RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy18005
(135 letters)
>3vh1_A Ubiquitin-like modifier-activating enzyme ATG7; autophagy, zinc
binding, metal binding protein; 3.00A {Saccharomyces
cerevisiae} PDB: 3vh2_A
Length = 598
Score = 123 bits (311), Expect = 3e-34
Identities = 35/137 (25%), Positives = 69/137 (50%), Gaps = 13/137 (9%)
Query: 7 SPGTILNFIP-FVSSIEPTFWYKLSEIKLDEDKLKETPRPIQGYFNH------NGSCRLY 59
S +L++ P F S ++ +F+ +LS +KLD KL T +P+ + L+
Sbjct: 5 SSERVLSYAPAFKSFLDTSFFQELSRLKLDVLKLDSTCQPLTVNLDLHNIPKSADQVPLF 64
Query: 60 INSSSFSSTSSESFDHF-AEGTLLNLNSLESFKSYDKTELLLKRGQIILQAMEDGDIFEN 118
+ + SF +++ + +G++ N N L+ FK+ DK L +R + D ++
Sbjct: 65 LTNRSFEKHNNKRTNEVPLQGSIFNFNVLDEFKNLDKQLFLHQRALECWE-----DGIKD 119
Query: 119 LKLLTSFFVLTFANLQK 135
+ SF +++FA+L+K
Sbjct: 120 INKCVSFVIISFADLKK 136
>3t7h_A Ubiquitin-like modifier-activating enzyme ATG7; autophagy, ligase;
1.60A {Saccharomyces cerevisiae} PDB: 3t7f_A 3t7g_A
3ruj_A
Length = 291
Score = 104 bits (261), Expect = 1e-28
Identities = 35/137 (25%), Positives = 69/137 (50%), Gaps = 13/137 (9%)
Query: 7 SPGTILNFIP-FVSSIEPTFWYKLSEIKLDEDKLKETPRPIQGYFNH------NGSCRLY 59
S +L++ P F S ++ +F+ +LS +KLD KL T +P+ + L+
Sbjct: 4 SSERVLSYAPAFKSFLDTSFFQELSRLKLDVLKLDSTCQPLTVNLDLHNIPKSADQVPLF 63
Query: 60 INSSSFSSTSSESFDHF-AEGTLLNLNSLESFKSYDKTELLLKRGQIILQAMEDGDIFEN 118
+ + SF +++ + +G++ N N L+ FK+ DK L +R + D ++
Sbjct: 64 LTNRSFEKHNNKRTNEVPLQGSIFNFNVLDEFKNLDKQLFLHQRALECWE-----DGIKD 118
Query: 119 LKLLTSFFVLTFANLQK 135
+ SF +++FA+L+K
Sbjct: 119 INKCVSFVIISFADLKK 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 = 32.5 bits (73), Expect = 0.034
Identities = 17/105 (16%), Positives = 35/105 (33%), Gaps = 22/105 (20%)
Query: 25 FWYKLSEIKLDEDKLKETPRPIQGYFNHNGSCRLYINSSSFSSTSSESFDHFAEGTLLNL 84
FW L E L+ +Q +L + DH + L +
Sbjct: 185 FWLNLKNCNSPETVLE----MLQ---------KLLYQ---IDPNWTSRSDH-SSNIKLRI 227
Query: 85 NSLESFKSYDKTELLLKRGQIILQAMEDGDIFE--NLK---LLTS 124
+S+++ + ++L +++ + NL LLT+
Sbjct: 228 HSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTT 272
>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 = 30.4 bits (68), Expect = 0.17
Identities = 23/106 (21%), Positives = 37/106 (34%), Gaps = 22/106 (20%)
Query: 24 TFWYKLSEIKLDEDKLKETPRPIQGYFNHNGSCRLYINSSSFSSTSSESFDHFAEGTLLN 83
T+ + + +I + P + +F R+ N S+ F+ +G L
Sbjct: 1656 TYGFSILDI------VINNPVNLTIHFGGEKGKRIRENYSAM------IFETIVDGKLKT 1703
Query: 84 LNSL----ESFKSY----DKTELLLKRG-QIILQAMEDGDIFENLK 120
E SY +K L + Q L ME FE+LK
Sbjct: 1704 EKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKA-AFEDLK 1748
>2bzy_A CRK-like protein, CRKL SH3C; SH3 domain, dimer, nuclear export;
2.5A {Homo sapiens} PDB: 2bzx_A
Length = 67
Score = 27.7 bits (62), Expect = 0.32
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 89 SFKSYDKTELLLKRGQII--LQAMEDG 113
+YDKT L L+ G I+ + +G
Sbjct: 11 VPCAYDKTALALEVGDIVKVTRMNING 37
>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR,
immune system; 2.30A {Eptatretus burgeri}
Length = 177
Score = 29.2 bits (66), Expect = 0.34
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 57 RLYINSSSFSSTSSESFDHFAEGTLLNL--NSLESFKS--YDK----TELLLKRGQIILQ 108
RL + S+ S FD + T L+L N ++S +DK T L L + LQ
Sbjct: 32 RLELESNKLQSLPHGVFDKLTQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHENK--LQ 89
Query: 109 AMEDGDIFENLKLLT 123
++ +G +F+ L L
Sbjct: 90 SLPNG-VFDKLTQLK 103
>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte
receptors, VLR, leucine-rich repeat, LRR adaptive
immunity, immune system; HET: DR2; 1.67A {Petromyzon
marinus}
Length = 229
Score = 28.9 bits (65), Expect = 0.37
Identities = 17/75 (22%), Positives = 26/75 (34%), Gaps = 11/75 (14%)
Query: 57 RLYINSSSFSSTSSESFDHFAEGTLLNL--NSLESFKS--YDK----TELLLKRGQIILQ 108
LY++ + + FD L L N L + +D T L L Q L
Sbjct: 44 ILYLHDNQITKLEPGVFDSLINLKELYLGSNQLGALPVGVFDSLTQLTVLDLGTNQ--LT 101
Query: 109 AMEDGDIFENLKLLT 123
+ +F+ L L
Sbjct: 102 VLPSA-VFDRLVHLK 115
>2dbk_A CRK-like protein; structural genomics, NPPSFA, national project on
protein structural and functional analyses; NMR {Homo
sapiens}
Length = 88
Score = 27.4 bits (61), Expect = 0.53
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 89 SFKSYDKTELLLKRGQII--LQAMEDG 113
+YDKT L L+ G I+ + +G
Sbjct: 26 VPCAYDKTALALEVGDIVKVTRMNING 52
>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY,
crystallography, immune system; 1.55A {Petromyzon
marinus} PDB: 3g3a_A 3g3b_A 3twi_D
Length = 170
Score = 28.4 bits (64), Expect = 0.63
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 57 RLYINSSSFSSTSSESFDHFAEGTLLNL--NSLESFKS--YDK----TELLLKRGQIILQ 108
LY+ + + FD + T L+L N L + +DK T+L L Q L+
Sbjct: 34 VLYLYDNQITKLEPGVFDRLTQLTRLDLDNNQLTVLPAGVFDKLTQLTQLSLNDNQ--LK 91
Query: 109 AMEDGDIFENLKLLT 123
++ G F+NLK LT
Sbjct: 92 SIPRG-AFDNLKSLT 105
>2dm2_A Palladin; beta-sandwich, KIAA0992, actin-associated scaffold,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 110
Score = 27.3 bits (61), Expect = 0.85
Identities = 7/41 (17%), Positives = 16/41 (39%), Gaps = 6/41 (14%)
Query: 26 WYKLSEIKLDEDKLKETPRPIQGYFNHNGSCRLYINSSSFS 66
W+K D ++ + +G+C L+ +S+
Sbjct: 42 WFK------DGKQISPKSDHYTIQRDLDGTCSLHTTASTLD 76
>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR,
immune system; 1.50A {Eptatretus burgeri}
Length = 208
Score = 27.7 bits (62), Expect = 1.1
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 57 RLYINSSSFSSTSSESFDHFAEGTLLNL--NSLESFKS--YDK----TELLLKRGQIILQ 108
L + ++S S + FD T L L N L+S + ++K T L L Q LQ
Sbjct: 32 YLDLETNSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQ--LQ 89
Query: 109 AMEDGDIFENLKLLT 123
++ +G +F+ L L
Sbjct: 90 SLPNG-VFDKLTQLK 103
>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein
binding, plasma; 1.70A {Listeria monocytogenes} PDB:
3rfj_A
Length = 272
Score = 27.7 bits (62), Expect = 1.2
Identities = 22/75 (29%), Positives = 31/75 (41%), Gaps = 11/75 (14%)
Query: 57 RLYINSSSFSSTSSESFDHFAEGTLLNL--NSLESFKS--YDK----TELLLKRGQIILQ 108
L + + S + FD L L N L+S +DK T L L Q LQ
Sbjct: 89 YLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLNLAHNQ--LQ 146
Query: 109 AMEDGDIFENLKLLT 123
++ G +F+ L LT
Sbjct: 147 SLPKG-VFDKLTNLT 160
Score = 26.9 bits (60), Expect = 2.0
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 9/71 (12%)
Query: 59 YINSSSFSSTSSESFDHFAEGTLLNL--NSLESFKSYDK----TELLLKRGQIILQAMED 112
I +++ S + + L L N L + + T L+L Q LQ++ +
Sbjct: 45 QIIANNSDIKSVQGIQYLPNVRYLALGGNKLHDISALKELTNLTYLILTGNQ--LQSLPN 102
Query: 113 GDIFENLKLLT 123
G +F+ L L
Sbjct: 103 G-VFDKLTNLK 112
>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity,
antibody, T cell, leucine-rich repeat, immune system;
1.70A {Petromyzon marinus} PDB: 3m18_A
Length = 251
Score = 27.4 bits (61), Expect = 1.5
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 57 RLYINSSSFSSTSSESFDHFAEGTLLNL--NSLESFKS--YDK----TELLLKRGQIILQ 108
+L + S+ ++ S +F + T LNL N L++ + +D L L Q L
Sbjct: 39 KLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQ--LA 96
Query: 109 AMEDGDIFENLKLLT 123
++ G +F++L L
Sbjct: 97 SLPLG-VFDHLTQLD 110
>2eyx_A V-CRK sarcoma virus CT10 oncogene homolog isoform A; SH3, signaling
protein; NMR {Homo sapiens}
Length = 67
Score = 25.7 bits (57), Expect = 1.8
Identities = 8/25 (32%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 91 KSYDKTELLLKRGQII--LQAMEDG 113
+YDKT L L+ G+++ + G
Sbjct: 18 NAYDKTALALEVGELVKVTKINVSG 42
>2dyb_A Neutrophil cytosol factor 4; P40(PHOX), NADPH oxidase,
oxidoreductase; HET: CAF; 3.15A {Homo sapiens}
Length = 341
Score = 26.9 bits (58), Expect = 2.5
Identities = 13/77 (16%), Positives = 22/77 (28%)
Query: 30 SEIKLDEDKLKETPRPIQGYFNHNGSCRLYINSSSFSSTSSESFDHFAEGTLLNLNSLES 89
+ +DED + + R + + S + +L
Sbjct: 123 VWVLMDEDVRIFFYQSPYDSEQVPQALRRLRPRTRKVKSVSPQGNSVDRMAAPRAEALFD 182
Query: 90 FKSYDKTELLLKRGQII 106
F K EL K G +I
Sbjct: 183 FTGNSKLELNFKAGDVI 199
>2ebp_A SAM and SH3 domain-containing protein 1; proline-glutamate
repeat-containing protein, structural genomics, NPPSFA;
NMR {Homo sapiens} PDB: 2kea_A
Length = 73
Score = 24.7 bits (54), Expect = 4.7
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 89 SFKSYDKTELLLKRGQII--LQAMEDG 113
+ YD L LK+G II + G
Sbjct: 19 TPSPYDTDSLKLKKGDIIDIISKPPMG 45
>2i24_N NEW antigen receptor PBLA8; immunoglobulin fold, immune system;
1.35A {Ginglymostoma cirratum} PDB: 2i25_N 2i27_N 2i26_N
Length = 121
Score = 24.6 bits (54), Expect = 8.2
Identities = 6/31 (19%), Positives = 15/31 (48%)
Query: 56 CRLYINSSSFSSTSSESFDHFAEGTLLNLNS 86
C+ S+ + + D + GT++ +N+
Sbjct: 83 CKPESRYGSYDAVCAALNDQYGGGTVVTVNA 113
>2ke9_A Caskin-2; SH3 domain, ANK repeat, cytoplasm, phosphoprotein,
protein binding; NMR {Homo sapiens}
Length = 83
Score = 24.4 bits (53), Expect = 8.2
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 92 SYDKTELLLKRGQII--LQAMEDG 113
+D T L ++ G +I L+ DG
Sbjct: 30 LHDPTALNVRAGDVITVLEQHPDG 53
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 0.134 0.384
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,934,593
Number of extensions: 99921
Number of successful extensions: 281
Number of sequences better than 10.0: 1
Number of HSP's gapped: 273
Number of HSP's successfully gapped: 32
Length of query: 135
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 51
Effective length of database: 4,356,429
Effective search space: 222177879
Effective search space used: 222177879
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 (21.6 bits)
S2: 52 (24.0 bits)