RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2224
(504 letters)
>3ho1_A Argonaute; argonaute, protein-DNA-RNA complex, nucleic acid binding
Pro RNA complex; 2.60A {Thermus thermophilus} PDB:
3dlb_A* 3dlh_A* 3f73_A* 3hm9_A 3hvr_A 3hxm_A* 3hk2_A
3hjf_A
Length = 685
Score = 288 bits (738), Expect = 6e-90
Identities = 65/557 (11%), Positives = 135/557 (24%), Gaps = 102/557 (18%)
Query: 2 PTWTLNLYRIDFNPPEDIMGVKRGLLRDHKDKIGAYVFDGTMMFTPNTI-IGKEMKLMSK 60
+ +PP V L + + G V G + + + + +++
Sbjct: 22 EELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLAR 81
Query: 61 KRDETPVELTIRHVRVLEYGDAQYTQLFNILIRQTLRALDLKLLGR--NYFDPAAKEDIP 118
L + R L+ D + + L R+ L+ +L G +E
Sbjct: 82 MGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHAR 141
Query: 119 QYRLEVWPGWDTSMRQ-MENDIMLCVELSHKVLRKETVLDAWEQCRNDKYFYYRKFEAQM 177
V G + +L V+ ++++L + ++ Q
Sbjct: 142 GPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPL------------ 189
Query: 178 TNSIVLTKYNNKTYRVDDIQYDVTPCSTFPMKGENVSYIDYYQKKYNETIRNRNQPMIVH 237
V Y+ +T+ + + P+ +S +DY+ K R + V
Sbjct: 190 -PKRVRNAYDRRTWELLRL--GEEDPKELPL-PGGLSLLDYHASKGRLQGREGGRVAWVA 245
Query: 238 KSKLRELRAGQSEIIYLVPELCYLTGLSDDMRADFRLMKPLGEITRVRPRERVAKFNVFR 297
K I +L L + L D + L + ER
Sbjct: 246 DPKDPRKP-----IPHLTGLLVPVLTLEDLHEEEGSLA------LSLPWEERR------- 287
Query: 298 KRIENSEAKEVLKRWELALDTNLARVQGHILPPDSIIFSDPLKPFPVGPDANWTTPTRSS 357
R A + +R L + R Q + L ++ +
Sbjct: 288 -RRTREIASWIGRRLGLGTPEAV-RAQAYRLSIPKLMGRRA---------VSKPADALRV 336
Query: 358 VFRAPNLERWCVLTTGFMMADTENFLQLINKAAQGMRFKVNRPNVI-------------- 403
F +L E + + +A + +
Sbjct: 337 GFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALR 396
Query: 404 ------------------------VKKNLASKGALT-------------IATKVAIQLCC 426
+K L +G + + L
Sbjct: 397 KAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLA 456
Query: 427 KIGGAPWSVAVPLKGLMVLGFDVTHDSDLKGSSYGALVASIDPQMSSWFSRVSPHRSGNE 486
K G +++ + +GFD + V +
Sbjct: 457 KAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEA--QAGERI 514
Query: 487 LSNDIAVSVVHALHKYR 503
+ + L +R
Sbjct: 515 PQEVVWDLLEETLWAFR 531
>4f3t_A Protein argonaute-2; hydrolase/gene regulation, RNAI, slicer,
hydrolase-RNA; 2.25A {Homo sapiens} PDB: 4ei1_A 4ei3_A*
1r4k_A 1si2_A 1si3_A
Length = 861
Score = 234 bits (597), Expect = 2e-68
Identities = 91/616 (14%), Positives = 195/616 (31%), Gaps = 123/616 (19%)
Query: 1 MPTWTLNLYRIDFNPPEDIMGVKRGLLRDHKDKIGA-------YVFDG-TMMFTPNTIIG 52
+P + Y +D P + V R ++ VFDG ++T +
Sbjct: 51 IPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPI 110
Query: 53 KEMKL-----MSKKRDETPVELTIRHVRVL-------------EYGDAQYTQLFNILIRQ 94
K+ + + + +++I+ V + + Q ++++R
Sbjct: 111 GRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRH 170
Query: 95 TLRALDLKLLGRNYFDPAAKEDIP-QYRLEVWPGWDTSMRQMENDIMLCVELSHKVLRKE 153
L ++ +GR++F + P EVW G+ S+R +ML +++S K
Sbjct: 171 -LPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKA 229
Query: 154 -TVLDAWEQCRNDKY----------FYYRKFEAQMTNSIVLTKYN---NKTYRVDDIQYD 199
V++ + + K KF ++ V + + YRV ++
Sbjct: 230 QPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRR 289
Query: 200 VTPCSTFPMK-----GENVSYIDYYQKKYNETIRNRNQPMIVHKSKLRELRAGQSEIIYL 254
TFP++ + Y++ ++ +R + P + + + E+ +
Sbjct: 290 PASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPL-EVCNI 348
Query: 255 VPELCYLTGLSDDMRADFRLMKPLGEITRVRPRERVAKFNVFRKRIENSEAKEVLKRWEL 314
V + L+D+ + T +R + + + + ++ + +
Sbjct: 349 VAGQRCIKKLTDNQTSTMIRA------TARSAPDRQEEISKLMRSA-SFNTDPYVREFGI 401
Query: 315 ALDTNLARVQGHILPPDSIIFSDPLKPFPVGPDANWTTPTRSSVFRAPNLERWCVLTTGF 374
+ + V G +L P SI++ K W ++ W +
Sbjct: 402 MVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDM-RNKQFHTGIEIKVWAIACFAP 460
Query: 375 M----MADTENFLQLINKAAQGMRFKVNRPNVI--------------------------- 403
++F + + K ++ +
Sbjct: 461 QRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLV 520
Query: 404 -------------VKK-----------NLASKGALTIATKVAIQLCCKI----GGAPWSV 435
VK+ + K + LC KI GG +
Sbjct: 521 VVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNIL 580
Query: 436 A------VPLKGLMVLGFDVTHDS--DLKGSSYGALVASIDPQMSSWFSRVSPHRSGNEL 487
V + ++ LG DVTH D K S A+V S+D + + + V + E+
Sbjct: 581 LPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEI 640
Query: 488 SNDIAVSVVHALHKYR 503
D+A V L ++
Sbjct: 641 IQDLAAMVRELLIQFY 656
>1yvu_A Hypothetical protein AQ_1447; RNAse H fold, RNA binding protein,
gene regulation; 2.90A {Aquifex aeolicus} SCOP:
b.34.14.1 c.55.3.10 PDB: 2f8s_A 2f8t_A 2nub_A
Length = 706
Score = 213 bits (542), Expect = 2e-61
Identities = 79/575 (13%), Positives = 181/575 (31%), Gaps = 99/575 (17%)
Query: 6 LNLYRIDFNPPEDIMGVKRGLLRDHKDKIGAYVFDGTMMFTPNTIIGKEMKLMSKKRDET 65
LNLYRI++ P + V + K+K+ + + T ++ + K ++
Sbjct: 7 LNLYRIEYRPKDTTFTVFKPTHEIQKEKLNKVRWRVFLQTGLPTFRREDEFWCAGKVEKD 66
Query: 66 PVELTIRHVRVLEY---GDAQYTQLFNILIRQTLRALDLKLLGRNYFDPAAKEDIPQYRL 122
+ LT+ + ++E G+ ++ N + + L R++ +D ++
Sbjct: 67 TLYLTLSNGEIVELKRVGEEEFRGFQNER--------ECQELFRDFLTKTKVKD--KFIS 116
Query: 123 EVWPGW--DTSMRQMENDIMLCVELSHKVLRKETVLDAWEQCRNDKYFYYRKFEAQMTNS 180
+ + + +++ I L E++ KVL+ E D F + FE +
Sbjct: 117 DFYKKFRDKITVQGKNRKIALIPEVNEKVLKSEEGYFLLHL---DLKFRIQPFE-TLQTL 172
Query: 181 IVLTKYNNKTYRVD--DIQYDVTPCSTFPMKGENVSYI-DYYQKKYNETIRNRNQPMIVH 237
+ +N K RV I + F K + + ++ +++ + + ++ +
Sbjct: 173 LERNDFNPKRIRVKPIGIDFVGRVQDVFKAKEKGEEFFRLCMERSTHKSSKKAWEELLKN 232
Query: 238 KSKLRELRAGQSEIIYLVPELCYLTGLSDDMRADFRLMKPLGEITRVRPRERVAKFNVFR 297
+ + E Y P L+ + D + +I R+ P +R+
Sbjct: 233 RELREKAFLVVLEKGYTYPATILKPVLTYENLEDEE-RNEVADIVRMEPGKRLNLIRYIL 291
Query: 298 KRIENSEAKEVLKRWELALDTNLARVQGHILPPDSIIFSDPLKPFPVGPDANWTTPTRSS 357
+R + L+ + + R +G + D+++ + K V +
Sbjct: 292 RR-----YVKALRDYGWYISPEEERAKGKLNFKDTVLDAKG-KNTKVITNLRKFLELC-R 344
Query: 358 VFRAPNLERWCVLTTGFM---MADTENFLQLINKAAQGMRFKVNRPNVI----------- 403
F ++ +++ E FL+ + + K+
Sbjct: 345 PFVKKDVLSVEIISVSVYKKLEWRKEEFLKELINFLKNKGIKLKIKGKSLILAQTREEAK 404
Query: 404 -------------------------------------VKKNLASKGALT----------- 415
VK+ L K +
Sbjct: 405 EKLIPVINKIKDVDLVIVFLEEYPKVDPYKSFLLYDFVKRELLKKMIPSQVILNRTLKNE 464
Query: 416 ----IATKVAIQLCCKIGGAPWSVA-VPLKGLMVLGFDVTHDSDLKGS-SYGALVASIDP 469
+ VA Q+ K G P+ + + K +G D++ + + + A +
Sbjct: 465 NLKFVLLNVAEQVLAKTGNIPYKLKEIEGKVDAFVGIDISRITRDGKTVNAVAFTKIFNS 524
Query: 470 Q-MSSWFSRVSPHRSGNELSNDIAVSVVHALHKYR 503
+ + S G +L+ V L K
Sbjct: 525 KGELVRYYLTSYPAFGEKLTEKAIGDVFSLLEKLG 559
>1u04_A Argonaute, hypothetical protein PF0537; RNAI, silencing, PIWI, PAZ,
RISC, slicer, RNAse H hydrolase-gene regulation complex;
2.25A {Pyrococcus furiosus} SCOP: b.34.14.1 c.55.3.10
PDB: 1z25_A 1z26_A
Length = 771
Score = 202 bits (515), Expect = 2e-57
Identities = 56/425 (13%), Positives = 136/425 (32%), Gaps = 44/425 (10%)
Query: 4 WTLNLYRIDFNPPEDIMGVKRGLLRDHKDKIGAYVFDGTMMFTPNTIIGKEMKLMSKKRD 63
+ +YR+ +P E++ + R + +G + ++ + + K
Sbjct: 20 DKIYVYRLFNDPEEELQKEGYSIYRLAYENVGIVIDPENLI------------IATTKEL 67
Query: 64 ETPVELT-IRHVRVLEYGDAQYTQLF-NILIRQTLRALDLKLLGRNYFDPAAKEDIPQYR 121
E E + E + ++L +L + +L L R + P
Sbjct: 68 EYEGEFIPEGEISFSELRNDYQSKLVLRLLKENGIGEYELSKLLRKFRKPKTFG-----D 122
Query: 122 LEVWPGWDTSMRQMENDIMLCVELSHKVLRKETVLDAWEQCRNDKYFYYRKFEAQMTNSI 181
+V P + S+ + + D L + + H++ +T+ + + + +F ++
Sbjct: 123 YKVIPSVEMSVIKHDEDFYLVIHIIHQIQSMKTLWELVNKDPKE----LEEFLMTHKENL 178
Query: 182 VLTKYNNKTYRVDDIQYDVTPCSTFPMK-------GENVSYIDYYQKKY-------NETI 227
+L + V ++ N Y+
Sbjct: 179 MLKDIASPLKTVYKPCFEEYTKKPKLDHNQEIVKYWYNYHIERYWNTPEAKLEFYRKFGQ 238
Query: 228 RNRNQPMIVHKSKLRELRAGQSEIIYLVPELCYLTGLSDDMRADFRLMKPLGEITRVRPR 287
+ QP I+ K +++ ++ IYL+P+L T + + + + K + E T++ P
Sbjct: 239 VDLKQPAILAKFA-SKIKKNKNYKIYLLPQLVVPTYNA--EQLESDVAKEILEYTKLMPE 295
Query: 288 ERVAKFNVFRKRI---ENSEAKEVLKRWELALDTNLARVQGHILPPDSIIFSDPLKPFPV 344
ER + ++ ++ ++A + I ++ +
Sbjct: 296 ERKELLENILAEVDSDIIDKSLSEIEVEKIAQELENKIRVRDDKGNSVPISQLNVQKSQL 355
Query: 345 GPDANWTTPTRSSV-FRAPNLERWCVLTTGFMMADTENFLQLINKAAQGMRFKVNRPNVI 403
N++ + + P R F++ D+ + N A R V
Sbjct: 356 LLWTNYSRKYPVILPYEVPEKFRKIREIPMFIILDSGLLADIQNFATNEFRELVKSMYYS 415
Query: 404 VKKNL 408
+ K
Sbjct: 416 LAKKY 420
Score = 82.2 bits (202), Expect = 1e-16
Identities = 14/100 (14%), Positives = 34/100 (34%), Gaps = 3/100 (3%)
Query: 405 KKNLASKGALTIATKVAIQLCCKIGGAPWSVAVPLKGLMVLGFDVTHDSDLKGSSYG-AL 463
K ++ L + + Q+ K+G + + ++G DV +G G A+
Sbjct: 516 DKYDRNRLDLFVRHNLLFQVLSKLGVKYYVLDYRFNYDYIIGIDVAPMKRSEGYIGGSAV 575
Query: 464 VASIDPQMSSWFSRVSPHRSGNELSNDIAVSVVHALHKYR 503
+ + + G + D+ + K++
Sbjct: 576 MFDSQGYIRKIVPIKIGEQRGESV--DMNEFFKEMVDKFK 613
>3qir_A PIWI-like protein 2; structural genomics consortium, SGC, PAZ
domain, RNAI, RNA B RNA binding protein; 2.45A {Homo
sapiens} PDB: 3o7x_A
Length = 148
Score = 153 bits (388), Expect = 8e-45
Identities = 46/146 (31%), Positives = 86/146 (58%), Gaps = 4/146 (2%)
Query: 151 RKETVLDAWEQC-RNDKYFYYRKFEAQMTNSIVLTKYNNKTYRVDDIQYDVTPCSTFPMK 209
R + VLD + +K + + + +IV+T+YNN+TYR+DD+ ++ TP +F M
Sbjct: 1 RNDCVLDVMHAIYQQNKEHFQDECTKLLVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMS 60
Query: 210 -GENVSYIDYYQKKYNETIRNRNQPMIVHKSKLRELRAG--QSEIIYLVPELCYLTGLSD 266
G+ +++++YY K Y T++ +QP+++H+ R+ G I L+PEL ++TG+ +
Sbjct: 61 DGKEITFLEYYSKNYGITVKEEDQPLLIHRPSERQDNHGMLLKGEILLLPELSFMTGIPE 120
Query: 267 DMRADFRLMKPLGEITRVRPRERVAK 292
M+ DFR MK L + + P++ +
Sbjct: 121 KMKKDFRAMKDLAQQINLSPKQHHSA 146
>2xfm_A MIWI, PIWI-like protein 1; RNA-protein complex, differentiation,
RNA interference; HET: OMU; NMR {Mus musculus}
Length = 150
Score = 150 bits (381), Expect = 7e-44
Identities = 64/150 (42%), Positives = 89/150 (59%), Gaps = 4/150 (2%)
Query: 151 RKETVLDAWEQC--RNDKYFYYRKFEAQMTNSIVLTKYNNKTYRVDDIQYDVTPCSTFPM 208
R ETVLD + +++ + + ++ IVLTKYNNKTYRVDDI +D P STF
Sbjct: 1 RSETVLDFMFNLYQQTEEHKFQEQVSKELIGLIVLTKYNNKTYRVDDIDWDQNPKSTFKK 60
Query: 209 K-GENVSYIDYYQKKYNETIRNRNQPMIVHKSKLRELRAG-QSEIIYLVPELCYLTGLSD 266
G VS+++YY+K+YN+ I + QP++V + K R G L+PELCYLTGL+D
Sbjct: 61 ADGSEVSFLEYYRKQYNQEITDLKQPVLVSQPKRRRGPGGTLPGPAMLIPELCYLTGLTD 120
Query: 267 DMRADFRLMKPLGEITRVRPRERVAKFNVF 296
MR DF +MK L TR+ P +R +
Sbjct: 121 KMRNDFNVMKDLAVHTRLTPEQRQREVGRL 150
>3o7v_X PIWI-like protein 1; PIWI, RNA silencing, PI-RNA, HIWI1, HILI, PAZ
domain, RNA BI protein; HET: OMU; 2.10A {Homo sapiens}
PDB: 2l5c_A 2l5d_A 3o3i_X 3o6e_X*
Length = 124
Score = 138 bits (348), Expect = 2e-39
Identities = 55/123 (44%), Positives = 76/123 (61%), Gaps = 4/123 (3%)
Query: 153 ETVLDAWEQC--RNDKYFYYRKFEAQMTNSIVLTKYNNKTYRVDDIQYDVTPCSTFPMK- 209
ETVLD + +++ + + ++ +VLTKYNNKTYRVDDI +D P STF
Sbjct: 2 ETVLDFMFNFYHQTEEHKFQEQVSKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKAD 61
Query: 210 GENVSYIDYYQKKYNETIRNRNQPMIVHKSKLRELRAG-QSEIIYLVPELCYLTGLSDDM 268
G VS+++YY+K+YN+ I + QPM+V + K R G L+PELCYLTGL+D M
Sbjct: 62 GSEVSFLEYYRKQYNQEITDLKQPMLVSQPKRRRGPGGTLPGPAMLIPELCYLTGLTDKM 121
Query: 269 RAD 271
R D
Sbjct: 122 RND 124
>4f1n_A Kpago; argonaute, RNAI, RNAse H, RNA binding protein-RNA complex;
3.19A {Vanderwaltozyma polyspora}
Length = 1046
Score = 105 bits (263), Expect = 3e-24
Identities = 36/352 (10%), Positives = 98/352 (27%), Gaps = 36/352 (10%)
Query: 79 YGDAQYTQLFNILIRQTLRALDLKLLGRNYFDPAAKEDIPQYRLEVWPGWDTSMRQMEND 138
+Y L + + +Y + P +
Sbjct: 288 IKHTKYLPGDPRFKNNEKEQFTLMDWIIECYHQSKAIRDIRYNPKTAPPPSVKDLNYFVE 347
Query: 139 IMLCVELSHKVLRKETVLDAWEQCRNDKYFYYRKFEAQMTNSIVLTKYNNKTYRVDDIQY 198
+ K L+ + ++ RK + T+ + + R + ++
Sbjct: 348 KNTDISALLKGLKVYRPYINYSINKDGTPKPPRKR--SSKGIVGFTRESAVSMRFNVLES 405
Query: 199 DVTPCSTFPM--KGENVSYIDYYQKKYNETIRNRNQPMIVHKSKLRELRAGQSEIIYLVP 256
+ S K N++ IDY+++KY+ T++ + ++ K + P
Sbjct: 406 SLKKNSAPKPNEKPININTIDYFKRKYDITLKYPDMKLVNLGGK----------NDVVPP 455
Query: 257 ELCYLTGLSDDMRADFRLMKPLGEITRVRPRERVAKFNVFRKRI---ENSEAKEVLKRWE 313
E + ++ K + + +RP E+ + +++++
Sbjct: 456 ECLTIVPGQ-KLKGQIFDTKTYIDFSAIRPTEKFDLISRLSMPAIKRGLTDSEKEESSAP 514
Query: 314 LALDTNLARVQGHILPPDSIIFSDPLKPFPVGPDANWTTPTRSS-------VFRAPNLER 366
RV IL + F + + ++ + P +
Sbjct: 515 HNSAYQFMRVPSRILDAPVVQFKESTFEYKDKSYGTKHEESKGNWNMKGHQFISTPAKQV 574
Query: 367 WCVL---------TTGFMMADTENFLQLINKAAQ--GMRFKVNRPNVIVKKN 407
M ++ + + + G+ F V+ +++ +
Sbjct: 575 NLRAIFINNANTAPPASMESELDISMDKFASDVKQLGVDFNVSGKPILINQF 626
Score = 75.9 bits (185), Expect = 1e-14
Identities = 24/113 (21%), Positives = 50/113 (44%), Gaps = 12/113 (10%)
Query: 402 VIVKKNLASKGALTIATKVAIQLCCKIGGAPWSVAVPLKGL----------MVLGFDVTH 451
+V N K ++ + V +++ K+ G+ S+++ L +VLG DVTH
Sbjct: 714 CVVWDNF-KKNSIQYNSNVVMKMNLKLLGSNHSLSIENNKLLIDKESNLPILVLGSDVTH 772
Query: 452 DSDLKGSSYGALVASIDPQMSSWFSRVSPHRS-GNELSNDIAVSVVHALHKYR 503
+ +S +LV S D + + + G E+ ++ +++ L Y+
Sbjct: 773 YPEKDQNSIASLVGSYDDKFTQFPGDYMLQDGPGEEIITNVGSLMLNRLKIYQ 825
>2w42_A PIWI, putative uncharacterized protein; RNAI, RISC, argonaute, PIWI
domain, protein/DNA complex; 1.90A {Archaeoglobus
fulgidus} PDB: 1ytu_A 2bgg_A 1w9h_A
Length = 427
Score = 86.3 bits (213), Expect = 2e-18
Identities = 13/104 (12%), Positives = 40/104 (38%), Gaps = 5/104 (4%)
Query: 402 VIVKKNLASKGALTIATKVAIQLCCKIGGAPWSVAV--PLKGLMVLGFDVTHDSDLKGSS 459
+ L+++ + +Q K+GG PW + V +++G T ++
Sbjct: 138 FMRYDILSNRNLTFYVDNLLVQFVSKLGGKPWILNVDPEKGSDIIIGTGATRIDNVNLFC 197
Query: 460 YGALVASIDPQMSSWFSRVSPHRSGNELSNDIAVSVVHALHKYR 503
+ + ++ +SP + +E + ++ ++ ++
Sbjct: 198 F---AMVFKKDGTMLWNEISPIVTSSEYLTYLKSTIKKVVYGFK 238
>2yha_A Post-transcriptional gene silencing protein QDE-2; RNA binding
protein, argonaute, miRNA, siRNA; HET: GOL; 1.85A
{Neurospora crassa} PDB: 2xdy_A
Length = 388
Score = 71.3 bits (174), Expect = 1e-13
Identities = 30/115 (26%), Positives = 52/115 (45%), Gaps = 13/115 (11%)
Query: 402 VIVKKNLASKGALTIATKVAIQLCCKIGGAPWSVAVPLKGL-----MVLGFDVTHDSDL- 455
+ +K L++KG L V +++ K GG ++ P+ L MV+G+DVTH ++L
Sbjct: 112 CVAEKFLSTKGQLGYFANVGLKVNLKFGGTNHNIKTPIPLLAKGKTMVVGYDVTHPTNLA 171
Query: 456 ------KGSSYGALVASIDPQMSSWFSRVSPHRSGNE-LSNDIAVSVVHALHKYR 503
S LV++ID + W + V + G E ++ L +R
Sbjct: 172 AGQSPASAPSIVGLVSTIDQHLGQWPAMVWNNPHGQESMTEQFTDKFKTRLELWR 226
>2yhb_A QDE-2, post-transcriptional gene silencing protein QDE-2; RNA
binding protein, argonaute, miRNA, siRNA; 3.65A
{Neurospora crassa}
Length = 437
Score = 69.4 bits (169), Expect = 7e-13
Identities = 30/115 (26%), Positives = 50/115 (43%), Gaps = 13/115 (11%)
Query: 402 VIVKKNLASKGALTIATKVAIQLCCKIGGAPWSVAVPLKGL-----MVLGFDVTH----- 451
+ +K L++KG L V +++ K GG ++ P+ L MV+G+DVTH
Sbjct: 112 CVAEKFLSTKGQLGYFANVGLKVNLKFGGTNHNIKTPIPLLAKGKTMVVGYDVTHPTNLA 171
Query: 452 --DSDLKGSSYGALVASIDPQMSSWFSRVSPHRSGNE-LSNDIAVSVVHALHKYR 503
S S LV++ID + W + V + G E ++ L +R
Sbjct: 172 AGQSPASAPSIVGLVSTIDQHLGQWPAMVWNNPHGQESMTEQFTDKFKTRLELWR 226
>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 = 49.5 bits (117), Expect = 3e-06
Identities = 61/419 (14%), Positives = 113/419 (26%), Gaps = 118/419 (28%)
Query: 4 WTLNLYRID----------FNPP---EDIMGVKRGLLRDHKDKIGAYVFDGTMMFTPNTI 50
L LY+ID N I R LL+ + V +
Sbjct: 203 QKL-LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN--VQNAKAW 259
Query: 51 IGKEMKLMSKKRDETPVELTIRHVRVLEYGDAQ-YTQLFNILIRQTL---RALDL--KLL 104
L K + LT R +V ++ A T + TL L K L
Sbjct: 260 --NAFNLSCK------ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL 311
Query: 105 GRNYFD--PAAKEDIPQY------RLEVWPG-WDTSMRQMEND-----IMLCVE-LSHKV 149
D P+ + WD + + D I + L
Sbjct: 312 DCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNW-KHVNCDKLTTIIESSLNVLEPAE 370
Query: 150 LRK---------------ETVLDA-WEQCRNDKYFYYRKFEAQMTNSIVLTKYNNK-TYR 192
RK +L W + ++ ++ K + T
Sbjct: 371 YRKMFDRLSVFPPSAHIPTILLSLIWF---DVIKSDVMVVVNKLHKYSLVEKQPKESTIS 427
Query: 193 VDDIQYDVTPCSTFPMKGENVSY-----IDYYQ--KKY--NETIRNRNQPMIV-----HK 238
+ I ++ +K EN +D+Y K + ++ I H
Sbjct: 428 IPSIYLELK------VKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHH- 480
Query: 239 SKLRELRAGQSEIIYLVPELCYLTGLSDDMRADFRLMK------PLGEITRVRPRERVAK 292
L+ E + L + +L DFR ++ + +
Sbjct: 481 --LKN--IEHPERMTLFRMV-FL---------DFRFLEQKIRHDSTAWNASGSILNTLQQ 526
Query: 293 FNVFRKRIENSEAK-----EVLKRWELALDTNLAR------VQGHILPPDSIIFSDPLK 340
++ I +++ K + + ++ NL ++ ++ D IF + K
Sbjct: 527 LKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHK 585
Score = 49.1 bits (116), Expect = 3e-06
Identities = 44/350 (12%), Positives = 105/350 (30%), Gaps = 102/350 (29%)
Query: 129 DTSMRQME---NDIML-----------C---VELSHKVLRKETVLDAWEQCRNDKYFYYR 171
D + + DI+ C ++ +L KE + ++ R
Sbjct: 8 DFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMS-KDAVSGTLR 66
Query: 172 KFEAQMTNSIVLTKYNNKTYR----VDDIQYD--VTPCSTFPMK--GENVSYIDYYQKKY 223
F +L+K + V I Y ++P T + YI+ + Y
Sbjct: 67 LFW------TLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY 120
Query: 224 NETIR------NRNQPMIVHKSKLRELRAGQSEIIY---------LVPELC--------- 259
N+ +R QP + + L ELR ++ +I + ++C
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKM 180
Query: 260 -----YLT-GLSDDMRADFRLMKPLGEITRVRPRERVAKFNVFRKRIENSEAKEVLKRWE 313
+L + +++ L + ++ P + ++ + L+R
Sbjct: 181 DFKIFWLNLKNCNSPETVLEMLQKL--LYQIDPNWTSRSDHSSNIKLRIHSIQAELRR-- 236
Query: 314 LALDTNLARVQGH-----ILPPDSIIFSDP--LKPFPVGPDANWTT--PTR-SSVFRAPN 363
L + + + +L ++ + F + + TR V +
Sbjct: 237 ------LLKSKPYENCLLVL--LNV--QNAKAWNAF----NLSCKILLTTRFKQVTDFLS 282
Query: 364 LERWCVLT-----TGFMMADTEN-FLQLINKAAQGMRFKVNRPNVIVKKN 407
++ + ++ L+ ++ Q + P ++ N
Sbjct: 283 AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL------PREVLTTN 326
Score = 30.6 bits (68), Expect = 1.4
Identities = 37/266 (13%), Positives = 73/266 (27%), Gaps = 77/266 (28%)
Query: 6 LNLYRIDFNPPEDIMGVKRGLLRDHKDKIGAYVF-DGTMMFTPNTIIGK----------- 53
N+ R + + +++ LL + + V DG + GK
Sbjct: 129 YNVSR-----LQPYLKLRQALL---ELRPAKNVLIDG--VLG----SGKTWVALDVCLSY 174
Query: 54 --EMKL------MSKKRDETPVELTIRHVRVLEYGDAQYTQLFNILIRQTLRALDLKLLG 105
+ K+ ++ K +P + ++L D +T + LR ++
Sbjct: 175 KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234
Query: 106 RNYFDPAAKEDIPQYRL---EVWPGWDTSMRQMENDIMLCVELSHKVL---RKETVLDAW 159
R + L V C K+L R + V D
Sbjct: 235 RRLL---KSKPYENCLLVLLNVQNAKA--WNAFNLS---C-----KILLTTRFKQVTDFL 281
Query: 160 EQCRNDKYFYYRKFEAQMTNSIVLTKYNNKTY--RVDDIQYDVTP---CSTFP------- 207
+ +S+ LT K+ + D + P +T P
Sbjct: 282 S-------AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIA 334
Query: 208 -MKGENVSYIDYYQ----KKYNETIR 228
+ ++ D ++ K I
Sbjct: 335 ESIRDGLATWDNWKHVNCDKLTTIIE 360
>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase;
3.00A {Giardia intestinalis} PDB: 2ffl_A
Length = 756
Score = 48.4 bits (115), Expect = 4e-06
Identities = 26/115 (22%), Positives = 44/115 (38%), Gaps = 11/115 (9%)
Query: 165 DKYFYYRKFEAQMTNSIVLT-KYNNKTYRVDDIQYDVTPCSTFPMKGENVSYIDYYQKKY 223
D+Y Y A + +V T + + Y V I T S F E+++Y+ YY +
Sbjct: 144 DEYTDYSTLSASLHGRMVATPEISWSLYVVLGIDSTQTSLSYFTRANESITYMRYYATAH 203
Query: 224 NETIRNRNQPMIVHKS----------KLRELRAGQSEIIYLVPELCYLTGLSDDM 268
N +R + P++ ++ +L PELC L D+
Sbjct: 204 NIHLRAADLPLVAAVRLDDLKDHQIPAPGSWDDLAPKLRFLPPELCLLLPDEFDL 258
>3mj0_A Protein argonaute-2; argonaut, PAZ domain, 3'-END 2'-O-methylated
ssRNA, RNA-RNA protein complex; HET: OMU; 2.31A
{Drosophila melanogaster} PDB: 1t2r_A 1t2s_A
Length = 124
Score = 37.9 bits (88), Expect = 0.001
Identities = 15/77 (19%), Positives = 28/77 (36%), Gaps = 9/77 (11%)
Query: 185 KYNNKTYRVDDIQYDVTPCSTFPMKGENVSYIDYYQKKYNETIRNRNQPMIVHKSKLREL 244
+ + YRV+ + TF G+ V+ Y+ N ++ + S ++
Sbjct: 49 QSAPRVYRVNGLSRAPASSETFEHDGKKVTIASYF-HSRNYPLKFPQLHCLNVGSSIKS- 106
Query: 245 RAGQSEIIYLVPELCYL 261
I L ELC +
Sbjct: 107 -------ILLPIELCSI 116
>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 = 40.0 bits (93), Expect = 0.002
Identities = 45/246 (18%), Positives = 65/246 (26%), Gaps = 115/246 (46%)
Query: 269 RADFRLMKPLG----EITRVRPRERVAKFNVFR-KRI-ENSEAKEVLKRWELALDTNLAR 322
RAD G +I P F + KRI EN A + +T
Sbjct: 1648 RADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSA--------MIFET---- 1695
Query: 323 VQGHILPPDSIIFSDPLKPFPVGPDANWTTPTRSSVFRAPNLERWCVLTTGFMMADTENF 382
D + ++ + F + S FR+ G + A T+
Sbjct: 1696 ------IVDGKLKTEKI--FK-----EINEHSTSYTFRSEK---------GLLSA-TQF- 1731
Query: 383 LQLINKAAQGMRFKVNRPNVIVKKNLASKGALTIATKVAIQLCCKIGGAPWSVAVPLK-- 440
Q P ALT + A + LK
Sbjct: 1732 -------TQ--------P------------ALT-LMEKAA----------FED---LKSK 1750
Query: 441 GLMVLGFDVTHDSDLKGSS---YGALVASIDPQMSSWFSRVSPHRSGNELSNDIAVSVVH 497
GL + D+ G S Y AL + + V +S + V VV
Sbjct: 1751 GL------IPADATFAGHSLGEYAALAS---------LADV--------MSIESLVEVVF 1787
Query: 498 ALHKYR 503
YR
Sbjct: 1788 ----YR 1789
>1vyn_A Argonaute2; nucleic acid binding, RNA interference; NMR {Drosophila
melanogaster} SCOP: b.34.14.1
Length = 143
Score = 34.5 bits (79), Expect = 0.023
Identities = 15/94 (15%), Positives = 29/94 (30%), Gaps = 16/94 (17%)
Query: 185 KYNNKTYRVDDIQYDVTPCSTFPMKGENVSYIDYYQKKYNETIRNRNQPMIVHKSKLREL 244
+ + YRV+ + TF G+ V+ Y+ + ++ + S ++
Sbjct: 51 QSAPRVYRVNGLSRAPASSETFEHDGKKVTIASYFHSRNY-PLKFPQLHCLNVGSSIKS- 108
Query: 245 RAGQSEIIYLVPELC-------YLTGLSDDMRAD 271
I L ELC A+
Sbjct: 109 -------ILLPIELCSIEEGQALNRKDGATQVAN 135
>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 = 28.8 bits (63), Expect = 2.4
Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 9/25 (36%)
Query: 93 RQTLRALD--LKLLGRNYFD---PA 112
+Q L+ L LKL Y D PA
Sbjct: 19 KQALKKLQASLKL----YADDSAPA 39
>2zgc_A Granzyme M; serine protease, cytolysis, glycoprotein, hydrolase,
secrete zymogen; 1.96A {Homo sapiens} PDB: 2zgh_A 2zks_A
2zgj_A
Length = 240
Score = 28.3 bits (64), Expect = 5.0
Identities = 9/30 (30%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 126 PGWDTSMRQMENDIMLCVELSHKVLRKETV 155
P + + +END+ L ++L KV T+
Sbjct: 75 PRYK-PVPALENDLAL-LQLDGKVKPSRTI 102
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
0.321 0.137 0.415
Gapped
Lambda K H
0.267 0.0519 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,873,289
Number of extensions: 475712
Number of successful extensions: 887
Number of sequences better than 10.0: 1
Number of HSP's gapped: 842
Number of HSP's successfully gapped: 33
Length of query: 504
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 406
Effective length of database: 3,965,535
Effective search space: 1610007210
Effective search space used: 1610007210
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: 59 (27.0 bits)