Complet list of 1fu9 hssp file
Complete list of 1fu9.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1FU9
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 2014-04-29
HEADER TRANSCRIPTION 14-SEP-00 1FU9
COMPND MOL_ID: 1; MOLECULE: U-SHAPED TRANSCRIPTIONAL COFACTOR; CHAIN: A; FRAG
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; ORGANISM_COMM
AUTHOR C.K.LIEW,K.KOWALSKI,A.H.FOX,A.NEWTON,B.K.SHARPE,M.CROSSLEY, J.P.MACKAY
DBREF 1FU9 A 3 36 UNP Q9VPQ6 USH_DROME 587 620
SEQLENGTH 36
NCHAIN 1 chain(s) in 1FU9 data set
NALIGN 46
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 : B3N7R3_DROER 0.94 1.00 1 36 1110 1145 36 0 0 1190 B3N7R3 GG24725 OS=Drosophila erecta GN=Dere\GG24725 PE=4 SV=1
2 : B4ICY0_DROSE 0.94 1.00 1 36 1110 1145 36 0 0 1190 B4ICY0 GM16748 OS=Drosophila sechellia GN=Dsec\GM16748 PE=4 SV=1
3 : B4P2F3_DROYA 0.94 1.00 1 36 1116 1151 36 0 0 1196 B4P2F3 GE16880 OS=Drosophila yakuba GN=Dyak\GE16880 PE=4 SV=1
4 : B4Q650_DROSI 0.94 1.00 1 36 595 630 36 0 0 675 B4Q650 GD23030 OS=Drosophila simulans GN=Dsim\GD23030 PE=4 SV=1
5 : C1C573_DROME 0.94 1.00 1 36 1118 1153 36 0 0 1198 C1C573 SD10668p OS=Drosophila melanogaster GN=ush-RA PE=2 SV=1
6 : M9PBN1_DROME 0.94 1.00 1 36 1111 1146 36 0 0 1212 M9PBN1 U-shaped, isoform C OS=Drosophila melanogaster GN=ush PE=4 SV=1
7 : M9PC12_DROME 0.94 1.00 1 36 1118 1153 36 0 0 1198 M9PC12 U-shaped, isoform B OS=Drosophila melanogaster GN=ush PE=4 SV=1
8 : M9PDU3_DROME 0.94 1.00 1 36 1095 1130 36 0 0 1175 M9PDU3 U-shaped, isoform D OS=Drosophila melanogaster GN=ush PE=4 SV=1
9 : USH_DROME 0.94 1.00 1 36 1111 1146 36 0 0 1191 Q9VPQ6 Zinc finger protein ush OS=Drosophila melanogaster GN=ush PE=1 SV=2
10 : B4LTM2_DROVI 0.89 0.94 1 35 1394 1428 35 0 0 1485 B4LTM2 GJ17781 OS=Drosophila virilis GN=Dvir\GJ17781 PE=4 SV=1
11 : B3MUG5_DROAN 0.86 0.94 1 36 1159 1194 36 0 0 1239 B3MUG5 GF20666 OS=Drosophila ananassae GN=Dana\GF20666 PE=4 SV=1
12 : B4JDQ5_DROGR 0.86 0.94 1 36 1155 1190 36 0 0 1232 B4JDQ5 GH11230 OS=Drosophila grimshawi GN=Dgri\GH11230 PE=4 SV=1
13 : B4N0W0_DROWI 0.86 0.97 1 35 1139 1173 35 0 0 1225 B4N0W0 GK24402 OS=Drosophila willistoni GN=Dwil\GK24402 PE=4 SV=1
14 : B4G892_DROPE 0.83 0.94 1 36 1069 1104 36 0 0 1159 B4G892 GL18881 OS=Drosophila persimilis GN=Dper\GL18881 PE=4 SV=1
15 : Q29N50_DROPS 0.83 0.94 1 36 1146 1181 36 0 0 1236 Q29N50 GA15455 OS=Drosophila pseudoobscura pseudoobscura GN=Dpse\GA15455 PE=4 SV=2
16 : B0WGK0_CULQU 0.74 0.93 10 36 448 474 27 0 0 521 B0WGK0 Zinc finger protein OS=Culex quinquefasciatus GN=CpipJ_CPIJ005813 PE=4 SV=1
17 : W8BZI5_CERCA 0.74 0.89 1 35 148 182 35 0 0 225 W8BZI5 Zinc finger protein ush (Fragment) OS=Ceratitis capitata GN=USH PE=2 SV=1
18 : W5JPD6_ANODA 0.66 0.79 6 34 1759 1787 29 0 0 1848 W5JPD6 Zinc finger protein OS=Anopheles darlingi GN=AND_003488 PE=4 SV=1
19 : Q17FQ5_AEDAE 0.62 0.86 6 34 1182 1210 29 0 0 1249 Q17FQ5 AAEL003327-PA OS=Aedes aegypti GN=AAEL003327 PE=4 SV=1
20 : D6WKC2_TRICA 0.61 0.82 9 36 886 913 28 0 0 936 D6WKC2 U-shaped OS=Tribolium castaneum GN=ush PE=4 SV=1
21 : B7PEB5_IXOSC 0.57 0.89 9 36 985 1012 28 0 0 1028 B7PEB5 Zinc finger protein, putative OS=Ixodes scapularis GN=IscW_ISCW003495 PE=4 SV=1
22 : E2AQS7_CAMFO 0.57 0.82 9 36 855 882 28 0 0 914 E2AQS7 Zinc finger protein ush OS=Camponotus floridanus GN=EAG_09000 PE=4 SV=1
23 : E2C1Z2_HARSA 0.57 0.86 9 36 534 561 28 0 0 594 E2C1Z2 Zinc finger protein ush OS=Harpegnathos saltator GN=EAI_06417 PE=4 SV=1
24 : E9J384_SOLIN 0.57 0.86 9 36 873 900 28 0 0 934 E9J384 Putative uncharacterized protein (Fragment) OS=Solenopsis invicta GN=SINV_00337 PE=4 SV=1
25 : F4WU34_ACREC 0.57 0.86 9 36 529 556 28 0 0 590 F4WU34 Zinc finger protein ush OS=Acromyrmex echinatior GN=G5I_09389 PE=4 SV=1
26 : H9KHC5_APIME 0.57 0.86 9 36 979 1006 28 0 0 1038 H9KHC5 Uncharacterized protein OS=Apis mellifera GN=LOC100577801 PE=4 SV=1
27 : W4VVC6_ATTCE 0.57 0.86 9 36 863 890 28 0 0 924 W4VVC6 Uncharacterized protein OS=Atta cephalotes PE=4 SV=1
28 : N6TGJ7_DENPD 0.56 0.85 10 36 791 817 27 0 0 839 N6TGJ7 Uncharacterized protein (Fragment) OS=Dendroctonus ponderosae GN=YQE_03987 PE=4 SV=1
29 : U4URZ3_DENPD 0.56 0.85 10 36 736 762 27 0 0 784 U4URZ3 Uncharacterized protein OS=Dendroctonus ponderosae GN=D910_10138 PE=4 SV=1
30 : V3ZHZ8_LOTGI 0.56 0.78 10 36 1063 1089 27 0 0 1099 V3ZHZ8 Uncharacterized protein OS=Lottia gigantea GN=LOTGIDRAFT_170471 PE=4 SV=1
31 : G6CL67_DANPL 0.55 0.74 4 34 753 783 31 0 0 807 G6CL67 U-shaped OS=Danaus plexippus GN=KGM_17148 PE=4 SV=1
32 : K1QZW3_CRAGI 0.55 0.72 7 35 1206 1234 29 0 0 1246 K1QZW3 Zinc finger protein ush OS=Crassostrea gigas GN=CGI_10024972 PE=4 SV=1
33 : H9J935_BOMMO 0.54 0.77 1 35 718 752 35 0 0 774 H9J935 Uncharacterized protein OS=Bombyx mori PE=4 SV=1
34 : W8BPP2_CERCA 0.54 0.71 1 35 363 397 35 0 0 1105 W8BPP2 Zinc finger protein ush (Fragment) OS=Ceratitis capitata GN=USH PE=2 SV=1
35 : W8C7U9_CERCA 0.54 0.71 1 35 386 420 35 0 0 1128 W8C7U9 Zinc finger protein ush (Fragment) OS=Ceratitis capitata GN=USH PE=2 SV=1
36 : C3YFM2_BRAFL 0.52 0.76 8 36 1196 1224 29 0 0 1230 C3YFM2 Putative uncharacterized protein OS=Branchiostoma floridae GN=BRAFLDRAFT_92618 PE=4 SV=1
37 : E0VJN6_PEDHC 0.52 0.76 8 36 991 1019 29 0 0 1037 E0VJN6 Zinc finger protein ush, putative OS=Pediculus humanus subsp. corporis GN=Phum_PHUM248250 PE=4 SV=1
38 : M7BKK5_CHEMY 0.52 0.74 10 36 998 1024 27 0 0 1415 M7BKK5 Zinc finger protein OS=Chelonia mydas GN=UY3_06589 PE=4 SV=1
39 : R7UJC7_CAPTE 0.52 0.68 6 36 833 863 31 0 0 875 R7UJC7 Uncharacterized protein OS=Capitella teleta GN=CAPTEDRAFT_212172 PE=4 SV=1
40 : T1IRZ0_STRMM 0.52 0.77 6 36 749 779 31 0 0 789 T1IRZ0 Uncharacterized protein OS=Strigamia maritima PE=4 SV=1
41 : B4KFH7_DROMO 0.51 0.74 1 35 319 353 35 0 0 873 B4KFH7 GI21745 OS=Drosophila mojavensis GN=Dmoj\GI21745 PE=4 SV=1
42 : Q3S409_CALVI 0.50 0.71 2 35 74 107 34 0 0 110 Q3S409 U-shaped-like protein (Fragment) OS=Calliphora vicina PE=2 SV=1
43 : B0WGJ9_CULQU 0.48 0.70 3 35 350 382 33 0 0 773 B0WGJ9 Zinc finger protein OS=Culex quinquefasciatus GN=CpipJ_CPIJ005812 PE=4 SV=1
44 : T1HJH8_RHOPR 0.46 0.80 1 35 947 981 35 0 0 997 T1HJH8 Uncharacterized protein (Fragment) OS=Rhodnius prolixus PE=4 SV=1
45 : T1HJH9_RHOPR 0.46 0.80 1 35 651 685 35 0 0 699 T1HJH9 Uncharacterized protein (Fragment) OS=Rhodnius prolixus PE=4 SV=1
46 : S4RWV3_PETMA 0.44 0.72 1 36 640 675 36 0 0 680 S4RWV3 Uncharacterized protein (Fragment) OS=Petromyzon marinus PE=4 SV=1
## ALIGNMENTS 1 - 46
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A G 0 0 136 24 49 AAAAAAAAAPAPAAA A DGG E AAS
2 2 A S - 0 0 121 25 60 AAAAAAAAASASAAA T NSS SG PPA
3 3 A A + 0 0 108 26 55 AAAAAAAAAAAAAAA A DSS SPPPPA
4 4 A A + 0 0 72 27 49 AAAAAAAAAAAAAAA A D ASS SAPTTA
5 5 A E - 0 0 158 27 56 EEEEEEEEEEEEEEE A E EQQ QPPNNN
6 6 A V + 0 0 100 31 85 VVVVVVVVVAAAAAA VPS D EQQ IVQQQTTG
7 7 A M + 0 0 118 32 86 MMMMMMMMMMMLMMM NGG TTTTT TGIVVGGN
8 8 A K + 0 0 139 34 83 KKKKKKKKKKKKKKK LPP PDPDDTI ASDDDPPG
9 9 A K S S+ 0 0 82 42 38 KKKKKKKKKKKKKKK KKNKKRRRRRR NKNRRKN KKRRRRRK
10 10 A Y E -A 17 0A 92 47 8 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYFYYYYYYEYYYYYYYY
11 11 A C E >>> -A 16 0A 0 47 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
12 12 A S T 345S+ 0 0 85 47 70 SSSSSSSSSSSSSSSDQDDKKDRRRRRKKHKRKSSRETKKSSSKKR
13 13 A T T 345S+ 0 0 74 47 75 TTTTTTTTTTVTTVVTTTASSSSSSSSSSSSHSDDSSAQSDDDSSL
14 14 A C T <45S- 0 0 26 47 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
15 15 A D T <5 + 0 0 119 47 8 DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDNDDDDDDRDDDDDDDD
16 16 A I E < -A 11 0A 83 47 0 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
17 17 A S E -A 10 0A 71 47 38 SSSSSSSSSSSSSSSTSTTSSSSSSSSSSSSSSRRSSSSSRRRSSH
18 18 A F - 0 0 37 47 0 FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
19 19 A N S S+ 0 0 148 47 36 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNTKTKNNTNNTTNSSNNS
20 20 A Y S >> S- 0 0 153 47 44 YYYYYYYYYYYYYYYYYYYYYFYYYYYYYYYYYNNNYSYYNSSYYN
21 21 A V H 3> S+ 0 0 82 47 57 VVVVVVVVVVVVVVVVMTVYLYLLLLLPPQVKVVVLLLLLITTLLL
22 22 A K H 3> S+ 0 0 162 47 65 KKKKKKKKKKKKKKKNKKNSSHSSSSSTTANNNKKSSDSSKKKSSS
23 23 A T H <> S+ 0 0 48 47 20 TTTTTTTTTTTTTTTTTTTTTTTTTTTSSSTSTTTTSSTTTTTTTT
24 24 A Y H X S+ 0 0 49 47 6 YYYYYYYYYFYFFFFFYFFFFFFFFFFFFFYYYYYFLYFFYYYFFF
25 25 A L H X S+ 0 0 109 47 62 LLLLLLLLLLLLLLLIVIIIILIIIIIIIIKLKRRIILLIRRRIII
26 26 A A H X S+ 0 0 46 47 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27 27 A H H X>S+ 0 0 11 47 0 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
28 28 A K H <5S+ 0 0 94 47 0 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK
29 29 A Q H <5S- 0 0 126 47 55 QQQQQQQQQQQQQQQKQNKKKRKKKKKKKKQKQLLKKKKKQQQKKK
30 30 A F H <5S+ 0 0 163 47 28 FFFFFFFFFFFFFFFFYFFFYFFFFFFFFYFYYHHFFYYYHHHFFF
31 31 A Y T <5S+ 0 0 187 47 0 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY
32 32 A C S