RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4090
(112 letters)
>3gjx_A Exportin-1; transport, cytoplasm, nucleus, RNA-binding,
acetylation, GTP-binding, HOST-virus interaction,
nucleotide-binding, phosphoprotein; HET: GTP; 2.50A {Mus
musculus} PDB: 3nby_A* 3nbz_A* 3nc0_A* 3nc1_A* 3gb8_A
Length = 1073
Score = 101 bits (253), Expect = 1e-26
Identities = 63/86 (73%), Positives = 72/86 (83%)
Query: 13 KLLDFNQKLDITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQ 72
+LLDF+QKLDI LLDN+V C+Y G G +Q+ AQEVLT LKEHPDAWTRVDTILE+S N
Sbjct: 17 QLLDFSQKLDINLLDNVVNCLYHGEGAQQRMAQEVLTHLKEHPDAWTRVDTILEFSQNMN 76
Query: 73 TKFYALQILEQVIKTRWKALPREQCD 98
TK+Y LQILE VIKTRWK LPR QC+
Sbjct: 77 TKYYGLQILENVIKTRWKILPRNQCE 102
>3m1i_C Exportin-1; heat repeat, GTP-binding, nucleotide-binding, NUCL
protein transport, transport, cytoplasm, GTPase
activation; HET: GTP; 2.00A {Saccharomyces cerevisiae}
PDB: 2l1l_B
Length = 1049
Score = 101 bits (251), Expect = 2e-26
Identities = 42/86 (48%), Positives = 60/86 (69%)
Query: 13 KLLDFNQKLDITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQ 72
+LDF+ LDI LLD +V Y G GV+QK AQE+LT +++PDAW + D IL++S+N Q
Sbjct: 5 GILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAWQKADQILQFSTNPQ 64
Query: 73 TKFYALQILEQVIKTRWKALPREQCD 98
+KF AL IL+++I +WK LP +
Sbjct: 65 SKFIALSILDKLITRKWKLLPNDHRI 90
>2x1g_F Cadmus; transport protein, developmental protein, mRNA
processing, nuclear transport, mRNA splicing, mRNA
transport; 3.35A {Drosophila melanogaster}
Length = 971
Score = 77.4 bits (189), Expect = 4e-18
Identities = 18/80 (22%), Positives = 32/80 (40%)
Query: 19 QKLDITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYAL 78
+ +DI L+ V Y Q E LT + P AW +++ +Q+ +F+
Sbjct: 2 EPIDIARLEEAVVSFYRSNSQNQAITHEWLTDAEASPQAWQFSWQLMQLGKSQEVQFFGA 61
Query: 79 QILEQVIKTRWKALPREQCD 98
L + W +P E +
Sbjct: 62 ITLHSKLMKHWHEVPPENRE 81
>2x19_B Importin-13; nuclear transport, protein transport; HET: GTP;
2.80A {Homo sapiens} PDB: 2xwu_B
Length = 963
Score = 72.6 bits (177), Expect = 2e-16
Identities = 18/94 (19%), Positives = 35/94 (37%), Gaps = 5/94 (5%)
Query: 6 PPNEQFKKLLDFNQKLDITLLDNIVECMYTGMGVEQK-AAQEVLTALKEHPDAWTRVDTI 64
LDF + ++ + +Y +E K AQ+ L + P AW +
Sbjct: 10 AAGAGAAPALDF----TVENVEKALHQLYYDPNIENKNLAQKWLMQAQVSPQAWHFSWQL 65
Query: 65 LEYSSNQQTKFYALQILEQVIKTRWKALPREQCD 98
L+ + +++ L I W +P +Q +
Sbjct: 66 LQPDKVPEIQYFGASALHIKISRYWSDIPTDQYE 99
>3ibv_A Exportin-T; karyopherin, heat repeat, cytoplasm, nucleus, RNA-
binding, transport, tRNA processing, tRNA-binding, RNA
binding protein; 3.10A {Schizosaccharomyces pombe} PDB:
3icq_T*
Length = 980
Score = 72.6 bits (177), Expect = 2e-16
Identities = 11/82 (13%), Positives = 27/82 (32%), Gaps = 4/82 (4%)
Query: 21 LDITLLDNIVECMYTGMG--VEQKAAQEVLTALKEHPDAWTRVDTIL--EYSSNQQTKFY 76
+ ++N VE + ++ A + + +L+ W I + T+
Sbjct: 3 MSAQDVENAVEAALDPSVGPIIKQQATDFIGSLRSSSTGWKICHEIFSEKTKYKPSTRLI 62
Query: 77 ALQILEQVIKTRWKALPREQCD 98
LQ L + ++ +
Sbjct: 63 CLQTLSEKVREWNNESNLLELQ 84
>3a6p_A Exportin-5; exportin-5, RANGTP, nuclearexport, importin-BE
family, nucleus, phosphoprotein, protein transport;
HET: GTP; 2.92A {Homo sapiens}
Length = 1204
Score = 60.4 bits (145), Expect = 3e-12
Identities = 17/76 (22%), Positives = 27/76 (35%), Gaps = 3/76 (3%)
Query: 26 LDNIVECMYTGMGVEQ--KAAQEVLTALKEHPDAWTRVD-TILEYSSNQQTKFYALQILE 82
L V M ++ A + KE + E + + + LQILE
Sbjct: 13 LVKAVTVMMDPNSTQRYRLEALKFCEEFKEKCPICVPCGLRLAEKTQVAIVRHFGLQILE 72
Query: 83 QVIKTRWKALPREQCD 98
V+K RW + R +
Sbjct: 73 HVVKFRWNGMSRLEKV 88
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 41.4 bits (96), Expect = 1e-05
Identities = 22/130 (16%), Positives = 40/130 (30%), Gaps = 41/130 (31%)
Query: 8 NEQFKKLL---DFNQKLDITLLDNI----------VEC---MYTGMGVEQKAAQEVLTAL 51
+ ++LL + L + L N+ + C + T ++V L
Sbjct: 231 QAELRRLLKSKPYENCLLV--LLNVQNAKAWNAFNLSCKILLTT-------RFKQVTDFL 281
Query: 52 KEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDV------------ 99
A T L++ S T +L + + R + LPRE
Sbjct: 282 ----SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI 337
Query: 100 KEEKEREQNW 109
++ NW
Sbjct: 338 RDGLATWDNW 347
Score = 33.3 bits (75), Expect = 0.012
Identities = 11/74 (14%), Positives = 23/74 (31%), Gaps = 21/74 (28%)
Query: 51 LKEHPDAWT--------RVDTILEYSSNQ------QTKFYALQIL-------EQVIKTRW 89
+++ W ++ TI+E S N + F L + ++ W
Sbjct: 337 IRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW 396
Query: 90 KALPREQCDVKEEK 103
+ + V K
Sbjct: 397 FDVIKSDVMVVVNK 410
Score = 32.9 bits (74), Expect = 0.015
Identities = 16/112 (14%), Positives = 36/112 (32%), Gaps = 22/112 (19%)
Query: 4 VIPPNEQ-FKKLLDFNQKLDITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRV- 61
++ E F D D + +I+ + +E+ + DA +
Sbjct: 21 ILSVFEDAFVDNFDCKDVQD--MPKSIL------------SKEEIDHIIMS-KDAVSGTL 65
Query: 62 ---DTILEYSSNQQTKFY--ALQILEQVIKTRWKALPREQCDVKEEKEREQN 108
T+L KF L+I + + + K R+ + +++
Sbjct: 66 RLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRD 117
>4fdd_A Transportin-1; heat repeats, karyopherin, nuclear import, protein
transport importin, transportin, transport protein;
2.30A {Homo sapiens} PDB: 2ot8_A 2h4m_A 2z5k_A 2z5j_A
2qmr_A 2z5m_A 2z5n_A 2z5o_A 1qbk_B*
Length = 852
Score = 31.7 bits (71), Expect = 0.033
Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 40 EQKAAQEVLTALKEHPDAWTRVDTILEY--SSNQQTKFYALQILEQVIKTRWKALPREQ 96
Q+ Q+ L L ++PD + +L S ++ T+ + IL+ +K ++ P
Sbjct: 29 IQRTVQQKLEQLNQYPDFNNYLIFVLTKLKSEDEPTRSLSGLILKNNVKAHFQNFPNGV 87
>2nx2_A Hypothetical protein YPSA; structural genomics, unknown function,
PSI, protein structure initiative; 2.00A {Bacillus
subtilis} SCOP: c.129.1.2
Length = 181
Score = 27.8 bits (62), Expect = 0.56
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 23 ITLLDNIVECMYTGM--GVEQKAAQEVLTALKEHPD 56
I LD +E + GVE AA+ +E+PD
Sbjct: 37 IAFLDEGLEWILISGQLGVELWAAEAAYDLQEEYPD 72
>2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein;
2.60A {Homo sapiens}
Length = 232
Score = 26.6 bits (58), Expect = 1.8
Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 2/48 (4%)
Query: 40 EQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKT 87
+Q A+Q++L L H W + Y + VI+
Sbjct: 185 KQLASQKILQLLHPHVKNWG--SLLRMYGRESSKMVKQETSDKSVIEL 230
>3nxb_A CAT eye syndrome critical region protein 2; structural genomics
consortium, SGC, CECR2, CAT eye syndrome chromosome
region candidate 2, bromodomain; 1.83A {Homo sapiens}
Length = 116
Score = 26.1 bits (58), Expect = 2.0
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 40 EQKAAQEVLTALKEHPDAW 58
+ A +VL +K H D+W
Sbjct: 17 DFTAMYKVLDVVKAHKDSW 35
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 26.1 bits (56), Expect = 2.4
Identities = 5/19 (26%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 40 EQKAAQEVLTALKEH-PDA 57
E++A +++ +LK + D+
Sbjct: 18 EKQALKKLQASLKLYADDS 36
>2yyn_A Transcription intermediary factor 1-alpha; bromo domain,
structural genomics, NPPSFA; 2.50A {Homo sapiens}
Length = 135
Score = 25.4 bits (56), Expect = 3.1
Identities = 3/19 (15%), Positives = 9/19 (47%)
Query: 40 EQKAAQEVLTALKEHPDAW 58
+++ + +L L H +
Sbjct: 21 DKRKCERLLLFLYCHEMSL 39
>3d7c_A General control of amino acid synthesis protein 5; GCN5,
bromodomain, structural genomics consortium, SGC,
HOST-virus interaction, nucleus; 2.06A {Homo sapiens}
SCOP: a.29.2.1 PDB: 1f68_A 1jm4_B* 1n72_A 1wug_A*
1wum_A* 1zs5_A* 2rnw_A* 2rnx_A* 3gg3_A
Length = 112
Score = 24.9 bits (55), Expect = 3.8
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 41 QKAAQEVLTALKEHPDAW 58
+ +L +K HP AW
Sbjct: 9 YTTLKNLLAQIKSHPSAW 26
>1e6i_A Transcriptional activator GCN5; gene regulation, bromodomain,
histone binding, N-acetyl lysine; HET: ALY; 1.87A
{Saccharomyces cerevisiae} SCOP: a.29.2.1
Length = 121
Score = 25.0 bits (55), Expect = 4.7
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 40 EQKAAQEVLTALKEHPDAW 58
A Q +LT L+ H AW
Sbjct: 14 HDAAIQNILTELQNHAAAW 32
>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomic
protein structure initiative; 2.10A {Mycobacterium
tuberculosis}
Length = 242
Score = 25.2 bits (56), Expect = 5.7
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 40 EQKAAQEVLTALKEHPDA 57
EQKAA AL+ +A
Sbjct: 218 EQKAAAAAWKALEVLDNA 235
>3g0l_A Hwalp4, bromodomain adjacent to zinc finger domain protei; BAZB2,
KIAA1 WALP4, structural genomics consortium, SGC,
transcription; 2.03A {Homo sapiens} PDB: 3q2f_A* 2e7o_A
Length = 117
Score = 24.6 bits (54), Expect = 6.0
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 40 EQKAAQEVLTALKEHPDAW 58
+ +LT ++ H DAW
Sbjct: 14 DLALCSMILTEMETHEDAW 32
>3fkm_X Signaling protein; bromodomain, malaria, structural genomics,
structural genomi consortium, SGC; 2.50A {Plasmodium
falciparum 3D7}
Length = 166
Score = 24.8 bits (54), Expect = 6.0
Identities = 2/19 (10%), Positives = 8/19 (42%)
Query: 40 EQKAAQEVLTALKEHPDAW 58
A +++ +L ++
Sbjct: 22 WYLLANQLILSLSKYEGGH 40
>3ble_A Citramalate synthase from leptospira interrogans; TIM barrel,
licmsn, substrate specificity, acyltransferase,
amino-acid biosynthesis; 2.00A {Leptospira interrogans}
PDB: 3blf_A 3bli_A*
Length = 337
Score = 24.8 bits (55), Expect = 6.4
Identities = 2/18 (11%), Positives = 10/18 (55%)
Query: 46 EVLTALKEHPDAWTRVDT 63
++T + + ++ T ++
Sbjct: 260 ALVTTIHDKSNSKTNINE 277
>1wa5_C Importin alpha RE-exporter; nuclear transport/complex, nuclear
transport, exportin, RAN GTPase, protein transport; HET:
GTP; 2.0A {Saccharomyces cerevisiae} SCOP: a.118.1.1
PDB: 1z3h_A
Length = 960
Score = 24.9 bits (53), Expect = 9.4
Identities = 9/67 (13%), Positives = 17/67 (25%), Gaps = 1/67 (1%)
Query: 40 EQKAAQEVLTALKEHPDAWTR-VDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCD 98
K ++ L L+ + I + T+ + IK +W
Sbjct: 19 TAKTSERNLRQLETQDGFGLTLLHVIASTNLPLSTRLAGALFFKNFIKRKWVDENGNHLL 78
Query: 99 VKEEKER 105
E
Sbjct: 79 PANNVEL 85
>2ljh_A Double-stranded RNA-specific editase ADAR; DSRBD, DSRBM, editing,
hydrolase; NMR {Drosophila melanogaster}
Length = 114
Score = 24.1 bits (52), Expect = 9.4
Identities = 7/29 (24%), Positives = 10/29 (34%), Gaps = 5/29 (17%)
Query: 34 YTGMGV-----EQKAAQEVLTALKEHPDA 57
Y G G +AA L + + D
Sbjct: 77 YLGQGRSKKVARIEAAATALRSFIQFKDG 105
>4alg_A Bromodomain-containing protein 2; signaling protein, inhibitor,
histone, epigenetic reader; HET: 1GH; 1.60A {Homo
sapiens} PDB: 4a9e_A 4a9h_A* 4a9i_A* 4a9j_A* 4a9m_A*
4a9n_A* 4a9o_A* 4a9p_A* 4a9f_A* 4alh_A* 4akn_A* 2yek_A*
2ydw_A* 2yw5_A
Length = 154
Score = 24.3 bits (53), Expect = 9.5
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 41 QKAAQEVLTALKEHPDAW 58
Q + V+ AL +H AW
Sbjct: 34 QYLHKVVMKALWKHQFAW 51
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.131 0.387
Gapped
Lambda K H
0.267 0.0494 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,697,562
Number of extensions: 85506
Number of successful extensions: 332
Number of sequences better than 10.0: 1
Number of HSP's gapped: 324
Number of HSP's successfully gapped: 50
Length of query: 112
Length of database: 6,701,793
Length adjustment: 76
Effective length of query: 36
Effective length of database: 4,579,797
Effective search space: 164872692
Effective search space used: 164872692
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.0 bits)