RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8772
(234 letters)
>2ebm_A RWD domain-containing protein 1; alpha+beta sandwich fold, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 128
Score = 106 bits (266), Expect = 1e-29
Identities = 52/117 (44%), Positives = 79/117 (67%)
Query: 2 DYQEEQSNEIEALDSIYYGDMEILEKDPHVFTIPIQSECVDDEHQMNCLLRFQYTPKYPE 61
DY EEQ NE+EAL+SIY +L ++P FTI + SE +++ + L+F Y+ KYP+
Sbjct: 10 DYGEEQRNELEALESIYPDSFTVLSENPPSFTITVTSEAGENDETVQTTLKFTYSEKYPD 69
Query: 62 EIPIIEIENCDNIDEDVERELKEYLLTQANENLGMVMIFTLVSSAQEWLSTKSDQLK 118
E P+ EI + +N++++ ++ + L QA ENLGMVMIFTLV++ QE L+ DQ+K
Sbjct: 70 EAPLYEIFSQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVDQIK 126
>1ukx_A GCN2, GCN2 EIF2alpha kinase; UBC-like fold, triple beta-turns,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: d.20.1.3
Length = 137
Score = 98.2 bits (244), Expect = 3e-26
Identities = 33/118 (27%), Positives = 56/118 (47%), Gaps = 8/118 (6%)
Query: 2 DYQEEQSNEIEALDSIYYGDMEILEKD-------PHVFTIPIQSECVDDEHQMNCL-LRF 53
Y + Q +E++AL++IY D + L D P + + + + E + LR
Sbjct: 10 SYSQRQDHELQALEAIYGSDFQDLRPDARGRVREPPEINLVLYPQGLAGEEVYVQVELRV 69
Query: 54 QYTPKYPEEIPIIEIENCDNIDEDVERELKEYLLTQANENLGMVMIFTLVSSAQEWLS 111
+ P YP+ +P I+++N + + LK +L A + G VMIF L Q +LS
Sbjct: 70 KCPPTYPDVVPEIDLKNAKGLSNESVNLLKSHLEELAKKQCGEVMIFELAHHVQSFLS 127
>2ebk_A RWD domain-containing protein 3; alpha+beta sandwich fold, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 128
Score = 96.4 bits (240), Expect = 8e-26
Identities = 33/120 (27%), Positives = 45/120 (37%), Gaps = 7/120 (5%)
Query: 2 DYQEEQSNEIEALDSIYYGDMEIL-----EKDPHVFTIPIQSECVDDEHQMNCLLRFQYT 56
E E+ L +I+ E E D VF I ++E D + L F
Sbjct: 7 GMAEPVQEELSVLAAIFCRPHEWEVLSRSETDGTVFRIHTKAEGFMDA-DIPLELVFHLP 65
Query: 57 PKYPEEIPIIEIENCDNIDEDVERELKEYLLTQANENLGMVMIFTLVSSAQEWLSTKSDQ 116
YP +P I I N + + +KE LL QA L M+ LV Q+ L Q
Sbjct: 66 VNYPSCLPGISI-NSEQLTRAQCVTVKEKLLEQAESLLSEPMVHELVLWIQQNLRHILSQ 124
>2day_A Ring finger protein 25; ligase, metal-binding, UB1 conjugation, UB1
conjugation pathway, RWD domain, alpha+beta sandwich
fold, structural genomics; NMR {Homo sapiens} SCOP:
d.20.1.3 PDB: 2dmf_A
Length = 128
Score = 91.1 bits (226), Expect = 1e-23
Identities = 27/116 (23%), Positives = 52/116 (44%), Gaps = 6/116 (5%)
Query: 2 DYQEEQSNEIEALDSIYYGDMEILEKD----PHVFTIPIQSECVDDEHQMNC--LLRFQY 55
+ +E+E L+SIY ++++++ + P I + +D+ L Q
Sbjct: 8 EEDWVLPSEVEVLESIYLDELQVIKGNGRTSPWEIYITLHPATAEDQDSQYVCFTLVLQV 67
Query: 56 TPKYPEEIPIIEIENCDNIDEDVERELKEYLLTQANENLGMVMIFTLVSSAQEWLS 111
+YP E+P I I N + ++ + + L A LG M++ L+ +E LS
Sbjct: 68 PAEYPHEVPQISIRNPRGLSDEQIHTILQVLGHVAKAGLGTAMLYELIEKGKEILS 123
>2yz0_A Serine/threonine-protein kinase GCN2; A-B-B-B-B-A-A, amino acid
starvation signal response, EIF2alpha kinase,
transferase; NMR {Saccharomyces cerevisiae}
Length = 138
Score = 88.6 bits (219), Expect = 1e-22
Identities = 38/130 (29%), Positives = 55/130 (42%), Gaps = 9/130 (6%)
Query: 2 DYQEEQSNEIEALDSIYYGDMEILEKDPH--------VFTIPIQSECVDDEHQMNCLLRF 53
Y E Q NE+EA+ SIY D L K +F I ++S + + + L F
Sbjct: 10 QYYEIQCNELEAIRSIYMDDFTDLTKRKSSWDKQPQIIFEITLRSV-DKEPVESSITLHF 68
Query: 54 QYTPKYPEEIPIIEIENCDNIDEDVERELKEYLLTQANENLGMVMIFTLVSSAQEWLSTK 113
TP YP P IE +N N+ + + LK N + G +IF + S QE L
Sbjct: 69 AMTPMYPYTAPEIEFKNVQNVMDSQLQMLKSEFKKIHNTSRGQEIIFEITSFTQEKLDEF 128
Query: 114 SDQLKKDKEE 123
+ + E
Sbjct: 129 QNVVNTQSLE 138
>2dax_A Protein C21ORF6; RWD domain, alpha+beta sandwich fold, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.20.1.3
Length = 152
Score = 57.4 bits (138), Expect = 1e-10
Identities = 27/149 (18%), Positives = 47/149 (31%), Gaps = 28/149 (18%)
Query: 1 MDYQEEQSNEIEALDSIYYGDMEILEKDPHV---------------------FTIPIQSE 39
+ E Q E++ L S++ G+ E++ D FTI + +
Sbjct: 7 GEQAEAQLAELDLLASMFPGENELIVNDQLAVAELKDCIEKKTMEGRSSKVYFTINMNLD 66
Query: 40 CVDDEHQMNCLLRFQYTPKYPEEIPIIEIENCDNIDEDVERELKEYLLTQANEN-LGMVM 98
V DE L KYP +P I + + + +L L ++ G V
Sbjct: 67 -VSDEKMAMFSLACILPFKYPAVLPEITV-RSVLLSRSQQTQLNTDLTAFLQKHCHGDVC 124
Query: 99 IFTLVSSAQEWLSTKSDQLKKDKEEAEEK 127
I EW+ + +
Sbjct: 125 ILNAT----EWVREHASGYVSRDTSSSGP 149
>2daw_A RWD domain containing protein 2; alpha+beta sandwich fold,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.20.1.3
Length = 154
Score = 54.3 bits (130), Expect = 1e-09
Identities = 19/143 (13%), Positives = 43/143 (30%), Gaps = 22/143 (15%)
Query: 1 MDYQEEQSNEIEALDSIYYGDMEILEKDPHVF----------------TIPIQSECVDDE 44
+ + Q E+E L S++ E+ +D + I +E
Sbjct: 13 KESLQLQLLEMEMLFSMFPNQGEVKLEDVNALTNIKRYLEGTREALPPKIEFVITLQIEE 72
Query: 45 HQMNCLLRFQYTPKYPEEIPIIEIENCDNIDEDVERELKEYLLTQANEN-LGMVMIFTLV 103
++ L+ YP + +D + L + L + G + + +
Sbjct: 73 PKVKIDLQVTMPHSYPYLALQLFG-RSSELDRHQQLLLNKGLTSYIGTFDPGELCVCAAI 131
Query: 104 SSAQEWLSTKSDQLKKDKEEAEE 126
+WL S +++
Sbjct: 132 ----QWLQDNSASYFLNRKLVSG 150
>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 = 36.8 bits (84), Expect = 0.005
Identities = 33/239 (13%), Positives = 71/239 (29%), Gaps = 78/239 (32%)
Query: 11 IEALDSI----YYGDMEILEKDPHVFTIPIQSECV--------DDEHQMNCLLRFQYTPK 58
+ L+ + + + H IP + D +N L ++ K
Sbjct: 363 LNVLEPAEYRKMFDRLSVFPPSAH---IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEK 419
Query: 59 YPEE----IPIIEIENCDNIDEDVE--RELKE------------------------YL-- 86
P+E IP I +E ++ + R + + ++
Sbjct: 420 QPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH 479
Query: 87 -LTQANENLGMVMIFTLVSSAQEWLSTKSDQLKKDKEEAE---------------EKRIK 130
L E+ + +F +V +L K ++ D + I
Sbjct: 480 HLKNI-EHPERMTLFRMVFLDFRFLEQK---IRHDSTAWNASGSILNTLQQLKFYKPYIC 535
Query: 131 AEEAAEQKRFEGTVVTLETFI------AWKAKFDKDMAHIIFEEKNKAKEKTAGKLTGR 183
+ ++E V + F+ +K+ D+ I +++A + A K R
Sbjct: 536 DNDP----KYERLVNAILDFLPKIEENLICSKY-TDLLRIALMAEDEAIFEEAHKQVQR 589
Score = 34.8 bits (79), Expect = 0.021
Identities = 34/220 (15%), Positives = 73/220 (33%), Gaps = 55/220 (25%)
Query: 1 MDYQEEQSNEIEALDSIYYGDMEILEKDPHVFTIPIQSECVDDEHQMNCLLRFQYTPKYP 60
MD++ + E + Y +IL VF + VD+ + P
Sbjct: 7 MDFE---TGEHQ------YQYKDIL----SVF----EDAFVDN-------FDCKDVQDMP 42
Query: 61 EEIPIIEIENCDNIDEDVERELKEYLLTQANENLGMVMIFTLVSSAQEWLSTKSDQLKKD 120
+ I+ E D+I + + G + +F + S QE + ++K
Sbjct: 43 K--SILSKEEIDHI------------IMSKDAVSGTLRLFWTLLSKQE------EMVQKF 82
Query: 121 KEEAEEKRIKAEEAAEQKRFEGTVVTLETFIAWKAKFDKDMAHIIFEEKNKAKEKTAGKL 180
EE K + + + +I + + D +F + N ++ + KL
Sbjct: 83 VEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQ--VFAKYNVSRLQPYLKL 140
Query: 181 TGREMFMQDKSMNESDLKFIEESGDGGLDATESVEVNETL 220
R+ ++ + K + G G + ++ +
Sbjct: 141 --RQALLELRPA-----KNVLIDGVLG--SGKTWVALDVC 171
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 34.0 bits (77), Expect = 0.019
Identities = 16/98 (16%), Positives = 40/98 (40%), Gaps = 24/98 (24%)
Query: 105 SAQEWLSTKSDQLKKDKEEAEEKRIKAEEAAEQKRFEGTVVTLETFIAWKAKFDKDMAHI 164
+ + L+ + + ++K +EE + KR++ +AA + + W+ K KD+
Sbjct: 75 AQADRLTQEPESIRKWREE-QRKRLQELDAASKVMEQ----------EWREKAKKDLEE- 122
Query: 165 IFEEKNKAKEKTAGKLTGREMFMQDKSMNESDLKFIEE 202
+ +++ EK + +D F ++
Sbjct: 123 WNQRQSEQVEKNK------------INNRIADKAFYQQ 148
Score = 30.9 bits (69), Expect = 0.22
Identities = 11/69 (15%), Positives = 29/69 (42%), Gaps = 16/69 (23%)
Query: 76 EDVERELKEYLLTQANENLGMVMIFTLVSSAQEWLSTKSDQLKKDKEEAEEKRIKAEEAA 135
+ + +++ +A ++L +EW +S+Q++K+K A++A
Sbjct: 102 DAASKVMEQEWREKAKKDL------------EEWNQRQSEQVEKNKINNRI----ADKAF 145
Query: 136 EQKRFEGTV 144
Q+ +
Sbjct: 146 YQQPDADII 154
>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 = 32.7 bits (74), Expect = 0.12
Identities = 21/116 (18%), Positives = 35/116 (30%), Gaps = 44/116 (37%)
Query: 148 ETFIAWKAKFDK-D----------MAHIIFEEKNKAKEKTA--GKLTG---REMFMQ--- 188
+T A + +++ D + I+ N T G G RE +
Sbjct: 1637 KTSKAAQDVWNRADNHFKDTYGFSILDIV---INNPVNLTIHFGGEKGKRIRENYSAMIF 1693
Query: 189 -------------DKSMNESDLKFIEESGDGGLDATES-------VEVNETLFQDM 224
K +NE + S G L AT+ +E F+D+
Sbjct: 1694 ETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEK--AAFEDL 1747
Score = 28.5 bits (63), Expect = 2.4
Identities = 21/111 (18%), Positives = 40/111 (36%), Gaps = 34/111 (30%)
Query: 51 LRFQYTPKYPE-EIPIIEIENCDNIDE----------DVERELKEYLLTQANENL---GM 96
+R YP +P +E+ +E ++ +E + + + N +L
Sbjct: 308 VRCYEA--YPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQ 365
Query: 97 VMIFTLVSSAQ--------EWLSTKSDQLKKDKEEAEEKRIKAEEAAEQKR 139
V I +LV+ A+ + L + L+K KA +Q R
Sbjct: 366 VEI-SLVNGAKNLVVSGPPQSLYGLNLTLRK---------AKAPSGLDQSR 406
>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 = 29.5 bits (65), Expect = 0.55
Identities = 9/53 (16%), Positives = 17/53 (32%), Gaps = 24/53 (45%)
Query: 168 EKNKAKEKTAGKLTGREMFMQDKSMNESDLKFIEESGDGGLDATESVEVNETL 220
EK K KL ++ LK + D+ ++ + T+
Sbjct: 18 EKQALK-----KL-------------QASLKLYAD------DSAPALAIKATM 46
>3un6_A Hypothetical protein saouhsc_00137; structural genomics, center for
structural genomics of infec diseases, csgid; 2.01A
{Staphylococcus aureus subsp}
Length = 341
Score = 27.1 bits (60), Expect = 5.2
Identities = 7/42 (16%), Positives = 11/42 (26%), Gaps = 6/42 (14%)
Query: 129 IKAEEAAEQKRFEGTVVTLETFIAWKAKFDK------DMAHI 164
+ ++ Q + L F W D D A
Sbjct: 68 MMTKKLLSQYNHPKYKLELVKFNNWPDLMDALNSGRIDGAST 109
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
0.312 0.130 0.359
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,553,054
Number of extensions: 211730
Number of successful extensions: 534
Number of sequences better than 10.0: 1
Number of HSP's gapped: 507
Number of HSP's successfully gapped: 45
Length of query: 234
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 143
Effective length of database: 4,160,982
Effective search space: 595020426
Effective search space used: 595020426
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 56 (26.1 bits)