Complet list of 1yui hssp file
Complete list of 1yui.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1YUI
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 2014-05-14
HEADER DNA BINDING PROTEIN/DNA 31-DEC-96 1YUI
COMPND MOL_ID: 1; MOLECULE: DNA (5'-D(*GP*CP*CP*GP*AP*GP*AP*GP*TP*AP*C)-3');
SOURCE MOL_ID: 1; SYNTHETIC: YES; MOL_ID: 2; SYNTHETIC: YES; MOL_ID: 3; ORGAN
AUTHOR G.M.CLORE,J.G.OMICHINSKI,A.M.GRONENBORN
DBREF 1YUI A 10 63 UNP Q08605 GAGA_DROME 319 372
DBREF 1YUI B 101 111 PDB 1YUI 1YUI 101 111
DBREF 1YUI C 112 122 PDB 1YUI 1YUI 112 122
SEQLENGTH 54
NCHAIN 1 chain(s) in 1YUI data set
NALIGN 33
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 : A4V1Y6_DROME 1.00 1.00 1 54 319 372 54 0 0 582 A4V1Y6 Trithorax-like, isoform F OS=Drosophila melanogaster GN=Trl PE=4 SV=1
2 : A4V1Y7_DROME 1.00 1.00 1 54 319 372 54 0 0 519 A4V1Y7 Trithorax-like, isoform C OS=Drosophila melanogaster GN=Trl PE=4 SV=1
3 : B4HHS8_DROSE 1.00 1.00 1 54 319 372 54 0 0 565 B4HHS8 GM24533 OS=Drosophila sechellia GN=Dsec\GM24533 PE=4 SV=1
4 : B4QK25_DROSI 1.00 1.00 1 54 319 372 54 0 0 500 B4QK25 GD12604 OS=Drosophila simulans GN=Dsim\GD12604 PE=4 SV=1
5 : C3KGN3_DROME 1.00 1.00 1 54 133 186 54 0 0 396 C3KGN3 MIP04022p (Fragment) OS=Drosophila melanogaster GN=Trl-RA PE=2 SV=1
6 : GAGA_DROME 1YUJ 1.00 1.00 1 54 319 372 54 0 0 581 Q08605 Transcription factor GAGA OS=Drosophila melanogaster GN=Trl PE=1 SV=2
7 : M9PFM7_DROME 1.00 1.00 1 54 319 372 54 0 0 623 M9PFM7 Trithorax-like, isoform K OS=Drosophila melanogaster GN=Trl PE=4 SV=1
8 : Q2PDY1_DROME 1.00 1.00 1 54 319 372 54 0 0 608 Q2PDY1 Trithorax-like, isoform J OS=Drosophila melanogaster GN=Trl PE=4 SV=2
9 : Q2PDY2_DROME 1.00 1.00 1 54 319 372 54 0 0 567 Q2PDY2 Trithorax-like, isoform I OS=Drosophila melanogaster GN=Trl PE=4 SV=1
10 : B4J3T8_DROGR 0.98 1.00 1 54 324 377 54 0 0 552 B4J3T8 GH16792 OS=Drosophila grimshawi GN=Dgri\GH16792 PE=4 SV=1
11 : B4NM24_DROWI 0.98 1.00 1 54 326 379 54 0 0 532 B4NM24 GK10585 OS=Drosophila willistoni GN=Dwil\GK10585 PE=4 SV=1
12 : B4PIG5_DROYA 0.98 1.00 1 54 319 372 54 0 0 558 B4PIG5 GE20006 OS=Drosophila yakuba GN=Dyak\GE20006 PE=4 SV=1
13 : B3MAW3_DROAN 0.96 1.00 1 54 315 368 54 0 0 513 B3MAW3 GF25184 OS=Drosophila ananassae GN=Dana\GF25184 PE=4 SV=1
14 : B3ND55_DROER 0.96 1.00 1 54 319 372 54 0 0 556 B3ND55 GG13712 OS=Drosophila erecta GN=Dere\GG13712 PE=4 SV=1
15 : B4LF53_DROVI 0.96 1.00 1 54 324 377 54 0 0 570 B4LF53 Trithorax-like OS=Drosophila virilis GN=Trl PE=4 SV=1
16 : B5DQS4_DROPS 0.96 1.00 1 54 322 375 54 0 0 584 B5DQS4 GA23656 OS=Drosophila pseudoobscura pseudoobscura GN=Dpse\GA23656 PE=4 SV=1
17 : I1V4Y9_DROME 0.96 0.96 1 54 319 372 54 0 0 581 I1V4Y9 Trithorax-like protein variant A OS=Drosophila melanogaster GN=Trl PE=4 SV=1
18 : I1V4Z0_DROME 0.96 0.96 1 54 276 329 54 0 0 476 I1V4Z0 Trithorax-like protein variant G OS=Drosophila melanogaster GN=Trl PE=4 SV=1
19 : I1V4Z1_DROME 0.96 0.96 1 54 319 372 54 0 0 519 I1V4Z1 Trithorax-like protein variant B OS=Drosophila melanogaster GN=Trl PE=4 SV=1
20 : I1V4Z2_DROME 0.96 0.96 1 54 319 372 54 0 0 566 I1V4Z2 Trithorax-like protein variant I OS=Drosophila melanogaster GN=Trl PE=4 SV=1
21 : O76940_DROVI 0.96 1.00 1 54 324 377 54 0 0 556 O76940 GAGA factor class A-isoform OS=Drosophila virilis GN=Trl PE=2 SV=1
22 : O76941_DROVI 0.96 1.00 1 54 228 281 54 0 0 494 O76941 GAGA factor class B-specific isoform (Fragment) OS=Drosophila virilis GN=Trl PE=2 SV=1
23 : Q20C82_DROVI 0.96 1.00 1 54 324 377 54 0 0 748 Q20C82 Trl OS=Drosophila virilis GN=Trl PE=4 SV=1
24 : B4KVL0_DROMO 0.94 1.00 1 54 322 375 54 0 0 545 B4KVL0 GI13806 OS=Drosophila mojavensis GN=Dmoj\GI13806 PE=4 SV=1
25 : T1PMR8_MUSDO 0.87 0.92 3 54 18 68 52 1 1 213 T1PMR8 GAGA factor protein (Fragment) OS=Musca domestica PE=2 SV=1
26 : T1E204_9DIPT 0.83 0.93 14 54 309 349 41 0 0 511 T1E204 Putative transcription factor gaga OS=Psorophora albipes PE=2 SV=1
27 : T1E206_9DIPT 0.83 0.93 14 54 299 339 41 0 0 501 T1E206 Putative transcription factor gaga OS=Psorophora albipes PE=2 SV=1
28 : B0W2I6_CULQU 0.81 0.88 11 53 289 331 43 0 0 621 B0W2I6 Putative uncharacterized protein OS=Culex quinquefasciatus GN=CpipJ_CPIJ001236 PE=4 SV=1
29 : Q17MR3_AEDAE 0.80 0.89 11 54 285 328 44 0 0 618 Q17MR3 AAEL000970-PA OS=Aedes aegypti GN=AAEL000970 PE=4 SV=1
30 : B4GUJ7_DROPE 0.77 0.89 2 54 103 155 53 0 0 366 B4GUJ7 GL26106 OS=Drosophila persimilis GN=Dper\GL26106 PE=4 SV=1
31 : W5J545_ANODA 0.70 0.76 1 54 273 326 54 0 0 813 W5J545 Uncharacterized protein OS=Anopheles darlingi GN=AND_009315 PE=4 SV=1
32 : E1ZYF9_CAMFO 0.61 0.85 10 50 414 454 41 0 0 624 E1ZYF9 Transcription factor GAGA OS=Camponotus floridanus GN=EAG_06500 PE=4 SV=1
33 : K7J1M9_NASVI 0.41 0.66 1 44 252 295 44 0 0 374 K7J1M9 Uncharacterized protein OS=Nasonia vitripennis PE=4 SV=1
## ALIGNMENTS 1 - 33
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 10 A P 0 0 160 27 0 PPPPPPPPPPPPPPPPPPPPPPPP P P
2 11 A K - 0 0 147 28 62 KKKKKKKKKKKKKKKKKKKKKKKK RD A
3 12 A A - 0 0 89 29 31 AAAAAAAAAAAAAAATAAAAAAAAG NG A
4 13 A K - 0 0 158 29 51 KKKKKKKKKKKKKKKKKKKKKKKKK KT H
5 14 A R - 0 0 232 29 68 RRRRRRRRRRRRRRRRRRRRRRRRR LP N
6 15 A A - 0 0 64 29 76 AAAAAAAAATTATATTAAAATTTTT LI S
7 16 A K S S+ 0 0 179 29 47 KKKKKKKKKKKKKKKKKKKKKKKKK KD T
8 17 A H + 0 0 188 28 70 HHHHHHHHHHHHHHHHHHHHHHHH. QT T
9 18 A P S S- 0 0 73 29 65 PPPPPPPPPPPPPPPPPPPPPPPPN GK T
10 19 A P S S+ 0 0 125 30 74 PPPPPPPPPPPPPPPPPPPPPPPPL LDST
11 20 A G + 0 0 75 32 24 GGGGGGGGGGGGGGGGGGGGGGGGS GGSGGS
12 21 A T - 0 0 90 32 51 TTTTTTTTTTTSTSTTTTTTTTTTG IITIDT
13 22 A E - 0 0 168 32 65 EEEEEEEEEEEEDDEEEEEEEEEEE IIQIGQ
14 23 A K - 0 0 192 34 47 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKEKLS
15 24 A P >> - 0 0 64 30 76 PPPPPPPPPPPPPPPPXXXXPPPPPIIIIPIST
16 25 A R H 3>>S+ 0 0 188 34 32 RRRRRRRRRRRRRRRRRRRRRRRRRKKKKRKKK
17 26 A S H 345S+ 0 0 94 34 58 SSSSSSSSSSSSSSSSSSSSSSSSSNNNNSSAI
18 27 A R H <45S+ 0 0 178 34 19 RRRRRRRRRRRRRRRRRRRRRRRRRKKKKRKRR
19 28 A S H <5S+ 0 0 76 34 14 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSG
20 29 A Q T <5S+ 0 0 145 34 37 QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQLA
21 30 A S S - 0 0 0 34 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
28 37 A P T 4 S+ 0 0 107 34 0 PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP
29 38 A I T 4 S+ 0 0 91 30 19 IIIIIIIIIIIIIIIIXXXXIIIIIIIIIIILL
30 39 A C T 4 S- 0 0 63 34 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
31 40 A Y < + 0 0 176 34 104 YYYYYYYYYYYYYYYYYYYYYYYYYQQQQYQGG
32 41 A A - 0 0 25 34 17 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAS
33 42 A V E +A 26 0A 116 34 25 VVVVVVVVVVVVVVVVVVVVVVVIVVVVVVVIT
34 43 A I E -A 25 0A 34 34 18 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIILL
35 44 A R S S+ 0 0 209 34 0 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR
36 45 A Q S > S- 0 0 56 34 0 QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
37 46 A S H > S+ 0 0 61 34 17 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSA
38 47 A R H > S+ 0 0 125 34 0 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR
39 48 A N H > S+ 0 0 42 34 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
40 49 A L H X S+ 0 0 39 34 0 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
41 50 A R H >X S+ 0 0 196 34 0 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR
42 51 A R H 3X S+ 0 0 149 34 0 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR
43 52 A H H 3X S+ 0 0 21 34 7 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHRHHH
44 53 A L H S+ 0 0 47 34 0 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
45 54 A E H <5S+ 0 0 133 33 0 EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
46 55 A L H <5S+ 0 0 107 33 0 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
47 56 A R H <5S+ 0 0 170 33 26 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRWRL
48 57 A H T ><5S+ 0 0 41 33 0 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
49 58 A F T 3