RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3409
(139 letters)
>2j3w_A Sedlin, trafficking protein particle complex protein 2;
multisubunit tethering factor, trapp, palmitate,
transport, lipoprotein; HET: PLM; 2.1A {Mus musculus}
SCOP: d.110.4.3 PDB: 1h3q_A
Length = 142
Score = 154 bits (391), Expect = 9e-50
Identities = 70/138 (50%), Positives = 106/138 (76%), Gaps = 2/138 (1%)
Query: 1 MANRYYFVMVGREDNPLYQRGF--SCKEANDNENKYYYEFIAHASLDLLDEQVWQTDHMY 58
M+ +YFV+VG DNP+++ F K + +++++ +FIAHA+LDL+DE +W +++MY
Sbjct: 3 MSGSFYFVIVGHHDNPVFEMEFLPPGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMY 62
Query: 59 LKTIDKFNDMMVSAFVTPTGVKFLMVHDSKNEEGIKKFFTSVYELFIKYSLNPFYKINTP 118
LKT+DKFN+ VSAFVT ++F+M+HD + E+GIK FFT VY+L+IK+++NPFY+ N+P
Sbjct: 63 LKTVDKFNEWFVSAFVTAGHMRFIMLHDVRQEDGIKNFFTDVYDLYIKFAMNPFYEPNSP 122
Query: 119 INSTYFDSKVNFLGRKFL 136
I S+ FD KV FLG+K L
Sbjct: 123 IRSSAFDRKVQFLGKKHL 140
>3pr6_A Trapp-associated protein TCA17; longin fold, vesicle tethering
regulation, trapp complex, TR network, transport
protein; 1.80A {Saccharomyces cerevisiae}
Length = 162
Score = 70.8 bits (173), Expect = 1e-16
Identities = 26/140 (18%), Positives = 50/140 (35%), Gaps = 18/140 (12%)
Query: 6 YFVMVGREDNPLYQRGFSCKEANDNENKYYYEFIAHASLDLLDEQV--WQTDHMYLKTID 63
+ ++ D P+ + E N+ Y +++ SLD + + W +
Sbjct: 12 FVSLIDESDKPILIYVPNEAENEMNDVLKYN-VLSNISLDYFESALVEWHSLDSKPLLKS 70
Query: 64 KFNDMMVSAF---VTPTGVKFLMVHDSKN-------EEGIKKFFTSVYELFIKYSLNPFY 113
F VS F + TG+K ++ + K+ E I + F +V +++I+ NP
Sbjct: 71 IFQLEGVSVFAMLIKQTGLKIVIGFEQKSLSGADDEFEAINQIFETVRKIYIRVKCNPLL 130
Query: 114 KIN-----TPINSTYFDSKV 128
FD
Sbjct: 131 VSGDEKSIIKSLERKFDELF 150
>2j3t_D Trafficking protein particle complex subunit 4; trapp, palmitate,
transport, lipoprotein, ER-golgi transport apparatus,
protein transport; HET: PLM; 2.4A {Homo sapiens} PDB:
2zmv_A 2jsn_A
Length = 219
Score = 63.2 bits (153), Expect = 3e-13
Identities = 25/131 (19%), Positives = 50/131 (38%), Gaps = 4/131 (3%)
Query: 2 ANRYYFVMVGREDNPLYQRGFSCKEANDNENKYYYEFIAHASLDLLDEQVWQTDHMYLKT 61
+ +G N F NE H+ + + + ++
Sbjct: 78 DGKEVLEYLGNPANYPVSIRFGRPRLTSNEKLMLASMF-HSLFAIGSQLSPEQGSSGIEM 136
Query: 62 IDKFNDMMVSAFVTPTGVKFLMVHDSKNEEGIKKFFTSVYELFIKYSL-NPFYKINTPIN 120
+ + + + + T TG+KF+++ D + GI +YE++ ++L NPFY + PI
Sbjct: 137 L-ETDTFKLHCYQTLTGIKFVVLAD-PRQAGIDSLLRKIYEIYSDFALKNPFYSLEMPIR 194
Query: 121 STYFDSKVNFL 131
FD +
Sbjct: 195 CELFDQNLKLA 205
>3cue_A Transport protein particle 23 kDa subunit; membrane traffic, GEF,
tethering complex, RAB activation, GU nucleotide
exchange factor; HET: PLM; 3.70A {Saccharomyces
cerevisiae}
Length = 219
Score = 52.0 bits (123), Expect = 4e-09
Identities = 20/90 (22%), Positives = 31/90 (34%), Gaps = 24/90 (26%)
Query: 70 VSAFVTPTGVKFLMVHDSK-----------------------NEEGIKKFFTSVYELFIK 106
+ + T TG+KF+ + S + F VY L+
Sbjct: 129 MFIYQTLTGLKFVAISSSVMPQRQPTIATTDKPDRPKSTSNLAIQIADNFLRKVYCLYSD 188
Query: 107 YSL-NPFYKINTPINSTYFDSKVNFLGRKF 135
Y + +P Y + PI S FD KV +
Sbjct: 189 YVMKDPSYSMEMPIRSNLFDEKVKKMVENL 218
>2j3t_C Trafficking protein particle complex subunit 1, trafficking protein
particle complex subunit 3; trapp, palmitate, transport,
lipoprotein, ER-golgi transport apparatus, protein
transport; HET: PLM; 2.4A {Mus musculus}
Length = 145
Score = 46.4 bits (110), Expect = 1e-07
Identities = 20/133 (15%), Positives = 52/133 (39%), Gaps = 13/133 (9%)
Query: 5 YYFVMVGREDNPLYQRGFSCKEANDNENKYYYEFIA------HASLDLLDEQVWQTDHMY 58
+ + R L+ + K+ + Y+ + + + + + +
Sbjct: 4 HNLYLFDRNGVCLHYSEWHRKKQAGIPKEEEYKLMYGMLFSIRSFVSKMSPLDMKDGFLS 63
Query: 59 LKTIDKFNDMMVSAFVTPTGVKFLMVHDSKNEEGIKKFFTSVYE-LFIKYSL-NPFYKIN 116
+T ++ + + TPTG+K +M D I+ +Y L++++ + NP +
Sbjct: 64 FQT-SRYK---LHYYETPTGIKVVMNTD-LGVGPIRDVLHHIYSALYVEFVVKNPLCPLG 118
Query: 117 TPINSTYFDSKVN 129
+ S F S+++
Sbjct: 119 QTVQSELFRSRLD 131
>3cue_C Transport protein particle 18 kDa subunit; membrane traffic, GEF,
tethering complex, RAB activation, GU nucleotide
exchange factor; HET: PLM; 3.70A {Saccharomyces
cerevisiae}
Length = 159
Score = 36.8 bits (85), Expect = 6e-04
Identities = 9/57 (15%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 73 FVTPTGVKFLMVHDSKNEEGIKKFFTSVY-ELFIKYSL-NPFYKINTPINSTYFDSK 127
+ T +G+ F+++ D ++ + +Y +++KY N + N +
Sbjct: 80 YCTASGLWFVLLSD-FKQQSYTQVLQYIYSHIYVKYVSNNLLSPYDFAENENEMRGQ 135
>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 = 34.1 bits (77), Expect = 0.012
Identities = 20/122 (16%), Positives = 39/122 (31%), Gaps = 26/122 (21%)
Query: 18 YQ--RGFSC-KEANDNENKYYYEFIAHASLDLLDEQVWQTDHMYLKTIDKFNDMMVSAFV 74
Y + F ++Y+Y I H H+ + + F+
Sbjct: 453 YNIPKTFDSDDLIPPYLDQYFYSHIGH--------------HLKNIEHPERMTLFRMVFL 498
Query: 75 TPTGVKFL---MVHDSKNEEGIKKFFTSVYELFIKYSLNPFYKINTPINSTYFDSKVNFL 131
+FL + HDS ++ +L Y P+ N P ++ ++FL
Sbjct: 499 D---FRFLEQKIRHDSTAWNASGSILNTLQQL-KFYK--PYICDNDPKYERLVNAILDFL 552
Query: 132 GR 133
+
Sbjct: 553 PK 554
Score = 31.4 bits (70), Expect = 0.078
Identities = 18/110 (16%), Positives = 39/110 (35%), Gaps = 23/110 (20%)
Query: 30 NENKYYYEFIAHASLDLLDEQVWQTDHMYLKTID--KFNDMMVSAFVTPTGVKFLMVHDS 87
E++Y Y+ D+L V++ ++ D DM S + + + +
Sbjct: 12 GEHQYQYK-------DIL--SVFEDA--FVDNFDCKDVQDMPKSIL-SKEEIDHI-IMSK 58
Query: 88 KNEEGIKKFF-------TSVYELFIKYSLNPFYK-INTPINSTYFDSKVN 129
G + F + + F++ L YK + +PI + +
Sbjct: 59 DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMM 108
>3edf_A FSPCMD, cyclomaltodextrinase; alpha-cyclodextrin complex,
glycosidase, hydrolase; HET: CE6 ACX; 1.65A
{Flavobacterium SP} PDB: 3edj_A* 3edk_A* 3ede_A 3edd_A*
1h3g_A
Length = 601
Score = 27.5 bits (61), Expect = 1.8
Identities = 10/64 (15%), Positives = 19/64 (29%)
Query: 4 RYYFVMVGREDNPLYQRGFSCKEANDNENKYYYEFIAHASLDLLDEQVWQTDHMYLKTID 63
Y FV + + + +Y Y +A + D +Y D
Sbjct: 56 NYLFVDLEIGPEAQPGSFDIVFKGDGRSERYRYRLLAREQGSAQRQGFGPGDAIYQIMPD 115
Query: 64 KFND 67
+F +
Sbjct: 116 RFAN 119
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 25.8 bits (56), Expect = 6.3
Identities = 24/132 (18%), Positives = 41/132 (31%), Gaps = 42/132 (31%)
Query: 27 ANDNENK----YYYEFIAHASLDLLDEQVWQTDHMYLKTIDKF-------NDMMVSAFVT 75
A D+E +F+ + S + +V Q D + + +F ND + A
Sbjct: 49 AADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGND--IHALA- 105
Query: 76 PTGVKFLMVHDS---KNEEGIKKFFTSVYELFIKYSLNP--------------FYKI--- 115
K L +D+ K +E IK + T+ + I
Sbjct: 106 ---AKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGG 162
Query: 116 --NTPINSTYFD 125
N YF+
Sbjct: 163 QGN---TDDYFE 171
>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable
holliday junction DNA helicase; HET: ADP; 2.69A
{Campylobacter jejuni subsp}
Length = 338
Score = 25.6 bits (57), Expect = 6.3
Identities = 7/31 (22%), Positives = 13/31 (41%), Gaps = 3/31 (9%)
Query: 39 IAHASLDLL--DEQ-VWQTDHMYLKTIDKFN 66
A+ +L+ L +E D YL+ +
Sbjct: 246 RANEALNSLGVNELGFDAMDLRYLELLTAAK 276
>1e7u_A Phosphatidylinositol 3-kinase catalytic subunit; phosphoinositide
3-kinase gamma, secondary messenger generation, PI3K, PI
3K, wortmannin; HET: KWT; 2.0A {Sus scrofa} SCOP:
a.118.1.6 b.7.1.1 d.15.1.5 d.144.1.4 PDB: 1e8x_A*
1e8w_A* 1e7v_A* 1e90_A* 3l54_A* 3s2a_A* 3qaq_A* 3qjz_A*
3qk0_A* 3qar_A* 3apc_A* 3apd_A* 3apf_A* 3dbs_A* 3l13_A*
3r7q_A* 3cst_A* 3csf_A* 3l16_A* 3l17_A* ...
Length = 961
Score = 26.0 bits (56), Expect = 6.6
Identities = 19/128 (14%), Positives = 36/128 (28%), Gaps = 20/128 (15%)
Query: 16 PLYQRGFSCKEANDNENKYYYEFIAHASLDLLDEQVWQTDHMYLKTIDKFNDM------- 68
PL+ + F L + D + L+ + +
Sbjct: 669 PLWLEFKCADPTALSNETIGIIFKHGDDL--------RQDMLILQILRIMESIWETESLD 720
Query: 69 --MVSAFVTPTGVKFLM---VHDSKNEEGIKKFFTSVYELFIKYSLNPFYKINTPINSTY 123
++ TG K M V D+ I++ F L+ + K PI +
Sbjct: 721 LCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLSHWLKEKCPIEEKF 780
Query: 124 FDSKVNFL 131
+ F+
Sbjct: 781 QAAVERFV 788
>1ys1_X Lipase; CIS peptide Leu 234, Ca2+ ION, inhibitor hexylphosphonic
acid (R) 2-methyl-3-phenylpropyl ester, hydrolase; HET:
2HR; 1.10A {Burkholderia cepacia} PDB: 1ys2_X* 4lip_D
1hqd_A 2lip_A 1oil_A* 3lip_A 2nw6_A 5lip_A* 1cvl_A
2es4_A 1tah_B 1qge_D 1qge_E
Length = 320
Score = 25.4 bits (55), Expect = 6.9
Identities = 10/69 (14%), Positives = 18/69 (26%), Gaps = 3/69 (4%)
Query: 3 NRYYFVMVGREDNPLYQRGFSCKEANDNENKYYYEFIAHASLDLLDEQVWQTDHMYLKTI 62
+ G P G + +LD ++ T + +
Sbjct: 203 THLLYSWAGTAIQPTISVGGV---TGATDTSTIPLVDPANALDPSTLALFGTGTVMVNRG 259
Query: 63 DKFNDMMVS 71
ND +VS
Sbjct: 260 SGQNDGVVS 268
>1cxq_A Avian sarcoma virus integrase; mixed beta-sheet surrounded by
alpha-helices, transferase; HET: EPE; 1.02A {Avian
sarcoma virus} SCOP: c.55.3.2 PDB: 1cxu_A* 1czb_A*
1cz9_A* 1asu_A* 1asw_A* 1asv_A 1a5v_A* 1a5w_A* 1a5x_A*
1vsf_A* 1vse_A* 3o4n_A* 1vsm_A 3o4q_A* 1vsd_A* 1vsh_A*
1vsi_A* 1vsj_A* 1vsk_A 1vsl_A
Length = 162
Score = 24.8 bits (54), Expect = 9.7
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 50 QVWQTDHMYLKTIDKFNDMMVS 71
Q+WQTD + + + V+
Sbjct: 12 QIWQTDFTLEPRMAPRSWLAVT 33
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
0.322 0.138 0.415
Gapped
Lambda K H
0.267 0.0633 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,124,010
Number of extensions: 110547
Number of successful extensions: 220
Number of sequences better than 10.0: 1
Number of HSP's gapped: 209
Number of HSP's successfully gapped: 27
Length of query: 139
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 55
Effective length of database: 4,356,429
Effective search space: 239603595
Effective search space used: 239603595
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 (21.9 bits)
S2: 52 (24.0 bits)