Complet list of 1jn7 hssp file
Complete list of 1jn7.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1JN7
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 TRANSCRIPTION 23-JUL-01 1JN7
COMPND MOL_ID: 1; MOLECULE: U-SHAPED TRANSCRIPTIONAL COFACTOR; CHAIN: A; FRAG
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; ORGANISM_COMM
AUTHOR K.KOWALSKI,J.P.MACKAY
DBREF 1JN7 A 3 36 UNP Q9VPQ6 USH_DROME 587 620
SEQLENGTH 36
NCHAIN 1 chain(s) in 1JN7 data set
NALIGN 39
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 0.92 0.97 1 36 1110 1145 36 0 0 1190 B3N7R3 GG24725 OS=Drosophila erecta GN=Dere\GG24725 PE=4 SV=1
2 : B4ICY0_DROSE 0.92 0.97 1 36 1110 1145 36 0 0 1190 B4ICY0 GM16748 OS=Drosophila sechellia GN=Dsec\GM16748 PE=4 SV=1
3 : B4P2F3_DROYA 0.92 0.97 1 36 1116 1151 36 0 0 1196 B4P2F3 GE16880 OS=Drosophila yakuba GN=Dyak\GE16880 PE=4 SV=1
4 : B4Q650_DROSI 0.92 0.97 1 36 595 630 36 0 0 675 B4Q650 GD23030 OS=Drosophila simulans GN=Dsim\GD23030 PE=4 SV=1
5 : C1C573_DROME 0.92 0.97 1 36 1118 1153 36 0 0 1198 C1C573 SD10668p OS=Drosophila melanogaster GN=ush-RA PE=2 SV=1
6 : M9PBN1_DROME 0.92 0.97 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 0.92 0.97 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 0.92 0.97 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 0.92 0.97 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 0.86 0.91 1 35 1394 1428 35 0 0 1485 B4LTM2 GJ17781 OS=Drosophila virilis GN=Dvir\GJ17781 PE=4 SV=1
11 : B3MUG5_DROAN 0.83 0.92 1 36 1159 1194 36 0 0 1239 B3MUG5 GF20666 OS=Drosophila ananassae GN=Dana\GF20666 PE=4 SV=1
12 : B4JDQ5_DROGR 0.83 0.92 1 36 1155 1190 36 0 0 1232 B4JDQ5 GH11230 OS=Drosophila grimshawi GN=Dgri\GH11230 PE=4 SV=1
13 : B4N0W0_DROWI 0.83 0.94 1 35 1139 1173 35 0 0 1225 B4N0W0 GK24402 OS=Drosophila willistoni GN=Dwil\GK24402 PE=4 SV=1
14 : B4G892_DROPE 0.81 0.92 1 36 1069 1104 36 0 0 1159 B4G892 GL18881 OS=Drosophila persimilis GN=Dper\GL18881 PE=4 SV=1
15 : Q29N50_DROPS 0.81 0.92 1 36 1146 1181 36 0 0 1236 Q29N50 GA15455 OS=Drosophila pseudoobscura pseudoobscura GN=Dpse\GA15455 PE=4 SV=2
16 : W8BZI5_CERCA 0.71 0.86 1 35 148 182 35 0 0 225 W8BZI5 Zinc finger protein ush (Fragment) OS=Ceratitis capitata GN=USH PE=2 SV=1
17 : B0WGK0_CULQU 0.70 0.89 10 36 448 474 27 0 0 521 B0WGK0 Zinc finger protein OS=Culex quinquefasciatus GN=CpipJ_CPIJ005813 PE=4 SV=1
18 : W5JPD6_ANODA 0.62 0.76 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 0.59 0.83 6 34 1182 1210 29 0 0 1249 Q17FQ5 AAEL003327-PA OS=Aedes aegypti GN=AAEL003327 PE=4 SV=1
20 : D6WKC2_TRICA 0.57 0.79 9 36 886 913 28 0 0 936 D6WKC2 U-shaped OS=Tribolium castaneum GN=ush PE=4 SV=1
21 : B7PEB5_IXOSC 0.54 0.86 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 0.54 0.79 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 0.54 0.82 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 0.54 0.82 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 0.54 0.82 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 0.54 0.82 9 36 979 1006 28 0 0 1038 H9KHC5 Uncharacterized protein OS=Apis mellifera GN=LOC100577801 PE=4 SV=1
27 : W4VVC6_ATTCE 0.54 0.82 9 36 863 890 28 0 0 924 W4VVC6 Uncharacterized protein OS=Atta cephalotes PE=4 SV=1
28 : G6CL67_DANPL 0.52 0.71 4 34 753 783 31 0 0 807 G6CL67 U-shaped OS=Danaus plexippus GN=KGM_17148 PE=4 SV=1
29 : K1QZW3_CRAGI 0.52 0.69 7 35 1206 1234 29 0 0 1246 K1QZW3 Zinc finger protein ush OS=Crassostrea gigas GN=CGI_10024972 PE=4 SV=1
30 : N6TGJ7_DENPD 0.52 0.81 10 36 791 817 27 0 0 839 N6TGJ7 Uncharacterized protein (Fragment) OS=Dendroctonus ponderosae GN=YQE_03987 PE=4 SV=1
31 : U4URZ3_DENPD 0.52 0.81 10 36 736 762 27 0 0 784 U4URZ3 Uncharacterized protein OS=Dendroctonus ponderosae GN=D910_10138 PE=4 SV=1
32 : V3ZHZ8_LOTGI 0.52 0.74 10 36 1063 1089 27 0 0 1099 V3ZHZ8 Uncharacterized protein OS=Lottia gigantea GN=LOTGIDRAFT_170471 PE=4 SV=1
33 : H9J935_BOMMO 0.51 0.74 1 35 718 752 35 0 0 774 H9J935 Uncharacterized protein OS=Bombyx mori PE=4 SV=1
34 : W8BPP2_CERCA 0.51 0.69 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 0.51 0.69 1 35 386 420 35 0 0 1128 W8C7U9 Zinc finger protein ush (Fragment) OS=Ceratitis capitata GN=USH PE=2 SV=1
36 : B4KFH7_DROMO 0.49 0.71 1 35 319 353 35 0 0 873 B4KFH7 GI21745 OS=Drosophila mojavensis GN=Dmoj\GI21745 PE=4 SV=1
37 : R7UJC7_CAPTE 0.48 0.65 6 36 833 863 31 0 0 875 R7UJC7 Uncharacterized protein OS=Capitella teleta GN=CAPTEDRAFT_212172 PE=4 SV=1
38 : T1IRZ0_STRMM 0.48 0.74 6 36 749 779 31 0 0 789 T1IRZ0 Uncharacterized protein OS=Strigamia maritima PE=4 SV=1
39 : Q3S409_CALVI 0.47 0.68 2 35 74 107 34 0 0 110 Q3S409 U-shaped-like protein (Fragment) OS=Calliphora vicina PE=2 SV=1
## ALIGNMENTS 1 - 39
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A G 0 0 104 21 55 AAAAAAAAAPAPAAAA DGGE
2 2 A S + 0 0 90 22 62 AAAAAAAAASASAAAT NSSS G
3 3 A A S S+ 0 0 98 22 56 AAAAAAAAAAAAAAAA DSSS P
4 4 A A S S- 0 0 85 23 42 AAAAAAAAAAAAAAAA D ASSS A
5 5 A E S S+ 0 0 178 23 43 EEEEEEEEEEEEEEEA E EQQQ P
6 6 A V + 0 0 90 27 84 VVVVVVVVVAAAAAAV PS D EQQQIVQ
7 7 A M - 0 0 91 28 82 MMMMMMMMMMMLMMMN GG TT TTTITGV
8 8 A K S S- 0 0 137 28 79 KKKKKKKKKKKKKKKL PP PD PDDDASD
9 9 A K S S+ 0 0 42 36 37 KKKKKKKKKKKKKKKK KNKKRRRRRRNK NRRRKKR
10 10 A Y E -A 17 0A 97 40 0 YYYYYYYYYYYYYYYYYYYYYYYYYYYFYYYYYYYYYYY
11 11 A C E >> -A 16 0A 7 40 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
12 12 A S T 45S+ 0 0 78 40 69 SSSSSSSSSSSSSSSQDDDKKDRRRRRKRKKHKSSSKKS
13 13 A T T 45S+ 0 0 114 40 74 TTTTTTTTTTVTTVVTTTASSSSSSSSSHSSSSDDDQSD
14 14 A C T 45S- 0 0 26 40 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
15 15 A D T <5 + 0 0 113 40 3 DDDDDDDDDDDDDDDDDDDDDDDDDDDNDDDDDDDDDDD
16 16 A I E < -A 11 0A 75 40 0 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
17 17 A S E -A 10 0A 88 40 35 SSSSSSSSSSSSSSSSTTTSSSSSSSSSSSSSSRRRSSR
18 18 A F - 0 0 37 40 0 FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
19 19 A N S S+ 0 0 139 40 33 NNNNNNNNNNNNNNNNNNNNNNNNNNNKTNNTKNNNTTS
20 20 A Y S >> S- 0 0 148 40 30 YYYYYYYYYYYYYYYYYYYYYFYYYYYYYYYYYNNNYYS
21 21 A V H 3> S+ 0 0 83 40 57 VVVVVVVVVVVVVVVMVTVYLYLLLLLVKPPQVVVILLT
22 22 A K H 3> S+ 0 0 139 40 63 KKKKKKKKKKKKKKKKNKNSSHSSSSSNNTTANKKKSSK
23 23 A T H <> S+ 0 0 49 40 17 TTTTTTTTTTTTTTTTTTTTTTTTTTTTSSSSTTTTTTT
24 24 A Y H X S+ 0 0 40 40 3 YYYYYYYYYFYFFFFYFFFFFFFFFFFYYFFFYYYYFFY
25 25 A L H X S+ 0 0 109 40 64 LLLLLLLLLLLLLLLVIIIIILIIIIIKLIIIKRRRLIR
26 26 A A H X S+ 0 0 54 40 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27 27 A H H X>S+ 0 0 21 40 0 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
28 28 A K H <5S+ 0 0 117 40 0 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK
29 29 A Q H <5S+ 0 0 132 40 57 QQQQQQQQQQQQQQQQKNKKKRKKKKKQKKKKQLLQKKQ
30 30 A F H ><5S+ 0 0 168 40 28 FFFFFFFFFFFFFFFYFFFFYFFFFFFFYFFYYHHHYYH
31 31 A Y T 3<5S+ 0 0 149 40 0 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY
32 32 A H T 3