25 A 0 0 0 0 14 0 21 7 7 0 21 25 0 0 0 4 0 0 0 0 28 0 0 1.781 59 0.12
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 28 0 0 0.000 0 1.00
27 27 A 0 0 0 0 0 0 0 0 0 0 4 0 96 0 0 0 0 0 0 0 28 0 0 0.154 5 0.96
28 28 A 0 0 7 0 0 0 0 0 0 93 0 0 0 0 0 0 0 0 0 0 28 0 0 0.257 8 0.82
29 29 A 0 7 0 0 37 0 56 0 0 0 0 0 0 0 0 0 0 0 0 0 27 0 0 0.887 29 0.88
30 30 A 0 0 0 0 0 0 0 0 0 20 76 0 0 0 0 0 0 0 4 0 25 0 0 0.659 22 0.65
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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