RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12566
(220 letters)
>2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form,
hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A
2fbv_A 2fbx_A 2fbt_A 2fc0_A*
Length = 208
Score = 74.1 bits (182), Expect = 1e-16
Identities = 26/133 (19%), Positives = 50/133 (37%), Gaps = 15/133 (11%)
Query: 80 PNSIILVDTADKFASALQDF-ARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRD-RV 137
P SI+ A + +D RL +G D EW P G +A++Q+ + +
Sbjct: 14 PGSIVYSYEASDCSFLSEDISMRLSDGDVVGFDMEWPPIYKPGKRSRVAVIQLCVSESKC 73
Query: 138 YILDIITLSKLPCYAQLCHDLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKT 197
Y+ I ++S P L + N + K G + D +
Sbjct: 74 YLFHISSMSVFP--QGLKM-----LLENKSIKKAGVGIEGDQWKLLRDFDVKLE------ 120
Query: 198 SYLDLQLLWSKLV 210
S+++L + ++ +
Sbjct: 121 SFVELTDVANEKL 133
>1vk0_A Hypothetical protein; homohexamer, AT5G06450, struc genomics,
protein structure initiative, center for eukaryot
structural genomics, CESG; 2.10A {Arabidopsis thaliana}
SCOP: c.55.3.5 PDB: 2q3s_A
Length = 206
Score = 46.1 bits (109), Expect = 2e-06
Identities = 15/113 (13%), Positives = 32/113 (28%), Gaps = 27/113 (23%)
Query: 83 IILVDTADKFASALQDFARLDHNSH---LGLDTEWKPNLSGGSPPT------LALLQIAT 133
I V ++ + L + + D W T L+ ++++T
Sbjct: 21 TIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLST 80
Query: 134 RDRVYILDIITLSKLPCYAQLCHDLELI------VFANDDLLKIGFNLMPDVS 180
R+ L +L FA+ + +G + D+
Sbjct: 81 RNLCLFL------------RLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLD 121
>2hbj_A Exosome complex exonuclease RRP6; RNA metabolism, RNA surveillance,
RNA processing, hydrolase, gene regulation; 2.10A
{Saccharomyces cerevisiae} SCOP: a.60.8.4 c.55.3.5 PDB:
2hbk_A 2hbl_A* 2hbm_A*
Length = 410
Score = 42.9 bits (101), Expect = 4e-05
Identities = 29/107 (27%), Positives = 49/107 (45%), Gaps = 18/107 (16%)
Query: 68 KPAEEYYSLTLPPNSIILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGS-PPTL 126
+ EE S + + I VDT+ + S L L + + +D E S +
Sbjct: 72 QIREEIPSKSWDDSVPIWVDTSTELESML---EDLKNTKEIAVDLEH---HDYRSYYGIV 125
Query: 127 ALLQIATRDRVYILDIITLSKLPCYAQLCHDLELI--VFANDDLLKI 171
L+QI+TR+R Y++D TL L +L ++ VF N ++K+
Sbjct: 126 CLMQISTRERDYLVD--TLK-------LRENLHILNEVFTNPSIVKV 163
>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 = 42.1 bits (98), Expect = 9e-05
Identities = 42/247 (17%), Positives = 72/247 (29%), Gaps = 76/247 (30%)
Query: 11 ELQKELIDLCVQYYDCKEAYYWCQ------KFKLNPNCVGFDLRDKIAEEESEQD---VD 61
+ + L L Q D W KL + + +LR + + E +
Sbjct: 197 TVLEMLQKLLYQI-DPN----WTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL 251
Query: 62 NGWDV---------CKPAEEYYSLTLPPNSIILVDTADKFASALQDFARLDHNSHLGLDT 112
N + CK IL+ T K + DF +H+ LD
Sbjct: 252 NVQNAKAWNAFNLSCK---------------ILLTTRFK---QVTDFLSAATTTHISLD- 292
Query: 113 EWKPNLSGGSPP-TLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELIVFA---NDDL 168
+ +P +LL + LD LP + L + A D L
Sbjct: 293 ---HHSMTLTPDEVKSLL-------LKYLDC-RPQDLPREVLTTNPRRLSIIAESIRDGL 341
Query: 169 LKIGF----NLMPDVSIIKTSLPFSECSSYNKTSYLD--------------LQLLWSKLV 210
N +II++SL E + + + L L+W ++
Sbjct: 342 ATWDNWKHVNCDKLTTIIESSLNVLE-PAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVI 400
Query: 211 AETTLQL 217
+ +
Sbjct: 401 KSDVMVV 407
Score = 36.4 bits (83), Expect = 0.007
Identities = 35/209 (16%), Positives = 69/209 (33%), Gaps = 70/209 (33%)
Query: 6 VKDNPELQKELIDLCVQYYDCKEAYYWCQKFKLNPNCVGFDLRDKIAEEESEQDVDNGWD 65
+++ L + ++D +Y+ + + D
Sbjct: 439 LENEYALHRSIVD----HYNIPKTFDS-------------------------------DD 463
Query: 66 VCKPAEEYYSLT-----LPPNSIILVDTADKFASALQDF----ARLDHNSHLGLDTEWKP 116
+ P + Y + L +I + F DF ++ H+ T W
Sbjct: 464 LIPPYLDQYFYSHIGHHL--KNIEHPERMTLFRMVFLDFRFLEQKIRHD-----STAW-- 514
Query: 117 NLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELIVFANDDLLKIGFNLM 176
N SG TL L+ + YI D P Y +L + + D L KI NL+
Sbjct: 515 NASGSILNTLQQLKFY---KPYICD-----NDPKYERLVNAIL------DFLPKIEENLI 560
Query: 177 --PDVSIIKTSLPFSECSSYNKTSYLDLQ 203
+++ +L +E + + ++ +Q
Sbjct: 561 CSKYTDLLRIAL-MAEDEAIFEEAHKQVQ 588
Score = 34.8 bits (79), Expect = 0.020
Identities = 43/241 (17%), Positives = 85/241 (35%), Gaps = 67/241 (27%)
Query: 13 QKELIDLCVQYYDCK------EAYYWCQKFKLNP---NCVGFDLRDKIA---------EE 54
E+ L ++Y DC+ E NP + + +RD +A +
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREV---L---TTNPRRLSIIAESIRDGLATWDNWKHVNCD 353
Query: 55 ESEQDVDNGWDVCKPAEE---YYSLT-LPPNSIILVDT-----ADKFASALQDFARLDHN 105
+ +++ +V +PAE + L+ PP++ I D S + H
Sbjct: 354 KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK 413
Query: 106 SHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSK--LPCYAQLCHDLELIVF 163
L ++ + K + T+++ I +V + + L + + Y F
Sbjct: 414 YSL-VEKQPKES-------TISIPSIYLELKVKLENEYALHRSIVDHYNIPKT------F 459
Query: 164 ANDDLLK----------IGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVAET 213
+DDL+ IG +L + +L F +LD + L K+ ++
Sbjct: 460 DSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTL-FRMV-------FLDFRFLEQKIRHDS 511
Query: 214 T 214
T
Sbjct: 512 T 512
Score = 32.1 bits (72), Expect = 0.15
Identities = 39/207 (18%), Positives = 68/207 (32%), Gaps = 47/207 (22%)
Query: 24 YDCKEAYYWCQKFKLNPNCVGFDLRDKIAEEESEQDVDNGWDVCKPA---EEYYSLTLPP 80
++ E Y + + D + +DV D+ K EE + +
Sbjct: 9 FETGEHQYQYKD-------ILSVFEDAFVDNFDCKDVQ---DMPKSILSKEEIDHIIMSK 58
Query: 81 NSI----ILVDT-ADKFASALQDFARLDHNSHLG-LDTEWKPNLSGGSPPTLALLQIATR 134
+++ L T K +Q F + L + K S T + I R
Sbjct: 59 DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTR--MYIEQR 116
Query: 135 DRVY----ILDIITLSKLPCYAQLCHDLELIVFANDDLLKIGFNLMPDVSII-------- 182
DR+Y + +S+L Y +L LL+ L P +++
Sbjct: 117 DRLYNDNQVFAKYNVSRLQPYLKL----------RQALLE----LRPAKNVLIDGVLGSG 162
Query: 183 KTSLPFSECSSYNKTSYLDLQLLWSKL 209
KT + C SY +D ++ W L
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNL 189
>3saf_A Exosome component 10; exoribonuclease, RNA exosome, hydrolase;
2.50A {Homo sapiens} PDB: 3sag_A 3sah_A 2cpr_A
Length = 428
Score = 41.0 bits (96), Expect = 1e-04
Identities = 15/107 (14%), Positives = 37/107 (34%), Gaps = 18/107 (16%)
Query: 68 KPAEEYYSLTLPPNSIILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGS-PPTL 126
+ + + + + D+ +L + ++ E S S
Sbjct: 95 QKPQPQLYRPIEETPCHFISSLDELVELN---EKLLNCQEFAVNLEH---HSYRSFLGLT 148
Query: 127 ALLQIATRDRVYILDIITLSKLPCYAQLCHDLELI--VFANDDLLKI 171
L+QI+TR +I+D + L D+ ++ + ++K+
Sbjct: 149 CLMQISTRTEDFIIDTLELR---------SDMYILNESLTDPAIVKV 186
>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 = 41.2 bits (96), Expect = 2e-04
Identities = 21/104 (20%), Positives = 32/104 (30%), Gaps = 26/104 (25%)
Query: 71 EEY-------YSLTLPPNSIILVDTADKFASALQDFARLDHNSH----LGLD-TEWKPNL 118
++Y Y T L+ + A L + R ++ GL+ EW L
Sbjct: 167 DDYFEELRDLYQ-TYHVLVGDLIKFS---AETLSELIRTTLDAEKVFTQGLNILEW---L 219
Query: 119 SGGS--PPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLEL 160
S P LL I +I + +L Y L
Sbjct: 220 ENPSNTPDKDYLLSIP-----ISCPLIGVIQLAHYVVTAKLLGF 258
Score = 34.3 bits (78), Expect = 0.033
Identities = 21/135 (15%), Positives = 35/135 (25%), Gaps = 46/135 (34%)
Query: 3 LDIVKDNPELQKELIDLCVQYYDCK--EAYYWCQKFKLNPNCVGFDLRDKIAEEESEQDV 60
LDIV +NP L + E Y G +KI +E +E
Sbjct: 1662 LDIVINNP---VNLTIHFGGEKGKRIRENY---SAMIFETIVDGKLKTEKIFKEINEHST 1715
Query: 61 DNGWDVCKPAEEYYSLTLPPNS---IILVDTA--------------DKFA-------SAL 96
+ L+ + + L++ A FA +AL
Sbjct: 1716 SYTFR--SEKGL---LSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAAL 1770
Query: 97 ---------QDFARL 102
+ +
Sbjct: 1771 ASLADVMSIESLVEV 1785
Score = 30.0 bits (67), Expect = 0.71
Identities = 15/84 (17%), Positives = 28/84 (33%), Gaps = 23/84 (27%)
Query: 77 TLPPNSIILVDTADKFASALQDFARLD---HNSHLGL---DTE-WKPNLSGGSPP-TLAL 128
P +S +LV +D +D + + + + + DT +L S + +
Sbjct: 424 ASPFHSHLLVPASDLI---NKDLVKNNVSFNAKDIQIPVYDTFDGS-DLRVLSGSISERI 479
Query: 129 LQIATRDRVY-----------ILD 141
+ R V ILD
Sbjct: 480 VDCIIRLPVKWETTTQFKATHILD 503
Score = 27.7 bits (61), Expect = 4.0
Identities = 21/134 (15%), Positives = 39/134 (29%), Gaps = 56/134 (41%)
Query: 11 ELQ----------KELID--------LCVQYYDCKEAYYWCQKFKLNPNCVGFDLRDKIA 52
EL+ +LI L D ++ + G ++ + +
Sbjct: 172 ELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQ-----------GLNILEWLE 220
Query: 53 EEESEQDVDNGWDVCKPAEEYYSLTLPPNS---IILVDTADKFASALQDFARLDHNSHLG 109
+ P ++Y L P S I ++ A + A+L LG
Sbjct: 221 NPSN-----------TPDKDY--LLSIPISCPLIGVIQLA-HYVV----TAKL-----LG 257
Query: 110 LDT-EWKPNLSGGS 122
E + L G +
Sbjct: 258 FTPGELRSYLKGAT 271
>1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase,
tRNA processing, hydrolase,translation; 1.60A
{Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5
Length = 375
Score = 39.3 bits (92), Expect = 6e-04
Identities = 14/91 (15%), Positives = 34/91 (37%), Gaps = 15/91 (16%)
Query: 82 SIILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGS-PPTLALLQIATRDRVYIL 140
+ ++ T D AS + + LDTE+ + + P L L+Q+ + + ++
Sbjct: 2 NYQMITTDDALASLC---EAVRAFPAIALDTEF---VRTRTYYPQLGLIQLFDGEHLALI 55
Query: 141 DIITLSKLPCYAQLCHDLELIVFANDDLLKI 171
D + ++ + + + K
Sbjct: 56 DPLGITDWSPLKAI--------LRDPSITKF 78
>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown
function; 2.10A {Bifidobacterium adolescentis atcc
1570ORGANISM_TAXID}
Length = 440
Score = 38.7 bits (90), Expect = 9e-04
Identities = 21/105 (20%), Positives = 32/105 (30%), Gaps = 14/105 (13%)
Query: 70 AEEYYSLTLPPNSI-ILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGS-PPTLA 127
+E L P + ++DT F + A + L D E SG
Sbjct: 4 TDEPKLLAEPREGVPNVIDTLPAFRDYCSELAS--SHGSLAADAER---ASGFRYGHEDW 58
Query: 128 LLQIATRDR-VYILDIITLSKLPCYAQLCHDLELIVFANDDLLKI 171
L+Q + +LD L+ D A D + I
Sbjct: 59 LVQFKRDGAGIGLLDPQALA------AAGADWNDFNRAVGDAVWI 97
>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 = 0.48
Identities = 8/32 (25%), Positives = 13/32 (40%), Gaps = 9/32 (28%)
Query: 97 QDFARLDHNSHLGLDTEWKPNLSGGSPPTLAL 128
Q +L + L L + + S P LA+
Sbjct: 20 QALKKLQ--ASLKL---YADD----SAPALAI 42
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 0.137 0.423
Gapped
Lambda K H
0.267 0.0610 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,430,579
Number of extensions: 198379
Number of successful extensions: 416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 413
Number of HSP's successfully gapped: 18
Length of query: 220
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 130
Effective length of database: 4,188,903
Effective search space: 544557390
Effective search space used: 544557390
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: 55 (25.2 bits)