Query         537021.9.peg.817_1
Match_columns 148
No_of_seqs    127 out of 965
Neff          6.6 
Searched_HMMs 33803
Date          Wed May 25 01:25:21 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_817.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >3c1y_A DNA integrity scanning  97.7 7.2E-05 2.1E-09   51.8   5.5   50   51-101    17-66  (74)
  2 >1kft_A UVRC, excinuclease ABC  97.6 5.9E-05 1.7E-09   52.4   4.1   40   59-98     36-75  (78)
  3 >1z00_A DNA excision repair pr  97.6 0.00011 3.3E-09   50.6   5.5   50   49-99     22-71  (89)
  4 >1pzn_A RAD51, DNA repair and   97.2 0.00055 1.6E-08   46.1   4.7   50   49-99     38-88  (95)
  5 >2nrt_A Uvrabc system protein   96.7 0.00075 2.2E-08   45.3   2.1   41   50-91     16-56  (64)
  6 >3c65_A Uvrabc system protein   96.3 0.00073 2.2E-08   45.3   0.0   49   49-99    176-224 (226)
  7 >1ixr_A Holliday junction DNA   96.0    0.01 3.1E-07   37.9   4.6   97   38-140    66-166 (191)
  8 >2a1j_A DNA repair endonucleas  95.8   0.013 3.9E-07   37.2   4.5   48   50-99      8-55  (63)
  9 >1z00_B DNA repair endonucleas  95.6  0.0074 2.2E-07   38.9   2.5   40   50-90     22-61  (71)
 10 >1pu6_A 3-methyladenine DNA gl  95.0   0.046 1.4E-06   33.7   5.0   63   35-97     51-117 (123)
 11 >1m3q_A 8-oxoguanine DNA glyco  94.3   0.083 2.5E-06   32.1   4.9   58   40-97     62-126 (133)
 12 >1kg2_A A/G-specific adenine g  94.1   0.084 2.5E-06   32.0   4.7   59   40-98      9-69  (86)
 13 >1wcn_A Transcription elongati  93.7    0.16 4.7E-06   30.2   5.5   41   58-98     18-59  (70)
 14 >2ztd_A Holliday junction ATP-  92.3    0.25 7.3E-06   29.0   4.8   40   58-97     20-62  (75)
 15 >1cuk_A RUVA protein; DNA repa  91.9    0.29 8.7E-06   28.5   4.8   46   58-105    19-67  (79)
 16 >1x2i_A HEF helicase/nuclease;  91.3    0.13 3.9E-06   30.8   2.5   32   50-82     18-49  (49)
 17 >1kea_A Possible G-T mismatche  91.2    0.68   2E-05   26.2   6.0   64   41-104    10-76  (111)
 18 >3fhf_A Mjogg, N-glycosylase/D  91.0   0.013   4E-07   37.2  -2.8   69   26-97     29-106 (113)
 19 >2bgw_A XPF endonuclease; hydr  90.7    0.18 5.2E-06   30.0   2.6   31   51-82     19-49  (49)
 20 >1orn_A Endonuclease III; DNA   90.6    0.26 7.7E-06   28.9   3.5   60   42-101    10-72  (110)
 21 >1szp_A DNA repair protein RAD  90.6     0.3 8.9E-06   28.4   3.7   30   69-98      2-31  (56)
 22 >3fsp_A A/G-specific adenine g  90.0     1.5 4.5E-05   23.9   7.2   65   41-105     9-76  (110)
 23 >1lb2_B DNA-directed RNA polym  89.9    0.85 2.5E-05   25.5   5.6   41   60-100    21-63  (84)
 24 >1z3e_B DNA-directed RNA polym  89.9    0.83 2.5E-05   25.6   5.5   42   59-100    19-62  (73)
 25 >3gfk_B DNA-directed RNA polym  89.8    0.57 1.7E-05   26.6   4.7   42   59-100    26-69  (79)
 26 >1orn_A Endonuclease III; DNA   89.7    0.87 2.6E-05   25.5   5.5   60   35-97     42-104 (110)
 27 >1ngn_A Methyl-CPG binding pro  89.2     1.1 3.4E-05   24.7   5.8   63   40-102    33-98  (129)
 28 >1coo_A RNA polymerase alpha s  88.6    0.81 2.4E-05   25.7   4.7   41   60-100    35-77  (98)
 29 >3bzc_A TEX; helix-turn-helix,  87.0    0.71 2.1E-05   26.0   3.7   32   73-104     4-35  (70)
 30 >2edu_A Kinesin-like protein K  86.2    0.96 2.8E-05   25.2   4.0   33   70-102    31-63  (98)
 31 >2a1j_B DNA excision repair pr  85.5    0.63 1.9E-05   26.4   2.7   31   52-82     37-67  (67)
 32 >2duy_A Competence protein com  85.0    0.74 2.2E-05   25.9   2.9   32   70-101    18-49  (75)
 33 >1kea_A Possible G-T mismatche  85.0    0.54 1.6E-05   26.8   2.2   61   34-97     42-105 (111)
 34 >3bz1_U Photosystem II 12 kDa   84.9    0.52 1.5E-05   26.9   2.1   34   67-100    21-54  (104)
 35 >1dgs_A DNA ligase; AMP comple  84.4     0.8 2.4E-05   25.7   2.9   37   45-82     80-116 (116)
 36 >2abk_A Endonuclease III; DNA-  80.3       2   6E-05   23.1   3.7   54   40-96     48-104 (111)
 37 >1s5l_U Photosystem II 12 kDa   80.3    0.57 1.7E-05   26.7   0.8   30   69-98      6-35  (87)
 38 >1b22_A DNA repair protein RAD  78.3     1.8 5.3E-05   23.4   2.9   39   59-97     37-76  (114)
 39 >2h56_A DNA-3-methyladenine gl  77.8     3.7 0.00011   21.4   4.4   62   41-102     5-69  (77)
 40 >1u9l_A Transcription elongati  76.4     5.9 0.00017   20.1   5.2   40   58-97     17-57  (70)
 41 >2a1j_A DNA repair endonucleas  76.1    0.99 2.9E-05   25.1   1.0   52   77-128     2-57  (63)
 42 >1d8b_A SGS1 RECQ helicase; fi  75.2     5.6 0.00017   20.2   4.7   41   70-110    39-79  (81)
 43 >2w9m_A Polymerase X; SAXS, DN  74.3     3.5  0.0001   21.6   3.5   48   53-102    33-80  (118)
 44 >2kp7_A Crossover junction end  73.9     6.8  0.0002   19.7   6.1   57   41-102    24-81  (87)
 45 >3i0w_A 8-oxoguanine-DNA-glyco  71.9     7.6 0.00022   19.4   6.0   33   65-97     15-51  (58)
 46 >2csb_A Topoisomerase V, TOP61  70.2     8.2 0.00024   19.2   5.1   39   57-96      7-45  (48)
 47 >2jhn_A ALKA, 3-methyladenine   65.5     8.3 0.00024   19.2   3.8   43   57-100    73-129 (134)
 48 >2ihm_A POL MU, DNA polymerase  65.2     4.9 0.00014   20.6   2.6   25   77-101    59-83  (129)
 49 >2h56_A DNA-3-methyladenine gl  64.1     5.8 0.00017   20.2   2.8   21   77-97     59-79  (156)
 50 >2fmp_A DNA polymerase beta; n  62.3     5.4 0.00016   20.4   2.4   42   56-102    38-80  (119)
 51 >2jhn_A ALKA, 3-methyladenine   59.8     7.7 0.00023   19.4   2.8   38   58-96     10-48  (55)
 52 >1mpg_A ALKA, 3-methyladenine   59.0      13 0.00039   17.8   6.1   47   50-96     72-120 (127)
 53 >2a6h_A DNA-directed RNA polym  57.9     2.4 7.2E-05   22.6   0.0   41   60-100   140-182 (190)
 54 >1kg2_A A/G-specific adenine g  57.1     7.7 0.00023   19.4   2.4   25   75-99     19-43  (139)
 55 >1vdd_A Recombination protein   55.1     9.4 0.00028   18.8   2.6   19   78-96     11-29  (66)
 56 >2bcq_A DNA polymerase lambda;  52.9      16 0.00047   17.4   3.5   50   48-102    29-80  (128)
 57 >1exn_A 5'-exonuclease, 5'-nuc  51.9     3.3 9.7E-05   21.8  -0.2   37   70-106    13-49  (80)
 58 >1jms_A Terminal deoxynucleoti  51.9      11 0.00034   18.3   2.6   41   57-102    62-103 (154)
 59 >1a76_A Flap endonuclease-1 pr  51.0     8.6 0.00025   19.1   1.9   22   81-102    18-39  (65)
 60 >1rxw_A Flap structure-specifi  48.6     9.9 0.00029   18.7   1.9   24   82-105    18-41  (68)
 61 >1r4t_A Exoenzyme S; EXOS, GAP  47.3      20  0.0006   16.6   4.9   72   47-126    63-151 (153)
 62 >3i1m_M 30S ribosomal protein   46.1      12 0.00037   18.0   2.1   23   79-101    17-39  (63)
 63 >2zkq_m 40S ribosomal protein   45.1      10 0.00031   18.5   1.5   24   79-102    28-51  (88)
 64 >2izo_A FEN1, flap structure-s  44.3      13 0.00039   17.8   2.0   19   81-99     18-36  (82)
 65 >3e1s_A Exodeoxyribonuclease V  42.1     7.1 0.00021   19.6   0.3   87   41-131     9-108 (149)
 66 >2i5h_A Hypothetical protein A  40.5      15 0.00046   17.4   1.8   59   72-130   125-185 (205)
 67 >1b43_A Protein (FEN-1); nucle  39.8      17 0.00049   17.2   1.9   18   58-75     37-54  (77)
 68 >2owo_A DNA ligase; protein/DN  39.7      27 0.00079   15.9   6.6   58   46-104     9-66  (168)
 69 >2e1f_A Werner syndrome ATP-de  39.6      27 0.00079   15.9   5.4   49   71-119    49-97  (103)
 70 >2vqe_M 30S ribosomal protein   39.1      14 0.00041   17.7   1.4   24   79-102    17-40  (64)
 71 >2dgz_A Werner syndrome protei  39.1      21 0.00063   16.5   2.4   46   70-115    55-100 (113)
 72 >2r4f_A 3-hydroxy-3-methylglut  37.3      21 0.00063   16.5   2.1   29   27-55     15-46  (85)
 73 >2zbk_B Type 2 DNA topoisomera  36.4      21 0.00063   16.5   2.0   23   79-101    29-51  (82)
 74 >3bq0_A POL IV, DBH, DNA polym  35.1      21 0.00063   16.5   1.8   34   62-97      9-44  (51)
 75 >1jei_A Emerin; membrane prote  35.0      13 0.00039   17.9   0.7   33   34-66      3-35  (53)
 76 >2dla_A 397AA long hypothetica  33.4      14 0.00041   17.7   0.7   18   59-76     11-28  (134)
 77 >2ziu_A MUS81 protein; helix-h  32.1      33 0.00098   15.3   2.4   20   79-98      8-27  (82)
 78 >2rhf_A DNA helicase RECQ; HRD  29.7      38  0.0011   14.9   4.7   35   71-105    39-74  (77)
 79 >2w9m_A Polymerase X; SAXS, DN  26.2      44  0.0013   14.5   2.3   56   77-137    11-66  (123)
 80 >5csm_A Chorismate mutase; cho  25.9      30  0.0009   15.5   1.3   37   85-121   138-175 (256)
 81 >1t6c_A Exopolyphosphatase; al  25.5      34   0.001   15.2   1.5   94   23-116    35-159 (162)
 82 >3bqs_A Uncharacterized protei  24.8      23 0.00069   16.3   0.6   21   77-97      2-22  (93)
 83 >2ziu_B Crossover junction end  23.5      50  0.0015   14.1   2.5   19   57-75     24-42  (100)
 84 >3cer_A Possible exopolyphosph  23.0      28 0.00084   15.7   0.7   44   70-113   126-169 (185)
 85 >2p6r_A Afuhel308 helicase; pr  22.8      50  0.0015   14.1   2.0   35   59-96     10-45  (68)
 86 >1ul1_X Flap endonuclease-1; p  22.0      53  0.0016   13.9   2.3   26   82-107    32-57  (89)
 87 >1wud_A ATP-dependent DNA heli  20.7      56  0.0017   13.8   4.3   37   70-106    46-83  (89)

No 1  
>>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* (A:304-377)
Probab=97.70  E-value=7.2e-05  Score=51.84  Aligned_cols=50  Identities=22%  Similarity=0.297  Sum_probs=41.9

Q ss_pred             CCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             998988999999997379978985099789973789889999997549999
Q 537021.9.peg.8   51 IPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVA  101 (148)
Q Consensus        51 ~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~El  101 (148)
                      .|+.. ...|+.|+.+|||+..+.+||+++|.+++|||+.+|..|...+.-
T Consensus        17 I~giG-~~~a~~L~~~fgsl~~i~~as~~~L~~v~GiG~~~A~~i~~~~~~   66 (74)
T 3c1y_A           17 VARIP-LSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISS   66 (74)
T ss_dssp             TSCCC-HHHHHHHHHHHCSHHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHH
T ss_pred             CCCCC-HHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             99998-999999999853899998579988854478469999999999999


No 2  
>>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} (A:)
Probab=97.62  E-value=5.9e-05  Score=52.40  Aligned_cols=40  Identities=20%  Similarity=0.246  Sum_probs=37.0

Q ss_pred             HHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             9999997379978985099789973789889999997549
Q 537021.9.peg.8   59 IAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLV   98 (148)
Q Consensus        59 lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~   98 (148)
                      .|+.|+++|||+.++.+|+.+||.+|+|||+.+|..|.-.
T Consensus        36 ~a~~L~~~Fgs~~~i~~As~eeL~~v~gIG~~~A~~I~~~   75 (78)
T 1kft_A           36 RRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWS   75 (78)
T ss_dssp             HHHHHHHHHSCHHHHHHCCHHHHTTSSSTTSHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
T ss_conf             9999999909989998578999973899899999999999


No 3  
>>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (A:)
Probab=97.61  E-value=0.00011  Score=50.63  Aligned_cols=50  Identities=20%  Similarity=0.181  Sum_probs=42.1

Q ss_pred             CCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             379989889999999973799789850997899737898899999975499
Q 537021.9.peg.8   49 RLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVS   99 (148)
Q Consensus        49 ~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~   99 (148)
                      +|.|+..- ..|+.|+.+|||+..+.+|++++|.+++|||+.+|..|.-.+
T Consensus        22 ~~I~gIG~-~~a~~L~~~F~s~~~i~~A~~~~L~~v~GiG~~~A~~i~~~~   71 (89)
T 1z00_A           22 TTVKSVNK-TDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVL   71 (89)
T ss_dssp             TTSSSCCH-HHHHHHHHHTCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             CCCCCCCH-HHHHHHHHHHCCCHHHHHHHHHHHCHHCCCCHHHHHHHHHHH
T ss_conf             58997699-999999999099478766547510000332799999999998


No 4  
>>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} (A:1-95)
Probab=97.18  E-value=0.00055  Score=46.14  Aligned_cols=50  Identities=22%  Similarity=0.249  Sum_probs=41.2

Q ss_pred             CCCCCCCHHHHHHHHHHH-CCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             379989889999999973-799789850997899737898899999975499
Q 537021.9.peg.8   49 RLIPRKDTKSIAKALLKR-FATLGGVFGAPLHLLQEINRIGKRVALELKLVS   99 (148)
Q Consensus        49 ~g~~~~~~~~lA~~lL~~-fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~   99 (148)
                      .+.|+.. ...|+.|+.+ |+++..+.+|++++|.+|+|||+.+|..|...+
T Consensus        38 l~I~gIG-~~~a~~L~~~~~~s~e~i~~As~e~L~~i~Gig~~~A~~I~~~~   88 (95)
T 1pzn_A           38 EDLPGVG-PATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAA   88 (95)
T ss_dssp             SCCTTCC-HHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             HHCCCCC-HHHHHHHHHCCCCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             4379979-99999999859971999982899999975498999999999999


No 5  
>>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A (A:157-220)
Probab=96.71  E-value=0.00075  Score=45.26  Aligned_cols=41  Identities=17%  Similarity=0.223  Sum_probs=34.4

Q ss_pred             CCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHH
Q ss_conf             799898899999999737997898509978997378988999
Q 537021.9.peg.8   50 LIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRV   91 (148)
Q Consensus        50 g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~ak   91 (148)
                      |.|+-.. ..|+.|+++|||+..+.+||.+||++|+|||+..
T Consensus        16 ~I~gIG~-~~a~~L~~~F~s~~~i~~As~eeL~~v~gig~~A   56 (64)
T 2nrt_A           16 NVPGIGP-IRKKKLIEHFGSLENIRSASLEEIARVIGSTEIA   56 (64)
T ss_dssp             TSTTCCH-HHHHHHHHHHCSHHHHHTSCHHHHHHHHTCHHHH
T ss_pred             CCCCCCH-HHHHHHHHHCCCHHHHHCCCHHHHHHCCCCHHHH
T ss_conf             0531079-9999999986899999709999998687929999


No 6  
>>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} (A:)
Probab=96.31  E-value=0.00073  Score=45.33  Aligned_cols=49  Identities=27%  Similarity=0.219  Sum_probs=39.3

Q ss_pred             CCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             379989889999999973799789850997899737898899999975499
Q 537021.9.peg.8   49 RLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVS   99 (148)
Q Consensus        49 ~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~   99 (148)
                      .+.|+- -...|+.|+++|||+..+.+||.+||++| |||+.+|..|...+
T Consensus       176 ~~I~~I-G~~~a~~Ll~~Fgsl~~i~~As~eeL~~v-giG~~~A~~I~~~f  224 (226)
T 3c65_A          176 DDIPGV-GEKRKKALLNYFGSVKKMKEATVEELQRA-NIPRAVAEKIYEKL  224 (226)
T ss_dssp             ---------------------------------------------------
T ss_pred             HHHHHH-CHHHHHHHHHHCCCHHHHHHCCHHHHHHC-CCCHHHHHHHHHHH
T ss_conf             899874-79999999998589999983999999877-99999999999996


No 7  
>>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} (A:)
Probab=95.98  E-value=0.01  Score=37.89  Aligned_cols=97  Identities=18%  Similarity=0.245  Sum_probs=55.9

Q ss_pred             CHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCC---HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             98999999973379989889999999973799---789850997899737898899999975499999999998764067
Q 537021.9.peg.8   38 AYYEILELILFRLIPRKDTKSIAKALLKRFAT---LGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKK  114 (148)
Q Consensus        38 sD~ELLallL~~g~~~~~~~~lA~~lL~~fGs---L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~  114 (148)
                      .+-|+-..++.  .++-- --.|..+|++|+.   ...+.++|+++|+++||||+..|-+|..  ||-..+.........
T Consensus        66 ~er~~F~~L~~--V~GIG-pk~Al~iL~~~~~~el~~aI~~~d~~~L~~ipGIG~KtA~rIi~--eLk~k~~~~~~~~~~  140 (191)
T 1ixr_A           66 ENLALFELLLS--VSGVG-PKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIAL--ELKGKVPPHLLAGEK  140 (191)
T ss_dssp             HHHHHHHHHHS--SSCCC-HHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHH--HHTTTSCSCC-----
T ss_pred             HHHHHHHHHHC--CCCCC-HHHHHHHHHCCCHHHHHHHHHCCCHHHHCCCCCCCHHHHHHHHH--HHHHHCCCCCCCCCC
T ss_conf             99999999857--58847-78899998559999999999828999851388845688999999--998642521001123


Q ss_pred             CCCCH-HHHHHHHHHHHCCCCEEEEEE
Q ss_conf             78898-999999999845978000252
Q 537021.9.peg.8  115 FLTPG-QPCLISVERHYPMKNANNFAY  140 (148)
Q Consensus       115 ~l~s~-~~v~~yl~~~l~~~~~E~F~v  140 (148)
                      ..+++ +++..-| ..||+.+.|.-.+
T Consensus       141 ~~~~~~~e~~~aL-~~LGy~~~ea~~a  166 (191)
T 1ixr_A          141 VESEAAEEAVMAL-AALGFKEAQARAV  166 (191)
T ss_dssp             ---------------------------
T ss_pred             CCCCCHHHHHHHH-HHCCCCHHHHHHH
T ss_conf             3555689999999-9869999999999


No 8  
>>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} (A:)
Probab=95.80  E-value=0.013  Score=37.20  Aligned_cols=48  Identities=13%  Similarity=0.108  Sum_probs=36.6

Q ss_pred             CCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             79989889999999973799789850997899737898899999975499
Q 537021.9.peg.8   50 LIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVS   99 (148)
Q Consensus        50 g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~   99 (148)
                      +.|+... ..|+.|+.+|||+.++.+||.+||.+|+| |+.+|-.|.-.+
T Consensus         8 ~IpgVG~-~~a~~Ll~~f~Si~~i~~As~eeL~~i~g-g~~~A~~i~~~l   55 (63)
T 2a1j_A            8 KMPGVNA-KNCRSLMHHVKNIAELAALSQDELTSILG-NAANAKQLYDFI   55 (63)
T ss_dssp             TSTTCCH-HHHHHHHHHCSSHHHHHTCCHHHHHHHHS-CHHHHHHHHHHH
T ss_pred             CCCCCCH-HHHHHHHHHHCCHHHHHHCCHHHHHHCCC-CHHHHHHHHHHH
T ss_conf             1999899-99999999807899998699999977859-689999999998


No 9  
>>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} (B:1-71)
Probab=95.58  E-value=0.0074  Score=38.87  Aligned_cols=40  Identities=13%  Similarity=0.204  Sum_probs=33.2

Q ss_pred             CCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHH
Q ss_conf             79989889999999973799789850997899737898899
Q 537021.9.peg.8   50 LIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKR   90 (148)
Q Consensus        50 g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~a   90 (148)
                      +.|+-..+. ++.|+.+|||+.++.+||.+||.+++|++..
T Consensus        22 ~ipGIg~k~-~~~Ll~~f~si~~i~~As~eeL~~v~G~~~~   61 (71)
T 1z00_B           22 KMPGVNAKN-CRSLMHHVKNIAELAALSQDELTSILGNAAN   61 (71)
T ss_dssp             TCSSCCHHH-HHHHHHHSSCHHHHHHSCHHHHHHHHSCHHH
T ss_pred             CCCCCCHHH-HHHHHHHCCCHHHHHHCCHHHHHHCCCCHHH
T ss_conf             089988999-9999999079999987899999887597899


No 10 
>>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} (A:23-145)
Probab=94.97  E-value=0.046  Score=33.69  Aligned_cols=63  Identities=16%  Similarity=0.148  Sum_probs=50.1

Q ss_pred             HHCCHHHHHHHHHHCCCC---CCCHHHHHHHHHHHCCCHHHHHC-CCHHHHHHCCCCCHHHHHHHHH
Q ss_conf             218989999999733799---89889999999973799789850-9978997378988999999754
Q 537021.9.peg.8   35 NALAYYEILELILFRLIP---RKDTKSIAKALLKRFATLGGVFG-APLHLLQEINRIGKRVALELKL   97 (148)
Q Consensus        35 ~~LsD~ELLallL~~g~~---~~~~~~lA~~lL~~fGsL~~ll~-as~~eL~~i~GIG~aka~~l~a   97 (148)
                      ..+++.||.+++=..|..   -+....+|+.+.+.++++.++-. ...++|++++|||+..|-.++.
T Consensus        51 ~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~~~~~~~~l~~~~~~~~~~~L~~l~GIG~~tA~~ill  117 (123)
T 1pu6_A           51 AYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILC  117 (123)
T ss_dssp             HHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHHHHSSHHHHHHHCCHHHHHTSTTCCHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             7799999999999879958999999999999998663103799467999998489966999999999


No 11 
>>1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG, 8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET: DRZ ANG; 1.90A {Homo sapiens} (A:123-255)
Probab=94.26  E-value=0.083  Score=32.06  Aligned_cols=58  Identities=19%  Similarity=0.047  Sum_probs=42.1

Q ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH---CCC----HHHHHHCCCCCHHHHHHHHH
Q ss_conf             99999997337998988999999997379978985---099----78997378988999999754
Q 537021.9.peg.8   40 YEILELILFRLIPRKDTKSIAKALLKRFATLGGVF---GAP----LHLLQEINRIGKRVALELKL   97 (148)
Q Consensus        40 ~ELLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll---~as----~~eL~~i~GIG~aka~~l~a   97 (148)
                      .+.+.-.-.++.+-+....+|+.+.++||+.-.+-   +.+    .++|++++|||+..|-.+..
T Consensus        62 ~~~l~~~g~~~~ka~~i~~~a~~~~~~~~g~~~~~~~~~~~~~~~~~~L~~lpGIG~~tA~~ill  126 (133)
T 1m3q_A           62 VEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICL  126 (133)
T ss_dssp             HHHHHHHTTCTTHHHHHHHHHHHHHHTSCSHHHHHHTTTSCHHHHHHHHTTSTTCCHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             89999864747899999999999874245435799771399899999998468837999999999


No 12 
>>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} (A:24-109)
Probab=94.13  E-value=0.084  Score=32.02  Aligned_cols=59  Identities=17%  Similarity=0.187  Sum_probs=51.4

Q ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHH-CCCCCHH-HHHHHHHH
Q ss_conf             99999997337998988999999997379978985099789973-7898899-99997549
Q 537021.9.peg.8   40 YEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQE-INRIGKR-VALELKLV   98 (148)
Q Consensus        40 ~ELLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~-i~GIG~a-ka~~l~a~   98 (148)
                      .-|++.+|..-++..+|.....+|.++|.+...+.+++.++|.. |+++|-- ||..|+.+
T Consensus         9 ~~Lia~iLsq~T~~~~~~~~~~~L~~~~~t~~~l~~a~~~~l~~~i~~~G~~~Ka~~i~~~   69 (86)
T 1kg2_A            9 KVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKA   69 (86)
T ss_dssp             HHHHHHHHHTSSCHHHHHHHHHHHHHHCSSHHHHHHSCHHHHHHHHTTSCCTHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             9999999981184999999999999987999999860899999998846899999999999


No 13 
>>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B (A:)
Probab=93.72  E-value=0.16  Score=30.24  Aligned_cols=41  Identities=22%  Similarity=0.211  Sum_probs=35.4

Q ss_pred             HHHHHHHHH-CCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             999999973-79978985099789973789889999997549
Q 537021.9.peg.8   58 SIAKALLKR-FATLGGVFGAPLHLLQEINRIGKRVALELKLV   98 (148)
Q Consensus        58 ~lA~~lL~~-fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~   98 (148)
                      ..|+.|-+. |.++..|..+++++|..|+|||..+|..|...
T Consensus        18 ~~a~~L~~aGi~TvedLa~a~~~eL~~i~Gi~~~~A~~ii~~   59 (70)
T 1wcn_A           18 DLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMA   59 (70)
T ss_dssp             HHHHHHHTTTCCSHHHHHTSCHHHHHTSSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHCHHHHHHHCCCCHHHHHHHHHH
T ss_conf             999999996997599998729999976517999999999999


No 14 
>>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A (A:80-154)
Probab=92.31  E-value=0.25  Score=29.01  Aligned_cols=40  Identities=25%  Similarity=0.210  Sum_probs=32.2

Q ss_pred             HHHHHHHHHCCC---HHHHHCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf             999999973799---7898509978997378988999999754
Q 537021.9.peg.8   58 SIAKALLKRFAT---LGGVFGAPLHLLQEINRIGKRVALELKL   97 (148)
Q Consensus        58 ~lA~~lL~~fGs---L~~ll~as~~eL~~i~GIG~aka~~l~a   97 (148)
                      -+|-.+|..|+-   ...+.+.+...|+++||||+..|-+|..
T Consensus        20 k~Al~iLs~~~~~el~~aI~~~D~~~L~~ipGIG~KtA~rii~   62 (75)
T 2ztd_A           20 RLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVL   62 (75)
T ss_dssp             HHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHHHHHCCCCHHHHHHHHHCCCHHHHHCCCCCCHHHHHHHHH
T ss_conf             6662322157767777888536889985088835688999999


No 15 
>>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} (A:66-144)
Probab=91.91  E-value=0.29  Score=28.53  Aligned_cols=46  Identities=24%  Similarity=0.297  Sum_probs=35.2

Q ss_pred             HHHHHHHHHCCC---HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             999999973799---789850997899737898899999975499999999
Q 537021.9.peg.8   58 SIAKALLKRFAT---LGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRI  105 (148)
Q Consensus        58 ~lA~~lL~~fGs---L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~  105 (148)
                      -+|-.+|..|+-   ...+.+.+.+.|+++||||+..|-+|.  .||-.++
T Consensus        19 k~Al~iLs~~~~~el~~aI~~~D~~~L~~ipGIG~KtAerii--~eLk~K~   67 (79)
T 1cuk_A           19 KLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLI--VEMKDRF   67 (79)
T ss_dssp             HHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHH--HHHHHHG
T ss_pred             HHHHHHHCCCCHHHHHHHHHHCCHHHHHHCCCCCHHHHHHHH--HHHHHHH
T ss_conf             999999757999999999992899998419998899999999--9999888


No 16 
>>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} (A:1-49)
Probab=91.31  E-value=0.13  Score=30.76  Aligned_cols=32  Identities=31%  Similarity=0.510  Sum_probs=25.5

Q ss_pred             CCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHH
Q ss_conf             799898899999999737997898509978997
Q 537021.9.peg.8   50 LIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQ   82 (148)
Q Consensus        50 g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~   82 (148)
                      |.|+-.. ..|+.|+++|||+.++.+||.+||+
T Consensus        18 ~I~gVG~-~~ak~Ll~~Fgsi~~i~~As~eeL~   49 (49)
T 1x2i_A           18 GLPHVSA-TLARRLLKHFGSVERVFTASVAELM   49 (49)
T ss_dssp             TSTTCCH-HHHHHHHHHHCSHHHHHHCCHHHHT
T ss_pred             CCCCCCH-HHHHHHHHHCCHHHHHHHCCHHHHH
T ss_conf             8999789-9999999970628888626798886


No 17 
>>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} (A:29-139)
Probab=91.20  E-value=0.68  Score=26.16  Aligned_cols=64  Identities=14%  Similarity=0.196  Sum_probs=50.5

Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHC---CCCCHHHHHHHHHHHHHHHH
Q ss_conf             99999973379989889999999973799789850997899737---89889999997549999999
Q 537021.9.peg.8   41 EILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEI---NRIGKRVALELKLVSVASQR  104 (148)
Q Consensus        41 ELLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i---~GIG~aka~~l~a~~El~rR  104 (148)
                      -|++.+|...+....+..+..++.+.||+...+..++.+++...   -|....||..|..+.+.-..
T Consensus        10 ~Lv~~Il~qq~s~~~a~~~~~~l~~~~~~~~~l~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~~~~   76 (111)
T 1kea_A           10 ILITEILLRRTTAGHVKKIYDKFFVKYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVIN   76 (111)
T ss_dssp             HHHHHHHTTTSCHHHHHHHHHHHHHHCCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             9999999831969999999999999788999998399889999989768899999999999998887


No 18 
>>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} (A:38-150)
Probab=91.04  E-value=0.013  Score=37.19  Aligned_cols=69  Identities=13%  Similarity=-0.070  Sum_probs=44.1

Q ss_pred             HHHHHHCCHHHCCHHHHHHHHHHCCCC-----CCCHHHHHHHHHHHCCCHHHHHCCC----HHHHHHCCCCCHHHHHHHH
Q ss_conf             999982392218989999999733799-----8988999999997379978985099----7899737898899999975
Q 537021.9.peg.8   26 RDRFLQKGENALAYYEILELILFRLIP-----RKDTKSIAKALLKRFATLGGVFGAP----LHLLQEINRIGKRVALELK   96 (148)
Q Consensus        26 RErll~~G~~~LsD~ELLallL~~g~~-----~~~~~~lA~~lL~~fGsL~~ll~as----~~eL~~i~GIG~aka~~l~   96 (148)
                      -.||.+. ....+..++.+++-..|..     -+....+|+.+.++++  ..+.+.+    .++|+++||||+..|-.++
T Consensus        29 ~~~l~~~-~~~~~~~~~~~~~~~~g~~~~~~ka~~l~~~a~~~~~~~~--~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l  105 (113)
T 3fhf_A           29 QKEIGDG-FLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDI--VESFENEKVAREFLVRNIKGIGYKEASHFL  105 (113)
T ss_dssp             HHHHTTH-HHHSCHHHHHHHHHHTTCTTHHHHHHHHHHHGGGCCHHHH--HHHSSSHHHHHHHHHHHSTTCCHHHHHHHH
T ss_pred             HHHHHHH-HHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH--HHHCCCCCCCHHHHHHHCCCCCHHHHHHHH
T ss_conf             9999999-8718976799999994524667889999999999988767--776068897639999878583299999999


Q ss_pred             H
Q ss_conf             4
Q 537021.9.peg.8   97 L   97 (148)
Q Consensus        97 a   97 (148)
                      .
T Consensus       106 ~  106 (113)
T 3fhf_A          106 R  106 (113)
T ss_dssp             H
T ss_pred             H
T ss_conf             9


No 19 
>>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} (A:149-197)
Probab=90.71  E-value=0.18  Score=29.97  Aligned_cols=31  Identities=26%  Similarity=0.405  Sum_probs=23.9

Q ss_pred             CCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHH
Q ss_conf             99898899999999737997898509978997
Q 537021.9.peg.8   51 IPRKDTKSIAKALLKRFATLGGVFGAPLHLLQ   82 (148)
Q Consensus        51 ~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~   82 (148)
                      .|+..- .-++.||.+|||+.++..||.+||.
T Consensus        19 IpGIG~-k~~~~LL~~FgSi~~i~~As~eeLa   49 (49)
T 2bgw_A           19 FPGIGR-RTAERILERFGSLERFFTASKAEIS   49 (49)
T ss_dssp             STTCCH-HHHHHHHHHHSSHHHHTTCCHHHHH
T ss_pred             CCCCCH-HHHHHHHHHCCCHHHHHHCCHHHHH
T ss_conf             568997-8999999986999999858999996


No 20 
>>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} (A:28-137)
Probab=90.62  E-value=0.26  Score=28.86  Aligned_cols=60  Identities=18%  Similarity=0.319  Sum_probs=30.0

Q ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHH-CCCCCH--HHHHHHHHHHHH
Q ss_conf             999997337998988999999997379978985099789973-789889--999997549999
Q 537021.9.peg.8   42 ILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQE-INRIGK--RVALELKLVSVA  101 (148)
Q Consensus        42 LLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~-i~GIG~--aka~~l~a~~El  101 (148)
                      |++.+|...++...+..+-.+|.++||+...+..++.+++.. ++++|-  .|+..|..+.+.
T Consensus        10 Li~~Il~Qqt~~~~a~~~~~~l~~~~~~~~~~~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~   72 (110)
T 1orn_A           10 LIAVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAM   72 (110)
T ss_dssp             HHHHHHHTTSCHHHHHHHHHHHHHHCCSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHCCCCHHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHH
T ss_conf             999999810869999999999986049989986078999999999732499999999998789


No 21 
>>1szp_A DNA repair protein RAD51; homologous recombination, asymmetry, RAD51 filament, DNA binding protein; HET: DNA; 3.25A {Saccharomyces cerevisiae} (A:26-81)
Probab=90.56  E-value=0.3  Score=28.44  Aligned_cols=30  Identities=33%  Similarity=0.138  Sum_probs=26.6

Q ss_pred             CHHHHHCCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             978985099789973789889999997549
Q 537021.9.peg.8   69 TLGGVFGAPLHLLQEINRIGKRVALELKLV   98 (148)
Q Consensus        69 sL~~ll~as~~eL~~i~GIG~aka~~l~a~   98 (148)
                      ++.++..+++.+|+.|+||+++|+..|..+
T Consensus         2 Tve~ia~at~k~L~~ikGisE~ka~KIi~a   31 (56)
T 1szp_A            2 TAEAVAYAPRKDLLEIKGISEAKADKLLNE   31 (56)
T ss_dssp             SHHHHHHSCSHHHHTSTTCCHHHHHHHHHH
T ss_pred             CHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             399997389999987639999999999999


No 22 
>>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* (A:34-143)
Probab=89.95  E-value=1.5  Score=23.88  Aligned_cols=65  Identities=14%  Similarity=0.063  Sum_probs=51.2

Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHH-C--CCCCHHHHHHHHHHHHHHHHH
Q ss_conf             9999997337998988999999997379978985099789973-7--898899999975499999999
Q 537021.9.peg.8   41 EILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQE-I--NRIGKRVALELKLVSVASQRI  105 (148)
Q Consensus        41 ELLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~-i--~GIG~aka~~l~a~~El~rR~  105 (148)
                      -|+..+|...+....+..+-.+|.++||+...+..++..+|.. +  -|....|+..+.++.++....
T Consensus         9 ~Li~~Il~q~~s~~~a~~~~~rl~~~~~t~~~~~~~~~~~l~~~l~~~g~~~~k~~~i~~~~~~~~~~   76 (110)
T 3fsp_A            9 VWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRY   76 (110)
T ss_dssp             HHHHHHHTTTSCHHHHHHHHHHHHHHCCSHHHHHTSCHHHHHHTTTTSSCTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             99999986108788999999999997799999977899999999872671999999999899986863


No 23 
>>1lb2_B DNA-directed RNA polymerase alpha chain; protein-DNA complex, gene-regulatory, gene regulation/DNA complex; HET: CMP; 3.10A {Escherichia coli} (B:)
Probab=89.88  E-value=0.85  Score=25.53  Aligned_cols=41  Identities=22%  Similarity=0.184  Sum_probs=34.3

Q ss_pred             HHHHHHHC--CCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             99999737--997898509978997378988999999754999
Q 537021.9.peg.8   60 AKALLKRF--ATLGGVFGAPLHLLQEINRIGKRVALELKLVSV  100 (148)
Q Consensus        60 A~~lL~~f--GsL~~ll~as~~eL~~i~GIG~aka~~l~a~~E  100 (148)
                      +.+.|.+.  ..++.|...+.++|.+++|+|+...-+|....+
T Consensus        21 ~~n~L~~agI~ti~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~   63 (84)
T 1lb2_B           21 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA   63 (84)
T ss_dssp             HHHHHHHTTCCBHHHHHTCCHHHHHHSTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             9999989189469998728999997488987889999999999


No 24 
>>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} (B:)
Probab=89.86  E-value=0.83  Score=25.61  Aligned_cols=42  Identities=17%  Similarity=0.145  Sum_probs=35.5

Q ss_pred             HHHHHHHHC--CCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             999999737--997898509978997378988999999754999
Q 537021.9.peg.8   59 IAKALLKRF--ATLGGVFGAPLHLLQEINRIGKRVALELKLVSV  100 (148)
Q Consensus        59 lA~~lL~~f--GsL~~ll~as~~eL~~i~GIG~aka~~l~a~~E  100 (148)
                      -|.+.|.+.  .+++.|...+.+||.+|+|+|+...-+|..+.+
T Consensus        19 R~~N~L~~~gI~ti~dL~~~s~~dLl~i~n~G~kSl~EI~~~L~   62 (73)
T 1z3e_B           19 RSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLE   62 (73)
T ss_dssp             HHHHHHHHTTCCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             99999988389479999877999997588976605999999999


No 25 
>>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} (B:)
Probab=89.80  E-value=0.57  Score=26.65  Aligned_cols=42  Identities=17%  Similarity=0.145  Sum_probs=35.3

Q ss_pred             HHHHHHHHC--CCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             999999737--997898509978997378988999999754999
Q 537021.9.peg.8   59 IAKALLKRF--ATLGGVFGAPLHLLQEINRIGKRVALELKLVSV  100 (148)
Q Consensus        59 lA~~lL~~f--GsL~~ll~as~~eL~~i~GIG~aka~~l~a~~E  100 (148)
                      -+.+.|.+.  .+++.|...+.++|.+|+|+|+...-+|+...+
T Consensus        26 R~~n~L~~~gI~tv~dL~~~s~~dLl~i~nlG~ksl~EI~~~L~   69 (79)
T 3gfk_B           26 RSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLE   69 (79)
T ss_dssp             HHHHHHHHTTCCBHHHHTTCCHHHHTTSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             99999989189679999878999998578986736999999999


No 26 
>>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} (A:28-137)
Probab=89.74  E-value=0.87  Score=25.49  Aligned_cols=60  Identities=12%  Similarity=0.112  Sum_probs=46.7

Q ss_pred             HHCCHHHHHHHHHHCCCC---CCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf             218989999999733799---898899999999737997898509978997378988999999754
Q 537021.9.peg.8   35 NALAYYEILELILFRLIP---RKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKL   97 (148)
Q Consensus        35 ~~LsD~ELLallL~~g~~---~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a   97 (148)
                      ...+..|+.+.+-..|.+   -....++|+.+.+.+++   -.....++|++++|||+..|..++.
T Consensus        42 ~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~~~~~~~~---~~~~~~~~L~~l~GIG~~ta~~~ll  104 (110)
T 1orn_A           42 IAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNG---EVPRDRDELMKLPGVGRKTANVVVS  104 (110)
T ss_dssp             HSSCHHHHHHHTGGGSSHHHHHHHHHHHHHHHHHHSTT---SCCSCHHHHTTSTTCCHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCC---CCCCCHHHHHHCCCCCHHHHHHHHH
T ss_conf             60789999999997324999999999987899999399---8988899997587975258999999


No 27 
>>1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} (A:1-129)
Probab=89.20  E-value=1.1  Score=24.70  Aligned_cols=63  Identities=13%  Similarity=0.101  Sum_probs=51.9

Q ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHH-CCCCC--HHHHHHHHHHHHHH
Q ss_conf             99999997337998988999999997379978985099789973-78988--99999975499999
Q 537021.9.peg.8   40 YEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQE-INRIG--KRVALELKLVSVAS  102 (148)
Q Consensus        40 ~ELLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~-i~GIG--~aka~~l~a~~El~  102 (148)
                      .-|+..+|...+....+..+-++|..+||+...+..++..++.. ++.+|  ..|+..|..+.+..
T Consensus        33 e~Li~~Il~Qq~s~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~G~~~~Ka~~i~~~a~~~   98 (129)
T 1ngn_A           33 KLLIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFSDEY   98 (129)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHHHHHSCSHHHHHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             999999998618699999999999998879999971675868989812447999999999998246


No 28 
>>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} (A:)
Probab=88.64  E-value=0.81  Score=25.67  Aligned_cols=41  Identities=24%  Similarity=0.210  Sum_probs=34.6

Q ss_pred             HHHHHHHCC--CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             999997379--97898509978997378988999999754999
Q 537021.9.peg.8   60 AKALLKRFA--TLGGVFGAPLHLLQEINRIGKRVALELKLVSV  100 (148)
Q Consensus        60 A~~lL~~fG--sL~~ll~as~~eL~~i~GIG~aka~~l~a~~E  100 (148)
                      |.+.|.+.|  .++.|...+.++|++|+|+|+...-.|....+
T Consensus        35 s~N~Lk~~gI~ti~dL~~~s~~dLl~i~n~G~kSl~Ei~~~L~   77 (98)
T 1coo_A           35 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA   77 (98)
T ss_dssp             THHHHHTTTCCBHHHHHTSCHHHHTTSTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             9989999399759999858999998677987878999999999


No 29 
>>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} (A:499-568)
Probab=87.04  E-value=0.71  Score=26.04  Aligned_cols=32  Identities=22%  Similarity=0.160  Sum_probs=25.5

Q ss_pred             HHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             85099789973789889999997549999999
Q 537021.9.peg.8   73 VFGAPLHLLQEINRIGKRVALELKLVSVASQR  104 (148)
Q Consensus        73 ll~as~~eL~~i~GIG~aka~~l~a~~El~rR  104 (148)
                      +-.|+.++|+.++|||+.+|..|....+-.-+
T Consensus         4 iN~A~~~~L~~lpgig~~~A~~Ii~~R~~~G~   35 (70)
T 3bzc_A            4 VNTASAALLARISGLNSTLAQNIVAHRDANGA   35 (70)
T ss_dssp             TTTCCHHHHHTSTTCCHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCC
T ss_conf             68754888866069788999999999996699


No 30 
>>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} (A:)
Probab=86.21  E-value=0.96  Score=25.20  Aligned_cols=33  Identities=18%  Similarity=0.077  Sum_probs=26.2

Q ss_pred             HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             789850997899737898899999975499999
Q 537021.9.peg.8   70 LGGVFGAPLHLLQEINRIGKRVALELKLVSVAS  102 (148)
Q Consensus        70 L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~  102 (148)
                      .-++-.|+.++|++++|||+.+|..|..-.+..
T Consensus        31 ~idiNtAs~~eL~~lpgig~~~A~~Ii~~R~~~   63 (98)
T 2edu_A           31 LDLLNEGSARDLRSLQRIGPKKAQLIVGWRELH   63 (98)
T ss_dssp             HHHHHHSCHHHHHHSTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHCCCCCHHHHHHHHHHHHHC
T ss_conf             441357999999757898999999999999985


No 31 
>>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} (B:1-67)
Probab=85.48  E-value=0.63  Score=26.37  Aligned_cols=31  Identities=23%  Similarity=0.280  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHHHHHCCCHHHHHCCCHHHHH
Q ss_conf             9898899999999737997898509978997
Q 537021.9.peg.8   52 PRKDTKSIAKALLKRFATLGGVFGAPLHLLQ   82 (148)
Q Consensus        52 ~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~   82 (148)
                      .+.=-+.=|-.|+..||||.++++|+.++|.
T Consensus        37 ir~VNKTDa~tLls~FgSl~~ii~As~e~Ls   67 (67)
T 2a1j_B           37 VKSVNKTDSQTLLTTFGSLEQLIAASREDLA   67 (67)
T ss_dssp             STTCCHHHHHHHHHHHSSHHHHHSCCHHHHH
T ss_pred             CCCCCHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             9985999999999991893465553043787


No 32 
>>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} (A:)
Probab=85.04  E-value=0.74  Score=25.92  Aligned_cols=32  Identities=19%  Similarity=0.036  Sum_probs=24.7

Q ss_pred             HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             78985099789973789889999997549999
Q 537021.9.peg.8   70 LGGVFGAPLHLLQEINRIGKRVALELKLVSVA  101 (148)
Q Consensus        70 L~~ll~as~~eL~~i~GIG~aka~~l~a~~El  101 (148)
                      .-++-.|+.++|++++|||+..|..|..-.++
T Consensus        18 ~idiNtA~~~~L~~lpGig~~~A~~Ii~~R~f   49 (75)
T 2duy_A           18 PVSLNEASLEELXALPGIGPVLARRIVEGRPY   49 (75)
T ss_dssp             SEETTTCCHHHHTTSTTCCHHHHHHHHHTCCC
T ss_pred             CEECCCCCHHHHHHCCCCCHHHHHHHHHCCCC
T ss_conf             70061287999977789899999999986898


No 33 
>>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} (A:29-139)
Probab=85.03  E-value=0.54  Score=26.80  Aligned_cols=61  Identities=11%  Similarity=0.087  Sum_probs=43.5

Q ss_pred             HHHCCHHHHHHHHHHCCCCCC---CHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf             221898999999973379989---8899999999737997898509978997378988999999754
Q 537021.9.peg.8   34 ENALAYYEILELILFRLIPRK---DTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKL   97 (148)
Q Consensus        34 ~~~LsD~ELLallL~~g~~~~---~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a   97 (148)
                      ...++..||.+++-..|..+.   ....+|+.+.+.+++   =.....++|++++|||+..|-.++.
T Consensus        42 l~~~~~~~l~~~i~~~g~~~~ka~~i~~~a~~~~~~~~~---~~~~~~~~L~~l~GIG~~tA~~~ll  105 (111)
T 1kea_A           42 ILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGG---RVPRNRKAILDLPGVGKYTCAAVMC  105 (111)
T ss_dssp             HHHSCHHHHHHHTGGGSCHHHHHHHHHHHHHHHHHHHTT---SCCSCHHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC---CCCCHHHHHHCCCCCCHHHHHHHHH
T ss_conf             983998899999897688999999999999988875159---9973046765089876168999999


No 34 
>>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* 3a0b_U* 3a0h_U* (U:)
Probab=84.87  E-value=0.52  Score=26.93  Aligned_cols=34  Identities=3%  Similarity=-0.072  Sum_probs=25.4

Q ss_pred             CCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             7997898509978997378988999999754999
Q 537021.9.peg.8   67 FATLGGVFGAPLHLLQEINRIGKRVALELKLVSV  100 (148)
Q Consensus        67 fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~E  100 (148)
                      .+..-++-.|+.++|++++|||+.+|..|..-..
T Consensus        21 ~~~~vdIN~As~~~L~~ipGig~~~A~~Iv~~gp   54 (104)
T 3bz1_U           21 YGEKIDLNNTNIAAFIQYRGLYPTLAKLIVKNAP   54 (104)
T ss_dssp             BTTBEETTSSCGGGGGGSTTTTHHHHHHHHHSCC
T ss_pred             CCCCEECCCCCHHHHHHCCCCCHHHHHHHHHCCC
T ss_conf             5885677228999997775869999999997089


No 35 
>>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} (A:427-542)
Probab=84.42  E-value=0.8  Score=25.71  Aligned_cols=37  Identities=27%  Similarity=0.389  Sum_probs=27.8

Q ss_pred             HHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHH
Q ss_conf             99733799898899999999737997898509978997
Q 537021.9.peg.8   45 LILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQ   82 (148)
Q Consensus        45 llL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~   82 (148)
                      ++...|.|+---. -|+.|+++|||+.++.+||.+||+
T Consensus        80 ~l~algI~giG~~-~ak~L~~~f~s~~~i~~As~eeL~  116 (116)
T 1dgs_A           80 LLYALGLPGVGEV-LARNLARRFGTMDRLLEASLEELI  116 (116)
T ss_dssp             HHHHTTCSSCCHH-HHHHHHHTTSBHHHHTTCCHHHHH
T ss_pred             HHHHCCCCCCCHH-HHHHHHHHCCCHHHHHCCCHHHHH
T ss_conf             9997699754568-999998766899999728999995


No 36 
>>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} (A:23-133)
Probab=80.34  E-value=2  Score=23.11  Aligned_cols=54  Identities=11%  Similarity=0.081  Sum_probs=23.3

Q ss_pred             HHHHHHHHHCCCCC---CCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHH
Q ss_conf             99999997337998---9889999999973799789850997899737898899999975
Q 537021.9.peg.8   40 YEILELILFRLIPR---KDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELK   96 (148)
Q Consensus        40 ~ELLallL~~g~~~---~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~   96 (148)
                      .++.+.+=+.|..+   .....+|+.+++.+|+   -.....++|++++|||+..|..++
T Consensus        48 ~~~~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~---~~~~~~~~L~~l~GIG~~tA~~vl  104 (111)
T 2abk_A           48 EGVKTYIKTIGLYNSKAENIIKTCRILLEQHNG---EVPEDRAALEALPGVGRKTANVVL  104 (111)
T ss_dssp             HHHHHHHTTSTTHHHHHHHHHHHHHHHHHHTTT---SCCSCHHHHHHSTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             667777674115677888999999999986041---136779999989860635999999


No 37 
>>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} (U:48-134)
Probab=80.32  E-value=0.57  Score=26.66  Aligned_cols=30  Identities=3%  Similarity=-0.136  Sum_probs=20.7

Q ss_pred             CHHHHHCCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             978985099789973789889999997549
Q 537021.9.peg.8   69 TLGGVFGAPLHLLQEINRIGKRVALELKLV   98 (148)
Q Consensus        69 sL~~ll~as~~eL~~i~GIG~aka~~l~a~   98 (148)
                      ..-++-.|+.++|++++|||+..|..|..-
T Consensus         6 ~~vdiN~A~~~~L~~ipGig~~~A~~Iv~~   35 (87)
T 1s5l_U            6 EKIDLNNTNIAAFIQYRGLYPTLAKLIVKN   35 (87)
T ss_dssp             TSEETTTSCGGGGGGSTTCTHHHHHHHHHT
T ss_pred             CEEECCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             704164078999977103469999999982


No 38 
>>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: DNA; NMR {Homo sapiens} (A:)
Probab=78.29  E-value=1.8  Score=23.43  Aligned_cols=39  Identities=28%  Similarity=0.196  Sum_probs=31.3

Q ss_pred             HHHHHHH-HCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf             9999997-37997898509978997378988999999754
Q 537021.9.peg.8   59 IAKALLK-RFATLGGVFGAPLHLLQEINRIGKRVALELKL   97 (148)
Q Consensus        59 lA~~lL~-~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a   97 (148)
                      .|+.|-. .+-++..|..+++++|.++.|+|..+|..|..
T Consensus        37 ~~~~L~~~Gi~Tv~~la~~~~~~L~~i~G~~~~~a~~i~~   76 (114)
T 1b22_A           37 DVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILA   76 (114)
T ss_dssp             HHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHH
T ss_pred             HHHHHHHCCCCHHHHHHHCCHHHHHHHCCCCHHHHHHHHH
T ss_conf             9999999698539999858999998620636999999999


No 39 
>>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} (A:50-126)
Probab=77.81  E-value=3.7  Score=21.40  Aligned_cols=62  Identities=10%  Similarity=-0.038  Sum_probs=47.3

Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH---HHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             9999997337998988999999997379978---9850997899737898899999975499999
Q 537021.9.peg.8   41 EILELILFRLIPRKDTKSIAKALLKRFATLG---GVFGAPLHLLQEINRIGKRVALELKLVSVAS  102 (148)
Q Consensus        41 ELLallL~~g~~~~~~~~lA~~lL~~fGsL~---~ll~as~~eL~~i~GIG~aka~~l~a~~El~  102 (148)
                      -|+..+|..-+....+..+..+|.++||+..   ........++.+--|....||-.|+.+.+..
T Consensus         5 ~Li~~Ilsqqts~~~a~~~~~rl~~~~~~~~~~~~~~~~~~~~~ir~~G~~~~Ka~~i~~~a~~i   69 (77)
T 2h56_A            5 SLVSSIVEQQLSIKAASAIYGRVEQLVGGALEKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHV   69 (77)
T ss_dssp             HHHHHHHHTTSCHHHHHHHHHHHHHHHTSCCCCTHHHHTSCHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHHHCHHHHHHHHHHHH
T ss_conf             99999981700399999999999998600236889986379999877764100016899999999


No 40 
>>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} (A:)
Probab=76.36  E-value=5.9  Score=20.11  Aligned_cols=40  Identities=25%  Similarity=0.345  Sum_probs=33.8

Q ss_pred             HHHHHHHH-HCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf             99999997-37997898509978997378988999999754
Q 537021.9.peg.8   58 SIAKALLK-RFATLGGVFGAPLHLLQEINRIGKRVALELKL   97 (148)
Q Consensus        58 ~lA~~lL~-~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a   97 (148)
                      .+|+-|.. .|.|+-.+...+.++|..|.|...-.+..|+.
T Consensus        17 ~iA~lLV~EGFtslEEiAyvp~~El~~IegfDee~a~eL~~   57 (70)
T 1u9l_A           17 DFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRE   57 (70)
T ss_dssp             HHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCHHHHHCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf             99999998465879998658999997600447999999999


No 41 
>>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} (A:)
Probab=76.05  E-value=0.99  Score=25.10  Aligned_cols=52  Identities=6%  Similarity=-0.017  Sum_probs=37.8

Q ss_pred             CHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC----HHHHHHHHHH
Q ss_conf             978997378988999999754999999999987640677889----8999999999
Q 537021.9.peg.8   77 PLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTP----GQPCLISVER  128 (148)
Q Consensus        77 s~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~~l~s----~~~v~~yl~~  128 (148)
                      ....|..|||||++.+..|..-+.-..++..+...+-..+.-    .+.+++|+..
T Consensus         2 ~~s~L~~IpgVG~~~a~~Ll~~f~Si~~i~~As~eeL~~i~gg~~~A~~i~~~l~~   57 (63)
T 2a1j_A            2 PQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHT   57 (63)
T ss_dssp             CCHHHHTSTTCCHHHHHHHHHHCSSHHHHHTCCHHHHHHHHSCHHHHHHHHHHHHC
T ss_pred             CHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCHHHHHHHHHHHCC
T ss_conf             68888519998999999999980789999869999997785968999999999822


No 42 
>>1d8b_A SGS1 RECQ helicase; five helices, three-helical bundle flanked by two helices, DNA binding protein; NMR {Saccharomyces cerevisiae} (A:)
Probab=75.16  E-value=5.6  Score=20.25  Aligned_cols=41  Identities=5%  Similarity=0.094  Sum_probs=32.5

Q ss_pred             HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             78985099789973789889999997549999999999876
Q 537021.9.peg.8   70 LGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANW  110 (148)
Q Consensus        70 L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~  110 (148)
                      +....=.+.++|.+|+|+|+.++...-...+...++..++.
T Consensus        39 ia~~~P~t~~eL~~i~G~~~~k~~~yG~~l~~I~~~~~e~~   79 (81)
T 1d8b_A           39 MAAILPMNDSAFATLGTVEDKYRRRFKYFKATIADLSKKRS   79 (81)
T ss_dssp             HHHHCCCSHHHHGGGSCCCHHHHHHGGGTHHHHHHHHHHTT
T ss_pred             HHHHCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             99978999999817999999999999999999999999856


No 43 
>>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:1-118)
Probab=74.32  E-value=3.5  Score=21.59  Aligned_cols=48  Identities=17%  Similarity=0.142  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             89889999999973799789850997899737898899999975499999
Q 537021.9.peg.8   53 RKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVAS  102 (148)
Q Consensus        53 ~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~  102 (148)
                      +.-+..-|-..+..++  ..+-.++.+++.+++|||+..|..|.-..+-+
T Consensus        33 r~~aYr~Aa~~i~~l~--~~i~~~~~~~l~~lpGIG~~~a~kI~E~l~tG   80 (118)
T 2w9m_A           33 KSRAYRSAARSLEELN--EETPELLAREFTGIPKVGKGIAAELSDFARSG   80 (118)
T ss_dssp             SHHHHHHHHHHHHSCC------------CCSSTTCCHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHCC--CHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHC
T ss_conf             8999999999999688--23667549886259998789999999999849


No 44 
>>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} (A:)
Probab=73.86  E-value=6.8  Score=19.70  Aligned_cols=57  Identities=16%  Similarity=0.021  Sum_probs=44.2

Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHCC-CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             9999997337998988999999997379-9789850997899737898899999975499999
Q 537021.9.peg.8   41 EILELILFRLIPRKDTKSIAKALLKRFA-TLGGVFGAPLHLLQEINRIGKRVALELKLVSVAS  102 (148)
Q Consensus        41 ELLallL~~g~~~~~~~~lA~~lL~~fG-sL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~  102 (148)
                      |+....-..|..+..+..-|-+.|..++ -+     .+..++..++|||+.-+..|.=..+=+
T Consensus        24 ~la~~~~~~g~~r~~aY~kA~~slk~~p~pi-----~s~~~l~~lpgiG~~ia~kI~e~l~tg   81 (87)
T 2kp7_A           24 EWRDEAASRGRHTRFVFQKALRSLQRYPLPL-----RSGKEAKILQHFGDRLCRMLDEKLKQH   81 (87)
T ss_dssp             HHHHHHHHHTCTTHHHHHHHHHHHHHCCSCC-----CSHHHHHTCTTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHCCCCC-----CCHHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf             9999999708468999999999999789887-----889998738998789999999999999


No 45 
>>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A (A:111-127,A:196-236)
Probab=71.85  E-value=7.6  Score=19.40  Aligned_cols=33  Identities=18%  Similarity=0.070  Sum_probs=24.2

Q ss_pred             HHCCCHHHHHCCCHHH----HHHCCCCCHHHHHHHHH
Q ss_conf             7379978985099789----97378988999999754
Q 537021.9.peg.8   65 KRFATLGGVFGAPLHL----LQEINRIGKRVALELKL   97 (148)
Q Consensus        65 ~~fGsL~~ll~as~~e----L~~i~GIG~aka~~l~a   97 (148)
                      ..-=++..+...+.+|    |++++|||+..|-.+..
T Consensus        15 ~~~Ldl~~L~~l~~eea~~~L~~i~GIGpwTAdciLL   51 (58)
T 3i0w_A           15 SANLNLEYIKSLNDNECHEELKKFMGVGPQVADCIML   51 (58)
T ss_dssp             HTTSCHHHHHHSCHHHHHHHHTTSTTCCHHHHHHHHH
T ss_pred             HHHCCHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             7457989973135446789998268812999999999


No 46 
>>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix- hairpin-helix, HHH motif, three helix bundle; 2.30A {Methanopyrus kandleri} (A:472-519)
Probab=70.19  E-value=8.2  Score=19.17  Aligned_cols=39  Identities=28%  Similarity=0.335  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHH
Q ss_conf             9999999973799789850997899737898899999975
Q 537021.9.peg.8   57 KSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELK   96 (148)
Q Consensus        57 ~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~   96 (148)
                      .+-|.+||+.||+.+.+-.|..++|.. .|+.++....++
T Consensus         7 reraerllkkyggyskvreagveelre-dgltdaqirelk   45 (48)
T 2csb_A            7 RERAERLLKKYGGYSKVREAGVEELRE-DGLTDAQIRELK   45 (48)
T ss_dssp             HHHHHHHHHHHTSHHHHHTSCHHHHHH-TTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHH-CCCCHHHHHHHC
T ss_conf             899999999837805888850899987-577488888750


No 47 
>>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A (A:1-66,A:131-198)
Probab=65.51  E-value=8.3  Score=19.16  Aligned_cols=43  Identities=21%  Similarity=0.297  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHCC--------------CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             999999997379--------------97898509978997378988999999754999
Q 537021.9.peg.8   57 KSIAKALLKRFA--------------TLGGVFGAPLHLLQEINRIGKRVALELKLVSV  100 (148)
Q Consensus        57 ~~lA~~lL~~fG--------------sL~~ll~as~~eL~~i~GIG~aka~~l~a~~E  100 (148)
                      ..+..+|.++||              +...|..+++++|..+ |+|-.||..|..+.+
T Consensus        73 ~sIi~RLve~yGe~Ie~~g~~~yaFPTPEqLA~as~EeLRac-GlsyRKA~YI~~lAq  129 (134)
T 2jhn_A           73 EKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEGLREC-GLSRRKAELIVEIAK  129 (134)
T ss_dssp             HHHHHHHHHHHSCEEEETTEEEECCCCHHHHHHHHHHHHHHT-TCCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHCCCCCCCCHHHCCCCCHHHHHCCCHHHHHHH-CCCCHHHHHHHHCCC
T ss_conf             999999999855755666213215589999974999998541-023004566552011


No 48 
>>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} (A:1-129)
Probab=65.23  E-value=4.9  Score=20.63  Aligned_cols=25  Identities=12%  Similarity=0.142  Sum_probs=14.7

Q ss_pred             CHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             9789973789889999997549999
Q 537021.9.peg.8   77 PLHLLQEINRIGKRVALELKLVSVA  101 (148)
Q Consensus        77 s~~eL~~i~GIG~aka~~l~a~~El  101 (148)
                      +.+++..++|||+.-+..|.-..+-
T Consensus        59 s~~~~~~lpgIG~~ia~~I~E~l~t   83 (129)
T 2ihm_A           59 SLSQLHGLPYFGEHSTRVIQELLEH   83 (129)
T ss_dssp             SGGGGTTCTTCCHHHHHHHHHHHHH
T ss_pred             CHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             9999835999778999999999970


No 49 
>>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} (A:1-49,A:127-233)
Probab=64.12  E-value=5.8  Score=20.17  Aligned_cols=21  Identities=24%  Similarity=0.306  Sum_probs=17.2

Q ss_pred             CHHHHHHCCCCCHHHHHHHHH
Q ss_conf             978997378988999999754
Q 537021.9.peg.8   77 PLHLLQEINRIGKRVALELKL   97 (148)
Q Consensus        77 s~~eL~~i~GIG~aka~~l~a   97 (148)
                      ..++|++++|||+..|..+..
T Consensus        59 ~~~~LlsLPGIGpkTA~~ILl   79 (156)
T 2h56_A           59 VIEKLTAIKGIGQWTAEXFXX   79 (156)
T ss_dssp             HHHHHHTSTTCCHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHH
T ss_conf             888888738978789999998


No 50 
>>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} (A:1-119)
Probab=62.34  E-value=5.4  Score=20.35  Aligned_cols=42  Identities=7%  Similarity=0.199  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHCC-CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             8999999997379-9789850997899737898899999975499999
Q 537021.9.peg.8   56 TKSIAKALLKRFA-TLGGVFGAPLHLLQEINRIGKRVALELKLVSVAS  102 (148)
Q Consensus        56 ~~~lA~~lL~~fG-sL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~  102 (148)
                      +..-|-..|..+. .+     .+.+++.+++|||+.-+..|.-..+-+
T Consensus        38 aY~rAa~~l~~~p~~i-----~s~~~~~~lpgiG~~ia~~I~e~l~tG   80 (119)
T 2fmp_A           38 AYRKAASVIAKYPHKI-----KSGAEAKKLPGVGTKIAEKIDEFLATG   80 (119)
T ss_dssp             HHHHHHHHHHHCSSCC-----CCHHHHHTSTTCCHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHCCCCC-----CCHHHHHCCCCCCHHHHHHHHHHHHCC
T ss_conf             9999999998599554-----789998479996489999999999648


No 51 
>>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A (A:112-130,A:199-234)
Probab=59.85  E-value=7.7  Score=19.38  Aligned_cols=38  Identities=24%  Similarity=0.227  Sum_probs=24.1

Q ss_pred             HHHHHHHHHCCCHHHHHCC-CHHHHHHCCCCCHHHHHHHH
Q ss_conf             9999999737997898509-97899737898899999975
Q 537021.9.peg.8   58 SIAKALLKRFATLGGVFGA-PLHLLQEINRIGKRVALELK   96 (148)
Q Consensus        58 ~lA~~lL~~fGsL~~ll~a-s~~eL~~i~GIG~aka~~l~   96 (148)
                      .+|+.+++.- .|..+-+. =.++|.+++|||+..|-...
T Consensus        10 ~~~~~~~~~~-~L~~m~Deevi~~Lt~IkGIG~WTAem~L   48 (55)
T 2jhn_A           10 GIAKAIIQQQ-ELKEWGEEEAYEYLTSFKGIGRWTAELVL   48 (55)
T ss_dssp             HHHHHHHTTT-GGGGSCHHHHHHHHHTSTTCCHHHHHHHH
T ss_pred             HHHHHHHHCC-HHHHCCCHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             9999999751-31202431678898753782899999999


No 52 
>>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli} (A:105-231)
Probab=58.98  E-value=13  Score=17.82  Aligned_cols=47  Identities=21%  Similarity=0.203  Sum_probs=23.6

Q ss_pred             CCCCCCHHHHHHHHHHHCCCHH--HHHCCCHHHHHHCCCCCHHHHHHHH
Q ss_conf             7998988999999997379978--9850997899737898899999975
Q 537021.9.peg.8   50 LIPRKDTKSIAKALLKRFATLG--GVFGAPLHLLQEINRIGKRVALELK   96 (148)
Q Consensus        50 g~~~~~~~~lA~~lL~~fGsL~--~ll~as~~eL~~i~GIG~aka~~l~   96 (148)
                      +.+-+....+|+.+++..-++.  +=.....++|++++|||+..|-.+.
T Consensus        72 ~~ka~~i~~~a~~~~~~~l~~~~~~~~~~~~~~L~~lpGIG~~tA~~vl  120 (127)
T 1mpg_A           72 LKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFA  120 (127)
T ss_dssp             HHHHHHHHHHHHHHHHTCSCSSCCSCHHHHHHHHTTSTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             6589999999999982994213446789999999865897899999999


No 53 
>>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} (A:1-47,A:173-315)
Probab=57.95  E-value=2.4  Score=22.57  Aligned_cols=41  Identities=24%  Similarity=0.224  Sum_probs=32.7

Q ss_pred             HHHHHHHC--CCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             99999737--997898509978997378988999999754999
Q 537021.9.peg.8   60 AKALLKRF--ATLGGVFGAPLHLLQEINRIGKRVALELKLVSV  100 (148)
Q Consensus        60 A~~lL~~f--GsL~~ll~as~~eL~~i~GIG~aka~~l~a~~E  100 (148)
                      +.+.|++-  ..++.|+..+.+||.+++|+|....-+|+-..+
T Consensus       140 ~~n~Lk~a~I~ti~dL~~~s~~dL~~i~n~G~ksl~EI~~~L~  182 (190)
T 2a6h_A          140 VLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALE  182 (190)
T ss_dssp             -------------------------------------------
T ss_pred             HHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHH
T ss_conf             8867877589479998849999984599976055999999999


No 54 
>>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} (A:1-23,A:110-225)
Probab=57.14  E-value=7.7  Score=19.37  Aligned_cols=25  Identities=16%  Similarity=0.190  Sum_probs=20.0

Q ss_pred             CCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             0997899737898899999975499
Q 537021.9.peg.8   75 GAPLHLLQEINRIGKRVALELKLVS   99 (148)
Q Consensus        75 ~as~~eL~~i~GIG~aka~~l~a~~   99 (148)
                      .-+..+|++++|||+..|.-|.+-.
T Consensus        19 ~~~~~eL~~LpGIG~ktAd~Illfa   43 (139)
T 1kg2_A           19 RKTLPEVAALPGVGRSTAGAILSLS   43 (139)
T ss_dssp             CCCSGHHHTSTTCCHHHHHHHHHHH
T ss_pred             CCCCCHHHCCCCCCHHHHHHHHHHH
T ss_conf             9879998628987278999999984


No 55 
>>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} (A:1-66)
Probab=55.10  E-value=9.4  Score=18.80  Aligned_cols=19  Identities=26%  Similarity=0.398  Sum_probs=15.8

Q ss_pred             HHHHHHCCCCCHHHHHHHH
Q ss_conf             7899737898899999975
Q 537021.9.peg.8   78 LHLLQEINRIGKRVALELK   96 (148)
Q Consensus        78 ~~eL~~i~GIG~aka~~l~   96 (148)
                      +++|.++||||+..|..+.
T Consensus        11 I~~l~~LPGIG~KsA~Rla   29 (66)
T 1vdd_A           11 IRELSRLPGIGPKSAQRLA   29 (66)
T ss_dssp             HHHHHTSTTCCHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHH
T ss_conf             9999678998899999999


No 56 
>>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} (A:1-128)
Probab=52.95  E-value=16  Score=17.35  Aligned_cols=50  Identities=20%  Similarity=0.116  Sum_probs=27.9

Q ss_pred             HCCCCCC-CHHHHHHHHHHHCC-CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             3379989-88999999997379-9789850997899737898899999975499999
Q 537021.9.peg.8   48 FRLIPRK-DTKSIAKALLKRFA-TLGGVFGAPLHLLQEINRIGKRVALELKLVSVAS  102 (148)
Q Consensus        48 ~~g~~~~-~~~~lA~~lL~~fG-sL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~  102 (148)
                      ..|.+.+ .+..-|-..|..++ .+     .+.+++.+++|||+.-+..|.-..+-+
T Consensus        29 ~~g~~~r~~aY~kAa~~i~~lp~~I-----~s~~~~~~lpgIG~~ia~~I~E~l~tG   80 (128)
T 2bcq_A           29 VQGDKWRALGYAKAINALKSFHKPV-----TSYQEACSIPGIGKRMAEKIIEILESG   80 (128)
T ss_dssp             HTTCHHHHHHHHHHHHHHHSCCSCC-----CCHHHHHTSTTCCHHHHHHHHHHHHSS
T ss_pred             HCCCCHHHHHHHHHHHHHHHCCCCC-----CCHHHHHCCCCCCHHHHHHHHHHHHCC
T ss_conf             8499589999999999998598665-----899998279996489999999999739


No 57 
>>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} (A:182-261)
Probab=51.92  E-value=3.3  Score=21.76  Aligned_cols=37  Identities=14%  Similarity=0.150  Sum_probs=19.1

Q ss_pred             HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             7898509978997378988999999754999999999
Q 537021.9.peg.8   70 LGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRIL  106 (148)
Q Consensus        70 L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~  106 (148)
                      +..|..-+.+-.-.|+|||+.+|..|..-..--..+.
T Consensus        13 ~~~L~GD~sD~ipGV~GIG~ktA~~Li~~~gsle~i~   49 (80)
T 1exn_A           13 LKAIXGDLGDNIRGVEGIGAKRGYNIIREFGNVLDII   49 (80)
T ss_dssp             HHHHHCBGGGTBCCCTTCCHHHHHHHHHHHCSHHHHH
T ss_pred             HHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHH
T ss_conf             9997198313689999767999999999959999999


No 58 
>>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} (A:1-154)
Probab=51.87  E-value=11  Score=18.26  Aligned_cols=41  Identities=15%  Similarity=0.175  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHCC-CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             999999997379-9789850997899737898899999975499999
Q 537021.9.peg.8   57 KSIAKALLKRFA-TLGGVFGAPLHLLQEINRIGKRVALELKLVSVAS  102 (148)
Q Consensus        57 ~~lA~~lL~~fG-sL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~  102 (148)
                      ..-|-..|..++ .+     .+.+++.+++|||+.-+..|.-..+-+
T Consensus        62 Yr~Aa~~l~~~p~~I-----~s~~~l~~lpgIG~~ia~~I~E~l~tG  103 (154)
T 1jms_A           62 FMRASSVLKSLPFPI-----TSMKDTEGIPCLGDKVKSIIEGIIEDG  103 (154)
T ss_dssp             HHHHHHHHHTCSSCC-----CSGGGGTTCSSCCHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHCCCCC-----CCHHHHHCCCCCCHHHHHHHHHHHHHC
T ss_conf             999999998599777-----999998379996499999999999969


No 59 
>>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanococcus jannaschii} (A:210-274)
Probab=50.98  E-value=8.6  Score=19.05  Aligned_cols=22  Identities=32%  Similarity=0.277  Sum_probs=14.7

Q ss_pred             HHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             9737898899999975499999
Q 537021.9.peg.8   81 LQEINRIGKRVALELKLVSVAS  102 (148)
Q Consensus        81 L~~i~GIG~aka~~l~a~~El~  102 (148)
                      +..|+|||+.+|..|..-..--
T Consensus        18 ipGV~GIGpKtA~~li~~~~~l   39 (65)
T 1a76_A           18 PGGVKGIGFKRAYELVRSGVAK   39 (65)
T ss_dssp             TTTTTTCCHHHHHHHHHHTCHH
T ss_pred             CCCCCCEEHHHHHHHHHHCCCH
T ss_conf             5556856299999999972999


No 60 
>>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase/DNA complex; 2.00A {Archaeoglobus fulgidus} (A:221-288)
Probab=48.58  E-value=9.9  Score=18.65  Aligned_cols=24  Identities=17%  Similarity=0.140  Sum_probs=14.3

Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             737898899999975499999999
Q 537021.9.peg.8   82 QEINRIGKRVALELKLVSVASQRI  105 (148)
Q Consensus        82 ~~i~GIG~aka~~l~a~~El~rR~  105 (148)
                      -.|+|||+.+|..|..-..-...+
T Consensus        18 pGV~GIG~ktA~~li~~~~sle~i   41 (68)
T 1rxw_A           18 EGVKGVGVKKALNYIKTYGDIFRA   41 (68)
T ss_dssp             CCCTTCCHHHHHHHHHHHSSHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHCCHHHH
T ss_conf             899995789999999994999999


No 61 
>>1r4t_A Exoenzyme S; EXOS, GAP, toxin, virulence factor, signal transduction; NMR {Pseudomonas aeruginosa} (A:)
Probab=47.29  E-value=20  Score=16.63  Aligned_cols=72  Identities=19%  Similarity=0.124  Sum_probs=48.1

Q ss_pred             HHCCCCCCCHHHHHHHHHH---------HCCCHHH-----HHCCCHHHHHHCCCCCHHHHHHHHHH---HHHHHHHHHHH
Q ss_conf             7337998988999999997---------3799789-----85099789973789889999997549---99999999987
Q 537021.9.peg.8   47 LFRLIPRKDTKSIAKALLK---------RFATLGG-----VFGAPLHLLQEINRIGKRVALELKLV---SVASQRILKAN  109 (148)
Q Consensus        47 L~~g~~~~~~~~lA~~lL~---------~fGsL~~-----ll~as~~eL~~i~GIG~aka~~l~a~---~El~rR~~~~~  109 (148)
                      ++-+...+.....|..||+         .||+-++     |.+||+++|..+       +.+|..+   .+.-+|...+.
T Consensus        63 i~~~s~~~~~~~~A~~LL~~~VggipfqQWGT~GG~as~~v~~AS~e~L~~a-------~~~l~~v~~eva~L~~~V~aE  135 (153)
T 1r4t_A           63 IRAGSQVEESRIQAGRLLERSIGGIALQQWGTTGGAASQLVLDASPELRREI-------TDQLHQVMSEVALLRQAVESE  135 (153)
T ss_dssp             HHTTCSSHHHHHHHHHHHTSEETTEEGGGTTSSSSHHHHHHHHCSHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHHCCCCCCCHHHHHCCCHHHHHHHHHCCHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH
T ss_conf             7404168889999999874643563198731333589999985599999999-------999999999999999999998


Q ss_pred             HHHCCCCCCHHHHHHHH
Q ss_conf             64067788989999999
Q 537021.9.peg.8  110 WSIKKFLTPGQPCLISV  126 (148)
Q Consensus       110 ~~~~~~l~s~~~v~~yl  126 (148)
                      +.. ..-..|.++.||-
T Consensus       136 v~~-~~a~~~~~~~~~~  151 (153)
T 1r4t_A          136 VSR-VSADYPYDVPDYA  151 (153)
T ss_dssp             HHH-TC-----------
T ss_pred             HCC-CCCCCCCCCCCCC
T ss_conf             718-8788987753332


No 62 
>>3i1m_M 30S ribosomal protein S13; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F 1vs5_M 3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M ... (M:1-63)
Probab=46.10  E-value=12  Score=18.02  Aligned_cols=23  Identities=17%  Similarity=0.128  Sum_probs=18.2

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             89973789889999997549999
Q 537021.9.peg.8   79 HLLQEINRIGKRVALELKLVSVA  101 (148)
Q Consensus        79 ~eL~~i~GIG~aka~~l~a~~El  101 (148)
                      -.|..|.|||+..|.+|.....+
T Consensus        17 ~aLt~i~GIG~~~A~~Ic~~~gi   39 (63)
T 3i1m_M           17 IALTSIYGVGKTRSKAILAAAGI   39 (63)
T ss_dssp             HHGGGSTTCCHHHHHHHHTTTTC
T ss_pred             EEEECEECCCHHHHHHHHHHCCC
T ss_conf             87534457389999999999198


No 63 
>>2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M (m:1-88)
Probab=45.14  E-value=10  Score=18.54  Aligned_cols=24  Identities=17%  Similarity=0.191  Sum_probs=19.7

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             899737898899999975499999
Q 537021.9.peg.8   79 HLLQEINRIGKRVALELKLVSVAS  102 (148)
Q Consensus        79 ~eL~~i~GIG~aka~~l~a~~El~  102 (148)
                      -.|..|.|||+..|.+|.....+.
T Consensus        28 ~ALt~I~GIG~~~A~~Ic~~lgi~   51 (88)
T 2zkq_m           28 FAITAIKGVGRRYAHVVLRKADID   51 (88)
T ss_dssp             HHGGGSTTCCHHHHHHHHHHHTCC
T ss_pred             EEHHCCCCCCHHHHHHHHHHCCCC
T ss_conf             603024662899999999982999


No 64 
>>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-binding, excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} (A:219-300)
Probab=44.26  E-value=13  Score=17.82  Aligned_cols=19  Identities=26%  Similarity=0.214  Sum_probs=12.4

Q ss_pred             HHHCCCCCHHHHHHHHHHH
Q ss_conf             9737898899999975499
Q 537021.9.peg.8   81 LQEINRIGKRVALELKLVS   99 (148)
Q Consensus        81 L~~i~GIG~aka~~l~a~~   99 (148)
                      +..|+|||+.+|..|..-.
T Consensus        18 i~GV~GiG~ktA~~li~~~   36 (82)
T 2izo_A           18 PDGIRGIGPERALKIIKKY   36 (82)
T ss_dssp             TTCSTTCCHHHHHHHHHHS
T ss_pred             CCCCCCCCHHHHHHHHHHC
T ss_conf             3347994488999999983


No 65 
>>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, hydrolase; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A* (A:1-149)
Probab=42.09  E-value=7.1  Score=19.60  Aligned_cols=87  Identities=16%  Similarity=0.029  Sum_probs=54.7

Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHCC-CHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH-----------HHHHHH
Q ss_conf             9999997337998988999999997379-9789850997899737898899999975499999-----------999998
Q 537021.9.peg.8   41 EILELILFRLIPRKDTKSIAKALLKRFA-TLGGVFGAPLHLLQEINRIGKRVALELKLVSVAS-----------QRILKA  108 (148)
Q Consensus        41 ELLallL~~g~~~~~~~~lA~~lL~~fG-sL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~-----------rR~~~~  108 (148)
                      ++.+.+-..|.+    ..+|..+.+.|| .--.++..+|-.|+.+.|||-.+|-.|..-..+.           ...+.+
T Consensus         9 ~~~~~L~~~Gi~----~~~a~ki~~~yg~~a~~~i~~nPY~L~~i~gigF~~aD~iA~~~gi~~dd~~Ri~a~i~~~L~~   84 (149)
T 3e1s_A            9 RLLAGLQGLGLT----INQAQRAVKHFGADALDRLEKDLFTLTEVEGIGFLTADKLWQARGGALDDPRRLTAAAVYALQL   84 (149)
T ss_dssp             ---------------------------------------CGGGTSSSCCHHHHHTTC-------CCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCC----HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             999999877999----9999999999849999999949935541589995999999997698989999999999999999


Q ss_pred             H-HHHCCCCCCHHHHHHHHHHHHC
Q ss_conf             7-6406778898999999999845
Q 537021.9.peg.8  109 N-WSIKKFLTPGQPCLISVERHYP  131 (148)
Q Consensus       109 ~-~~~~~~l~s~~~v~~yl~~~l~  131 (148)
                      . .......-..+.+..-+...++
T Consensus        85 ~~~~~Ght~l~~~~L~~~~~~lL~  108 (149)
T 3e1s_A           85 AGTQAGHSFLPRSRAEKGVVHYTR  108 (149)
T ss_dssp             HHHHTCCSCEEHHHHHHHHHHHHC
T ss_pred             HHHCCCCEEEEHHHHHHHHHHHHC
T ss_conf             733489872149999999999867


No 66 
>>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} (A:)
Probab=40.52  E-value=15  Score=17.40  Aligned_cols=59  Identities=7%  Similarity=-0.026  Sum_probs=36.4

Q ss_pred             HHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHH
Q ss_conf             98509978997378988999999754999999999987640677889--899999999984
Q 537021.9.peg.8   72 GVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTP--GQPCLISVERHY  130 (148)
Q Consensus        72 ~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~~l~s--~~~v~~yl~~~l  130 (148)
                      ..-++....|..|+|||+.+|-.|....+-+.=...+...++..+..  .+.+.+=+...|
T Consensus       125 ~~n~~i~~~L~~I~GiG~~~a~~Iie~Re~g~F~S~eDl~~Rv~~~~~~~~~l~~~~le~L  185 (205)
T 2i5h_A          125 DSITTRMHQLELLPGVGKKMMWAIIEERKKRPFESFEDIAQRVKGIQRPEKLIVSRIIYEI  185 (205)
T ss_dssp             CCBCSSSBGGGGSTTCCHHHHHHHHHHHHHSCCCSHHHHHHHSTTCCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             8761878988744451589999999997548988999999885467789999999999996


No 67 
>>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication; 2.00A {Pyrococcus furiosus} (A:212-288)
Probab=39.83  E-value=17  Score=17.22  Aligned_cols=18  Identities=11%  Similarity=0.023  Sum_probs=10.2

Q ss_pred             HHHHHHHHHCCCHHHHHC
Q ss_conf             999999973799789850
Q 537021.9.peg.8   58 SIAKALLKRFATLGGVFG   75 (148)
Q Consensus        58 ~lA~~lL~~fGsL~~ll~   75 (148)
                      ..|-+|+++|||+.+++.
T Consensus        37 ktA~kli~~~gsle~i~~   54 (77)
T 1b43_A           37 KKALEIVRHSKDPLAKFQ   54 (77)
T ss_dssp             HHHHHHHHTCSSGGGGTG
T ss_pred             HHHHHHHHHHCCHHHHHC
T ss_conf             999999999599999752


No 68 
>>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} (A:504-671)
Probab=39.75  E-value=27  Score=15.88  Aligned_cols=58  Identities=21%  Similarity=0.184  Sum_probs=44.7

Q ss_pred             HHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             97337998988999999997379978985099789973789889999997549999999
Q 537021.9.peg.8   46 ILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVASQR  104 (148)
Q Consensus        46 lL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR  104 (148)
                      |-..|.++. ....|+.|.+++++...+..++.+++..+.++++..+..+.........
T Consensus         9 l~~l~i~~~-g~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   66 (168)
T 2owo_A            9 LYALGIREV-GEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAEESN   66 (168)
T ss_dssp             HHHTTCTTC-CHHHHHHHHHHHCSHHHHHTCCHHHHTTSTTCCHHHHHHHHHHHTCHHH
T ss_pred             HHHHHCCCC-CCCHHHHHHCCCCCHHHHHCCCHHHHHCCCCHHHHHHHHHHHHHCCHHH
T ss_conf             998631454-4320234310348899997089999867598019999999999759899


No 69 
>>2e1f_A Werner syndrome ATP-dependent helicase; HRDC domain, hydrolase; 2.00A {Homo sapiens} (A:)
Probab=39.62  E-value=27  Score=15.87  Aligned_cols=49  Identities=8%  Similarity=0.072  Sum_probs=37.2

Q ss_pred             HHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH
Q ss_conf             8985099789973789889999997549999999999876406778898
Q 537021.9.peg.8   71 GGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTPG  119 (148)
Q Consensus        71 ~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~~l~s~  119 (148)
                      ....=.+.++|.+|+|+|+.+....-.......++........+.+..+
T Consensus        49 A~~~P~~~~~L~~i~g~~~~~~~~~g~~l~~i~~~~~~~~~~~~~~p~~   97 (103)
T 2e1f_A           49 AKMRPTTVENVKRIDGVSEGKAAMLAPLLEVIKHFCQTNSVQTDLFSST   97 (103)
T ss_dssp             HHHCCCSHHHHTTSTTCCHHHHHHTHHHHHHHHHHHHHTTCCCCCCCC-
T ss_pred             HHHCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             9809999999837899999999999999999999998759988766777


No 70 
>>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (M:1-64)
Probab=39.06  E-value=14  Score=17.72  Aligned_cols=24  Identities=29%  Similarity=0.076  Sum_probs=19.3

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             899737898899999975499999
Q 537021.9.peg.8   79 HLLQEINRIGKRVALELKLVSVAS  102 (148)
Q Consensus        79 ~eL~~i~GIG~aka~~l~a~~El~  102 (148)
                      -.|..|.|||+..|.+|.....+.
T Consensus        17 ~aLt~I~GIG~~~A~~Ic~~lgi~   40 (64)
T 2vqe_M           17 VALTYIYGIGKARAKEALEKTGIN   40 (64)
T ss_dssp             HHHTTSSSCCSHHHHHHTTTTTCC
T ss_pred             EEEEEEECCCHHHHHHHHHHCCCC
T ss_conf             873306581899999999982998


No 71 
>>2dgz_A Werner syndrome protein variant; HRDC domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:)
Probab=39.06  E-value=21  Score=16.49  Aligned_cols=46  Identities=9%  Similarity=0.068  Sum_probs=35.4

Q ss_pred             HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             7898509978997378988999999754999999999987640677
Q 537021.9.peg.8   70 LGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKF  115 (148)
Q Consensus        70 L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~~  115 (148)
                      +....=.+.++|.+|+|||+.+....-....+..+.........+.
T Consensus        55 iA~~~P~t~~~L~~i~g~~~~~~~~~g~~l~~I~~~~~~~~~~~p~  100 (113)
T 2dgz_A           55 MAKMRPTTVENVKRIDGVSEGKAAMLAPLWEVIKHFCQTNSVQTDL  100 (113)
T ss_dssp             HHHHCCCSHHHHHHSSSCCTTGGGGGHHHHHHHHHHHHTTTCCCCC
T ss_pred             HHHHHCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             9983249999994689989999999999999999999983998665


No 72 
>>2r4f_A 3-hydroxy-3-methylglutaryl-coenzyme A reductase; oxidoreductase, cholesterol, biocynthesis, HMG-COA, NADPH, statin, alternative splicing; HET: RIE; 1.70A {Homo sapiens} PDB: 2q1l_A* 2q6c_A* 2q6b_A* 3bgl_A* 3cct_A* 3ccw_A* 3ccz_A* 3cd0_A* 3cd5_A* 3cd7_A* 3cda_A* 3cdb_A* 1dqa_A* 1dq9_A* 1dq8_A* 1hw8_A* 1hw9_A* 1hwi_A* 1hwj_A* 1hwk_A* ... (A:1-85)
Probab=37.28  E-value=21  Score=16.50  Aligned_cols=29  Identities=31%  Similarity=0.392  Sum_probs=22.7

Q ss_pred             HHHHH---CCHHHCCHHHHHHHHHHCCCCCCC
Q ss_conf             99982---392218989999999733799898
Q 537021.9.peg.8   27 DRFLQ---KGENALAYYEILELILFRLIPRKD   55 (148)
Q Consensus        27 Erll~---~G~~~LsD~ELLallL~~g~~~~~   55 (148)
                      ..+++   .|+.+|+|.|++.++...-.|.+.
T Consensus        15 ~~i~~~~~~~~~~lsDeEIi~lv~~g~Ip~Y~   46 (85)
T 2r4f_A           15 LQILGNAEKGAKFLSDAEIIQLVNAKHIPAYK   46 (85)
T ss_dssp             HHHHHSTTTGGGSSCHHHHHHHHHTTSSCGGG
T ss_pred             HHHHHCCCCCCCCCCHHHHHHHHHCCCCCHHH
T ss_conf             99872633477779989999999759976066


No 73 
>>2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae} (B:229-310)
Probab=36.37  E-value=21  Score=16.51  Aligned_cols=23  Identities=22%  Similarity=0.267  Sum_probs=17.9

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             89973789889999997549999
Q 537021.9.peg.8   79 HLLQEINRIGKRVALELKLVSVA  101 (148)
Q Consensus        79 ~eL~~i~GIG~aka~~l~a~~El  101 (148)
                      -.|..|.|||...|.+|.....+
T Consensus        29 ~aLt~i~GIG~~~A~~I~~~~gi   51 (82)
T 2zbk_B           29 FLVNEFQSIGDTTADKILELAGL   51 (82)
T ss_dssp             HHHTTSTTCCHHHHHHHHHHTTC
T ss_pred             HHHCCCCCCCHHHHHHHHHHHCC
T ss_conf             55157646760877766655236


No 74 
>>3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA; 2.60A {Sulfolobus acidocaldarius} (A:185-235)
Probab=35.15  E-value=21  Score=16.52  Aligned_cols=34  Identities=26%  Similarity=0.315  Sum_probs=26.6

Q ss_pred             HHHHHCC--CHHHHHCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf             9997379--97898509978997378988999999754
Q 537021.9.peg.8   62 ALLKRFA--TLGGVFGAPLHLLQEINRIGKRVALELKL   97 (148)
Q Consensus        62 ~lL~~fG--sL~~ll~as~~eL~~i~GIG~aka~~l~a   97 (148)
                      +-|++.|  -|..+++.+..+|.++  ||.+||.-|.-
T Consensus         9 ~kL~~lGInkL~Dil~~~f~klk~i--iG~aKa~YL~~   44 (51)
T 3bq0_A            9 RRLNELGIQKLRDILSKNYNELEKI--TGKAKALYLLK   44 (51)
T ss_dssp             HHHTTTTCCBGGGGGGSCHHHHHHH--HCHHHHHHHHH
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHH--HCCCHHHHHHH
T ss_conf             5545327874788876426678876--06403578897


No 75 
>>1jei_A Emerin; membrane protein; NMR {Synthetic} (A:)
Probab=34.96  E-value=13  Score=17.88  Aligned_cols=33  Identities=18%  Similarity=0.170  Sum_probs=27.7

Q ss_pred             HHHCCHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             221898999999973379989889999999973
Q 537021.9.peg.8   34 ENALAYYEILELILFRLIPRKDTKSIAKALLKR   66 (148)
Q Consensus        34 ~~~LsD~ELLallL~~g~~~~~~~~lA~~lL~~   66 (148)
                      ...|||.||.+-+..+|.+.-.+.+.-+.+..+
T Consensus         3 ~~~LSd~ELr~~L~~~G~~~GPIt~tTR~vy~k   35 (53)
T 1jei_A            3 YADLSDTELTTLLRRYNIPHGPVVGSTRRLYEK   35 (53)
T ss_dssp             TTTCCHHHHHHHHSSSCCSCCCCCSGGGHHHHH
T ss_pred             HHHHCHHHHHHHHHHHCCCCCCCCCCHHHHHHH
T ss_conf             656168999999999299988800613999999


No 76 
>>2dla_A 397AA long hypothetical protein; helix bundle, twisted beta-sheet, replication; 2.90A {Pyrococcus horikoshii OT3} (A:1-105,A:194-222)
Probab=33.40  E-value=14  Score=17.70  Aligned_cols=18  Identities=39%  Similarity=0.560  Sum_probs=14.6

Q ss_pred             HHHHHHHHCCCHHHHHCC
Q ss_conf             999999737997898509
Q 537021.9.peg.8   59 IAKALLKRFATLGGVFGA   76 (148)
Q Consensus        59 lA~~lL~~fGsL~~ll~a   76 (148)
                      -|++|++.|||+..++++
T Consensus        11 kAk~LlkeFG~in~fLe~   28 (134)
T 2dla_A           11 KAKELLKGFGSINDFMDA   28 (134)
T ss_dssp             HHHHHTTTTSSHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHH
T ss_conf             999999985059999987


No 77 
>>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A (A:230-311)
Probab=32.14  E-value=33  Score=15.28  Aligned_cols=20  Identities=15%  Similarity=0.071  Sum_probs=10.9

Q ss_pred             HHHHHCCCCCHHHHHHHHHH
Q ss_conf             89973789889999997549
Q 537021.9.peg.8   79 HLLQEINRIGKRVALELKLV   98 (148)
Q Consensus        79 ~eL~~i~GIG~aka~~l~a~   98 (148)
                      ..|++|+||++.+|..|...
T Consensus         8 ~~L~qi~gvs~~~A~aI~~~   27 (82)
T 2ziu_A            8 RQLMQISGVSGDKAAAVLEH   27 (82)
T ss_dssp             HHHTTBTTCCHHHHHHHHHH
T ss_pred             HHHHCCCCCCHHHHHHHHHH
T ss_conf             99980899999999999997


No 78 
>>2rhf_A DNA helicase RECQ; HRDC, D. radiodurans, ATP-binding, hydrolase, nucleotide-binding; HET: DNA; 1.10A {Deinococcus radiodurans R1} (A:)
Probab=29.72  E-value=38  Score=14.85  Aligned_cols=35  Identities=14%  Similarity=0.078  Sum_probs=23.5

Q ss_pred             HHHHCCCHHHHHHCCCCCHHHHHH-HHHHHHHHHHH
Q ss_conf             898509978997378988999999-75499999999
Q 537021.9.peg.8   71 GGVFGAPLHLLQEINRIGKRVALE-LKLVSVASQRI  105 (148)
Q Consensus        71 ~~ll~as~~eL~~i~GIG~aka~~-l~a~~El~rR~  105 (148)
                      ....-.+.++|.+|+|||+.++.. -..+.++.+.+
T Consensus        39 A~~~P~t~~eL~~i~gi~~~~~~~~G~~il~~i~~~   74 (77)
T 2rhf_A           39 AARQPRTLAELAEVPGLGEKRIEAYGERILDAINTV   74 (77)
T ss_dssp             HHHCCCSHHHHTTSTTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             860934999973799989999999999999999998


No 79 
>>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:119-241)
Probab=26.20  E-value=44  Score=14.46  Aligned_cols=56  Identities=11%  Similarity=-0.017  Sum_probs=41.8

Q ss_pred             CHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEEE
Q ss_conf             9789973789889999997549999999999876406778898999999999845978000
Q 537021.9.peg.8   77 PLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTPGQPCLISVERHYPMKNANN  137 (148)
Q Consensus        77 s~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~~l~s~~~v~~yl~~~l~~~~~E~  137 (148)
                      ..+.+.+++|+|+.....|+...+....     ...+..+.....+.+.+...+...+.|.
T Consensus        11 ~~~~i~~l~gfG~K~~~~il~gl~~~~~-----~~~ri~~~ea~~~a~~i~~~l~~~~~~~   66 (123)
T 2w9m_A           11 ESGELAGLKGFGAKSAATILENVVFLFE-----ARQRQSLRAGLAVAEELAGALTDLSPAP   66 (123)
T ss_dssp             HHTTTTTSTTCCHHHHHHHHHHHHHHHH-----HCSSEEHHHHHHHHHHHHHHTGGGCCEE
T ss_pred             HCCCHHHHHCCCHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             6088012110138899999987878887-----5356699999999999997544766997


No 80 
>>5csm_A Chorismate mutase; chorismate pyruvatemutase, allosteric protein, complex (isomerase/peptide), transition state analog; HET: TRP; 2.00A {Saccharomyces cerevisiae} (A:)
Probab=25.89  E-value=30  Score=15.52  Aligned_cols=37  Identities=14%  Similarity=0.122  Sum_probs=28.1

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCHHH
Q ss_conf             8988999999754999999999987640677-889899
Q 537021.9.peg.8   85 NRIGKRVALELKLVSVASQRILKANWSIKKF-LTPGQP  121 (148)
Q Consensus        85 ~GIG~aka~~l~a~~El~rR~~~~~~~~~~~-l~s~~~  121 (148)
                      ..-|.+.++-+.|...|+||++..+..-... -++|+.
T Consensus       138 ~NyGSta~cDi~cLQALSrRIHyGKFVAEaKF~~~p~~  175 (256)
T 5csm_A          138 NNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPL  175 (256)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHTCHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH
T ss_conf             31178999999999999988764346768776419999


No 81 
>>1t6c_A Exopolyphosphatase; alpha/beta protein, actin-like fold, hydrolase; 1.53A {Aquifex aeolicus VF5} (A:137-298)
Probab=25.52  E-value=34  Score=15.20  Aligned_cols=94  Identities=9%  Similarity=-0.017  Sum_probs=55.8

Q ss_pred             HHHHHHHHHCCHHHCCHHHHHHHHHHCCC----C--------CCCHHHHHHHHHHHC-----------------CC-HHH
Q ss_conf             01999998239221898999999973379----9--------898899999999737-----------------99-789
Q 537021.9.peg.8   23 NRLRDRFLQKGENALAYYEILELILFRLI----P--------RKDTKSIAKALLKRF-----------------AT-LGG   72 (148)
Q Consensus        23 ~R~RErll~~G~~~LsD~ELLallL~~g~----~--------~~~~~~lA~~lL~~f-----------------Gs-L~~   72 (148)
                      -|++|+|...++..-.+++.+.-.+....    .        +-.+..+|+-.....                 -. ...
T Consensus        35 vrl~e~f~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~ig~gGt~r~la~l~~~~~~~~~~~~~g~~i~~~~l~~~~~~  114 (162)
T 1t6c_A           35 VNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDT  114 (162)
T ss_dssp             HHHHHHHCCSSSCCHHHHHHHHHHHHHHHTTTCCCCSEEEEESHHHHHHHHHHTTCCSCCHHHHTTCEEEHHHHHHHHHH
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             88999844689976789999999999997542033366999537446588887541347843342200126889999999


Q ss_pred             HHCCCHHHH-HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             850997899-73789889999997549999999999876406778
Q 537021.9.peg.8   73 VFGAPLHLL-QEINRIGKRVALELKLVSVASQRILKANWSIKKFL  116 (148)
Q Consensus        73 ll~as~~eL-~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~~~l  116 (148)
                      +...+.++. .+++|+++..+-.|.+...+...+++.--.+...+
T Consensus       115 l~~~~~~e~~~~~~gl~~~Ra~~i~~g~~il~~l~~~~~~~~i~v  159 (162)
T 1t6c_A          115 FKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDCLIV  159 (162)
T ss_dssp             HTTSCHHHHHHHSTTSCGGGTTTHHHHHHHHHHHHHHHTCSEEEE
T ss_pred             HHCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             972999999875589996899859999999999999719898999


No 82 
>>3bqs_A Uncharacterized protein; 10114F, NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.42A {Listeria monocytogenes str} PDB: 3bqt_A (A:)
Probab=24.79  E-value=23  Score=16.25  Aligned_cols=21  Identities=33%  Similarity=0.400  Sum_probs=15.0

Q ss_pred             CHHHHHHCCCCCHHHHHHHHH
Q ss_conf             978997378988999999754
Q 537021.9.peg.8   77 PLHLLQEINRIGKRVALELKL   97 (148)
Q Consensus        77 s~~eL~~i~GIG~aka~~l~a   97 (148)
                      +..+|..+||||++.+..|..
T Consensus         2 a~~~l~~LPNiG~~~e~~L~~   22 (93)
T 3bqs_A            2 SLANLSELPNIGKVLEQDLIK   22 (93)
T ss_dssp             CCSCGGGSTTCCHHHHHHHHH
T ss_pred             CHHHHHHCCCCCHHHHHHHHH
T ss_conf             757785689999999999998


No 83 
>>2ziu_B Crossover junction endonuclease EME1; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Homo sapiens} PDB: 2ziw_B 2zix_B 2ziv_B (B:242-341)
Probab=23.53  E-value=50  Score=14.14  Aligned_cols=19  Identities=11%  Similarity=0.167  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHCCCHHHHHC
Q ss_conf             9999999973799789850
Q 537021.9.peg.8   57 KSIAKALLKRFATLGGVFG   75 (148)
Q Consensus        57 ~~lA~~lL~~fGsL~~ll~   75 (148)
                      .+.|..+.++|.+...|+.
T Consensus        24 ~~kA~aI~~~YPTp~~L~~   42 (100)
T 2ziu_B           24 LEMASAVVNAYPSPQLLVQ   42 (100)
T ss_dssp             HHHHHHHHHHSCSHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHH
T ss_conf             9999999997899999999


No 84 
>>3cer_A Possible exopolyphosphatase-like protein; NESG, BLR13, Q8G5J2, X-RAY, structure, structural genomics, PSI-2; 2.40A {Bifidobacterium longum NCC2705} (A:142-326)
Probab=23.04  E-value=28  Score=15.71  Aligned_cols=44  Identities=11%  Similarity=-0.116  Sum_probs=34.6

Q ss_pred             HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             78985099789973789889999997549999999999876406
Q 537021.9.peg.8   70 LGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIK  113 (148)
Q Consensus        70 L~~ll~as~~eL~~i~GIG~aka~~l~a~~El~rR~~~~~~~~~  113 (148)
                      +..+...+.++..+++|+.+..+-.|.+..-+...+.+.--.++
T Consensus       126 ~~~l~~~~~~~r~~~~gl~~~Rad~i~~g~~il~~l~~~~~~~~  169 (185)
T 3cer_A          126 DDKFLRXTRAERREYKTIHPGRIDVVGGGAVVWSRVLARVSEAA  169 (185)
T ss_dssp             HHHHHSSCHHHHHTCTTSCTTTTTTHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             99997799999975579897799989999999999999876520


No 85 
>>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} (A:635-702)
Probab=22.76  E-value=50  Score=14.11  Aligned_cols=35  Identities=14%  Similarity=0.230  Sum_probs=21.9

Q ss_pred             HHHHHHH-HCCCHHHHHCCCHHHHHHCCCCCHHHHHHHH
Q ss_conf             9999997-3799789850997899737898899999975
Q 537021.9.peg.8   59 IAKALLK-RFATLGGVFGAPLHLLQEINRIGKRVALELK   96 (148)
Q Consensus        59 lA~~lL~-~fGsL~~ll~as~~eL~~i~GIG~aka~~l~   96 (148)
                      -|+.|.+ .|.|+..+..++ +.+.++  ||+..|.+|.
T Consensus        10 RAR~Ly~aGiks~~dla~ap-~~l~~~--iG~k~A~~I~   45 (68)
T 2p6r_A           10 RARKLYNAGIRNAEDIVRHR-EKVASL--IGRGIAERVV   45 (68)
T ss_dssp             HHHHHHTTTCCSHHHHHHTH-HHHHHH--HCHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHCCC-HHHHHH--HCCCHHHHHH
T ss_conf             99999987999999997498-878977--6346389999


No 86 
>>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} (X:1-14,X:218-292)
Probab=22.03  E-value=53  Score=13.95  Aligned_cols=26  Identities=23%  Similarity=0.378  Sum_probs=14.0

Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             73789889999997549999999999
Q 537021.9.peg.8   82 QEINRIGKRVALELKLVSVASQRILK  107 (148)
Q Consensus        82 ~~i~GIG~aka~~l~a~~El~rR~~~  107 (148)
                      ..|+|||+.+|..|..-..=...+..
T Consensus        32 pGV~GIG~KtA~kLI~~ygsle~ii~   57 (89)
T 1ul1_X           32 ESIRGIGPKRAVDLIQKHKSIEEIVR   57 (89)
T ss_dssp             CCCTTCCHHHHHHHHHHSSSHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHCCCHHHHHH
T ss_conf             55788569999999998099999999


No 87 
>>1wud_A ATP-dependent DNA helicase RECQ; DNA-binding domain, HRDC, hydrolase; 2.20A {Escherichia coli} (A:)
Probab=20.68  E-value=56  Score=13.77  Aligned_cols=37  Identities=11%  Similarity=0.055  Sum_probs=26.1

Q ss_pred             HHHHHCCCHHHHHHCCCCCHHHHHHH-HHHHHHHHHHH
Q ss_conf             78985099789973789889999997-54999999999
Q 537021.9.peg.8   70 LGGVFGAPLHLLQEINRIGKRVALEL-KLVSVASQRIL  106 (148)
Q Consensus        70 L~~ll~as~~eL~~i~GIG~aka~~l-~a~~El~rR~~  106 (148)
                      +....=.+.++|.+|.|+|+.++..- ..+.++..++.
T Consensus        46 iA~~~P~t~~eL~~i~g~~~~~~~~yG~~il~~i~~~~   83 (89)
T 1wud_A           46 XAEQXPITASEXLSVNGVGXRKLERFGKPFXALIRAHV   83 (89)
T ss_dssp             HHHHCCCSHHHHHTSTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             99978899999807999899999999999999999998


Done!