RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8972
(170 letters)
>2j3w_B ZGC 92866, trafficking protein particle complex protein 2;
multisubunit tethering factor, trapp, palmitate,
transport, lipoprotein; HET: PLM; 2.1A {Brachydanio
rerio} SCOP: d.278.1.2 PDB: 2j3r_B*
Length = 188
Score = 127 bits (321), Expect = 6e-38
Identities = 57/95 (60%), Positives = 76/95 (80%)
Query: 1 MKLAKFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKDKGSLNCAIF 60
+ + F+K+N+WK +FGKE DKLE+ANDD++TYY+IE+E L+N +ISVPK+ +LNCA F
Sbjct: 83 LNILLFIKVNVWKALFGKEADKLEQANDDDKTYYIIEKEPLINAYISVPKENSTLNCAAF 142
Query: 61 VAGIVEAVLNNCGFKSTVTAHWHKGTTYMIQFDEQ 95
GIVEA+L + GF + VT HWHKGTT MI+FDE
Sbjct: 143 TGGIVEAILTHSGFPAKVTVHWHKGTTLMIKFDES 177
>3cue_B Transport protein particle 31 kDa subunit; membrane traffic, GEF,
tethering complex, RAB activation, GU nucleotide
exchange factor; HET: PLM; 3.70A {Saccharomyces
cerevisiae}
Length = 283
Score = 124 bits (311), Expect = 1e-35
Identities = 29/97 (29%), Positives = 49/97 (50%), Gaps = 10/97 (10%)
Query: 5 KFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKDKGSLNCAIFVAGI 64
+F+ LW +F D L ++++ + Y +++ + +FI +++C FV GI
Sbjct: 181 QFIHGTLWSYLFNHVSDDLVKSSERDNEYMIVDNFPTLTQFIPGE----NVSCEYFVCGI 236
Query: 65 VEAVLNNCGFKSTVTAH------WHKGTTYMIQFDEQ 95
++ L N GF VTAH + T Y+IQFD Q
Sbjct: 237 IKGFLFNAGFPCGVTAHRMPQGGHSQRTVYLIQFDRQ 273
>2bjn_A TPC6, trafficking protein particle complex subunit 6B; trapp
complex, tethering, transport protein; 1.7A {Homo
sapiens} PDB: 3kxc_C* 2cfh_C*
Length = 160
Score = 89.6 bits (222), Expect = 2e-23
Identities = 21/96 (21%), Positives = 37/96 (38%), Gaps = 6/96 (6%)
Query: 3 LAKFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKDKGSLNCAI--F 60
+ KF+ + W +F K+ D L + Y L + + + +S K F
Sbjct: 66 IMKFICKDFWTTVFKKQIDNLRTNHQG--IYVLQDNKFRLLTQMSAGKQYLEHASKYLAF 123
Query: 61 VAGIVEAVLNNCGFKSTVTAHWHK--GTTYMIQFDE 94
G++ L+N G KS VTA + + +
Sbjct: 124 TCGLIRGGLSNLGIKSIVTAEVSSMPACKFQVMIQK 159
>2c0j_B R32611_2; palmitate; HET: PLM; 2.20A {Homo sapiens} PDB: 2j3t_B*
Length = 160
Score = 82.2 bits (203), Expect = 1e-20
Identities = 19/98 (19%), Positives = 38/98 (38%), Gaps = 6/98 (6%)
Query: 1 MKLAKFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKD--KGSLNCA 58
+ + KF+ +LW +F K+ D L + TY L + + ++ + +
Sbjct: 64 LDVLKFLCKDLWVAVFQKQMDSLRTNHQG--TYVLQDNSFPLLLPMASGLQYLEEAPKFL 121
Query: 59 IFVAGIVEAVLNNCGFKSTVTAHWHK--GTTYMIQFDE 94
F G++ L G +S VTA + + +
Sbjct: 122 AFTCGLLRGALYTLGIESVVTASVAALPVCKFQVVIPK 159
>1sz7_A BET3 homolog, trafficking protein particle complex subunit 3;
alpha-beta plait, trapp complex, palmitoylated,
transport PR; HET: PLM; 1.55A {Homo sapiens} PDB:
2cfh_A* 2pwn_A* 3kxc_A* 1wc8_A* 2j3w_D* 2j3r_A* 2j3t_A*
1wc9_A* 2c0j_A*
Length = 200
Score = 80.4 bits (198), Expect = 1e-19
Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 6/98 (6%)
Query: 3 LAKFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKDKGSLNCAIFVA 62
A + +K G + + ++E LV+ F+ +P + SL + +
Sbjct: 83 TADVIAKVAFKMYLGITPSITNWSPAGDEFSLILENNPLVD-FVELPDNHSSLIYSNLLC 141
Query: 63 GIVEAVLNNCGFKSTVTAH-----WHKGTTYMIQFDEQ 95
G++ L T ++F +
Sbjct: 142 GVLRGALEMVQMAVEAKFVQDTLKGDGVTEIRMRFIRR 179
>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 = 38.3 bits (88), Expect = 7e-04
Identities = 21/139 (15%), Positives = 43/139 (30%), Gaps = 23/139 (16%)
Query: 3 LAKFVK-------INLWKNIFGK-ECDK-LERANDDERTYYLI-----EQESLVNKFI-- 46
FV ++ K+I K E D + + T L +QE +V KF+
Sbjct: 26 EDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEE 85
Query: 47 SVPKDKGSLNCAIFVAGIVEAVLNNCGFKSTVTAHWHKGTTYMIQFDEQEGKFTALQIM- 105
+ + L I + + + ++ + + + L+
Sbjct: 86 VLRINYKFLMSPIKTEQR-QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQAL 144
Query: 106 -----EENIASQWRRGAGK 119
+N+ G+GK
Sbjct: 145 LELRPAKNVLIDGVLGSGK 163
Score = 35.6 bits (81), Expect = 0.005
Identities = 26/178 (14%), Positives = 46/178 (25%), Gaps = 60/178 (33%)
Query: 3 LAKFVK--INLWKNIFGKECDKLERAND---------DERTYYLIEQESLVNKFISVPKD 51
+A+ ++ + W N CDKL + + R + + L F P
Sbjct: 333 IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMF----DRLS-VF---PPS 384
Query: 52 KGSLNCAIFVAGI---------VEAVLNNCGFKSTVTAHWHKGTT--YMIQFDEQEGKFT 100
+ + + V V+N S V + T I + + K
Sbjct: 385 ---AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKV-KLE 440
Query: 101 ALQIMEENIASQWRRGAGKVGRGACKGNQQLNYNLMAKPSGHDFCIILEPPLVRPRGY 158
+ +I YN+ D + P L Y
Sbjct: 441 NEYALHRSIVDH--------------------YNIPKTFDSDDL---IPPYL---DQY 472
Score = 26.7 bits (58), Expect = 4.7
Identities = 16/116 (13%), Positives = 30/116 (25%), Gaps = 40/116 (34%)
Query: 27 NDDERTYYLIEQESLVNKFISVPKD-------KGS-LNCAIFVAGIVEAVLNNCGFKSTV 78
+ T E +SL+ K++ + +I I + +
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGL---------- 341
Query: 79 TAHW-------HKGTTYMIQ-------FDEQEGKFTALQIMEE--NIASQ-----W 113
A W T +I+ E F L + +I + W
Sbjct: 342 -ATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW 396
>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 = 28.7 bits (63), Expect = 1.2
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 66 EAVLNNCGFKSTVTAHWHKGTTYMIQFDEQEGKFTALQIMEENIASQW 113
+ +L F+ A W K + + KF AL I+++ I +W
Sbjct: 37 QEILTK--FQDNPDA-WQKADQILQFSTNPQSKFIALSILDKLITRKW 81
>1b7y_B Phers, protein (phenylalanyl-tRNA synthetase); enzyme, alpha/beta
homodimer, ligase; HET: FYA; 2.50A {Thermus
thermophilus} SCOP: a.6.1.1 a.6.1.1 b.40.4.4 b.153.1.1
d.58.13.1 d.104.1.1 PDB: 1b70_B* 1eiy_B 1jjc_B* 1pys_B
2akw_B* 2aly_B* 2amc_B* 3hfz_B* 3teh_B* 2iy5_B*
Length = 785
Score = 28.2 bits (64), Expect = 1.6
Identities = 9/38 (23%), Positives = 15/38 (39%), Gaps = 4/38 (10%)
Query: 63 GIVEAVLNNCGFKSTVTA----HWHKGTTYMIQFDEQE 96
G +EA+ G V A H G + + + +E
Sbjct: 611 GYLEALFARLGLAFRVEAQAFPFLHPGVSGRVLVEGEE 648
>3e6s_A Ferritin; iron storage, ferroxidase, oxidoreductase; 1.95A
{Pseudo-nitzschia multiseries} PDB: 3e6r_A
Length = 168
Score = 27.6 bits (62), Expect = 1.6
Identities = 3/26 (11%), Positives = 8/26 (30%)
Query: 21 DKLERANDDERTYYLIEQESLVNKFI 46
K+ N ++ S + +
Sbjct: 140 AKVTDENRTPGLLRSLDVVSFLGPCL 165
>2r58_A Polycomb protein SCM; MBT repeat, sex COMB on midleg, DI-methyl
lysine, regulator, developmental protein, metal-binding,
nucleus; HET: MLY; 2.00A {Drosophila melanogaster} PDB:
2r57_A* 2r5a_A* 2r5m_A*
Length = 265
Score = 27.2 bits (60), Expect = 2.7
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 139 PSGHDFCIILEPPLVRPRGYCEK 161
S +DF +++ + G+CEK
Sbjct: 73 DSQNDFWRLVDSTEIHAIGHCEK 95
>2biv_A SCML2 protein, sex COMB on midleg-like protein 2; MBT, malignant
brain tumor, transcription factor; 1.7A {Homo sapiens}
SCOP: b.34.9.3 b.34.9.3 PDB: 1oi1_A 2vyt_A* 2p0k_A
Length = 243
Score = 26.9 bits (59), Expect = 3.0
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 139 PSGHDFCIILEPPLVRPRGYCEK 161
+ +DF +++ P ++P G CEK
Sbjct: 101 DNRNDFWRLVDSPDIQPVGTCEK 123
>3a6p_A Exportin-5; exportin-5, RANGTP, nuclearexport, importin-BE family,
nucleus, phosphoprotein, protein transport; HET: GTP;
2.92A {Homo sapiens}
Length = 1204
Score = 26.9 bits (58), Expect = 3.8
Identities = 8/48 (16%), Positives = 13/48 (27%), Gaps = 2/48 (4%)
Query: 66 EAVLNNCGFKSTVTAHWHKGTTYMIQFDEQEGKFTALQIMEENIASQW 113
FK G + + LQI+E + +W
Sbjct: 34 LKFCEE--FKEKCPICVPCGLRLAEKTQVAIVRHFGLQILEHVVKFRW 79
>2rhq_B Phenylalanyl-tRNA synthetase beta chain; heterotetramer,
phenylalanine, aminoacyl-tRNA synthetase, ATP-binding,
cytoplasm, ligase; HET: GAX; 2.20A {Staphylococcus
haemolyticus} PDB: 2rhs_B*
Length = 795
Score = 26.7 bits (60), Expect = 4.1
Identities = 8/38 (21%), Positives = 16/38 (42%), Gaps = 4/38 (10%)
Query: 63 GIVEAVLNNCGFKSTVTA----HWHKGTTYMIQFDEQE 96
G+V+ V + + A H G T ++ + Q+
Sbjct: 623 GVVDRVAEKLNLEFSYKAGKIEGLHPGRTAIVSLEGQD 660
>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 = 26.8 bits (58), Expect = 5.3
Identities = 6/50 (12%), Positives = 15/50 (30%), Gaps = 5/50 (10%)
Query: 66 EAVLNNCGFKSTVTAHWHKGTTYMIQFD--EQEGKFTALQIMEENIASQW 113
+ + +S+ T W + + + LQ + E +
Sbjct: 29 TDFIGS--LRSSSTG-WKICHEIFSEKTKYKPSTRLICLQTLSEKVREWN 75
>3pco_B Phenylalanyl-tRNA synthetase, beta chain; aminoacylation,
tRNA-binding, DNA-binding domain, four-helix
aminoacyl-tRNA synthetase, ATP-binding; HET: PHE AMP;
3.02A {Escherichia coli}
Length = 795
Score = 26.3 bits (59), Expect = 6.6
Identities = 9/42 (21%), Positives = 16/42 (38%), Gaps = 6/42 (14%)
Query: 61 VAGIVEAVLNNCGFKSTVT------AHWHKGTTYMIQFDEQE 96
+ G +E+VL+ G + V H G + I +
Sbjct: 617 LKGDLESVLDLTGKLNEVEFRAEANPALHPGQSAAIYLKGER 658
>1ixk_A Methyltransferase; open beta sheet; 1.90A {Pyrococcus horikoshii}
SCOP: c.66.1.38
Length = 315
Score = 25.6 bits (57), Expect = 9.2
Identities = 2/27 (7%), Positives = 10/27 (37%)
Query: 9 INLWKNIFGKECDKLERANDDERTYYL 35
+ + ++G+ ++ A +
Sbjct: 21 ADRYFQLWGERAIRIAEAMEKPLPRCF 47
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
0.320 0.136 0.421
Gapped
Lambda K H
0.267 0.0840 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,547,425
Number of extensions: 136386
Number of successful extensions: 251
Number of sequences better than 10.0: 1
Number of HSP's gapped: 245
Number of HSP's successfully gapped: 20
Length of query: 170
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 83
Effective length of database: 4,272,666
Effective search space: 354631278
Effective search space used: 354631278
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.4 bits)