Query         537021.9.peg.410_1
Match_columns 952
No_of_seqs    254 out of 5600
Neff          9.9 
Searched_HMMs 23785
Date          Wed May 25 02:25:51 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_410.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 1w36_B RECB, exodeoxyribonucle 100.0       0       0  764.5  53.0  756  124-948   326-1172(1180)
  2 1pjr_A PCRA; DNA repair, DNA r 100.0       0       0  504.4  37.6  440  127-669   170-622 (724)
  3 2is6_A DNA helicase II; hydrol 100.0       0       0  478.3  42.7  440  125-670   165-618 (680)
  4 1uaa_A REP helicase, protein ( 100.0       0       0  457.0  43.9  440  126-670   160-615 (673)
  5 1w36_C RECC, exodeoxyribonucle 100.0 2.1E-26 8.7E-31  206.3  36.7  543  340-946   380-1022(1122)
  6 2gk6_A Regulator of nonsense t  99.7   2E-14 8.3E-19  119.5  18.0   87  174-282   337-430 (624)
  7 2wjy_A Regulator of nonsense t  99.6 2.2E-13 9.4E-18  111.8  21.6   87  174-282   513-606 (800)
  8 3dmn_A Putative DNA helicase;   99.5 9.5E-15   4E-19  121.8   6.2   56  569-668    99-154 (174)
  9 3h4r_A Exodeoxyribonuclease 8;  99.3 1.4E-11   6E-16   98.8   8.0  188  756-948    12-232 (265)
 10 3l0a_A Putative exonuclease; R  99.3 3.3E-10 1.4E-14   88.8  14.7  160  775-951    51-225 (266)
 11 1w36_D RECD, exodeoxyribonucle  99.2 1.1E-11 4.7E-16   99.5   4.7   54  175-238   261-314 (608)
 12 3e1s_A Exodeoxyribonuclease V,  98.7 3.4E-09 1.4E-13   81.6   3.1   81  175-280   278-361 (574)
 13 3b85_A Phosphate starvation-in  97.0  0.0016 6.9E-08   40.3   6.7   79  178-275   124-204 (208)
 14 3e1s_A Exodeoxyribonuclease V,  96.6   0.006 2.5E-07   36.3   6.7   47  575-667   494-540 (574)
 15 2vld_A NUCS, UPF0286 protein p  96.0    0.02 8.2E-07   32.5   6.9   55  865-928   156-211 (251)
 16 3dmn_A Putative DNA helicase;   95.5   0.064 2.7E-06   28.8   7.8   20  261-280     2-21  (174)
 17 3e2i_A Thymidine kinase; Zn-bi  89.9    0.47   2E-05   22.6   5.1   37  174-220    99-135 (219)
 18 1xx6_A Thymidine kinase; X-RAY  88.5    0.79 3.3E-05   20.9   5.4   49  169-227    74-125 (191)
 19 2j9r_A Thymidine kinase; TK1,   86.8     0.8 3.4E-05   20.9   4.6   45  173-227    98-145 (214)
 20 2orw_A Thymidine kinase; TMTK,  85.2    0.71   3E-05   21.3   3.7   44  173-226    73-119 (184)
 21 2b8t_A Thymidine kinase; deoxy  75.2     2.5  0.0001   17.3   4.8   35  175-219    88-122 (223)
 22 2orv_A Thymidine kinase; TP4A   58.4     5.2 0.00022   15.0   4.6   35  175-220    89-123 (234)
 23 1w4r_A Thymidine kinase; type   55.8     5.7 0.00024   14.7   4.9   26  175-201    90-115 (195)
 24 1cu1_A Protein (protease/helic  49.9       7 0.00029   14.1   3.7   19  211-229    42-60  (645)
 25 2z4s_A Chromosomal replication  37.5      11 0.00044   12.8   7.0   22  646-667   214-235 (440)
 26 2i4r_A V-type ATP synthase sub  35.3      11 0.00048   12.5   1.5   24  211-235     7-30  (102)
 27 3llm_A ATP-dependent RNA helic  35.3      11 0.00048   12.5   3.6   19  193-222    67-85  (235)
 28 1l8q_A Chromosomal replication  32.1      13 0.00054   12.2   6.3   83  147-240    71-156 (324)
 29 3fov_A UPF0102 protein RPA0323  29.2      14  0.0006   11.8   7.3   62  865-928    50-116 (134)
 30 2hwk_A Helicase NSP2; rossman   28.5       7  0.0003   14.0  -0.7   41  173-226   135-176 (320)
 31 3kqn_A Serine protease/ntpase/  23.9      17 0.00073   11.2   3.6   27  175-201    94-120 (437)
 32 1ob8_A Holliday-junction resol  23.9      17 0.00073   11.2   1.8   28  861-888    31-58  (135)
 33 2jok_A Putative G-nucleotide e  23.6      16 0.00067   11.5   0.3   13  219-231     3-15  (186)

No 1  
>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*
Probab=100.00  E-value=0  Score=764.48  Aligned_cols=756  Identities=16%  Similarity=0.192  Sum_probs=460.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCEEEEECHHCCCHHHHHHHHHHHHHC
Q ss_conf             89999999999999999998699775899999999831584248999998617989998071019999999999984100
Q 537021.9.peg.4  124 LASLTLAKYLNAHYEEAKKKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRSLTEDF  203 (952)
Q Consensus       124 ~~l~~~~~~~~~~y~~~k~~~~~ldf~Dl~~~a~~lL~~~~~~~~~~~~l~~~~~~ilVDEfQDT~~~Q~~il~~L~~~~  203 (952)
                      ..+.+++..+.+.|.+.|+++|.+||+||++.+.++|.+++ .+.++.+++.+|+|||||||||||++||+||+.|+.+ 
T Consensus       326 ~~l~~~~~~~~~~y~~~k~~~~~ldf~Dl~~~a~~ll~~~~-~~~l~~~l~~r~~~ilVDEfQDTn~~Q~~il~~L~~~-  403 (1180)
T 1w36_B          326 LVITRALAEIRETVAREKRRRGELGFDDMLSRLDSALRSES-GEVLAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWHH-  403 (1180)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTEECHHHHHHHHHHHHHSTT-HHHHHHHHHHHCSEEEECSGGGCCHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCC-HHHHHHHHHHHCCEEEEEHHHCCHHHHHHHHHHHHHC-
T ss_conf             99999999999999999998399980999999999975212-6999999996398999961532399999999999716-


Q ss_pred             CCCCCCCCCCCEEEEEECCHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHCCCC
Q ss_conf             24676667686499996665676542488847899999996652134576531200686668878999999999711210
Q 537021.9.peg.4  204 FVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELPLSFRSTADILTVVDKVFSIPEN  283 (952)
Q Consensus       204 ~~~~~~~~~~~~l~~VGD~kQSIY~FRGAd~~~~~~~~~~f~~~~~~~~~~~~~~~L~~N~RS~~~Ii~~~N~~f~~~~~  283 (952)
                             ..++++|+|||||||||+||||||.+|.++.+.+.          +.+.|++||||+++||+++|.+|.+...
T Consensus       404 -------~~~~~l~~VGDpkQSIY~FRgAd~~~~~~~~~~~~----------~~~~L~~N~RS~~~Il~~~N~lf~~~~~  466 (1180)
T 1w36_B          404 -------QPETALLLIGDPKQAIYAFRGADIFTYMKARSEVH----------AHYTLDTNWRSAPGMVNSVNKLFSQTDD  466 (1180)
T ss_dssp             -------CTTCEEEEEECGGGCCCGGGTCCHHHHHHHHHHCC----------CEEECCEETTSCHHHHHHHHHHHHSSSS
T ss_pred             -------CCCCEEEEEECCCCEEECCCCCCHHHHHHHHHHHH----------HHCCCCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             -------89871899807865330335777799999987643----------4202442457748999999999972522


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC-
Q ss_conf             0123322122212233447888743651134443223343101111100011133336888999999999999835862-
Q 537021.9.peg.4  284 AQGLSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQHDSQCNPQQESWTSYFDSLPQESSASILARRIAYTISNMIGTDTI-  362 (952)
Q Consensus       284 ~~~~~~~~~~~~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~I~~l~~~~~~-  362 (952)
                      ..........+  ..+.....  .....   .   .....+....+....+...........|+.++..|++++..+.. 
T Consensus       467 ~~~~~~~~~~~--~~~~~~~~--~~~~~---~---~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~ia~~I~~ll~~~~~~  536 (1180)
T 1w36_B          467 AFMFREIPFIP--VKSAGKNQ--ALRFV---F---KGETQPAMKMWLMEGESCGVGDYQSTMAQVCAAQIRDWLQAGQRG  536 (1180)
T ss_dssp             TTSSTTSCCCC--CEECGGGT--TEEEE---E---TTEEECSEEEEECCSSCCCTTHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCC--HHCCCCCC--CCCCC---C---CCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             11123345310--00025554--43324---6---666665420220466664310377789999999999999820011


Q ss_pred             ----CCCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCEE-ECCCCCCCCCCCHHHHHHHHHHHHCCCCCHHH
Q ss_conf             ----2125436878244689861531012248999998741697366-04862112331052268768887481311024
Q 537021.9.peg.4  363 ----FSNGKKRVIQAKDILVLVRKRKDTPLITFLTRFLKNDYKISVV-GNDRFILTDHLAIKDLMALGRFILSQEDDLSF  437 (952)
Q Consensus       363 ----~~~~~~r~~~~~diaVL~r~~~~~~~~~~~l~al~~~~~ip~~-~~~~~~~~~~~~v~~l~a~l~~l~~p~~~~~~  437 (952)
                          ......|+++++|||||||++++...+...|    ..+|||+. ..++.++++++++.+++++|+++.+|.++..+
T Consensus       537 ~~~~~~~~~~r~~~~~DIaILvR~~~~~~~i~~~L----~~~gIp~~~~~~~~~~~~~~ev~~ll~ll~~l~~p~~~~~l  612 (1180)
T 1w36_B          537 EALLMNGDDARPVRASDISVLVRSRQEAAQVRDAL----TLLEIPSVYLSNRDSVFETLEAQEMLWLLQAVMTPERENTL  612 (1180)
T ss_dssp             CEEEEETTEEEECCGGGEEEEESSHHHHHHHHHHH----HTTTCCEEETTCCCBGGGSSHHHHHHHHHHHHTCTTSHHHH
T ss_pred             HHHHCCCCCCCCCCCCCEEEEECCCHHHHHHHHHH----HHCCCCEEEECCCHHHHHCHHHHHHHHHHHHHCCCCCHHHH
T ss_conf             12321454346778142799971537689999889----87499849946731364088999999999861484538999


Q ss_pred             HHHCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHH
Q ss_conf             54305877478888999987301268657888764311115899999999999998642199899999998503469999
Q 537021.9.peg.4  438 VCMLKSPLFNFSEDDIFKICTQRHETETVYEYIQKFANCGISKFQHVIKYIHELIHIAQFCSPHDFFTLILGAKKGRQQF  517 (952)
Q Consensus       438 ~~~L~spl~g~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  517 (952)
                      ..+|+||++|++..++..+....                  ..+....+.+..++.......+.++++.++........+
T Consensus       613 ~~~l~s~~~g~~~~~l~~l~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~l  674 (1180)
T 1w36_B          613 RSALATSMMGLNALDIETLNNDE------------------HAWDVVVEEFDGYRQIWRKRGVMPMLRALMSARNIAENL  674 (1180)
T ss_dssp             HHHHHSGGGTCCHHHHHHHHHCH------------------HHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTHHHHH
T ss_pred             HHHHHCCCCCCCHHHHHHHHHCH------------------HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
T ss_conf             99983734599999999984345------------------778999998999999998667089999999876799999


Q ss_pred             HHCCC-HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC-------CCCCCCCCCCCCCEEECHHHCCCCCCCEEE
Q ss_conf             81135-2389999999999999852056898999998850100-------132112357885303001221456777799
Q 537021.9.peg.4  518 ISRFG-NEVIDVLDEFLNFTLRNEQNSYSSLQELISELEQYPP-------TIKRAHSANHNEVRIMTVHTAKGLESPVVF  589 (952)
Q Consensus       518 ~~~~~-~~~~~~l~~l~~~a~~~e~~~~~~l~~f~~~l~~~~~-------~~~~~~~~~~d~V~imTiH~SKGLEfpvV~  589 (952)
                      ....+ .....|+..+.+.+..+ .....++..|+.|+.....       .......++.++|+|||||+|||||||+||
T Consensus       675 ~~~~~~~~~~~~l~~l~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~V~imTiHkSKGLEfpvV~  753 (1180)
T 1w36_B          675 LATAGGERRLTDILHISELLQEA-GTQLESEHALVRWLSQHILEPDSNASSQQMRLESDKHLVQIVTIHKSKGLEYPLVW  753 (1180)
T ss_dssp             HHSSSHHHHHHHHHHHHHHHHHH-HTTCSCHHHHHHHHHHHHHSCCCCSTTBCCCCTTGGGSEEEEETTTTSSCCEEEEE
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHH-HHHCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCEEEEEEEEECCCCCCCEEE
T ss_conf             86057689999999999999999-87423278999999999860121124554212203670689741541676678899


Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCC
Q ss_conf             81588776776544422234455566663123544457874779999999764444678878751146652899983167
Q 537021.9.peg.4  590 LVDTGSQVFSHKHIKKMHIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIICKHSN  669 (952)
Q Consensus       590 i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ee~RLlYVAlTRAk~~L~l~~~~~  669 (952)
                      ||+++++.++.......    . .......        ............+.+..+|++|||||||||||++|+|++...
T Consensus       754 v~~~~~~~~~~~~~~~~----~-~~~~~~~--------~~~~~~~~~~~~~~e~l~Ee~RLlYVAlTRAk~~L~l~~~~~  820 (1180)
T 1w36_B          754 LPFITNFRVQEQAFYHD----R-HSFEAVL--------DLNAAPESVDLAEAERLAEDLRLLYVALTRSVWHCSLGVAPL  820 (1180)
T ss_dssp             ETTTTCCCCCCSCEEEC----T-TTCCEEE--------ESSCCHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEECCC
T ss_pred             EECCCCCCCCCCCCCCC----C-CCCCCCC--------CCCCCHHHHHHHHHHHHHHHHHHHHEEEECCCCEEEEEEEEC
T ss_conf             93675677766666653----1-0100014--------655465677687899888887876304522335689998401


Q ss_pred             CCCCCCCCC--CCCHHHHHHCCCCCCCCCCCCC---CCCCCCCCCC--------CCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             777666543--2106887310356433222234---5444433222--------11012235544321000122221000
Q 537021.9.peg.4  670 TSNEKKSNQ--RTWYDMVYDSFHNDERVKKIKL---TNSINKDEWI--------AYEWSTHHPENTPLEREETIKQLMDE  736 (952)
Q Consensus       670 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~  736 (952)
                      .........  ......+...............   ..........        ................. ........
T Consensus       821 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~  899 (1180)
T 1w36_B          821 VRRRGDKKGDTDVHQSALGRLLQKGEPQDAAGLRTCIEALCDDDIAWQTAQTGDNQPWQVNDVSTAELNAK-TLQRLPGD  899 (1180)
T ss_dssp             CCSCSCCSSCCGGGGSHHHHHHTCSSCCCHHHHHHHHHHSCSTTEEEEECCCCCCCCCCCCCCCCCCCCCC-CCCCCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCC-CCCCCCCC
T ss_conf             33457766652556766788862677554146899888753776432245543233334565541121221-24556554


Q ss_pred             HHHHHHHCCCCCCC------CCCCCCCCHHHCCHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             01124530334433------233423361110010015554446630155677999999985668996568999999985
Q 537021.9.peg.4  737 QKIPKKLFSPIKND------INEPYILNPSTIDTKGKTNLESLLSDNQTFNRGLIIHKLLQVIFTLPEHKRKNFITSYCT  810 (952)
Q Consensus       737 ~~~~~~~~~~~~~~------~~~~~~l~~s~~~~~~~~~~~~~~~~~~a~~~Gt~vH~~lE~l~~~~~~~~~~~~~~~l~  810 (952)
                      ......+.......      ..................+.......+.|+.+||++|++||++++....+. ..+.+.+.
T Consensus       900 ~~~~~s~s~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ga~~Gt~~H~ilE~ldf~~~~~~-~~i~~~l~  978 (1180)
T 1w36_B          900 NWRVTSYSGLQQRGHGIAQDLMPRLDVDAAGVASVVEEPTLTPHQFPRGASPGTFLHSLFEDLDFTQPVDP-NWVREKLE  978 (1180)
T ss_dssp             CEEEESSCSSSCSSCTTHHHHCTTSCTTCCCCCCSCCCSSCCGGGSCCSHHHHHHHHHHTTSCCSSSCCCH-HHHHHHHH
T ss_pred             CCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHCCCCCCCCH-HHHHHHHH
T ss_conf             32203726664401345554454545553344210027767800147637689999999984899999999-99999998


Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHCCHH------HHHHHCCCCCCCEEEEEEEEC--------------------------C
Q ss_conf             00458998899999999999862965------578717778561137888623--------------------------8
Q 537021.9.peg.4  811 KNAKLWPAKEYKNLLLSITRLLENPM------MTTAMSCDSYSEVSVSGKINC--------------------------P  858 (952)
Q Consensus       811 ~~~~~~~~~~~~~~~~~~~~~l~~~~------~~~~~~~~~~~Ev~~e~~~~~--------------------------~  858 (952)
                      ..  .........+.+.+..++..+.      +..+.......|++|..++..                          .
T Consensus       979 ~~--~~~~~~~~~~~~~l~~~l~~pL~~~~~~l~~~~~~~~~~E~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1056 (1180)
T 1w36_B          979 LG--GFESQWEPVLTEWITAVLQAPLNETGVSLSQLSARNKQVEMEFYLPISEPLIASQLDTLIRQFDPLSAGCPPLEFM 1056 (1180)
T ss_dssp             HT--TCCGGGHHHHHHHHHHHHSSCSSSSSCCGGGCCGGGEEEEEEEEEEECSCCCHHHHHHHHHHHCSSTTSCCCCCSC
T ss_pred             HC--CCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHCCHHCCEEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             54--9970225999999999980858776766544772021650153222562202888999997336300125432343


Q ss_pred             CCCEEEEEEEEEEEEECCEEEEEECCCCCCCCCC----HHH-----HHHHHHHHHHHHHHHHHHHC----CCCCE-----
Q ss_conf             8858999797789997998999972580138999----899-----99988999999999999967----99827-----
Q 537021.9.peg.4  859 KKDIIISGRIDQISISQQNIFIFEYKTHHHVPQE----IEH-----IPYTHIAQLSIYEKILKDSY----PNKSL-----  920 (952)
Q Consensus       859 ~~~~~i~G~IDri~~~~~~~~IiDyKT~~~~~~~----~~~-----~~~~Y~~QL~~Y~~al~~~~----p~~~V-----  920 (952)
                      ...++|+|+||++|.++|+++|||||||+..++.    .+.     ..++|..||.+|+.||+++.    |+...     
T Consensus      1057 ~~~g~l~G~IDlvf~~dg~~~IvDYKTd~lg~~~~~y~~~~l~~~m~~~~Y~lQ~~lY~~AL~r~L~~r~~~y~~~~h~G 1136 (1180)
T 1w36_B         1057 QVRGMLKGFIDLVFRHEGRYYLLDYKSNWLGEDSSAYTQQAMAAAMQAHRYDLQYQLYTLALHRYLRHRIADYDYEHHFG 1136 (1180)
T ss_dssp             CCEEEEEEEEEEEEBSSSCBCCEEEECCCCCSSGGGSBHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHSSSCCHHHHCC
T ss_pred             CCEEEEEEEEEEEEEECCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHCC
T ss_conf             54146999999999999999999727899899841029999999988786199999999999999707077987455178


Q ss_pred             EEEEEECCC--------CEEEECCHHHHHHHHHHHH
Q ss_conf             899998559--------8789879899999999765
Q 537021.9.peg.4  921 VCLLIYVSE--------PKVFIIPQNKLNKAFAEIS  948 (952)
Q Consensus       921 ~~~l~y~~~--------~~~~~~~~~~l~~~~~~~~  948 (952)
                      .++.+|+++        |-..+.|+.+|=.+|+++-
T Consensus      1137 g~~YlFlRG~~~~~~~~G~~~~~p~~~~i~~ld~l~ 1172 (1180)
T 1w36_B         1137 GVIYLFLRGVDKEHPQQGIYTTRPNAGLIALMDEMF 1172 (1180)
T ss_dssp             CCEEEESSSCCTTCTTBSCCBCCCCSSHHHHHHHHH
T ss_pred             CEEEEEECCCCCCCCCCCEEEECCCHHHHHHHHHHH
T ss_conf             279999479899999996685059999999999985


No 2  
>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=100.00  E-value=0  Score=504.36  Aligned_cols=440  Identities=24%  Similarity=0.325  Sum_probs=319.6

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCEEEEECHHCCCHHHHHHHHHHHHHCCCC
Q ss_conf             99999999999999998699775899999999831584248999998617989998071019999999999984100246
Q 537021.9.peg.4  127 LTLAKYLNAHYEEAKKKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRSLTEDFFVG  206 (952)
Q Consensus       127 ~~~~~~~~~~y~~~k~~~~~ldf~Dl~~~a~~lL~~~~~~~~~~~~l~~~~~~ilVDEfQDT~~~Q~~il~~L~~~~~~~  206 (952)
                      ......++..|+..+.+.+.+||+|++..+..++.+.+.   ++..++.+|+|||||||||||++|++|++.|++     
T Consensus       170 ~~~~~~~y~~y~~~l~~~~~~d~~d~~~~~~~ll~~~~~---~~~~~~~~~~~ilvDE~QDt~~~q~~il~~L~~-----  241 (724)
T 1pjr_A          170 EKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPD---VLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAE-----  241 (724)
T ss_dssp             HHHHHHHHHHHHHHHHHTTEECTTHHHHHHHHHHHHCHH---HHHHHHHHCSEEEESSGGGCCHHHHHHHHHHHT-----
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHH---HHHHHHHHCCEECCCCCCCCHHHHHHHHHHHHC-----
T ss_conf             999999999999999984999868999999998616999---999987632342132332005889999998733-----


Q ss_pred             CCCCCCCCEEEEEECCHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHCCCCCCC
Q ss_conf             76667686499996665676542488847899999996652134576531200686668878999999999711210012
Q 537021.9.peg.4  207 KNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELPLSFRSTADILTVVDKVFSIPENAQG  286 (952)
Q Consensus       207 ~~~~~~~~~l~~VGD~kQSIY~FRGAd~~~~~~~~~~f~~~~~~~~~~~~~~~L~~N~RS~~~Ii~~~N~~f~~~~~~~~  286 (952)
                           ...++|+|||||||||+||||++.+|.+|.+.|+.        .+.+.|++||||++.|++++|.+|.++..+..
T Consensus       242 -----~~~~l~~vGD~dQsIY~frGA~~~~~~~f~~~~~~--------~~~~~L~~NyRs~~~I~~~an~li~~~~~~~~  308 (724)
T 1pjr_A          242 -----RFQNICAVGDADQSIYRWRGADIQNILSFERDYPN--------AKVILLEQNYRSTKRILQAANEVIEHNVNRKP  308 (724)
T ss_dssp             -----TTCCEEEEECGGGCCCGGGTCCTHHHHTHHHHSTT--------CEEEEECBCSSSCHHHHHHHHHHHTTCSSCCC
T ss_pred             -----CCCCEEEECCCHHCCCCCCCCCHHHHHHHHHHCCC--------CEEEECCCCCCCCHHHHHHHHHHHHHCCCCCC
T ss_conf             -----45645885373110245689888999999985566--------76997634557650589999999975224575


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             33221222122334478887436511344432233431011111000111333368889999999999998358622125
Q 537021.9.peg.4  287 LSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQHDSQCNPQQESWTSYFDSLPQESSASILARRIAYTISNMIGTDTIFSNG  366 (952)
Q Consensus       287 ~~~~~~~~~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~I~~l~~~~~~~~~~  366 (952)
                      .....         ....+..+.+.                          ........+..++..|..++..+.     
T Consensus       309 k~~~~---------~~~~g~~i~~~--------------------------~~~~~~~e~~~~~~~i~~~~~~~~-----  348 (724)
T 1pjr_A          309 KRIWT---------ENPEGKPILYY--------------------------EAMNEADEAQFVAGRIREAVERGE-----  348 (724)
T ss_dssp             CCCBC---------SSCCCCCEEEE--------------------------EEEEHHHHHHHHHHHHHHHHTTTS-----
T ss_pred             CCCCC---------CCCCCCCEEEE--------------------------ECCCHHHHHHHHHHHHHHHHHHCC-----
T ss_conf             42234---------47889832788--------------------------449889999987768999998079-----


Q ss_pred             CCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHCCCCCC
Q ss_conf             43687824468986153101224899999874169736604862112331052268768887481311024543058774
Q 537021.9.peg.4  367 KKRVIQAKDILVLVRKRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRFILSQEDDLSFVCMLKSPLF  446 (952)
Q Consensus       367 ~~r~~~~~diaVL~r~~~~~~~~~~~l~al~~~~~ip~~~~~~~~~~~~~~v~~l~a~l~~l~~p~~~~~~~~~L~spl~  446 (952)
                          .+++|||||+|++.+...++..|    ...|||+...++.++++++++++++++|+++.+|.++.++.+++.+|..
T Consensus       349 ----~~~~diAIL~R~n~~~~~le~~L----~~~~Ip~~~~~~~~~~~~~eikdlla~lr~l~~~~d~~s~~ril~~p~~  420 (724)
T 1pjr_A          349 ----RRYRDFAVLYRTNAQSRVMEEML----LKANIPYQIVGGLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINVPKR  420 (724)
T ss_dssp             ----CCGGGEEEEESSGGGHHHHHHHH----HHTTCCEEEETSCCGGGSHHHHHHHHHHHHHHCTTCHHHHHHHTTSSCC
T ss_pred             ----CCCCCEEEEEECHHHHHHHHHHH----HHCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCC
T ss_conf             ----98200168760567799999999----9879999996897611479999999999998098866999999846433


Q ss_pred             CCCHHHHHHHHHHCCC-CCCHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHHHHC
Q ss_conf             7888899998730126-865788-----8764311115899999999999998642199899999998503469999811
Q 537021.9.peg.4  447 NFSEDDIFKICTQRHE-TETVYE-----YIQKFANCGISKFQHVIKYIHELIHIAQFCSPHDFFTLILGAKKGRQQFISR  520 (952)
Q Consensus       447 g~~~~~l~~l~~~~~~-~~~~~~-----~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  520 (952)
                      |+....+..+...... ....++     .................................+++..++...+....+...
T Consensus       421 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~l~~~  500 (724)
T 1pjr_A          421 GIGASTIDKLVRYAADHELSLFEALGELEMIGLGAKAAGALAAFRSQLEQWTQLQEYVSVTELVEEVLDKSGYREMLKAE  500 (724)
T ss_dssp             TTTSCCCC------------CTTTTTSHHHHCCTTTTTTTTHHHHHHHHHHHHHTTTSCHHHHHHHHHHHTSHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHC
T ss_conf             56724678999999860211799987644310003445567788898888777652034999999999854708887520


Q ss_pred             CCHH---HHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHHCCCCCCC---CCCCCCCCCEEECHHHCCCCCCCEEEECCC
Q ss_conf             3523---8999999999999985-20568989999988501001321---123578853030012214567777998158
Q 537021.9.peg.4  521 FGNE---VIDVLDEFLNFTLRNE-QNSYSSLQELISELEQYPPTIKR---AHSANHNEVRIMTVHTAKGLESPVVFLVDT  593 (952)
Q Consensus       521 ~~~~---~~~~l~~l~~~a~~~e-~~~~~~l~~f~~~l~~~~~~~~~---~~~~~~d~V~imTiH~SKGLEfpvV~i~~l  593 (952)
                      ....   ...+..++......+. ......+..|+..+.........   ......++|+|||||+|||||||+|||+|+
T Consensus       501 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~l~~~~~~~~~~~~~~~~~~V~l~TiH~sKGlEfd~V~l~g~  580 (724)
T 1pjr_A          501 RTIEAQSRLENLDEFLSVTKHFENVSDDKSLIAFLTDLALISDLDELDGTEQAAEGDAVMLMTLHAAKGLEFPVVFLIGM  580 (724)
T ss_dssp             CSHHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHHHHTTTCC-------------CCCEEEEEGGGGTTCCEEEEEECCC
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEHHHCCCCCCCEEEECCC
T ss_conf             37668999998999999999987513400399999999863203334301345557807998330046766788998177


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCC
Q ss_conf             8776776544422234455566663123544457874779999999764444678878751146652899983167
Q 537021.9.peg.4  594 GSQVFSHKHIKKMHIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIICKHSN  669 (952)
Q Consensus       594 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ee~RLlYVAlTRAk~~L~l~~~~~  669 (952)
                      .++.+|+....                                  .....++||||||||||||||++|||+++..
T Consensus       581 ~eg~fP~~~~~----------------------------------~~~~~leEERRLfYVA~TRAk~~L~lt~~~~  622 (724)
T 1pjr_A          581 EEGIFPHNRSL----------------------------------EDDDEMEEERRLAYVGITRAEEELVLTSAQM  622 (724)
T ss_dssp             BTBTTTBGGGG----------------------------------TCHHHHHHHHHHHHHHHTTEEEEEEEEEEEE
T ss_pred             CCCCCCCCCCC----------------------------------CCCHHHHHHHHHHHHHHHHHHCEEEEEEECC
T ss_conf             56778530014----------------------------------7715479999999988836854789997270


No 3  
>2is6_A DNA helicase II; hydrolase/DNA complex; HET: DNA ADP; 2.20A {Escherichia coli} PDB: 2is2_A* 2is1_A* 2is4_A*
Probab=100.00  E-value=0  Score=478.30  Aligned_cols=440  Identities=21%  Similarity=0.276  Sum_probs=312.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCEEEEECHHCCCHHHHHHHHHHHHHCC
Q ss_conf             99999999999999999986997758999999998315842489999986179899980710199999999999841002
Q 537021.9.peg.4  125 ASLTLAKYLNAHYEEAKKKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRSLTEDFF  204 (952)
Q Consensus       125 ~l~~~~~~~~~~y~~~k~~~~~ldf~Dl~~~a~~lL~~~~~~~~~~~~l~~~~~~ilVDEfQDT~~~Q~~il~~L~~~~~  204 (952)
                      ........++..|.+.+..+|.+||+|++..+.+++...+.   ++..++.+|+||+||||||||++|++|++.+.+   
T Consensus       165 ~~~~~~~~~~~~y~~~~~~~~~~~f~~~~~~~~~l~~~~~~---i~~~~~~~~~~i~vDE~QD~~~~q~~~l~~l~~---  238 (680)
T 2is6_A          165 PVEQTWQKVYQAYQEACDRAGLVDFAELLLRAHELWLNKPH---ILQHYRERFTNILVDEFQDTNNIQYAWIRLLAG---  238 (680)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTEEEHHHHHHHHHHHHHHCHH---HHHHHHHHCCEEEESSGGGCCHHHHHHHHHHHT---
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCHH---HHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHC---
T ss_conf             89999999999999999886997868899999999860999---999999754700206666679999999987635---


Q ss_pred             CCCCCCCCCCEEEEEECCHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHCCCCC
Q ss_conf             46766676864999966656765424888478999999966521345765312006866688789999999997112100
Q 537021.9.peg.4  205 VGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELPLSFRSTADILTVVDKVFSIPENA  284 (952)
Q Consensus       205 ~~~~~~~~~~~l~~VGD~kQSIY~FRGAd~~~~~~~~~~f~~~~~~~~~~~~~~~L~~N~RS~~~Ii~~~N~~f~~~~~~  284 (952)
                             .+.++++|||||||||+||||++..|.++...|+        +.+.+.|++||||+++|++++|.+|.+...+
T Consensus       239 -------~~~~~~~vGD~~QsIy~frga~~~~~~~~~~~~~--------~~~~~~L~~NyRs~~~I~~~an~l~~~~~~~  303 (680)
T 2is6_A          239 -------DTGKVMIVGDDDQSIYGWRGAQVENIQRFLNDFP--------GAETIRLEQNYRSTSNILSAANALIENNNGR  303 (680)
T ss_dssp             -------TTCEEEEEECGGGCCCGGGTCCTHHHHHHHHHST--------TCEEEECCBCCSSCHHHHHHHHHHHHTSSSC
T ss_pred             -------CCCCEEEECCHHHHHHHHCCHHHHHHHHHHHHCC--------CCEEEECCCCCCCCHHHHHHHHHHHHHCCCC
T ss_conf             -------7874278548576444650035789999998778--------9869978987798789999999999727333


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             12332212221223344788874365113444322334310111110001113333688899999999999983586221
Q 537021.9.peg.4  285 QGLSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQHDSQCNPQQESWTSYFDSLPQESSASILARRIAYTISNMIGTDTIFS  364 (952)
Q Consensus       285 ~~~~~~~~~~~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~I~~l~~~~~~~~  364 (952)
                      .....        .+ ....++.+.+..                          .......+..|+..|..+..++    
T Consensus       304 ~~~~l--------~~-~~~~~~~i~~~~--------------------------~~~~~~e~~~i~~~i~~~~~~g----  344 (680)
T 2is6_A          304 LGKKL--------WT-DGADGEPISLYC--------------------------AFNELDEARFVVNRIKTWQDNG----  344 (680)
T ss_dssp             CCCCC--------BC-CSCCCSCEEEEE--------------------------EEEHHHHHHHHHHHHHHHHHTT----
T ss_pred             CCCCC--------CC-CCCCCCCEEEEE--------------------------CCCHHHHHHHHHHHHHHHHHCC----
T ss_conf             56533--------45-567899627994--------------------------5986899999999999998759----


Q ss_pred             CCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHCCCC
Q ss_conf             25436878244689861531012248999998741697366048621123310522687688874813110245430587
Q 537021.9.peg.4  365 NGKKRVIQAKDILVLVRKRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRFILSQEDDLSFVCMLKSP  444 (952)
Q Consensus       365 ~~~~r~~~~~diaVL~r~~~~~~~~~~~l~al~~~~~ip~~~~~~~~~~~~~~v~~l~a~l~~l~~p~~~~~~~~~L~sp  444 (952)
                            ..++||+||+|++.....+...|    ...|||+...++.++++++++++++++|+++.+|.++.++..++.+|
T Consensus       345 ------~~~~diaiL~r~~~~~~~l~~~L----~~~~Ip~~~~~~~~~~~~~ev~~~l~~l~~l~~~~d~~~~~~~l~~~  414 (680)
T 2is6_A          345 ------GALAECAILYRSNAQSRVLEEAL----LQASMPYRIYGGMRFFERQEIKDALSYLRLIVNRNDDAAFERVVNTP  414 (680)
T ss_dssp             ------CCGGGEEEEESSGGGHHHHHHHH----HHTTCCEEECSSSCGGGSHHHHHHHHHHHHHHCTTCHHHHHHHTTSS
T ss_pred             ------CCHHHHHHHHHHHHHHHHHHHHH----HHCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCC
T ss_conf             ------97567344874067799999999----97699889958976103499999999999980988669999998353


Q ss_pred             CCCCCHHHHHHHHHHCCCCC-CHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHH
Q ss_conf             74788889999873012686-57888764------311115899999999999998642199899999998503469999
Q 537021.9.peg.4  445 LFNFSEDDIFKICTQRHETE-TVYEYIQK------FANCGISKFQHVIKYIHELIHIAQFCSPHDFFTLILGAKKGRQQF  517 (952)
Q Consensus       445 l~g~~~~~l~~l~~~~~~~~-~~~~~~~~------~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  517 (952)
                      ++|++...+..+........ .+......      ...........+...+..................+.........+
T Consensus       415 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  494 (680)
T 2is6_A          415 TRGIGDRTLDVVRQTSRDRQLTLWQACRELLQEKALAGRAASALQRFMELIDALAQETADMPLHVQTDRVIKDSGLRTMY  494 (680)
T ss_dssp             CCSCCHHHHHHHHHHHHHHTCCHHHHHHHHHTTTCSCHHHHHHHHHHHHHHHHHHHHTSSSCHHHHHHHHHHHTSHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf             34889999999999887410257888887643100134568999999998777888741020578999998766679998


Q ss_pred             HHCCCHHHH---HHHHHHHHHHHHHHHCC----CCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEECHHHCCCCCCCEEEE
Q ss_conf             811352389---99999999999985205----68989999988501001321123578853030012214567777998
Q 537021.9.peg.4  518 ISRFGNEVI---DVLDEFLNFTLRNEQNS----YSSLQELISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFL  590 (952)
Q Consensus       518 ~~~~~~~~~---~~l~~l~~~a~~~e~~~----~~~l~~f~~~l~~~~~~~~~~~~~~~d~V~imTiH~SKGLEfpvV~i  590 (952)
                      .........   ..+..++..+..+....    ...+..++.........  .......++|+|||||+|||||||+|||
T Consensus       495 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~--~~~~~~~d~V~l~TiH~sKGLEfd~Vil  572 (680)
T 2is6_A          495 EQEKGEKGQTRIENLEELVTATRQFSYNEEDEDLMPLQAFLSHAALEAGE--GQADTWQDAVQLMTLHSAKGLEFPQVFI  572 (680)
T ss_dssp             HTTCSHHHHHHHHHHHHHHHHHHHCCCCCCC--CCHHHHHHHHHHHTGGG--CSCCCSSCCEEEEEHHHHTTCCEEEEEE
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCC--CCCCCCCCEEEEEEHHCCCCCCCCEEEE
T ss_conf             73247566788899999999999876315421013799999998752023--4346779959995142001125888999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf             15887767765444222344555666631235444578747799999997644446788787511466528999831677
Q 537021.9.peg.4  591 VDTGSQVFSHKHIKKMHIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIICKHSNT  670 (952)
Q Consensus       591 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ee~RLlYVAlTRAk~~L~l~~~~~~  670 (952)
                      +|+.++.+|+....                                  ......+||||||||||||||++|+|+++...
T Consensus       573 ~~~~~g~fP~~~~~----------------------------------~~~~~~eEErRL~YVA~TRAk~~L~l~~~~~~  618 (680)
T 2is6_A          573 VGMEEGMFPSQMSL----------------------------------DEGGRLEEERRLAYVGVTRAMQKLTLTYAETR  618 (680)
T ss_dssp             CCCBTBTTTBHHHH----------------------------------SSSSTHHHHHHHHHHHHTTEEEEEEEEEEEEE
T ss_pred             ECCCCCCCCCCCCC----------------------------------CCCHHHHHHHHHHHHHHHHHHCEEEEEEECCC
T ss_conf             67818998752458----------------------------------87421699998999898368457899986602


No 4  
>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=100.00  E-value=0  Score=457.04  Aligned_cols=440  Identities=20%  Similarity=0.296  Sum_probs=302.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCEEEEECHHCCCHHHHHHHHHHHHHCCC
Q ss_conf             99999999999999999869977589999999983158424899999861798999807101999999999998410024
Q 537021.9.peg.4  126 SLTLAKYLNAHYEEAKKKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRSLTEDFFV  205 (952)
Q Consensus       126 l~~~~~~~~~~y~~~k~~~~~ldf~Dl~~~a~~lL~~~~~~~~~~~~l~~~~~~ilVDEfQDT~~~Q~~il~~L~~~~~~  205 (952)
                      .......+...|...+...+.+||+|++..+..++...+.   ++..++.+|+||+||||||||++|++|+..++.    
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~vDE~QD~~~~q~~l~~~l~~----  232 (673)
T 1uaa_A          160 RDRIFAHCYGLYDAHLKACNVLDFDDLILLPTLLLQANEE---VRKRWQNKIRYLLVDEYQDTNTSQYELVKLLVG----  232 (673)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHH---HHHHHHTTCSEEEESCGGGCBHHHHHHHHHHHT----
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCHH---HHHHHHHHCEEEECCCHHHCCHHHHHHHHCCCC----
T ss_conf             8999999999999999981777815789999998620858---999998642477425134349888865430147----


Q ss_pred             CCCCCCCCCEEEEEECCHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHCCCCCC
Q ss_conf             67666768649999666567654248884789999999665213457653120068666887899999999971121001
Q 537021.9.peg.4  206 GKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELPLSFRSTADILTVVDKVFSIPENAQ  285 (952)
Q Consensus       206 ~~~~~~~~~~l~~VGD~kQSIY~FRGAd~~~~~~~~~~f~~~~~~~~~~~~~~~L~~N~RS~~~Ii~~~N~~f~~~~~~~  285 (952)
                            .+.++++|||||||||+||||++..|..+...|+.        .+.+.|++||||++.|++++|.+|..+....
T Consensus       233 ------~~~~l~~vGD~~QsIy~frga~~~~~~~~~~~~~~--------~~~~~L~~nyRs~~~I~~~~~~li~~~~~~~  298 (673)
T 1uaa_A          233 ------SRARFTVVGDDDQSIYSWRGARPQNLVLLSQDFPA--------LKVIKLEQNYRSSGRILKAANILIANNPHVF  298 (673)
T ss_dssp             ------TTCCEEEECCGGGCCCGGGTBCTTHHHHHHHHSTT--------CEEECCCCBSSSCHHHHHHHHHHHHTSCCSS
T ss_pred             ------CCCEEEEECCHHHHHHHHCCCCHHHHHHHHHCCCC--------CEEEECCCCCCCCHHHHHHHHHHHHHCCCCC
T ss_conf             ------88536762350355455337741221002201798--------7698687655888788899999986074111


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             23322122212233447888743651134443223343101111100011133336888999999999999835862212
Q 537021.9.peg.4  286 GLSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQHDSQCNPQQESWTSYFDSLPQESSASILARRIAYTISNMIGTDTIFSN  365 (952)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~I~~l~~~~~~~~~  365 (952)
                      ......         .....+.+....                          .......+..+...|.......     
T Consensus       299 ~~~~~~---------~~~~~~~~~~~~--------------------------~~~~~~~~~~~~~~i~~~~~~~-----  338 (673)
T 1uaa_A          299 EKRLFS---------ELGYGAELKVLS--------------------------ANNEEHEAERVTGELIAHHFVN-----  338 (673)
T ss_dssp             CCCCCB---------SSCCCCCBEEEE--------------------------CSSHHHHHHHHHHHHHHHHHHH-----
T ss_pred             CCCCCC---------CCCCCCCCCCHH--------------------------CCCHHHHHHHHHHHHHHHHHCC-----
T ss_conf             000132---------124686522000--------------------------0104899988888876542025-----


Q ss_pred             CCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHCCCCC
Q ss_conf             54368782446898615310122489999987416973660486211233105226876888748131102454305877
Q 537021.9.peg.4  366 GKKRVIQAKDILVLVRKRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRFILSQEDDLSFVCMLKSPL  445 (952)
Q Consensus       366 ~~~r~~~~~diaVL~r~~~~~~~~~~~l~al~~~~~ip~~~~~~~~~~~~~~v~~l~a~l~~l~~p~~~~~~~~~L~spl  445 (952)
                          ...++||+||+|++.+...+...|.    ..|||+...++..+++++++++++++|+++.+|.++.++..++.+|.
T Consensus       339 ----~~~~~~iavL~r~~~~~~~~~~~L~----~~~Ip~~~~~~~~~~~~~ei~~ll~~l~~~~~~~~~~~~~rll~~~~  410 (673)
T 1uaa_A          339 ----KTQYKDYAILYRGNHQSRVFEKFLM----QNRIPYKISGGTSFFSRPEIKDLLAYLRVLTNPDDDSAFLRIVNTPK  410 (673)
T ss_dssp             ----CCCTTTEEEEESSSGGGTTHHHHHH----HTTCCEEESCCCCGGGCHHHHHHHHHHHHHHCTTCHHHHHHHSSTTC
T ss_pred             ----CCCCCCEEEEECCHHHHHHHHHHHH----HCCCCEEEECCCCHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHCCC
T ss_conf             ----6773214541002144899999999----77998899578650023999999999999809885699999982720


Q ss_pred             CCCCHHHHHHHHHHCCCC-CCHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHHH
Q ss_conf             478888999987301268-657888764------3111158999999999999986421998999999985034699998
Q 537021.9.peg.4  446 FNFSEDDIFKICTQRHET-ETVYEYIQK------FANCGISKFQHVIKYIHELIHIAQFCSPHDFFTLILGAKKGRQQFI  518 (952)
Q Consensus       446 ~g~~~~~l~~l~~~~~~~-~~~~~~~~~------~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  518 (952)
                      .++.......+....... ...+.....      ...............+......... .+...+..............
T Consensus       411 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  489 (673)
T 1uaa_A          411 REIGPATLKKLGEWAMTRNKSMFTASFDMGLSQTLSGRGYEALTRFTHWLAEIQRLAER-EPIAAVRDLIHGMDYESWLY  489 (673)
T ss_dssp             CCCCHHHHHHHHHHHHHTTSCHHHHTTCTTHHHHSCSHHHHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHH
T ss_conf             01355689999999987077577898876553100045677888899999999997523-84789999999863566666


Q ss_pred             HC-C----CHHHHHHHHHHHHHHHHHHHC----CCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEECHHHCCCCCCCEEE
Q ss_conf             11-3----523899999999999998520----56898999998850100132112357885303001221456777799
Q 537021.9.peg.4  519 SR-F----GNEVIDVLDEFLNFTLRNEQN----SYSSLQELISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVF  589 (952)
Q Consensus       519 ~~-~----~~~~~~~l~~l~~~a~~~e~~----~~~~l~~f~~~l~~~~~~~~~~~~~~~d~V~imTiH~SKGLEfpvV~  589 (952)
                      .. .    ......++.++++.+..+...    ...++..++.++...............|+|+|||||+|||||||+||
T Consensus       490 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~V~l~TiH~sKGLEfd~Vi  569 (673)
T 1uaa_A          490 ETSPSPKAAEMRMKNVNQLFSWMTEMLEGSELDEPMTLTQVVTRFTLRDMMERGESEEELDQVQLMTLHASKGLEFPYVY  569 (673)
T ss_dssp             HHSSSHHHHHHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHTTCCCCC---CCCCCSEEEEESTTTSSCCEEEEE
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHHHCCCCEEE
T ss_conf             64114306999999999999999999841554532459999999986545542655566996899767653321589899


Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCC
Q ss_conf             81588776776544422234455566663123544457874779999999764444678878751146652899983167
Q 537021.9.peg.4  590 LVDTGSQVFSHKHIKKMHIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIICKHSN  669 (952)
Q Consensus       590 i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ee~RLlYVAlTRAk~~L~l~~~~~  669 (952)
                      |+|+.++.||+...                                   ......+||+|||||||||||++|||++...
T Consensus       570 v~g~~~g~~P~~~~-----------------------------------~d~~~~eEErRL~YVA~TRAk~~L~l~~~~~  614 (673)
T 1uaa_A          570 MVGMEEGFLPHQSS-----------------------------------IDEDNIDEERRLAYVGITRAQKELTFTLCKE  614 (673)
T ss_dssp             ECCCBSSTTTTHHH-----------------------------------HTTTCCHHHHHHHHHHHHTEEEEEEEEECSS
T ss_pred             EECCCCCCCCCCCC-----------------------------------CCCCCHHHHHHHHHHHHHHHHCEEEEEEECC
T ss_conf             96680799977545-----------------------------------8953288999999989987850789999551


Q ss_pred             C
Q ss_conf             7
Q 537021.9.peg.4  670 T  670 (952)
Q Consensus       670 ~  670 (952)
                      .
T Consensus       615 ~  615 (673)
T 1uaa_A          615 R  615 (673)
T ss_dssp             C
T ss_pred             C
T ss_conf             5


No 5  
>1w36_C RECC, exodeoxyribonuclease V gamma chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.25 PDB: 3k70_C*
Probab=99.97  E-value=2.1e-26  Score=206.27  Aligned_cols=543  Identities=11%  Similarity=0.090  Sum_probs=276.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHH----CCCCEEECCCCCCCCC
Q ss_conf             368889999999999998358622125436878244689861531012248999998741----6973660486211233
Q 537021.9.peg.4  340 SSASILARRIAYTISNMIGTDTIFSNGKKRVIQAKDILVLVRKRKDTPLITFLTRFLKND----YKISVVGNDRFILTDH  415 (952)
Q Consensus       340 ~~~~~~a~~i~~~I~~l~~~~~~~~~~~~r~~~~~diaVL~r~~~~~~~~~~~l~al~~~----~~ip~~~~~~~~~~~~  415 (952)
                      ......++.|+.+|.+++..+.        .++|+||+|+++....   |...+.+.+..    .+||+...++..+..+
T Consensus       380 ~s~~rEvE~l~~~Il~ll~~~~--------~l~p~DIaVl~pdi~~---Y~p~I~avF~~~~~~~~IP~~i~~~~~~~~~  448 (1122)
T 1w36_C          380 HSPQREVEVLHDRLLAMLEEDP--------TLTPRDIIVMVADIDS---YSPFIQAVFGSAPADRYLPYAISDRRARQSH  448 (1122)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHST--------TCCGGGEEEEESCHHH---HHHHHHHHTSCCSSTTCCCCEECSEETGGGC
T ss_pred             CCHHHHHHHHHHHHHHHHHCCC--------CCCCCCEEEECCCHHH---HHHHHHHHHHCCCCCCCCCEEECCCHHHHCC
T ss_conf             9989999999999999974288--------8882126787288798---8999999861024567887241352043205


Q ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHCCCCC----CCCCHHHHHHHHHHCCC---------------------CCCHHHHH
Q ss_conf             105226876888748131102454305877----47888899998730126---------------------86578887
Q 537021.9.peg.4  416 LAIKDLMALGRFILSQEDDLSFVCMLKSPL----FNFSEDDIFKICTQRHE---------------------TETVYEYI  470 (952)
Q Consensus       416 ~~v~~l~a~l~~l~~p~~~~~~~~~L~spl----~g~~~~~l~~l~~~~~~---------------------~~~~~~~~  470 (952)
                      +.+..+++++....+......+..+|.+|.    ++++..++..+..-...                     ..++....
T Consensus       449 pl~~~l~~lL~l~~~r~~~~~vl~lL~~p~l~~~f~l~~~~~~~l~~~~~~~gir~g~~~~~~~~~~~~~~~~~tw~~~l  528 (1122)
T 1w36_C          449 PVLEAFISLLSLPDSRFVSEDVLALLDVPVLAARFDITEEGLRYLRQWVNESGIRWGIDDDNVRELELPATGQHTWRFGL  528 (1122)
T ss_dssp             HHHHHHHHHTTGGGCCCCHHHHHHHTTSHHHHHHTTCCHHHHHHHHHHHHHHTCCSCSCHHHHHHTTCCCCSSSSHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCCCCCHHHHH
T ss_conf             89999999998741799999999997681423213898789999999999808765743566787604521113487767


Q ss_pred             HHH-------------------------HHHHHHHHHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHCCHHHHHHHCCCHH
Q ss_conf             643-------------------------1111589999999999999864219-98999999985034699998113523
Q 537021.9.peg.4  471 QKF-------------------------ANCGISKFQHVIKYIHELIHIAQFC-SPHDFFTLILGAKKGRQQFISRFGNE  524 (952)
Q Consensus       471 ~~~-------------------------~~~~~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~~  524 (952)
                      ...                         .......+..+...+..+....... +..+....+..   ....+......+
T Consensus       529 ~Rlllg~~~~~~~~~~~~~~p~~~~~~~~~~~l~~~~~~l~~L~~~~~~l~~~~t~~~w~~~l~~---lL~~~~~~~~~~  605 (1122)
T 1w36_C          529 TRMLLGYAMESAQGEWQSVLPYDESSGLIAELVGHLASLLMQLNIWRRGLAQERPLEEWLPVCRD---MLNAFFLPDAET  605 (1122)
T ss_dssp             HHHHHHHSSCSTTCCSSSCCCCTTSCSSTHHHHHHHHHHHHHHHHHHHHTSSCEEHHHHTTHHHH---HHHHHCCCCSHH
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH---HHHHHHCCCHHH
T ss_conf             77765432013455641234500122226999999999999999999997188989999999999---999974888668


Q ss_pred             ------HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEECHHHCCCCCCCEEEECCCCCCCC
Q ss_conf             ------89999999999999852056898999998850100132112357885303001221456777799815887767
Q 537021.9.peg.4  525 ------VIDVLDEFLNFTLRNEQNSYSSLQELISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVF  598 (952)
Q Consensus       525 ------~~~~l~~l~~~a~~~e~~~~~~l~~f~~~l~~~~~~~~~~~~~~~d~V~imTiH~SKGLEfpvV~i~~l~~~~~  598 (952)
                            ..+.+.++++...........++..|...+...-...........|+|+|+|+|.+||++|++|||.|++++.+
T Consensus       606 ~~~~~~~~~~l~~l~~~~~~~~~~~~l~l~~~~~~L~~~l~~~~~~~~~~~~~V~v~tl~~~R~ipfkvVfllGlndg~f  685 (1122)
T 1w36_C          606 EAAMTLIEQQWQAIIAEGLGAQYGDAVPLSLLRDELAQRLDQERISQRFLAGPVNICTLMPMRSIPFKVVCLLGMNDGVY  685 (1122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCCCSEECHHHHHHHHHHHHHHCEECTTTTSSSCEEECCCTTCCCCEEEEEEECCBTTTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCEEEECCHHHCCCCCCEEEEEECCCCCC
T ss_conf             99999999999999999987236764389999999998740134567898997698112553578867699973366757


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCC-CCCCCC
Q ss_conf             7654442223445556666312354445787477999999976444467887875114665289998316777-766654
Q 537021.9.peg.4  599 SHKHIKKMHIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIICKHSNTS-NEKKSN  677 (952)
Q Consensus       599 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ee~RLlYVAlTRAk~~L~l~~~~~~~-~~~~~~  677 (952)
                      |.......+.......         ...             .....+|++++||+|+|+|+++||||++.... +.....
T Consensus       686 P~~~~~~~fdl~~~~~---------~~g-------------d~~~~~edr~lfl~al~sA~~~L~lSy~~~~~~~~~~~~  743 (1122)
T 1w36_C          686 PRQLAPLGFDLMSQKP---------KRG-------------DRSRRDDDRYLFLEALISAQQKLYISYIGRSIQDNSERF  743 (1122)
T ss_dssp             SCCCCCCSSCHHHHSC---------CTT-------------CCCHHHHHHHHHHHHHHHEEEEEEEEEECBCSSSCCBCC
T ss_pred             CCCCCCCCCCCHHHCC---------CCC-------------CCHHHHHHHHHHHHHHHHHHHHHEEEEECCCCCCCCCCC
T ss_conf             6656666653154423---------668-------------810657899999999997544231444123278998348


Q ss_pred             CCCCHHHHHHCCCCCCCCCCCCCCCC------CCCCCCCCCCCC---CCC--CCCCCCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             32106887310356433222234544------443322211012---235--5443210001222210000112453033
Q 537021.9.peg.4  678 QRTWYDMVYDSFHNDERVKKIKLTNS------INKDEWIAYEWS---THH--PENTPLEREETIKQLMDEQKIPKKLFSP  746 (952)
Q Consensus       678 ~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~---~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~  746 (952)
                      ++.+...+..................      ............   ...  ..........................  
T Consensus       744 PS~~l~eL~d~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~h~l~~fs~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~--  821 (1122)
T 1w36_C          744 PSVLVQELIDYIGQSHYLPGDEALNCDESEARVKAHLTCLHTRMPFDPQNYQPGERQSYAREWLPAASQAGKAHSEFV--  821 (1122)
T ss_dssp             BCHHHHHHHHHHHTTEECSSCSSSCHHHHHHHHHHHHCCBCCSSTTSGGGSSSSTTCCSCGGGHHHHTTCCCCCCCSC--
T ss_pred             CCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCC--
T ss_conf             778999999999742357774334632004678865401266788885553004323440999876325455676445--


Q ss_pred             CCCCCCCCCCCCHHHCCHHCCCCCCCCC--------------------CCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             4433233423361110010015554446--------------------63015567799999998566899656899999
Q 537021.9.peg.4  747 IKNDINEPYILNPSTIDTKGKTNLESLL--------------------SDNQTFNRGLIIHKLLQVIFTLPEHKRKNFIT  806 (952)
Q Consensus       747 ~~~~~~~~~~l~~s~~~~~~~~~~~~~~--------------------~~~~a~~~Gt~vH~~lE~l~~~~~~~~~~~~~  806 (952)
                      .......+..++.|.+.....||.....                    -..++...+.+.|.+++.+-....  ...+..
T Consensus       822 ~~l~~~~~~~ls~s~L~~f~~~P~~~fl~~~L~~~~~~~~~~~~d~Ep~~ld~L~~~~l~~~ll~~~l~~~~--~~~~~~  899 (1122)
T 1w36_C          822 QPLPFTLPETVPLETLQRFWAHPVRAFFQMRLQVNFRTEDSEIPDTEPFILEGLSRYQINQQLLNALVEQDD--AERLFR  899 (1122)
T ss_dssp             CCCCCCCCSCEEHHHHHHHSSSHHHHHHHTTTCCCCCCSCCCCCSSCCSSCCHHHHHHHHHHHHHHHHTTCC--HHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCC--HHHHHH
T ss_conf             689987788448999999997968999997448888621224555686667706552499999999871899--999999


Q ss_pred             HHHHHHCCCCCHH-----HHHHHHHHHHHHHCCHHHHHHHCCCCCCCEEEEEEEECCCCCEEEEEEEEEEEEECCEEEEE
Q ss_conf             9985004589988-----99999999999862965578717778561137888623888589997977899979989999
Q 537021.9.peg.4  807 SYCTKNAKLWPAK-----EYKNLLLSITRLLENPMMTTAMSCDSYSEVSVSGKINCPKKDIIISGRIDQISISQQNIFIF  881 (952)
Q Consensus       807 ~~l~~~~~~~~~~-----~~~~~~~~~~~~l~~~~~~~~~~~~~~~Ev~~e~~~~~~~~~~~i~G~IDri~~~~~~~~Ii  881 (952)
                      +... .+ .++..     ..+.....+..+++.  +...  .....++++    ....++..|+|+||.|.  +++  +|
T Consensus       900 ~~~~-~g-~LP~g~~g~~~~~~~~~~~~~l~~~--~~~~--~~~~~~~~~----~l~~~~~~L~G~l~~v~--~~~--~v  965 (1122)
T 1w36_C          900 RFRA-AG-DLPYGAFGEIFWETQCQEMQQLADR--VIAC--RQPGQSMEI----DLACNGVQITGWLPQVQ--PDG--LL  965 (1122)
T ss_dssp             HHHH-HT-CSCSHHHHHHHHHHHHHHHHHHHHH--HHTT--CCCCEEEEE----EEEETTEEEEEEEEEEC--SSE--EE
T ss_pred             HHHH-CC-CCCCCHHHHHHHHHHHHHHHHHHHH--HHHH--CCCCCCEEE----EEEECCEEEEEEECCCC--CCC--EE
T ss_conf             9997-59-9998255699999999999999999--9870--688886348----98409889999889862--683--59


Q ss_pred             ECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCEE--EECCHHHHHHHHHH
Q ss_conf             725801389998999998899999999999996799827899998559878--98798999999997
Q 537021.9.peg.4  882 EYKTHHHVPQEIEHIPYTHIAQLSIYEKILKDSYPNKSLVCLLIYVSEPKV--FIIPQNKLNKAFAE  946 (952)
Q Consensus       882 DyKT~~~~~~~~~~~~~~Y~~QL~~Y~~al~~~~p~~~V~~~l~y~~~~~~--~~~~~~~l~~~~~~  946 (952)
                      .|++++..   ..     ...++-+...+++..  +.+....++....+.+  -+++++.-...|..
T Consensus       966 ~~~~~~~~---~~-----~~l~~wl~hL~~~a~--~~~~~~~~~~~~~~~~~~~p~~~~~A~~~L~~ 1022 (1122)
T 1w36_C          966 RWRPSLLS---VA-----QGMQLWLEHLVYCAS--GGNGESRLFLRKDGEWRFPPLAAEQALHYLSQ 1022 (1122)
T ss_dssp             EECSSCCC---HH-----HHHHHHHHHHHHHHT--SCCCEEEEECGGGCEEEECCCCHHHHHHHHHH
T ss_pred             EEEECCCC---HH-----HHHHHHHHHHHHHHC--CCCCCEEEEEECCCEEEECCCCHHHHHHHHHH
T ss_conf             99727898---78-----899999999999826--99997289997696799899897999999999


No 6  
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A
Probab=99.66  E-value=2e-14  Score=119.46  Aligned_cols=87  Identities=20%  Similarity=0.211  Sum_probs=62.3

Q ss_pred             HCCCCEEEEECHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCHH-------HHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             617989998071019999999999984100246766676864999966656-------7654248884789999999665
Q 537021.9.peg.4  174 DQEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAVGDEKQ-------SIYSFHGAEPKRVLREKRINQK  246 (952)
Q Consensus       174 ~~~~~~ilVDEfQDT~~~Q~~il~~L~~~~~~~~~~~~~~~~l~~VGD~kQ-------SIY~FRGAd~~~~~~~~~~f~~  246 (952)
                      ...|++++|||.......+.-+-  |..          ..+.+++|||++|       ....+.|-+-++|.+....   
T Consensus       337 ~~~fd~viIDEA~Q~~e~~~lip--l~~----------~~~~~ilvGD~~QL~p~v~s~~~~~~~l~~Slf~r~~~~---  401 (624)
T 2gk6_A          337 KMQFRSILIDESTQATEPECMVP--VVL----------GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL---  401 (624)
T ss_dssp             TCCCSEEEETTGGGSCHHHHHHH--HTT----------TBSEEEEEECTTSCCCCCSCHHHHHHTTTSCHHHHHHHT---
T ss_pred             HCCCCEEEEEHHHCCCHHHHHHH--HHH----------CCCCEEEECCCCCCCCCEECHHHHHCCCHHHHHHHHHHC---
T ss_conf             06877788504212256999999--985----------044289813224467513115555435200189998751---


Q ss_pred             HCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHCCC
Q ss_conf             213457653120068666887899999999971121
Q 537021.9.peg.4  247 RATNAGQKFSIIELPLSFRSTADILTVVDKVFSIPE  282 (952)
Q Consensus       247 ~~~~~~~~~~~~~L~~N~RS~~~Ii~~~N~~f~~~~  282 (952)
                             +...+.|.++||+.+.|.++.|..|....
T Consensus       402 -------~~~~~~L~~qyRm~~~I~~f~s~~fy~~~  430 (624)
T 2gk6_A          402 -------GIRPIRLQVQYRMHPALSAFPSNIFYEGS  430 (624)
T ss_dssp             -------TCCCEECCEECSSCHHHHHHHHHHHSTTC
T ss_pred             -------CCCCEECHHCCCCCHHHHHCCHHHHCCCC
T ss_conf             -------67831211006677789970167653886


No 7  
>2wjy_A Regulator of nonsense transcripts 1; alternative splicing, nonsense mediated decay, zinc-finger, ATP-binding, polymorphism, metal-binding, UPF2; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A
Probab=99.64  E-value=2.2e-13  Score=111.84  Aligned_cols=87  Identities=20%  Similarity=0.214  Sum_probs=61.9

Q ss_pred             HCCCCEEEEECHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCHHH-------HHHHCCCCHHHHHHHHHHHHH
Q ss_conf             6179899980710199999999999841002467666768649999666567-------654248884789999999665
Q 537021.9.peg.4  174 DQEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAVGDEKQS-------IYSFHGAEPKRVLREKRINQK  246 (952)
Q Consensus       174 ~~~~~~ilVDEfQDT~~~Q~~il~~L~~~~~~~~~~~~~~~~l~~VGD~kQS-------IY~FRGAd~~~~~~~~~~f~~  246 (952)
                      ..+|++++|||....+..+.-|  .|..          +.+.+++|||++|-       -...-|-+.++|.++...   
T Consensus       513 ~~~Fd~vIIDEAsQ~~epe~li--pL~~----------~~k~lILVGD~~QLpP~v~s~~a~~~gl~~SLFeRl~~~---  577 (800)
T 2wjy_A          513 KMQFRSILIDESTQATEPECMV--PVVL----------GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL---  577 (800)
T ss_dssp             TCCCSEEEETTGGGSCHHHHHH--HHTT----------TBSEEEEEECTTSCCCCCCCHHHHHTTTTSCHHHHHHHT---
T ss_pred             CCCCCEEEEEHHHCCCCHHHHH--HHHH----------CCCEEEECCCCCCCCCCCCCHHHHHCCCCCCHHHHHHHC---
T ss_conf             5798989975653377389999--9985----------241377766711368842457777547200099999762---


Q ss_pred             HCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHCCC
Q ss_conf             213457653120068666887899999999971121
Q 537021.9.peg.4  247 RATNAGQKFSIIELPLSFRSTADILTVVDKVFSIPE  282 (952)
Q Consensus       247 ~~~~~~~~~~~~~L~~N~RS~~~Ii~~~N~~f~~~~  282 (952)
                             +...+.|.++||+.|.|.+|.|..|-...
T Consensus       578 -------~~~~~~L~~QYRmhp~I~~fps~~FY~g~  606 (800)
T 2wjy_A          578 -------GIRPIRLQVQYRMHPALSAFPSNIFYEGS  606 (800)
T ss_dssp             -------TCCCEECCEECSSCHHHHHHHHHHHSTTC
T ss_pred             -------CCCCEEHHHHCCCCHHHHHHHHHHHHCCC
T ss_conf             -------58822488874867799983077761877


No 8  
>3dmn_A Putative DNA helicase; APC89291.2, lactobacillus plantarum WCFS1, structural genomics, PSI-2, midwest center for structural genomics; HET: MSE; 1.66A {Lactobacillus plantarum}
Probab=99.53  E-value=9.5e-15  Score=121.77  Aligned_cols=56  Identities=25%  Similarity=0.353  Sum_probs=46.9

Q ss_pred             CCCCEEECHHHCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             88530300122145677779981588776776544422234455566663123544457874779999999764444678
Q 537021.9.peg.4  569 HNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYN  648 (952)
Q Consensus       569 ~d~V~imTiH~SKGLEfpvV~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ee~  648 (952)
                      .+.|.+||||++||||||+|||+++.....+.                                            .+++
T Consensus        99 ~~~I~v~Tih~~KGlEfd~Vil~~~~~~~~~~--------------------------------------------~~~~  134 (174)
T 3dmn_A           99 APGVIVVPSFLAKGLEFDAVIVWNANQENYQR--------------------------------------------EDER  134 (174)
T ss_dssp             CSSEEEEEGGGCTTCCEEEEEEETCBTTTSCS--------------------------------------------GGGH
T ss_pred             CCCEEEEEEECCCCCCCCEEEEECCCCCCCCC--------------------------------------------HHHH
T ss_conf             68479986030367647999995661033468--------------------------------------------5565


Q ss_pred             HHHHHHCCCCCCEEEEEECC
Q ss_conf             87875114665289998316
Q 537021.9.peg.4  649 RLLYVGMTRASDQLIICKHS  668 (952)
Q Consensus       649 RLlYVAlTRAk~~L~l~~~~  668 (952)
                      ||||||||||+++|+|+...
T Consensus       135 ~llYVa~TRAk~~L~i~~~~  154 (174)
T 3dmn_A          135 QLLYTICSRAMHELTLVAVG  154 (174)
T ss_dssp             HHHHHHHTTEEEEEEEEEES
T ss_pred             HHHHHHHHHCCCEEEEEECC
T ss_conf             46521450100289999899


No 9  
>3h4r_A Exodeoxyribonuclease 8; exonuclease, recombination, hydrolase; 2.80A {Escherichia coli k-12}
Probab=99.26  E-value=1.4e-11  Score=98.77  Aligned_cols=188  Identities=15%  Similarity=0.176  Sum_probs=109.9

Q ss_pred             CCCHHHCCHHCCCCCCC--------CCCCCHHHHHHHHHHHHHHHCCC----CC---HHHH-----HHHHHHH----HHH
Q ss_conf             33611100100155544--------46630155677999999985668----99---6568-----9999999----850
Q 537021.9.peg.4  756 ILNPSTIDTKGKTNLES--------LLSDNQTFNRGLIIHKLLQVIFT----LP---EHKR-----KNFITSY----CTK  811 (952)
Q Consensus       756 ~l~~s~~~~~~~~~~~~--------~~~~~~a~~~Gt~vH~~lE~l~~----~~---~~~~-----~~~~~~~----l~~  811 (952)
                      .+|+|.+.....||..+        ......++.+||++|.+++....    ..   ....     .......    ...
T Consensus        12 ~lS~S~l~~~~~cP~~~~~~~~~~~~~~~t~a~~~Gt~vH~~lle~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (265)
T 3h4r_A           12 GISKSQLDDIADTPALYLWRKNAPVDTTKTKTLDLGTAFHCRVLELEEFSNRFIVAPEFNRRTNAGKEEEKAFLMECAST   91 (265)
T ss_dssp             CBCHHHHHHHHHCHHHHHHHTTSCCCCCCCSCCTHHHHHHHHHSSHHHHTCC----------------------------
T ss_pred             CCCHHHHHHHHHCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             83988899998699999999727899999879986499999885755523432226502331567899999999886632


Q ss_pred             HCCCCCHHHHHHHHHHHHHHHCCHHHHHHHCCCCCCCEEEEEEEECCCCCEEEEEEEEEEEEECCEEEEEECCCCCCCCC
Q ss_conf             04589988999999999998629655787177785611378886238885899979778999799899997258013899
Q 537021.9.peg.4  812 NAKLWPAKEYKNLLLSITRLLENPMMTTAMSCDSYSEVSVSGKINCPKKDIIISGRIDQISISQQNIFIFEYKTHHHVPQ  891 (952)
Q Consensus       812 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~Ev~~e~~~~~~~~~~~i~G~IDri~~~~~~~~IiDyKT~~~~~~  891 (952)
                      ....+...+.+.+...+..+..++....+.......|+.+  .+.....+..+.|+||++  .+++..||||||+..+..
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~--~~~~~~~g~~~kgriD~~--~~d~~~iiD~Kt~~~~~~  167 (265)
T 3h4r_A           92 GKTVITAEEGRKIELMYQSVMALPLGQWLVESAGHAESSI--YWEDPETGILCRCRPDKI--IPEFHWIMDVKTTADIQR  167 (265)
T ss_dssp             ------CCCTTHHHHHHHHHTTSHHHHHHHSSSCBSSCCE--EEECTTTCCEEEECCSEE--EGGGTEEEEEEEESCHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCHHHHHHCCCCCEEEEEE--EEEECCCCEEEEEEEEEE--ECCCCEEEEEEECCCHHH
T ss_conf             7764458999999999999984855676503455379989--899657775888878998--568855676400366777


Q ss_pred             C-HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCC--------CEEEECCHHHHHHHHHHHH
Q ss_conf             9-8999998899999999999996799827899998559--------8789879899999999765
Q 537021.9.peg.4  892 E-IEHIPYTHIAQLSIYEKILKDSYPNKSLVCLLIYVSE--------PKVFIIPQNKLNKAFAEIS  948 (952)
Q Consensus       892 ~-~~~~~~~Y~~QL~~Y~~al~~~~p~~~V~~~l~y~~~--------~~~~~~~~~~l~~~~~~~~  948 (952)
                      - .....-+|..|+++|+.++++.+ ++..+-.++.+..        -.+++++++.|+.+...+.
T Consensus       168 ~~~~~~~~~Y~~Q~a~Y~~~~~~~~-g~~~~f~fi~vek~~~~~~~~v~v~~~~~~~l~~g~~~~~  232 (265)
T 3h4r_A          168 FKTAYYDYRYHVQDAFYSDGYEAQF-GVQPTFVFLVASTTIECGRYPVEIFMMGEEAKLAGQQEYH  232 (265)
T ss_dssp             HHHHHHHHTTTHHHHHHHHHHHHHH-SSCCEEEEEEEESSCBTTBCCEEEEECCHHHHHHHHHHHH
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHH-CCCCCEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHH
T ss_conf             7776651378999999999999962-9998459999986577886138999589999999999999


No 10 
>3l0a_A Putative exonuclease; RER070207002219, structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: PE4; 2.19A {Eubacterium rectale}
Probab=99.25  E-value=3.3e-10  Score=88.83  Aligned_cols=160  Identities=13%  Similarity=0.109  Sum_probs=100.8

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH-CCCCCHHHHHHHHHHHHHHHCCHHHHHHHCCCCCCCEEEEE
Q ss_conf             63015567799999998566899656899999998500-45899889999999999986296557871777856113788
Q 537021.9.peg.4  775 SDNQTFNRGLIIHKLLQVIFTLPEHKRKNFITSYCTKN-AKLWPAKEYKNLLLSITRLLENPMMTTAMSCDSYSEVSVSG  853 (952)
Q Consensus       775 ~~~~a~~~Gt~vH~~lE~l~~~~~~~~~~~~~~~l~~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~Ev~~e~  853 (952)
                      ....++.+||++|.++|...    ..   ......... ....-..+.+.+...+..+++++....+..  ...|+++..
T Consensus        51 ~~t~al~~Gt~vH~~le~~~----~~---~~~~~~~~~~~~~~~~~e~~~~~~m~~~~~~~~~~~~~~~--~~~E~~~~~  121 (266)
T 3l0a_A           51 EKSTALLVGSYVDSYFEGSL----DQ---FKKDNPEIFTQKGELKANFKQAEEIIARIERDEYFMKYMS--GQKQVIMTG  121 (266)
T ss_dssp             CCCHHHHHHHHHHHHHHTCH----HH---HHHHCGGGBCTTSSBCHHHHHHHHHHHHHHTCHHHHHHTT--SEEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHHHCHH----HH---HHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHCC--CCCEEEEEE
T ss_conf             99879987189999865745----53---4201842013331448999999999999996700355515--772478999


Q ss_pred             EEECCCCCEEEEEEEEEEEEECCEEEEEECCCCCCCCCC---------HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             862388858999797789997998999972580138999---------89999988999999999999967998278999
Q 537021.9.peg.4  854 KINCPKKDIIISGRIDQISISQQNIFIFEYKTHHHVPQE---------IEHIPYTHIAQLSIYEKILKDSYPNKSLVCLL  924 (952)
Q Consensus       854 ~~~~~~~~~~i~G~IDri~~~~~~~~IiDyKT~~~~~~~---------~~~~~~~Y~~QL~~Y~~al~~~~p~~~V~~~l  924 (952)
                      .    ..|+.+.|+||++.. ++  .|+|+||.+.....         ..-....|..||++|+.++++.+ +.++..++
T Consensus       122 ~----~~gv~~kg~iD~i~~-~~--~ivDlKtt~~~~~~~~~~~~~~~~~~~~~~Y~~Q~a~Y~~~l~~~~-g~~~~~~~  193 (266)
T 3l0a_A          122 E----LFGAKWKIKMDSYIP-GV--AIVDLKVMASITDLKWVKDIGYLDFVRYWGYDIQGAVYQEIVRQNT-GEKLPFFI  193 (266)
T ss_dssp             E----ETTEEEEEEEEEEET-TT--EEEEEEEESCSSCCEEETTTEEECHHHHTTHHHHHHHHHHHHHHHH-SCCCCEEE
T ss_pred             E----ECCEEEEEEEEEEEC-CC--CEEEEEEEECCCCCCCCCCCCHHHHHHHCCHHHHHHHHHHHHHHHH-CCCCCEEE
T ss_conf             7----758587406789956-89--7267677411563224432103557775288999999999999986-89863799


Q ss_pred             EECCC-----CEEEECCHHHHHHHHHHHHHCC
Q ss_conf             98559-----8789879899999999765158
Q 537021.9.peg.4  925 IYVSE-----PKVFIIPQNKLNKAFAEISTKI  951 (952)
Q Consensus       925 ~y~~~-----~~~~~~~~~~l~~~~~~~~~~~  951 (952)
                      +++..     ..++.++++.++.++..+..++
T Consensus       194 v~v~k~~p~~~~~~~~~~~~l~~~~~~v~~~i  225 (266)
T 3l0a_A          194 AGATKQTEPDIRIIHVTDNYLQEALHMVEMNM  225 (266)
T ss_dssp             EEEECSSSCCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCCEEEECCHHHHHHHHHHHHHHH
T ss_conf             99978888760489779899999999999999


No 11 
>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=99.19  E-value=1.1e-11  Score=99.54  Aligned_cols=54  Identities=15%  Similarity=0.136  Sum_probs=42.9

Q ss_pred             CCCCEEEEECHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCHHHHHHHCCCCHHHHH
Q ss_conf             1798999807101999999999998410024676667686499996665676542488847899
Q 537021.9.peg.4  175 QEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVL  238 (952)
Q Consensus       175 ~~~~~ilVDEfQDT~~~Q~~il~~L~~~~~~~~~~~~~~~~l~~VGD~kQSIY~FRGAd~~~~~  238 (952)
                      ..++.++|||.+..+..+...+....          ..+..+.+|||++|-+..++|+....+.
T Consensus       261 ~~~~~~ivDE~sm~~~~~~~~~~~a~----------~~~~~l~l~gD~~Ql~~v~~g~~~~~l~  314 (608)
T 1w36_D          261 LHLDVLVVDEASMIDLPMMSRLIDAL----------PDHARVIFLGDRDQLASVEAGAVLGDIC  314 (608)
T ss_dssp             CSCSEEEECSGGGCBHHHHHHHHHTC----------CTTCEEEEEECTTSGGGTSTTBCHHHHG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH----------HCCCEEEEECCHHHHHHHHCCCHHHHHH
T ss_conf             12236776788654199887787762----------0564799833301201111351388899


No 12 
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, hydrolase; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*
Probab=98.74  E-value=3.4e-09  Score=81.56  Aligned_cols=81  Identities=17%  Similarity=0.183  Sum_probs=51.7

Q ss_pred             CCCCEEEEECHHCCCHHHHHHH-HHHHHHCCCCCCCCCCCCEEEEEECCHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf             1798999807101999999999-998410024676667686499996665676542488847899999996652134576
Q 537021.9.peg.4  175 QEINHILIDEVQDTSLIQWEVI-RSLTEDFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQ  253 (952)
Q Consensus       175 ~~~~~ilVDEfQDT~~~Q~~il-~~L~~~~~~~~~~~~~~~~l~~VGD~kQSIY~FRGAd~~~~~~~~~~f~~~~~~~~~  253 (952)
                      ..+++|+|||+--.|.-++.-+ +.+           +.+..+++|||++|---=-.|.   .|..+.+.          
T Consensus       278 ~~~dvlIIDEaSMv~~~~~~~Ll~a~-----------~~g~rlIlvGD~~QLppV~~G~---~~~~l~~~----------  333 (574)
T 3e1s_A          278 APYDLLIVDEVSMMGDALMLSLLAAV-----------PPGARVLLVGDTDQLPPVDAGL---PLLALAQA----------  333 (574)
T ss_dssp             CSCSEEEECCGGGCCHHHHHHHHTTS-----------CTTCEEEEEECTTSCCCSSSCC---HHHHHHHH----------
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHC-----------CCCCEEEEECCHHHCCCCCCCC---HHHHHHHC----------
T ss_conf             65868999266622399999998645-----------3688798506867547755684---78988513----------


Q ss_pred             CCCEEECCCCCCCCH--HHHHHHHHHHHC
Q ss_conf             531200686668878--999999999711
Q 537021.9.peg.4  254 KFSIIELPLSFRSTA--DILTVVDKVFSI  280 (952)
Q Consensus       254 ~~~~~~L~~N~RS~~--~Ii~~~N~~f~~  280 (952)
                       ...+.|+++||...  .++..++.+...
T Consensus       334 -~~~~~Lt~i~RQ~~~s~i~~~a~~i~~g  361 (574)
T 3e1s_A          334 -APTIKLTQVYRQAAKNPIIQAAHGLLHG  361 (574)
T ss_dssp             -SCEEECCCCCHHHHTCHHHHHHHHHHTT
T ss_pred             -CCEEEEEEEEECCCCCHHHHHHHHHHCC
T ss_conf             -8848966776244746899999998749


No 13 
>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, structural genomics, PSI-2; 2.35A {Corynebacterium glutamicum atcc 13032}
Probab=97.02  E-value=0.0016  Score=40.34  Aligned_cols=79  Identities=18%  Similarity=0.220  Sum_probs=47.9

Q ss_pred             CEEEEECHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCE
Q ss_conf             89998071019999999999984100246766676864999966656765424888478999999966521345765312
Q 537021.9.peg.4  178 NHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSI  257 (952)
Q Consensus       178 ~~ilVDEfQDT~~~Q~~il~~L~~~~~~~~~~~~~~~~l~~VGD~kQSIY~FRGAd~~~~~~~~~~f~~~~~~~~~~~~~  257 (952)
                      ..|+|||.|..++-|...+-.  +        -+.+..++++||+.|+=-.  +-..+.+..+.+.+...     .....
T Consensus       124 ~~vIvDEaQN~t~~~~~~ilT--R--------ig~~sKli~~GD~~Q~d~~--~~~~sGl~~~~~~l~~~-----~~~~~  186 (208)
T 3b85_A          124 AFVILDEAQNTTPAQMKMFLT--R--------LGFGSKMVVTGDITQVDLP--GGQKSGLRLVRHILRGV-----DDVHF  186 (208)
T ss_dssp             EEEEECSGGGCCHHHHHHHHT--T--------BCTTCEEEEEEC--------------CCHHHHHHTTTC-----TTEEE
T ss_pred             CEEEECHHHCCCHHHHHHHHH--H--------CCCCCEEEEECCHHHCCCC--CCCCCCHHHHHHHHCCC-----CCCEE
T ss_conf             677731564699999999998--7--------1788569992787761688--88877299999997399-----98559


Q ss_pred             EECCCC--CCCCHHHHHHHH
Q ss_conf             006866--688789999999
Q 537021.9.peg.4  258 IELPLS--FRSTADILTVVD  275 (952)
Q Consensus       258 ~~L~~N--~RS~~~Ii~~~N  275 (952)
                      +.|+.+  .||.  ++..+.
T Consensus       187 ~~l~~~divRs~--l~~~i~  204 (208)
T 3b85_A          187 SELTSSDVVRHQ--LVGHIV  204 (208)
T ss_dssp             EECCGGGCCCCH--HHHHHH
T ss_pred             EEECCCCEEECH--HHHHHH
T ss_conf             997289728278--999999


No 14 
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, hydrolase; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*
Probab=96.56  E-value=0.006  Score=36.26  Aligned_cols=47  Identities=30%  Similarity=0.338  Sum_probs=35.8

Q ss_pred             ECHHHCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00122145677779981588776776544422234455566663123544457874779999999764444678878751
Q 537021.9.peg.4  575 MTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVG  654 (952)
Q Consensus       575 mTiH~SKGLEfpvV~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ee~RLlYVA  654 (952)
                      ||||||.|.|||.||++- .....+                                             .-.++|+|||
T Consensus       494 ~TvHKsQGse~d~Viv~l-~~~~~~---------------------------------------------~l~r~llYvA  527 (574)
T 3e1s_A          494 LTVHRAQGSEWGTVLGVL-HEAHMP---------------------------------------------MLSRNLVYTA  527 (574)
T ss_dssp             EEHHHHTTCCEEEEEEEE-CGGGGG---------------------------------------------GCCHHHHHHH
T ss_pred             EEEECCCCCCCCEEEEEC-CCCCCC---------------------------------------------CCCCCEEEHH
T ss_conf             367422004768799988-987665---------------------------------------------4552637462


Q ss_pred             CCCCCCEEEEEEC
Q ss_conf             1466528999831
Q 537021.9.peg.4  655 MTRASDQLIICKH  667 (952)
Q Consensus       655 lTRAk~~L~l~~~  667 (952)
                      +||||++|+|.|.
T Consensus       528 iTRAk~~l~ivg~  540 (574)
T 3e1s_A          528 LTRARDRFFSAGS  540 (574)
T ss_dssp             HHTEEEEEEEEEC
T ss_pred             HHHHHCEEEEEEC
T ss_conf             6666384899998


No 15 
>2vld_A NUCS, UPF0286 protein pyrab01260; endonuclease, hydrolase; 2.60A {Pyrococcus abyssi}
Probab=96.03  E-value=0.02  Score=32.54  Aligned_cols=55  Identities=24%  Similarity=0.456  Sum_probs=42.5

Q ss_pred             EEEEEEEEEEC-CEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECC
Q ss_conf             97977899979-98999972580138999899999889999999999999679982789999855
Q 537021.9.peg.4  865 SGRIDQISISQ-QNIFIFEYKTHHHVPQEIEHIPYTHIAQLSIYEKILKDSYPNKSLVCLLIYVS  928 (952)
Q Consensus       865 ~G~IDri~~~~-~~~~IiDyKT~~~~~~~~~~~~~~Y~~QL~~Y~~al~~~~p~~~V~~~l~y~~  928 (952)
                      .|+||+++.+. +..+||..|.++..   .+     +..||..|...+++-+ +.+|++-|+--+
T Consensus       156 ~G~iDll~~D~~g~~VvIElKr~~~~---~~-----~V~QL~rYv~~lr~~~-~~~VrGIlvA~~  211 (251)
T 2vld_A          156 HGIVDVMGVDKDGNIVVLELKRRKAD---LH-----AVSQMKRYVDSLKEEY-GENVRGILVAPS  211 (251)
T ss_dssp             TEEEEEEEECTTSCEEEEEECSSCBC---HH-----HHHHHHHHHHHHHHHH-CSCEEEEEEESC
T ss_pred             CCCEEEEEEECCCCEEEEEEEECCCC---HH-----HHHHHHHHHHHHHHCC-CCCCEEEEECCC
T ss_conf             89655899907999999999704798---60-----7999999999987406-998269998686


No 16 
>3dmn_A Putative DNA helicase; APC89291.2, lactobacillus plantarum WCFS1, structural genomics, PSI-2, midwest center for structural genomics; HET: MSE; 1.66A {Lactobacillus plantarum}
Probab=95.49  E-value=0.064  Score=28.80  Aligned_cols=20  Identities=25%  Similarity=0.353  Sum_probs=17.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHC
Q ss_conf             86668878999999999711
Q 537021.9.peg.4  261 PLSFRSTADILTVVDKVFSI  280 (952)
Q Consensus       261 ~~N~RS~~~Ii~~~N~~f~~  280 (952)
                      ++||||+++|++++|.++..
T Consensus         2 ~~sYR~t~~I~~~a~~~l~~   21 (174)
T 3dmn_A            2 NASYRSTQQITDFTKEILVN   21 (174)
T ss_dssp             -CCCCCCHHHHHHHHTTSCC
T ss_pred             CCCCCCHHHHHHHHHHHHHC
T ss_conf             98889839999999999866


No 17 
>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide- binding, transferase; HET: MSE; 2.01A {Staphylococcus aureus}
Probab=89.94  E-value=0.47  Score=22.57  Aligned_cols=37  Identities=24%  Similarity=0.239  Sum_probs=28.6

Q ss_pred             HCCCCEEEEECHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEE
Q ss_conf             61798999807101999999999998410024676667686499996
Q 537021.9.peg.4  174 DQEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAVG  220 (952)
Q Consensus       174 ~~~~~~ilVDEfQDT~~~Q~~il~~L~~~~~~~~~~~~~~~~l~~VG  220 (952)
                      ...+++|+|||.|=-++.|..++..+..+          +..+++.|
T Consensus        99 ~~~~d~I~IDEaQFf~~~~i~~l~~l~~~----------~~~Viv~G  135 (219)
T 3e2i_A           99 LTNVDVIGIDEVQFFDDEIVSIVEKLSAD----------GHRVIVAG  135 (219)
T ss_dssp             CTTCSEEEECCGGGSCTHHHHHHHHHHHT----------TCEEEEEE
T ss_pred             CCCCCEEEEECHHHCCHHHHHHHHHHHCC----------CCEEEEEE
T ss_conf             03588999952563326899999997336----------97179985


No 18 
>1xx6_A Thymidine kinase; X-RAY, NESG, northeast structural genomics consortium, protein structure initiative, PSI; HET: ADP; 2.00A {Clostridium acetobutylicum atcc 824} SCOP: c.37.1.24 g.39.1.14
Probab=88.53  E-value=0.79  Score=20.91  Aligned_cols=49  Identities=22%  Similarity=0.229  Sum_probs=34.0

Q ss_pred             HHHHHHCCCCEEEEECHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEEEE---ECCHHHHH
Q ss_conf             999986179899980710199999999999841002467666768649999---66656765
Q 537021.9.peg.4  169 IRYKIDQEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAV---GDEKQSIY  227 (952)
Q Consensus       169 ~~~~l~~~~~~ilVDEfQDT~~~Q~~il~~L~~~~~~~~~~~~~~~~l~~V---GD~kQSIY  227 (952)
                      +...+...+++|+|||.|=-+..|.+++..+...          +..+++.   ||-++-.+
T Consensus        74 ~~~~~~~~~dvI~IDEaQFf~~~~v~~~~~l~~~----------~~~Vi~~GLd~Df~~~~F  125 (191)
T 1xx6_A           74 ILKYFEEDTEVIAIDEVQFFDDEIVEIVNKIAES----------GRRVICAGLDMDFRGKPF  125 (191)
T ss_dssp             HHHHCCTTCSEEEECSGGGSCTHHHHHHHHHHHT----------TCEEEEEECSBCTTSCBC
T ss_pred             HHHHHCCCCCEEEEECHHHCCHHHHHHHHHHHHC----------CCEEEEEEECCCCCCCCH
T ss_conf             5563034577999930554677799999999715----------760698873465043834


No 19 
>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate acceptor; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*
Probab=86.81  E-value=0.8  Score=20.87  Aligned_cols=45  Identities=27%  Similarity=0.235  Sum_probs=32.5

Q ss_pred             HHCCCCEEEEECHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEEEE---ECCHHHHH
Q ss_conf             86179899980710199999999999841002467666768649999---66656765
Q 537021.9.peg.4  173 IDQEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAV---GDEKQSIY  227 (952)
Q Consensus       173 l~~~~~~ilVDEfQDT~~~Q~~il~~L~~~~~~~~~~~~~~~~l~~V---GD~kQSIY  227 (952)
                      +...+++|+|||.|=-++.+.+++..+..          .+..+++.   ||-++-.+
T Consensus        98 ~~~~~dvI~IDEaQFF~~~~~~~~~~l~~----------~~~~Viv~GLd~Df~~~~F  145 (214)
T 2j9r_A           98 ITEEMDVIAIDEVQFFDGDIVEVVQVLAN----------RGYRVIVAGLDQDFRGLPF  145 (214)
T ss_dssp             CCSSCCEEEECCGGGSCTTHHHHHHHHHH----------TTCEEEEEECSBCTTSCBC
T ss_pred             HHCCCCEEEEECHHCCCHHHHHHHHHHHH----------CCCEEEEEEECCCCCCCCH
T ss_conf             63158899995300074779999999982----------4864899873556056860


No 20 
>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*
Probab=85.24  E-value=0.71  Score=21.26  Aligned_cols=44  Identities=27%  Similarity=0.373  Sum_probs=31.9

Q ss_pred             HHCCCCEEEEECHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEEEE---ECCHHHH
Q ss_conf             86179899980710199999999999841002467666768649999---6665676
Q 537021.9.peg.4  173 IDQEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAV---GDEKQSI  226 (952)
Q Consensus       173 l~~~~~~ilVDEfQDT~~~Q~~il~~L~~~~~~~~~~~~~~~~l~~V---GD~kQSI  226 (952)
                      +...+++|+|||.|=-++.|.+++..+..          .+..+++.   ||-++--
T Consensus        73 ~~~~~~~I~IDEaQFf~~~~~~~l~~~~~----------~g~~Viv~GLd~Df~~~~  119 (184)
T 2orw_A           73 IEEDTRGVFIDEVQFFNPSLFEVVKDLLD----------RGIDVFCAGLDLTHKQNP  119 (184)
T ss_dssp             CCTTEEEEEECCGGGSCTTHHHHHHHHHH----------TTCEEEEEEESBCTTSCB
T ss_pred             HHCCCEEEEEEEHHHCCHHHHHHHHHHHH----------CCCEEEEEEECCCCCCCC
T ss_conf             52242189983155331669999999982----------798999999657514586


No 21 
>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*
Probab=75.20  E-value=2.5  Score=17.32  Aligned_cols=35  Identities=31%  Similarity=0.147  Sum_probs=25.3

Q ss_pred             CCCCEEEEECHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEEEE
Q ss_conf             179899980710199999999999841002467666768649999
Q 537021.9.peg.4  175 QEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAV  219 (952)
Q Consensus       175 ~~~~~ilVDEfQDT~~~Q~~il~~L~~~~~~~~~~~~~~~~l~~V  219 (952)
                      ..+++|+|||.|=-++....++..+..          .+..+++.
T Consensus        88 ~~~dvI~IDEaQFf~d~i~~~~~~~~~----------~g~~Viv~  122 (223)
T 2b8t_A           88 DETKVIGIDEVQFFDDRICEVANILAE----------NGFVVIIS  122 (223)
T ss_dssp             TTCCEEEECSGGGSCTHHHHHHHHHHH----------TTCEEEEE
T ss_pred             CCCCEEEEEHHHHHHHHHHHHHHHHHH----------HCCEEEEE
T ss_conf             677789985255425679999999986----------08689999


No 22 
>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14
Probab=58.44  E-value=5.2  Score=15.01  Aligned_cols=35  Identities=23%  Similarity=0.168  Sum_probs=23.5

Q ss_pred             CCCCEEEEECHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEE
Q ss_conf             1798999807101999999999998410024676667686499996
Q 537021.9.peg.4  175 QEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAVG  220 (952)
Q Consensus       175 ~~~~~ilVDEfQDT~~~Q~~il~~L~~~~~~~~~~~~~~~~l~~VG  220 (952)
                      ..+++|+|||.|=-+.+ .+++..+..          .+..+++-|
T Consensus        89 ~~~dvI~IDEaQFF~dl-~~~v~~l~~----------~gk~VivaG  123 (234)
T 2orv_A           89 LGVAVIGIDEGQFFPDI-VEFCEAMAN----------AGKTVIVAA  123 (234)
T ss_dssp             TTCSEEEESSGGGCTTH-HHHHHHHHH----------TTCEEEEEC
T ss_pred             CCCCEEEEECHHHHHHH-HHHHHHHHH----------CCCCEEEEE
T ss_conf             67778998234366879-999999981----------587079998


No 23 
>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*
Probab=55.81  E-value=5.7  Score=14.71  Aligned_cols=26  Identities=23%  Similarity=0.045  Sum_probs=18.5

Q ss_pred             CCCCEEEEECHHCCCHHHHHHHHHHHH
Q ss_conf             179899980710199999999999841
Q 537021.9.peg.4  175 QEINHILIDEVQDTSLIQWEVIRSLTE  201 (952)
Q Consensus       175 ~~~~~ilVDEfQDT~~~Q~~il~~L~~  201 (952)
                      ..+++|+|||.|=-+. ..++++.+..
T Consensus        90 ~~~d~I~IDEaQFf~d-i~~~v~~l~~  115 (195)
T 1w4r_A           90 LGVAVIGIDEGQFFPD-IVEFCEAMAN  115 (195)
T ss_dssp             HTCSEEEESSGGGCTT-HHHHHHHHHH
T ss_pred             CCCCEEEEEHHHHHHH-HHHHHHHHHH
T ss_conf             5687999962456587-9999999982


No 24 
>1cu1_A Protein (protease/helicase NS3); bifunctional,protease-helicase, hydrolase; 2.50A {Hepatitis c virus} SCOP: b.47.1.3 c.37.1.14 c.37.1.14
Probab=49.85  E-value=7  Score=14.06  Aligned_cols=19  Identities=16%  Similarity=0.101  Sum_probs=11.2

Q ss_pred             CCCCEEEEEECCHHHHHHH
Q ss_conf             7686499996665676542
Q 537021.9.peg.4  211 SSPRTLFAVGDEKQSIYSF  229 (952)
Q Consensus       211 ~~~~~l~~VGD~kQSIY~F  229 (952)
                      ...+++++.|---|+=.|+
T Consensus        42 ~~~g~~~vl~t~tq~~~G~   60 (645)
T 1cu1_A           42 QVEGEVQVVSTATQSFLAT   60 (645)
T ss_dssp             CCCSSEEEEECSSCEEEEE
T ss_pred             CCCCEEEEEEECCEEEEEE
T ss_conf             5533599987011104689


No 25 
>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*
Probab=37.55  E-value=11  Score=12.76  Aligned_cols=22  Identities=14%  Similarity=0.285  Sum_probs=10.6

Q ss_pred             HHHHHHHHHCCCCCCEEEEEEC
Q ss_conf             6788787511466528999831
Q 537021.9.peg.4  646 EYNRLLYVGMTRASDQLIICKH  667 (952)
Q Consensus       646 Ee~RLlYVAlTRAk~~L~l~~~  667 (952)
                      |+.=-+|=++.....++++++.
T Consensus       214 eelf~~fN~l~~~gkqIvitsd  235 (440)
T 2z4s_A          214 TELFHTFNELHDSGKQIVICSD  235 (440)
T ss_dssp             HHHHHHHHHHHTTTCEEEEEES
T ss_pred             HHHHHHHHHHHHCCCEEEEECC
T ss_conf             9999999999863985999689


No 26 
>2i4r_A V-type ATP synthase subunit F; NESG, GR52A, ATP synthesis, hydrolase, structural genomics, PSI-2, protein structure initiative; 2.80A {Archaeoglobus fulgidus} SCOP: c.149.1.1
Probab=35.34  E-value=11  Score=12.52  Aligned_cols=24  Identities=25%  Similarity=0.191  Sum_probs=18.5

Q ss_pred             CCCCEEEEEECCHHHHHHHCCCCHH
Q ss_conf             7686499996665676542488847
Q 537021.9.peg.4  211 SSPRTLFAVGDEKQSIYSFHGAEPK  235 (952)
Q Consensus       211 ~~~~~l~~VGD~kQSIY~FRGAd~~  235 (952)
                      .....+.+|||. -+++|||-|-++
T Consensus         7 ~~s~~IaVIGd~-dtv~GFrLaGi~   30 (102)
T 2i4r_A            7 HHSHMLAVVGDP-DFTIGFMLAGIS   30 (102)
T ss_dssp             --CCEEEEEECH-HHHHHHHHTTCC
T ss_pred             CCCEEEEEEECH-HHHHHHHHCCCC
T ss_conf             541699999488-988989982887


No 27 
>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}
Probab=35.27  E-value=11  Score=12.51  Aligned_cols=19  Identities=11%  Similarity=0.305  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCEEEEEECC
Q ss_conf             999999841002467666768649999666
Q 537021.9.peg.4  193 WEVIRSLTEDFFVGKNTHSSPRTLFAVGDE  222 (952)
Q Consensus       193 ~~il~~L~~~~~~~~~~~~~~~~l~~VGD~  222 (952)
                      .+|+..|-           .+..++++|++
T Consensus        67 ~~il~~i~-----------~n~vvvV~G~T   85 (235)
T 3llm_A           67 SEILEAIS-----------QNSVVIIRGAT   85 (235)
T ss_dssp             HHHHHHHH-----------HCSEEEEECCT
T ss_pred             HHHHHHHH-----------HCCEEEEEECC
T ss_conf             99999999-----------79979999389


No 28 
>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, replication initiation; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 2hcb_A*
Probab=32.06  E-value=13  Score=12.16  Aligned_cols=83  Identities=18%  Similarity=0.175  Sum_probs=48.1

Q ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCEEEEECHHCC---CHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCH
Q ss_conf             775899999999831584248999998617989998071019---99999999998410024676667686499996665
Q 537021.9.peg.4  147 LDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDT---SLIQWEVIRSLTEDFFVGKNTHSSPRTLFAVGDEK  223 (952)
Q Consensus       147 ldf~Dl~~~a~~lL~~~~~~~~~~~~l~~~~~~ilVDEfQDT---~~~Q~~il~~L~~~~~~~~~~~~~~~~l~~VGD~k  223 (952)
                      ++..|........+..... ..+..+++ .++.++||+.|-.   ...|..+|..+-.-       ...++.+++.+|- 
T Consensus        71 ~~~~~~~~~~~~a~~~~~~-~~~~~~~~-~~dlLiiDDi~~l~~~~~~qe~lf~l~n~~-------~~~~k~iiits~~-  140 (324)
T 1l8q_A           71 SSADDFAQAMVEHLKKGTI-NEFRNMYK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTL-------YLLEKQIILASDR-  140 (324)
T ss_dssp             EEHHHHHHHHHHHHHHTCH-HHHHHHHH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHH-------HHTTCEEEEEESS-
T ss_pred             EEHHHHHHHHHHHHHCCCH-HHHHHHHH-CCCEEECCCHHHHCCCHHHHHHHHHHHHHH-------HHCCCCEEEECCC-
T ss_conf             4499999999999864878-99998851-256400030665415557899999999999-------8709968985698-


Q ss_pred             HHHHHHCCCCHHHHHHH
Q ss_conf             67654248884789999
Q 537021.9.peg.4  224 QSIYSFHGAEPKRVLRE  240 (952)
Q Consensus       224 QSIY~FRGAd~~~~~~~  240 (952)
                       +...+.+-++++..++
T Consensus       141 -~P~~l~~~~~~L~SRl  156 (324)
T 1l8q_A          141 -HPQKLDGVSDRLVSRF  156 (324)
T ss_dssp             -CGGGCTTSCHHHHHHH
T ss_pred             -CHHHHCCCCHHHHHHH
T ss_conf             -8565413226788786


No 29 
>3fov_A UPF0102 protein RPA0323; structural genomics, APC7380, PSI-2, protein structure initiative; 1.88A {Rhodopseudomonas palustris CGA009}
Probab=29.20  E-value=14  Score=11.83  Aligned_cols=62  Identities=18%  Similarity=0.129  Sum_probs=33.7

Q ss_pred             EEEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHH-----HHHCCCCCEEEEEEECC
Q ss_conf             97977899979989999725801389998999998899999999999-----99679982789999855
Q 537021.9.peg.4  865 SGRIDQISISQQNIFIFEYKTHHHVPQEIEHIPYTHIAQLSIYEKIL-----KDSYPNKSLVCLLIYVS  928 (952)
Q Consensus       865 ~G~IDri~~~~~~~~IiDyKT~~~~~~~~~~~~~~Y~~QL~~Y~~al-----~~~~p~~~V~~~l~y~~  928 (952)
                      .|-||+|..+++.++.|.-||-.......+.+  ....|-.+.+.|-     ...++..+++-=++.+.
T Consensus        50 ~GEIDLIa~~~~~lvFVEVK~R~~~~~~~~~v--~~~K~~ri~~aA~~~l~~~~~~~~~~~RFDvi~v~  116 (134)
T 3fov_A           50 CGEIDLVAQRDALVAFVEVKARGNVDDAAYAV--TPRQQSRIVAAAEAWLSRHPEHAMSELRFDAILIA  116 (134)
T ss_dssp             TEEEEEEEEETTEEEEEEEEEC------CCCC--CHHHHHHHHHHHHHHHHHCGGGTTSEEEEEEEEEC
T ss_pred             CCCCCEEEEECCEEEEEEEEEECCCCCHHHCC--CHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEE
T ss_conf             99608899849999999999703789976718--99999999999999999788789998899999990


No 30 
>2hwk_A Helicase NSP2; rossman fold, alpha/beta/alpha, multi-domain, hydrolase; 2.45A {Venezuelan equine encephalitis virus}
Probab=28.51  E-value=7  Score=14.02  Aligned_cols=41  Identities=22%  Similarity=0.438  Sum_probs=24.8

Q ss_pred             HHCCCCEEEEECHHCCCHHHHHHH-HHHHHHCCCCCCCCCCCCEEEEEECCHHHH
Q ss_conf             861798999807101999999999-998410024676667686499996665676
Q 537021.9.peg.4  173 IDQEINHILIDEVQDTSLIQWEVI-RSLTEDFFVGKNTHSSPRTLFAVGDEKQSI  226 (952)
Q Consensus       173 l~~~~~~ilVDEfQDT~~~Q~~il-~~L~~~~~~~~~~~~~~~~l~~VGD~kQSI  226 (952)
                      +.+|..|.||+|++...+.-++-| ..|            .++++.+||| +-.|
T Consensus       135 ~NRrLPHaLV~~~~~~~~~~~~~f~~k~------------~g~tvL~Vge-~~~~  176 (320)
T 2hwk_A          135 VNRRLPHALVLHHNEHPQSDFSSFVSKL------------KGRTVLVVGE-KLSV  176 (320)
T ss_dssp             TTSCCSSCCCSCCCCCCCCCCHHHHHTS------------SCSEEEEEES-CCCC
T ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHC------------CCCEEEEECC-CCCC
T ss_conf             4467883200002435877789999648------------8967999525-3357


No 31 
>3kqn_A Serine protease/ntpase/helicase NS3; helicase-substrate transition-state complex, HCV, NS3 protein, helicase, DNA-binding; HET: ADP; 2.05A {Hepatitis c virus} PDB: 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 2zjo_A* 8ohm_A 1a1v_A* 2f55_A 1hei_A 1jr6_A 1onb_A
Probab=23.90  E-value=17  Score=11.17  Aligned_cols=27  Identities=19%  Similarity=0.176  Sum_probs=21.8

Q ss_pred             CCCCEEEEECHHCCCHHHHHHHHHHHH
Q ss_conf             179899980710199999999999841
Q 537021.9.peg.4  175 QEINHILIDEVQDTSLIQWEVIRSLTE  201 (952)
Q Consensus       175 ~~~~~ilVDEfQDT~~~Q~~il~~L~~  201 (952)
                      .++++|+|||++-.+.-+...+..+..
T Consensus        94 ~~~~~VVIDEaH~~d~~~~~~l~~i~~  120 (437)
T 3kqn_A           94 GAYDIIICDECHSTDSTTILGIGTVLD  120 (437)
T ss_dssp             TCCSEEEETTTTCCSHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEEEECCCCHHHHHHHHHH
T ss_conf             344648998765237120034668987


No 32 
>1ob8_A Holliday-junction resolvase; hydrolase, enzyme, homologous recombination, holliday junction resolving enzyme, nuclease, archaea; 1.8A {Sulfolobus solfataricus} SCOP: c.52.1.18 PDB: 1ob9_A
Probab=23.85  E-value=17  Score=11.16  Aligned_cols=28  Identities=11%  Similarity=0.076  Sum_probs=22.4

Q ss_pred             CEEEEEEEEEEEEECCEEEEEECCCCCC
Q ss_conf             5899979778999799899997258013
Q 537021.9.peg.4  861 DIIISGRIDQISISQQNIFIFEYKTHHH  888 (952)
Q Consensus       861 ~~~i~G~IDri~~~~~~~~IiDyKT~~~  888 (952)
                      +..-.|-||.+...++.++.|.-||.+.
T Consensus        31 ~~~~~g~iDiiA~~~~~~~~IEvKs~~~   58 (135)
T 1ob8_A           31 NSSPNPLPDIFATKGNTLLSIECKSTWE   58 (135)
T ss_dssp             ----CCSCSEEEEETTEEEEEEEEEESS
T ss_pred             CCCCCCCCCEEEECCCEEEEEEEEECCC
T ss_conf             8888899888995399999999996349


No 33 
>2jok_A Putative G-nucleotide exchange factor; guanine nucleotide exchange factor, type III secretion, SOPE, SOPE2, cell invasion; NMR {Burkholderia pseudomallei} SCOP: a.168.1.1 PDB: 2jol_A
Probab=23.60  E-value=16  Score=11.47  Aligned_cols=13  Identities=46%  Similarity=0.652  Sum_probs=9.8

Q ss_pred             EECCHHHHHHHCC
Q ss_conf             9666567654248
Q 537021.9.peg.4  219 VGDEKQSIYSFHG  231 (952)
Q Consensus       219 VGD~kQSIY~FRG  231 (952)
                      .||+||.|-.|--
T Consensus         3 ~gd~k~~ir~~~d   15 (186)
T 2jok_A            3 TGDAKQAIRHFVD   15 (186)
T ss_dssp             CTTTTTHHHHHHH
T ss_pred             CCCHHHHHHHHHH
T ss_conf             8758999999999


Done!