Query         gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 340
No_of_seqs    142 out of 1377
Neff          5.5 
Searched_HMMs 23785
Date          Tue May 24 02:40:14 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780237.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3lu0_A DNA-directed RNA polyme 100.0       0       0  810.3  20.7  324    2-331     1-328 (329)
  2 2a6h_A DNA-directed RNA polyme 100.0       0       0  755.4  22.6  298   20-318    13-314 (315)
  3 1bdf_A RNA polymerase alpha su 100.0       0       0  589.1  24.6  230    2-234     1-234 (235)
  4 2pa8_D DNA-directed RNA polyme 100.0   1E-36 4.3E-41  256.6  10.0  208   22-233     7-258 (265)
  5 3h0g_C DNA-directed RNA polyme 100.0 1.9E-32 8.1E-37  228.9   7.6  211   19-233     8-261 (297)
  6 1twf_C B44.5, DNA-directed RNA 100.0 3.8E-31 1.6E-35  220.5  10.7  211   19-233     9-260 (318)
  7 1coo_A RNA polymerase alpha su  99.9 2.9E-27 1.2E-31  195.4   5.0   85  247-331    13-97  (98)
  8 3k4g_A DNA-directed RNA polyme  99.9 7.8E-27 3.3E-31  192.6   4.7   83  249-331     3-85  (86)
  9 3gfk_B DNA-directed RNA polyme  99.9 6.4E-22 2.7E-26  160.8   6.5   74  247-320     5-78  (79)
 10 1z3e_B DNA-directed RNA polyme  99.8 1.2E-21 5.1E-26  158.9   7.6   70  251-320     2-71  (73)
 11 1b22_A DNA repair protein RAD5  96.5   0.002 8.4E-08   41.0   4.1   56  258-313    23-81  (114)
 12 3lda_A DNA repair protein RAD5  96.0    0.02 8.5E-07   34.5   6.8   58  256-313    79-139 (400)
 13 1pzn_A RAD51, DNA repair and r  95.8  0.0097 4.1E-07   36.6   4.6   57  257-313    34-91  (349)
 14 2zj8_A DNA helicase, putative   94.9    0.04 1.7E-06   32.6   5.4   45  267-312   657-701 (720)
 15 2i1q_A DNA repair and recombin  94.3   0.098 4.1E-06   30.1   6.1   24  200-223   143-166 (322)
 16 1vq8_Y 50S ribosomal protein L  93.1   0.013 5.7E-07   35.6   0.0   18  299-316   211-228 (241)
 17 2pa8_L DNA-directed RNA polyme  93.0    0.24 9.9E-06   27.6   6.2   48  180-233    38-85  (92)
 18 2z43_A DNA repair and recombin  93.0   0.015 6.2E-07   35.4   0.0   20  201-220   143-162 (324)
 19 1dgs_A DNA ligase; AMP complex  92.6    0.32 1.3E-05   26.8   6.4   49  264-312   448-497 (667)
 20 1v5w_A DMC1, meiotic recombina  91.2   0.032 1.3E-06   33.3   0.0   23  199-221   156-178 (343)
 21 1twf_K B13.6, DNA-directed RNA  90.5    0.84 3.5E-05   24.0   6.8   36  198-233    68-103 (120)
 22 3h0g_K DNA-directed RNA polyme  90.1    0.38 1.6E-05   26.2   4.8   36  198-233    67-102 (123)
 23 2pa8_L DNA-directed RNA polyme  89.9    0.32 1.4E-05   26.7   4.3   39   22-65      7-45  (92)
 24 1xpp_A TA1416, DNA-directed RN  89.5    0.69 2.9E-05   24.6   5.6   47  180-233    48-94  (115)
 25 2owo_A DNA ligase; protein/DNA  89.1    0.86 3.6E-05   24.0   5.9   44   56-99    107-162 (671)
 26 3h0g_K DNA-directed RNA polyme  89.0     0.5 2.1E-05   25.5   4.7   41   13-59     16-56  (123)
 27 1u9l_A Transcription elongatio  88.9    0.99 4.1E-05   23.6   6.1   59  255-313     4-62  (70)
 28 1z00_A DNA excision repair pro  87.4     1.1 4.6E-05   23.3   5.5   44  268-313    31-74  (89)
 29 1im4_A DBH; DNA polymerase PAL  86.0    0.41 1.7E-05   26.1   2.7   40  255-294   181-221 (221)
 30 3bq0_A POL IV, DBH, DNA polyme  84.8       1 4.2E-05   23.5   4.3   53  255-309   176-229 (354)
 31 3gqc_A DNA repair protein REV1  84.2     1.7   7E-05   22.1   5.2   54  254-309   311-365 (504)
 32 1jx4_A DNA polymerase IV (fami  83.9    0.96   4E-05   23.7   3.8   52  255-308   175-227 (352)
 33 3im1_A Protein SNU246, PRE-mRN  79.8       3 0.00013   20.4   8.6   94  214-314   113-214 (328)
 34 1kft_A UVRC, excinuclease ABC   79.6     2.2 9.4E-05   21.3   4.5   42  268-311    36-77  (78)
 35 1wcn_A Transcription elongatio  78.7     3.3 0.00014   20.2   5.4   47  264-310    14-60  (70)
 36 3osn_A DNA polymerase IOTA; ho  76.0     3.8 0.00016   19.8   4.8   49  259-309   235-284 (420)
 37 1x2i_A HEF helicase/nuclease;   75.7       4 0.00017   19.6   5.1   51  259-312    18-68  (75)
 38 2a1j_B DNA excision repair pro  72.7     4.6 0.00019   19.3   4.5   41  271-312    46-86  (91)
 39 1feu_A 50S ribosomal protein L  70.8     2.5  0.0001   21.0   2.8   34  113-149    68-102 (206)
 40 2bgw_A XPF endonuclease; hydro  69.6     5.5 0.00023   18.7   8.1   48  264-312   169-216 (219)
 41 2kp7_A Crossover junction endo  69.0     4.1 0.00017   19.6   3.6   41  268-314    42-82  (87)
 42 3mr3_A DNA polymerase ETA; POL  63.9     7.1  0.0003   18.0   4.3   52  257-310   252-305 (435)
 43 2w9m_A Polymerase X; SAXS, DNA  60.0     6.1 0.00026   18.4   3.1   23  302-324   471-493 (578)
 44 2q0z_X Protein Pro2281; SEC63,  59.0     8.7 0.00036   17.5   4.2   96  215-313   117-217 (339)
 45 2zjr_S 50S ribosomal protein L  58.1     2.7 0.00011   20.7   1.0   24  114-137   147-171 (237)
 46 2x7i_A Mevalonate kinase; tran  55.9     9.7 0.00041   17.1   4.5   77  260-338   207-295 (308)
 47 1zco_A 2-dehydro-3-deoxyphosph  52.3     7.9 0.00033   17.7   2.6   15   77-91     70-84  (262)
 48 2aq4_A DNA repair protein REV1  52.1      11 0.00047   16.8   3.8   50  257-308   240-293 (434)
 49 3bz1_U Photosystem II 12 kDa e  51.3     6.1 0.00026   18.4   1.9   41  267-315    44-84  (104)
 50 1s5l_U Photosystem II 12 kDa e  46.2     8.8 0.00037   17.4   2.1   39  267-313    74-112 (134)
 51 2a1j_A DNA repair endonuclease  42.9      15 0.00065   15.8   3.9   47  264-312    11-57  (63)
 52 3bqs_A Uncharacterized protein  42.4      16 0.00066   15.8   3.0   77  259-338     5-84  (93)
 53 1kea_A Possible G-T mismatches  41.0      10 0.00044   17.0   1.8   53  256-308    78-133 (221)
 54 3c1y_A DNA integrity scanning   36.0      20 0.00083   15.2   3.8   50  264-313   308-370 (377)
 55 1kg2_A A/G-specific adenine gl  35.9      12 0.00051   16.5   1.5   51  258-308    75-127 (225)
 56 2e1f_A Werner syndrome ATP-dep  35.6      13 0.00056   16.2   1.7   47  270-316    37-90  (103)
 57 1gm5_A RECG; helicase, replica  34.3      13 0.00055   16.3   1.4   22   68-89    113-134 (780)
 58 1x40_A ARAP2; ASAP-related pro  34.2      21 0.00088   15.0   3.6   40  259-299    21-62  (91)
 59 1vr6_A Phospho-2-dehydro-3-deo  33.5      22 0.00091   14.9   2.6   17  204-220   217-233 (350)
 60 1t94_A Polymerase (DNA directe  33.1      22 0.00092   14.8   3.8   49  255-306   279-328 (459)
 61 2cz9_A Probable galactokinase;  31.7      23 0.00097   14.7   8.2   62  259-321   239-300 (350)
 62 2rrd_A BLM HRDC domain, HRDC d  30.9      15 0.00063   15.9   1.3   45  269-313    43-91  (101)
 63 3fsp_A A/G-specific adenine gl  30.0      18 0.00076   15.4   1.6   17  287-303   115-131 (369)
 64 1vs1_A 3-deoxy-7-phosphoheptul  29.0      26  0.0011   14.4   2.3   11   82-92     54-64  (276)
 65 2duy_A Competence protein come  28.0      13 0.00054   16.3   0.5   24  287-310    50-73  (75)
 66 1wuu_A Galactokinase; galactos  27.9      27  0.0011   14.3   2.4   63  260-322   289-351 (399)
 67 1ow5_A Serine/threonine-protei  26.9      28  0.0012   14.2   4.0   53  258-313    20-74  (85)
 68 3cqj_A L-ribulose-5-phosphate   26.7      11 0.00044   16.9  -0.1   49  169-229   239-287 (295)
 69 3fhf_A Mjogg, N-glycosylase/DN  25.5      30  0.0012   14.0   3.6   41  267-307    95-142 (214)
 70 2kg5_A ARF-GAP, RHO-GAP domain  24.1      31  0.0013   13.8   4.4   49  260-312    33-81  (100)
 71 1npy_A Hypothetical shikimate   23.6     6.4 0.00027   18.3  -1.7   15   37-51     17-31  (271)
 72 1dxs_A P53-like transcription   22.6      33  0.0014   13.7   2.8   50  260-313    13-64  (80)
 73 2h56_A DNA-3-methyladenine gly  22.6      34  0.0014   13.7   5.2   48  259-306    97-154 (233)
 74 2abk_A Endonuclease III; DNA-r  21.6      35  0.0015   13.5   2.1   53  256-308    72-127 (211)
 75 1ucv_A Ephrin type-A receptor   21.4      35  0.0015   13.5   2.6   35  260-295    14-48  (81)
 76 1z00_B DNA repair endonuclease  21.4      35  0.0015   13.5   4.2   47  264-312    25-71  (84)
 77 1orn_A Endonuclease III; DNA r  21.2      33  0.0014   13.7   1.5   52  256-307    76-130 (226)
 78 2hfs_A Mevalonate kinase, puta  21.0      36  0.0015   13.4   8.5  114  200-339   188-312 (332)
 79 2rhf_A DNA helicase RECQ; HRDC  21.0      21  0.0009   14.9   0.6   37  269-305    26-62  (77)
 80 1pie_A Galactokinase; galactos  20.4      37  0.0016   13.4   3.0   61  261-321   305-365 (419)
 81 2edu_A Kinesin-like protein KI  20.3      37  0.0016   13.4   7.0   54  283-336    33-90  (98)
 82 2ihm_A POL MU, DNA polymerase   20.2      37  0.0016   13.3   4.6   11   38-48     68-78  (360)

No 1  
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A
Probab=100.00  E-value=0  Score=810.30  Aligned_cols=324  Identities=45%  Similarity=0.798  Sum_probs=304.0

Q ss_pred             CCCHHHHCCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHH
Q ss_conf             52205751797420158636788815899996169756678889999987416983068899988714431466462444
Q gi|254780237|r    2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED   81 (340)
Q Consensus         2 ~~~~~~~~~~P~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~ED   81 (340)
                      |+..|++|++|+.+++   ++.+++||||+++||+||||+|||||||||||||++|+|||+|||+||.|||++|+||+||
T Consensus         1 m~~~~~~~~~p~~i~~---~~~~~~yg~f~i~Ple~G~g~TlGnaLRRvLLssi~G~ait~vkI~gv~HEfsti~GV~Ed   77 (329)
T 3lu0_A            1 MQGSVTEFLKPRLVDI---EQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQED   77 (329)
T ss_dssp             CCCSTTTSSSCCCCCE---EECTTSEEEEEECCCCTTCHHHHHHHHHHHTTTSSCEEEEEEEEESSCSSTTCCCTTBSSC
T ss_pred             CCCHHHHHCCCCEEEE---ECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCC
T ss_conf             9613666138857787---2268867899997688862636688999998856984588999989965545568996237


Q ss_pred             HHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEEC-CCCEEEEEEEEECCCCCEECCC
Q ss_conf             999998401141777279827999999447169963351389859988880899977-8964999999746876320344
Q gi|254780237|r   82 LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKH  160 (340)
Q Consensus        82 V~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~-~~~~l~iel~ie~G~GY~~~e~  160 (340)
                      |++|+||||+|+|+.+++.+..++|+++|||+|||+||++|++++|+||||||||++ +++.|+|+++|++|+||++++.
T Consensus        78 v~~IilNLK~i~~~~~~~~~~~~~l~~~Gpg~vtA~di~~p~~veivNpdq~IaTl~~~~~~l~~e~~i~~G~GY~~~~~  157 (329)
T 3lu0_A           78 ILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPAST  157 (329)
T ss_dssp             HHHHHHHHHSCCCEESSCSCEEEEECCCSSSCEETTSSCCCSSEECSCTTCEEECBCSSCCCCCEEEEEEEESSEECTTT
T ss_pred             HHHHHHHCCCCCEEECCCCCEEEEEEEECCCCEEECCCCCCCCEEEECCCEEEEEECCCCCEEEEEEEEEECCCEEECCC
T ss_conf             99999846733156426872589999616776681136667987995899889996588926999999990565264200


Q ss_pred             CC---CCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             44---655754302124311114422357764116887762189999993896177799999999999988876224444
Q gi|254780237|r  161 HR---TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP  237 (340)
Q Consensus       161 ~~---~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~  237 (340)
                      ++   ....++|+||+||+||||+||||.|+++|+|++++||+|+|||||||||+|++||++||++|++||++|.++++.
T Consensus       158 ~~~~~~~~~~ig~i~iDa~FsPV~kVny~Ve~~rv~~~~~~e~L~lEI~TnGsI~P~eAl~~AakiL~~~f~~f~~~~~~  237 (329)
T 3lu0_A          158 RIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV  237 (329)
T ss_dssp             SCCCSTTSSSCCCEECCEECCCEEEEEEEEEEECCSSCSCEEEEEEEEEECSSSCHHHHHHHHHHHHHHHTTTSSSCC--
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             23554334667834036655563789999864355667751038999983898898999999999999999976263101


Q ss_pred             CCCCCCHHHCCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             32210000000001123331112210110588898988398371888744988886188988644999999999808312
Q gi|254780237|r  238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL  317 (340)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~l  317 (340)
                      .....   ..+..+.++.+.++||+||||+||+||||||||+|||||+++|++||+++||||+||++||+++|+++||+|
T Consensus       238 ~~~~~---~~~~~~~~~~l~~~Ie~LeLSvRs~NcLkra~I~ti~dLv~~s~~dLl~ikNfGkKSl~EI~~kL~~~gl~l  314 (329)
T 3lu0_A          238 RQPEV---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL  314 (329)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCCCC---CCCCCCCCHHHHCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHCCCCC
T ss_conf             34444---444444265763879885277888865757189189997647999995589976200999999999749777


Q ss_pred             CCCCCCCCHHHHHH
Q ss_conf             67687898677999
Q gi|254780237|r  318 GMNLPDWPPESIEE  331 (340)
Q Consensus       318 g~~l~~~~~~~~~~  331 (340)
                      ||++++|||+++++
T Consensus       315 gm~l~~~~~~~~~~  328 (329)
T 3lu0_A          315 GMRLENWPPASIAD  328 (329)
T ss_dssp             --------------
T ss_pred             CCCCCCCCCCCCCC
T ss_conf             78789999534356


No 2  
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* 2gho_A 1hqm_A ...
Probab=100.00  E-value=0  Score=755.37  Aligned_cols=298  Identities=37%  Similarity=0.567  Sum_probs=276.2

Q ss_pred             CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCC
Q ss_conf             36788815899996169756678889999987416983068899988714431466462444999998401141777279
Q gi|254780237|r   20 LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD   99 (340)
Q Consensus        20 ~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~   99 (340)
                      .++.+++||||+++||+||||+|+||||||+||||++|+|||+|||+||.|||++||||+|||+||+||||+|+|++.++
T Consensus        13 ~~~~~~~Yg~F~i~Pl~~G~g~TlGnaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~Edv~eIllNLK~i~~k~~~~   92 (315)
T 2a6h_A           13 VRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNP   92 (315)
T ss_dssp             EEEETTTEEEEEEEEECTTCHHHHHHHHHHHHHHTCEEEEEEEEEESSCCSTTCBCTTBSSBHHHHHHHHHTCCEEECST
T ss_pred             EEECCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHCCCEEEEECC
T ss_conf             88668856899996688972304678999999856985489999999954423458885105899998530446997148


Q ss_pred             --CCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEECCCCCH
Q ss_conf             --827999999447169963351389859988880899977896499999974687632034444655754302124311
Q gi|254780237|r  100 --SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY  177 (340)
Q Consensus       100 --~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~iDa~F  177 (340)
                        ++..++++++||++|||+||++|++++|+||||||||+++++.|+||++|++||||++++.++.. .++|+|++||+|
T Consensus        93 ~~~~~~~~l~~~Gp~~vtA~di~~p~~ieivNpdq~IaTl~~~~~l~~el~i~~G~Gy~~~e~~~~~-~~~g~i~iDa~F  171 (315)
T 2a6h_A           93 SLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIK-DRINAIPVDAVF  171 (315)
T ss_dssp             TCSBCCEEEEEESSCEEEGGGSCCCTTEEESCTTCEEEEBCSSCEEEEEEEEEEEESEECHHHHCCC-SSTTCEECCEEC
T ss_pred             CCCEEEEEEECCCCEEEEEECCCCCCCEEEECCCEEEEEECCCCEEEEEEEEEECCCEEECCCCCCC-CCCCCCCCCCCC
T ss_conf             8615999996499848995414689858997898799997789669999999925754402335664-656751677652


Q ss_pred             HEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHH--CCCCHHHHH
Q ss_conf             114422357764116887762189999993896177799999999999988876224444322100000--000011233
Q gi|254780237|r  178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--VKSLPFNPA  255 (340)
Q Consensus       178 sPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~--~~~~~~~~~  255 (340)
                      |||+||||.|+++|+||+++||+|+|||||||||+|++||++||+||++||.+|.++++..........  ......+..
T Consensus       172 sPV~kVny~V~~~rvg~~~~~ekL~lEIwTnGsi~P~~Al~~Aa~iL~~~f~~f~~~~~~~~~~~~~~~~~~~~~~~~~~  251 (315)
T 2a6h_A          172 SPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPPEQEEE  251 (315)
T ss_dssp             CCEEEEEEEEEECCBTTBCCCEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHTTCSCC----------------------
T ss_pred             CCEEEEEEEEEECCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf             35257899999711367777654699998289899899999999999999997528310022333323342222200354


Q ss_pred             HHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             311122101105888989883983718887449888861889886449999999998083126
Q gi|254780237|r  256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG  318 (340)
Q Consensus       256 L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg  318 (340)
                      ++++|++|+||+|++||||+|||+|||||+++|++||+++||||+||++||+++|+++||+|.
T Consensus       252 l~~~Ie~L~LSvRs~NcLk~a~I~ti~dLv~~s~~eLl~i~N~G~KSl~EI~ekL~~~Gl~L~  314 (315)
T 2a6h_A          252 LDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLK  314 (315)
T ss_dssp             ---------------------------------------------------------------
T ss_pred             HCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHCCCCCC
T ss_conf             368099822879888678785994899987399999847999851039999999998599889


No 3  
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1
Probab=100.00  E-value=0  Score=589.06  Aligned_cols=230  Identities=43%  Similarity=0.757  Sum_probs=220.3

Q ss_pred             CCCHHHHCCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHH
Q ss_conf             52205751797420158636788815899996169756678889999987416983068899988714431466462444
Q gi|254780237|r    2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED   81 (340)
Q Consensus         2 ~~~~~~~~~~P~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~ED   81 (340)
                      |+.+|++|++|+.+++   ++.+++||||.++||+||||+||||||||+||||++|+|||+|||+|+.|||++||||+||
T Consensus         1 m~~~~~~~~~p~~i~~---~~~~~~~~~f~i~Ple~G~g~TlGnaLRRvLLs~i~G~ait~vkI~gv~hEfs~i~GV~Ed   77 (235)
T 1bdf_A            1 MQGSVTEFLKPRLVDI---EQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVEIDGVLHEYSTKEGVQED   77 (235)
T ss_dssp             -CCCSSCSCCCCEEEE---EESSSSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCCEEEEEEEETTCCSTTCCCTTBSSC
T ss_pred             CCCHHHHHCCCCEEEE---ECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCHHH
T ss_conf             9504666038857887---0378867899997788962525788999988865985499999957765465468880563


Q ss_pred             HHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECC-CCEEEEEEEEECCCCCEECCC
Q ss_conf             9999984011417772798279999994471699633513898599888808999778-964999999746876320344
Q gi|254780237|r   82 LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKH  160 (340)
Q Consensus        82 V~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~-~~~l~iel~ie~G~GY~~~e~  160 (340)
                      |+||+||||+|+|+.+++++..++|+++|||+|||+||++|++++|+||||||||+++ ++.|+||++|++|+||++++.
T Consensus        78 v~eIilNLK~i~~~~~~~~~~~~~l~~~Gp~~vtA~di~~p~~ieivNpdq~IaTlt~~~~~l~ie~~ie~G~Gy~~~~~  157 (235)
T 1bdf_A           78 ILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPAST  157 (235)
T ss_dssp             HHHHHHHHHTCCEECSSCSEEEEEEEEESSEEEEGGGBCCCSSCEESCTTCEEEEECSTTCEEEEEEEEEECCSEECGGG
T ss_pred             HHHHHHHCCCCEEEECCCCCEEEEEEEECCCCEEEECCCCCCCEEEECCCEEEEEECCCCCEEEEEEEEECCCCEECCCC
T ss_conf             99999726755367516884179999515743897156678987996899899997678957999999945786343533


Q ss_pred             C---CCCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             4---4655754302124311114422357764116887762189999993896177799999999999988876224
Q gi|254780237|r  161 H---RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF  234 (340)
Q Consensus       161 ~---~~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~  234 (340)
                      +   +.+..++|+|++||+||||++|||.|+++|+|++++||+|+|||||||||+|++||++||++|++||++|+++
T Consensus       158 ~~~~~~~~~~~g~i~iDa~fsPV~~Vny~Ve~~rv~~~~~~e~L~leI~TdGsI~P~~Al~~Aa~iL~~~f~~f~~~  234 (235)
T 1bdf_A          158 RIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDL  234 (235)
T ss_dssp             TC-----CCCCSCCBCCEECCSEEEEEEECCBCCCSSCSSEEEEEEEEEECSSSCHHHHHHHHHHHHHHHGGGGC--
T ss_pred             CCCCCCCCCCCCCEECCCCCCCEEEEEEEEEECCCCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             44554333567833336543555789999997124789860699999997998999999999999999999987537


No 4  
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D
Probab=100.00  E-value=1e-36  Score=256.56  Aligned_cols=208  Identities=17%  Similarity=0.155  Sum_probs=177.6

Q ss_pred             CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE---------CCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             78881589999616975667888999998741698306889998---------871443146646244499999840114
Q gi|254780237|r   22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKGI   92 (340)
Q Consensus        22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI---------~gv~HEfs~i~GV~EDV~eIiLNLK~I   92 (340)
                      +.++++.+|.+.    |+|.|+||||||+|||++||+||++|+|         +++.|+|+.||++.|++.++++|+|.+
T Consensus         7 ~~~~~~~~f~~~----g~~~si~NaLRR~lls~ip~~ai~~v~I~~Nts~~~dE~i~hrl~lIP~~~e~~~~~~~~~~~~   82 (265)
T 2pa8_D            7 HKDDTRIDLVFE----GYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPEEC   82 (265)
T ss_dssp             EECSSEEEEEEE----SSCHHHHHHHHHHHHHSCCEEEEEEEEEEEECSSSCHHHHHHHHTTSCBCCTTHHHHSCCGGGC
T ss_pred             ECCCCEEEEEEE----CCCCHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCCCCCEEEEECCCCCCCCCHHHHCCCHHE
T ss_conf             737988999997----8882799999999997496367999999866654667750689851675013502321160210


Q ss_pred             EEEECCCC--CEEEEEE---EECCEEEEEEEEECC-CCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCC---
Q ss_conf             17772798--2799999---944716996335138-98599888808999778964999999746876320344446---
Q gi|254780237|r   93 NLKMSGDS--HKRVTIF---KRGPGVVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---  163 (340)
Q Consensus        93 ~~k~~~~~--~~~~~l~---~~Gp~~vtA~Di~~p-~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~---  163 (340)
                      ........  ....++.   ..||+.++|+|++.+ +.+++++|+++||+|..+..|.+++++..|+|+..+..+..   
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~di~~~~~~~~~~~~~i~I~~L~~~q~L~l~~~~~~g~Gk~hak~~~v~~~  162 (265)
T 2pa8_D           83 IECTENCEKCYTKIYIEAEAPNEPRMIYSKDIKSEDPSVVPISGDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLS  162 (265)
T ss_dssp             TTCCSSCTTTEEEEEEEEECCSSCEEEEGGGCEESSTTCCBSCSCCEEEEECTTCEEEEEEEEEEECTTTCGGGCCEEEE
T ss_pred             EECCCCCCCEEEEEEEEEECCCCCCEEEHHHCCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEECCCCCCCCCCCCC
T ss_conf             22158898238999998882789837873332467997221148806999379976778999996364212212766543


Q ss_pred             --------------------------CCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHH
Q ss_conf             --------------------------557543021243111144223577641168877621899999938961777999
Q gi|254780237|r  164 --------------------------ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV  217 (340)
Q Consensus       164 --------------------------~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl  217 (340)
                                                ........+.|+.++|+.+++|...+..+....++++++|+|||+|+++|++|+
T Consensus       163 ~y~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~f~f~IET~G~i~p~~il  242 (265)
T 2pa8_D          163 VVRYYPKVEILANCEKAVNVCPEGVFELKDGKLSVKNELSCTLCEECLRYCNGSIRISFVEDKYILEIESVGSLKPERIL  242 (265)
T ss_dssp             EEEEEEEEEECSCCTTHHHHCTTCCEEEETTEEEESCGGGCCCCCHHHHHHTTSEEEEEEEEEEEEEEEECSSSCHHHHH
T ss_pred             CCCCCCCHHHHCCHHHHHHHCCCCCCCCCCCCEEECCCHHCCEEEEEEEECCCCEEECCCCCEEEEEEEECCCCCHHHHH
T ss_conf             31213404330004677664732430125675267452328714676542575200033676899999974761999999


Q ss_pred             HHHHHHHHHHHHHHHC
Q ss_conf             9999999998887622
Q gi|254780237|r  218 ALASRILQDQLGMFIN  233 (340)
Q Consensus       218 ~~Aa~iL~~~l~~f~~  233 (340)
                      .+|+++|+++|..|.+
T Consensus       243 ~~A~~iL~~kl~~l~~  258 (265)
T 2pa8_D          243 LEAGKSIIRKIEELEK  258 (265)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999999999999


No 5  
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=99.97  E-value=1.9e-32  Score=228.88  Aligned_cols=211  Identities=18%  Similarity=0.227  Sum_probs=172.1

Q ss_pred             ECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE---------CCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             63678881589999616975667888999998741698306889998---------871443146646244499999840
Q gi|254780237|r   19 VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNI   89 (340)
Q Consensus        19 ~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI---------~gv~HEfs~i~GV~EDV~eIiLNL   89 (340)
                      .+.+.+++..+|.++    |.+.|++|||||+|||++|++||+.|+|         +++.|+|+.||++.|++.++.+|+
T Consensus         8 ~i~~~~~~~~~f~l~----~~~~s~aNaLRR~lls~ip~~ai~~v~I~~Nts~l~dE~i~hRl~lIPi~~~~~~~~~~~~   83 (297)
T 3h0g_C            8 TIRNISKNSVDFVLT----NTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPPVG   83 (297)
T ss_dssp             CCCCBCSSEEEEEEC----SCCHHHHHHHHHHHHSSCCEEEEEEEEEEEECSSSCHHHHHHHHHHSCBCCTTCSSCSSSC
T ss_pred             EEEECCCCEEEEEEE----CCCCHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCCEEEEECCCCCEECCCCCCCHHH
T ss_conf             999845987999997----8880677899999987384207999999767864555312677314675202522022001


Q ss_pred             CCCEEEECCCC-----CEEEEEEE----ECCEEEEEEEEECCCCEE--------EECCCEEEEEECCCCEEEEEEEEECC
Q ss_conf             11417772798-----27999999----447169963351389859--------98888089997789649999997468
Q gi|254780237|r   90 KGINLKMSGDS-----HKRVTIFK----RGPGVVTAGDIQTVNDIE--------VLNPDHVICNLDVDAVVRMELTVSKG  152 (340)
Q Consensus        90 K~I~~k~~~~~-----~~~~~l~~----~Gp~~vtA~Di~~p~~ve--------ivNpd~~IaTl~~~~~l~iel~ie~G  152 (340)
                      +...++.....     ....++.+    .||+.|+|+|+++++.-+        .++|+++||+|..+..|+|++++..|
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~s~dl~~~~~~~~~~~~~~~~~~~~i~I~~L~~gq~L~le~~a~~G  163 (297)
T 3h0g_C           84 LEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILADPKSRGPLICKLRKEQEISLRCIAKKG  163 (297)
T ss_dssp             CCCSSSCSSSSSCGGGSCEEEEEECCCCSSCEEEEGGGCBCCSCCSSCCBCCCSTTSCCSEEEEECSSCCEEEEEEEEEE
T ss_pred             EEEEEECCCCCCCCCCEEEEEEEEECCCCCCEEEEECCEEECCCCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEEEEEC
T ss_conf             00111014456776525899998870567843676031687786430586433555689627980367369999999948


Q ss_pred             CCCEECCCCC-------------CCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCC----CEEEEEEEECCCCCHHH
Q ss_conf             7632034444-------------655754302124311114422357764116887762----18999999389617779
Q gi|254780237|r  153 HGYVPAKHHR-------------TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY----DKLSMTIDTDGSITGED  215 (340)
Q Consensus       153 ~GY~~~e~~~-------------~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~----dkL~lEI~TnGsi~P~e  215 (340)
                      +|+..|..+.             ......+....+..+.|..++.+..+..+.++..++    ++++|+|||+|+++|++
T Consensus       164 ~Gk~hak~spvs~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~F~IES~G~l~p~~  243 (297)
T 3h0g_C          164 IAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWPKSKNADWEEPPREGEPFNFQEEPRRFYMDVESVGSIPPNE  243 (297)
T ss_dssp             CGGGCTTSCCBCCCCCCSSSSCSSCCSCCCCSSCSTTTSCCCGGGTTCCCCSCCSCCCSSCCCCCEEEEEEBCSSSCTTT
T ss_pred             CCCCCCCCCCCCEEEEEECCCHHHHCCCCCCCCCCHHHCCCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCCCCHHH
T ss_conf             72222524663025653145101102433321231121356532137860455530577605768999999516659999


Q ss_pred             HHHHHHHHHHHHHHHHHC
Q ss_conf             999999999998887622
Q gi|254780237|r  216 SVALASRILQDQLGMFIN  233 (340)
Q Consensus       216 Al~~Aa~iL~~~l~~f~~  233 (340)
                      ||.+|+++|+++|..|..
T Consensus       244 il~~A~~iL~~kl~~~~~  261 (297)
T 3h0g_C          244 IMVQGLRILQEKLAVLVR  261 (297)
T ss_dssp             TTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999


No 6  
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ...
Probab=99.97  E-value=3.8e-31  Score=220.53  Aligned_cols=211  Identities=17%  Similarity=0.186  Sum_probs=161.2

Q ss_pred             ECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE---------CCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             63678881589999616975667888999998741698306889998---------871443146646244499999840
Q gi|254780237|r   19 VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNI   89 (340)
Q Consensus        19 ~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI---------~gv~HEfs~i~GV~EDV~eIiLNL   89 (340)
                      ++.+.++++.+|.++    |++.|+||||||+|||++|++||+.|+|         +++.|+|+.||++.||+.++..|+
T Consensus         9 ~i~~~~~~~~~f~l~----g~~~siaNaLRR~lLseIp~~Ai~~V~I~~Nts~l~dE~i~HRlglIPi~~~d~~~~~~~~   84 (318)
T 1twf_C            9 KIREASKDNVDFILS----NVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSR   84 (318)
T ss_dssp             CCSCCCSSEECCEEB----SSCHHHHHHHHHHHHHCCCEEEEEEEEEEEECSSSCHHHHHHHHHTSCEEETTGGGSCCTT
T ss_pred             EEEECCCCEEEEEEE----CCCHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCCEEEEEECCCCCCCCHHHHHHCC
T ss_conf             999867998999997----8881799999999987395127999999767764566623688632676335777832111


Q ss_pred             CCCEEEECCCCCEEEEEEEEC----CEEEEEEEEECCCCE-----------EEECCCEEEEEECCCCEEEEEEEEECCCC
Q ss_conf             114177727982799999944----716996335138985-----------99888808999778964999999746876
Q gi|254780237|r   90 KGINLKMSGDSHKRVTIFKRG----PGVVTAGDIQTVNDI-----------EVLNPDHVICNLDVDAVVRMELTVSKGHG  154 (340)
Q Consensus        90 K~I~~k~~~~~~~~~~l~~~G----p~~vtA~Di~~p~~v-----------eivNpd~~IaTl~~~~~l~iel~ie~G~G  154 (340)
                      +.+.+...+.......|++++    |..|+|+|+..++..           .+.+++.+||+|..+..|+|++++..|+|
T Consensus        85 ~~~~~~~~~~~~v~~~L~v~~~~~~~~~Vts~Di~~~~~~~~~~~~~p~~~~~~~~~IlI~kL~~gq~l~l~~~~~~G~g  164 (318)
T 1twf_C           85 DCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIA  164 (318)
T ss_dssp             TSSSSSCCTTTEEEEEEEEECCSSSCEEEEGGGEEECSCCTTCSEEEECCCSTTSCCSEEEEECTTCEEEEEEEEEEECT
T ss_pred             CCCCCCCCCCCEEEEEEEEECCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEEECCC
T ss_conf             34210368873599999964577765401135534567544467788655466789759999668957999999983873


Q ss_pred             CEECCCC-------------CCCCCCCCEECCCCCHHEEEEEEE----EEEEECCCCCCCCCEEEEEEEECCCCCHHHHH
Q ss_conf             3203444-------------465575430212431111442235----77641168877621899999938961777999
Q gi|254780237|r  155 YVPAKHH-------------RTENDPIGLITIDALYSPIKKVSY----TVESAREGQVLDYDKLSMTIDTDGSITGEDSV  217 (340)
Q Consensus       155 Y~~~e~~-------------~~~~~~ig~i~iDa~FsPV~~Vny----~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl  217 (340)
                      +..|..+             +...........+..+.|..+...    ..+..++......+++.|+|||+|+++|+++|
T Consensus       165 kehak~~pvs~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~F~IET~G~~~p~~il  244 (318)
T 1twf_C          165 KEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVV  244 (318)
T ss_dssp             TTCGGGCCEEEEEEEECSSTTSCCSCCCCSSCHHHHSCCCGGGTTSCCCCSSSCCCTTCCCCCEEEEEEECSSSCHHHHH
T ss_pred             CCCCEECCCCEEEEEECCCCCCCCCCCCEECCCHHHCCCCCCEEEECCCCCCCEEEEECCCCEEEEEEEECCCCCHHHHH
T ss_conf             33556555412676515543335553332204331088653036862344554058743664899999945877999999


Q ss_pred             HHHHHHHHHHHHHHHC
Q ss_conf             9999999998887622
Q gi|254780237|r  218 ALASRILQDQLGMFIN  233 (340)
Q Consensus       218 ~~Aa~iL~~~l~~f~~  233 (340)
                      .+|+++|++.|..|..
T Consensus       245 ~~A~~iL~~Kl~~l~~  260 (318)
T 1twf_C          245 VRGIDTLQKKVASILL  260 (318)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999999999999


No 7  
>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} SCOP: a.60.3.1 PDB: 2jzb_A
Probab=99.93  E-value=2.9e-27  Score=195.40  Aligned_cols=85  Identities=54%  Similarity=0.970  Sum_probs=79.1

Q ss_pred             CCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCH
Q ss_conf             00001123331112210110588898988398371888744988886188988644999999999808312676878986
Q gi|254780237|r  247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP  326 (340)
Q Consensus       247 ~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~  326 (340)
                      .+....++.|.++|++|+||+|++|||+++||+|||||+++|++||+++||||+||++||+++|+++||+|||++++|||
T Consensus        13 ee~~~~~~~L~~~I~eL~LSvRs~N~L~~~gI~tvgdLv~~se~dLl~~~n~G~KSl~EIk~~L~~~gL~lgm~l~~~~p   92 (98)
T 1coo_A           13 EEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPP   92 (98)
T ss_dssp             -----CCHHHHSBGGGGTCCTTTHHHHHTTTCCBHHHHHTSCHHHHTTSTTCCHHHHHHHHHHHHHTTCCTTCCCSSSSC
T ss_pred             CCCHHHHHHHCCCHHHHCCCHHHHHHHHHHCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             00034528860969882778999998738179389999857999997588976878999999999859777997899893


Q ss_pred             HHHHH
Q ss_conf             77999
Q gi|254780237|r  327 ESIEE  331 (340)
Q Consensus       327 ~~~~~  331 (340)
                      .++++
T Consensus        93 ~~~~~   97 (98)
T 1coo_A           93 ASIAD   97 (98)
T ss_dssp             STTCC
T ss_pred             CCCCC
T ss_conf             13235


No 8  
>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} PDB: 1lb2_B* 1xs9_D
Probab=99.93  E-value=7.8e-27  Score=192.58  Aligned_cols=83  Identities=53%  Similarity=0.938  Sum_probs=78.3

Q ss_pred             CCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHH
Q ss_conf             00112333111221011058889898839837188874498888618898864499999999980831267687898677
Q gi|254780237|r  249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES  328 (340)
Q Consensus       249 ~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~  328 (340)
                      ..+.++.|.++|++|+||+|++|||+++||+|||||+++|++||+++||||+||++||+++|+++||+|||++++|||.+
T Consensus         3 ~~e~~~~L~~~I~eL~LSvR~~N~Lk~~gI~tvgdLv~~se~dLl~i~NfG~kSl~EI~~~L~~~gL~lgm~l~~~~p~~   82 (86)
T 3k4g_A            3 XPEFDPILLRPVDDLELTVRSANCLXAEAIHYIGDLVQRTEVELLXTPNLGXXSLTEIXDVLASRGLSLGMRLENWPPAS   82 (86)
T ss_dssp             CCCCCGGGGSBGGGGCCCHHHHHHHHHTTCCBHHHHHHSCHHHHHTSTTCCHHHHHHHHHHHHTTTCCSSCCEESBSCCE
T ss_pred             CCCCCHHHCCCHHHHCCCHHHHHHHCCCCCCCHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             42108887196987278899998725543937999984899998178898772699999999985988899799989412


Q ss_pred             HHH
Q ss_conf             999
Q gi|254780237|r  329 IEE  331 (340)
Q Consensus       329 ~~~  331 (340)
                      +++
T Consensus        83 ~~~   85 (86)
T 3k4g_A           83 IAD   85 (86)
T ss_dssp             ECC
T ss_pred             CCC
T ss_conf             133


No 9  
>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis}
Probab=99.85  E-value=6.4e-22  Score=160.79  Aligned_cols=74  Identities=41%  Similarity=0.565  Sum_probs=69.7

Q ss_pred             CCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             00001123331112210110588898988398371888744988886188988644999999999808312676
Q gi|254780237|r  247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN  320 (340)
Q Consensus       247 ~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~  320 (340)
                      .++.+.++.|.++|++|+||+|++|||+++||+||+||+++|++||++++|||+||++||+++|+++||+|||+
T Consensus         5 ~~~~~~~~~L~~~I~~L~LS~R~~n~L~~~gI~tv~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~~~gL~l~~~   78 (79)
T 3gfk_B            5 KEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLRKD   78 (79)
T ss_dssp             CCCSSCCCGGGCBGGGSCCBHHHHHHHHHTTCCBHHHHTTCCHHHHTTSTTCHHHHHHHHHHHHHHTTCCCC--
T ss_pred             CCCCHHHHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             42024678854959984798999999989289679999868899997578986737999999999858989999


No 10 
>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B
Probab=99.85  E-value=1.2e-21  Score=158.95  Aligned_cols=70  Identities=43%  Similarity=0.616  Sum_probs=67.6

Q ss_pred             HHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             1123331112210110588898988398371888744988886188988644999999999808312676
Q gi|254780237|r  251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN  320 (340)
Q Consensus       251 ~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~  320 (340)
                      +.++.|+++|++|+||+|++|||+++||+|||||+++|++||+++||||+||++||+++|+++||+|||+
T Consensus         2 e~~~~L~~~I~~L~LS~R~~N~L~~~~I~tv~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~~~gl~l~~~   71 (73)
T 1z3e_B            2 EKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLRKD   71 (73)
T ss_dssp             -CHHHHTCBGGGSCCBHHHHHHHHHTTCCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHHTTCCCC--
T ss_pred             CHHHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             5067626889884698999999989489679999868999997478986605999999999849987999


No 11 
>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1
Probab=96.53  E-value=0.002  Score=41.02  Aligned_cols=56  Identities=5%  Similarity=0.145  Sum_probs=51.8

Q ss_pred             CCHHHC---CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             112210---11058889898839837188874498888618898864499999999980
Q gi|254780237|r  258 KKVEEL---ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       258 ~~IeeL---eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      .+|+.|   .++....+-|+.|||+||.+|+..+..+|.++++||.+..+-|.+.-..+
T Consensus        23 ~~I~~L~~~Gvg~~~i~KL~~aG~~Tv~~Ia~~t~~eL~~i~Gi~e~~A~KIi~aark~   81 (114)
T 1b22_A           23 QPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKL   81 (114)
T ss_dssp             CCHHHHHHTTCSHHHHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHHHHH
T ss_pred             CCHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             22899976899999999999969744999984899999766698899999999999987


No 12 
>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*
Probab=95.97  E-value=0.02  Score=34.51  Aligned_cols=58  Identities=10%  Similarity=0.194  Sum_probs=49.7

Q ss_pred             HHCCHHHCC---CCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             311122101---1058889898839837188874498888618898864499999999980
Q gi|254780237|r  256 LLKKVEELE---LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       256 L~~~IeeLe---LSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      ...+|++|.   .+....+-|+.|||+|+.+|+..+..+|.++++++..-++.|.+.-.++
T Consensus        79 ~~~~~~~l~~~gi~~~~i~kL~~aG~~t~~~i~~~~~~~L~~~~g~s~~~a~ki~~~a~k~  139 (400)
T 3lda_A           79 SFVPIEKLQVNGITMADVKKLRESGLHTAEAVAYAPRKDLLEIKGISEAKADKLLNEAARL  139 (400)
T ss_dssp             CSCBGGGGCCTTCCHHHHHHHHHTTCCBHHHHHHSCHHHHHTSTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             8766999986699989999999869851999971799999872399999999999999986


No 13 
>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11
Probab=95.82  E-value=0.0097  Score=36.58  Aligned_cols=57  Identities=11%  Similarity=0.196  Sum_probs=38.4

Q ss_pred             HCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             1112210-11058889898839837188874498888618898864499999999980
Q gi|254780237|r  257 LKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       257 ~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      ..++++| .++....+-|+.|||+|+.||+..+..+|.++.+++...+.+|.....+.
T Consensus        34 ~~~l~~l~gv~~~~~~kL~~aG~~t~~~l~~~~~~~L~~~~gis~~~a~kii~~a~~~   91 (349)
T 1pzn_A           34 IRSIEDLPGVGPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAARKA   91 (349)
T ss_dssp             -CCSSCCTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             1576337996999999999869972999970899999986498999999999999975


No 14 
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Probab=94.93  E-value=0.04  Score=32.57  Aligned_cols=45  Identities=20%  Similarity=0.330  Sum_probs=38.9

Q ss_pred             HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             5888989883983718887449888861889886449999999998
Q gi|254780237|r  267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT  312 (340)
Q Consensus       267 vRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~  312 (340)
                      +|+..|+ ++|+.++.|++..++++|.+++++|.|..+.|.+.+..
T Consensus       657 ~~ar~L~-~~G~~s~~~i~~~~~~~l~~v~g~g~k~a~~i~~~~~~  701 (720)
T 2zj8_A          657 RRARALY-NSGFRSIEDISQARPEELLKIEGIGVKTVEAIFKFLGK  701 (720)
T ss_dssp             HHHHHHH-TTTCCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHC-
T ss_pred             HHHHHHH-HCCCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHCH
T ss_conf             9999999-87999999997499889852769489999999974450


No 15 
>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ewa_A* 3ew9_A* 3etl_A* 2gdj_A*
Probab=94.30  E-value=0.098  Score=30.08  Aligned_cols=24  Identities=25%  Similarity=0.382  Sum_probs=16.5

Q ss_pred             EEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             899999938961777999999999
Q gi|254780237|r  200 KLSMTIDTDGSITGEDSVALASRI  223 (340)
Q Consensus       200 kL~lEI~TnGsi~P~eAl~~Aa~i  223 (340)
                      .-.+-|+|+++.+|...-..|...
T Consensus       143 ~~~l~i~t~~~~~~~~~~~~~~~~  166 (322)
T 2i1q_A          143 PKAVYIDTEGTFRPERIMQMAEHA  166 (322)
T ss_dssp             EEEEEEESSSCCCHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHC
T ss_conf             649999778888989999999764


No 16 
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...
Probab=93.12  E-value=0.013  Score=35.65  Aligned_cols=18  Identities=17%  Similarity=0.207  Sum_probs=7.5

Q ss_pred             CHHHHHHHHHHHHHHCCC
Q ss_conf             864499999999980831
Q gi|254780237|r  299 GRKSLVEIKGVLGTMGLF  316 (340)
Q Consensus       299 G~KSl~EI~~~L~~~gl~  316 (340)
                      |+|.=-.|.++=+++|+.
T Consensus       211 SsKtd~lIl~KA~eLGIk  228 (241)
T 1vq8_Y          211 GARKRERIEEEAEDAGIR  228 (241)
T ss_dssp             CHHHHHHHHHHHHHTTCC
T ss_pred             CCCCCHHHHHHHHHCCCC
T ss_conf             466779999999985994


No 17 
>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L
Probab=93.02  E-value=0.24  Score=27.60  Aligned_cols=48  Identities=29%  Similarity=0.317  Sum_probs=37.3

Q ss_pred             EEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             442235776411688776218999999389617779999999999998887622
Q gi|254780237|r  180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN  233 (340)
Q Consensus       180 V~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~  233 (340)
                      |.-+.|.+..      ...++..|-|.|+|+.+|.+||..|++-+++.+..|.+
T Consensus        38 V~fagY~~pH------Pl~~~i~i~i~t~~~~~p~~~l~~a~~~l~~~~~~~~~   85 (92)
T 2pa8_L           38 VSFASYYQPH------PLSDKIIVKILTDGSITPKDALLKAIENIRGMTSHYID   85 (92)
T ss_dssp             EEEEEEECSS------TTSCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEECCC------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             1698875678------87781599999699999899999999999999999999


No 18 
>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular switch, RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus P2} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*
Probab=92.97  E-value=0.015  Score=35.42  Aligned_cols=20  Identities=30%  Similarity=0.368  Sum_probs=12.3

Q ss_pred             EEEEEEECCCCCHHHHHHHH
Q ss_conf             99999938961777999999
Q gi|254780237|r  201 LSMTIDTDGSITGEDSVALA  220 (340)
Q Consensus       201 L~lEI~TnGsi~P~eAl~~A  220 (340)
                      -++-|.|.|+.+|+.....+
T Consensus       143 ~vvyidtE~~f~~~rl~~~~  162 (324)
T 2z43_A          143 KAVYIDTEGTFRWERIENMA  162 (324)
T ss_dssp             EEEEEESSSCCCHHHHHHHH
T ss_pred             EEEEEECCCCCHHHHHHHHH
T ss_conf             49999743511799999999


No 19 
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*
Probab=92.62  E-value=0.32  Score=26.78  Aligned_cols=49  Identities=18%  Similarity=0.255  Sum_probs=30.0

Q ss_pred             CCCHHHHHHHHHCC-CCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             11058889898839-83718887449888861889886449999999998
Q gi|254780237|r  264 ELSVRSTNCLRGEN-IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT  312 (340)
Q Consensus       264 eLSvRs~NcLk~a~-I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~  312 (340)
                      +|+.....-|-.+| |.++.||..++.++|+++.+||.||.+-+.+.++.
T Consensus       448 GlG~~~i~~L~e~g~I~~i~Diy~L~~~~l~~l~gfg~ksa~nll~sIe~  497 (667)
T 1dgs_A          448 GLGEKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEE  497 (667)
T ss_dssp             TCCHHHHHHHHHTTSCSSGGGGGGGCCHHHHTTSSCCSTTHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCHHHHHCCCHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf             60899999998678727678841378877635776340237899999876


No 20 
>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A
Probab=91.21  E-value=0.032  Score=33.26  Aligned_cols=23  Identities=17%  Similarity=0.206  Sum_probs=13.5

Q ss_pred             CEEEEEEEECCCCCHHHHHHHHH
Q ss_conf             18999999389617779999999
Q gi|254780237|r  199 DKLSMTIDTDGSITGEDSVALAS  221 (340)
Q Consensus       199 dkL~lEI~TnGsi~P~eAl~~Aa  221 (340)
                      +..++-|-|.|+..|.-....+.
T Consensus       156 ~g~vvyIdTE~~f~~~Rl~~i~~  178 (343)
T 1v5w_A          156 GGKIIFIDTENTFRPDRLRDIAD  178 (343)
T ss_dssp             CCEEEEEESSSCCCHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHH
T ss_conf             88468997789888999999998


No 21 
>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ...
Probab=90.48  E-value=0.84  Score=24.01  Aligned_cols=36  Identities=17%  Similarity=0.355  Sum_probs=31.5

Q ss_pred             CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             218999999389617779999999999998887622
Q gi|254780237|r  198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN  233 (340)
Q Consensus       198 ~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~  233 (340)
                      .++.+|-|.|+++.+|.+||..|++-|++.+..+..
T Consensus        68 ~~~i~lrI~t~~~~~p~~~l~~a~~~l~~~~~~i~~  103 (120)
T 1twf_K           68 FARFKLRIQTTEGYDPKDALKNACNSIINKLGALKT  103 (120)
T ss_dssp             SCEEEEEEEECTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             781279999699999999999999999999999999


No 22 
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=90.14  E-value=0.38  Score=26.23  Aligned_cols=36  Identities=11%  Similarity=0.100  Sum_probs=31.4

Q ss_pred             CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             218999999389617779999999999998887622
Q gi|254780237|r  198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN  233 (340)
Q Consensus       198 ~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~  233 (340)
                      .++.++-|.|+|+.+|.+|+..|++-|+..+..+..
T Consensus        67 ~~~i~irI~t~~~~~p~~~l~~a~~~li~~~~~i~~  102 (123)
T 3h0g_K           67 NHNFILRVQTVEDCSPKQVIVDAAKSLITHLEEIKV  102 (123)
T ss_dssp             SCEEEEEEECCSSSCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             880389999699999999999999999999999999


No 23 
>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L
Probab=89.94  E-value=0.32  Score=26.70  Aligned_cols=39  Identities=26%  Similarity=0.295  Sum_probs=29.2

Q ss_pred             CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             78881589999616975667888999998741698306889998
Q gi|254780237|r   22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI   65 (340)
Q Consensus        22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI   65 (340)
                      +.+++...|.+    .|.+||+||+||..|+.. ++....+-++
T Consensus         7 ~~~~n~~~i~i----~~EdhTlgnlL~~~L~~~-~~V~fagY~~   45 (92)
T 2pa8_L            7 KSESNYLELEI----EGEDHTLGNLIAGTLRRI-SGVSFASYYQ   45 (92)
T ss_dssp             EEETTEEEEEE----ETCCHHHHHHHHHHHHTS-TTEEEEEEEC
T ss_pred             ECCCCEEEEEE----ECCCCHHHHHHHHHHHCC-CCCEEEEEEC
T ss_conf             37998899999----489822999999999449-9916988756


No 24 
>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2
Probab=89.45  E-value=0.69  Score=24.57  Aligned_cols=47  Identities=11%  Similarity=0.147  Sum_probs=33.7

Q ss_pred             EEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             442235776411688776218999999389617779999999999998887622
Q gi|254780237|r  180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN  233 (340)
Q Consensus       180 V~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~  233 (340)
                      |.-+.|.+..      .--++..|-|.|+|. +|.+||..|++-|.+.+.-|..
T Consensus        48 V~fAgY~ipH------Pl~~~~~lrIkt~~~-~p~e~l~~a~~~l~~~~~~l~~   94 (115)
T 1xpp_A           48 VDEARYYIKH------PVIDNPQIYVRVKSG-KPQSAIKRAVRKLSKLYEDLGT   94 (115)
T ss_dssp             EEEEEEECSS------TTTSCCEEEEEESSS-CHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEECCC------CCCCCEEEEEEECCC-CHHHHHHHHHHHHHHHHHHHHH
T ss_conf             1699867799------887852899996799-9799999999999999999999


No 25 
>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12}
Probab=89.05  E-value=0.86  Score=23.97  Aligned_cols=44  Identities=25%  Similarity=0.416  Sum_probs=27.5

Q ss_pred             CCEEEEEEEECCCCCC-----------CCCCCCC-HHHHHHHHHHHCCCEEEECCC
Q ss_conf             8306889998871443-----------1466462-444999998401141777279
Q gi|254780237|r   56 RGAAITAVQIDGVLHE-----------ISSIKGV-HEDLTDIILNIKGINLKMSGD   99 (340)
Q Consensus        56 ~G~ait~vkI~gv~HE-----------fs~i~GV-~EDV~eIiLNLK~I~~k~~~~   99 (340)
                      .+.-+..-||||+.=.           +|.=.|. =|||++-+..++.|..+....
T Consensus       107 ~~~~~~e~KiDGls~~L~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~ip~~~~~~  162 (671)
T 2owo_A          107 KVTWCCELKLDGLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGE  162 (671)
T ss_dssp             CCCEEEEEEESSEEEEEEEETTEEEEEECCTTSSEEEBCHHHHHTCTTSCSBCCSS
T ss_pred             CCEEEEEEECCEEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHCCCCCCCCCC
T ss_conf             82289986135279999998999989764799964348476565531577642335


No 26 
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=89.02  E-value=0.5  Score=25.47  Aligned_cols=41  Identities=24%  Similarity=0.332  Sum_probs=30.9

Q ss_pred             CCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEE
Q ss_conf             42015863678881589999616975667888999998741698306
Q gi|254780237|r   13 NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA   59 (340)
Q Consensus        13 ~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~a   59 (340)
                      .+|.+ ..+...+|.+.|.+    .|..|||||+||..|+.. ++..
T Consensus        16 ~ki~~-~~~tk~~N~~~~~i----~~EDHTLGNlL~~~L~~~-~~V~   56 (123)
T 3h0g_K           16 PKVTY-ELDSKSPNAAVVTL----EKEDHTLANMLANQLLSD-ERVL   56 (123)
T ss_dssp             CSCCE-EECSSSTTEEEEEE----ESCCSSHHHHHHHTGGGS-TTCS
T ss_pred             CCEEE-EECCCCCCEEEEEE----ECCCCHHHHHHHHHHHCC-CCCE
T ss_conf             51698-64478885689999----589842999999999539-9834


No 27 
>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A
Probab=88.93  E-value=0.99  Score=23.57  Aligned_cols=59  Identities=10%  Similarity=0.138  Sum_probs=52.4

Q ss_pred             HHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             33111221011058889898839837188874498888618898864499999999980
Q gi|254780237|r  255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       255 ~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      .+++-++.|++.--..+.|-..|+.+|.++.--+.++|+.|.+|...-.+|+++.=+++
T Consensus         4 ~~~~F~e~LdvDe~iA~lLv~EGF~siEeIAy~~~~eL~~IegfDee~a~eL~~RA~~~   62 (70)
T 1u9l_A            4 AIDTFTKYLDIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERAKNA   62 (70)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             89999998486399999999865597999875999999763155899999999999999


No 28 
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5
Probab=87.39  E-value=1.1  Score=23.29  Aligned_cols=44  Identities=18%  Similarity=0.190  Sum_probs=36.7

Q ss_pred             HHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             8889898839837188874498888618898864499999999980
Q gi|254780237|r  268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       268 Rs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      ++.+-+++  ..++.+|.+-+.++|.+++++|.+..+.|.+.+.+-
T Consensus        31 ~a~~L~~~--Fgsl~~i~~As~eeL~~i~GiG~~~A~~I~~~f~~p   74 (89)
T 1z00_A           31 DSQTLLTT--FGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEP   74 (89)
T ss_dssp             HHHHHHHH--TCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSC
T ss_pred             HHHHHHHH--HCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCH
T ss_conf             99999999--488899999878777268996999999999998084


No 29 
>1im4_A DBH; DNA polymerase PALM, thumb, fingers, helix-hairpin-helix, fidelity, processivity, transferase; 2.30A {Sulfolobus solfataricus} SCOP: e.8.1.7
Probab=85.99  E-value=0.41  Score=26.06  Aligned_cols=40  Identities=10%  Similarity=0.160  Sum_probs=34.5

Q ss_pred             HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHC
Q ss_conf             331112210-1105888989883983718887449888861
Q gi|254780237|r  255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLR  294 (340)
Q Consensus       255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~  294 (340)
                      +-.++|++| .+.-|..-.|++.||+|+|||.+++.++|.+
T Consensus       181 L~~lpl~~l~GiG~~~~~~L~~~Gi~ti~dl~~~~~~~L~r  221 (221)
T 1im4_A          181 LNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEK  221 (221)
T ss_dssp             HHTCBGGGSTTCCHHHHHHHHHTTCCBTTC-----------
T ss_pred             HHCCCHHHHCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHCC
T ss_conf             85798754189479999999992992099985799998119


No 30 
>3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA; 2.60A {Sulfolobus acidocaldarius} SCOP: d.240.1.1 e.8.1.7 PDB: 3bq1_A* 3bq2_A* 1k1q_A 1k1s_A
Probab=84.84  E-value=1  Score=23.52  Aligned_cols=53  Identities=9%  Similarity=0.142  Sum_probs=41.9

Q ss_pred             HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             331112210-1105888989883983718887449888861889886449999999
Q gi|254780237|r  255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV  309 (340)
Q Consensus       255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~  309 (340)
                      .-..+|++| .+.-|...-|++.||+|++||.+.+.++|.+  -||.+....+.+.
T Consensus       176 l~~lpv~~l~GiG~~~~~~L~~~Gi~t~~dl~~~~~~~l~~--~fG~~~g~~l~~~  229 (354)
T 3bq0_A          176 LNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEK--ITGKAKALYLLKL  229 (354)
T ss_dssp             HHHCBSTTSTTCCHHHHHHHTTTTCCBGGGGGGSCHHHHHH--HHCHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHH--HHCHHHHHHHHHH
T ss_conf             98610666159647899999981896999954589878998--8481788999998


No 31 
>3gqc_A DNA repair protein REV1; protein-DNA complex, alternative splicing, DNA damage, DNA repair, DNA synthesis; HET: DNA DOC DCP; 2.50A {Homo sapiens}
Probab=84.19  E-value=1.7  Score=22.09  Aligned_cols=54  Identities=22%  Similarity=0.111  Sum_probs=42.9

Q ss_pred             HHHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             3331112210-1105888989883983718887449888861889886449999999
Q gi|254780237|r  254 PALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV  309 (340)
Q Consensus       254 ~~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~  309 (340)
                      -+...+|.+| .+.-+...-|++.||+|++||...+.+.|.+.  ||.+....+.+.
T Consensus       311 fL~~lpv~~lpGIG~~~~~kL~~lGI~Ti~DL~~l~~~~L~~~--fG~k~g~~L~~~  365 (504)
T 3gqc_A          311 FIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKE--FGPKTGQMLYRF  365 (504)
T ss_dssp             HHHHSBGGGSTTCCHHHHHHHHHTTCCBHHHHTTSCHHHHHHH--HCHHHHHHHHHH
T ss_pred             HHHHHCCCCCCCCCHHHHHHHHHHCCCCHHHHHCCCHHHHHHH--HCCHHHHHHHHH
T ss_conf             8864133344787878999998616850999855999999988--471789999996


No 32 
>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family, transferase/DNA complex; HET: DNA MSE ADI; 1.70A {Sulfolobus solfataricus} SCOP: d.240.1.1 e.8.1.7 PDB: 1jxl_A* 1n48_A* 1n56_A* 1ryr_A* 1rys_A* 1s0m_A* 1s0n_A* 1s0o_A* 1s10_A* 1s97_A* 1s9f_A* 2ia6_A* 2ibk_A* 2r8g_A* 2r8h_A* 2r8i_A* 2rdj_A* 3fds_A* 3m9m_B* 3m9n_B* ...
Probab=83.87  E-value=0.96  Score=23.66  Aligned_cols=52  Identities=8%  Similarity=0.012  Sum_probs=42.2

Q ss_pred             HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             331112210-110588898988398371888744988886188988644999999
Q gi|254780237|r  255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG  308 (340)
Q Consensus       255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~  308 (340)
                      +-..+|.+| .+.-++..-|++.||+|++||.+.+.+.|.+  -||.+....+.+
T Consensus       175 L~~lpv~~l~Gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~--~fG~~~~~~l~~  227 (352)
T 1jx4_A          175 IRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKG--MIGEAKAKYLIS  227 (352)
T ss_dssp             HHHSBGGGSTTCCHHHHHHHHTTTCCBGGGGGSSCHHHHHH--HHCHHHHHHHHH
T ss_pred             CCCCCEEEECCCCCHHHHHHHHHCCCCHHHHHCCCHHHHHH--HHCHHHHHHHHH
T ss_conf             02676024148870468899984686825413279789997--858487999999


No 33 
>3im1_A Protein SNU246, PRE-mRNA-splicing helicase BRR2; ATPase, RNA helicase, rnpase, RNA unwindase, molecular modeling; 1.65A {Saccharomyces cerevisiae} PDB: 3im2_A* 3hib_A
Probab=79.83  E-value=3  Score=20.41  Aligned_cols=94  Identities=5%  Similarity=0.104  Sum_probs=62.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCCCCHHHHHH-------HCCHHHC-CCCHHHHHHHHHCCCCCHHHHH
Q ss_conf             7999999999999888762244443221000000000112333-------1112210-1105888989883983718887
Q gi|254780237|r  214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL-------LKKVEEL-ELSVRSTNCLRGENIVYMGDLI  285 (340)
Q Consensus       214 ~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~~~~~~~~~~L-------~~~IeeL-eLSvRs~NcLk~a~I~tigdLv  285 (340)
                      ...+..|.+++...+.......-.. ..      ......+-+       ..++-+| .+..+...-|++.+|.++++|.
T Consensus       113 ~~I~~~~~Ril~al~ei~~~~~~~~-a~------~~l~l~q~i~q~~w~~~~~L~Qlp~i~~~~~~~l~~~~i~~l~~l~  185 (328)
T 3im1_A          113 KDILEKVVPLINVVVDILSANGYLN-AT------TAMDLAQMLIQGVWDVDNPLRQIPHFNNKILEKCKEINVETVYDIM  185 (328)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTBTT-HH------HHHHHHHHHHHTSCTTSCGGGGSTTCCHHHHHHHHHTTCCSHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHH-HH------HHHHHHHHHHHHCCCCCCHHHHHHHCCHHHHHHHHHCCCCCHHHHH
T ss_conf             9999999999999999996168799-99------9999999988655899866676620799999999975999999998


Q ss_pred             HCCHHHHHCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             44988886188988644999999999808
Q gi|254780237|r  286 QRTEADMLRMANFGRKSLVEIKGVLGTMG  314 (340)
Q Consensus       286 ~~s~~dLl~ikNfG~KSl~EI~~~L~~~g  314 (340)
                      ..+++++..+-++...-.++|.+.+..+-
T Consensus       186 ~~~~~~~~~~l~~~~~~~~~i~~~~~~~P  214 (328)
T 3im1_A          186 ALEDEERDEILTLTDSQLAQVAAFVNNYP  214 (328)
T ss_dssp             HSCHHHHHHHCCCCHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf             75176799997107789999999986489


No 34 
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3
Probab=79.62  E-value=2.2  Score=21.29  Aligned_cols=42  Identities=12%  Similarity=0.060  Sum_probs=35.1

Q ss_pred             HHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf             88898988398371888744988886188988644999999999
Q gi|254780237|r  268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG  311 (340)
Q Consensus       268 Rs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~  311 (340)
                      |+..-++.  ..++.++..-+.+||.+++++|++..++|.+.|.
T Consensus        36 ~ak~Ll~~--F~si~~i~~As~eeL~~v~GIg~~~A~~I~~~l~   77 (78)
T 1kft_A           36 RRQMLLKY--MGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK   77 (78)
T ss_dssp             HHHHHHHH--HSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHHHT
T ss_pred             HHHHHHHH--HCCHHHHHHHCHHHHHCCCCCCHHHHHHHHHHHC
T ss_conf             99999999--2994999883799998079989999999999966


No 35 
>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B
Probab=78.66  E-value=3.3  Score=20.18  Aligned_cols=47  Identities=9%  Similarity=0.067  Sum_probs=39.7

Q ss_pred             CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             11058889898839837188874498888618898864499999999
Q gi|254780237|r  264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL  310 (340)
Q Consensus       264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L  310 (340)
                      .++....--|..+||+|+.||...+-++|+.+-++.......+.-+-
T Consensus        14 G~~~~~~~~L~e~gI~t~edLAdls~dEL~ei~~i~ee~A~~lIM~A   60 (70)
T 1wcn_A           14 GVDRDLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMAA   60 (70)
T ss_dssp             TCCHHHHHHHHTTTCCSHHHHHTSCHHHHHTSSSCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCHHHHHHHCHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             98999999999969974999987289999876168999999999999


No 36 
>3osn_A DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA complex, Y-family DNA polym translesion synthesis, nucleoside triphosphate; HET: DNA DOC 6OG TTP; 1.90A {Homo sapiens} PDB: 2dpj_A* 2fll_A* 2fln_A* 2flp_A* 3epg_A* 3epi_A* 2dpi_A* 3g6v_A* 3g6y_A* 3g6x_A* 3gv7_B* 3gv8_B* 3ngd_A* 3gv5_B* 3h4d_A* 3h4b_A* 2alz_A* 3h40_A* 1t3n_A* 1zet_A*
Probab=75.99  E-value=3.8  Score=19.78  Aligned_cols=49  Identities=16%  Similarity=0.293  Sum_probs=39.0

Q ss_pred             CHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             12210-1105888989883983718887449888861889886449999999
Q gi|254780237|r  259 KVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV  309 (340)
Q Consensus       259 ~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~  309 (340)
                      +|.+| .+.-+....|++.||+|++||...+..+|.  +-||.+.-..+.+.
T Consensus       235 pv~~l~GiG~~~~~~L~~~Gi~ti~dl~~~~~~~L~--~~fG~~~g~~l~~~  284 (420)
T 3osn_A          235 HIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILE--KELGISVAQRIQKL  284 (420)
T ss_dssp             SGGGSTTCCHHHHHHHHHTTCCSHHHHHHSCHHHHH--HHHHHHHHHHHHHH
T ss_pred             CHHHHCCCCHHHHHHHHHHCCCCHHHHHCCCHHHHH--HHHCCHHHHHHHHH
T ss_conf             688856888789999864256609987527553699--88593999999999


No 37 
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5
Probab=75.68  E-value=4  Score=19.65  Aligned_cols=51  Identities=14%  Similarity=0.223  Sum_probs=38.9

Q ss_pred             CHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             122101105888989883983718887449888861889886449999999998
Q gi|254780237|r  259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT  312 (340)
Q Consensus       259 ~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~  312 (340)
                      .|..++-  ...+.|-+. ..++.++..-|.++|++++++|.+..+.|.+.+..
T Consensus        18 ~IpgIG~--~~a~~L~~~-F~s~~~i~~As~eeL~~v~GIG~~~a~~i~~~~~~   68 (75)
T 1x2i_A           18 GLPHVSA--TLARRLLKH-FGSVERVFTASVAELMKVEGIGEKIAKEIRRVITA   68 (75)
T ss_dssp             TSTTCCH--HHHHHHHHH-HCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHS
T ss_pred             CCCCCCH--HHHHHHHHH-HCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCC
T ss_conf             8999429--999999999-68889899978999985589799999999999857


No 38 
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5
Probab=72.73  E-value=4.6  Score=19.26  Aligned_cols=41  Identities=17%  Similarity=0.201  Sum_probs=34.5

Q ss_pred             HHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             989883983718887449888861889886449999999998
Q gi|254780237|r  271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT  312 (340)
Q Consensus       271 NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~  312 (340)
                      ..|-+. ..++.+|..-+.++|.+++++|.+-.+.|.+.+.+
T Consensus        46 ~~L~~~-F~Si~~l~~As~eeL~~i~GIG~~~A~~I~~~f~~   86 (91)
T 2a1j_B           46 QTLLTT-FGSLEQLIAASREDLALCPGLGPQKARRLFDVLHE   86 (91)
T ss_dssp             HHHHHH-HSSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHS
T ss_pred             HHHHHH-HCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHC
T ss_conf             999999-58829899989997557799699999999999848


No 39 
>1feu_A 50S ribosomal protein L25; general stress protein CTC, 5S rRNA-protein complex, cadmium IONS, ribosome; 2.30A {Thermus thermophilus} SCOP: b.53.1.1 PDB: 2j01_Z 1vsp_T 2hgj_Y 2hgq_Y 2hgu_Y 1vsa_T 2j03_Z 2jl6_Z 2jl8_Z 2v47_Z 2v49_Z 2wdi_Z 2wdj_Z 2wdl_Z 2wdn_Z 2wh2_Z 2wh4_Z 2wrj_Z 2wrl_Z 2wro_Z ...
Probab=70.80  E-value=2.5  Score=20.98  Aligned_cols=34  Identities=12%  Similarity=0.082  Sum_probs=17.4

Q ss_pred             EEEEEEEECC-CCEEEECCCEEEEEECCCCEEEEEEEE
Q ss_conf             6996335138-985998888089997789649999997
Q gi|254780237|r  113 VVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTV  149 (340)
Q Consensus       113 ~vtA~Di~~p-~~veivNpd~~IaTl~~~~~l~iel~i  149 (340)
                      .+--+|+|.. -.=.++.=|.|..  + +..+.+++-|
T Consensus        68 ~vlikevQ~~pv~~~i~HvDF~~v--~-~~~i~v~VPv  102 (206)
T 1feu_A           68 PTLVRQVNLDKRRRRPEHVDFFVL--S-DEPVEMYVPL  102 (206)
T ss_dssp             EEEEEEEEECSSSSCEEEEEEEEC--C-SSCEEEEEEE
T ss_pred             EEEEEEEEECCCCCCCEEEEEEEC--C-CCEEEEEECE
T ss_conf             999999874122577379998815--8-9769999665


No 40 
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A
Probab=69.64  E-value=5.5  Score=18.74  Aligned_cols=48  Identities=19%  Similarity=0.297  Sum_probs=38.0

Q ss_pred             CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             1105888989883983718887449888861889886449999999998
Q gi|254780237|r  264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT  312 (340)
Q Consensus       264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~  312 (340)
                      +.|......|-+. ..++.+|.+.+.++|.+++++|.+-..+|.+.|..
T Consensus       169 gi~~~~A~~Ll~~-f~Sl~~l~~as~~eL~~v~giG~~~A~~I~~~l~~  216 (219)
T 2bgw_A          169 GIGRRTAERILER-FGSLERFFTASKAEISKVEGIGEKRAEEIKKILMT  216 (219)
T ss_dssp             TCCHHHHHHHHHH-HSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHH-CCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHCC
T ss_conf             9899999999998-69999998688999960899799999999999638


No 41 
>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus}
Probab=68.96  E-value=4.1  Score=19.58  Aligned_cols=41  Identities=15%  Similarity=0.135  Sum_probs=30.5

Q ss_pred             HHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             88898988398371888744988886188988644999999999808
Q gi|254780237|r  268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG  314 (340)
Q Consensus       268 Rs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~g  314 (340)
                      ||.+.|++--      +--.+.+|+..++++|.+..+-|.++|+++-
T Consensus        42 kA~~sLk~~p------~~I~s~~~l~~l~GIG~~i~~ki~e~L~~yc   82 (87)
T 2kp7_A           42 KALRSLQRYP------LPLRSGKEAKILQHFGDRLCRMLDEKLKQHL   82 (87)
T ss_dssp             HHHHHHHHCC------SCCCSHHHHHTCTTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCC------CCCCCHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf             9999999789------9888899997279977899999999999999


No 42 
>3mr3_A DNA polymerase ETA; POL ETA, polymerase, thymine dimer, CPD, XPV, xeroderma PIGM variant, DNA damage; HET: DNA TTD DZ4; 1.75A {Homo sapiens} PDB: 3mr2_A* 3mr5_A* 3mr6_A*
Probab=63.86  E-value=7.1  Score=18.01  Aligned_cols=52  Identities=23%  Similarity=0.306  Sum_probs=37.8

Q ss_pred             HCCHHHC-CCCHHH-HHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             1112210-110588-89898839837188874498888618898864499999999
Q gi|254780237|r  257 LKKVEEL-ELSVRS-TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL  310 (340)
Q Consensus       257 ~~~IeeL-eLSvRs-~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L  310 (340)
                      ..+|.+| ...-+. ..-|++.||+|++||...+..+|.+.  ||.+.-..+.+..
T Consensus       252 ~lpi~~l~GiG~k~~~~~L~~~gi~ti~dl~~~~~~~L~~~--~G~~~g~~l~~~a  305 (435)
T 3mr3_A          252 QMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSH--FGEKNGSWLYAMC  305 (435)
T ss_dssp             TCBGGGSTTCSSHHHHHHHHHHTCCBGGGGGGSCHHHHHHH--HCHHHHHHHHHHT
T ss_pred             HCCCCEECCCCHHHHHHHHHHHCCCCHHHHHHCCHHHHHHH--HCHHHHHHHHHHH
T ss_conf             37677607767578999999958947899873999899999--7868899999996


No 43 
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans}
Probab=60.03  E-value=6.1  Score=18.43  Aligned_cols=23  Identities=17%  Similarity=0.177  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             49999999998083126768789
Q gi|254780237|r  302 SLVEIKGVLGTMGLFLGMNLPDW  324 (340)
Q Consensus       302 Sl~EI~~~L~~~gl~lg~~l~~~  324 (340)
                      -+++|.+.+++.|..+=+|-..|
T Consensus       471 d~e~v~~~~~~~g~~lEINts~~  493 (578)
T 2w9m_A          471 DLDAVLGACEANGTVVEINANAA  493 (578)
T ss_dssp             CHHHHHHHHHHHTCEEEEECSTT
T ss_pred             HHHHHHHHHHHHCCEEEEECCCC
T ss_conf             79999999998199999949999


No 44 
>2q0z_X Protein Pro2281; SEC63, SEC, NESG, HR1979, structural genomics, translocase, northeast structural genomics consortium, PSI-2; 2.00A {Homo sapiens} SCOP: a.289.1.1 b.1.18.22
Probab=59.00  E-value=8.7  Score=17.47  Aligned_cols=96  Identities=6%  Similarity=0.067  Sum_probs=59.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCH---HHCCC-CHHHHHHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCH
Q ss_conf             999999999999888762244443221000---00000-01123331112210-11058889898839837188874498
Q gi|254780237|r  215 DSVALASRILQDQLGMFINFEEPKKEVKED---INVKS-LPFNPALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTE  289 (340)
Q Consensus       215 eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~---~~~~~-~~~~~~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~  289 (340)
                      -.+..|.+++...+................   .-..+ .-.+   ..++-+| .++....+-|.+.+|.++.||...+.
T Consensus       117 ~I~~~~~Ril~al~ei~~~~~~~~~~~~~l~l~q~i~q~~w~~---~~pL~Qlp~i~~~~~~~l~~~~i~sl~~l~~~~~  193 (339)
T 2q0z_X          117 EILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWSK---DSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMED  193 (339)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHTCCTT---SCGGGGSTTCCHHHHHHHHHTTCCSHHHHHHSCH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCC---CCHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCH
T ss_conf             9999899999999999986598999999999999988663899---7732324658999999998669998999972899


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             888618898864499999999980
Q gi|254780237|r  290 ADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       290 ~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      +++..+-++......+|.+.+..+
T Consensus       194 ~~~~~~l~l~~~~~~~i~~~~~~~  217 (339)
T 2q0z_X          194 EERNALLQLTDSQIADVARFCNRY  217 (339)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHTTS
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             999877523768999999988758


No 45 
>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W 1vou_W 1vow_W ...
Probab=58.09  E-value=2.7  Score=20.75  Aligned_cols=24  Identities=25%  Similarity=0.536  Sum_probs=8.1

Q ss_pred             EEEEEEECCCCEEEE-CCCEEEEEE
Q ss_conf             996335138985998-888089997
Q gi|254780237|r  114 VTAGDIQTVNDIEVL-NPDHVICNL  137 (340)
Q Consensus       114 vtA~Di~~p~~veiv-Npd~~IaTl  137 (340)
                      ++++||.+|.+++++ +|+..||++
T Consensus       147 i~v~Dl~lp~gv~l~~d~d~~V~~V  171 (237)
T 2zjr_S          147 ITAGDIKLPEGCTLAADPELTVVSV  171 (237)
T ss_dssp             EETTTSCCSTTCCCCSCTTCEEEEE
T ss_pred             EEEEEECCCCCEEECCCCCCEEEEE
T ss_conf             9998442799808825999579999


No 46 
>2x7i_A Mevalonate kinase; transferase; HET: CIT; 2.20A {Staphylococcus aureus}
Probab=55.85  E-value=9.7  Score=17.13  Aligned_cols=77  Identities=13%  Similarity=0.274  Sum_probs=53.9

Q ss_pred             HHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCC--CC---------CHH
Q ss_conf             2210-11058889898839837188874498888618898864499999999980831267687--89---------867
Q gi|254780237|r  260 VEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP--DW---------PPE  327 (340)
Q Consensus       260 IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~--~~---------~~~  327 (340)
                      ++.+ ++..++..+|++.++..+++|+..+...|.++ +.....++++.+...+.|- +|.++.  +|         +.+
T Consensus       207 ~~~i~~~~~~~~~al~~~d~~~lg~lm~~~~~~l~~l-~vs~p~l~~l~~~~~~~Ga-~gaklsGaG~Gg~~~al~~~~~  284 (308)
T 2x7i_A          207 VKHIGKLVLRASDVIEHHKFEALADIFNECHADLKAL-TVSHDKIEQLMKIGKENGA-IAGKLTGAGRGGSMLLLAKDLP  284 (308)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHTTC-SEEEESBTTTCSSEEEEESSHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHCCC-CEEEEECCCCCCEEEEEECCHH
T ss_conf             9997478999999998657789999999999999871-7898899999999997899-5899977785226999979878


Q ss_pred             HHHHHHHHHHC
Q ss_conf             79999987750
Q gi|254780237|r  328 SIEELAKKYED  338 (340)
Q Consensus       328 ~~~~~~~~~~~  338 (340)
                      ..+.+.+++++
T Consensus       285 ~a~~i~~~l~~  295 (308)
T 2x7i_A          285 TAKNIVKAVEK  295 (308)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999997


No 47 
>1zco_A 2-dehydro-3-deoxyphosphoheptonate aldolase; arabino-heptulosonate, synthase, shikimate, DAHP, DAH7P, dahps, DAH7PS, lyase; HET: PEP; 2.25A {Pyrococcus furiosus}
Probab=52.30  E-value=7.9  Score=17.71  Aligned_cols=15  Identities=13%  Similarity=0.085  Sum_probs=8.8

Q ss_pred             CCHHHHHHHHHHHCC
Q ss_conf             624449999984011
Q gi|254780237|r   77 GVHEDLTDIILNIKG   91 (340)
Q Consensus        77 GV~EDV~eIiLNLK~   91 (340)
                      |.-|.-++++...|+
T Consensus        70 g~g~~gl~~l~~ik~   84 (262)
T 1zco_A           70 GYGEKALRWMREAAD   84 (262)
T ss_dssp             CCTHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH
T ss_conf             761588999998776


No 48 
>2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop, transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces cerevisiae} PDB: 3bjy_A*
Probab=52.13  E-value=11  Score=16.75  Aligned_cols=50  Identities=18%  Similarity=0.131  Sum_probs=35.7

Q ss_pred             HCCHHHC-CCCHHHHHHHHHC--CCCCHHHHHH-CCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             1112210-1105888989883--9837188874-4988886188988644999999
Q gi|254780237|r  257 LKKVEEL-ELSVRSTNCLRGE--NIVYMGDLIQ-RTEADMLRMANFGRKSLVEIKG  308 (340)
Q Consensus       257 ~~~IeeL-eLSvRs~NcLk~a--~I~tigdLv~-~s~~dLl~ikNfG~KSl~EI~~  308 (340)
                      ..++.+| ...-++..-|++.  ||+|++||.+ .+.+.|.+.  ||.|.-..+.+
T Consensus       240 ~lpv~~LpGIG~~~~~kL~~~~~Gi~ti~DL~~~~~~~~L~~~--fG~~~g~~l~~  293 (434)
T 2aq4_A          240 SFKLDDLPGVGHSTLSRLESTFDSPHSLNDLRKRYTLDALKAS--VGSKLGMKIHL  293 (434)
T ss_dssp             TCCGGGSTTCCHHHHHHHHHHTTCCCSHHHHHHHCCHHHHHHH--HCSSHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHCCCEEHHHHHHHCCHHHHHHH--HCCHHHHHHHH
T ss_conf             6672106686789999999876588079997632829899999--67489999999


No 49 
>3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3kzi_U* 3a0b_U* 3a0h_U*
Probab=51.27  E-value=6.1  Score=18.43  Aligned_cols=41  Identities=7%  Similarity=0.126  Sum_probs=28.5

Q ss_pred             HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             5888989883983718887449888861889886449999999998083
Q gi|254780237|r  267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL  315 (340)
Q Consensus       267 vRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl  315 (340)
                      ..|....+...+.        +-+||++++++|.+.++-|+..|..+-.
T Consensus        44 ~~A~~Iv~~gpf~--------s~~dL~~V~Gig~~~~e~ik~yl~~~~~   84 (104)
T 3bz1_U           44 TLAKLIVKNAPYE--------SVEDVLNIPGLTERQKQILRENLEHFTV   84 (104)
T ss_dssp             HHHHHHHHSCCCS--------SGGGGGGCTTCCHHHHHHHHHHGGGEEC
T ss_pred             HHHHHHHHCCCCC--------CHHHHHCCCCCCHHHHHHHHHHHCCCEE
T ss_conf             9999999749979--------8999963899899999999986545544


No 50 
>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus}
Probab=46.18  E-value=8.8  Score=17.43  Aligned_cols=39  Identities=8%  Similarity=0.127  Sum_probs=27.4

Q ss_pred             HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             58889898839837188874498888618898864499999999980
Q gi|254780237|r  267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       267 vRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      .++....++..+.        +-+||++++++|.|.++-+++.|..+
T Consensus        74 ~~A~~Iv~~gpf~--------svedl~~v~Gig~~~~e~l~~~l~~f  112 (134)
T 1s5l_U           74 TLAKLIVKNAPYE--------SVEDVLNIPGLTERQKQILRENLEHF  112 (134)
T ss_dssp             HHHHHHHHTCCCS--------SGGGGGGCTTCCHHHHHHHHHHHTTE
T ss_pred             HHHHHHHHCCCCC--------CHHHHHCCCCCCHHHHHHHHHHHCCC
T ss_conf             9999999827848--------79999617757999999999865353


No 51 
>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A*
Probab=42.90  E-value=15  Score=15.84  Aligned_cols=47  Identities=6%  Similarity=0.191  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             1105888989883983718887449888861889886449999999998
Q gi|254780237|r  264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT  312 (340)
Q Consensus       264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~  312 (340)
                      +.+......|-+ ...++.+|.+.|.+||.++.+ |++....|.+.|..
T Consensus        11 GIg~~~~~~Ll~-~fgSi~~l~~as~eeL~~v~G-~~~~A~~i~~~l~~   57 (63)
T 2a1j_A           11 GVNAKNCRSLMH-HVKNIAELAALSQDELTSILG-NAANAKQLYDFIHT   57 (63)
T ss_dssp             TCCHHHHHHHHH-HCSSHHHHHTCCHHHHHHHHS-CHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHH-HCCCHHHHHHCCHHHHHHCCC-CHHHHHHHHHHHCC
T ss_conf             988999999999-867999998799999987869-89999999999802


No 52 
>3bqs_A Uncharacterized protein; 10114F, NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.42A {Listeria monocytogenes str} PDB: 3bqt_A 3mab_A
Probab=42.41  E-value=16  Score=15.79  Aligned_cols=77  Identities=17%  Similarity=0.123  Sum_probs=46.9

Q ss_pred             CHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHH-HCCCCCCHH-HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             12210-11058889898839837188874498888-618898864-4999999999808312676878986779999987
Q gi|254780237|r  259 KVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADM-LRMANFGRK-SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK  335 (340)
Q Consensus       259 ~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dL-l~ikNfG~K-Sl~EI~~~L~~~gl~lg~~l~~~~~~~~~~~~~~  335 (340)
                      .+.+| +++..+..-|.+.||+++.||......++ .+++-.|.. ++.-   -..--|.--|..-...+.+.-++|++.
T Consensus         5 ~L~~LPNig~~~e~~L~~iGI~~~~~L~~~ga~~~y~rLk~~~~~~~~~~---L~aL~gAl~g~~w~~l~~e~K~~L~~~   81 (93)
T 3bqs_A            5 NLSELPNIGKVLEQDLIKAGIKTPVELKDVGSKEAFLRIWENDSSVCMSE---LYALEGAVQGIRWHGLDEAKKIELKKF   81 (93)
T ss_dssp             CGGGSTTCCHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHTTCTTCCHHH---HHHHHHHHHTSCGGGSCHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHHHCCCCCHHH---HHHHHHHHCCCCHHHCCHHHHHHHHHH
T ss_conf             77248999999999999939998999986799999999998689960999---999999994998676999999999999


Q ss_pred             HHC
Q ss_conf             750
Q gi|254780237|r  336 YED  338 (340)
Q Consensus       336 ~~~  338 (340)
                      |..
T Consensus        82 ~~~   84 (93)
T 3bqs_A           82 HQS   84 (93)
T ss_dssp             HHH
T ss_pred             HHH
T ss_conf             998


No 53 
>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} SCOP: a.96.1.2
Probab=40.96  E-value=10  Score=16.96  Aligned_cols=53  Identities=19%  Similarity=0.326  Sum_probs=36.7

Q ss_pred             HHCCHHHCCCC-HHHHHHHHHCCCC--CHHHHHHCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             31112210110-5888989883983--71888744988886188988644999999
Q gi|254780237|r  256 LLKKVEELELS-VRSTNCLRGENIV--YMGDLIQRTEADMLRMANFGRKSLVEIKG  308 (340)
Q Consensus       256 L~~~IeeLeLS-vRs~NcLk~a~I~--tigdLv~~s~~dLl~ikNfG~KSl~EI~~  308 (340)
                      +..-|..++|. .||.+..+-+.+-  .-+.-+..+.++|+++|+.|+|+..-|-.
T Consensus        78 l~~~i~~~G~~~~KA~~l~~~a~~i~~~~~g~vp~~~~eL~~LPGVG~ktA~~vl~  133 (221)
T 1kea_A           78 IAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGVGKYTCAAVMC  133 (221)
T ss_dssp             HHHHTGGGSCHHHHHHHHHHHHHHHHHHHTTSCCSCHHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             99999987899999999999999998860587301288874489876567999999


No 54 
>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A*
Probab=36.03  E-value=20  Score=15.15  Aligned_cols=50  Identities=14%  Similarity=0.252  Sum_probs=40.2

Q ss_pred             CCCHHHHHHHHH-------------CCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf             110588898988-------------39837188874498888618898864499999999980
Q gi|254780237|r  264 ELSVRSTNCLRG-------------ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       264 eLSvRs~NcLk~-------------a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~  313 (340)
                      -+|.|-|-.|.+             ....++..|+.-|.+||.++.+.|++-..-|++-|..+
T Consensus       308 ~v~pRGyRiLskiprlp~~vienLV~~FgsLq~Ll~AS~EeL~eVeGIGe~RAr~IreGL~Rl  370 (377)
T 3c1y_A          308 LVSARGYRLLKTVARIPLSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISSL  370 (377)
T ss_dssp             BCCCCSHHHHHHTSCCCHHHHHHHHHHHCSHHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             657417888723899978899999998468999985899889645885899999999999998


No 55 
>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A
Probab=35.92  E-value=12  Score=16.49  Aligned_cols=51  Identities=18%  Similarity=0.183  Sum_probs=34.8

Q ss_pred             CCHHHCCCCHHHHHHHHHCCCC--CHHHHHHCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             1122101105888989883983--71888744988886188988644999999
Q gi|254780237|r  258 KKVEELELSVRSTNCLRGENIV--YMGDLIQRTEADMLRMANFGRKSLVEIKG  308 (340)
Q Consensus       258 ~~IeeLeLSvRs~NcLk~a~I~--tigdLv~~s~~dLl~ikNfG~KSl~EI~~  308 (340)
                      .-|..+.+..|+.|-.+.+.+-  .-+.-+..+.++|+++|+.|+|+.+-|-.
T Consensus        75 ~~i~~~gy~~ka~~l~~~a~~i~~~~~g~~p~~~~~L~~LpGVG~kTA~~il~  127 (225)
T 1kg2_A           75 HLWTGLGYYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILS  127 (225)
T ss_dssp             HHHTTSCCTHHHHHHHHHHHHHHHHSTTSCCCSHHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCHHHHHHHHH
T ss_conf             99861673277999999999999870799974299997589874789999999


No 56 
>2e1f_A Werner syndrome ATP-dependent helicase; HRDC domain, hydrolase; 2.00A {Homo sapiens} SCOP: a.60.8.1 PDB: 2e1e_A
Probab=35.58  E-value=13  Score=16.24  Aligned_cols=47  Identities=15%  Similarity=0.089  Sum_probs=29.5

Q ss_pred             HHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHH-------HHHHHHHHHCCC
Q ss_conf             89898839837188874498888618898864499-------999999980831
Q gi|254780237|r  270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV-------EIKGVLGTMGLF  316 (340)
Q Consensus       270 ~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~-------EI~~~L~~~gl~  316 (340)
                      +..+.+.-+.-+....-.|.++|..+++||.+-++       -|.+...+.++.
T Consensus        37 ~~I~~d~~L~~ia~~~P~t~~eL~~I~G~g~~k~~ryG~~l~~I~~~~~~~~~~   90 (103)
T 2e1f_A           37 AILATNKILVDMAKMRPTTVENVKRIDGVSEGKAAMLAPLLEVIKHFCQTNSVQ   90 (103)
T ss_dssp             HHHCCHHHHHHHHHHCCCSHHHHTTSTTCCHHHHHHTHHHHHHHHHHHHHTTCC
T ss_pred             EEEECHHHHHHHHHHCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             044789999999987899999993789989999999989999999999984998


No 57 
>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19
Probab=34.27  E-value=13  Score=16.29  Aligned_cols=22  Identities=18%  Similarity=0.270  Sum_probs=15.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             1443146646244499999840
Q gi|254780237|r   68 VLHEISSIKGVHEDLTDIILNI   89 (340)
Q Consensus        68 v~HEfs~i~GV~EDV~eIiLNL   89 (340)
                      ....-+.++||=.-..+.+-.|
T Consensus       113 l~~~i~~lkGVGpk~a~~L~kl  134 (780)
T 1gm5_A          113 LSTDIQYAKGVGPNRKKKLKKL  134 (780)
T ss_dssp             SCCCSSSSSSCCHHHHHHHHTT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHC
T ss_conf             9998601788159999999976


No 58 
>1x40_A ARAP2; ASAP-related protein2, GTPase activity, signal transduction, SAM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.1.2
Probab=34.23  E-value=21  Score=14.97  Aligned_cols=40  Identities=8%  Similarity=0.100  Sum_probs=31.3

Q ss_pred             CHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCC--CCCC
Q ss_conf             1221011058889898839837188874498888618--8988
Q gi|254780237|r  259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM--ANFG  299 (340)
Q Consensus       259 ~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~i--kNfG  299 (340)
                      =++.+.|+ +=...+++.+|.++.+|...++++|.++  .++|
T Consensus        21 WL~~igL~-~Y~~~F~~~~~~~~~~l~~l~~~dL~~lGI~~~g   62 (91)
T 1x40_A           21 FLMSINLE-QYLLHFHESGFTTVKDCAAINDSLLQKIGISPTG   62 (91)
T ss_dssp             HHHTTTCG-GGHHHHHHHTCCBSGGGGGCCHHHHHHHTCCCHH
T ss_pred             HHHHCCCH-HHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHH
T ss_conf             99888559-9999999949982899987999999786999899


No 59 
>1vr6_A Phospho-2-dehydro-3-deoxyheptonate aldolase; TM0343, structural genomics, joint center for structural genomics, JCSG; 1.92A {Thermotoga maritima} SCOP: c.1.10.4 PDB: 1rzm_A*
Probab=33.46  E-value=22  Score=14.89  Aligned_cols=17  Identities=18%  Similarity=-0.097  Sum_probs=7.4

Q ss_pred             EEEECCCCCHHHHHHHH
Q ss_conf             99938961777999999
Q gi|254780237|r  204 TIDTDGSITGEDSVALA  220 (340)
Q Consensus       204 EI~TnGsi~P~eAl~~A  220 (340)
                      .+.-.-..+|++-+.-|
T Consensus       217 ~lKkG~~~s~~e~l~aa  233 (350)
T 1vr6_A          217 LLKRGFMNTIEEFLLSA  233 (350)
T ss_dssp             EEECCTTCCHHHHHHHH
T ss_pred             EECCCCCCCHHHHHHHH
T ss_conf             94175548999987789


No 60 
>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family DNA polymerase, translesion DNA synthesis, lesion bypass; 2.40A {Homo sapiens} SCOP: d.240.1.1 e.8.1.7 PDB: 2oh2_A* 2w7o_A* 2w7p_A* 3hed_A* 3in5_A*
Probab=33.06  E-value=22  Score=14.85  Aligned_cols=49  Identities=14%  Similarity=0.108  Sum_probs=36.3

Q ss_pred             HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHH
Q ss_conf             331112210-1105888989883983718887449888861889886449999
Q gi|254780237|r  255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI  306 (340)
Q Consensus       255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI  306 (340)
                      +-..+|.+| +..-+...-|++.||.|++||.+.. ..|.  +-||++...-+
T Consensus       279 L~~lpv~~l~GIG~~~~~~L~~~gI~ti~dL~~~~-~~l~--~~~g~~~~~~~  328 (459)
T 1t94_A          279 IKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQR-ALLS--LLFSETSWHYF  328 (459)
T ss_dssp             HTTCBGGGCTTSCHHHHHHHHHTTCCBHHHHHHTH-HHHH--HHSCHHHHHHH
T ss_pred             HHHCCCCEECCCCCHHHHHHHHHCCCCHHHHHHHH-HHHH--HHHCCHHHHHH
T ss_conf             86298353368884137889870784999999858-8899--98451366646


No 61 
>2cz9_A Probable galactokinase; structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.50A {Pyrococcus horikoshii} PDB: 2dei_A* 2dej_A* 1s4e_A*
Probab=31.66  E-value=23  Score=14.70  Aligned_cols=62  Identities=18%  Similarity=0.193  Sum_probs=48.0

Q ss_pred             CHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             122101105888989883983718887449888861889886449999999998083126768
Q gi|254780237|r  259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL  321 (340)
Q Consensus       259 ~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l  321 (340)
                      -+.+-+........|++.++..+|+|+..+-..|++.-+..-..++++.+...+.|. +|-++
T Consensus       239 v~~e~~~~~~~~~~~~~~d~~~~g~lm~~~~~~L~~~~~vs~~~ld~lv~~a~~~Ga-~GaKl  300 (350)
T 2cz9_A          239 IVRENARVLEVRDALKEGNVEEVGKILTTAHWDLAKNYEVSCKELDFFVERALKLGA-YGARL  300 (350)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTC-SEEEE
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCC-CEEEE
T ss_conf             999999999999875027899999999999999987208996899999999997799-38998


No 62 
>2rrd_A BLM HRDC domain, HRDC domain from bloom syndrome protein; DNA helicase, RECQ family, HRDC DOMA binding protein; NMR {Homo sapiens}
Probab=30.85  E-value=15  Score=15.91  Aligned_cols=45  Identities=13%  Similarity=0.187  Sum_probs=31.3

Q ss_pred             HHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHH----HHHHHHHHH
Q ss_conf             889898839837188874498888618898864499----999999980
Q gi|254780237|r  269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV----EIKGVLGTM  313 (340)
Q Consensus       269 s~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~----EI~~~L~~~  313 (340)
                      .+..+.+..+.-+....-.|.++|++|++||.+.++    +|.+.+.++
T Consensus        43 ~~~I~~d~~L~eia~~~P~t~~eL~~I~Gv~~~k~~~yG~~il~~I~~~   91 (101)
T 2rrd_A           43 YFNIFNTVTLKKLAESLSSDPEVLLQIDGVTEDKLEKYGAEVISVLQKY   91 (101)
T ss_dssp             HHHHCCHHHHHHHHHHCCCCHHHHHTSTTCCHHHHHHTHHHHHHHHHHH
T ss_pred             CEEEECHHHHHHHHHHCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             5455779999999986859999982677879999999999999999999


No 63 
>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A*
Probab=30.05  E-value=18  Score=15.38  Aligned_cols=17  Identities=12%  Similarity=0.307  Sum_probs=6.4

Q ss_pred             CCHHHHHCCCCCCHHHH
Q ss_conf             49888861889886449
Q gi|254780237|r  287 RTEADMLRMANFGRKSL  303 (340)
Q Consensus       287 ~s~~dLl~ikNfG~KSl  303 (340)
                      .+.++|+++++.|+++.
T Consensus       115 ~~~~~L~~LpGVG~~TA  131 (369)
T 3fsp_A          115 DDPDEFSRLKGVGPYTV  131 (369)
T ss_dssp             CSHHHHHTSTTCCHHHH
T ss_pred             CCHHHHHHCCCHHHHHH
T ss_conf             87999852422588999


No 64 
>1vs1_A 3-deoxy-7-phosphoheptulonate synthase; (beta/alpha)8 barrel, transferase; HET: PEP; 2.30A {Aeropyrum pernix}
Probab=29.03  E-value=26  Score=14.42  Aligned_cols=11  Identities=18%  Similarity=0.338  Sum_probs=4.4

Q ss_pred             HHHHHHHHCCC
Q ss_conf             99999840114
Q gi|254780237|r   82 LTDIILNIKGI   92 (340)
Q Consensus        82 V~eIiLNLK~I   92 (340)
                      ..++..-+|++
T Consensus        54 ~~~~a~~~k~~   64 (276)
T 1vs1_A           54 VREAALAVKEA   64 (276)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999984


No 65 
>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} SCOP: a.60.2.7
Probab=28.02  E-value=13  Score=16.33  Aligned_cols=24  Identities=21%  Similarity=0.421  Sum_probs=16.3

Q ss_pred             CCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             498888618898864499999999
Q gi|254780237|r  287 RTEADMLRMANFGRKSLVEIKGVL  310 (340)
Q Consensus       287 ~s~~dLl~ikNfG~KSl~EI~~~L  310 (340)
                      .|-+||.+++++|.+.++.|+..|
T Consensus        50 ~s~~dL~~v~gi~~~~~~~i~~~l   73 (75)
T 2duy_A           50 ARVEDLLKVKGIGPATLERLRPYL   73 (75)
T ss_dssp             SSGGGGGGSTTCCHHHHHHHGGGE
T ss_pred             CCHHHHHHCCCCCHHHHHHHHHHC
T ss_conf             989999757898999999999772


No 66 
>1wuu_A Galactokinase; galactosemia, GHMP superfamily, transferase; HET: GLA ANP; 2.50A {Homo sapiens} SCOP: d.14.1.5 d.58.26.7
Probab=27.93  E-value=27  Score=14.29  Aligned_cols=63  Identities=13%  Similarity=0.149  Sum_probs=48.8

Q ss_pred             HHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             221011058889898839837188874498888618898864499999999980831267687
Q gi|254780237|r  260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP  322 (340)
Q Consensus       260 IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~  322 (340)
                      +.+.....++..+|+..+...+|+|+..+-+.|+..-+..--+|+.|.+...+.+=.+|-++-
T Consensus       289 ~~e~~~~~~~~~al~~~d~~~lG~Lm~~~h~~L~~~lgVS~p~Ld~lv~~a~~~~Ga~gaKlt  351 (399)
T 1wuu_A          289 VGEIRRTAQAAAALRRGDYRAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMT  351 (399)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTSCCCCHHHHHHHHHHHTSTTEEEEEEC
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             778888888998775389999999999999999986479979999999999874997398973


No 67 
>1ow5_A Serine/threonine-protein kinase STE11; MAP kinase, MAPKKK, SAM domain, pointed domain, SCM domain, STE50 regulator, transferase; NMR {Saccharomyces cerevisiae} SCOP: a.60.1.2 PDB: 1x9x_A
Probab=26.86  E-value=28  Score=14.17  Aligned_cols=53  Identities=11%  Similarity=0.154  Sum_probs=36.8

Q ss_pred             CCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCC--CCCCHHHHHHHHHHHHHH
Q ss_conf             11221011058889898839837188874498888618--898864499999999980
Q gi|254780237|r  258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM--ANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       258 ~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~i--kNfG~KSl~EI~~~L~~~  313 (340)
                      .=++++.|+ +-..++.++|+.+...|+..+++||..+  .++|.+  .-|...+..+
T Consensus        20 ~WL~~igL~-~Y~~~F~~~g~i~~~~L~~L~~~dL~~lGI~~~ghR--~rIl~ai~~L   74 (85)
T 1ow5_A           20 LFLEEIGCT-QYLDSFIQCNLVTEEEIKYLDKDILIALGVNKIGDR--LKILRKSKSF   74 (85)
T ss_dssp             HHHHHHSCT-HHHHHHHHHTCCCHHHHHHCCHHHHHHHTCCCHHHH--HHHHHHHHHT
T ss_pred             HHHHHCCCH-HHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHH--HHHHHHHHHH
T ss_conf             999998449-999999984887399967389999978599988999--9999999999


No 68 
>3cqj_A L-ribulose-5-phosphate 3-epimerase ULAE; TIM-barrel, isomerase, phosphate-binding motif, structural genomics; 2.04A {Escherichia coli} PDB: 3cqi_A 3cqh_A 3cqk_A
Probab=26.69  E-value=11  Score=16.92  Aligned_cols=49  Identities=12%  Similarity=0.259  Sum_probs=29.1

Q ss_pred             CEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             3021243111144223577641168877621899999938961777999999999999888
Q gi|254780237|r  169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG  229 (340)
Q Consensus       169 g~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~  229 (340)
                      |.|+.+..|.-++..+|..            -+++|+|+.+.-.|.+++..|...|.+.+.
T Consensus       239 G~id~~~~~~~L~~~gy~G------------~~~~E~~~~~~~~~~~~~~~~~~~l~~~l~  287 (295)
T 3cqj_A          239 GVVDFERCFETLKQSGYCG------------PYLIEMWSETAEDPAAEVAKARDWVKARMA  287 (295)
T ss_dssp             SSCCHHHHHHHHHHTTCCS------------CEEECCCGGGSSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHCCCE------------EEEEEECCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             4619999999999969971------------799972687677999999999999999999


No 69 
>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} PDB: 3knt_A*
Probab=25.51  E-value=30  Score=14.01  Aligned_cols=41  Identities=12%  Similarity=0.130  Sum_probs=28.8

Q ss_pred             HHHHHHHHHCCCCCHHHHH-------HCCHHHHHCCCCCCHHHHHHHH
Q ss_conf             5888989883983718887-------4498888618898864499999
Q gi|254780237|r  267 VRSTNCLRGENIVYMGDLI-------QRTEADMLRMANFGRKSLVEIK  307 (340)
Q Consensus       267 vRs~NcLk~a~I~tigdLv-------~~s~~dLl~ikNfG~KSl~EI~  307 (340)
                      .||.+....+.+....++.       ..++++|+++|+.|+|+.+-+-
T Consensus        95 ~KAk~I~~~a~~~~~~~l~~~~~~~~~~~~~~L~~l~GIG~ktA~~~L  142 (214)
T 3fhf_A           95 KRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYKEASHFL  142 (214)
T ss_dssp             HHHHHHHHHGGGCCHHHHHHHSSSHHHHHHHHHHHSTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCHHHHHHHH
T ss_conf             999999999999999888897399898739999748887699999999


No 70 
>2kg5_A ARF-GAP, RHO-GAP domain, ANK repeat and PH domain-containing protein 3; SAM domain, helix bundle, cell membrane, cell projection, cytoplasm; NMR {Homo sapiens}
Probab=24.10  E-value=31  Score=13.84  Aligned_cols=49  Identities=12%  Similarity=0.178  Sum_probs=33.6

Q ss_pred             HHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             22101105888989883983718887449888861889886449999999998
Q gi|254780237|r  260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT  312 (340)
Q Consensus       260 IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~  312 (340)
                      ++.++|+--+ ..+.+.+|.++.+|...+++||.+   +|-++.-..+..|..
T Consensus        33 L~~igL~~Y~-~~F~~~gi~~~~~l~~lt~~DL~~---lGI~~~ghrkkil~a   81 (100)
T 2kg5_A           33 LATVHLEQYA-DTFRRHGLATAGAARGLGHEELKQ---LGISATGHRKRILRL   81 (100)
T ss_dssp             HGGGTCGGGH-HHHHHTTCCBHHHHTTCCHHHHHH---HTCCCHHHHHHHHHH
T ss_pred             HHHCCCHHHH-HHHHHCCCCCHHHHHHCCHHHHHH---CCCCCHHHHHHHHHH
T ss_conf             9988429999-999996998399997777978998---599988999999999


No 71 
>1npy_A Hypothetical shikimate 5-dehydrogenase-like protein HI0607; structural genomics, PSI, protein structure initiative; 1.75A {Haemophilus influenzae} SCOP: c.2.1.7 c.58.1.5
Probab=23.59  E-value=6.4  Score=18.30  Aligned_cols=15  Identities=33%  Similarity=0.363  Sum_probs=9.2

Q ss_pred             CCHHHHHHHHHHHHH
Q ss_conf             756678889999987
Q gi|254780237|r   37 RGFAHTLGNALRRVL   51 (340)
Q Consensus        37 ~G~g~TlGNaLRRvL   51 (340)
                      ..++-|+=|+.=+-|
T Consensus        17 ~s~sp~iHn~~f~~l   31 (271)
T 1npy_A           17 SNFGTTFHNYLYDKL   31 (271)
T ss_dssp             CSHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHC
T ss_conf             656999999999987


No 72 
>1dxs_A P53-like transcription factor; P73 SAM-like domain, gene regulation, P53 P63 homologue, sterIle alpha motif, tumour supressor; 2.54A {Homo sapiens} SCOP: a.60.1.2 PDB: 1cok_A
Probab=22.62  E-value=33  Score=13.66  Aligned_cols=50  Identities=12%  Similarity=0.043  Sum_probs=34.1

Q ss_pred             HHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHC--CCCCCHHHHHHHHHHHHHH
Q ss_conf             22101105888989883983718887449888861--8898864499999999980
Q gi|254780237|r  260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR--MANFGRKSLVEIKGVLGTM  313 (340)
Q Consensus       260 IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~--ikNfG~KSl~EI~~~L~~~  313 (340)
                      ++.|.|+ .=..++..+|+.++.+|...+++||..  |+ .|-  -.-|-..+..+
T Consensus        13 L~~igL~-qY~~~F~~~g~~~~~~l~~lt~~dL~~lgI~-~gH--r~kIl~~i~~l   64 (80)
T 1dxs_A           13 LTGLGCP-NCIEYFTSQGLQSIYHLQNLTIEDLGALKIP-EQY--RMTIWRGLQDL   64 (80)
T ss_dssp             HHHTTCT-TSHHHHHTTTCCCHHHHHTCCHHHHHHTTCC-TTT--HHHHHHHHHHC
T ss_pred             HHHCCHH-HHHHHHHHCCCCCHHHHHCCCHHHHHHCCCC-HHH--HHHHHHHHHHH
T ss_conf             9888739-9999999848865688870599999771999-999--99999999999


No 73 
>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans}
Probab=22.59  E-value=34  Score=13.66  Aligned_cols=48  Identities=10%  Similarity=0.151  Sum_probs=34.8

Q ss_pred             CHHHCCCCHHHHHHHHH------CCCCCHHHHHHCCHHH----HHCCCCCCHHHHHHH
Q ss_conf             12210110588898988------3983718887449888----861889886449999
Q gi|254780237|r  259 KVEELELSVRSTNCLRG------ENIVYMGDLIQRTEAD----MLRMANFGRKSLVEI  306 (340)
Q Consensus       259 ~IeeLeLSvRs~NcLk~------a~I~tigdLv~~s~~d----Ll~ikNfG~KSl~EI  306 (340)
                      .+-++.||-|...+++.      .|...+..+...+.++    |+++|++|.++.+-+
T Consensus        97 ~Lr~~Gls~~K~~~i~~la~~~~~g~~~~~~l~~~~~~e~~~~L~~ikGIGpWTA~~i  154 (233)
T 2h56_A           97 ALRQAGVSKRKIEYIRHVCEHVESGRLDFTELEGAEATTVIEKLTAIKGIGQWTAEMF  154 (233)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHHHHTTSSCHHHHTTSCHHHHHHHHHTSTTCCHHHHHHH
T ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHH
T ss_conf             9977799787899999999999817752001012688899999880688487899999


No 74 
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1
Probab=21.60  E-value=35  Score=13.53  Aligned_cols=53  Identities=13%  Similarity=0.219  Sum_probs=32.6

Q ss_pred             HHCCHHHCCCC-HHHHHHHHHCCCC--CHHHHHHCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf             31112210110-5888989883983--71888744988886188988644999999
Q gi|254780237|r  256 LLKKVEELELS-VRSTNCLRGENIV--YMGDLIQRTEADMLRMANFGRKSLVEIKG  308 (340)
Q Consensus       256 L~~~IeeLeLS-vRs~NcLk~a~I~--tigdLv~~s~~dLl~ikNfG~KSl~EI~~  308 (340)
                      +..-|.-+++. .|+.+-...+.+-  .-+.-+..+.++|+++|+.|+|+..-|--
T Consensus        72 l~~~i~~~G~y~~Ka~~l~~~a~~i~~~~~g~~p~~~~~L~~LpGVG~kTA~~il~  127 (211)
T 2abk_A           72 VKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLN  127 (211)
T ss_dssp             HHHHHTTSTTHHHHHHHHHHHHHHHHHHTTTSCCSCHHHHHHSTTCCHHHHHHHHH
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCHHHHHHHHH
T ss_conf             99999862179999999999999999984899983299987178873699999999


No 75 
>1ucv_A Ephrin type-A receptor 8; receptor oligomerization, developmental regulation, tyrosine kinase, riken structural genomics/proteomics initiative; NMR {Homo sapiens} SCOP: a.60.1.2
Probab=21.38  E-value=35  Score=13.50  Aligned_cols=35  Identities=9%  Similarity=0.286  Sum_probs=27.9

Q ss_pred             HHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCC
Q ss_conf             221011058889898839837188874498888618
Q gi|254780237|r  260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM  295 (340)
Q Consensus       260 IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~i  295 (340)
                      ++.|.|+ +-..++.+.+|.+...|...+++||..+
T Consensus        14 L~~igL~-qY~~~F~~~g~~~~~~l~~lt~~dL~~l   48 (81)
T 1ucv_A           14 LDSIRMG-RYRDHFAAGGYSSLGMVLRMNAQDVRAL   48 (81)
T ss_dssp             HHHTTCG-GGHHHHHHTTCCBHHHHTTCCHHHHHHH
T ss_pred             HHHCCCH-HHHHHHHHCCCCCHHHHHHCCHHHHHHC
T ss_conf             9888689-9999999969998999976789999886


No 76 
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*
Probab=21.37  E-value=35  Score=13.50  Aligned_cols=47  Identities=6%  Similarity=0.191  Sum_probs=37.9

Q ss_pred             CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             1105888989883983718887449888861889886449999999998
Q gi|254780237|r  264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT  312 (340)
Q Consensus       264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~  312 (340)
                      +.+...+-.|-+ .+.++.+|...|.+||..+.+ |.+....|.+.|..
T Consensus        25 GIg~k~~~~Ll~-~f~sl~~i~~AS~eeL~~v~G-~~~~Ak~i~~~lh~   71 (84)
T 1z00_B           25 GVNAKNCRSLMH-HVKNIAELAALSQDELTSILG-NAANAKQLYDFIHT   71 (84)
T ss_dssp             SCCHHHHHHHHH-HSSCHHHHHHSCHHHHHHHHS-CHHHHHHHHHHHTS
T ss_pred             CCCHHHHHHHHH-HCCCHHHHHHCCHHHHHHCCC-CHHHHHHHHHHHCC
T ss_conf             999999999999-966999998599999988759-79999999999855


No 77 
>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A*
Probab=21.25  E-value=33  Score=13.73  Aligned_cols=52  Identities=13%  Similarity=0.245  Sum_probs=34.9

Q ss_pred             HHCCHHHCCCC-HHHHHHHHHCCC--CCHHHHHHCCHHHHHCCCCCCHHHHHHHH
Q ss_conf             31112210110-588898988398--37188874498888618898864499999
Q gi|254780237|r  256 LLKKVEELELS-VRSTNCLRGENI--VYMGDLIQRTEADMLRMANFGRKSLVEIK  307 (340)
Q Consensus       256 L~~~IeeLeLS-vRs~NcLk~a~I--~tigdLv~~s~~dLl~ikNfG~KSl~EI~  307 (340)
                      +...|..+.+. .|+.|-.+.+.+  ..-+.-+..+.++|+++|+.|.|+..-|-
T Consensus        76 l~~~i~~~g~y~~ka~~i~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~kTA~~il  130 (226)
T 1orn_A           76 LEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVV  130 (226)
T ss_dssp             HHHHTGGGSSHHHHHHHHHHHHHHHHHHSTTSCCSCHHHHTTSTTCCHHHHHHHH
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCHHHHHHHH
T ss_conf             9898874221999999999999999999299798789999748775367999999


No 78 
>2hfs_A Mevalonate kinase, putative; GHMP kinase, trypanosomatid parasite, transferase; 1.75A {Leishmania major} PDB: 2hfu_A*
Probab=21.00  E-value=36  Score=13.45  Aligned_cols=114  Identities=16%  Similarity=0.216  Sum_probs=66.7

Q ss_pred             EEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCC
Q ss_conf             89999993896177799999999999988876224444322100000000011233311122101105888989883983
Q gi|254780237|r  200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIV  279 (340)
Q Consensus       200 kL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~  279 (340)
                      .-++=+||+.+.+-.+.+..-..........+..                      +...+.  +++.++..+|+...+.
T Consensus       188 ~~l~l~~tg~~~~T~~~~~~~~~~~~~~~~~~~~----------------------~~~~i~--~i~~~~~~al~~~~~~  243 (332)
T 2hfs_A          188 LYLVVVGTGINASTAKVVNDVHKMKQQQPVQFKR----------------------LYDNYT--HIVSQAREALQKGDLQ  243 (332)
T ss_dssp             EEEEEEECSCCCCHHHHHHHHHHHHHHCHHHHHH----------------------HHHHHH--HHHHHHHHHHHHTCHH
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHCHHHHHH----------------------HHHHHH--HHHHHHHHHHHHHHHH
T ss_conf             4799981897622499997644555534277776----------------------666789--9999999877500045


Q ss_pred             CHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCC--C---------CHHHHHHHHHHHHCC
Q ss_conf             71888744988886188988644999999999808312676878--9---------867799999877503
Q gi|254780237|r  280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD--W---------PPESIEELAKKYEDK  339 (340)
Q Consensus       280 tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~--~---------~~~~~~~~~~~~~~~  339 (340)
                      .+++|+..+.+-|.++ +..-..++++.+...+.|- +|.++.+  |         .++..+.+.+.++++
T Consensus       244 ~lg~lm~~~~~~l~~l-~vs~p~l~~l~~~a~~~Ga-lgaklsGaG~Gg~~ial~~~~~~~~~i~~~l~~~  312 (332)
T 2hfs_A          244 RLGQLMNANHDLCRQI-DVSCRELESIVQTCRTYGA-LGAKLSGTGRGGIAVALAASSDQRDAIVKGLKAK  312 (332)
T ss_dssp             HHHHHHHHHHHHHHHT-TCCCHHHHHHHHHHHHTTC-SEEEEESSCSSSEEEEEESSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHCCC-CEEEECCCCCCCEEEEEECCHHHHHHHHHHHHHH
T ss_conf             6789999999999853-8998899999999997899-4899927898664999987878899999999998


No 79 
>2rhf_A DNA helicase RECQ; HRDC, D. radiodurans, ATP-binding, hydrolase, nucleotide-binding; HET: DNA; 1.10A {Deinococcus radiodurans R1}
Probab=20.99  E-value=21  Score=14.92  Aligned_cols=37  Identities=14%  Similarity=0.214  Sum_probs=26.6

Q ss_pred             HHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHH
Q ss_conf             8898988398371888744988886188988644999
Q gi|254780237|r  269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE  305 (340)
Q Consensus       269 s~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~E  305 (340)
                      .|..+.+.-+.-+....-.|.++|+.|+++|.+-++.
T Consensus        26 ~~~I~~d~~L~~ia~~~P~t~~eL~~I~Gig~~k~~~   62 (77)
T 2rhf_A           26 AFVVFTNATLEALAARQPRTLAELAEVPGLGEKRIEA   62 (77)
T ss_dssp             HHHHCCHHHHHHHHHHCCCSHHHHTTSTTTCHHHHHH
T ss_pred             CEEEECHHHHHHHHHHCCCCHHHHHCCCCCCHHHHHH
T ss_conf             6565789999999983978999980799979999999


No 80 
>1pie_A Galactokinase; galactose, galactosemia, transferase; HET: GLA; 2.10A {Lactococcus lactis} SCOP: d.14.1.5 d.58.26.7
Probab=20.36  E-value=37  Score=13.36  Aligned_cols=61  Identities=13%  Similarity=0.134  Sum_probs=46.5

Q ss_pred             HHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             2101105888989883983718887449888861889886449999999998083126768
Q gi|254780237|r  261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL  321 (340)
Q Consensus       261 eeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l  321 (340)
                      .+-....+...+|++.++..+|+|+..+...|...-+..-..|+++.+.....+=.+|-++
T Consensus       305 ~e~~rv~~~~~al~~~d~~~lG~Lm~esh~sL~~~~~vS~peLd~lv~~a~~~~Ga~GaKl  365 (419)
T 1pie_A          305 YENNRTKIAQKAFVAGNLTKFGELLNASHASLKDDYEVTGLELDTLAETAQKQAGVLGARM  365 (419)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTSCCCCHHHHHHHHHHHHSTTEEEEEE
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEE
T ss_conf             6889999999875327788899999999999999757997999999999998489579897


No 81 
>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7
Probab=20.28  E-value=37  Score=13.35  Aligned_cols=54  Identities=19%  Similarity=0.166  Sum_probs=39.0

Q ss_pred             HHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC----CCCCCCCHHHHHHHHHHH
Q ss_conf             887449888861889886449999999998083126----768789867799999877
Q gi|254780237|r  283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG----MNLPDWPPESIEELAKKY  336 (340)
Q Consensus       283 dLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg----~~l~~~~~~~~~~~~~~~  336 (340)
                      +|=.-+.++|+.++++|.+-...|.+.-...|-.-.    ++++++.+..++.+.+.+
T Consensus        33 ~iNtAs~~eL~~lpgIg~~~A~~Iv~~R~~~G~f~sledL~~v~Gi~~k~~eki~k~~   90 (98)
T 2edu_A           33 LLNEGSARDLRSLQRIGPKKAQLIVGWRELHGPFSQVEDLERVEGITGKQMESFLKAN   90 (98)
T ss_dssp             HHHHSCHHHHHHSTTCCHHHHHHHHHHHHHHCCCSSGGGGGGSTTCCHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHCC
T ss_conf             0437899999647998999999999999985992889998448998999999999838


No 82 
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus}
Probab=20.23  E-value=37  Score=13.35  Aligned_cols=11  Identities=9%  Similarity=0.156  Sum_probs=4.0

Q ss_pred             CHHHHHHHHHH
Q ss_conf             56678889999
Q gi|254780237|r   38 GFAHTLGNALR   48 (340)
Q Consensus        38 G~g~TlGNaLR   48 (340)
                      |.|-.+..-+.
T Consensus        68 gIG~~i~~kI~   78 (360)
T 2ihm_A           68 YFGEHSTRVIQ   78 (360)
T ss_dssp             TCCHHHHHHHH
T ss_pred             CCCHHHHHHHH
T ss_conf             98789999999


Done!