Query 000509
Match_columns 1456
No_of_seqs 352 out of 1728
Neff 6.0
Searched_HMMs 29240
Date Tue Mar 26 17:39:06 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000509.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_281-285//hhsearch_pdb/000509hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 4b3f_X DNA-binding protein smu 1.0 1 1 574.3 34.9 407 818-1311 188-632 (646)
2 2xzl_A ATP-dependent helicase 1.0 1 1 490.8 35.7 394 818-1314 359-787 (802)
3 2wjy_A Regulator of nonsense t 1.0 1 1 488.8 35.0 397 818-1315 355-786 (800)
4 2gk6_A Regulator of nonsense t 1.0 1 1 487.5 32.1 397 818-1316 179-611 (624)
5 3e1s_A Exodeoxyribonuclease V, 1.0 1 1 225.5 20.6 278 817-1292 187-546 (574)
6 3lfu_A DNA helicase II; SF1 he 1.0 1 1 222.3 30.2 344 818-1226 8-372 (647)
7 1pjr_A PCRA; DNA repair, DNA r 1.0 1 1 214.7 22.4 342 818-1223 10-373 (724)
8 1uaa_A REP helicase, protein ( 1.0 1 1 208.2 25.5 334 818-1222 1-363 (673)
9 3upu_A ATP-dependent DNA helic 1.0 1 1 196.9 21.5 293 818-1284 24-459 (459)
10 1w36_D RECD, exodeoxyribonucle 1.0 1 1 194.6 22.8 325 821-1292 151-588 (608)
No 1
>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A
Probab=1.00 E-value=1 Score=574.26 Aligned_cols=407 Identities=26% Similarity=0.295 Sum_probs=301.6
Q ss_pred CCCCHHHHHHHHHCC-CCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCEEE
Q ss_conf 889999999999613-8990999947999968999999999998099994799925789999999999834999653887
Q 000509 818 VRFTPTQVGAIISGI-QPGLTMVVGPPGTGKTDTAVQILNVLYHNCPSQRTLIITHSNQALNDLFEKIMQRDVPARYLLR 896 (1456)
Q Consensus 818 i~Ln~sQ~eAI~s~l-~~gltLI~GPPGTGKT~via~iI~~Ll~~~p~~kILIva~SN~Ald~L~ekL~~l~i~~~~llR 896 (1456)
-.||++|.+||..++ ++++++|+||||||||+|++++|..++++ +.+||+|||||.|+|++.+||...+.. ++|
T Consensus 188 ~~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~--~~~ILv~a~TN~AvD~i~erL~~~~~~---ilR 262 (646)
T 4b3f_X 188 TCLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ--GLKVLCCAPSNIAVDNLVERLALCKQR---ILR 262 (646)
T ss_dssp TTCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHHHHTTCC---EEE
T ss_pred CCCCHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEECCCHHHHHHHHHHHHHCCCC---EEE
T ss_conf 888999999999996589965998899988899999999999848--982999918518887999999862776---588
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 06761001223320245678999999999999999999862999763442001003567645789999999962038997
Q 000509 897 LGQGEQELATDLDFSRQGRVNAMLVRRLELLSEVERLARSLQLPEDVGYTCETAGYFWLLHVYSRWEQFLAACADNEGKP 976 (1456)
Q Consensus 897 lG~~e~~l~~~~~~s~~gRv~~~l~~r~~lL~ev~kLa~~l~~~~~~~~sceta~~f~~~~i~~~w~~f~~~~~~~~~~~ 976 (1456)
+|+..+..+....++....+ ... ... ..+......+.......
T Consensus 263 lG~~~r~~~~~~~~~l~~~~---------------------~~~-------~~~---------~~~~~~~~~~~~~~~~~ 305 (646)
T 4b3f_X 263 LGHPARLLESIQQHSLDAVL---------------------ARS-------DSA---------QIVADIRKDIDQVFVKN 305 (646)
T ss_dssp CSCCSSCCHHHHTTBHHHHH---------------------TTT-------TCS---------STHHHHHHHHTTSSTTT
T ss_pred ECCHHHHHHHHHHHHHHHHH---------------------HHC-------HHH---------HHHHHHHHHHHHHHHHH
T ss_conf 23656520255430188898---------------------504-------178---------89999998889999863
Q ss_pred CCCCCCCCHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCHH
Q ss_conf 31123464124520699999877417899999989999999999999998989997977988777521157499974435
Q 000509 977 TFVRDRFPFKEFFSNTPQPIFTGDSFEKDMRAAKGCFRHLQTLFQELEECRAFELLKSTADRANYLMTKQAKIVAMTCTH 1056 (1456)
Q Consensus 977 ~~i~~~fpf~~~f~~~p~~l~~~~s~e~~l~~a~~~~~~i~~if~eL~e~r~felLr~~~dr~~~lllk~arIIa~T~t~ 1056 (1456)
. .. .+..........+..+..++.+. ........+..+++|++||+.
T Consensus 306 ~----------~~--------------~~~~~~~~~~~~~~~l~~~l~~~---------~~~~~~~~l~~~~vv~~t~~~ 352 (646)
T 4b3f_X 306 K----------KT--------------QDKREKSNFRNEIKLLRKELKER---------EEAAMLESLTSANVVLATNTG 352 (646)
T ss_dssp T----------C--------------------CCSSHHHHHHHHHHHHHH---------HHHHHHHHHHHCSEEEEETTT
T ss_pred H----------HH--------------HHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHCCEEEEEHHH
T ss_conf 4----------32--------------23788877788999999999888---------888889887633542222012
Q ss_pred HHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHC-------CCCCCCCEECCHHHHHHCCCCCCHHHHHHHC--CC
Q ss_conf 76644677430897798999439899927898778717-------9888886011423331037952089999981--99
Q 000509 1057 AALKRKDFLQLGFKYDNLLMEESAQILEIETFIPMLLN-------DRRMLPPVVKNMAFQKYSHMDQSLFTRFVRL--GI 1127 (1456)
Q Consensus 1057 aa~~~~~l~~lg~~fD~VIIDEAsQitE~EtlIPLll~-------Dh~QLpPvV~s~~~~~~~~l~qSLFeRL~r~--g~ 1127 (1456)
++...........+||+||||||+|++|+++++|+..+ ||+||||++.+..... .+++.|+|+|+... +.
T Consensus 353 a~~~~~~~~~~~~~Fd~vIIDEAsQ~~e~~~lipL~~~~~~ILVGD~~QLpP~v~~~~a~~-~gl~~SlferL~~~~~~~ 431 (646)
T 4b3f_X 353 ASADGPLKLLPESYFDVVVIDECAQALEASCWIPLLKARKCILAGDHKQLPPTTVSHKAAL-AGLSLSLMERLAEEYGAR 431 (646)
T ss_dssp TCSSSGGGGSCTTCCSEEEETTGGGSCHHHHTTTGGGSSEEEEEECTTSCCCCCSCHHHHH-TTTTCCHHHHHHHHHGGG
T ss_pred HHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHCCCCCEEEECCCCCCCCCEECCHHHHH-CCCCCHHHHHHHHHCCCC
T ss_conf 2233588764312688899717544455788752035542897078655685012436666-054112999999866986
Q ss_pred CEEECCCCCCCCHHHHHHHHHHHCCCC-------------CCCC------------EEECCCCCCCCCCCCCCCCCCCHH
Q ss_conf 814045554673347999999741489-------------9992------------253389999876689988668999
Q 000509 1128 PYIELNAQGRARPSIAQLYNWRYRDLG-------------DLPF------------LVDVPDYNGRGESAPSPWFYQNEG 1182 (1456)
Q Consensus 1128 p~i~L~~QYRs~PsIa~l~n~~yy~l~-------------dlp~------------fIdV~~~~g~~e~~~~~~S~~N~~ 1182 (1456)
+..+|+.||||||.|+.|+|..||+.. ++|. |+|+.+..........+.|+.|..
T Consensus 432 ~v~~L~~qYRmhp~I~~f~n~~fY~g~L~~~~~~~~~~~~~lp~~~~~~~~~~p~~f~d~~g~~~~~~~~~~~~s~~N~~ 511 (646)
T 4b3f_X 432 VVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAATEETGVPLLLVDTAGCGLFELEEEDEQSKGNPG 511 (646)
T ss_dssp TEEECCEESSSCHHHHHHHHHHHSTTCCEECTTTTTCCGGGSTTCCCCTTTTCSEEEEECTTSSCCCCC-----CCCCHH
T ss_pred EEEECCCCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCHH
T ss_conf 15535201277688886557763188454584066554203666666645688527885488764322026886646789
Q ss_pred HHHHHHHHHHHHHHHCCCCCCEEEECCCHHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCCCCCCCCEEEEEECCCC---
Q ss_conf 99999999999999199999779843778899999999973189999889993251256898755779999702369---
Q 000509 1183 EAEYVVSVYIYMRLLGYPANKISILTTYNGQKLLIRDVINRQCVPYPFIGPPSKVTTVDKFQGQQNDFILLSLVRTR--- 1259 (1456)
Q Consensus 1183 EAe~VV~iv~~L~~~Gy~~~kIaIITpY~aQ~~lIr~~L~~r~~~~~~~g~~vkV~TVD~fQG~E~DiVIlSlVRs~--- 1259 (1456)
||++|+.+++.+...|+++++|||||||++|+.+|++.|..+. ..+.|+|||+|||+|+|+||+|+||++
T Consensus 512 EA~~V~~~v~~L~~~gv~~~dIgVItpYraQ~~~l~~~l~~~~-------~~i~v~TVd~fQG~E~dvII~S~vrsn~~~ 584 (646)
T 4b3f_X 512 EVRLVSLHIQALVDAGVPARDIAVVSPYNLQVDLLRQSLVHRH-------PELEIKSVDGFQGREKEAVILSFVRSNRKG 584 (646)
T ss_dssp HHHHHHHHHHHHHHHTCCGGGEEEEESCHHHHHHHHHHHTTTC-------TTCEEEEGGGGTTCCEEEEEEECCCCCTTC
T ss_pred HHHHHHHHHHHHHHCCCCCCCEEEECCCHHHHHHHHHHHHHHC-------CCCEECCHHHCCCCCCCEEEEEECCCCCCC
T ss_conf 9999999999999669896849998997999999999999759-------997987843166454788999950679999
Q ss_pred CCCCCCCCHHHHHHHHHHHCCEEEEECHHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf 8665565102578875432257999120256530140689999970921103
Q 000509 1260 FVGHLRDVRRLVVAMSRARLGLYVFCRRSLFEQCYELQPTFRLLLQRPDKLA 1311 (1456)
Q Consensus 1260 ~vGfL~d~rRLNVAlSRAK~~LiIVGn~~~l~~~~~~~~~~~~ll~~~~~l~ 1311 (1456)
.+||+.+.||||||+||||.+||||||..++++. +.|+.|++++...+
T Consensus 585 ~iGFl~~~rRlNVAlTRAk~~liivGn~~~l~~~----~~~~~li~~~~~~g 632 (646)
T 4b3f_X 585 EVGFLAEDRRINVAVTRARRHVAVICDSRTVNNH----AFLKTLVEYFTQHG 632 (646)
T ss_dssp CCCSTTCHHHHHHHHHTEEEEEEEEECHHHHTTS----HHHHHHHHHHHHSS
T ss_pred CCCCCCCCCCEEEEHHHHHCEEEEEECHHHHCCC----HHHHHHHHHHHHCC
T ss_conf 9664489684872745661808999726896478----79999999999879
No 2
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}
Probab=1.00 E-value=1 Score=490.81 Aligned_cols=394 Identities=26% Similarity=0.358 Sum_probs=293.2
Q ss_pred CCCCHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCEEEC
Q ss_conf 88999999999961389909999479999689999999999980999947999257899999999998349996538870
Q 000509 818 VRFTPTQVGAIISGIQPGLTMVVGPPGTGKTDTAVQILNVLYHNCPSQRTLIITHSNQALNDLFEKIMQRDVPARYLLRL 897 (1456)
Q Consensus 818 i~Ln~sQ~eAI~s~l~~gltLI~GPPGTGKT~via~iI~~Ll~~~p~~kILIva~SN~Ald~L~ekL~~l~i~~~~llRl 897 (1456)
..||++|.+||..++..++++|+||||||||+|++.++..++.. ++.+||+||+||.|+|++.++|.+.++. ++|+
T Consensus 359 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~~l~~~-~~~~ILv~a~tn~A~d~l~~rL~~~g~~---ilR~ 434 (802)
T 2xzl_A 359 AQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKI-HKDRILVCAPSNVAVDHLAAKLRDLGLK---VVRL 434 (802)
T ss_dssp CCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHHHHHHH-HCCCEEEEESSHHHHHHHHHHHHHTTCC---EEEC
T ss_pred CCCCHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHHHHHHHHHCCC---EEEE
T ss_conf 56899999999998639977998789977899999999999867-9972999848579999999999862750---7862
Q ss_pred CCCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 6761001-223320245678999999999999999999862999763442001003567645789999999962038997
Q 000509 898 GQGEQEL-ATDLDFSRQGRVNAMLVRRLELLSEVERLARSLQLPEDVGYTCETAGYFWLLHVYSRWEQFLAACADNEGKP 976 (1456)
Q Consensus 898 G~~e~~l-~~~~~~s~~gRv~~~l~~r~~lL~ev~kLa~~l~~~~~~~~sceta~~f~~~~i~~~w~~f~~~~~~~~~~~ 976 (1456)
|+..... ...... ..+...+ .. +... ....+........
T Consensus 435 g~~~r~~i~~~~~~---~tl~~~~--------------~~----------~~~~----------~l~~l~~~~~~~~--- 474 (802)
T 2xzl_A 435 TAKSREDVESSVSN---LALHNLV--------------GR----------GAKG----------ELKNLLKLKDEVG--- 474 (802)
T ss_dssp CCGGGTTSCCTTGG---GBHHHHH--------------HT----------TCCT----------HHHHHHHHHHHHS---
T ss_pred CCCCHHHHCCHHHH---HHHHHHH--------------HH----------HCHH----------HHHHHHHHHHHHC---
T ss_conf 22322210315656---4299999--------------85----------1689----------9999999988644---
Q ss_pred CCCCCCCCHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCHH
Q ss_conf 31123464124520699999877417899999989999999999999998989997977988777521157499974435
Q 000509 977 TFVRDRFPFKEFFSNTPQPIFTGDSFEKDMRAAKGCFRHLQTLFQELEECRAFELLKSTADRANYLMTKQAKIVAMTCTH 1056 (1456)
Q Consensus 977 ~~i~~~fpf~~~f~~~p~~l~~~~s~e~~l~~a~~~~~~i~~if~eL~e~r~felLr~~~dr~~~lllk~arIIa~T~t~ 1056 (1456)
.+ + ..+ .+.|..+ .......+++.++||++||.+
T Consensus 475 -------------------~l---s-~~~--------------------~~~~~~~---~~~~~~~~l~~a~VI~~T~~~ 508 (802)
T 2xzl_A 475 -------------------EL---S-ASD--------------------TKRFVKL---VRKTEAEILNKADVVCCTCVG 508 (802)
T ss_dssp -------------------CC---C-HHH--------------------HHHHHHH---HHHHHHHHHHTCSEEEEETTG
T ss_pred -------------------CC---C-HHH--------------------HHHHHHH---HHHHHHHHHCCCCEEEECHHH
T ss_conf -------------------57---8-889--------------------9888999---999999875239999833233
Q ss_pred HHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHC--------CCCCCCCEECCHHHHHHCCCCCCHHHHHHHCCCC
Q ss_conf 76644677430897798999439899927898778717--------9888886011423331037952089999981998
Q 000509 1057 AALKRKDFLQLGFKYDNLLMEESAQILEIETFIPMLLN--------DRRMLPPVVKNMAFQKYSHMDQSLFTRFVRLGIP 1128 (1456)
Q Consensus 1057 aa~~~~~l~~lg~~fD~VIIDEAsQitE~EtlIPLll~--------Dh~QLpPvV~s~~~~~~~~l~qSLFeRL~r~g~p 1128 (1456)
++..+ +. .+||+||||||+|+++++.++|++.. ||+||||++.+..... .++++|+|+|+...+.+
T Consensus 509 ~~~~~--L~---~~fd~viIDEA~q~~e~~~li~l~~~~~~lilvGD~~QL~pvv~s~~a~~-~gl~~slferl~~~~~~ 582 (802)
T 2xzl_A 509 AGDKR--LD---TKFRTVLIDESTQASEPECLIPIVKGAKQVILVGDHQQLGPVILERKAAD-AGLKQSLFERLISLGHV 582 (802)
T ss_dssp GGCTT--CC---SCCSEEEETTGGGSCHHHHHHHHTTTBSEEEEEECTTSCCCCCCCHHHHH-TTTTCCHHHHHHHTTCC
T ss_pred CCHHH--HH---CCCCEEEEECCCCCCHHHHHHHHHHCCCEEEEEECCCCCCCEECHHHHHH-CCCCHHHHHHHHHCCCC
T ss_conf 17277--75---56999999885032447899999857998999807611387141054656-58743599999866998
Q ss_pred EEECCCCCCCCHHHHHHHHHHHCCCCC---------------CC-------C-EEECCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf 140455546733479999997414899---------------99-------2-253389999876689988668999999
Q 000509 1129 YIELNAQGRARPSIAQLYNWRYRDLGD---------------LP-------F-LVDVPDYNGRGESAPSPWFYQNEGEAE 1185 (1456)
Q Consensus 1129 ~i~L~~QYRs~PsIa~l~n~~yy~l~d---------------lp-------~-fIdV~~~~g~~e~~~~~~S~~N~~EAe 1185 (1456)
.+.|++||||||+|++|+|..||+... .+ . |+++. |..+....+.|+.|..||+
T Consensus 583 ~~~L~~qYRm~p~I~~f~n~~fY~g~L~~~~~~~~r~~~~~~~~~~~~~~p~~f~~~~---g~~~~~~~~~s~~N~~EA~ 659 (802)
T 2xzl_A 583 PIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWANY---GREEISANGTSFLNRIEAM 659 (802)
T ss_dssp CEECCEECSSCHHHHHHHHHHHSTTCCEESSCTTTTCCTTCCCCCSSTTCCEEEEECC---CCCEECTTSSSEECHHHHH
T ss_pred CEEEEEECCCCHHHHHHHHHHHCCCCCCCCCCHHHHCCCCCCCCCCCCCCCEEEEECC---CCEEECCCCCCCCCHHHHH
T ss_conf 3475200488868999889875288465687534311455567777899987999868---9502137898868999999
Q ss_pred HHHHHHHHHHHHCCCCCCEEEECCCHHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCCCCCCCCEEEEEECCCC---CCC
Q ss_conf 99999999999199999779843778899999999973189999889993251256898755779999702369---866
Q 000509 1186 YVVSVYIYMRLLGYPANKISILTTYNGQKLLIRDVINRQCVPYPFIGPPSKVTTVDKFQGQQNDFILLSLVRTR---FVG 1262 (1456)
Q Consensus 1186 ~VV~iv~~L~~~Gy~~~kIaIITpY~aQ~~lIr~~L~~r~~~~~~~g~~vkV~TVD~fQG~E~DiVIlSlVRs~---~vG 1262 (1456)
+|+.++..+...|+++++|||||||++|+.+|++.|...+........++.|+|||+|||+|+|+||+|+||++ .+|
T Consensus 660 ~V~~~v~~L~~~g~~~~~IgVItpy~~Q~~~I~~~L~~~~~l~~~~~~~v~V~TVd~fQG~E~dvVIlS~vrs~~~~~~g 739 (802)
T 2xzl_A 660 NCERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIG 739 (802)
T ss_dssp HHHHHHHHHHHTTCCGGGEEEEESCHHHHHHHHHHHHHHCSSCHHHHHTSEEEEHHHHTTCCEEEEEEECCCCCTTCCCG
T ss_pred HHHHHHHHHHHCCCCCCCEEEECCCHHHHHHHHHHHHHCCCCCCCCCCCEEECCHHHCCCCCCCEEEEEECCCCCCCCCC
T ss_conf 99999999997599834289983669999999999987256550013665982354348872677999823688877734
Q ss_pred CCCCCHHHHHHHHHHHCCEEEEECHHHHHHHCCCHHHHHHHHCCCCCCCCCC
Q ss_conf 5565102578875432257999120256530140689999970921103445
Q 000509 1263 HLRDVRRLVVAMSRARLGLYVFCRRSLFEQCYELQPTFRLLLQRPDKLALTM 1314 (1456)
Q Consensus 1263 fL~d~rRLNVAlSRAK~~LiIVGn~~~l~~~~~~~~~~~~ll~~~~~l~l~~ 1314 (1456)
|+.+.||||||+||||.+||||||..++.+. +.|+.+++++...+.+.
T Consensus 740 fl~d~rrLNVAlTRAk~~LiIvg~~~~l~~~----~~w~~ll~~~~~~~~~~ 787 (802)
T 2xzl_A 740 FLRDPRRLNVGLTRAKYGLVILGNPRSLARN----TLWNHLLIHFREKGCLV 787 (802)
T ss_dssp GGGCHHHHHHHHSSEEEEEEEEECHHHHTTS----HHHHHHHHHHHHHTCEE
T ss_pred CCCCCCCEEEEHHHHHCEEEEEECHHHHCCC----HHHHHHHHHHHHCCCEE
T ss_conf 1258451112574652839999887996117----69999999999859962
No 3
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A
Probab=1.00 E-value=1 Score=488.79 Aligned_cols=397 Identities=28% Similarity=0.396 Sum_probs=294.7
Q ss_pred CCCCHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCEEEC
Q ss_conf 88999999999961389909999479999689999999999980999947999257899999999998349996538870
Q 000509 818 VRFTPTQVGAIISGIQPGLTMVVGPPGTGKTDTAVQILNVLYHNCPSQRTLIITHSNQALNDLFEKIMQRDVPARYLLRL 897 (1456)
Q Consensus 818 i~Ln~sQ~eAI~s~l~~gltLI~GPPGTGKT~via~iI~~Ll~~~p~~kILIva~SN~Ald~L~ekL~~l~i~~~~llRl 897 (1456)
..||++|.+||..++..++++|+||||||||+|++.++..+... ++.+||+||+||.|++++.+++.+.+++ ++|+
T Consensus 355 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~g~~---vvRl 430 (800)
T 2wjy_A 355 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQTGLK---VVRL 430 (800)
T ss_dssp CCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHHHHHHHHTT-CSSCEEEEESSHHHHHHHHHHHHTTTCC---EEEC
T ss_pred CCCCHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHC-CCCCEEEECCCHHHHHHHHHHHHHHCCC---EEEE
T ss_conf 67799999999874259917998699999899999999999974-8981999869689999999999872754---1762
Q ss_pred CCCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 6761001-223320245678999999999999999999862999763442001003567645789999999962038997
Q 000509 898 GQGEQEL-ATDLDFSRQGRVNAMLVRRLELLSEVERLARSLQLPEDVGYTCETAGYFWLLHVYSRWEQFLAACADNEGKP 976 (1456)
Q Consensus 898 G~~e~~l-~~~~~~s~~gRv~~~l~~r~~lL~ev~kLa~~l~~~~~~~~sceta~~f~~~~i~~~w~~f~~~~~~~~~~~ 976 (1456)
|+..+.. .....+ ..+...+ .. +.. .+...++..... ..
T Consensus 431 g~~~r~~i~~~~~~---~tlh~~~--------------~~----------~~~---------~~~l~~l~~~~~-~~--- 470 (800)
T 2wjy_A 431 CAKSREAIDSPVSF---LALHNQI--------------RN----------MDS---------MPELQKLQQLKD-ET--- 470 (800)
T ss_dssp CCGGGGGCCCTTGG---GBHHHHH--------------HT----------CTT---------CHHHHHHHHHHT-TT---
T ss_pred CCCCHHHHCCHHHH---HHHHHHH--------------HC----------CCC---------HHHHHHHHHHHH-HH---
T ss_conf 33214331361556---5399999--------------72----------764---------999999999987-53---
Q ss_pred CCCCCCCCHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCHH
Q ss_conf 31123464124520699999877417899999989999999999999998989997977988777521157499974435
Q 000509 977 TFVRDRFPFKEFFSNTPQPIFTGDSFEKDMRAAKGCFRHLQTLFQELEECRAFELLKSTADRANYLMTKQAKIVAMTCTH 1056 (1456)
Q Consensus 977 ~~i~~~fpf~~~f~~~p~~l~~~~s~e~~l~~a~~~~~~i~~if~eL~e~r~felLr~~~dr~~~lllk~arIIa~T~t~ 1056 (1456)
..+. . .+. + .|..++ ......+++.++||++||.+
T Consensus 471 ------------------~~~~---~-~~~-----------~---------~~~~~~---~~~~~~~l~~a~VI~~T~~~ 505 (800)
T 2wjy_A 471 ------------------GELS---S-ADE-----------K---------RYRALK---RTAERELLMNADVICCTCVG 505 (800)
T ss_dssp ------------------SCCC---H-HHH-----------H---------HHHHHH---HHHHHHHHHHCSEEEEETGG
T ss_pred ------------------CCCC---H-HHH-----------H---------HHHHHH---HHHHHHHHCCCCEEEECHHH
T ss_conf ------------------3468---6-789-----------9---------999999---87777543369899974045
Q ss_pred HHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHC--------CCCCCCCEECCHHHHHHCCCCCCHHHHHHHCCCC
Q ss_conf 76644677430897798999439899927898778717--------9888886011423331037952089999981998
Q 000509 1057 AALKRKDFLQLGFKYDNLLMEESAQILEIETFIPMLLN--------DRRMLPPVVKNMAFQKYSHMDQSLFTRFVRLGIP 1128 (1456)
Q Consensus 1057 aa~~~~~l~~lg~~fD~VIIDEAsQitE~EtlIPLll~--------Dh~QLpPvV~s~~~~~~~~l~qSLFeRL~r~g~p 1128 (1456)
++... +. ...||+||||||+|+++++.++|++.. ||+||||++.+..... .++++|+|+|+...+.+
T Consensus 506 ~~~~~--l~--~~~fd~viIDEAsQ~~e~~~li~l~~~~~~~ilvGD~~QLpPvv~s~~a~~-~gl~~SlFerL~~~g~~ 580 (800)
T 2wjy_A 506 AGDPR--LA--KMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAK-AGLSQSLFERLVVLGIR 580 (800)
T ss_dssp GGCTT--TT--TCCCSEEEETTGGGSCHHHHHHHHTTTBSEEEEEECTTSCCCCCCCHHHHH-TTTTSCHHHHHHHTTCC
T ss_pred HCCHH--HH--CCCCCEEEEECCCCCCCHHHHHHHHHCCCEEEEECCCCCCCCEECCHHHHH-CCCCHHHHHHHHHCCCC
T ss_conf 28724--54--589898999897787769999999846885999615213798455555655-57435899999867999
Q ss_pred EEECCCCCCCCHHHHHHHHHHHCCCC---------------CCC-------C-EEECCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf 14045554673347999999741489---------------999-------2-253389999876689988668999999
Q 000509 1129 YIELNAQGRARPSIAQLYNWRYRDLG---------------DLP-------F-LVDVPDYNGRGESAPSPWFYQNEGEAE 1185 (1456)
Q Consensus 1129 ~i~L~~QYRs~PsIa~l~n~~yy~l~---------------dlp-------~-fIdV~~~~g~~e~~~~~~S~~N~~EAe 1185 (1456)
.+.|++||||||+|++|+|..||+.. +.| . |+++. |..+....+.|+.|..||+
T Consensus 581 ~~~L~~qYRm~p~I~~f~n~~fY~g~L~~~~~~~~r~~~~~~~~~~~~~~p~~f~~~~---g~e~~~~~~~S~~N~~Ea~ 657 (800)
T 2wjy_A 581 PIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQ---GQEEIASSGTSYLNRTEAA 657 (800)
T ss_dssp CEECCEECSSCHHHHHHHHHHHSTTCCEESSCSGGGSCTTCCCCCSSTTSCEEEEECC---CCCEECSSBSCEECHHHHH
T ss_pred CEEEHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHCCCCCCCCCCCCCCCEEEEECC---CCEEECCCCCCCCCHHHHH
T ss_conf 5484453288817877518975298154677513310135666566899888999868---8512047887646899999
Q ss_pred HHHHHHHHHHHHCCCCCCEEEECCCHHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCCCCCCCCEEEEEECCCC---CCC
Q ss_conf 99999999999199999779843778899999999973189999889993251256898755779999702369---866
Q 000509 1186 YVVSVYIYMRLLGYPANKISILTTYNGQKLLIRDVINRQCVPYPFIGPPSKVTTVDKFQGQQNDFILLSLVRTR---FVG 1262 (1456)
Q Consensus 1186 ~VV~iv~~L~~~Gy~~~kIaIITpY~aQ~~lIr~~L~~r~~~~~~~g~~vkV~TVD~fQG~E~DiVIlSlVRs~---~vG 1262 (1456)
.|+.++..+...|+++++|||||||++|+.+|++.+.......+.....+.|+|||+|||+|+|+||+|+||++ ++|
T Consensus 658 ~V~~~v~~L~~~g~~~~dIgVItPy~~Q~~~I~~~L~~~~~~~~~~~~~v~V~TVd~fQG~E~dvVIlS~vrs~~~~~~g 737 (800)
T 2wjy_A 658 NVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIG 737 (800)
T ss_dssp HHHHHHHHHHHTTCCGGGEEEECSCHHHHHHHHHHHHHHCSSCHHHHHTSEEECGGGGTTCCEEEEEEECCCCSCCCCCG
T ss_pred HHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCEEECCCCCCCCCCCCEEEEEECCCCCCCCCC
T ss_conf 99999999997599805599990658999999999986476541236866984211268875787999805788766633
Q ss_pred CCCCCHHHHHHHHHHHCCEEEEECHHHHHHHCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf 55651025788754322579991202565301406899999709211034458
Q 000509 1263 HLRDVRRLVVAMSRARLGLYVFCRRSLFEQCYELQPTFRLLLQRPDKLALTMN 1315 (1456)
Q Consensus 1263 fL~d~rRLNVAlSRAK~~LiIVGn~~~l~~~~~~~~~~~~ll~~~~~l~l~~~ 1315 (1456)
|+.+.||||||+||||.+|||||+..+|... +.|+.+++++...+...+
T Consensus 738 fl~d~rrLNVAlTRAk~~LiIvG~~~~l~~~----~~w~~ll~~~~~~~~~~~ 786 (800)
T 2wjy_A 738 FLNDPRRLNVALTRARYGVIIVGNPKALSKQ----PLWNHLLNYYKEQKVLVE 786 (800)
T ss_dssp GGTCHHHHHHHHTSEEEEEEEEECHHHHTSS----HHHHHHHHHHHHTTCEEE
T ss_pred CCCCCCHHHHHHHHHHCCEEEEECHHHHCCC----HHHHHHHHHHHHCCCEEE
T ss_conf 1167134313087663119999877995427----899999999998799996
No 4
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A
Probab=1.00 E-value=1 Score=487.47 Aligned_cols=397 Identities=27% Similarity=0.389 Sum_probs=293.9
Q ss_pred CCCCHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCEEEC
Q ss_conf 88999999999961389909999479999689999999999980999947999257899999999998349996538870
Q 000509 818 VRFTPTQVGAIISGIQPGLTMVVGPPGTGKTDTAVQILNVLYHNCPSQRTLIITHSNQALNDLFEKIMQRDVPARYLLRL 897 (1456)
Q Consensus 818 i~Ln~sQ~eAI~s~l~~gltLI~GPPGTGKT~via~iI~~Ll~~~p~~kILIva~SN~Ald~L~ekL~~l~i~~~~llRl 897 (1456)
..||++|.+||..++..++++|+||||||||+|++.++..++.. ++.+||+||+||.|++++.+++.+.++. ++|+
T Consensus 179 ~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~~~~---~~R~ 254 (624)
T 2gk6_A 179 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQTGLK---VVRL 254 (624)
T ss_dssp CCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHHHHHHHHTS-SSCCEEEEESSHHHHHHHHHHHHTTTCC---EEEC
T ss_pred CCCCHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHC-CCCEEEEEECCHHHHHHHHHHHHHCCCE---EEEE
T ss_conf 78999999999999628976998999987899999999999974-8980999927189999999999861975---8960
Q ss_pred CCCCCCC-CCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 6761001-2233-2024567899999999999999999986299976344200100356764578999999996203899
Q 000509 898 GQGEQEL-ATDL-DFSRQGRVNAMLVRRLELLSEVERLARSLQLPEDVGYTCETAGYFWLLHVYSRWEQFLAACADNEGK 975 (1456)
Q Consensus 898 G~~e~~l-~~~~-~~s~~gRv~~~l~~r~~lL~ev~kLa~~l~~~~~~~~sceta~~f~~~~i~~~w~~f~~~~~~~~~~ 975 (1456)
|+..+.. .... .+..+..+ . .+... +...++. . ...
T Consensus 255 ~~~~r~~~~~~~~~~tl~~~~---------------------~-------~~~~~---------~~l~~l~---~-~~~- 292 (624)
T 2gk6_A 255 CAKSREAIDSPVSFLALHNQI---------------------R-------NMDSM---------PELQKLQ---Q-LKD- 292 (624)
T ss_dssp CCTGGGSCCCTTTTTBHHHHH---------------------T-------SCSSC---------HHHHHHH---T-TCC-
T ss_pred CCCCCHHHCCCHHHHHHHHHH---------------------H-------HCCCH---------HHHHHHH---H-HHH-
T ss_conf 532201111304566599999---------------------8-------05236---------9999999---9-987-
Q ss_pred CCCCCCCCCHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCH
Q ss_conf 73112346412452069999987741789999998999999999999999898999797798877752115749997443
Q 000509 976 PTFVRDRFPFKEFFSNTPQPIFTGDSFEKDMRAAKGCFRHLQTLFQELEECRAFELLKSTADRANYLMTKQAKIVAMTCT 1055 (1456)
Q Consensus 976 ~~~i~~~fpf~~~f~~~p~~l~~~~s~e~~l~~a~~~~~~i~~if~eL~e~r~felLr~~~dr~~~lllk~arIIa~T~t 1055 (1456)
... .+ +. .+ . +.|..++ ......+++.++||++||.
T Consensus 293 ----------------~~~-~~---~~-~~-----------~---------~~~~~~~---~~~~~~~l~~~~vI~~T~~ 328 (624)
T 2gk6_A 293 ----------------ETG-EL---SS-AD-----------E---------KRYRALK---RTAERELLMNADVICCTCV 328 (624)
T ss_dssp ---------------------C---CH-HH-----------H---------HHHHHHH---HHHHHHHHHTCSEEEEETG
T ss_pred ----------------HHC-CC---CH-HH-----------H---------HHHHHHH---HHHHHHHHHCCCEEEECCH
T ss_conf ----------------642-13---77-78-----------9---------9999999---9889998714999999270
Q ss_pred HHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHC--------CCCCCCCEECCHHHHHHCCCCCCHHHHHHHCCC
Q ss_conf 576644677430897798999439899927898778717--------988888601142333103795208999998199
Q 000509 1056 HAALKRKDFLQLGFKYDNLLMEESAQILEIETFIPMLLN--------DRRMLPPVVKNMAFQKYSHMDQSLFTRFVRLGI 1127 (1456)
Q Consensus 1056 ~aa~~~~~l~~lg~~fD~VIIDEAsQitE~EtlIPLll~--------Dh~QLpPvV~s~~~~~~~~l~qSLFeRL~r~g~ 1127 (1456)
+++... +. ..+||+||||||+|+++++.++|++.. ||+||||++.+..... .++++|+|+|+...+.
T Consensus 329 ~~~~~~--l~--~~~fd~viIDEAsQ~~e~~~li~l~~~~~~~ilvGD~~QL~p~v~~~~~~~-~gl~~Slferl~~~~~ 403 (624)
T 2gk6_A 329 GAGDPR--LA--KMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAK-AGLSQSLFERLVVLGI 403 (624)
T ss_dssp GGGCGG--GT--TCCCSEEEETTGGGSCHHHHHHHHTTTBSEEEEEECTTSCCCCCSCHHHHH-HTTTSCHHHHHHHTTC
T ss_pred HHCCHH--HH--CCCCCEEEEECCCCCCCHHHHHHHHHCCCEEEEECCHHCCCCEEECHHHHH-CCCCHHHHHHHHHCCC
T ss_conf 115146--64--679887999630146758999999846874999167010698520488887-5874569999986699
Q ss_pred CEEECCCCCCCCHHHHHHHHHHHCCCCC---------------CC-------C-EEECCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 8140455546733479999997414899---------------99-------2-25338999987668998866899999
Q 000509 1128 PYIELNAQGRARPSIAQLYNWRYRDLGD---------------LP-------F-LVDVPDYNGRGESAPSPWFYQNEGEA 1184 (1456)
Q Consensus 1128 p~i~L~~QYRs~PsIa~l~n~~yy~l~d---------------lp-------~-fIdV~~~~g~~e~~~~~~S~~N~~EA 1184 (1456)
+.+.|++||||||+|++|+|..||+... .+ . |+++. |..+....+.|+.|..||
T Consensus 404 ~~~~L~~qYR~~~~I~~~~n~~fY~~~L~~~~~~~~r~~~~~~~~~~~~~~p~~~~~~~---g~~~~~~~~~s~~N~~Ea 480 (624)
T 2gk6_A 404 RPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQ---GQEEIASSGTSYLNRTEA 480 (624)
T ss_dssp CCEECCEECSSCHHHHHHHHHHHSTTCCEESSCTGGGCCTTCCCCCSSTTCCEEEEECC---CCEECCTTSSCCEEHHHH
T ss_pred CCEEEHHHHCCCHHHHHHHHHHHCCCCCCCCCCHHHHCCCCCCCCCCCCCCCEEEEECC---CCCEECCCCCCCCCHHHH
T ss_conf 92783023076845876548865576465688634410135677888999998999858---830333789885289999
Q ss_pred HHHHHHHHHHHHHCCCCCCEEEECCCHHHHHHHHHHHHHCCCCCCCCCCCCEEECCCCCCCCCCCEEEEEECCCC---CC
Q ss_conf 999999999999199999779843778899999999973189999889993251256898755779999702369---86
Q 000509 1185 EYVVSVYIYMRLLGYPANKISILTTYNGQKLLIRDVINRQCVPYPFIGPPSKVTTVDKFQGQQNDFILLSLVRTR---FV 1261 (1456)
Q Consensus 1185 e~VV~iv~~L~~~Gy~~~kIaIITpY~aQ~~lIr~~L~~r~~~~~~~g~~vkV~TVD~fQG~E~DiVIlSlVRs~---~v 1261 (1456)
+.++.++..+...|+++.+|||||||++|+..|++.+...+.........+.|+|||+|||+|+|+||+|+||++ ++
T Consensus 481 ~~v~~~v~~l~~~g~~~~dIgVItpy~~Q~~~i~~~l~~~~~~~~~~~~~v~v~TVd~fQG~E~dvVIls~vrs~~~~~~ 560 (624)
T 2gk6_A 481 ANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGI 560 (624)
T ss_dssp HHHHHHHHHHHTTTCCGGGEEEECSCHHHHHHHHHHHHHSCSSCHHHHHHSEEECHHHHTTCCEEEEEEEECC------C
T ss_pred HHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCCCCEEEECHHHCCCCCCCEEEEEEECCCCCCCC
T ss_conf 99999999999759997809998688999999999998602232002476189322324886057899995047987874
Q ss_pred CCCCCCHHHHHHHHHHHCCEEEEECHHHHHHHCCCHHHHHHHHCCCCCCCCCCCC
Q ss_conf 6556510257887543225799912025653014068999997092110344588
Q 000509 1262 GHLRDVRRLVVAMSRARLGLYVFCRRSLFEQCYELQPTFRLLLQRPDKLALTMNE 1316 (1456)
Q Consensus 1262 GfL~d~rRLNVAlSRAK~~LiIVGn~~~l~~~~~~~~~~~~ll~~~~~l~l~~~e 1316 (1456)
||+.+.||||||+||||.+||||||..+|... +.|+.+++++...+...+.
T Consensus 561 gfl~~~~rlnVAlTRAk~~L~ivg~~~~l~~~----~~~~~li~~~~~~~~~~~~ 611 (624)
T 2gk6_A 561 GFLNDPRRLNVALTRARYGVIIVGNPKALSKQ----PLWNHLLNYYKEQKVLVEG 611 (624)
T ss_dssp CTTTCHHHHHHHTTSEEEEEEEEECHHHHTTS----HHHHHHHHHHHHTTCCCCS
T ss_pred CCCCCCCEEEEEHHHHHCCEEEEECHHHHCCC----HHHHHHHHHHHHCCCEEEC
T ss_conf 64588350210344653858999888997347----6999999999987988958
No 5
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*
Probab=1.00 E-value=1 Score=225.54 Aligned_cols=278 Identities=18% Similarity=0.194 Sum_probs=184.8
Q ss_pred CCCCCHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCEEE
Q ss_conf 98899999999996138990999947999968999999999998099994799925789999999999834999653887
Q 000509 817 SVRFTPTQVGAIISGIQPGLTMVVGPPGTGKTDTAVQILNVLYHNCPSQRTLIITHSNQALNDLFEKIMQRDVPARYLLR 896 (1456)
Q Consensus 817 ~i~Ln~sQ~eAI~s~l~~gltLI~GPPGTGKT~via~iI~~Ll~~~p~~kILIva~SN~Ald~L~ekL~~l~i~~~~llR 896 (1456)
.+.||++|.+|+..++..++.+|.||||||||+++..++..+... +.+|+++|||+.|++.+.+.+.. + ..
T Consensus 187 ~~~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~~l~~~l~~~--g~~Vl~~ApT~~Aa~~L~e~~~~---~---a~- 257 (574)
T 3e1s_A 187 RKGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVADLAESL--GLEVGLCAPTGKAARRLGEVTGR---T---AS- 257 (574)
T ss_dssp TTTCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHHTS---C---EE-
T ss_pred CCCCCHHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEECCCHHHHHHHHHHHCC---C---HH-
T ss_conf 379999999999999768879999599998899999999999856--98299964858999976766363---0---98-
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 06761001223320245678999999999999999999862999763442001003567645789999999962038997
Q 000509 897 LGQGEQELATDLDFSRQGRVNAMLVRRLELLSEVERLARSLQLPEDVGYTCETAGYFWLLHVYSRWEQFLAACADNEGKP 976 (1456)
Q Consensus 897 lG~~e~~l~~~~~~s~~gRv~~~l~~r~~lL~ev~kLa~~l~~~~~~~~sceta~~f~~~~i~~~w~~f~~~~~~~~~~~ 976 (1456)
T Consensus 258 -------------------------------------------------------------------------------- 257 (574)
T 3e1s_A 258 -------------------------------------------------------------------------------- 257 (574)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
T ss_conf --------------------------------------------------------------------------------
Q ss_pred CCCCCCCCHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCHH
Q ss_conf 31123464124520699999877417899999989999999999999998989997977988777521157499974435
Q 000509 977 TFVRDRFPFKEFFSNTPQPIFTGDSFEKDMRAAKGCFRHLQTLFQELEECRAFELLKSTADRANYLMTKQAKIVAMTCTH 1056 (1456)
Q Consensus 977 ~~i~~~fpf~~~f~~~p~~l~~~~s~e~~l~~a~~~~~~i~~if~eL~e~r~felLr~~~dr~~~lllk~arIIa~T~t~ 1056 (1456)
.+++++...+ ..+
T Consensus 258 -------Tih~ll~~~~-~~~----------------------------------------------------------- 270 (574)
T 3e1s_A 258 -------TVHRLLGYGP-QGF----------------------------------------------------------- 270 (574)
T ss_dssp -------EHHHHTTEET-TEE-----------------------------------------------------------
T ss_pred -------HHHHHHCCCC-CHH-----------------------------------------------------------
T ss_conf -------9999876792-032-----------------------------------------------------------
Q ss_pred HHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHC-----------CCCCCCCEECCHHHHHHCCCCCCHHHHHHHC
Q ss_conf 76644677430897798999439899927898778717-----------9888886011423331037952089999981
Q 000509 1057 AALKRKDFLQLGFKYDNLLMEESAQILEIETFIPMLLN-----------DRRMLPPVVKNMAFQKYSHMDQSLFTRFVRL 1125 (1456)
Q Consensus 1057 aa~~~~~l~~lg~~fD~VIIDEAsQitE~EtlIPLll~-----------Dh~QLpPvV~s~~~~~~~~l~qSLFeRL~r~ 1125 (1456)
. +. ......+|.||||||+++... .+-.++.. |+.||||+.... .|..+..
T Consensus 271 -~--~~--~~~~~~~dvlIIDEasml~~~-~~~~Ll~~~~~~~~lilvGD~~QL~~v~~g~-----------~~~~l~~- 332 (574)
T 3e1s_A 271 -R--HN--HLEPAPYDLLIVDEVSMMGDA-LMLSLLAAVPPGARVLLVGDTDQLPPVDAGL-----------PLLALAQ- 332 (574)
T ss_dssp -S--CS--SSSCCSCSEEEECCGGGCCHH-HHHHHHTTSCTTCEEEEEECTTSCCCSSSCC-----------HHHHHHH-
T ss_pred -H--HH--HCCCCCCCEEEECCCCCCCHH-HHHHHHHHCCCCCEEEEEECCCCCCCCCCCC-----------HHHHHHH-
T ss_conf -3--20--103565888997175677899-9999998376898899995433268766883-----------7999996-
Q ss_pred CCCEEECCCCCCCC--HHHHHHHHHHHCCCCCCCC------EEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99814045554673--3479999997414899992------253389999876689988668999999999999999991
Q 000509 1126 GIPYIELNAQGRAR--PSIAQLYNWRYRDLGDLPF------LVDVPDYNGRGESAPSPWFYQNEGEAEYVVSVYIYMRLL 1197 (1456)
Q Consensus 1126 g~p~i~L~~QYRs~--PsIa~l~n~~yy~l~dlp~------fIdV~~~~g~~e~~~~~~S~~N~~EAe~VV~iv~~L~~~ 1197 (1456)
..+.+.|+.+||++ +.|..+.+.... +..|. |+...+ ....++.+++++.
T Consensus 333 ~~~~~~L~~~~R~~~~s~I~~~a~~i~~--g~~~~~~~d~~~~~~~~---------------~~~~~~~i~~~~~----- 390 (574)
T 3e1s_A 333 AAPTIKLTQVYRQAAKNPIIQAAHGLLH--GEAPAWGDKRLNLTEIE---------------PDGGARRVALMVR----- 390 (574)
T ss_dssp HSCEEECCCCCHHHHTCHHHHHHHHHHT--TCCCCCCBTTEEEEECC---------------STTCHHHHHHHHH-----
T ss_pred CCCEEECCEEEECCCCCHHHHHHHHHHC--CCCCCCCCCEEEEECCC---------------HHHHHHHHHHHHH-----
T ss_conf 3988985201818996189999999867--99866678769983799---------------9999999999986-----
Q ss_pred CCCC-CCEEEECCCHHH---HHHHHHHHHHCCCC----------------------CC----CC----C-------CC--
Q ss_conf 9999-977984377889---99999999731899----------------------99----88----9-------99--
Q 000509 1198 GYPA-NKISILTTYNGQ---KLLIRDVINRQCVP----------------------YP----FI----G-------PP-- 1234 (1456)
Q Consensus 1198 Gy~~-~kIaIITpY~aQ---~~lIr~~L~~r~~~----------------------~~----~~----g-------~~-- 1234 (1456)
|+.+ .+|.||||.+.. +..+...+.....+ +. ++ | ..
T Consensus 391 ~~~~~~~~~VL~~~~~g~~gv~~lN~~l~~~lnp~~~~~~~~~~~~~~Gd~V~~~~N~~~~~v~NGdiG~i~~~~~~~l~ 470 (574)
T 3e1s_A 391 ELGGPGAVQVLTPMRKGPLGMDHLNYHLQALFNPGEGGVRIAEGEARPGDTVVQTKNDYNNEIFNGTLGMVLKAEGARLT 470 (574)
T ss_dssp HTTSGGGCEEEESCSSSTTSHHHHHHHHHHHHSCCSCCEECSSSEECTTCEEEECSCBTTTTBCTTCEEEEEEECSSCEE
T ss_pred CCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHCCCCCCEEECCEEEECCCEEEEEECCCCCCEECCCEEEEECCCCCEEE
T ss_conf 45843574899863388535999999999975888872212781774699799930375246345863689717799899
Q ss_pred --------------------CEEECCCCCCCCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEECHHHHHH
Q ss_conf --------------------3251256898755779999702369866556510257887543225799912025653
Q 000509 1235 --------------------SKVTTVDKFQGQQNDFILLSLVRTRFVGHLRDVRRLVVAMSRARLGLYVFCRRSLFEQ 1292 (1456)
Q Consensus 1235 --------------------vkV~TVD~fQG~E~DiVIlSlVRs~~vGfL~d~rRLNVAlSRAK~~LiIVGn~~~l~~ 1292 (1456)
..+.|||++||.|+|.||+.+.... ..+.+.+++|||+||||..++|+|+...|..
T Consensus 471 v~fdg~~v~~~~~~l~~~~~ayA~TIHksQGsEfd~Vil~l~~~~--~~~l~r~LlYvAiTRAk~~l~lvg~~~~l~~ 546 (574)
T 3e1s_A 471 VDFDGNVVELTGAELFNLQLGYALTVHRAQGSEWGTVLGVLHEAH--MPMLSRNLVYTALTRARDRFFSAGSASAWQI 546 (574)
T ss_dssp EEETTEEEEECGGGGTTEEECSEEEHHHHTTCCEEEEEEEECGGG--GGGCCHHHHHHHHHTEEEEEEEEECHHHHHH
T ss_pred EEECCEEEEECHHHHHHHHHEEEEEHHHHCCCCCCEEEEECCCCC--CCCCCCCEEEEEEEEEEEEEEEEECHHHHHH
T ss_conf 998996999726774201011330088747866886999867765--5534536189871301668999978999999
No 6
>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*
Probab=1.00 E-value=1 Score=222.31 Aligned_cols=344 Identities=17% Similarity=0.151 Sum_probs=173.8
Q ss_pred CCCCHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCC--CCCCEEEEECCHHHHHHHHHHHHHC-CCCCCCE
Q ss_conf 889999999999613899099994799996899999999999809--9994799925789999999999834-9996538
Q 000509 818 VRFTPTQVGAIISGIQPGLTMVVGPPGTGKTDTAVQILNVLYHNC--PSQRTLIITHSNQALNDLFEKIMQR-DVPARYL 894 (1456)
Q Consensus 818 i~Ln~sQ~eAI~s~l~~gltLI~GPPGTGKT~via~iI~~Ll~~~--p~~kILIva~SN~Ald~L~ekL~~l-~i~~~~l 894 (1456)
-.||++|.+||.+. .|..+|.||||||||+|++..|.+++... +..+||++|+||.|++++.+++.+. +... .-
T Consensus 8 ~~Ln~~Q~~av~~~--~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~~~~~-~~ 84 (647)
T 3lfu_A 8 DSLNDKQREAVAAP--RSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMGTSQ-GG 84 (647)
T ss_dssp TTCCHHHHHHHTCC--SSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHHCSCC-TT
T ss_pred HCCCHHHHHHHHCC--CCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCHHHHHHHHHHHHHHHCCCC-CC
T ss_conf 54999999998188--9987999789987899999999999983799952589895618999999999998725556-78
Q ss_pred EECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 87067610012233202456789999999999999999998629997634420010035676457899999999620389
Q 000509 895 LRLGQGEQELATDLDFSRQGRVNAMLVRRLELLSEVERLARSLQLPEDVGYTCETAGYFWLLHVYSRWEQFLAACADNEG 974 (1456)
Q Consensus 895 lRlG~~e~~l~~~~~~s~~gRv~~~l~~r~~lL~ev~kLa~~l~~~~~~~~sceta~~f~~~~i~~~w~~f~~~~~~~~~ 974 (1456)
+.++. +..+..+ ++ .......+.+....... .......++...........
T Consensus 85 ~~v~T----------------fhs~~~~---il---~~~~~~~~~~~~~~i~~-------~~~~~~~~~~~~~~~~~~~~ 135 (647)
T 3lfu_A 85 MWVGT----------------FHGLAHR---LL---RAHHMDANLPQDFQILD-------SEDQLRLLKRLIKAMNLDEK 135 (647)
T ss_dssp CEEEE----------------HHHHHHH---HH---HHTTGGGTCCTTCEEEC-------HHHHHHHHHHHHHHTTCCTT
T ss_pred CEEEC----------------HHHHHHH---HH---HHHHHHHCCCCCCEEEC-------HHHHHHHHHHHHHHCCCCCC
T ss_conf 08972----------------8999999---99---99799709998988857-------89999999999987699821
Q ss_pred CCCCCCCCCCHHHHHH---CCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf 9731123464124520---69999987-7417899999989999999999999998989997977988777521157499
Q 000509 975 KPTFVRDRFPFKEFFS---NTPQPIFT-GDSFEKDMRAAKGCFRHLQTLFQELEECRAFELLKSTADRANYLMTKQAKIV 1050 (1456)
Q Consensus 975 ~~~~i~~~fpf~~~f~---~~p~~l~~-~~s~e~~l~~a~~~~~~i~~if~eL~e~r~felLr~~~dr~~~lllk~arII 1050 (1456)
.........+...+. ..|..+.. ..... ..+..++...++... ... .+...+++
T Consensus 136 -~~~~~~~~~~i~~~k~~~~~~~~~~~~~~~~~----------~~~~~i~~~y~~~~~------~~~-----~~df~dl~ 193 (647)
T 3lfu_A 136 -QWPPRQAMWYINSQKDEGLRPHHIQSYGNPVE----------QTWQKVYQAYQEACD------RAG-----LVDFAELL 193 (647)
T ss_dssp -TSCHHHHHHHHHHHHHTTCCCCCC----CCHH----------HHHHHHHHHHHHHHH------HHT-----EEEHHHHH
T ss_pred -CCCHHHHHHHHHHHHHCCCCHHHHHHCCCHHH----------HHHHHHHHHHHHHHH------HCC-----CCCHHHHH
T ss_conf -04899999999999875999899875024689----------999999999999999------869-----97899999
Q ss_pred EECCHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHH-HHC---------CCCCCCCEECCHHHHHHCCCCCCHHH
Q ss_conf 97443576644677430897798999439899927898778-717---------98888860114233310379520899
Q 000509 1051 AMTCTHAALKRKDFLQLGFKYDNLLMEESAQILEIETFIPM-LLN---------DRRMLPPVVKNMAFQKYSHMDQSLFT 1120 (1456)
Q Consensus 1051 a~T~t~aa~~~~~l~~lg~~fD~VIIDEAsQitE~EtlIPL-ll~---------Dh~QLpPvV~s~~~~~~~~l~qSLFe 1120 (1456)
..++............+..+|++|+|||+++++..+.-+.. +.. |++|-- +. +.+-+...|.
T Consensus 194 ~~~~~~l~~~~~~~~~~~~~~~~ilVDE~QD~~~~q~~ll~~l~~~~~~l~~vGD~~QsI-----y~---frga~~~~~~ 265 (647)
T 3lfu_A 194 LRAHELWLNKPHILQHYRERFTNILVDEFQDTNNIQYAWIRLLAGDTGKVMIVGDDDQSI-----YG---WRGAQVENIQ 265 (647)
T ss_dssp HHHHHHHHHCHHHHHHHHHHCCEEEESSGGGCCHHHHHHHHHHHTTTCEEEEEECGGGCC-----CG---GGTCCTTHHH
T ss_pred HHHHHHHHHCHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHH-----CC---CCCCCHHHHH
T ss_conf 999999876989999998319899997800398999999999966898799980760212-----13---2587889999
Q ss_pred HHHHC--CCCEEECCCCCCCCHHHHHHHHHHHCCCCCC-CC-EEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 99981--9981404555467334799999974148999-92-25338999987668998866899999999999999999
Q 000509 1121 RFVRL--GIPYIELNAQGRARPSIAQLYNWRYRDLGDL-PF-LVDVPDYNGRGESAPSPWFYQNEGEAEYVVSVYIYMRL 1196 (1456)
Q Consensus 1121 RL~r~--g~p~i~L~~QYRs~PsIa~l~n~~yy~l~dl-p~-fIdV~~~~g~~e~~~~~~S~~N~~EAe~VV~iv~~L~~ 1196 (1456)
++.+. +...+.|+.||||++.|.++.|..++..... +. ..... +.+.....-.......|+++|+..+..+..
T Consensus 266 ~~~~~~~~~~~~~L~~nyRs~~~I~~~~n~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~e~~~ia~~I~~l~~ 342 (647)
T 3lfu_A 266 RFLNDFPGAETIRLEQNYRSTSNILSAANALIENNNGRLGKKLWTDG---ADGEPISLYCAFNELDEARFVVNRIKTWQD 342 (647)
T ss_dssp HHHHHCTTCEEEEECBCSSSCHHHHHHHHHHHTTCSSCCCCCCBCSS---CCCCCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred HHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCC---CCCCCEEEEECCCHHHHHHHHHHHHHHHHH
T ss_conf 99986899859976657899779999999999854202377442678---899962899669859999999999999997
Q ss_pred HCCCCCCEEEECCCHHHHHHHHHHHHHCCC
Q ss_conf 199999779843778899999999973189
Q 000509 1197 LGYPANKISILTTYNGQKLLIRDVINRQCV 1226 (1456)
Q Consensus 1197 ~Gy~~~kIaIITpY~aQ~~lIr~~L~~r~~ 1226 (1456)
.|++.++|+||++++.|...|.+.|.....
T Consensus 343 ~g~~~~diaVL~r~~~~~~~l~~~l~~~~I 372 (647)
T 3lfu_A 343 NGGALAECAILYRSNAQSRVLEEALLQASM 372 (647)
T ss_dssp TTCCGGGEEEEESSGGGHHHHHHHHHHTTC
T ss_pred CCCCCCCEEEEEECCHHHHHHHHHHHHCCC
T ss_conf 698806789998474439999999997799
No 7
>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*
Probab=1.00 E-value=1 Score=214.73 Aligned_cols=342 Identities=15% Similarity=0.118 Sum_probs=168.9
Q ss_pred CCCCHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCC--CCCCEEEEECCHHHHHHHHHHHHHC-CCCCCCE
Q ss_conf 889999999999613899099994799996899999999999809--9994799925789999999999834-9996538
Q 000509 818 VRFTPTQVGAIISGIQPGLTMVVGPPGTGKTDTAVQILNVLYHNC--PSQRTLIITHSNQALNDLFEKIMQR-DVPARYL 894 (1456)
Q Consensus 818 i~Ln~sQ~eAI~s~l~~gltLI~GPPGTGKT~via~iI~~Ll~~~--p~~kILIva~SN~Ald~L~ekL~~l-~i~~~~l 894 (1456)
-.||++|.+||.+. .|..+|.|+||||||+|++..|.+++... +..+||++|+||.|++++.+|+.+. +.....
T Consensus 10 ~~Ln~~Q~~av~~~--~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l~~~~~~- 86 (724)
T 1pjr_A 10 AHLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAED- 86 (724)
T ss_dssp TTSCHHHHHHHHCC--SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHGGGGTT-
T ss_pred HHCCHHHHHHHHCC--CCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCHHHHHHHHHHHHHHHCCCCCC-
T ss_conf 52899999998288--998899974999789999999999999669988996878266999999999999972465568-
Q ss_pred EECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 87067610012233202456789999999999999999998629997634420010035676457899999999620389
Q 000509 895 LRLGQGEQELATDLDFSRQGRVNAMLVRRLELLSEVERLARSLQLPEDVGYTCETAGYFWLLHVYSRWEQFLAACADNEG 974 (1456)
Q Consensus 895 lRlG~~e~~l~~~~~~s~~gRv~~~l~~r~~lL~ev~kLa~~l~~~~~~~~sceta~~f~~~~i~~~w~~f~~~~~~~~~ 974 (1456)
+.+ +.+..+..+ + +.+....+|.+......-+ ......++..........
T Consensus 87 ~~v----------------~Tfhs~~~~---i---lr~~~~~~g~~~~f~i~d~-------~d~~~l~~~~~~~~~~~~- 136 (724)
T 1pjr_A 87 VWI----------------STFHSMCVR---I---LRRDIDRIGINRNFSILDP-------TDQLSVMKTILKEKNIDP- 136 (724)
T ss_dssp SEE----------------EEHHHHHHH---H---HHHHGGGGTCCTTCEECCH-------HHHHHHHHHHHHTTSCTT-
T ss_pred CEE----------------EEHHHHHHH---H---HHHHHHHHCCCCCCEECCH-------HHHHHHHHHHHHHCCCCC-
T ss_conf 199----------------619999999---9---9999998588989777789-------999999999998769982-
Q ss_pred CCCCCCCCCCHH---HHHHCCCCCCCCCCCHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf 973112346412---45206999998774178999999-89999999999999998989997977988777521157499
Q 000509 975 KPTFVRDRFPFK---EFFSNTPQPIFTGDSFEKDMRAA-KGCFRHLQTLFQELEECRAFELLKSTADRANYLMTKQAKIV 1050 (1456)
Q Consensus 975 ~~~~i~~~fpf~---~~f~~~p~~l~~~~s~e~~l~~a-~~~~~~i~~if~eL~e~r~felLr~~~dr~~~lllk~arII 1050 (1456)
..++.. ..++........ .+.....+ ......+..++...++ . ... ...++..+++
T Consensus 137 ------~~~~~~~~~~~i~~~k~~~~~---~~~~~~~~~~~~~~~~~~iy~~Y~~------~---l~~--~~~lDf~Dll 196 (724)
T 1pjr_A 137 ------KKFEPRTILGTISAAKNELLP---PEQFAKRASTYYEKVVSDVYQEYQQ------R---LLR--NHSLDFDDLI 196 (724)
T ss_dssp ------TTCCHHHHHHHHHHHHHTTCC---HHHHTTC---CHHHHHHHHHHHHHH------H---HHH--TTEECTTHHH
T ss_pred ------CCCCHHHHHHHHHHHHHCCCC---HHHHHHHCCCHHHHHHHHHHHHHHH------H---HHH--CCCCCHHHHH
T ss_conf ------208999999999999876999---9999986237899999999999999------9---998--5999999999
Q ss_pred EECCHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHH-HHHHC---------CCCCCCCEECCHHHHHHCCCCCCHHH
Q ss_conf 974435766446774308977989994398999278987-78717---------98888860114233310379520899
Q 000509 1051 AMTCTHAALKRKDFLQLGFKYDNLLMEESAQILEIETFI-PMLLN---------DRRMLPPVVKNMAFQKYSHMDQSLFT 1120 (1456)
Q Consensus 1051 a~T~t~aa~~~~~l~~lg~~fD~VIIDEAsQitE~EtlI-PLll~---------Dh~QLpPvV~s~~~~~~~~l~qSLFe 1120 (1456)
..+................+|++|+|||+++++..+.-+ -++.. |+.|.- +.+ .+-+...|.
T Consensus 197 ~~~~~ll~~~~~v~~~~~~rf~~IlVDEfQDtn~~Q~~ll~~L~~~~~~l~vVGD~~QsI-----Y~f---RGA~~~~~~ 268 (724)
T 1pjr_A 197 MTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSI-----YRW---RGADIQNIL 268 (724)
T ss_dssp HHHHHHHHHCHHHHHHHHHHCSEEEESSGGGCCHHHHHHHHHHHTTTCCEEEEECGGGCC-----CGG---GTCCTHHHH
T ss_pred HHHHHHHHHCHHHHHHHHHHCCEEEEEHHHCCCHHHHHHHHHHHCCCCEEEEEECCHHHC-----CCC---CCCCHHHHH
T ss_conf 999999865979999998639899987676089999999999976898699997806624-----424---588989999
Q ss_pred HHHHC--CCCEEECCCCCCCCHHHHHHHHHHHCCCC-CCCC-EEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 99981--99814045554673347999999741489-9992-25338999987668998866899999999999999999
Q 000509 1121 RFVRL--GIPYIELNAQGRARPSIAQLYNWRYRDLG-DLPF-LVDVPDYNGRGESAPSPWFYQNEGEAEYVVSVYIYMRL 1196 (1456)
Q Consensus 1121 RL~r~--g~p~i~L~~QYRs~PsIa~l~n~~yy~l~-dlp~-fIdV~~~~g~~e~~~~~~S~~N~~EAe~VV~iv~~L~~ 1196 (1456)
++.+. +...+.|.++|||++.|.++.|..+.+.. ..+. .+.. .+.++....-.+.....|+++|+..+..+..
T Consensus 269 ~f~~~~~~~~~i~L~~NyRSt~~Il~~an~li~~n~~~~~k~l~~~---~~~g~~i~~~~~~~~~~Ea~~va~~I~~l~~ 345 (724)
T 1pjr_A 269 SFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTE---NPEGKPILYYEAMNEADEAQFVAGRIREAVE 345 (724)
T ss_dssp THHHHSTTCEEEEECBCSSSCHHHHHHHHHHHTTCSSCCCCCCBCS---SCCCCCEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred HHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCC---CCCCCCEEEEECCCHHHHHHHHHHHHHHHHH
T ss_conf 9998779981998998789978999999999985734467656665---6899954999559879999999999999998
Q ss_pred -HCCCCCCEEEECCCHHHHHHHHHHHHH
Q ss_conf -199999779843778899999999973
Q 000509 1197 -LGYPANKISILTTYNGQKLLIRDVINR 1223 (1456)
Q Consensus 1197 -~Gy~~~kIaIITpY~aQ~~lIr~~L~~ 1223 (1456)
.|++.++|+||++.+.|...|.+.|..
T Consensus 346 ~~g~~~~diAIL~R~~~~~~~le~~L~~ 373 (724)
T 1pjr_A 346 RGERRYRDFAVLYRTNAQSRVMEEMLLK 373 (724)
T ss_dssp TTSCCGGGEEEEESSGGGHHHHHHHHHH
T ss_pred HCCCCHHHEEEEEECCHHHHHHHHHHHH
T ss_conf 2699844635643052148999999987
No 8
>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19
Probab=1.00 E-value=1 Score=208.17 Aligned_cols=334 Identities=14% Similarity=0.107 Sum_probs=163.7
Q ss_pred CCCCHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHC--CCCCCEEEEECCHHHHHHHHHHHHHC-CCCCCCE
Q ss_conf 88999999999961389909999479999689999999999980--99994799925789999999999834-9996538
Q 000509 818 VRFTPTQVGAIISGIQPGLTMVVGPPGTGKTDTAVQILNVLYHN--CPSQRTLIITHSNQALNDLFEKIMQR-DVPARYL 894 (1456)
Q Consensus 818 i~Ln~sQ~eAI~s~l~~gltLI~GPPGTGKT~via~iI~~Ll~~--~p~~kILIva~SN~Ald~L~ekL~~l-~i~~~~l 894 (1456)
+.||++|.+||... .|..+|.|+||||||+|++..|.+++.+ .+..+||++|+||.|++++.+++.+. +.....-
T Consensus 1 ~~L~~~Q~~av~~~--~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~~~~~~~ 78 (673)
T 1uaa_A 1 MRLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGRKEARG 78 (673)
T ss_dssp -CCCHHHHHHHHCC--SSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSCTTTTTT
T ss_pred CCCCHHHHHHHHCC--CCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 99998999998388--9977999579997689999999999985699878958785468999999999998707323468
Q ss_pred EECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHH-----------HHHHHHHH
Q ss_conf 8706761001223320245678999999999999999999862999763442001003567-----------64578999
Q 000509 895 LRLGQGEQELATDLDFSRQGRVNAMLVRRLELLSEVERLARSLQLPEDVGYTCETAGYFWL-----------LHVYSRWE 963 (1456)
Q Consensus 895 lRlG~~e~~l~~~~~~s~~gRv~~~l~~r~~lL~ev~kLa~~l~~~~~~~~sceta~~f~~-----------~~i~~~w~ 963 (1456)
+.+ +.+..+..+ ++ ......++.........+....... ......+.
T Consensus 79 ~~v----------------~Tfhs~~~~---il---~~~~~~~g~~~~~~i~d~~~~~~l~~~~~~~~~~~~~~~~~~~~ 136 (673)
T 1uaa_A 79 LMI----------------STFHTLGLD---II---KREYAALGMKANFSLFDDTDQLALLKELTEGLIEDDKVLLQQLI 136 (673)
T ss_dssp SEE----------------EEHHHHHHH---HH---HHHHHHTTCCCCCCEECHHHHHHHHHHHTSTTSCSCHHHHHHHH
T ss_pred CEE----------------EEHHHHHHH---HH---HHHHHHHCCCCCCEEECHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 889----------------728787999---99---99899858999988707999999999999976434544699999
Q ss_pred HHHHHHHCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999620389973112346412452069999987741789999998999999999999999898999797798877752
Q 000509 964 QFLAACADNEGKPTFVRDRFPFKEFFSNTPQPIFTGDSFEKDMRAAKGCFRHLQTLFQELEECRAFELLKSTADRANYLM 1043 (1456)
Q Consensus 964 ~f~~~~~~~~~~~~~i~~~fpf~~~f~~~p~~l~~~~s~e~~l~~a~~~~~~i~~if~eL~e~r~felLr~~~dr~~~ll 1043 (1456)
............++. ..... . .. ....+..++...++.. .... .
T Consensus 137 ~~i~~~k~~~~~~~~---------~~~~~------~---~~-------~~~~~~~i~~~Y~~~l------~~~~-----~ 180 (673)
T 1uaa_A 137 STISNWKNDLKTPSQ---------AAASA------I---GE-------RDRIFAHCYGLYDAHL------KACN-----V 180 (673)
T ss_dssp HHHHHHHTTTCCTTH---------HHHTC------C---SH-------HHHHHHHHHHHHHHHH------HHHT-----C
T ss_pred HHHHHHHHCCCCHHH---------HHHHH------H---HH-------HHHHHHHHHHHHHHHH------HHCC-----C
T ss_conf 999999873999899---------99874------2---24-------8999999999999999------9869-----9
Q ss_pred HCCCCEEEECCHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHH-HHHC---------CCCCCCCEECCHHHHHHCC
Q ss_conf 11574999744357664467743089779899943989992789877-8717---------9888886011423331037
Q 000509 1044 TKQAKIVAMTCTHAALKRKDFLQLGFKYDNLLMEESAQILEIETFIP-MLLN---------DRRMLPPVVKNMAFQKYSH 1113 (1456)
Q Consensus 1044 lk~arIIa~T~t~aa~~~~~l~~lg~~fD~VIIDEAsQitE~EtlIP-Lll~---------Dh~QLpPvV~s~~~~~~~~ 1113 (1456)
+...+++..+................+|++|+|||+++++..+.-+- .+.. |++|.- +.+ .+
T Consensus 181 lDfdDll~~~~~lL~~~~~~~~~~~~~~~~ilVDEfQDt~~~Q~~ll~~L~~~~~~l~~vGD~~QsI-----y~f---rg 252 (673)
T 1uaa_A 181 LDFDDLILLPTLLLQANEEVRKRWQNKIRYLLVDEYQDTNTSQYELVKLLVGSRARFTVVGDDDQSI-----YSW---RG 252 (673)
T ss_dssp EEHHHHHHHHHHHHHHCHHHHHHHHTTCSEEEESCGGGCBHHHHHHHHHHHTTTCCEEEECCGGGCC-----CGG---GT
T ss_pred CCHHHHHHHHHHHHHHCHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEECCHHHH-----HHC---CC
T ss_conf 9889999999999874968999998308689986600189879999999966898599981752655-----450---59
Q ss_pred CCCCHHHHHHHC--CCCEEECCCCCCCCHHHHHHHHHHHCCCC-CCCC-EEECCCCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 952089999981--99814045554673347999999741489-9992-2533899998766899886689999999999
Q 000509 1114 MDQSLFTRFVRL--GIPYIELNAQGRARPSIAQLYNWRYRDLG-DLPF-LVDVPDYNGRGESAPSPWFYQNEGEAEYVVS 1189 (1456)
Q Consensus 1114 l~qSLFeRL~r~--g~p~i~L~~QYRs~PsIa~l~n~~yy~l~-dlp~-fIdV~~~~g~~e~~~~~~S~~N~~EAe~VV~ 1189 (1456)
-+...|.++... +...+.|..+||++++|+++.|..+.... ..+. ..... +.+.....-.+.....|+++|+.
T Consensus 253 a~~~~~~~~~~~~~~~~~~~L~~nyRs~~~I~~~an~~~~~~~~~~~~~l~~~~---~~g~~i~~~~~~~~~~e~~~va~ 329 (673)
T 1uaa_A 253 ARPQNLVLLSQDFPALKVIKLEQNYRSSGRILKAANILIANNPHVFEKRLFSEL---GYGAELKVLSANNEEHEAERVTG 329 (673)
T ss_dssp BCTTHHHHHHHHSTTCEEECCCCBSSSCHHHHHHHHHHHHTSCCSSCCCCCBSS---CCCCCBEEEECSSHHHHHHHHHH
T ss_pred CCHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHHCHHCCCCCCCCCC---CCCCCCEEEECCCHHHHHHHHHH
T ss_conf 988999999986899819978878899839999999999855311465445658---88997148846998999999999
Q ss_pred HHHHHH-HHCCCCCCEEEECCCHHHHHHHHHHHH
Q ss_conf 999999-919999977984377889999999997
Q 000509 1190 VYIYMR-LLGYPANKISILTTYNGQKLLIRDVIN 1222 (1456)
Q Consensus 1190 iv~~L~-~~Gy~~~kIaIITpY~aQ~~lIr~~L~ 1222 (1456)
.+..+. ..|++.++|+||++.+.|...|.+.|.
T Consensus 330 ~I~~l~~~~g~~~~diaVL~r~~~~~~~l~~~L~ 363 (673)
T 1uaa_A 330 ELIAHHFVNKTQYKDYAILYRGNHQSRVFEKFLM 363 (673)
T ss_dssp HHHHHHHHHCCCTTTEEEEESSSGGGTTHHHHHH
T ss_pred HHHHHHHCCCCCCCCEEEEEECHHHHHHHHHHHH
T ss_conf 9999886159980478999726264899999997
No 9
>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}
Probab=1.00 E-value=1 Score=196.86 Aligned_cols=293 Identities=15% Similarity=0.123 Sum_probs=176.1
Q ss_pred CCCCHHHHHHHHHCCC-----CCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCC
Q ss_conf 8899999999996138-----99099994799996899999999999809999479992578999999999983499965
Q 000509 818 VRFTPTQVGAIISGIQ-----PGLTMVVGPPGTGKTDTAVQILNVLYHNCPSQRTLIITHSNQALNDLFEKIMQRDVPAR 892 (1456)
Q Consensus 818 i~Ln~sQ~eAI~s~l~-----~gltLI~GPPGTGKT~via~iI~~Ll~~~p~~kILIva~SN~Ald~L~ekL~~l~i~~~ 892 (1456)
-.||+.|.+|+...+. .+..+|.||||||||+++..++..+.... ..+|+++|+||.|++.+.+++. ..
T Consensus 24 ~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~~~~~~l~~~~-~~~il~~a~T~~Aa~~l~~~~~---~~-- 97 (459)
T 3upu_A 24 DDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTKFIIEALISTG-ETGIILAAPTHAAKKILSKLSG---KE-- 97 (459)
T ss_dssp SCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHHHHHHHHHHTT-CCCEEEEESSHHHHHHHHHHHS---SC--
T ss_pred CCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHHHHC---CC--
T ss_conf 34899999999999998736897799996999989999999999998649-9609996675789998876616---54--
Q ss_pred CEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 38870676100122332024567899999999999999999986299976344200100356764578999999996203
Q 000509 893 YLLRLGQGEQELATDLDFSRQGRVNAMLVRRLELLSEVERLARSLQLPEDVGYTCETAGYFWLLHVYSRWEQFLAACADN 972 (1456)
Q Consensus 893 ~llRlG~~e~~l~~~~~~s~~gRv~~~l~~r~~lL~ev~kLa~~l~~~~~~~~sceta~~f~~~~i~~~w~~f~~~~~~~ 972 (1456)
...
T Consensus 98 -~~T---------------------------------------------------------------------------- 100 (459)
T 3upu_A 98 -AST---------------------------------------------------------------------------- 100 (459)
T ss_dssp -EEE----------------------------------------------------------------------------
T ss_pred -HHH----------------------------------------------------------------------------
T ss_conf -155----------------------------------------------------------------------------
Q ss_pred CCCCCCCCCCCCHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf 89973112346412452069999987741789999998999999999999999898999797798877752115749997
Q 000509 973 EGKPTFVRDRFPFKEFFSNTPQPIFTGDSFEKDMRAAKGCFRHLQTLFQELEECRAFELLKSTADRANYLMTKQAKIVAM 1052 (1456)
Q Consensus 973 ~~~~~~i~~~fpf~~~f~~~p~~l~~~~s~e~~l~~a~~~~~~i~~if~eL~e~r~felLr~~~dr~~~lllk~arIIa~ 1052 (1456)
+|.++...+. .......+..
T Consensus 101 ------------~h~~~~~~~~------------------------------------------------~~~~~~~~~~ 120 (459)
T 3upu_A 101 ------------IHSILKINPV------------------------------------------------TYEENVLFEQ 120 (459)
T ss_dssp ------------HHHHHTEEEE------------------------------------------------ECSSCEEEEE
T ss_pred ------------HHHHHCCCCC------------------------------------------------CCCCCCHHCC
T ss_conf ------------9988546855------------------------------------------------4553002000
Q ss_pred CCHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHH-----------CCCCCCCCEECCHHHHHHCCCCCCHHHH
Q ss_conf 44357664467743089779899943989992789877871-----------7988888601142333103795208999
Q 000509 1053 TCTHAALKRKDFLQLGFKYDNLLMEESAQILEIETFIPMLL-----------NDRRMLPPVVKNMAFQKYSHMDQSLFTR 1121 (1456)
Q Consensus 1053 T~t~aa~~~~~l~~lg~~fD~VIIDEAsQitE~EtlIPLll-----------~Dh~QLpPvV~s~~~~~~~~l~qSLFeR 1121 (1456)
. ....-.+++++|||||+++... .+-.+.. +|+.|+||+..+..... + ..++.
T Consensus 121 ~----------~~~~~~~~~~iiiDE~~~~~~~-~~~~l~~~~~~~~~~~~vGD~~Ql~~v~~g~~~~~---l-~~~~~- 184 (459)
T 3upu_A 121 K----------EVPDLAKCRVLICDEVSMYDRK-LFKILLSTIPPWCTIIGIGDNKQIRPVDPGENTAY---I-SPFFT- 184 (459)
T ss_dssp C----------SCCCCSSCSEEEESCGGGCCHH-HHHHHHHHSCTTCEEEEEECTTSCCCCCTTSCSCC---C-CGGGT-
T ss_pred C----------CCCCCCCCCEEEEECCHHCCHH-HHHHHHHHCCCCCEEEEECCHHHCCCCCCCCCHHH---H-HHHHH-
T ss_conf 3----------3333467889999880118999-99999984568988999887787688668862476---7-79985-
Q ss_pred HHHCCCCEEECCCCCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 99819981404555467334799999974148999922533899998766899886689999999999999999919999
Q 000509 1122 FVRLGIPYIELNAQGRARPSIAQLYNWRYRDLGDLPFLVDVPDYNGRGESAPSPWFYQNEGEAEYVVSVYIYMRLLGYPA 1201 (1456)
Q Consensus 1122 L~r~g~p~i~L~~QYRs~PsIa~l~n~~yy~l~dlp~fIdV~~~~g~~e~~~~~~S~~N~~EAe~VV~iv~~L~~~Gy~~ 1201 (1456)
..+.+.+.|+++||+++.|.++.+....+ ..+.. ...+ +.+... +.+..|+ ...+......+...
T Consensus 185 --~~~~~~~~L~~~~R~~~~I~~~a~~lr~g-~~~~~--~~~~--~~~v~~-----~~~~~~~---~~~i~~~~~~~~~~ 249 (459)
T 3upu_A 185 --HKDFYQCELTEVKRSNAPIIDVATDVRNG-KWIYD--KVVD--GHGVRG-----FTGDTAL---RDFMVNYFSIVKSL 249 (459)
T ss_dssp --CTTEEEEECCCCCCCCCHHHHHHHHHHTT-CCCCC--EEET--TEEEEE-----CCSSSSH---HHHHHHHHHHTTTC
T ss_pred --CCCCCEEECEEEEECCCHHHHHHHHHHCC-CCCCH--HCCC--CCCEEE-----CCCHHHH---HHHHHHHHHHCCCC
T ss_conf --68972875504640895799999999758-87610--0248--998375-----5866889---99999999760894
Q ss_pred C---CEEEECCCHHHHHHHHHHHHHCCCCCC--C----------------------------------------------
Q ss_conf 9---779843778899999999973189999--8----------------------------------------------
Q 000509 1202 N---KISILTTYNGQKLLIRDVINRQCVPYP--F---------------------------------------------- 1230 (1456)
Q Consensus 1202 ~---kIaIITpY~aQ~~lIr~~L~~r~~~~~--~---------------------------------------------- 1230 (1456)
. +++||++.++|+..+.+.++.+..... .
T Consensus 250 ~~~~~~aIL~rtN~~~~~~n~~lr~~~~~~~~~~~~gd~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~v~rv~~~~~~~ 329 (459)
T 3upu_A 250 DDLFENRVMAFTNKSVDKLNSIIRKKIFETDKDFIVGEIIVMQEPLFKTYKIDGKPVSEIIFNNGQLVRIIEAEYTSTFV 329 (459)
T ss_dssp SCCTTEEEEESSHHHHHHHHHHHHHHHTTCCCSCCTTCEEEESSCEEEEEEETTEEEEEEEECTTCEEEEEEEEEEEEEE
T ss_pred CHHHCEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCEEEEEEECCCCCCC
T ss_conf 30111699981176799999999998516688667887888501010345347875540898189889999960430111
Q ss_pred --------------------------------------------------------------------------C--CCC
Q ss_conf --------------------------------------------------------------------------8--999
Q 000509 1231 --------------------------------------------------------------------------I--GPP 1234 (1456)
Q Consensus 1231 --------------------------------------------------------------------------~--g~~ 1234 (1456)
+ ...
T Consensus 330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 409 (459)
T 3upu_A 330 KARGVPGEYLIRHWDLTVETYGDDEYYREKIKIISSDEELYKFNLFLGKTAETYKNWNKGGKAPWSDFWDAKSQFSKVKA 409 (459)
T ss_dssp CCTTSCSCEEEEEEEEEEEECSSSCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHSCCSSSSCCTHHHHHHHTTBCCEEE
T ss_pred CCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf 23466767747999999964578762058999517879999999999999999876102560678999999998761585
Q ss_pred CEEECCCCCCCCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEE
Q ss_conf 32512568987557799997023698665565102578875432257999
Q 000509 1235 SKVTTVDKFQGQQNDFILLSLVRTRFVGHLRDVRRLVVAMSRARLGLYVF 1284 (1456)
Q Consensus 1235 vkV~TVD~fQG~E~DiVIlSlVRs~~vGfL~d~rRLNVAlSRAK~~LiIV 1284 (1456)
+.+.|+|+.||.|+|.|++..........-.+.|.++||+||||..|+++
T Consensus 410 ~~~~t~h~~kG~e~~~v~~~~~~~~~~~~~~~~~~~yva~tRa~~~l~~~ 459 (459)
T 3upu_A 410 LPASTFHKAQGMSVDRAFIYTPCIHYADVELAQQLLYVGVTRGRYDVFYV 459 (459)
T ss_dssp SSEEETGGGTTCCEEEEEEECGGGGGSCHHHHHHHHHHHHHHEEEEEEEC
T ss_pred EEEEEEEECCCCCCCEEEEECCCCCCCCHHHHHHEEEEEECCEEEEEEEC
T ss_conf 79998882367778889995488887686887540465521230479959
No 10
>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*
Probab=1.00 E-value=1 Score=194.61 Aligned_cols=325 Identities=20% Similarity=0.174 Sum_probs=178.7
Q ss_pred CHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHC--CCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCEEECC
Q ss_conf 99999999961389909999479999689999999999980--9999479992578999999999983499965388706
Q 000509 821 TPTQVGAIISGIQPGLTMVVGPPGTGKTDTAVQILNVLYHN--CPSQRTLIITHSNQALNDLFEKIMQRDVPARYLLRLG 898 (1456)
Q Consensus 821 n~sQ~eAI~s~l~~gltLI~GPPGTGKT~via~iI~~Ll~~--~p~~kILIva~SN~Ald~L~ekL~~l~i~~~~llRlG 898 (1456)
++.|..||..++..++.+|+||||||||++++.++..+... ..+.+|+++|||+.|++++.+.+....
T Consensus 151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~APTg~AA~~L~e~~~~~~---------- 220 (608)
T 1w36_D 151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKAL---------- 220 (608)
T ss_dssp CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTHHH----------
T ss_pred CHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHH----------
T ss_conf 9999999999962998999949999789999999999998630579759999187368999999999887----------
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 76100122332024567899999999999999999986299976344200100356764578999999996203899731
Q 000509 899 QGEQELATDLDFSRQGRVNAMLVRRLELLSEVERLARSLQLPEDVGYTCETAGYFWLLHVYSRWEQFLAACADNEGKPTF 978 (1456)
Q Consensus 899 ~~e~~l~~~~~~s~~gRv~~~l~~r~~lL~ev~kLa~~l~~~~~~~~sceta~~f~~~~i~~~w~~f~~~~~~~~~~~~~ 978 (1456)
..+++...... ..
T Consensus 221 ------------------------------------~~l~l~~~~~~-------------------------------~~ 233 (608)
T 1w36_D 221 ------------------------------------RQLPLTDEQKK-------------------------------RI 233 (608)
T ss_dssp ------------------------------------HHSSCCSCCCC-------------------------------SC
T ss_pred ------------------------------------HCCCCCHHHHH-------------------------------CC
T ss_conf ------------------------------------50787788873-------------------------------24
Q ss_pred CCCCCCHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCHHHH
Q ss_conf 12346412452069999987741789999998999999999999999898999797798877752115749997443576
Q 000509 979 VRDRFPFKEFFSNTPQPIFTGDSFEKDMRAAKGCFRHLQTLFQELEECRAFELLKSTADRANYLMTKQAKIVAMTCTHAA 1058 (1456)
Q Consensus 979 i~~~fpf~~~f~~~p~~l~~~~s~e~~l~~a~~~~~~i~~if~eL~e~r~felLr~~~dr~~~lllk~arIIa~T~t~aa 1058 (1456)
-.....+|.++...+.. ..
T Consensus 234 ~~~~~Tih~ll~~~~~~-------------------------------------------------------------~~ 252 (608)
T 1w36_D 234 PEDASTLHRLLGAQPGS-------------------------------------------------------------QR 252 (608)
T ss_dssp SCCCBTTTSCC---------------------------------------------------------------------
T ss_pred CHHHHHHHHHHCCCCCC-------------------------------------------------------------HH
T ss_conf 05555057552058981-------------------------------------------------------------67
Q ss_pred HHHHHHHHCCCCCCEEEEECCCCCCHHH--HHHHHH--------HCCCCCCCCEECCHHHHHH-----CCCCCCHHHHHH
Q ss_conf 6446774308977989994398999278--987787--------1798888860114233310-----379520899999
Q 000509 1059 LKRKDFLQLGFKYDNLLMEESAQILEIE--TFIPML--------LNDRRMLPPVVKNMAFQKY-----SHMDQSLFTRFV 1123 (1456)
Q Consensus 1059 ~~~~~l~~lg~~fD~VIIDEAsQitE~E--tlIPLl--------l~Dh~QLpPvV~s~~~~~~-----~~l~qSLFeRL~ 1123 (1456)
..+... ...++|.+|||||+++.... .++..+ .+|+.||||+..+..+... .++..++++++.
T Consensus 253 ~~~~~~--~~l~~d~lIIDEAsml~~~~~~~Ll~~l~~~~~liLvGD~~QL~~V~~G~vl~dl~~~~~~g~~~~~~~~l~ 330 (608)
T 1w36_D 253 LRHHAG--NPLHLDVLVVDEASMIDLPMMSRLIDALPDHARVIFLGDRDQLASVEAGAVLGDICAYANAGFTAERARQLS 330 (608)
T ss_dssp ---CTT--SCCSCSEEEECSGGGCBHHHHHHHHHTCCTTCEEEEEECTTSGGGTSTTBCHHHHGGGGTTCCCHHHHHHHH
T ss_pred HHHCCC--CCCCCCEEEEECHHHCCHHHHHHHHHHCCCCCEEEEECCHHHCCCCCCCCHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 775268--987799999945250899999999984888988999766044588789807999998775366678899998
Q ss_pred HCC-----------CC-----EEECCCCCCCCHH--HHHHHHHHHCCCCCCCC-------------EEECCCCCC-----
Q ss_conf 819-----------98-----1404555467334--79999997414899992-------------253389999-----
Q 000509 1124 RLG-----------IP-----YIELNAQGRARPS--IAQLYNWRYRDLGDLPF-------------LVDVPDYNG----- 1167 (1456)
Q Consensus 1124 r~g-----------~p-----~i~L~~QYRs~Ps--Ia~l~n~~yy~l~dlp~-------------fIdV~~~~g----- 1167 (1456)
+.. .| .+.|+++||+++. |..+.+....+ +.+. |+...+...
T Consensus 331 ~~~~~~~~~~~~~~~~~~~~~~~~L~~~~R~~~~s~I~~la~~i~~g--~~~~~~~~l~~~~~d~~~~~~~~~~~~~~~~ 408 (608)
T 1w36_D 331 RLTGTHVPAGTGTEAASLRDSLCLLQKSYRFGSDSGIGQLAAAINRG--DKTAVKTVFQQDFTDIEKRLLQSGEDYIAML 408 (608)
T ss_dssp HHSSSCCCCCSTTTTHHHHTTEEECCCCCCSSCCTTHHHHHHHHTSC--HHHHHTTTSGGGCCSSBCCBCCSTTTHHHHH
T ss_pred HHCCCCCCCCCCCCCCCCCCCEEECCEEEEECCCCHHHHHHHHHHCC--CCHHHHHHHCCCCCCEEEEECCCHHHHHHHH
T ss_conf 73175434321123554446277622545207843599999998658--8156899854788865997268867899999
Q ss_pred -----------------C--C------CC----CCCCCC-----CCCH---------------HHHHHHH-HHHHHHH--
Q ss_conf -----------------8--7------66----899886-----6899---------------9999999-9999999--
Q 000509 1168 -----------------R--G------ES----APSPWF-----YQNE---------------GEAEYVV-SVYIYMR-- 1195 (1456)
Q Consensus 1168 -----------------~--~------e~----~~~~~S-----~~N~---------------~EAe~VV-~iv~~L~-- 1195 (1456)
. . .. .+.... ..|. .+..+-+ +-++..+
T Consensus 409 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~vL~~~~~g~~gv~~lN~~i~~~l~~~~~~~~~~~~~~~~Gd~Vm~~~Nd 488 (608)
T 1w36_D 409 EEALAGYGRYLDLLQARAEPDLIIQAFNEYQLLCALREGPFGVAGLNERIEQFMQQKRKIHRHPHSRWYEGRPVMIARND 488 (608)
T ss_dssp HHHHHHTHHHHHHHHTCCCSSTTHHHHTTEEEEESCSSSSSSHHHHHHHHHGGGTSCC----------------------
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEEC
T ss_conf 99999999999986512488999889866553277468836699999999998385676554666654289723675556
Q ss_pred -HHCCCCCCEEEECCCHHHHHHHHHHHHH---CC---CCCCCC-CCCCEEECCCCCCCCCCCEEEEEECCCCCCCCCCCC
Q ss_conf -9199999779843778899999999973---18---999988-999325125689875577999970236986655651
Q 000509 1196 -LLGYPANKISILTTYNGQKLLIRDVINR---QC---VPYPFI-GPPSKVTTVDKFQGQQNDFILLSLVRTRFVGHLRDV 1267 (1456)
Q Consensus 1196 -~~Gy~~~kIaIITpY~aQ~~lIr~~L~~---r~---~~~~~~-g~~vkV~TVD~fQG~E~DiVIlSlVRs~~vGfL~d~ 1267 (1456)
..|+-..+||+|++.... ++-.+.. +. ....+. -....+.|||+.||.|+|.||+.+..... .+.+.
T Consensus 489 ~~~gl~NGdiG~V~~~~~~---l~v~f~~~dg~~~~~~~~~l~~l~~~~a~TihksqG~e~~~v~~~~~~~~~--~~~~~ 563 (608)
T 1w36_D 489 SALGLFNGDIGIALDRGQG---TRVWFAMPDGNIKSVQPSRLPEHETTWAMTVHKSQGSEFDHAALILPSQRT--PVVTR 563 (608)
T ss_dssp -------------------------------------CCSCCCSCSSCSEEETTTTTTCCBSEEEEECCSSCC--SSSCH
T ss_pred HHHCCCCCCEEEEEECCCE---EEEEEECCCCCEEEECHHHCCCCCEEEEEEEEECCCCCCCEEEEEECCCCC--CHHHH
T ss_conf 1433637976999973881---799998899958995657777624489998781364348869999189866--13342
Q ss_pred HHHHHHHHHHHCCEEEEECHHHHHH
Q ss_conf 0257887543225799912025653
Q 000509 1268 RRLVVAMSRARLGLYVFCRRSLFEQ 1292 (1456)
Q Consensus 1268 rRLNVAlSRAK~~LiIVGn~~~l~~ 1292 (1456)
+.+|||+||||..++++|+...|..
T Consensus 564 ~~~Yva~tRa~~~l~l~~~~~~l~~ 588 (608)
T 1w36_D 564 ELVYTAVTRARRRLSLYADERILSA 588 (608)
T ss_dssp HHHHHHHTTBSSCEEEECCTTHHHH
T ss_pred HHHHHHHHHHHCEEEEEECHHHHHH
T ss_conf 2377316044366899988899999
Done!