Query 003516
Match_columns 813
No_of_seqs 163 out of 1062
Neff 7.5
Searched_HMMs 29240
Date Tue Mar 26 17:30:22 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/003516.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_1567-1571//hhsearch_pdb/003516hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 4f3t_A Protein argonaute-2; hy 1.0 1 1 1081.8 69.9 663 121-813 18-693 (861)
2 4f1n_A Kpago; argonaute, RNAI, 1.0 1 1 955.1 52.3 661 122-813 11-863 (1046)
3 1yvu_A Hypothetical protein AQ 1.0 1 1 554.3 27.7 551 146-813 6-586 (706)
4 1u04_A Argonaute, hypothetical 1.0 1 1 518.3 27.5 554 141-813 2-644 (771)
5 3ho1_A Argonaute; argonaute, p 1.0 1 1 444.8 32.0 522 141-796 5-546 (685)
6 2yha_A Post-transcriptional ge 1.0 1 1 399.2 21.2 247 542-813 2-266 (388)
7 2yhb_A QDE-2, post-transcripti 1.0 1 1 394.3 20.6 245 542-813 2-266 (437)
8 2w42_A PIWI, putative uncharac 1.0 1 1 244.3 5.5 249 516-813 5-272 (427)
9 4g0x_A Protein argonaute 1; MI 1.0 1 1 218.6 14.2 145 544-688 2-147 (147)
10 4g0o_A Protein argonaute 5; MI 1.0 1 1 211.6 12.2 138 544-688 2-139 (139)
No 1
>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
Probab=1.00 E-value=1 Score=1081.78 Aligned_cols=663 Identities=38% Similarity=0.669 Sum_probs=583.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEECCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEE
Q ss_conf 88998864678899999999848999557874519986135449992688894799999999999832484589852240
Q 003516 121 FPTSSKSLSFAPRPGYGQVGTKCIVKANHFFAELPDKDLNQYDVTITPEVASRTVNRAIMAELVRLYKESDLGMRLPAYD 200 (813)
Q Consensus 121 ~~~~~~~~~~~~RP~~Gt~G~~v~l~tN~f~i~~~~~~iy~YdV~i~p~v~~k~~~r~i~~~l~~~~~~~~~~~~~~~yD 200 (813)
||.+++.+.+|+||++||.|++|.|+||||++++++..+|||||+|.|+..++++++++++++++.++...|++..++||
T Consensus 18 ~~~~~~~~~~p~RPg~Gt~G~~i~l~aN~F~v~~~~~~ly~Y~V~i~p~~~~~~~~r~i~~~l~~~~~~~~~~~~~~afD 97 (861)
T 4f3t_A 18 PPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFD 97 (861)
T ss_dssp -------CCCCBCCCCCCCSEEEEEEESEEEEECCSCEEEEEEEEEESCSCCHHHHHHHHHHHHHHSCCCCCTTCCCEEC
T ss_pred CCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEECCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEC
T ss_conf 85445456679899789888478999556998778886265037847876767799999999998755665068607875
Q ss_pred CCCEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEEEEEEECHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf 86148974777897406999940577888999976269999999433043669988628999990679999999980233
Q 003516 201 GRKSLYTAGELPFVWKEFKIKLVDELDGINGPKRVREYKVVIKFAARANMHHLGQFLAGKRADAPQEALQILDIVLRELS 280 (813)
Q Consensus 201 G~~~LyS~~~L~~~~~~~~v~l~~~~~~~~~~~~~~~~~V~Ik~~~~i~~~~L~~~l~~~~~~~~~~~~q~Lniilr~~~ 280 (813)
|+++|||+.+||.+....++.+.... ..++++|+|+|++++++++.+|.+|+.|...+.+.+++|+||||+|+.+
T Consensus 98 G~~~l~s~~~L~~~~~~~~~~v~~~~-----~~~~~~~~V~I~~~~~i~l~~L~~~l~g~~~~~~~~~iq~Lniilr~~~ 172 (861)
T 4f3t_A 98 GRKNLYTAMPLPIGRDKVELEVTLPG-----EGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLP 172 (861)
T ss_dssp SSSEEEESSCCSCSSCEEEEECCC------------CEEEEEEEEEEEEHHHHHHHHHTCSSSCCHHHHHHHHHHHHHHH
T ss_pred CCCEEEECCCCCCCCCCEEEEEECCC-----CCCCCEEEEEEEEEEECCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf 86317888767877863699986378-----8987279999999024388999999649987882899999999997622
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCC---CCCC
Q ss_conf 4762467864469999985227997799632122265305625997634432212577399999999289865---8999
Q 003516 281 TKRYCPIGRSFFSPSIRTPQRLGDGLESWCGFYQSIRPTQMGLSLNIDMASAAFIEPLPVIEFVAQLLGKDVL---SRTL 357 (813)
Q Consensus 281 ~~~~~~~Gr~ff~~~~~~~~~l~~g~ei~~G~~~svr~~~~~l~LnID~s~~~F~~~~~lld~i~~~~~~~~~---~r~l 357 (813)
+.++..+||+||++..+...++++|+|+|+||++|||+++++++||+|+++++|+++++|+|+|.++++..+. .+.+
T Consensus 173 ~~~~~~vGR~Ff~~~~~~~~~lg~Gle~w~G~~~Svr~~~~~l~LnvDvs~~~F~~~~~v~d~~~~~~~~~~~~~~~~~~ 252 (861)
T 4f3t_A 173 SMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPL 252 (861)
T ss_dssp HHHSEEETTEEECCC---CCEEETTEEEEEEEEEEEEECSSSEEEEEEEEEEEEECCEEHHHHHHHHHTCSSCC---CCC
T ss_pred CCCCCCCCCCCCCCCCCCEECCCCCEEEEECEEEEEEECCCCCEEEECCCCEEEEECCCHHHHHHHHHCCCCHHHHCCCC
T ss_conf 12464268775589877501168987998450678985178527854143102760770999999986345502203565
Q ss_pred CHHHHHHHHHHHCCCEEEEEECCCCCCEEEEECCCCCCCCCEEEECC-CCC--CEEEHHHHHHHHHCCCCCCCCCCEEEE
Q ss_conf 95789999998539499993259745269994354789988166606-999--266399999988097535899974894
Q 003516 358 SDSDRVKIKKALRGVKVEVTHRGTVRRKYRVSGLTSQPTRELVFPVD-DNS--TMKSVVEYFQEMYGFTIQHTHLPCLQV 434 (813)
Q Consensus 358 ~~~~r~~i~~~Lkgl~V~~~~~~~~~r~yrI~~i~~~~a~~~~F~~~-~~g--~~iSv~~Yf~~~Y~i~Lk~p~lPli~~ 434 (813)
++.++.+++++|+|++|.++|.++.+|.|+|.||++.++.+.+|.++ ++| .++||+|||+++||++|+||+||||++
T Consensus 253 ~~~~~~~~~k~LkGl~V~~t~~~~~~r~yrI~~i~~~pa~~~~F~~~~~~g~~~~iSV~dYFk~kYni~L~~p~lPll~~ 332 (861)
T 4f3t_A 253 TDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQV 332 (861)
T ss_dssp CHHHHHHHHHHHTTCEEEESCC---CCEEEEEEEEEEETTTCEEEEECSSSCEEEEEHHHHHHHHHCCCCSCTTSEEEEE
T ss_pred CHHHHHHHHHHHCCCEEEEEECCCCCCEEEEEECCCCCCCCCEEEEECCCCCCEEEEHHHHHHHHCCCCCCCCCCCEEEE
T ss_conf 77899999998579389983037788659995378899877678765278984168889999875395247999763883
Q ss_pred CCCCCCCEECCCCEEECCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCHHHHHHCCEEECCCCEEEEE
Q ss_conf 67886410033350423774336669999999999993399545699999999841499417774319064475316533
Q 003516 435 GNQKKANYLPMEACKIVEGQRYTKRLNERQITALLKVTCQRPRDRENDILQTVQQNAYDQDLYAKEFGIKISEKLASVEA 514 (813)
Q Consensus 435 ~~~~k~~ylP~Elc~i~~gQr~~~~l~~~~~~~lik~t~~~P~~R~~~I~~~~~~~~~~~~~~l~~fGi~I~~~~~~V~a 514 (813)
|++++.+|||||||.|+|||+++++|+++|+++|+++++..|.+|.+.|.++++.++++.+++|++|||+|+++|++|+|
T Consensus 333 g~~~~~~ylP~Elc~i~~gQ~~~~~Lt~~q~s~mik~~~~~P~~R~~~I~~~~~~l~~~~~~~l~~fGi~i~~~~~~v~g 412 (861)
T 4f3t_A 333 GQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSASFNTDPYVREFGIMVKDEMTDVTG 412 (861)
T ss_dssp SCTTTTEEEEGGGEEECTTCBCCSCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCGGGCHHHHHTTCEECSSCEEEEE
T ss_pred CCCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCHHHHHCCCEEECCEEEEEE
T ss_conf 48888752565668940784455668989999999987549799999999999871689756899779788387568977
Q ss_pred EECCCCEEEECCCCCCCCCCCCCCCCCCCCEEEECCCEECEEEEEEECCC--CCHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 56299816414589743347877632333402314822000299993888--2478999999999999884194137899
Q 003516 515 RILPAPWLKYHENGKEKDCLPQVGQWNMMNKKMINGMTVSRWACINFSRS--VQESVARGFCNELAQMCQVSGMEFNPEP 592 (813)
Q Consensus 515 rvLppP~I~y~~~~~~~~v~p~~g~Wn~~~~kf~~~~~i~~W~~i~~~~~--~~~~~~~~f~~~L~~~~~~~Gi~i~~~p 592 (813)
||||||.|.|+++++ ..+.|.+|+|++++++|+.++.+++|+++++... .++..++.|++.|.+.|+.+||.+..+|
T Consensus 413 RvL~~P~I~y~~~~~-~~~~~~~g~W~~~~~~f~~~~~l~~W~vv~~~~~~~~~~~~~~~f~~~L~~~~~~~G~~i~~~p 491 (861)
T 4f3t_A 413 RVLQPPSILYGGRNK-AIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQP 491 (861)
T ss_dssp EECCCCCEECCSSSC-CEECCBTTBCCCTTCCCTBCCCBCCEEEEECSCTTTSCHHHHHHHHHHHHHHHHHHTCCBCSCC
T ss_pred EEECCCEEEECCCCC-CCCCCCCCCEECCCCEECCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 982586488568764-3337887851356988702754440599984575444589999999999999850786547997
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHH
Q ss_conf 30223799348999999999986201379972499999328998501225565420037024644213214468779999
Q 003516 593 VIPIHNARPDQVEKALKHVYHSSMSKTKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHVFKISKQYLAN 672 (813)
Q Consensus 593 ~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~liivIlp~~~~~~Y~~iK~~~e~~~GI~TQci~~~t~~K~~~q~~~N 672 (813)
.+.......+.++..++.+.+. ..+++|+|||+|++ .++|+.||++||+++||+||||+.+++.|.++||+.|
T Consensus 492 ~~~~~~~~~~~~~~~~~~l~~~------~~~~qlvl~Ilp~~-~~~Y~~IK~~~~~~~gI~TQcv~~~~~~k~~~q~~~n 564 (861)
T 4f3t_A 492 CFCKYAQGADSVEPMFRHLKNT------YAGLQLVVVILPGK-TPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSN 564 (861)
T ss_dssp SEEEECCSSSSHHHHHHHHHHH------STTCCEEEEEESSS-CTHHHHHHHHHHHTSCCEEEEEETHHHHSCCHHHHHH
T ss_pred EEEEECCCHHHHHHHHHHHHHH------CCCCCEEEEEECCC-CCHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHH
T ss_conf 3777258457899999999852------68983899995898-4289999997430678422899721225556789999
Q ss_pred HHHHHHHHCCCCCCEECCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCCCEEEEEECCCCEEH
Q ss_conf 99998840496230102322379886369996999785307899999998289999952889756420588852785101
Q 003516 673 VSLKINVKMGGRNTVLLDAISCRIPLVSDIPTIIFGADVTHPENGEDSSPSIAAVVASQDWPEVTKYAGLVCAQAHRQEL 752 (813)
Q Consensus 673 i~lKiN~KLGG~N~~l~~~~~~~ip~~~~~~tMIiG~DVsHp~~~~~~~pSi~avVaS~d~~~~tky~~~~~~Q~~~qE~ 752 (813)
|+||||+||||+||.+.+. ..|.+...+|||||+||+||+++....|||+|+|||+|+ .+++|++.+++|.+++|+
T Consensus 565 i~lKiN~KlGG~n~~l~~~---~~~~~~~~~tmiiG~DV~H~~~~~~~~pSiaa~vaS~d~-~~~~y~~~~~~Q~~~~E~ 640 (861)
T 4f3t_A 565 LCLKINVKLGGVNNILLPQ---GRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDA-HPNRYCATVRVQQHRQEI 640 (861)
T ss_dssp HHHHHHHHTTCBCCEECST---TSCGGGGSCEEEEEEEEECCC----CCCEEEEEEEECSS-SSCCEEEEEEEESTTCCS
T ss_pred HHHHHHHHCCCCCEECCCC---CCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEEECCC-CCCEEEEEEEECCCCCCH
T ss_conf 9999988619833044665---465346896589987721468887788659999998479-856587899975899558
Q ss_pred ECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECC-----HHHHHHHHHHHHHHHHC
Q ss_conf 10110115799766443689999999999972999984999845-----26799999999998429
Q 003516 753 IQDLYKTWHDPVRGTVSGGMIRDLLISFRKATGQKPLRIIFYRS-----LFLSVLRVKVEIISICV 813 (813)
Q Consensus 753 i~~l~~~~~d~~~~~~~~~~i~~~L~~f~~~~~~lP~rIIiYRD-----Qf~~Vl~~Ei~~Ir~a~ 813 (813)
|++| ++|++++|+.|++.++.+|+||||||| ||.+|+++|+++|++|+
T Consensus 641 i~~l-------------~~~~~~~L~~~~~~~~~~P~~IiiyRDGVsegq~~~v~~~Ev~~i~~a~ 693 (861)
T 4f3t_A 641 IQDL-------------AAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREAC 693 (861)
T ss_dssp CTTH-------------HHHHHHHHHHHHHHHSCCCSEEEEEEESCCGGGHHHHHHHHHHHHHHHH
T ss_pred HHHH-------------HHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 9989-------------9999999999999828998459999268776889999999999999999
No 2
>4f1n_A Kpago; argonaute, RNAI, RNAse H, RNA binding protein-RNA complex; 3.19A {Vanderwaltozyma polyspora}
Probab=1.00 E-value=1 Score=955.15 Aligned_cols=661 Identities=20% Similarity=0.303 Sum_probs=534.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEECCCC---------------------CCEEEEEEECCCCC---------
Q ss_conf 899886467889999999984899955787451998---------------------61354499926888---------
Q 003516 122 PTSSKSLSFAPRPGYGQVGTKCIVKANHFFAELPDK---------------------DLNQYDVTITPEVA--------- 171 (813)
Q Consensus 122 ~~~~~~~~~~~RP~~Gt~G~~v~l~tN~f~i~~~~~---------------------~iy~YdV~i~p~v~--------- 171 (813)
|.+...+.+|.||+|||.|++|.|+||||.+.+++. .||+|+|+|.|+..
T Consensus 11 ~~~~~~~~~p~Rp~yGt~G~~v~l~aN~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~i~~~~~~~~~~~~~~~~ 90 (1046)
T 4f1n_A 11 EDTHAIYKVENRHDYGTKGTKVDILTNHILLAVGNDVPTEKIDKELVPKLDGWWKTAFIFTYHIDFKPQQKGPPRRGKPV 90 (1046)
T ss_dssp -CCCCCCCCCBCCCCCCCSEEEEEEESEEEEECCTTSCTTTSCTTTSCCCCSTTTSCEEEEEEEEEC-------------
T ss_pred CCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCC
T ss_conf 77611354789998898996789996379985477754332211123344433354158998899756456654445667
Q ss_pred -----CHHHHHHHHHHHHHHHC-CCCCCCCCCEEECCCEEEECCCCC---CCCEEEEEEEC-----CCCCC---------
Q ss_conf -----94799999999999832-484589852240861489747778---97406999940-----57788---------
Q 003516 172 -----SRTVNRAIMAELVRLYK-ESDLGMRLPAYDGRKSLYTAGELP---FVWKEFKIKLV-----DELDG--------- 228 (813)
Q Consensus 172 -----~k~~~r~i~~~l~~~~~-~~~~~~~~~~yDG~~~LyS~~~L~---~~~~~~~v~l~-----~~~~~--------- 228 (813)
++..+++|+..|++... ...++ ..+||||+++|||..+|+ .....+.|.+. ++.++
T Consensus 91 ~~~~~~~~k~~~ii~~ll~e~~~~~~~~-~~ia~d~~~~L~s~~~L~~~~l~~~~~~v~~~~~~~~~~~~~~~~~~~~~~ 169 (1046)
T 4f1n_A 91 PPQELSKPKKYELIEALLDEDEILYKYR-DRIAFNGEDTIYSHVPLEEFTLFDGCWEVSNKQKKKVVPGMGAPSNKASLQ 169 (1046)
T ss_dssp ----CCHHHHHHHHHHHHHSCTTTGGGT-TSEEECSSSEEEESSCGGGSTTCTTCCC-----------------------
T ss_pred CCCCCCHHHHHHHHHHHHHHCCHHHHCC-CCEEECCCCCEEECCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf 6532212379999999997261356428-860464722168787677653577766986553344667766544332223
Q ss_pred --CCCCCCCCEEEEEEEEEEEECHHHHHHHHCCCCCCCH-----HHHHHHHHHHHHCCCCCC---CCCCCC-CCCCCCC-
Q ss_conf --8999976269999999433043669988628999990-----679999999980233476---246786-4469999-
Q 003516 229 --INGPKRVREYKVVIKFAARANMHHLGQFLAGKRADAP-----QEALQILDIVLRELSTKR---YCPIGR-SFFSPSI- 296 (813)
Q Consensus 229 --~~~~~~~~~~~V~Ik~~~~i~~~~L~~~l~~~~~~~~-----~~~~q~Lniilr~~~~~~---~~~~Gr-~ff~~~~- 296 (813)
.....+.++|+|+|++++++++.+|.+|+.+...+.. .+.+++|++++++.+... ...+|+ +||..+.
T Consensus 170 ~~~~~~~~~~~~~V~i~~~~~i~l~dL~~~l~~~~~~~~~~~~~~~~i~aL~~il~~~~~~~~~~i~~vg~nkFF~~~~~ 249 (1046)
T 4f1n_A 170 KKIDPELEEMVSQITLKFSGKVGLKDIYNDTTTQDTEVQESRMSAIDKTCLLSLLGAKFMSTDDLIFQVQGNKFFIFNNF 249 (1046)
T ss_dssp --------CGGGGEEEEEEEEEEGGGGGSCSSCCCTTHHHHHHTCHHHHHHHHHHHHHHHCSSSCEEEETTTEEEECSTT
T ss_pred CCCCCCCCCCEEEEEEEEEEECCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCC
T ss_conf 45555566845999998710517999999972898554433341678999999975565535896487578430467987
Q ss_pred CCCCCCCCCEEEEEEEEEEEEEECCEEEEEEECCCCCCCCC-----------------CCHHHHHHHHHCCCC-------
Q ss_conf 98522799779963212226530562599763443221257-----------------739999999928986-------
Q 003516 297 RTPQRLGDGLESWCGFYQSIRPTQMGLSLNIDMASAAFIEP-----------------LPVIEFVAQLLGKDV------- 352 (813)
Q Consensus 297 ~~~~~l~~g~ei~~G~~~svr~~~~~l~LnID~s~~~F~~~-----------------~~lld~i~~~~~~~~------- 352 (813)
+...++++|+|+|+|||+|||+++++++||||+++++||++ ++|+|+|.++++..+
T Consensus 250 ~~~~~Lg~Gle~wrGffqSvRpa~~rLlLNvdvs~~aF~k~~~~~~~~~~~~~~~~~p~~lid~l~~~~~~~~~~~~~~~ 329 (1046)
T 4f1n_A 250 AKAIPFQIGGYLLQGFTVSLTHVYGGVALNTVSVPAPFIKHTKYLPGDPRFKNNEKEQFTLMDWIIECYHQSKAIRDIRY 329 (1046)
T ss_dssp CCEEECSSSEEEEEEEEEEEEEETTEEEEEEEEEEEEEECCSSSCTTSHHHHHCTTCCCCHHHHHHHHHHHHHHHHSSSC
T ss_pred CCCCCCCCCEEEEEEEEEEEEECCCCEEEEEECCCEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCC
T ss_conf 75103788179997676667851894089972551117846666765310001356886099999998633333222222
Q ss_pred ---CCCCCCHHHH-------HHHHHHHCCCEEEEEECCC------------CCCEEEEECCCCCCCCCEEEECCCC----
Q ss_conf ---5899995789-------9999985394999932597------------4526999435478998816660699----
Q 003516 353 ---LSRTLSDSDR-------VKIKKALRGVKVEVTHRGT------------VRRKYRVSGLTSQPTRELVFPVDDN---- 406 (813)
Q Consensus 353 ---~~r~l~~~~r-------~~i~~~Lkgl~V~~~~~~~------------~~r~yrI~~i~~~~a~~~~F~~~~~---- 406 (813)
..+.++..++ .+++++|+|++|.++|.+. ..+.++|.||+..++.+.+|+++++
T Consensus 330 ~~~~~~~~~~~d~~~f~~~~~kl~k~LKgLkV~vth~~~~~~~~g~~~~~~~~r~k~I~GLs~~~a~~~~F~~~~~~~~~ 409 (1046)
T 4f1n_A 330 NPKTAPPPSVKDLNYFVEKNTDISALLKGLKVYRPYINYSINKDGTPKPPRKRSSKGIVGFTRESAVSMRFNVLESSLKK 409 (1046)
T ss_dssp TTTTSCCCCSSHHHHHHHHCHHHHHHHTTCEECCTTCC--------------CCCEECCEECSSCSSSCC----------
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEECCCCCCCC
T ss_conf 32235787556654456788999998489789998667544556652443466646986346899773199616875444
Q ss_pred ------C---CEEEHHHHHHHHHCCCCCCCCCCEEEECCCCCCCEECCCCEEECCCCCCCCCCCHHHHHHHHHHHCCCCH
Q ss_conf ------9---2663999999880975358999748946788641003335042377433666999999999999339954
Q 003516 407 ------S---TMKSVVEYFQEMYGFTIQHTHLPCLQVGNQKKANYLPMEACKIVEGQRYTKRLNERQITALLKVTCQRPR 477 (813)
Q Consensus 407 ------g---~~iSv~~Yf~~~Y~i~Lk~p~lPli~~~~~~k~~ylP~Elc~i~~gQr~~~~l~~~~~~~lik~t~~~P~ 477 (813)
| ..+||+|||+++||++|+||+||||++|+. .+|||||||.|+|||+++++|++ .++||++||++|.
T Consensus 410 ~~~~~~g~~~~~iTVadYFk~kYni~LkyP~LPcV~VG~~--~~ylPmElC~I~pGQr~~kKL~~--ts~MIKfAa~rP~ 485 (1046)
T 4f1n_A 410 NSAPKPNEKPININTIDYFKRKYDITLKYPDMKLVNLGGK--NDVVPPECLTIVPGQKLKGQIFD--TKTYIDFSAIRPT 485 (1046)
T ss_dssp -------------CHHHHHHHHSCCCCSCTTSCCEECSTT--TCEECGGGCCBCTTCBCCSCCCC--HHHHHHHHCCCHH
T ss_pred CCCCCCCCCCEEEEHHHHHHHHHCCCCCCCCCCEEEECCC--CCCCCCCEEEECCCCCCCCCCCC--HHHHHHHHCCCCH
T ss_conf 5666677675278899999987394047999877997897--74213104796689624512351--7899998756949
Q ss_pred HHHHHHHHHHHH-----CCCCCHHHHHHCCEEECCCCEEEEEEECCCCEEEECCCCCC-------CCCCCCCCCCCCCCE
Q ss_conf 569999999984-----14994177743190644753165335629981641458974-------334787763233340
Q 003516 478 DRENDILQTVQQ-----NAYDQDLYAKEFGIKISEKLASVEARILPAPWLKYHENGKE-------KDCLPQVGQWNMMNK 545 (813)
Q Consensus 478 ~R~~~I~~~~~~-----~~~~~~~~l~~fGi~I~~~~~~V~arvLppP~I~y~~~~~~-------~~v~p~~g~Wn~~~~ 545 (813)
+|.+.|.+.... +.++.++++++|| .|+.+|++|+|||||||.|.|+++... ..+.+++|.|||+++
T Consensus 486 eR~~~I~~~~~~~~~~~l~~~~~~~l~~FG-~I~~~m~~V~gRVLppP~L~Yg~~~~~~~~~p~~~~~~p~~G~Wnm~~~ 564 (1046)
T 4f1n_A 486 EKFDLISRLSMPAIKRGLTDSEKEESSAPH-NSAYQFMRVPSRILDAPVVQFKESTFEYKDKSYGTKHEESKGNWNMKGH 564 (1046)
T ss_dssp HHHHHHHHHHHHHHHHHTSCCC---------CCSSSCCEEEEEECCCCCEECSSCEECCCCCCSSSSGGGGTTBCCCTTC
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCHHHHHCC-CCCCCEEEEEEEECCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 999999999887541024666557678628-7568503677887489757616875455556543445766785268888
Q ss_pred EEECCCE-ECEEEEEEECCC------CCHHHHHHHHHHHHHHHHHCCCCCCCC--CCCC---------CCCC--------
Q ss_conf 2314822-000299993888------247899999999999988419413789--9302---------2379--------
Q 003516 546 KMINGMT-VSRWACINFSRS------VQESVARGFCNELAQMCQVSGMEFNPE--PVIP---------IHNA-------- 599 (813)
Q Consensus 546 kf~~~~~-i~~W~~i~~~~~------~~~~~~~~f~~~L~~~~~~~Gi~i~~~--p~~~---------~~~~-------- 599 (813)
+|+.++. +..|.++++... .....+..|+..|.+.|+.+||.+..+ |.+. +...
T Consensus 565 kf~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~Gm~i~~~~~p~~~~~~~~~~~~~~~~~~~~r~~~ 644 (1046)
T 4f1n_A 565 QFISTPAKQVNLRAIFINNANTAPPASMESELDISMDKFASDVKQLGVDFNVSGKPILINQFGPPIKKFQGGGRGGRGGR 644 (1046)
T ss_dssp CCSBCCSSCEEEEEEEEECSSSCCCGGGHHHHHHHHHHHHHHHHTTTCCEECCSCCEEEESCCSCBC-------------
T ss_pred EEECCCCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 77137866640799997278766654238999999999999998669854787787412134554311123343332333
Q ss_pred ------------------CCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCC-CCCCHHHHHHHHHHCCCCEEEEEECC
Q ss_conf ------------------93489999999999862013799724999993289-98501225565420037024644213
Q 003516 600 ------------------RPDQVEKALKHVYHSSMSKTKGKELELLLAILPDN-NGSLYGDLKRICETDLGIISQCCLTK 660 (813)
Q Consensus 600 ------------------~~~~~~~~L~~~~~~~~~~~~~~~~~liivIlp~~-~~~~Y~~iK~~~e~~~GI~TQci~~~ 660 (813)
..++.+..|..+++.+ ..++|||||||++ +.++|+.||++||+++||+||||+.+
T Consensus 645 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~------~~~~lvl~Ilp~~~~~~~Y~~IK~~~d~~~gV~TQcv~~~ 718 (1046)
T 4f1n_A 645 GSRGGRGGRGAPSGPPTFETSPGEISLLNLLENI------PSNTYILYVLRRGNDSAVYDRLKYITDLKFGALNSCVVWD 718 (1046)
T ss_dssp ---------------CCCBCCTTHHHHHHHHHTC------CTTEEEEEEESSSCCHHHHHHHHHHHTTTTCCCEEEEEHH
T ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHC------CCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCCCEEEEHH
T ss_conf 3333333333444432111231799999999745------8997899996688871689999997613578144898423
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCC----CCCCEEEEEEEECCCCCCCCCCCCEEEEEEECCCCCC
Q ss_conf 214468779999999988404962301023223798863----6999699978530789999999828999995288975
Q 003516 661 HVFKISKQYLANVSLKINVKMGGRNTVLLDAISCRIPLV----SDIPTIIFGADVTHPENGEDSSPSIAAVVASQDWPEV 736 (813)
Q Consensus 661 t~~K~~~q~~~Ni~lKiN~KLGG~N~~l~~~~~~~ip~~----~~~~tMIiG~DVsHp~~~~~~~pSi~avVaS~d~~~~ 736 (813)
++.|.+.||++||+||||+||||+||.|++.. ++++ +..+|||||+||+|++++ ..+||+|||||+|+ .+
T Consensus 719 t~~k~~~q~~~NI~lKiN~KLGG~n~~l~~~~---~~~l~~~~~~~ptMiiG~DVtH~p~~--~~~SiaavVaS~d~-~~ 792 (1046)
T 4f1n_A 719 NFKKNSIQYNSNVVMKMNLKLLGSNHSLSIEN---NKLLIDKESNLPILVLGSDVTHYPEK--DQNSIASLVGSYDD-KF 792 (1046)
T ss_dssp HHTTCCHHHHHHHHHHHHHHTTCBCCEECTTG---GGGGEETTTTEECEEEEEEEECCSST--TCEEEEEEEECCSS-SC
T ss_pred HHCCCCHHHHHHHHHHHHHHCCCEEEECCCCC---CCCCCCCCCCCCEEEEEEEEECCCCC--CCCEEEEEEEEECC-CC
T ss_conf 51354278999999999986098511436654---43234445677349985311117989--98726699999879-85
Q ss_pred CCCEEEEEECCC-CEEHECCCCCCCCCCCCCCCHHHHHHHHHHHHHHH-CCCCCCEEEEECC-----HHHHHHHHHHHHH
Q ss_conf 642058885278-51011011011579976644368999999999997-2999984999845-----2679999999999
Q 003516 737 TKYAGLVCAQAH-RQELIQDLYKTWHDPVRGTVSGGMIRDLLISFRKA-TGQKPLRIIFYRS-----LFLSVLRVKVEII 809 (813)
Q Consensus 737 tky~~~~~~Q~~-~qE~i~~l~~~~~d~~~~~~~~~~i~~~L~~f~~~-~~~lP~rIIiYRD-----Qf~~Vl~~Ei~~I 809 (813)
++|++.+++|.+ ++|+|++| ++|+.++|+.|++. ++.+|+||||||| ||.+|+++|+++|
T Consensus 793 t~y~s~~~~Q~~~~~Eii~~L-------------~~~~~~~L~~y~~~n~~~lP~~IIiYRDGVSEGQf~~Vl~~Ev~~I 859 (1046)
T 4f1n_A 793 TQFPGDYMLQDGPGEEIITNV-------------GSLMLNRLKIYQKHNNGKLPTKIMYFRDGVSVDQFSQVVKIEVKSI 859 (1046)
T ss_dssp CCCCEEEEEEEEETCCSCTTG-------------GGGHHHHHHHHHHTTTTCCCSSEEEEEESCCGGGHHHHHHTHHHHH
T ss_pred CEEEEEEEEECCCCCCHHHHH-------------HHHHHHHHHHHHHHCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHH
T ss_conf 858359998458872489889-------------9999999999998637999857999806876577899999999999
Q ss_pred HHHC
Q ss_conf 8429
Q 003516 810 SICV 813 (813)
Q Consensus 810 r~a~ 813 (813)
++|+
T Consensus 860 k~a~ 863 (1046)
T 4f1n_A 860 KESV 863 (1046)
T ss_dssp HHHH
T ss_pred HHHH
T ss_conf 9999
No 3
>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
Probab=1.00 E-value=1 Score=554.30 Aligned_cols=551 Identities=13% Similarity=0.105 Sum_probs=395.5
Q ss_pred EEEEEEEEC-CCCCCEEEEE-EECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCEEEECCCCCCCCEEEEEEEC
Q ss_conf 955787451-9986135449-99268889479999999999983248458985224086148974777897406999940
Q 003516 146 KANHFFAEL-PDKDLNQYDV-TITPEVASRTVNRAIMAELVRLYKESDLGMRLPAYDGRKSLYTAGELPFVWKEFKIKLV 223 (813)
Q Consensus 146 ~tN~f~i~~-~~~~iy~YdV-~i~p~v~~k~~~r~i~~~l~~~~~~~~~~~~~~~yDG~~~LyS~~~L~~~~~~~~v~l~ 223 (813)
.-|.|+++. |...-| .| +-+.++...+++..-++-++.. ..+.|....-.|+.++.+.+. .-....
T Consensus 6 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~--~~~~~~ 73 (706)
T 1yvu_A 6 LLNLYRIEYRPKDTTF--TVFKPTHEIQKEKLNKVRWRVFLQT--------GLPTFRREDEFWCAGKVEKDT--LYLTLS 73 (706)
T ss_dssp EESEEEEEECCSSCEE--BCCEESSCCCHHHHHHHHHHHHHHH--------CSCEEEETTEEEESSCCTTCC--CEEEEC
T ss_pred HHHHHEEEECCCCCEE--EEECCHHHHHHHHHHHEEEEEEEEC--------CCCCCCCCCCCEECCCCCCCE--EEEECC
T ss_conf 5354425513677336--7634507887876412014765101--------786520153103435201324--899817
Q ss_pred CCCCCCCCCCCCCEEEEEEEEEEEECHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC-C
Q ss_conf 577888999976269999999433043669988628999990679999999980233476246786446999998522-7
Q 003516 224 DELDGINGPKRVREYKVVIKFAARANMHHLGQFLAGKRADAPQEALQILDIVLRELSTKRYCPIGRSFFSPSIRTPQR-L 302 (813)
Q Consensus 224 ~~~~~~~~~~~~~~~~V~Ik~~~~i~~~~L~~~l~~~~~~~~~~~~q~Lniilr~~~~~~~~~~Gr~ff~~~~~~~~~-l 302 (813)
.+. .|+|++++++.. +.-..+.+++|+++++++.. ...+..+||+||++......+ .
T Consensus 74 ----------~~~--~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~-~l~~~~igr~~~~~~~~~~i~~~ 131 (706)
T 1yvu_A 74 ----------NGE--IVELKRVGEEEF---------RGFQNERECQELFRDFLTKT-KVKDKFISDFYKKFRDKITVQGK 131 (706)
T ss_dssp ----------SSS--CEEEEECCCEEC---------CCCSCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHEEECS
T ss_pred ----------CCC--EEEEEEEEEEEC---------CCCCCCHHHHHHHHHHHHHC-CCHHHHHCCCCCCCCCCCCCCCC
T ss_conf ----------997--899999988615---------67899989999999999975-77475517244583356205677
Q ss_pred CCCEEEEEEEEEEEEEEC-CEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCEEEEEECCC
Q ss_conf 997799632122265305-6259976344322125773999999992898658999957899999985394999932597
Q 003516 303 GDGLESWCGFYQSIRPTQ-MGLSLNIDMASAAFIEPLPVIEFVAQLLGKDVLSRTLSDSDRVKIKKALRGVKVEVTHRGT 381 (813)
Q Consensus 303 ~~g~ei~~G~~~svr~~~-~~l~LnID~s~~~F~~~~~lld~i~~~~~~~~~~r~l~~~~r~~i~~~Lkgl~V~~~~~~~ 381 (813)
.+++|+||||.+||+..+ ++++||+|++|+ |++..+|+|+|.+ +... . ..+..+|.
T Consensus 132 ~~~l~iwPG~~tsi~~~e~~~~~L~~DvshK-vlr~~Tvld~l~~-~~~~------~-------------~~~~~~y~-- 188 (706)
T 1yvu_A 132 NRKIALIPEVNEKVLKSEEGYFLLHLDLKFR-IQPFETLQTLLER-NDFN------P-------------KRIRVKPI-- 188 (706)
T ss_dssp SCEEEEEEEEEEEEEEBSSSCEEEEEEEEEE-EEESSCHHHHHHH-CCCC------C-------------TTCEEEET--
T ss_pred CCCEEECCCEEEEEEECCCCCEEEEEEEEEE-ECCCCHHHHHHHH-HHHC------C-------------HHHHHHCC--
T ss_conf 8767981686889885267875999973404-5566539999997-2304------6-------------56886432--
Q ss_pred CCCEE--EEECC-CCCCCCCEEEECCCCCCEEEHHHHHHHHHCCC--------CCCCCCCEEEECCCCC-CCEECCCCEE
Q ss_conf 45269--99435-47899881666069992663999999880975--------3589997489467886-4100333504
Q 003516 382 VRRKY--RVSGL-TSQPTRELVFPVDDNSTMKSVVEYFQEMYGFT--------IQHTHLPCLQVGNQKK-ANYLPMEACK 449 (813)
Q Consensus 382 ~~r~y--rI~~i-~~~~a~~~~F~~~~~g~~iSv~~Yf~~~Y~i~--------Lk~p~lPli~~~~~~k-~~ylP~Elc~ 449 (813)
+++| ||++| +|+.++.++|. + |..+| ||+++|++. .+.+.+++++.+.+.. ..++++ ||.
T Consensus 189 -n~ty~~riddi~~~~~~P~~~f~-~--g~~iS---Yyk~~~~~~q~ll~~r~~~~~~~~~~v~~~~~~p~~lL~p-lc~ 260 (706)
T 1yvu_A 189 -GIDFVGRVQDVFKAKEKGEEFFR-L--CMERS---THKSSKKAWEELLKNRELREKAFLVVLEKGYTYPATILKP-VLT 260 (706)
T ss_dssp -TCCCCEEEEEEEESTTSCHHHHH-H--HHHTC---SSHHHHHHHHHHHHCHHHHHHCEEEEETTSCEEEGGGEEE-CCC
T ss_pred -CCEECCCCCCCCCCCCCCCEEEC-C--CCCCC---EEECCCCCCHHHHHCCCCCCCCCEEEECCCCCCCCEEECC-CCC
T ss_conf -55633365740046889513842-8--99755---5851467541444302445677248842688778644300-121
Q ss_pred ECCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCHHHHHHCCEEECCCCEEEEEEECCCCEEEECCCCC
Q ss_conf 23774336669999999999993399545699999999841499417774319064475316533562998164145897
Q 003516 450 IVEGQRYTKRLNERQITALLKVTCQRPRDRENDILQTVQQNAYDQDLYAKEFGIKISEKLASVEARILPAPWLKYHENGK 529 (813)
Q Consensus 450 i~~gQr~~~~l~~~~~~~lik~t~~~P~~R~~~I~~~~~~~~~~~~~~l~~fGi~I~~~~~~V~arvLppP~I~y~~~~~ 529 (813)
+ ++|+++|+++|+++++.+|.+|.+.|.++++.. ++.|+.|||+|+.+|+.|+|||||||.|.++.+..
T Consensus 261 ~-------t~Ltd~q~~~mik~t~~~P~~R~~~i~~~~~~~----~~~L~~fGi~i~~~~~~v~gRVLp~P~i~~~~g~~ 329 (706)
T 1yvu_A 261 Y-------ENLEDEERNEVADIVRMEPGKRLNLIRYILRRY----VKALRDYGWYISPEEERAKGKLNFKDTVLDAKGKN 329 (706)
T ss_dssp C-------C------HHHHTSTTSCCHHHHHHHHHHHHHHH----HHHHHTTTEEECSSCEECCEECCCCCCEECSSCCE
T ss_pred C-------CCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHH----HHHHHHCCCEECCCEEECCCEECCCCEEECCCCCC
T ss_conf 3-------799999999999998259999999999999998----99999769888886422136873895066478974
Q ss_pred CCCCCCCCCCCCCCCEEEECCCEECE---EEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf 43347877632333402314822000---299993888247899999999999988419413789930223799348999
Q 003516 530 EKDCLPQVGQWNMMNKKMINGMTVSR---WACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARPDQVEK 606 (813)
Q Consensus 530 ~~~v~p~~g~Wn~~~~kf~~~~~i~~---W~~i~~~~~~~~~~~~~f~~~L~~~~~~~Gi~i~~~p~~~~~~~~~~~~~~ 606 (813)
.....+..|.|++. .+|+.++.++. |.+++..+ + ..++.|++.|.+.|+.+||.++.|+.......+.+.+
T Consensus 330 ~~~~~~~~~~~~~~-~~~~~~~~l~~~~lW~~i~~~~--~-~~~~~f~~~L~~~~~~~G~~i~~p~~~~~~~~~~~~~-- 403 (706)
T 1yvu_A 330 TKVITNLRKFLELC-RPFVKKDVLSVEIISVSVYKKL--E-WRKEEFLKELINFLKNKGIKLKIKGKSLILAQTREEA-- 403 (706)
T ss_dssp ECCSSCCHHHHHHC-CCCCSCSEEEEEEEEEEC--------CHHHHHHHHHHHHHHTTTCEEEEEEEEEEECSSTTHH--
T ss_pred CEECCCCCCCCCCC-CCEECCCCCCCCEEEEEEECCH--H-HHHHHHHHHHHHHHHHCCCEECCCCCCCCCCHHHHHH--
T ss_conf 30236875430003-7411143256433899981661--6-8999999999999987496206874223340019999--
Q ss_pred HHHHHHHHHHCCCCCCCCEEEEEEECCC-------CCCCHHHHHHHHHHCCCCEEEEEECCCCCCC-CHHHHHHHHHHHH
Q ss_conf 9999999862013799724999993289-------9850122556542003702464421321446-8779999999988
Q 003516 607 ALKHVYHSSMSKTKGKELELLLAILPDN-------NGSLYGDLKRICETDLGIISQCCLTKHVFKI-SKQYLANVSLKIN 678 (813)
Q Consensus 607 ~L~~~~~~~~~~~~~~~~~liivIlp~~-------~~~~Y~~iK~~~e~~~GI~TQci~~~t~~K~-~~q~~~Ni~lKiN 678 (813)
++.+...+. +..+++++|||+|++ +.++|+.||++|+ ++||+||||..+|+.+. ..+++.||+||||
T Consensus 404 -~~~l~~~~~---~~~~~qlvlvIlp~~~~~~~~~~~~~Y~~IK~~~~-~~GI~TQcv~~~tl~~~~~~q~~~NI~lkiN 478 (706)
T 1yvu_A 404 -KEKLIPVIN---KIKDVDLVIVFLEEYPKVDPYKSFLLYDFVKRELL-KKMIPSQVILNRTLKNENLKFVLLNVAEQVL 478 (706)
T ss_dssp -HHHHHHHHT---TTSSCSEEEEEEC----------CHHHHHHHHHHH-HTTCCCEEEEHHHHHHSCHHHHHHHHHHHHH
T ss_pred -HHHHHHHHC---CCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHH-CCCCCEEEEEHHHCCCCCHHHHHHHHHHHHH
T ss_conf -999998750---05899589999777444455567547999999985-2898549980102166530789999999999
Q ss_pred HHCCCCCCEECCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCEEEEEEECCCCC--CCCCEEEEEECCCCEEHECCC
Q ss_conf 404962301023223798863699969997853078999999982899999528897--564205888527851011011
Q 003516 679 VKMGGRNTVLLDAISCRIPLVSDIPTIIFGADVTHPENGEDSSPSIAAVVASQDWPE--VTKYAGLVCAQAHRQELIQDL 756 (813)
Q Consensus 679 ~KLGG~N~~l~~~~~~~ip~~~~~~tMIiG~DVsHp~~~~~~~pSi~avVaS~d~~~--~tky~~~~~~Q~~~qE~i~~l 756 (813)
+||||+||.|++ | ...+|||||+||+||+.+ ...||++|+|+|+| .. .++|.+....|. ++|++++
T Consensus 479 ~KLGG~nw~L~~------~--~~~~tmiIGiDVsH~~~~-~~~pSv~g~vas~d-~~g~~~~~~~~~~~q~-~~ei~~~- 546 (706)
T 1yvu_A 479 AKTGNIPYKLKE------I--EGKVDAFVGIDISRITRD-GKTVNAVAFTKIFN-SKGELVRYYLTSYPAF-GEKLTEK- 546 (706)
T ss_dssp HHTTCCSCEESC------C--TTCCSEEEEECEEECCCS-SSCCCEEEEEEEEC-TTSCEEEEEEEEECSC-TTHHHHH-
T ss_pred HHHCCEEEEECC------C--CCCCEEEEEEEEECCCCC-CCCCEEEEEEEEEC-CCCCEEEEEEEECCCC-CCHHHHH-
T ss_conf 984986156025------8--888559999988616878-88856999999985-8998899998733666-4269999-
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECC-HHHHHHHHHHHHHHHHC
Q ss_conf 0115799766443689999999999972999984999845-26799999999998429
Q 003516 757 YKTWHDPVRGTVSGGMIRDLLISFRKATGQKPLRIIFYRS-LFLSVLRVKVEIISICV 813 (813)
Q Consensus 757 ~~~~~d~~~~~~~~~~i~~~L~~f~~~~~~lP~rIIiYRD-Qf~~Vl~~Ei~~Ir~a~ 813 (813)
++..+|+.|.+.++.+|+||||||| -++ ++|+++|++|+
T Consensus 547 ---------------l~~~~l~~~~~~~~~~P~rIIiyRDGVse---~~El~~Ik~A~ 586 (706)
T 1yvu_A 547 ---------------AIGDVFSLLEKLGFKKGSKIVVHRDGRLY---RDEVAAFKKYG 586 (706)
T ss_dssp ---------------HHHHHHHHHHHTTCCTTCEEEEEESSCCC---HHHHHHHHHHH
T ss_pred ---------------HHHHHHHHHHHHCCCCCCEEEEEECCCCC---HHHHHHHHHHH
T ss_conf ---------------99999999998649998379999688885---89999999999
No 4
>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
Probab=1.00 E-value=1 Score=518.30 Aligned_cols=554 Identities=13% Similarity=0.081 Sum_probs=403.7
Q ss_pred CEEEEEEEEEEEEC---CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCE--EEECCCCCCCC
Q ss_conf 84899955787451---99861354499926888947999999999998324845898522408614--89747778974
Q 003516 141 TKCIVKANHFFAEL---PDKDLNQYDVTITPEVASRTVNRAIMAELVRLYKESDLGMRLPAYDGRKS--LYTAGELPFVW 215 (813)
Q Consensus 141 ~~v~l~tN~f~i~~---~~~~iy~YdV~i~p~v~~k~~~r~i~~~l~~~~~~~~~~~~~~~yDG~~~--LyS~~~L~~~~ 215 (813)
-+..+.+|||++.. |+ .+|+|+|++.|++.++ .+..++.. ++. .+| .++|||. . ||++.+|+-
T Consensus 2 ~~~~~~~n~~~~~~~~~~~-~~y~y~v~~~p~~~~~-~~~~~~~~----~~~-~~g--~~~fdg~-~~~l~~~~~l~~-- 69 (771)
T 1u04_A 2 MKAIVVINLVKINKKIIPD-KIYVYRLFNDPEEELQ-KEGYSIYR----LAY-ENV--GIVIDPE-NLIIATTKELEY-- 69 (771)
T ss_dssp CEEEEEBSEEEBCGGGSCS-CEEEEEC-------------CCHHH----HHH-HTT--EEEEETT-TTEEEESSCCCC--
T ss_pred CCEEEEEEEEEEECCCCCC-EEEEEEEECCCHHHHH-HHHHHHHH----HHH-HCC--CEEECCC-CEEEECCCEECC--
T ss_conf 5069994068873246887-0599986238758889-99989998----786-537--1896475-203222532146--
Q ss_pred EEEEEEECCCCCCCCCCCCCCEEEEEEEEEEEECHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCC-CCC-----CCCCCC
Q ss_conf 06999940577888999976269999999433043669988628999990679999999980233-476-----246786
Q 003516 216 KEFKIKLVDELDGINGPKRVREYKVVIKFAARANMHHLGQFLAGKRADAPQEALQILDIVLRELS-TKR-----YCPIGR 289 (813)
Q Consensus 216 ~~~~v~l~~~~~~~~~~~~~~~~~V~Ik~~~~i~~~~L~~~l~~~~~~~~~~~~q~Lniilr~~~-~~~-----~~~~Gr 289 (813)
.+..+.++++.+++++ +|++|+++|... ..+ +..+||
T Consensus 70 ------------------~~~~~~~~~~~~~~~~-------------------~~~~n~i~r~~l~~~~~~~~~l~~~~r 112 (771)
T 1u04_A 70 ------------------EGEFIPEGEISFSELR-------------------NDYQSKLVLRLLKENGIGEYELSKLLR 112 (771)
T ss_dssp ------------------SSCCEEEEEECGGGSC-------------------HHHHHHHHHHHHHHTTCSHHHHHHHHT
T ss_pred ------------------CCCEEEEEEEECCEEC-------------------HHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf ------------------8973789999904402-------------------999999999999874620588999766
Q ss_pred CCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 44699999852279977996321222653056259976344322125773999999992898658999957899999985
Q 003516 290 SFFSPSIRTPQRLGDGLESWCGFYQSIRPTQMGLSLNIDMASAAFIEPLPVIEFVAQLLGKDVLSRTLSDSDRVKIKKAL 369 (813)
Q Consensus 290 ~ff~~~~~~~~~l~~g~ei~~G~~~svr~~~~~l~LnID~s~~~F~~~~~lld~i~~~~~~~~~~r~l~~~~r~~i~~~L 369 (813)
+||++. . -..+++|+|+.+||+..+++++|++|++|++ .+..+|+|+|.+.. .....+....
T Consensus 113 ~~~~~~-----~-~~~~~~~~~~~tsi~~~e~~~ll~~di~hkv-~r~~t~~d~~~~~~-----------~~~~~~~~~~ 174 (771)
T 1u04_A 113 KFRKPK-----T-FGDYKVIPSVEMSVIKHDEDFYLVIHIIHQI-QSMKTLWELVNKDP-----------KELEEFLMTH 174 (771)
T ss_dssp TTSCCE-----E-ETTEEEEEEEEEEEEECSSCEEEEEEEEEEE-EESSCHHHHTTTCH-----------HHHHHHHHHS
T ss_pred HCCCCC-----C-CCCCEEEECCEEEEEECCCCEEEEEEEEEEE-EEHHHHHHHHHHHH-----------HHHHHHHHHC
T ss_conf 207983-----3-4662799873466885378438999866567-55567999999999-----------9999888735
Q ss_pred CCCEEEEE--------ECCCCCCEEEEECCCCCCCCCE--EE---ECCCC-CCEEEHHHHHHHHHCCCCCCCCCCEEEEC
Q ss_conf 39499993--------2597452699943547899881--66---60699-92663999999880975358999748946
Q 003516 370 RGVKVEVT--------HRGTVRRKYRVSGLTSQPTREL--VF---PVDDN-STMKSVVEYFQEMYGFTIQHTHLPCLQVG 435 (813)
Q Consensus 370 kgl~V~~~--------~~~~~~r~yrI~~i~~~~a~~~--~F---~~~~~-g~~iSv~~Yf~~~Y~i~Lk~p~lPli~~~ 435 (813)
.|..|.+. |.-| .+.|++++ +++..+.. +| ..+++ ++ +++.+||.++|++ ++++||+++++
T Consensus 175 ~g~~~~~~~~~~~~~vy~~n-~~~Y~~~~-~~d~~~~~~~~~~~~~~~~~~~~-~~~~~~y~~~y~i--~d~~QPllvs~ 249 (771)
T 1u04_A 175 KENLMLKDIASPLKTVYKPC-FEEYTKKP-KLDHNQEIVKYWYNYHIERYWNT-PEAKLEFYRKFGQ--VDLKQPAILAK 249 (771)
T ss_dssp TTTCEEEETTSTTCCEEEEC-BCTTSSCB-CEECCHHHHHHHHHHHHHHHCCS-HHHHHHHHHHHCS--CCTTSCEEEEE
T ss_pred CCCEEEEECCCCCEEEEECC-CCEEECCC-CCCCCCCCHHHEECEEECCCCCC-CCHHHHHHHHCCC--CCCCCCEEEEC
T ss_conf 67378531134442686046-62441588-51237898544013021377887-4116878876486--76788769851
Q ss_pred CC-------CCCCEECCCCEEECCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHC-----CCC--CHHHHHHC
Q ss_conf 78-------86410033350423774336669999999999993399545699999999841-----499--41777431
Q 003516 436 NQ-------KKANYLPMEACKIVEGQRYTKRLNERQITALLKVTCQRPRDRENDILQTVQQN-----AYD--QDLYAKEF 501 (813)
Q Consensus 436 ~~-------~k~~ylP~Elc~i~~gQr~~~~l~~~~~~~lik~t~~~P~~R~~~I~~~~~~~-----~~~--~~~~l~~f 501 (813)
.+ .+.+||+||||.++. ...+++.+.+++|..+|...|.+|.+.+.++.+++ .-+ ..+.++.|
T Consensus 250 ~~~~~~~~~~~~i~LiPELc~~TG---~~~~~~~~~MK~la~~trl~P~~R~~~l~~~~~~l~~~~~~~~~~~~~~l~~~ 326 (771)
T 1u04_A 250 FASKIKKNKNYKIYLLPQLVVPTY---NAEQLESDVAKEILEYTKLMPEERKELLENILAEVDSDIIDKSLSEIEVEKIA 326 (771)
T ss_dssp ESCC-----CCCEEECTTTEEEEE---EGGGC----CCHHHHHHCCCHHHHHHHHHHHHHHCCCSSBCSSCCEEEEEECC
T ss_pred CHHHCCCCCCCEEEECHHHHHHCC---CHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 443246788960364247653367---43566689999999987779899999999999986154430798899997555
Q ss_pred CEEECCCCEEEEEEECCCCEEEECCCCCCCCCCCCCCCCC--CCCEEEECCCE----ECE------EEEEEECCCCCHHH
Q ss_conf 9064475316533562998164145897433478776323--33402314822----000------29999388824789
Q 003516 502 GIKISEKLASVEARILPAPWLKYHENGKEKDCLPQVGQWN--MMNKKMINGMT----VSR------WACINFSRSVQESV 569 (813)
Q Consensus 502 Gi~I~~~~~~V~arvLppP~I~y~~~~~~~~v~p~~g~Wn--~~~~kf~~~~~----i~~------W~~i~~~~~~~~~~ 569 (813)
+ .++.. +.|.++++.+-.+.+.+- ..+..++|. +++.+++.+.. ++. |.+++. +. ...
T Consensus 327 ~-~l~~~-~~v~~~~~~~~~i~~~~~-----~~~~~adW~~~~~~~~~~~~~~~p~~l~~~~~i~~wil~~~-~~--~~~ 396 (771)
T 1u04_A 327 Q-ELENK-IRVRDDKGNSVPISQLNV-----QKSQLLLWTNYSRKYPVILPYEVPEKFRKIREIPMFIILDS-GL--LAD 396 (771)
T ss_dssp G-GGGSS-EEEECSSSCEEESCCC-------------CGGGGSCCCCCCCCSBCCTHHHHCCCCCEEEEEET-TS--CHH
T ss_pred H-CCCCC-CCCCCCCCCCCCEEECCC-----CCCCCCCCCHHHCCCCCEECCCCHHHHHCCCCCCEEEEEEC-CC--HHH
T ss_conf 4-11767-500254566453263276-----77766776055377851104654265504355535999957-71--688
Q ss_pred HHHHH---------HHHHHHHHHCC-----------CCCCCCC------CCCCCCCCCHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 99999---------99999988419-----------4137899------3022379934899999999998620137997
Q 003516 570 ARGFC---------NELAQMCQVSG-----------MEFNPEP------VIPIHNARPDQVEKALKHVYHSSMSKTKGKE 623 (813)
Q Consensus 570 ~~~f~---------~~L~~~~~~~G-----------i~i~~~p------~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~ 623 (813)
+.+|+ +.|.+.+..+| +.++.+. .+.....+.+.++..++.+.++.. +..
T Consensus 397 ~~~f~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~p~~~~~~~~~~i~~dl~~~~~i~~~l~~~~~~~~----~~~ 472 (771)
T 1u04_A 397 IQNFATNEFRELVKSMYYSLAKKYNSLAKKARSTNEIGLPFLDFRGKEKVITEDLNSDKGIIEVVEQVSSFMK----GKE 472 (771)
T ss_dssp HHHHHHHHHHHHHHHHCC-----------------------------CEEEEECTTSHHHHHHHHHHHHHHHT----TCS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHHHHHCC----CCC
T ss_conf 9988888766677899998753223101103566422578733346751431565534779999999997515----789
Q ss_pred CEEEEEEEC-CCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCC----C-----HHHHHHHHHHHHHHCCCCCCEECCCCC
Q ss_conf 249999932-899850122556542003702464421321446----8-----779999999988404962301023223
Q 003516 624 LELLLAILP-DNNGSLYGDLKRICETDLGIISQCCLTKHVFKI----S-----KQYLANVSLKINVKMGGRNTVLLDAIS 693 (813)
Q Consensus 624 ~~liivIlp-~~~~~~Y~~iK~~~e~~~GI~TQci~~~t~~K~----~-----~q~~~Ni~lKiN~KLGG~N~~l~~~~~ 693 (813)
++|++++++ .++.+.|+.||++| .+.||+||||..+|+.+. . .+++.||++|||+||||+||.|+.
T Consensus 473 ~~lvlv~l~~~~~~d~Y~~IK~~~-~~~gIpTQcV~~~Tl~~~~~k~~~~~l~~sia~NIalqIn~KLGG~pW~L~~--- 548 (771)
T 1u04_A 473 LGLAFIAARNKLSSEKFEEIKRRL-FNLNVISQVVNEDTLKNKRDKYDRNRLDLFVRHNLLFQVLSKLGVKYYVLDY--- 548 (771)
T ss_dssp CEEEEEEECTTSCHHHHHHHHHHH-HHTTEEEEEEEHHHHHHCEETTEEEEECHHHHHHHHHHHHHHTTCBCCEESC---
T ss_pred CCEEEEEECCCCCCCHHHHHHHHH-HCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEECC---
T ss_conf 878999975898866689999998-5489663998435006765443323132899999999999985983326068---
Q ss_pred CCCCCCCCCCEEEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCCCEEEEEECCCCEEHECCCCCCCCCCCCCCCHHHHH
Q ss_conf 79886369996999785307899999998289999952889756420588852785101101101157997664436899
Q 003516 694 CRIPLVSDIPTIIFGADVTHPENGEDSSPSIAAVVASQDWPEVTKYAGLVCAQAHRQELIQDLYKTWHDPVRGTVSGGMI 773 (813)
Q Consensus 694 ~~ip~~~~~~tMIiG~DVsHp~~~~~~~pSi~avVaS~d~~~~tky~~~~~~Q~~~qE~i~~l~~~~~d~~~~~~~~~~i 773 (813)
|. .+|||||+||+|+.++ ..+++++|.|+|.|+ ..++|.+....|.++ |.++ + ..|+
T Consensus 549 ---p~---~~tmiIGiDV~H~~~~-~~svs~~A~V~s~dg-~~~~~~s~~~~~~~~-E~i~-l-------------~~~l 605 (771)
T 1u04_A 549 ---RF---NYDYIIGIDVAPMKRS-EGYIGGSAVMFDSQG-YIRKIVPIKIGEQRG-ESVD-M-------------NEFF 605 (771)
T ss_dssp ---CC---SSSEEEEEEEEEECCT-TTCEEEEEEEEETTS-CEEEEEEEECCCCSS-SSCC-H-------------HHHH
T ss_pred ---CC---CCEEEEEEEEECCCCC-CCCEEEEEEEECCCC-CEEEEEEEEEECCCC-CEEC-H-------------HHHH
T ss_conf ---99---9879999998747989-974699999977999-789998887303776-3773-9-------------9999
Q ss_pred HHHHHHHHHH-CCCCCCEEEEECC-HHHHHHHHHHHHHHHHC
Q ss_conf 9999999997-2999984999845-26799999999998429
Q 003516 774 RDLLISFRKA-TGQKPLRIIFYRS-LFLSVLRVKVEIISICV 813 (813)
Q Consensus 774 ~~~L~~f~~~-~~~lP~rIIiYRD-Qf~~Vl~~Ei~~Ir~a~ 813 (813)
.++|..|++. ++.+|+||||||| . |+++|+++|++|+
T Consensus 606 ~~~L~~y~~~n~~~lP~RIIiyRDG~---v~~~El~~i~ea~ 644 (771)
T 1u04_A 606 KEMVDKFKEFNIKLDNKKILLLRDGR---ITNNEEEGLKYIS 644 (771)
T ss_dssp HHHHHHHHHTTCCCTTCEEEEECSBC---CCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCCCCEEEEECCCC---CCHHHHHHHHHHH
T ss_conf 99999999970799997799991888---8789999999999
No 5
>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
Probab=1.00 E-value=1 Score=444.77 Aligned_cols=522 Identities=15% Similarity=0.127 Sum_probs=374.8
Q ss_pred CEEEEEEEEEEEEC---CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCEEEECCCCCCC-CE
Q ss_conf 84899955787451---998613544999268889479999999999983248458985224086148974777897-40
Q 003516 141 TKCIVKANHFFAEL---PDKDLNQYDVTITPEVASRTVNRAIMAELVRLYKESDLGMRLPAYDGRKSLYTAGELPFV-WK 216 (813)
Q Consensus 141 ~~v~l~tN~f~i~~---~~~~iy~YdV~i~p~v~~k~~~r~i~~~l~~~~~~~~~~~~~~~yDG~~~LyS~~~L~~~-~~ 216 (813)
.++.|.-|-|.++- .+...|.|+|.+.|.....+ -..++..++.. +|. . +--..+.|.|.++ |.. ..
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-----~~~-~-~~~~~~~~~~~~~-~~~~~~ 75 (685)
T 3ho1_A 5 GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREE-VYPLLAQVARR-----AGG-V-TVRMGDGLASWSP-PEVLVL 75 (685)
T ss_dssp CCEEEEEEEEEEEECCTTTSSCEEEEEEEESCCCTTT-HHHHHHHHHHH-----TCS-S-EEEETTEEEESSC-TTTSCC
T ss_pred CCEEEEEEEEECCCCCHHHCCEEEEEEECCCCCCCCH-HHHHHHHHHHH-----HCC-E-EEEECCCEECCCC-CHHHHC
T ss_conf 5205897500345488534850589985079988414-77899999987-----387-4-7863274000467-055410
Q ss_pred EEEEEECCCCCCCCCCCCCCEEEEEEEEEEEECHHHHHHHHCCCCCCCHHHHHHH-----HHHHHHCCCCCCCCCCCCCC
Q ss_conf 6999940577888999976269999999433043669988628999990679999-----99998023347624678644
Q 003516 217 EFKIKLVDELDGINGPKRVREYKVVIKFAARANMHHLGQFLAGKRADAPQEALQI-----LDIVLRELSTKRYCPIGRSF 291 (813)
Q Consensus 217 ~~~v~l~~~~~~~~~~~~~~~~~V~Ik~~~~i~~~~L~~~l~~~~~~~~~~~~q~-----Lniilr~~~~~~~~~~Gr~f 291 (813)
+-.|. . ..+...|++.-.-...+|+.+-. .++++.. |+-.+++. .+...-|.-.
T Consensus 76 ~~~~~--~-------~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~ 134 (685)
T 3ho1_A 76 EGTLA--R-------MGQTYAYRLYPKGRRPLDPKDPG----------ERSVLSALARRLLQERLRRL--EGVWVEGLAV 134 (685)
T ss_dssp EEEEE--C-------SSCEEEEEEEEEEECCCCTTSHH----------HHHHHHHHHHHHHHHHHHTC--SSSEEETTEE
T ss_pred CCHHC--C-------CCCCCCEEEEECCCCCCCCCCHH----------HHHHHHHHHHHHHHHHHHHH--HCEEECCEEE
T ss_conf 22000--2-------36886636530566457889867----------88999999999999998765--3337764789
Q ss_pred CCCCCCCCCCCCCCEEEEEEEEEEEEEEC-CEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf 69999985227997799632122265305-62599763443221257739999999928986589999578999999853
Q 003516 292 FSPSIRTPQRLGDGLESWCGFYQSIRPTQ-MGLSLNIDMASAAFIEPLPVIEFVAQLLGKDVLSRTLSDSDRVKIKKALR 370 (813)
Q Consensus 292 f~~~~~~~~~l~~g~ei~~G~~~svr~~~-~~l~LnID~s~~~F~~~~~lld~i~~~~~~~~~~r~l~~~~r~~i~~~Lk 370 (813)
+... ..-|.|.|+.+|+...|.+.. ++++|.||..+. |+...++.+++++.+. |-
T Consensus 135 ~~~~----~~~~~~~~~~~g~~~~v~~~~~~~~~l~vd~~~r-~~~~~~~~~~l~~~~~-------------------~~ 190 (685)
T 3ho1_A 135 YRRE----HARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYR-ILCEMSLEAWLAQGHP-------------------LP 190 (685)
T ss_dssp EEEE----EEEETTEEEEEEEEEEEEECSSSEEEEEEEEEEE-EEECSCHHHHHHHSCC-------------------CC
T ss_pred EEEC----CCCCCCEEEECCEEEEEEECCCCCEEEEEEEHEE-ECCHHHHHHHHHHCCC-------------------CC
T ss_conf 8406----8877743884366999998778867999740301-1476449999981798-------------------32
Q ss_pred CCEEEEEECCCCCCEEEEECCCCCCCCCEEEECCCCCCEEEHHHHHHHHHCCCCCCCCCCEEEECCC----CC-----CC
Q ss_conf 9499993259745269994354789988166606999266399999988097535899974894678----86-----41
Q 003516 371 GVKVEVTHRGTVRRKYRVSGLTSQPTRELVFPVDDNSTMKSVVEYFQEMYGFTIQHTHLPCLQVGNQ----KK-----AN 441 (813)
Q Consensus 371 gl~V~~~~~~~~~r~yrI~~i~~~~a~~~~F~~~~~g~~iSv~~Yf~~~Y~i~Lk~p~lPli~~~~~----~k-----~~ 441 (813)
..|+.+|+ .++|.|.+|+ +.+|++.|.. + .+|++||++++|.+ +.-++|+|+...+ ++ .+
T Consensus 191 -~~v~~~y~---~~~~~~~~~~-~~~p~~~~l~---~-~~s~~~y~~~k~~~--~~~~~~~vv~~~~~~~~~~~i~~~~~ 259 (685)
T 3ho1_A 191 -KRVRNAYD---RRTWELLRLG-EEDPKELPLP---G-GLSLLDYHASKGRL--QGREGGRVAWVADPKDPRKPIPHLTG 259 (685)
T ss_dssp -SEEEESSS---CCEECCCEEE-CCCTTCC----------CSTTTTTTTSTT--TTSCCCSEEEECSCC---CCEEEETT
T ss_pred -HHHHHHCC---CCEEEEEECC-CCCCHHEECC---C-CCCHHHHHHHCCCC--CCCCCCEEEEEECCCCCCCCCEEEEE
T ss_conf -77764316---6248986336-6893323457---8-86599997542653--34678659999554457873324425
Q ss_pred EECCCCEEECCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCHHHHHHCCEEECCCCEEEEEEECCCCE
Q ss_conf 00333504237743366699999999999933995456999999998414994177743190644753165335629981
Q 003516 442 YLPMEACKIVEGQRYTKRLNERQITALLKVTCQRPRDRENDILQTVQQNAYDQDLYAKEFGIKISEKLASVEARILPAPW 521 (813)
Q Consensus 442 ylP~Elc~i~~gQr~~~~l~~~~~~~lik~t~~~P~~R~~~I~~~~~~~~~~~~~~l~~fGi~I~~~~~~V~arvLppP~ 521 (813)
||.|||| +. .|++.+.. .++...|.+|++.+.++.+. +++.|||. +.+|+.|+||+||||+
T Consensus 260 ~l~p~l~-m~-------~l~~~~~~---~~trlsP~~R~~~l~~~~~~-------i~~~~Gl~-~~~~i~v~gRvLppp~ 320 (685)
T 3ho1_A 260 LLVPVLT-LE-------DLHEEEGS---LALSLPWEERRRRTREIASW-------IGRRLGLG-TPEAVRAQAYRLSIPK 320 (685)
T ss_dssp SEEEECC-TT-------TTSSCSSC---CCCCCCHHHHHHHHHHHHHH-------HHHTTCSC-CCEEEEEEEEECCCCC
T ss_pred EECHHHH-HH-------HHHHHHHH---CCCCCCHHHHHHHHHHHHHH-------HHHHCCCC-CCCCCEEEEEECCHHH
T ss_conf 6322767-87-------77666640---62567989999999999999-------88853999-8971168778838899
Q ss_pred EEECCCCCCCCCCCCCCCCCCCCEEEECCCEECEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 64145897433478776323334023148220002999938882478999999999999884194137899302237993
Q 003516 522 LKYHENGKEKDCLPQVGQWNMMNKKMINGMTVSRWACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARP 601 (813)
Q Consensus 522 I~y~~~~~~~~v~p~~g~Wn~~~~kf~~~~~i~~W~~i~~~~~~~~~~~~~f~~~L~~~~~~~Gi~i~~~p~~~~~~~~~ 601 (813)
| +++. .+ .+.|++.+..|+.++.. .|+++++.+. ...++.|++.|.+.|+.+||.+..+......+..
T Consensus 321 I-~g~~----~~---~~~~d~~~~~~~~~~~~-~~ail~l~~~--~~~~~~f~~~L~~va~~~G~~i~~~~~~~~~~d~- 388 (685)
T 3ho1_A 321 L-MGRR----AV---SKPADALRVGFYRAQET-ALALLRLDGA--QGWPEFLRRALLRAFGASGASLRLHTLHAHPSQG- 388 (685)
T ss_dssp E-ESSS----BC---SSGGGHHHHCCSSCCCE-EEEEEECSSC--CSCCHHHHHHHHHHHHSSSSCEEEEECCCCGGGT-
T ss_pred H-CCCC----CC---CCCHHHCCCCCEECCCC-EEEEEECCCC--HHHHHHHHHHHHHHHHHCCCEECCCEEECCCCCH-
T ss_conf 5-5899----75---78621114753113673-5999962672--6789999999999887679376355110477736-
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf 48999999999986201379972499999328998501225565420037024644213214468779999999988404
Q 003516 602 DQVEKALKHVYHSSMSKTKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHVFKISKQYLANVSLKINVKM 681 (813)
Q Consensus 602 ~~~~~~L~~~~~~~~~~~~~~~~~liivIlp~~~~~~Y~~iK~~~e~~~GI~TQci~~~t~~K~~~q~~~Ni~lKiN~KL 681 (813)
..+...+++..+ .+++++|||+|+++.+.|+.||++| .+.||+||||. +++.+...+++.||+||||+||
T Consensus 389 ~~~~~~l~~~~~--------~~~qlvvvIlp~~~~~~y~~IKk~~-~~~GIpTQcV~-~tl~k~~~~ia~NIaLkINaKL 458 (685)
T 3ho1_A 389 LAFREALRKAKE--------EGVQAVLVLTPPMAWEDRNRLKALL-LREGLPSQILN-VPLREEERHRWENALLGLLAKA 458 (685)
T ss_dssp HHHHHHHHHHHH--------TTCCEEEEEESCCCHHHHHHHHHHH-HHTTCCEEEEE-SSCCTTCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH--------CCCCEEEEEECCCCCCHHHHHHHHH-HCCCCCCEEEE-CCCCCCCHHHHHHHHHHHHHHH
T ss_conf 999999998642--------3998899997799954789999998-63997638996-1225640719999999998873
Q ss_pred CCCCCEECCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCEEEEEEECCC-CCCCCCEEEEEECCCCEEHECCCCCCC
Q ss_conf 9623010232237988636999699978530789999999828999995288-975642058885278510110110115
Q 003516 682 GGRNTVLLDAISCRIPLVSDIPTIIFGADVTHPENGEDSSPSIAAVVASQDW-PEVTKYAGLVCAQAHRQELIQDLYKTW 760 (813)
Q Consensus 682 GG~N~~l~~~~~~~ip~~~~~~tMIiG~DVsHp~~~~~~~pSi~avVaS~d~-~~~tky~~~~~~Q~~~qE~i~~l~~~~ 760 (813)
||+||.|+. |. .+|||||+||+|++. .++++++++++. ...++| +....|.+.++.++++
T Consensus 459 GG~pW~L~~------P~---~~tmiIGiDVsH~~~-----~~~~~~aav~~~dg~~~~~-~~~~~Q~~e~l~~~~L---- 519 (685)
T 3ho1_A 459 GLQVVALSG------AY---PAELAVGFDAGGRES-----FRFGGAACAVGGDGGHLLW-TLPEAQAGERIPQEVV---- 519 (685)
T ss_dssp TCCCCEECS------CC---SCSEEEEEEEEETTE-----EEEEEEEEEECC--CCCEE-ECCCCCCSCCCHHHHH----
T ss_pred CCEEEEECC------CC---CCEEEEEEEEECCCC-----CCCCEEEEEEECCCCEEEE-EEEECCCCCEECHHHH----
T ss_conf 983578568------99---986999999973898-----9612399999788887776-7887267858649999----
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECC
Q ss_conf 799766443689999999999972999984999845
Q 003516 761 HDPVRGTVSGGMIRDLLISFRKATGQKPLRIIFYRS 796 (813)
Q Consensus 761 ~d~~~~~~~~~~i~~~L~~f~~~~~~lP~rIIiYRD 796 (813)
.+|+.++|..|++.++.+|+|||||||
T Consensus 520 ---------~~~l~eaL~~Y~k~ng~lP~RIIIyRD 546 (685)
T 3ho1_A 520 ---------WDLLEETLWAFRRKAGRLPSRVLLLRN 546 (685)
T ss_dssp ---------HHHHHHHHHHHHHHHSSCCSEEEEEEC
T ss_pred ---------HHHHHHHHHHHHHHHCCCCCEEEEEEC
T ss_conf ---------999999999999983899848999958
No 6
>2yha_A Post-transcriptional gene silencing protein QDE-2; RNA binding protein, argonaute, miRNA, siRNA; HET: GOL; 1.85A {Neurospora crassa} PDB: 2xdy_A
Probab=1.00 E-value=1 Score=399.16 Aligned_cols=247 Identities=22% Similarity=0.427 Sum_probs=209.6
Q ss_pred CCCEEEEC-CCEECEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 33402314-82200029999388824789999999999998841941378993-02237993489999999999862013
Q 003516 542 MMNKKMIN-GMTVSRWACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPV-IPIHNARPDQVEKALKHVYHSSMSKT 619 (813)
Q Consensus 542 ~~~~kf~~-~~~i~~W~~i~~~~~~~~~~~~~f~~~L~~~~~~~Gi~i~~~p~-~~~~~~~~~~~~~~L~~~~~~~~~~~ 619 (813)
|++++|++ ++++++|+++++.+..+...++.|++.|.+.|+.+||.++.|.. ....... +.+..+ .+++...
T Consensus 2 ~~~~~f~~p~~~l~~W~vv~~~~~~~~~~~~~f~~~l~~~~~~~G~~i~~p~~~~~~~~~~--~~~~~~--~~~~~~~-- 75 (388)
T 2yha_A 2 AMAVKVARPCRKIEKWTYLELKGSKANEGVPQAMTAFAEFLNRTGIPINPRFSPGMSMSVP--GSEKEF--FAKVKEL-- 75 (388)
T ss_dssp ---CCCSBCCSCBCSEEEEEEECSSCCCCHHHHHHHHHHHHHHTTCCBCSCCCCCEEEECC--SSHHHH--HHHHHHH--
T ss_pred CCCCEECCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEECCCCCCCEECCCC--CHHHHH--HHHHHHC--
T ss_conf 9888851699727789999902777879999999999999987697747998754103778--638785--8987504--
Q ss_pred CCCCCEEEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCCHH--HHHHHHHHHHHHCCCCCCEECCCCCCCCC
Q ss_conf 7997249999932899850122556542003702464421321446877--99999999884049623010232237988
Q 003516 620 KGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHVFKISKQ--YLANVSLKINVKMGGRNTVLLDAISCRIP 697 (813)
Q Consensus 620 ~~~~~~liivIlp~~~~~~Y~~iK~~~e~~~GI~TQci~~~t~~K~~~q--~~~Ni~lKiN~KLGG~N~~l~~~~~~~ip 697 (813)
..+++|+|||+|+++.++|+.||++||+++||+||||+.+++.|.+.| |++||+||||+||||+||.|++ .+|
T Consensus 76 -~~~~~lvl~ilp~~~~~~Y~~iK~~~~~~~GI~TQcv~~~~~~k~~~q~s~~~NI~lKiN~KlGG~n~~l~~----~~~ 150 (388)
T 2yha_A 76 -MSSHQFVVVLLPRKDVAIYNMVKRAADITFGVHTVCCVAEKFLSTKGQLGYFANVGLKVNLKFGGTNHNIKT----PIP 150 (388)
T ss_dssp -HHTCSEEEEEESSSCHHHHHHHHHHHHTTTCCEEEEEEHHHHHCSTTHHHHHHHHHHHHHHHTTCBCCCCCS----CCH
T ss_pred -CCCCEEEEEEECCCCHHHHHHHHHHHHCCCCCCEEEEEHHHHCCCCCHHHHHHHHHHHHHHHHCCCCEECCC----CCC
T ss_conf -589829999978998348999999871057975089834560576748999999999999971893312256----655
Q ss_pred CCCCCCEEEEEEEECCCC---CC--CCCCCCEEEEEEECCCCCCCCCEEEEEECC-CCEEHECCCCCCCCCCCCCCCHHH
Q ss_conf 636999699978530789---99--999982899999528897564205888527-851011011011579976644368
Q 003516 698 LVSDIPTIIFGADVTHPE---NG--EDSSPSIAAVVASQDWPEVTKYAGLVCAQA-HRQELIQDLYKTWHDPVRGTVSGG 771 (813)
Q Consensus 698 ~~~~~~tMIiG~DVsHp~---~~--~~~~pSi~avVaS~d~~~~tky~~~~~~Q~-~~qE~i~~l~~~~~d~~~~~~~~~ 771 (813)
++.+.+|||||+||+||+ ++ ....|||+|+|||+| +.+++|.+.+++|. +++|+|++| ++
T Consensus 151 ~~~~~~tmiiG~DV~H~~~~~~g~~~~~~pSiaavVaS~d-~~~~~y~~~~~~Q~~~~~E~i~~l-------------~~ 216 (388)
T 2yha_A 151 LLAKGKTMVVGYDVTHPTNLAAGQSPASAPSIVGLVSTID-QHLGQWPAMVWNNPHGQESMTEQF-------------TD 216 (388)
T ss_dssp HHHTSCEEEEEEEEECSCCCSSSSCCTTSCEEEEEEECCS-TTCCCCCEEEEEETTTHHHHHHHH-------------HH
T ss_pred CCCCCCEEEEEEEEECCCCCCCCCCCCCCCEEEEEEEECC-CCCCEEEEEEEECCCCCCCHHHHH-------------HH
T ss_conf 4577877999877751565677776789987999877759-997779789998688862579999-------------99
Q ss_pred HHHHHHHHHHH---HCCCCCCEEEEECC-----HHHHHHHHHHHHHHHHC
Q ss_conf 99999999999---72999984999845-----26799999999998429
Q 003516 772 MIRDLLISFRK---ATGQKPLRIIFYRS-----LFLSVLRVKVEIISICV 813 (813)
Q Consensus 772 ~i~~~L~~f~~---~~~~lP~rIIiYRD-----Qf~~Vl~~Ei~~Ir~a~ 813 (813)
|++++|+.|++ +++.+|+||||||| ||.+|+++|+++|++|+
T Consensus 217 ~~~~~L~~~~~~~~~~~~~P~rIiiyRDGVseGQf~~V~~~El~~i~~a~ 266 (388)
T 2yha_A 217 KFKTRLELWRSNPANNRSLPENILIFRDGVSEGQFQMVIKDELPLVRAAC 266 (388)
T ss_dssp HHHHHHHHHHHSGGGTTCCCSEEEEEEESCCGGGHHHHHHHTHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999987565437897528999468672579999999999999999
No 7
>2yhb_A QDE-2, post-transcriptional gene silencing protein QDE-2; RNA binding protein, argonaute, miRNA, siRNA; 3.65A {Neurospora crassa}
Probab=1.00 E-value=1 Score=394.30 Aligned_cols=245 Identities=22% Similarity=0.419 Sum_probs=209.1
Q ss_pred CCCEEEEC-CCEECEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCC-C--CCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf 33402314-82200029999388824789999999999998841941378993-0--22379934899999999998620
Q 003516 542 MMNKKMIN-GMTVSRWACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPV-I--PIHNARPDQVEKALKHVYHSSMS 617 (813)
Q Consensus 542 ~~~~kf~~-~~~i~~W~~i~~~~~~~~~~~~~f~~~L~~~~~~~Gi~i~~~p~-~--~~~~~~~~~~~~~L~~~~~~~~~ 617 (813)
+++++|++ ++.+++|+++++....+...++.|++.|.+.|+.+||.+..|.. . .......+.+ .+++...
T Consensus 2 ~~~~~f~~p~~~l~~W~vv~~~~~~~~~~~~~f~~~l~~~~~~~G~~i~~p~~~~~~~~~~~~~~~~--~~~~~~~---- 75 (437)
T 2yhb_A 2 AMAVKVARPCRKIEKWTYLELKGSKANEGVPQAMTAFAEFLNRTGIPINPRFSPGMSMSVPGSEKEF--FAKVKEL---- 75 (437)
T ss_dssp ---CCCSBCCCCBCSEEEEEEECSSCCCCHHHHHHHHHHHHHHTTCCBCSCCCCCEEEECCSSHHHH--HHHHHHH----
T ss_pred CCCCEECCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEECCCCCCCEECCCCCHHHHH--HHHHHHC----
T ss_conf 9888862699727779999912777879999999999999987697717998764103778658887--9987504----
Q ss_pred CCCCCCCEEEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCCHH--HHHHHHHHHHHHCCCCCCEECCCCCCC
Q ss_conf 137997249999932899850122556542003702464421321446877--999999998840496230102322379
Q 003516 618 KTKGKELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHVFKISKQ--YLANVSLKINVKMGGRNTVLLDAISCR 695 (813)
Q Consensus 618 ~~~~~~~~liivIlp~~~~~~Y~~iK~~~e~~~GI~TQci~~~t~~K~~~q--~~~Ni~lKiN~KLGG~N~~l~~~~~~~ 695 (813)
..+++|+|||+|+++.++|+.||++||+++||+||||..+++.|.+.| |++||+||||+||||+||.|++ .
T Consensus 76 ---~~~~~lvl~ilp~~~~~~Y~~iK~~~~~~~gI~TQcv~~~~~~k~~~q~s~~~Ni~lKiN~KlGG~n~~l~~----~ 148 (437)
T 2yhb_A 76 ---MSSHQFVVVLLPRKDVAIYNMVKRAADITFGVHTVCCVAEKFLSTKGQLGYFANVGLKVNLKFGGTNHNIKT----P 148 (437)
T ss_dssp ---HHTCSEEEEEESSCCHHHHHHHHHHHHTTSCCEEEEEEHHHHHCSTTHHHHHHHHHHHHHHHTTCBCCCCSS----C
T ss_pred ---CCCCCEEEEEECCCCHHHHHHHHHHHHCCCCCCCEEEEHHHHCCCCCHHHHHHHHHHHHHHHHCCCCEECCC----C
T ss_conf ---589838999978898348999999870156854189726672476628999999999999984992402366----6
Q ss_pred CCCCCCCCEEEEEEEECCCC---CC--CCCCCCEEEEEEECCCCCCCCCEEEEEECC-CCEEHECCCCCCCCCCCCCCCH
Q ss_conf 88636999699978530789---99--999982899999528897564205888527-8510110110115799766443
Q 003516 696 IPLVSDIPTIIFGADVTHPE---NG--EDSSPSIAAVVASQDWPEVTKYAGLVCAQA-HRQELIQDLYKTWHDPVRGTVS 769 (813)
Q Consensus 696 ip~~~~~~tMIiG~DVsHp~---~~--~~~~pSi~avVaS~d~~~~tky~~~~~~Q~-~~qE~i~~l~~~~~d~~~~~~~ 769 (813)
+|++.+.+|||||+||+||+ ++ ....|||+|+|||+| +.+++|.+.+++|. +++|+|++|
T Consensus 149 ~~~~~~~~tmiiG~DV~H~~~~~~g~~~~~~pSiaa~vaS~d-~~~~~y~~~~~~Q~~~~~E~i~~l------------- 214 (437)
T 2yhb_A 149 IPLLAKGKTMVVGYDVTHPTNLAAGQSPASAPSIVGLVSTID-QHLGQWPAMVWNNPHGQESMTEQF------------- 214 (437)
T ss_dssp CHHHHTTCEEEEEEEECCCSCCCTTCCSTTSCEEEEEEECCS-TTCCCCCEEEEEETTTHHHHHHHH-------------
T ss_pred CCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCEEEEEEEECC-CCCCEEEEEEEECCCCCHHHHHHH-------------
T ss_conf 454577877999888752565567776789997999987349-996744027898677644489999-------------
Q ss_pred HHHHHHHHHHHHH---HCCCCCCEEEEECC-----HHHHHHHHHHHHHHHHC
Q ss_conf 6899999999999---72999984999845-----26799999999998429
Q 003516 770 GGMIRDLLISFRK---ATGQKPLRIIFYRS-----LFLSVLRVKVEIISICV 813 (813)
Q Consensus 770 ~~~i~~~L~~f~~---~~~~lP~rIIiYRD-----Qf~~Vl~~Ei~~Ir~a~ 813 (813)
++|++++|+.|++ +++.+|+||||||| ||.+|+++|+++|++|+
T Consensus 215 ~~~~~~~L~~~~~~~~~~~~~P~rIiiyRDGVseGqf~~V~~~El~~i~~a~ 266 (437)
T 2yhb_A 215 TDKFKTRLELWRSNPANNRSLPENILIFRDGVSEGQFQMVIKDELPLVRAAC 266 (437)
T ss_dssp HHHHHHHHHHHHTCGGGTTCCCSEEEEEEESCCTTTHHHHHHHTHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999986554337998638999177566779999999999999999
No 8
>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
Probab=1.00 E-value=1 Score=244.28 Aligned_cols=249 Identities=13% Similarity=0.056 Sum_probs=166.8
Q ss_pred ECCCCEEEECCCCCCC-----CCCCCCCCCCCCCEEEECCCEE--CEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 6299816414589743-----3478776323334023148220--00299993888247899999999999988419413
Q 003516 516 ILPAPWLKYHENGKEK-----DCLPQVGQWNMMNKKMINGMTV--SRWACINFSRSVQESVARGFCNELAQMCQVSGMEF 588 (813)
Q Consensus 516 vLppP~I~y~~~~~~~-----~v~p~~g~Wn~~~~kf~~~~~i--~~W~~i~~~~~~~~~~~~~f~~~L~~~~~~~Gi~i 588 (813)
-|..|.+.|+.++... ..+|..| +.+...+..... .+|++|+..+.. ..++.|.+.+.... ..++.+
T Consensus 5 ~~~ep~~~~~~~~~~~~~~~~~~~~~~g---l~~~gpy~~~~~~~~~w~vI~~~~~~--~~l~~l~~~~~~~~-g~~f~~ 78 (427)
T 2w42_A 5 KIVENGLTYRIGNGASVPISNTGELIKG---LRNYGPYEVPSLKYNQIALIHNNQFS--SLINQLKSQISSKI-DEVWHI 78 (427)
T ss_dssp ------CEEECGGGCEEESSCHHHHHHH---HHHHCCSBCCCCSSSEEEEEESCTTC--HHHHHHHHHHHHHH-HHTTCC
T ss_pred CCCCCCCEEECCCCCCCCCCCCCCHHHH---HHHCCCCCCCCCCCCEEEEEECCCCH--HHHHHHHHHHHHCC-CCCEEE
T ss_conf 4478753441247973444456787899---98669974677889889999773308--99999987533128-984053
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEE--------CCCCCCCHHHHHHHHHHCCCCEEEEEECC
Q ss_conf 7899302237993489999999999862013799724999993--------28998501225565420037024644213
Q 003516 589 NPEPVIPIHNARPDQVEKALKHVYHSSMSKTKGKELELLLAIL--------PDNNGSLYGDLKRICETDLGIISQCCLTK 660 (813)
Q Consensus 589 ~~~p~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~liivIl--------p~~~~~~Y~~iK~~~e~~~GI~TQci~~~ 660 (813)
..+. .+.+.|.+++.+..+ .+++++|||+ |+++...| .+|+ ++.++||+||||..+
T Consensus 79 ~~~~------~~~~~y~~~i~~~l~--------~~~~lvlvilp~~~~~~~~~~~~~~y-~~K~-~~~~~gvptQ~I~~~ 142 (427)
T 2w42_A 79 HNIN------ISEFIYDSPHFDSIK--------SQVDNAIDTGVDGIMLVLPEYNTPLY-YKLK-SYLINSIPSQFMRYD 142 (427)
T ss_dssp CSCE------EEEEECSSSSHHHHH--------HHHHHHHHHCCSEEEEEESSCCHHHH-HHHH-HHHHTTSCEEEEEGG
T ss_pred CCCC------CCHHHHHHHHHHHHC--------CCCCEEEEEEECCCCCCCCCCCCCHH-HHHH-HHHCCCCCCEEEEHH
T ss_conf 5776------780789999999743--------79979999997601045898775059-9999-986799675898733
Q ss_pred CCCCCCH-HHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCCC
Q ss_conf 2144687-799999999884049623010232237988636999699978530789999999828999995288975642
Q 003516 661 HVFKISK-QYLANVSLKINVKMGGRNTVLLDAISCRIPLVSDIPTIIFGADVTHPENGEDSSPSIAAVVASQDWPEVTKY 739 (813)
Q Consensus 661 t~~K~~~-q~~~Ni~lKiN~KLGG~N~~l~~~~~~~ip~~~~~~tMIiG~DVsHp~~~~~~~pSi~avVaS~d~~~~tky 739 (813)
|+.+.+. .++.||++|||+||||+||.|+.. .|. .+|||||+||+|++.+ +++|++.+.| .+...+
T Consensus 143 tl~~~~~~~~~~nIalqi~~KlGG~pW~l~~~----~~~---~~~miiGidv~h~~~~-----~v~g~a~v~~-~~g~~~ 209 (427)
T 2w42_A 143 ILSNRNLTFYVDNLLVQFVSKLGGKPWILNVD----PEK---GSDIIIGTGATRIDNV-----NLFCFAMVFK-KDGTML 209 (427)
T ss_dssp GCCTTTHHHHHHHHHHHHHHHTTCBCCEECCC----TTS---SCSEEEEEEEEESSSS-----EEEEEEEEEC-TTSCEE
T ss_pred HCCCCCCHHHHHHHHHHHHHHHCCCCEECCCC----CCC---CCEEEEEEEEEECCCC-----CEEEEEEEEC-CCCCEE
T ss_conf 54556505699999999978738966064567----898---9869997899876999-----5799999983-899789
Q ss_pred EEEEEECCCCEEHECCCCCCCCCCCCCCCHHHHHHHHHHHHHH-HCCCCCC--EEEEECCHHHHHHHHHHHHHHHHC
Q ss_conf 0588852785101101101157997664436899999999999-7299998--499984526799999999998429
Q 003516 740 AGLVCAQAHRQELIQDLYKTWHDPVRGTVSGGMIRDLLISFRK-ATGQKPL--RIIFYRSLFLSVLRVKVEIISICV 813 (813)
Q Consensus 740 ~~~~~~Q~~~qE~i~~l~~~~~d~~~~~~~~~~i~~~L~~f~~-~~~~lP~--rIIiYRDQf~~Vl~~Ei~~Ir~a~ 813 (813)
...+..|.+++|++++| +.+++++|..|++ .|+.+|+ |||||. ||.+++++|+++|++|+
T Consensus 210 ~~~~~~~~~~~E~~~~l-------------~~~l~~aL~~y~~~~~~~~P~~~rIii~g-q~~~v~~~Ei~~i~~a~ 272 (427)
T 2w42_A 210 WNEISPIVTSSEYLTYL-------------KSTIKKVVYGFKKSNPDWDVEKLTLHVSG-KRPKMKDGETKILKETV 272 (427)
T ss_dssp EEEECCCEEGGGHHHHH-------------HHHHHHHHHHHHHHCTTCCCSEEEEEEES-SCCSCHHHHHHHHHHHH
T ss_pred EEEEEECCCHHHHHHHH-------------HHHHHHHHHHHHHHHCCCCCCCEEEEEEE-ECCCCCHHHHHHHHHHH
T ss_conf 99888427706799999-------------99999999999987427899825999992-14111699999999999
No 9
>4g0x_A Protein argonaute 1; MID domain, small RNA 5' nucleotide recognition, gene regula; 1.35A {Arabidopsis thaliana} PDB: 4g0q_A* 4g0p_A 4g0y_A* 4g0z_A* 3vna_A 3vnb_A
Probab=1.00 E-value=1 Score=218.65 Aligned_cols=145 Identities=76% Similarity=1.244 Sum_probs=130.4
Q ss_pred CEEEECCCEECEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC-CCC
Q ss_conf 4023148220002999938882478999999999999884194137899302237993489999999999862013-799
Q 003516 544 NKKMINGMTVSRWACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARPDQVEKALKHVYHSSMSKT-KGK 622 (813)
Q Consensus 544 ~~kf~~~~~i~~W~~i~~~~~~~~~~~~~f~~~L~~~~~~~Gi~i~~~p~~~~~~~~~~~~~~~L~~~~~~~~~~~-~~~ 622 (813)
+++|++|+++++|+++++++..++..++.|++.|.+.|+.+||.+++|+.+.+...+++++++.|+++++++.++. ++.
T Consensus 2 ~kkf~~~~~l~~Wavv~~~~~~~~~~~~~F~~~L~~~~~~~Gm~i~~p~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 81 (147)
T 4g0x_A 2 NKKMINGGTVNNWICINFSRQVQDNLARTFCQELAQMCYVSGMAFNPEPVLPPVSARPEQVEKVLKTRYHDATSKLSQGK 81 (147)
T ss_dssp CCCEEECCEECSEEEEECCTTCCHHHHHHHHHHHHHHHHHTTCEECSSCSSCCEECCGGGHHHHHHHHHHHHHHTSSTTC
T ss_pred CCEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 88770277467489998468776799999999999999984997799986521478817799999999999986404489
Q ss_pred CCEEEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCEE
Q ss_conf 724999993289985012255654200370246442132144687799999999884049623010
Q 003516 623 ELELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHVFKISKQYLANVSLKINVKMGGRNTVL 688 (813)
Q Consensus 623 ~~~liivIlp~~~~~~Y~~iK~~~e~~~GI~TQci~~~t~~K~~~q~~~Ni~lKiN~KLGG~N~~l 688 (813)
+++|+|||+|+++.++|+.||++||+++||+||||+.+++.|.++||++||+||||+||||+||.|
T Consensus 82 ~~~lv~~il~~~~~~~Y~~iK~~~~~~~gi~tqcv~~~~~~k~~~q~~~nv~lKiN~KlGG~N~~l 147 (147)
T 4g0x_A 82 EIDLLIVILPDNNGSLYGDLKRICETELGIVSQCCLTKHVFKMSKQYMANVALKINVKVGGRNTVL 147 (147)
T ss_dssp CCCEEEEEECSSCTTHHHHHHHHCCCCCCCCEEEEEHHHHHHCCHHHHHHHHHHHHHHTTCEECCC
T ss_pred CCEEEEEEECCCCCCHHHHHHHHHCCCCCCCCEEECHHHHCCCCHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 971999996899940789999987327891658854455167778899999999977657545639
No 10
>4g0o_A Protein argonaute 5; MID domain, small RNA 5' nucleotide recognition, gene regula; 2.19A {Arabidopsis thaliana}
Probab=1.00 E-value=1 Score=211.58 Aligned_cols=138 Identities=51% Similarity=1.003 Sum_probs=123.8
Q ss_pred CEEEECCCEECEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 40231482200029999388824789999999999998841941378993022379934899999999998620137997
Q 003516 544 NKKMINGMTVSRWACINFSRSVQESVARGFCNELAQMCQVSGMEFNPEPVIPIHNARPDQVEKALKHVYHSSMSKTKGKE 623 (813)
Q Consensus 544 ~~kf~~~~~i~~W~~i~~~~~~~~~~~~~f~~~L~~~~~~~Gi~i~~~p~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~ 623 (813)
+++|++|+++++|++++|++..++..++.|++.|.+.|+.+||.+++||.+.....++++++..|+++++++ .+
T Consensus 2 ~kkf~~~~~l~~W~vv~~~~~~~~~~~~~F~~~L~~~~~~~Gm~i~~p~~~~~~~~~~~~~e~~l~~~~~~~------~~ 75 (139)
T 4g0o_A 2 DKKMVNGAKVTSWTCVSFSTRIDRGLPQEFCKQLIGMCVSKGMEFKPQPAIPFISCPPEHIEEALLDIHKRA------PG 75 (139)
T ss_dssp CEEEEECCEECSEEEEECCSSSCTTHHHHHHHHHHHHHHHHTCEECSSCSSCCEECCGGGHHHHHHHHHHHC------TT
T ss_pred CCEECCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHC------CC
T ss_conf 886835852574899983697798999999999999999849834899887563688336999999999756------89
Q ss_pred CEEEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCEE
Q ss_conf 24999993289985012255654200370246442132144687799999999884049623010
Q 003516 624 LELLLAILPDNNGSLYGDLKRICETDLGIISQCCLTKHVFKISKQYLANVSLKINVKMGGRNTVL 688 (813)
Q Consensus 624 ~~liivIlp~~~~~~Y~~iK~~~e~~~GI~TQci~~~t~~K~~~q~~~Ni~lKiN~KLGG~N~~l 688 (813)
++|+|||+|+++.+ |+.||++||+++||+||||+.+++.|.++||++||+||||+||||+||.|
T Consensus 76 ~qlv~~ilp~~~~~-Y~~iK~~~~~~~gi~tQcv~~~~~~k~~~q~~~nv~lKiN~KlGG~N~~l 139 (139)
T 4g0o_A 76 LQLLIVILPDVTGS-YGKIKRICETELGIVSQCCQPRQVNKLNKQYMENVALKINVKTGGRNTVL 139 (139)
T ss_dssp CSEEEEECCSSSSC-HHHHHCCCCCCCCCCEEEECHHHHHHTCHHHHHHHHHHHHHHTTCEEEEC
T ss_pred CCEEEEEECCCCCC-HHHHHHHHHCCCCCCEEEECHHHHCCCCHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 96899998999975-89999988516883439961455057778899999999822127555719
Done!