Query         gi|254780239|ref|YP_003064652.1| 30S ribosomal protein S13 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 122
No_of_seqs    126 out of 1448
Neff          6.1 
Searched_HMMs 23785
Date          Tue May 24 00:41:44 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780239.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 2vqe_M 30S ribosomal protein S 100.0       0       0  311.5   5.6  122    1-122     1-122 (126)
  2 2zkq_m 40S ribosomal protein S 100.0 1.4E-45       0  302.1   8.4  119    1-122    12-152 (152)
  3 3ofp_M 30S ribosomal protein S 100.0 2.2E-43       0  289.5  -0.1  113    2-115     1-113 (113)
  4 3bbn_M Ribosomal protein S13;  100.0 5.4E-38 2.3E-42  256.0  -2.0  100    1-112    46-145 (145)
  5 1ee8_A MUTM (FPG) protein; bet  96.5  0.0023 9.8E-08   41.0   4.3   50   12-61    143-195 (266)
  6 3gpu_A DNA glycosylase; DNA gl  96.5  0.0026 1.1E-07   40.7   4.4   50   12-61    155-207 (256)
  7 1tdz_A Formamidopyrimidine-DNA  96.4   0.003 1.2E-07   40.4   4.5   49   13-61    155-206 (272)
  8 3a46_A Formamidopyrimidine-DNA  96.4  0.0029 1.2E-07   40.4   4.5   48   14-61    156-207 (289)
  9 1k3x_A Endonuclease VIII; hydr  96.3  0.0035 1.5E-07   39.9   4.3   52   11-62    149-203 (262)
 10 1k82_A Formamidopyrimidine-DNA  96.3  0.0043 1.8E-07   39.4   4.5   48   14-61    152-202 (268)
 11 1tdh_A NEI endonuclease VIII-l  89.4   0.075 3.1E-06   31.7   0.7   42   13-54    159-203 (364)
 12 1mu5_A Type II DNA topoisomera  88.7    0.37 1.6E-05   27.4   3.8   43   20-62    261-303 (471)
 13 1x2i_A HEF helicase/nuclease;   84.7    0.38 1.6E-05   27.3   2.1   52   15-66     12-72  (75)
 14 3fut_A Dimethyladenosine trans  83.8     1.3 5.6E-05   23.9   4.6   50   12-62    220-269 (271)
 15 1z00_A DNA excision repair pro  83.7    0.27 1.1E-05   28.3   1.0   50   14-65     16-76  (89)
 16 2a1j_B DNA excision repair pro  81.0    0.29 1.2E-05   28.0   0.3   49   14-64     29-88  (91)
 17 3ftd_A Dimethyladenosine trans  78.4     1.8 7.5E-05   23.1   3.7   34   30-63    214-247 (249)
 18 1qyr_A KSGA, high level kasuga  77.2    0.67 2.8E-05   25.7   1.2   45   12-62    206-250 (252)
 19 1s5l_U Photosystem II 12 kDa e  73.3     3.5 0.00015   21.3   4.0   54    9-62     55-111 (134)
 20 3bz1_U Photosystem II 12 kDa e  71.3       4 0.00017   21.0   4.0   54    9-62     25-81  (104)
 21 1kft_A UVRC, excinuclease ABC   70.2    0.81 3.4E-05   25.3   0.2   46    9-56     15-61  (78)
 22 2a1j_A DNA repair endonuclease  69.4     2.6 0.00011   22.1   2.7   37   19-57      6-42  (63)
 23 3fhg_A Mjogg, N-glycosylase/DN  67.7     4.2 0.00018   20.8   3.4   40   17-60    117-156 (207)
 24 1cuk_A RUVA protein; DNA repai  61.7     1.8 7.7E-05   23.0   0.7   20   18-37    109-128 (203)
 25 2nrt_A Uvrabc system protein C  59.8     5.1 0.00022   20.3   2.7   39   17-57    168-206 (220)
 26 1z00_B DNA repair endonuclease  59.8       5 0.00021   20.3   2.6   39   18-58     19-57  (84)
 27 1ixr_A Holliday junction DNA h  58.4     2.5 0.00011   22.2   0.9   21   18-38    108-128 (191)
 28 2ztd_A Holliday junction ATP-d  57.3     2.6 0.00011   22.2   0.8   21   18-38    124-144 (212)
 29 2ihm_A POL MU, DNA polymerase   55.1     7.5 0.00031   19.3   2.9   37   17-54    102-142 (360)
 30 2grj_A Dephospho-COA kinase; T  54.4      10 0.00042   18.5   3.4   54   12-65     10-67  (192)
 31 2w9m_A Polymerase X; SAXS, DNA  52.7       4 0.00017   20.9   1.2   23   17-40     97-119 (578)
 32 3fhf_A Mjogg, N-glycosylase/DN  51.9     4.3 0.00018   20.7   1.2   39   18-60    126-164 (214)
 33 1jms_A Terminal deoxynucleotid  51.7     4.1 0.00017   20.9   1.1   25   16-41    120-144 (381)
 34 1vq8_Y 50S ribosomal protein L  49.8     2.8 0.00012   21.9   0.0   45   12-57     10-54  (241)
 35 2duy_A Competence protein come  49.2     9.8 0.00041   18.5   2.7   49   12-60     22-73  (75)
 36 1mpg_A ALKA, 3-methyladenine D  47.7      13 0.00053   17.8   3.1   35   14-48    204-239 (282)
 37 3mr3_A DNA polymerase ETA; POL  47.5      16 0.00068   17.2   3.6   40   17-56    253-292 (435)
 38 1pu6_A 3-methyladenine DNA gly  45.6      17 0.00072   17.0   4.3   41   16-60    120-160 (218)
 39 1m3q_A 8-oxoguanine DNA glycos  45.5     5.3 0.00022   20.2   0.9   42   14-58    227-268 (317)
 40 3c65_A Uvrabc system protein C  44.1     3.9 0.00016   21.0   0.0   41   14-56    170-210 (226)
 41 2bgw_A XPF endonuclease; hydro  43.8      13 0.00053   17.8   2.6   22   17-38    162-183 (219)
 42 3i0w_A 8-oxoguanine-DNA-glycos  43.8     5.8 0.00024   20.0   0.9   30   15-44    209-238 (290)
 43 2fmp_A DNA polymerase beta; nu  43.4       7 0.00029   19.4   1.2   39   17-56     98-140 (335)
 44 2hnh_A DNA polymerase III alph  41.0      12 0.00052   17.9   2.2   50    9-58    825-884 (910)
 45 2h56_A DNA-3-methyladenine gly  39.6     6.1 0.00025   19.8   0.4   45   14-64    135-180 (233)
 46 2eo2_A Adult MALE hypothalamus  39.4      14 0.00059   17.5   2.3   26   33-59     36-61  (71)
 47 3e1s_A Exodeoxyribonuclease V,  38.6     3.6 0.00015   21.2  -0.9   28   16-43     43-70  (574)
 48 1im4_A DBH; DNA polymerase PAL  38.0      13 0.00054   17.8   1.9   20   70-89    130-149 (221)
 49 2edu_A Kinesin-like protein KI  37.1      23 0.00095   16.3   3.0   42   18-59     41-89  (98)
 50 3f2b_A DNA-directed DNA polyme  36.5      24   0.001   16.1   4.4   60   12-90    962-1021(1041)
 51 1gm5_A RECG; helicase, replica  35.1      13 0.00055   17.7   1.6   29   11-40    109-137 (780)
 52 2jhn_A ALKA, 3-methyladenine D  34.2     9.7 0.00041   18.6   0.7   33   15-48    208-241 (295)
 53 2bcq_A DNA polymerase lambda;   32.9     5.8 0.00024   19.9  -0.6   30   10-40     89-118 (335)
 54 1kg2_A A/G-specific adenine gl  30.9      13 0.00056   17.7   1.0   28    8-38    103-130 (225)
 55 2abk_A Endonuclease III; DNA-r  30.0      14 0.00057   17.7   0.9   22   16-37    108-129 (211)
 56 1orn_A Endonuclease III; DNA r  29.2      15 0.00065   17.3   1.1   27    8-37    107-133 (226)
 57 3fsp_A A/G-specific adenine gl  29.1      15 0.00062   17.4   1.0   28    7-37    111-138 (369)
 58 3doa_A Fibrinogen binding prot  28.7      13 0.00057   17.7   0.7   36   14-49    189-225 (288)
 59 3mfi_A DNA polymerase ETA; DNA  27.8      16 0.00065   17.3   0.9   40   17-56    307-352 (520)
 60 1kea_A Possible G-T mismatches  27.4      17 0.00073   17.0   1.1   25   17-41    115-139 (221)
 61 1zq9_A Probable dimethyladenos  25.1      37  0.0016   14.9   3.8   32   30-62    248-279 (285)
 62 3lay_A Zinc resistance-associa  23.1      41  0.0017   14.7   2.9   58    5-62     21-82  (175)
 63 3n5n_X A/G-specific adenine DN  23.0      22 0.00092   16.4   0.9   20   19-38    131-150 (287)
 64 1vdd_A Recombination protein R  22.6      26  0.0011   16.0   1.2   80   15-95     10-108 (228)
 65 2r6f_A Excinuclease ABC subuni  22.2      42  0.0018   14.6   3.6   85   27-113   336-442 (972)
 66 3hdt_A Putative kinase; struct  22.0      43  0.0018   14.6   3.1   34    7-40      7-41  (223)
 67 1ngn_A Methyl-CPG binding prot  21.3      28  0.0012   15.7   1.2   19   18-36    105-123 (155)

No 1  
>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} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ...
Probab=100.00  E-value=0  Score=311.47  Aligned_cols=122  Identities=59%  Similarity=0.919  Sum_probs=117.9

Q ss_pred             CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf             94551675899857666431200717689999999808882120022798999999986124564333788999999999
Q gi|254780239|r    1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKR   80 (122)
Q Consensus         1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~r   80 (122)
                      |+||+|+|||++|+|.+|||+|||||+++|.+||+.+||||++++++||++|+++|+++|+++|.+|+||++.+.+||+|
T Consensus         1 M~RI~g~~i~~~K~v~~aLt~I~GIG~~~A~~Ic~~lGId~~~kvg~Lt~~qi~~l~~~i~~~~~i~~~L~~~~~~~i~r   80 (126)
T 2vqe_M            1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKR   80 (126)
T ss_dssp             -CCCSTTCCCCSSBHHHHHTTSSSCCSHHHHHHTTTTTCCTTSBGGGCCHHHHHHHHHHHHTTSCCHHHHHHHHHHHHHH
T ss_pred             CCEECCCCCCCCCEEEEEECCEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             97265744899978787620434838999999999859796630163999999999999831451147899999998999


Q ss_pred             HHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             973031001233179878770778776577776655423469
Q gi|254780239|r   81 LMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR  122 (122)
Q Consensus        81 l~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk  122 (122)
                      |++|+||||+||.+|||||||||||||||+|+..+++.++||
T Consensus        81 l~~i~syrG~RH~~gLpvRGQrT~tn~rt~kg~~~~~~~kk~  122 (126)
T 2vqe_M           81 LMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKK  122 (126)
T ss_dssp             HHHTTCHHHHHHHTTCCSSSCCCSSCCHHHHCSCCCCCCCCS
T ss_pred             HHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             887431212334069987777787775567888553555667


No 2  
>2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M 3jyv_M*
Probab=100.00  E-value=1.4e-45  Score=302.09  Aligned_cols=119  Identities=29%  Similarity=0.472  Sum_probs=114.6

Q ss_pred             CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCC-----------------
Q ss_conf             945516758998576664312007176899999998088821200227989999999861245-----------------
Q gi|254780239|r    1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQD-----------------   63 (122)
Q Consensus         1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~-----------------   63 (122)
                      ||||+|+|||++|+|.+|||+|||||+++|.+||+.+||||++++++||++|+++|+++|+++                 
T Consensus        12 ivRI~g~dI~g~K~v~~aLt~I~GIG~~~A~~Ic~~lgI~~~~kvg~Lt~~ql~kl~~~I~~~~~~~ip~w~~nr~~d~~   91 (152)
T 2zkq_m           12 ILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIMQNPRQYKIPDWFLNRQKDVK   91 (152)
T ss_dssp             -CCCSTTCCCCSSBHHHHGGGSTTCCHHHHHHHHHHHTCCTTSBTTTSCHHHHHHHHHHHHTTCSCCSCCCSSCSSSCCC
T ss_pred             HHHEECCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             34132852799978876500210658999999999938995430151999999999999850001157558776566650


Q ss_pred             -----CCCCHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             -----64333788999999999973031001233179878770778776577776655423469
Q gi|254780239|r   64 -----YQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR  122 (122)
Q Consensus        64 -----~~i~~~L~~~~~~~i~rl~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk  122 (122)
                           |++|+||++.+++||+||++|+||||+||++|||||||||||||||++++   +|.+||
T Consensus        92 ~g~~~hli~~dL~~~~~~dI~rl~~i~syRG~RH~~gLpVRGQrT~tN~R~~~~~---gv~~kK  152 (152)
T 2zkq_m           92 DGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTGRRGRTV---GVSKKK  152 (152)
T ss_dssp             CCSSCCCSSHHHHHHHHHHHHHHHHSSCHHHHHHHHTCBSBCCCSSSSCCSSSCC---CCCCCC
T ss_pred             CCCCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC---CCCCCC
T ss_conf             4531022076799999997999998605889998758987877688777778866---767789


No 3  
>3ofp_M 30S ribosomal protein S13; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_M* 2wwl_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M 2qbf_M 2qbh_M* 2qbj_M* 2qou_M* 2qow_M* 2qoy_M* 2qp0_M* ...
Probab=100.00  E-value=2.2e-43  Score=289.50  Aligned_cols=113  Identities=56%  Similarity=0.875  Sum_probs=109.5

Q ss_pred             CEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             45516758998576664312007176899999998088821200227989999999861245643337889999999999
Q gi|254780239|r    2 ARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRL   81 (122)
Q Consensus         2 vrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~rl   81 (122)
                      +||+|+|||++|+|++|||+|||||+++|.+||+++||||++++++||++|++.|+++|+ +|.+|+||++.+.+||+||
T Consensus         1 aRI~g~dip~~K~v~~ALt~I~GIG~~~A~~Ic~~lgi~~~~rv~~Lt~~qi~~l~~~i~-~~~i~~~L~~~~~~~I~rl   79 (113)
T 3ofp_M            1 ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA-KFVVEGDLRREISMSIKRL   79 (113)
T ss_dssp             CCTTSSCCCCCCCHHHHHTSSSSCCSSHHHHGGGTTTCCSSCCSSSCCTTSSTTTHHHHH-SSCCHHHHHHHTTTHHHHG
T ss_pred             CEECCCCCCCCCEEEEEEECEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHH
T ss_conf             902686699997866550143474899999999984989874048599999999999986-1031025899999979999


Q ss_pred             HHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             7303100123317987877077877657777665
Q gi|254780239|r   82 MDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGK  115 (122)
Q Consensus        82 ~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~  115 (122)
                      ++|+||||+||.+|||||||||||||||+|+.++
T Consensus        80 ~~i~~yRG~RH~~gLpvRGQrT~tnart~k~~~k  113 (113)
T 3ofp_M           80 MDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK  113 (113)
T ss_dssp             GGSSCSTTTTTTTSSCSSSCCSSSCCSSSSCSCC
T ss_pred             HHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             8851042111226998887778777524588998


No 4  
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa}
Probab=100.00  E-value=5.4e-38  Score=256.01  Aligned_cols=100  Identities=48%  Similarity=0.740  Sum_probs=92.9

Q ss_pred             CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf             94551675899857666431200717689999999808882120022798999999986124564333788999999999
Q gi|254780239|r    1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKR   80 (122)
Q Consensus         1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~r   80 (122)
                      ||||+|+|||++|+|++|||+|||||+++|.+||+++|||+ .++++|+|+|+..+++.+           +.+++||+|
T Consensus        46 ~vRI~GvnIp~nK~V~~ALT~IyGIG~~~A~~Ic~~lgId~-kkv~dLteeel~~i~~~r-----------r~~~~dIkR  113 (145)
T 3bbn_M           46 CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDN-KVTKDLSEEEVIILRKEK-----------RFNRVAIER  113 (145)
T ss_dssp             -CCCSSSCCCCSSBTTTGGGGSTTCCSSTTTGGGTTTTCCS-CBTTSCCSSTTHHHHSSC-----------CCCSTTTHH
T ss_pred             EEEEECCCCCCCCEEEEHHHHHHCCCHHHHHHHHHHCCCCH-HHHHHCCHHHHHHHHHHH-----------HHHHHHHHH
T ss_conf             89984874899977212355674638899999999859974-667654787999999999-----------998999999


Q ss_pred             HHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             97303100123317987877077877657777
Q gi|254780239|r   81 LMDLGCYRGLRHRRGLPVRGQRTHTNARTRKK  112 (122)
Q Consensus        81 l~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~  112 (122)
                      |++|+||||+||.+|||||||||||||||+|+
T Consensus       114 Lk~I~sYRG~RH~~gLPVRGQRTrTNaRT~KG  145 (145)
T 3bbn_M          114 LKEIRCYRGIRHKLGLPVRGQRTKNNCRTLKG  145 (145)
T ss_dssp             HHCCCCSCCTTTTTTCCSSSCCTTTCCCSSCC
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
T ss_conf             99850055445524998687778777666687


No 5  
>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8} SCOP: a.156.1.2 b.113.1.1 g.39.1.8
Probab=96.51  E-value=0.0023  Score=41.03  Aligned_cols=50  Identities=20%  Similarity=0.284  Sum_probs=42.3

Q ss_pred             CCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             85766643---120071768999999980888212002279899999998612
Q gi|254780239|r   12 AKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE   61 (122)
Q Consensus        12 ~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~   61 (122)
                      +++|.-+|   ..|-|||...+..||..++|+|..++.+|+++|+..|-+.+.
T Consensus       143 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~L~~~e~~~L~~~~~  195 (266)
T 1ee8_A          143 ARPLKALLLDQRLAAGVGNIYADEALFRARLSPFRPARSLTEEEARRLYRALR  195 (266)
T ss_dssp             CSBHHHHHHHSSSSTTCCHHHHHHHHHHTTCCSSSBGGGCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHCCCCEECCCCHHHHHHHHHHHCCCHHHCCCCCCHHHHHHHHHHHH
T ss_conf             64065762157612246699999999985798023267289999999999999


No 6  
>3gpu_A DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 3go8_A* 2f5n_A 2f5o_A 2f5p_A 3gp1_A* 3gq4_A* 3gpy_A* 3gq5_A* 3gpp_A* 2f5q_A* 2f5s_A* 1l1z_A* 1l1t_A* 1l2b_A* 1l2c_A* 1l2d_A* 1r2z_A* 1r2y_A* ...
Probab=96.47  E-value=0.0026  Score=40.73  Aligned_cols=50  Identities=18%  Similarity=0.257  Sum_probs=42.3

Q ss_pred             CCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             85766643---120071768999999980888212002279899999998612
Q gi|254780239|r   12 AKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE   61 (122)
Q Consensus        12 ~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~   61 (122)
                      +.+|.-+|   ..|-|||...|..||..++|+|..++++||++|+..|-+.+-
T Consensus       155 ~~~Ik~~LlDQ~~iaGIGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~  207 (256)
T 3gpu_A          155 KRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMV  207 (256)
T ss_dssp             CSBHHHHHHCTTTSTTCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHCCCCEECCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             76455631136513343488999999973148376313389999999999999


No 7  
>1tdz_A Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1pji_A* 1pm5_A* 1xc8_A* 3c58_A* 1nnj_A 1kfv_A 1pjj_A*
Probab=96.45  E-value=0.003  Score=40.39  Aligned_cols=49  Identities=24%  Similarity=0.382  Sum_probs=41.3

Q ss_pred             CEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             5766643---120071768999999980888212002279899999998612
Q gi|254780239|r   13 KRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE   61 (122)
Q Consensus        13 K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~   61 (122)
                      ++|.-+|   ..|-|||...|..||..++|+|..++++|+++|+..|-+.+.
T Consensus       155 ~~Ik~~LlDQ~~iaGIGNiy~~EiLf~a~I~P~~~~~~L~~~e~~~L~~~~~  206 (272)
T 1tdz_A          155 KKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSII  206 (272)
T ss_dssp             SBHHHHHHTSSSSSCCCHHHHHHHHHHTTCCTTCBGGGCCHHHHHHHHHHHH
T ss_pred             CCCCEEEECCCEECCCCHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHH
T ss_conf             3200267507635444473798998872798676752407999999999999


No 8  
>3a46_A Formamidopyrimidine-DNA glycosylase; helix two turns helix, zinc-LESS finger, hydrolase, THF, glycosidase, lyase, multifunctional enzyme; HET: DNA 3DR; 2.20A {Acanthamoeba polyphaga mimivirus} PDB: 3a45_A* 3a42_A
Probab=96.44  E-value=0.0029  Score=40.40  Aligned_cols=48  Identities=23%  Similarity=0.288  Sum_probs=40.3

Q ss_pred             EEEEEE--EE-E-ECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             766643--12-0-071768999999980888212002279899999998612
Q gi|254780239|r   14 RVVRAL--CY-I-HGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE   61 (122)
Q Consensus        14 ~i~~aL--t~-I-~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~   61 (122)
                      ++.-+|  ++ | -|||.-.|..||..++|+|..++.+||++|+..|-+.+.
T Consensus       156 ~ik~~LLdq~~i~aGIGNiya~EiLf~a~I~P~~~~~~Ls~~e~~~L~~~i~  207 (289)
T 3a46_A          156 PIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIK  207 (289)
T ss_dssp             BHHHHHHCSSSSCBCCCHHHHHHHHHHTTBCTTCBGGGCCHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCCEECCCCHHHHHHHHHHHHCCHHHHHHHCCHHHHHHHHHHHH
T ss_conf             2457752466267064089999999985068546667499999999999999


No 9  
>1k3x_A Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A 2opf_A* 1q3b_A*
Probab=96.32  E-value=0.0035  Score=39.91  Aligned_cols=52  Identities=13%  Similarity=0.307  Sum_probs=44.0

Q ss_pred             CCCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf             985766643---1200717689999999808882120022798999999986124
Q gi|254780239|r   11 RAKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ   62 (122)
Q Consensus        11 ~~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~   62 (122)
                      .+++|.-+|   ..|-|||...|..||..++|+|..++.+||++|+..|-+.+.+
T Consensus       149 ~~~~Ik~~LlDQ~~iaGIGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~  203 (262)
T 1k3x_A          149 RNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLE  203 (262)
T ss_dssp             TTSCHHHHTTCTTTSBTCCHHHHHHHHHHHTCCSSCCGGGSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             0068999984177445656999999998720685450134447789999999999


No 10 
>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8
Probab=96.27  E-value=0.0043  Score=39.40  Aligned_cols=48  Identities=19%  Similarity=0.208  Sum_probs=40.7

Q ss_pred             EEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             766643---120071768999999980888212002279899999998612
Q gi|254780239|r   14 RVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE   61 (122)
Q Consensus        14 ~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~   61 (122)
                      .|.-+|   ..|-|||...+..||..++|+|..++++|+++|+..|-+.+.
T Consensus       152 ~ik~~LlDQ~~iaGIGN~y~~EiLf~a~IhP~~~~~~L~~~e~~~L~~~~~  202 (268)
T 1k82_A          152 AIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIK  202 (268)
T ss_dssp             BHHHHHTCTTTCSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHH
T ss_pred             CCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHH
T ss_conf             541488617604667588999999872798668632399999999999999


No 11 
>1tdh_A NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens} SCOP: a.156.1.2 b.113.1.1 g.39.1.8
Probab=89.44  E-value=0.075  Score=31.67  Aligned_cols=42  Identities=26%  Similarity=0.460  Sum_probs=34.3

Q ss_pred             CEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHH
Q ss_conf             5766643---12007176899999998088821200227989999
Q gi|254780239|r   13 KRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVI   54 (122)
Q Consensus        13 K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~   54 (122)
                      ++|.-+|   +.|-|||.-+|..||..++|+|..++.+|++++..
T Consensus       159 ~~IK~~LLDQ~iiaGIGNIYadEiLf~A~IhP~r~a~~ls~~~~~  203 (364)
T 1tdh_A          159 RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQ  203 (364)
T ss_dssp             SBHHHHTTCTTTSTTCCHHHHHHHHHHHTCCTTSBHHHHHGGGC-
T ss_pred             CCHHHHHHCCCEECCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHC
T ss_conf             608998724770225428899999998489966741234576641


No 12 
>1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} SCOP: a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A* 1z5a_A* 1z59_A* 1z5c_A* 2hkj_A*
Probab=88.66  E-value=0.37  Score=27.38  Aligned_cols=43  Identities=19%  Similarity=0.404  Sum_probs=38.8

Q ss_pred             EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf             1200717689999999808882120022798999999986124
Q gi|254780239|r   20 CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ   62 (122)
Q Consensus        20 t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~   62 (122)
                      ..+-.||..+|..||..+|++|+++..+|+++|+..|-+.+.+
T Consensus       261 ~~Fs~V~~~~a~~i~~~~g~~~~~~p~~l~~~e~~~l~~a~~~  303 (471)
T 1mu5_A          261 NEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK  303 (471)
T ss_dssp             TSSSSCCHHHHHHHHHHTTCCTTSBGGGCCTTHHHHHHHHHHH
T ss_pred             HHCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             7547769899999999749997777144999999999999985


No 13 
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5
Probab=84.66  E-value=0.38  Score=27.31  Aligned_cols=52  Identities=12%  Similarity=0.109  Sum_probs=36.0

Q ss_pred             EEEEEEEEECCCHHHHHHHHHHCC---------CCHHHHHCCCCHHHHHHHHHHHCCCCCC
Q ss_conf             666431200717689999999808---------8821200227989999999861245643
Q gi|254780239|r   15 VVRALCYIHGIGFKSSQDICNKLA---------IPPERRVHQLVESEVIQIRQAIEQDYQV   66 (122)
Q Consensus        15 i~~aLt~I~GIG~~~A~~Ic~~lg---------Id~~~kv~~Lt~~qi~~l~~~I~~~~~i   66 (122)
                      ..+.|+.|-|||+..|..|+...|         .+.-..+..+.+.-..+|.+++..+|.-
T Consensus        12 ~~~~L~~IpgIG~~~a~~L~~~F~s~~~i~~As~eeL~~v~GIG~~~a~~i~~~~~~~~~~   72 (75)
T 1x2i_A           12 QRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYIE   72 (75)
T ss_dssp             HHHHHTTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSCCCC
T ss_pred             HHHHHCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCHHHC
T ss_conf             9999848999429999999999688898999789999855897999999999998576320


No 14 
>3fut_A Dimethyladenosine transferase; methyltransferase, dimethyltransferase, dual-specific methyltransferase, 16S rRNA methyltransferase; 1.52A {Thermus thermophilus HB8} PDB: 3fuu_A* 3fuv_A 3fuw_A* 3fux_A*
Probab=83.79  E-value=1.3  Score=23.89  Aligned_cols=50  Identities=22%  Similarity=0.349  Sum_probs=39.6

Q ss_pred             CCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf             857666431200717689999999808882120022798999999986124
Q gi|254780239|r   12 AKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ   62 (122)
Q Consensus        12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~   62 (122)
                      .|.+.-+|..+ +........++..+||+|+.+..+||.+|+..|-+.+++
T Consensus       220 RK~l~n~L~~~-~~~~~~~~~~l~~~~i~~~~R~e~Ls~~~~~~L~~~l~~  269 (271)
T 3fut_A          220 RKTLLNALAAA-GYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLEG  269 (271)
T ss_dssp             TSCHHHHHHHT-TCCHHHHHHHHHHTTCCTTCCGGGCCHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHH-CCCHHHHHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHC
T ss_conf             57999998763-688889999999869796639154999999999999865


No 15 
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5
Probab=83.74  E-value=0.27  Score=28.26  Aligned_cols=50  Identities=10%  Similarity=0.207  Sum_probs=32.9

Q ss_pred             EEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCH-----------HHHHHHHHHHCCCCC
Q ss_conf             7666431200717689999999808882120022798-----------999999986124564
Q gi|254780239|r   14 RVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVE-----------SEVIQIRQAIEQDYQ   65 (122)
Q Consensus        14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~-----------~qi~~l~~~I~~~~~   65 (122)
                      ++..+|+.|.|||...|..++...|  .-..+-.-+.           ....+|.+++.++|.
T Consensus        16 ~~~~~L~~I~gIG~~~a~~L~~~Fg--sl~~i~~As~eeL~~i~GiG~~~A~~I~~~f~~pf~   76 (89)
T 1z00_A           16 RVTECLTTVKSVNKTDSQTLLTTFG--SLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFL   76 (89)
T ss_dssp             HHHHHHTTSSSCCHHHHHHHHHHTC--BHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSCSS
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHHC--CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCHHC
T ss_conf             9999875899759999999999948--889999987877726899699999999999808420


No 16 
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5
Probab=81.01  E-value=0.29  Score=28.03  Aligned_cols=49  Identities=10%  Similarity=0.244  Sum_probs=32.2

Q ss_pred             EEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHH-----------HHHHHHHCCCC
Q ss_conf             7666431200717689999999808882120022798999-----------99998612456
Q gi|254780239|r   14 RVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEV-----------IQIRQAIEQDY   64 (122)
Q Consensus        14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi-----------~~l~~~I~~~~   64 (122)
                      ++..+|+.|.|||...|..++...| + -..+..-+.+++           .+|.+++.++|
T Consensus        29 ~~~~~L~~I~gIGk~~A~~L~~~F~-S-i~~l~~As~eeL~~i~GIG~~~A~~I~~~f~~pf   88 (91)
T 2a1j_B           29 RVTECLTTVKSVNKTDSQTLLTTFG-S-LEQLIAASREDLALCPGLGPQKARRLFDVLHEPF   88 (91)
T ss_dssp             HHHHHHTTSTTCCHHHHHHHHHHHS-S-HHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHSCS
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHHC-C-CHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCH
T ss_conf             9999864688859999999999958-8-2989998999755779969999999999984814


No 17 
>3ftd_A Dimethyladenosine transferase; KSGA, rossmann-like fold, RNA methyltransferase, mtase, antibiotic resistance, methyltransferase; 1.44A {Aquifex aeolicus VF5} PDB: 3ftc_A 3fte_A 3ftf_A*
Probab=78.45  E-value=1.8  Score=23.13  Aligned_cols=34  Identities=24%  Similarity=0.466  Sum_probs=30.1

Q ss_pred             HHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             9999998088821200227989999999861245
Q gi|254780239|r   30 SQDICNKLAIPPERRVHQLVESEVIQIRQAIEQD   63 (122)
Q Consensus        30 A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~   63 (122)
                      ...++..+||+|+.++.+|+.+|+..|-+.++++
T Consensus       214 ~~~~l~~~~i~~~~R~e~Ls~~~~~~L~~~l~~~  247 (249)
T 3ftd_A          214 PEELLKEAGINPDARVEQLSLEDFFKLYRLIEDS  247 (249)
T ss_dssp             CHHHHHHTTCCTTCCGGGCCHHHHHHHHHHHHCC
T ss_pred             HHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHHC
T ss_conf             9999998795988894779999999999999971


No 18 
>1qyr_A KSGA, high level kasugamycin resistance protein, S-; adenosine dimethyltransferase, rRNA modification, transferase, translation; 2.10A {Escherichia coli} SCOP: c.66.1.24
Probab=77.19  E-value=0.67  Score=25.75  Aligned_cols=45  Identities=13%  Similarity=0.278  Sum_probs=34.4

Q ss_pred             CCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf             857666431200717689999999808882120022798999999986124
Q gi|254780239|r   12 AKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ   62 (122)
Q Consensus        12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~   62 (122)
                      .|.+.-+|..++.      ..+...+||+|+.+..+|+.+|+.+|-+.+++
T Consensus       206 RK~l~n~L~~~~~------~~~l~~~~i~~~~R~e~Ls~~~~~~L~~~l~~  250 (252)
T 1qyr_A          206 RKTIRNSLGNLFS------VEVLTGMGIDPAMRAENISVAQYCQMANYLAE  250 (252)
T ss_dssp             TSBHHHHTTTTCC------HHHHHHTTCCTTSBGGGSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCC------HHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHH
T ss_conf             2889998740441------99999779882339333999999999999984


No 19 
>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus}
Probab=73.27  E-value=3.5  Score=21.31  Aligned_cols=54  Identities=15%  Similarity=0.158  Sum_probs=40.0

Q ss_pred             CCCCCEEEEEEEEEECCCHHHHHHHHHHCC---CCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf             899857666431200717689999999808---882120022798999999986124
Q gi|254780239|r    9 IPRAKRVVRALCYIHGIGFKSSQDICNKLA---IPPERRVHQLVESEVIQIRQAIEQ   62 (122)
Q Consensus         9 i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lg---Id~~~kv~~Lt~~qi~~l~~~I~~   62 (122)
                      ++=|.--.-.|+.+.|||+..|..|...-.   ++.=..+.-+++.+++.|+++++.
T Consensus        55 idlN~A~~~eL~~lpGig~~~A~~Iv~~gpf~svedl~~v~Gig~~~~e~l~~~l~~  111 (134)
T 1s5l_U           55 IDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEH  111 (134)
T ss_dssp             EETTTSCGGGGGGSTTCTHHHHHHHHHTCCCSSGGGGGGCTTCCHHHHHHHHHHHTT
T ss_pred             EECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHHHCC
T ss_conf             416407899997710346999999998278487999961775799999999986535


No 20 
>3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3kzi_U* 3a0b_U* 3a0h_U*
Probab=71.27  E-value=4  Score=20.96  Aligned_cols=54  Identities=15%  Similarity=0.158  Sum_probs=39.9

Q ss_pred             CCCCCEEEEEEEEEECCCHHHHHHHHHHCC---CCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf             899857666431200717689999999808---882120022798999999986124
Q gi|254780239|r    9 IPRAKRVVRALCYIHGIGFKSSQDICNKLA---IPPERRVHQLVESEVIQIRQAIEQ   62 (122)
Q Consensus         9 i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lg---Id~~~kv~~Lt~~qi~~l~~~I~~   62 (122)
                      ++=|.--...|+.+-|||+..|..|+..=.   ++.-.++..+++..++.|..+++.
T Consensus        25 idlN~As~~eL~~lpGig~~~A~~Iv~~gpf~s~~dL~~V~Gig~~~~e~ik~yl~~   81 (104)
T 3bz1_U           25 IDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEH   81 (104)
T ss_dssp             EETTSSCGGGGGGSTTTTHHHHHHHHHSCCCSSGGGGGGCTTCCHHHHHHHHHHGGG
T ss_pred             EECCCCCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHHHCC
T ss_conf             578408999996589979999999997499798999963899899999999986545


No 21 
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3
Probab=70.20  E-value=0.81  Score=25.26  Aligned_cols=46  Identities=20%  Similarity=0.324  Sum_probs=32.6

Q ss_pred             CCCCCEEE-EEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHH
Q ss_conf             89985766-6431200717689999999808882120022798999999
Q gi|254780239|r    9 IPRAKRVV-RALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQI   56 (122)
Q Consensus         9 i~~~K~i~-~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l   56 (122)
                      ++-.|.+. -.|..|.|||+.++..++...+  .-..+.+.+.+|+.++
T Consensus        15 ~~R~K~~~~S~L~~IpGIG~k~ak~Ll~~F~--si~~i~~As~eeL~~v   61 (78)
T 1kft_A           15 VPRGSHMNTSSLETIEGVGPKRRQMLLKYMG--GLQGLRNASVEEIAKV   61 (78)
T ss_dssp             --------CCGGGGCTTCSSSHHHHHHHHHS--CHHHHHHCCHHHHTTS
T ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHC--CHHHHHHHCHHHHHCC
T ss_conf             6675442338265699932999999999929--9499988379999807


No 22 
>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A*
Probab=69.37  E-value=2.6  Score=22.10  Aligned_cols=37  Identities=16%  Similarity=0.271  Sum_probs=31.6

Q ss_pred             EEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHH
Q ss_conf             312007176899999998088821200227989999999
Q gi|254780239|r   19 LCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIR   57 (122)
Q Consensus        19 Lt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~   57 (122)
                      |..|-|||...+..++...|  .=..+.+.|.+|+.++.
T Consensus         6 L~~IPGIg~~~~~~Ll~~fg--Si~~l~~as~eeL~~v~   42 (63)
T 2a1j_A            6 LLKMPGVNAKNCRSLMHHVK--NIAELAALSQDELTSIL   42 (63)
T ss_dssp             HHTSTTCCHHHHHHHHHHCS--SHHHHHTCCHHHHHHHH
T ss_pred             HHCCCCCCHHHHHHHHHHCC--CHHHHHHCCHHHHHHCC
T ss_conf             85299988999999999867--99999879999998786


No 23 
>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus}
Probab=67.65  E-value=4.2  Score=20.84  Aligned_cols=40  Identities=18%  Similarity=0.360  Sum_probs=27.6

Q ss_pred             EEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHH
Q ss_conf             64312007176899999998088821200227989999999861
Q gi|254780239|r   17 RALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI   60 (122)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I   60 (122)
                      -.|+.+.|||+.+|..++.-++-.|..    ..+..+..+..-+
T Consensus       117 ~~L~~l~GIG~ktA~~~L~~~~~~~~~----~vD~hv~Ri~~r~  156 (207)
T 3fhg_A          117 ERLLNIKGIGMQEASHFLRNVGYFDLA----IIDRHIIDFMRRI  156 (207)
T ss_dssp             HHHTTSTTCCHHHHHHHHHHTTCCSSC----CCCHHHHHHHHHT
T ss_pred             HHHHHCCCCCHHHHHHHHHHHCCCCCC----CCCHHHHHHHHHH
T ss_conf             999987887299999999997688766----7847999999992


No 24 
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A
Probab=61.68  E-value=1.8  Score=23.05  Aligned_cols=20  Identities=30%  Similarity=0.511  Sum_probs=9.7

Q ss_pred             EEEEEECCCHHHHHHHHHHC
Q ss_conf             43120071768999999980
Q gi|254780239|r   18 ALCYIHGIGFKSSQDICNKL   37 (122)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~l   37 (122)
                      +|+++-|||.++|..|+-.|
T Consensus       109 ~L~~vpGIGkKtA~rIilEL  128 (203)
T 1cuk_A          109 ALVKLPGIGKKTAERLIVEM  128 (203)
T ss_dssp             HHHTSTTCCHHHHHHHHHHH
T ss_pred             HHHCCCCCCHHHHHHHHHHH
T ss_conf             86069987799999999999


No 25 
>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
Probab=59.76  E-value=5.1  Score=20.27  Aligned_cols=39  Identities=13%  Similarity=0.221  Sum_probs=33.8

Q ss_pred             EEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHH
Q ss_conf             64312007176899999998088821200227989999999
Q gi|254780239|r   17 RALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIR   57 (122)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~   57 (122)
                      ..|..|.|||+.+...++...|  .-..+.+-|.+|+.++.
T Consensus       168 S~Ld~I~GIG~k~~~~Ll~~Fg--s~~~I~~As~eeL~~v~  206 (220)
T 2nrt_A          168 SVLDNVPGIGPIRKKKLIEHFG--SLENIRSASLEEIARVI  206 (220)
T ss_dssp             HHHTTSTTCCHHHHHHHHHHHC--SHHHHHTSCHHHHHHHH
T ss_pred             CCCHHCCCCCHHHHHHHHHHCC--CHHHHHHCCHHHHHHCC
T ss_conf             6410037969999999999818--99999718999998686


No 26 
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*
Probab=59.76  E-value=5  Score=20.34  Aligned_cols=39  Identities=15%  Similarity=0.229  Sum_probs=31.0

Q ss_pred             EEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHH
Q ss_conf             43120071768999999980888212002279899999998
Q gi|254780239|r   18 ALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQ   58 (122)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~   58 (122)
                      -|..|-|||+..+..|+...|  .=..+.+.+.+++..+.-
T Consensus        19 ~L~~iPGIg~k~~~~Ll~~f~--sl~~i~~AS~eeL~~v~G   57 (84)
T 1z00_B           19 FLLKMPGVNAKNCRSLMHHVK--NIAELAALSQDELTSILG   57 (84)
T ss_dssp             HHHTCSSCCHHHHHHHHHHSS--CHHHHHHSCHHHHHHHHS
T ss_pred             HHHCCCCCCHHHHHHHHHHCC--CHHHHHHCCHHHHHHCCC
T ss_conf             998389999999999999966--999998599999988759


No 27 
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2
Probab=58.38  E-value=2.5  Score=22.21  Aligned_cols=21  Identities=24%  Similarity=0.349  Sum_probs=10.6

Q ss_pred             EEEEEECCCHHHHHHHHHHCC
Q ss_conf             431200717689999999808
Q gi|254780239|r   18 ALCYIHGIGFKSSQDICNKLA   38 (122)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~lg   38 (122)
                      +|+++-|||.++|..|+-.|.
T Consensus       108 ~L~~vpGIGkKtAerIilELk  128 (191)
T 1ixr_A          108 LLTSASGVGRRLAERIALELK  128 (191)
T ss_dssp             HHTTSTTCCHHHHHHHHHHHT
T ss_pred             HHHCCCCCCHHHHHHHHHHHH
T ss_conf             950188846889999999998


No 28 
>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
Probab=57.30  E-value=2.6  Score=22.15  Aligned_cols=21  Identities=29%  Similarity=0.472  Sum_probs=13.7

Q ss_pred             EEEEEECCCHHHHHHHHHHCC
Q ss_conf             431200717689999999808
Q gi|254780239|r   18 ALCYIHGIGFKSSQDICNKLA   38 (122)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~lg   38 (122)
                      +|+++-|||.++|..|+-.|.
T Consensus       124 ~L~~vpGIGkKtAeRIilELk  144 (212)
T 2ztd_A          124 ALTRVPGIGKRGAERMVLELR  144 (212)
T ss_dssp             HHHTSTTCCHHHHHHHHHHHT
T ss_pred             HHHHCCCCCHHHHHHHHHHHH
T ss_conf             985177824888999999997


No 29 
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus}
Probab=55.06  E-value=7.5  Score=19.26  Aligned_cols=37  Identities=11%  Similarity=0.302  Sum_probs=24.6

Q ss_pred             EEEEEEECCCHHHHHHHHHHCCCCHHH----HHCCCCHHHHH
Q ss_conf             643120071768999999980888212----00227989999
Q gi|254780239|r   17 RALCYIHGIGFKSSQDICNKLAIPPER----RVHQLVESEVI   54 (122)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~----kv~~Lt~~qi~   54 (122)
                      ..|+.|+|||+.+|..+-.. ||..-.    ....|+..|.-
T Consensus       102 ~~l~~i~GvGpk~a~~l~~~-Gi~si~dL~~~~~~l~~~q~~  142 (360)
T 2ihm_A          102 KLFTQVFGVGVKTANRWYQE-GLRTLDELREQPQRLTQQQKA  142 (360)
T ss_dssp             HHHHTSTTCCHHHHHHHHHT-TCCSHHHHHTCCTTCCHHHHH
T ss_pred             HHHHHCCCCCHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHH
T ss_conf             99975778789999999983-988799998778750154653


No 30 
>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme A kinase, structural genomics, joint center for structural genomics, JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}
Probab=54.41  E-value=10  Score=18.49  Aligned_cols=54  Identities=15%  Similarity=0.129  Sum_probs=37.0

Q ss_pred             CCEEEEEEEEEECCCHHHHHHHHH-HCCC---CHHHHHCCCCHHHHHHHHHHHCCCCC
Q ss_conf             857666431200717689999999-8088---82120022798999999986124564
Q gi|254780239|r   12 AKRVVRALCYIHGIGFKSSQDICN-KLAI---PPERRVHQLVESEVIQIRQAIEQDYQ   65 (122)
Q Consensus        12 ~K~i~~aLt~I~GIG~~~A~~Ic~-~lgI---d~~~kv~~Lt~~qi~~l~~~I~~~~~   65 (122)
                      .-++.+|||.--|-|.++...++. ++|+   |.+.-+++|-++-...|.+....+..
T Consensus        10 ~~~mIIgiTG~igSGKStv~~~l~~~~g~~vidaD~i~~~l~~~~~~~i~~~fg~~i~   67 (192)
T 2grj_A           10 HHHMVIGVTGKIGTGKSTVCEILKNKYGAHVVNVDRIGHEVLEEVKEKLVELFGGSVL   67 (192)
T ss_dssp             CCEEEEEEECSTTSSHHHHHHHHHHHHCCEEEEHHHHHHHHHHHTHHHHHHHHCGGGB
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             5777999878987889999999988539989970699999866458899887097222


No 31 
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans}
Probab=52.67  E-value=4  Score=20.94  Aligned_cols=23  Identities=22%  Similarity=0.245  Sum_probs=17.4

Q ss_pred             EEEEEEECCCHHHHHHHHHHCCCC
Q ss_conf             643120071768999999980888
Q gi|254780239|r   17 RALCYIHGIGFKSSQDICNKLAIP   40 (122)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~lgId   40 (122)
                      ..|+.|+|||+++|.++.+ .||.
T Consensus        97 ~~l~~I~GvGpk~A~~l~~-~Gi~  119 (578)
T 2w9m_A           97 LDLLGVRGLGPKKIRSLWL-AGID  119 (578)
T ss_dssp             HHHTTSTTCCHHHHHHHHH-TTCC
T ss_pred             HHHHCCCCCCHHHHHHHHH-HCCC
T ss_conf             9984789868999999998-0998


No 32 
>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} PDB: 3knt_A*
Probab=51.85  E-value=4.3  Score=20.73  Aligned_cols=39  Identities=13%  Similarity=0.249  Sum_probs=29.1

Q ss_pred             EEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHH
Q ss_conf             4312007176899999998088821200227989999999861
Q gi|254780239|r   18 ALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI   60 (122)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I   60 (122)
                      .|.++.|||+.+|..++..++-.|..-    -|..+..+.+-+
T Consensus       126 ~L~~l~GIG~ktA~~~L~~~~~~~~~i----vD~hv~Ri~~rl  164 (214)
T 3fhf_A          126 LVRNIKGIGYKEASHFLRNVGYDDVAI----IDRHILRELYEN  164 (214)
T ss_dssp             HHHHSTTCCHHHHHHHHHHTTCCSCCC----CCHHHHHHHHHT
T ss_pred             HHHHCCCCCHHHHHHHHHHHCCCCCCC----CCHHHHHHHHHH
T ss_conf             997488876999999999976998631----327999999993


No 33 
>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A*
Probab=51.65  E-value=4.1  Score=20.86  Aligned_cols=25  Identities=12%  Similarity=0.424  Sum_probs=19.6

Q ss_pred             EEEEEEEECCCHHHHHHHHHHCCCCH
Q ss_conf             66431200717689999999808882
Q gi|254780239|r   16 VRALCYIHGIGFKSSQDICNKLAIPP   41 (122)
Q Consensus        16 ~~aLt~I~GIG~~~A~~Ic~~lgId~   41 (122)
                      ...|+.|+|||+.+|..+.+ +||..
T Consensus       120 l~~l~~I~GiGpk~a~~l~~-~Gi~t  144 (381)
T 1jms_A          120 FKLFTSVFGVGLKTAEKWFR-MGFRT  144 (381)
T ss_dssp             HHHHHTSTTCCHHHHHHHHH-TTCCS
T ss_pred             HHHHHHCCCCCHHHHHHHHH-CCCCC
T ss_conf             89987377878999999998-69777


No 34 
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...
Probab=49.83  E-value=2.8  Score=21.92  Aligned_cols=45  Identities=16%  Similarity=0.215  Sum_probs=32.0

Q ss_pred             CCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHH
Q ss_conf             8576664312007176899999998088821200227989999999
Q gi|254780239|r   12 AKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIR   57 (122)
Q Consensus        12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~   57 (122)
                      .+.....|..|-|||+.++.+++. .|++.-..+..++++++..+.
T Consensus        10 ~~~~~~~l~~i~gvG~~~~~~l~~-~g~~~~~~i~~~~~~~L~~~~   54 (241)
T 1vq8_Y           10 AEEEYTELTDISGVGPSKAESLRE-AGFESVEDVRGADQSALADVS   54 (241)
T ss_dssp             ----------------------------------------------
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHH-CCCCCHHHHHHCCHHHHHHCC
T ss_conf             688674325889989999999997-689999999869999997468


No 35 
>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} SCOP: a.60.2.7
Probab=49.15  E-value=9.8  Score=18.53  Aligned_cols=49  Identities=14%  Similarity=0.199  Sum_probs=33.9

Q ss_pred             CCEEEEEEEEEECCCHHHHHHHHHHCC---CCHHHHHCCCCHHHHHHHHHHH
Q ss_conf             857666431200717689999999808---8821200227989999999861
Q gi|254780239|r   12 AKRVVRALCYIHGIGFKSSQDICNKLA---IPPERRVHQLVESEVIQIRQAI   60 (122)
Q Consensus        12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lg---Id~~~kv~~Lt~~qi~~l~~~I   60 (122)
                      |.--.-.|..+-|||+..|..|.+.=.   ++.-..+..+++..+++|..+|
T Consensus        22 N~As~~eL~~lpGig~~~A~~Iv~~R~f~s~~dL~~v~gi~~~~~~~i~~~l   73 (75)
T 2duy_A           22 NEASLEELMALPGIGPVLARRIVEGRPYARVEDLLKVKGIGPATLERLRPYL   73 (75)
T ss_dssp             TTCCHHHHTTSTTCCHHHHHHHHHTCCCSSGGGGGGSTTCCHHHHHHHGGGE
T ss_pred             CCCCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHHCCCCCHHHHHHHHHHC
T ss_conf             1287999977789899999999985898989999757898999999999772


No 36 
>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A* 3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A* 3d4v_A*
Probab=47.70  E-value=13  Score=17.84  Aligned_cols=35  Identities=11%  Similarity=0.061  Sum_probs=23.7

Q ss_pred             EEEEEEEEEECCCHHHHHHHHHHCCCCHHH-HHCCC
Q ss_conf             766643120071768999999980888212-00227
Q gi|254780239|r   14 RVVRALCYIHGIGFKSSQDICNKLAIPPER-RVHQL   48 (122)
Q Consensus        14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~-kv~~L   48 (122)
                      .+.-.|+.|.|||+.+|..++-..-=+|+. .++|+
T Consensus       204 e~~~~L~~l~GIGpWTA~~vll~~lg~~D~fp~~Dl  239 (282)
T 1mpg_A          204 QAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDY  239 (282)
T ss_dssp             HHHHHHTTSTTCCHHHHHHHHHHHSCCSSCCCTTCH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCHHH
T ss_conf             999999976798869999999997699883874349


No 37 
>3mr3_A DNA polymerase ETA; POL ETA, polymerase, thymine dimer, CPD, XPV, xeroderma PIGM variant, DNA damage; HET: DNA TTD DZ4; 1.75A {Homo sapiens} PDB: 3mr2_A* 3mr5_A* 3mr6_A*
Probab=47.50  E-value=16  Score=17.19  Aligned_cols=40  Identities=20%  Similarity=0.192  Sum_probs=29.6

Q ss_pred             EEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHH
Q ss_conf             6431200717689999999808882120022798999999
Q gi|254780239|r   17 RALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQI   56 (122)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l   56 (122)
                      ..+..+.|||.++...++..+||..-.-+..++.+++...
T Consensus       253 lpi~~l~GiG~k~~~~~L~~~gi~ti~dl~~~~~~~L~~~  292 (435)
T 3mr3_A          253 MPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSH  292 (435)
T ss_dssp             CBGGGSTTCSSHHHHHHHHHHTCCBGGGGGGSCHHHHHHH
T ss_pred             CCCCEECCCCHHHHHHHHHHHCCCCHHHHHHCCHHHHHHH
T ss_conf             7677607767578999999958947899873999899999


No 38 
>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A*
Probab=45.63  E-value=17  Score=17.01  Aligned_cols=41  Identities=17%  Similarity=0.078  Sum_probs=27.4

Q ss_pred             EEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHH
Q ss_conf             664312007176899999998088821200227989999999861
Q gi|254780239|r   16 VRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI   60 (122)
Q Consensus        16 ~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I   60 (122)
                      .-.|..+.|||+.+|..|+..+.=.|..    .-+..+..+-.-+
T Consensus       120 ~~~L~~lpGIG~kTA~~il~~~~~~~~~----~vD~~v~Rv~~Rl  160 (218)
T 1pu6_A          120 REWLLDQKGIGKESADAILCYACAKEVM----VVDKYSYLFLKKL  160 (218)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHHTTCCSCC----CCCHHHHHHHHHT
T ss_pred             HHHHHCCCCCCHHHHHHHHHHHCCCCCC----CCCHHHHHHHHHH
T ss_conf             9999848996699999999998799806----2042599999990


No 39 
>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} SCOP: a.96.1.3 d.129.1.2 PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A* 2nol_A* 3ktu_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* ...
Probab=45.51  E-value=5.3  Score=20.22  Aligned_cols=42  Identities=29%  Similarity=0.448  Sum_probs=25.3

Q ss_pred             EEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHH
Q ss_conf             766643120071768999999980888212002279899999998
Q gi|254780239|r   14 RVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQ   58 (122)
Q Consensus        14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~   58 (122)
                      .+.-.|+.|.|||+.+|..||-..==.++.-.  + +-.+.++.+
T Consensus       227 e~~~~L~~l~GIG~wtAd~ilLf~lg~~dafP--v-D~~v~r~~~  268 (317)
T 1m3q_A          227 EAHKALCILPGVGTKVADCICLMALDKPQAVP--V-EVHMWHIAQ  268 (317)
T ss_dssp             HHHHHHTTSTTCCHHHHHHHHHHHSCCTTCCC--C-SHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHCCCCCEEE--E-EHHHHHHHH
T ss_conf             99999985489488999999998579998677--5-299999999


No 40 
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus}
Probab=44.07  E-value=3.9  Score=21.03  Aligned_cols=41  Identities=17%  Similarity=0.233  Sum_probs=30.7

Q ss_pred             EEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHH
Q ss_conf             7666431200717689999999808882120022798999999
Q gi|254780239|r   14 RVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQI   56 (122)
Q Consensus        14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l   56 (122)
                      .....|..|-|||+.++..++...|  .-..+.+.|.+|+.++
T Consensus       170 ~~~S~Ld~I~GIG~~~~~~Ll~~Fg--s~~~i~~As~eeL~~v  210 (226)
T 3c65_A          170 MFHSVLDDIPGVGEKRKKALLNYFG--SVKKMKEATVEELQRA  210 (226)
T ss_dssp             -------------------------------------------
T ss_pred             HCCCCCCCCCCCCHHHHHHHHHHCC--CHHHHHHCCHHHHHHC
T ss_conf             2037110268869999999999818--9999973899999876


No 41 
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A
Probab=43.81  E-value=13  Score=17.83  Aligned_cols=22  Identities=23%  Similarity=0.400  Sum_probs=18.7

Q ss_pred             EEEEEEECCCHHHHHHHHHHCC
Q ss_conf             6431200717689999999808
Q gi|254780239|r   17 RALCYIHGIGFKSSQDICNKLA   38 (122)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~lg   38 (122)
                      ..|+.|.|||...|..|+...+
T Consensus       162 ~~L~~Ipgi~~~~A~~Ll~~f~  183 (219)
T 2bgw_A          162 YILQSFPGIGRRTAERILERFG  183 (219)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHHS
T ss_pred             HHHHCCCCCCHHHHHHHHHHCC
T ss_conf             9984079989999999999869


No 42 
>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
Probab=43.80  E-value=5.8  Score=19.95  Aligned_cols=30  Identities=13%  Similarity=-0.066  Sum_probs=21.3

Q ss_pred             EEEEEEEEECCCHHHHHHHHHHCCCCHHHH
Q ss_conf             666431200717689999999808882120
Q gi|254780239|r   15 VVRALCYIHGIGFKSSQDICNKLAIPPERR   44 (122)
Q Consensus        15 i~~aLt~I~GIG~~~A~~Ic~~lgId~~~k   44 (122)
                      +.-.|+.|.|||+.+|..||-..-=.++.-
T Consensus       209 ~~~~L~~i~GIG~wtAd~ilLf~lg~~d~f  238 (290)
T 3i0w_A          209 CHEELKKFMGVGPQVADCIMLFSMQKYSAF  238 (290)
T ss_dssp             HHHHHTTSTTCCHHHHHHHHHHHHCCTTCC
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHCCCCCEE
T ss_conf             999998679948899999999967999967


No 43 
>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ...
Probab=43.36  E-value=7  Score=19.44  Aligned_cols=39  Identities=18%  Similarity=0.239  Sum_probs=24.7

Q ss_pred             EEEEEEECCCHHHHHHHHHHCCCCHHHH----HCCCCHHHHHHH
Q ss_conf             6431200717689999999808882120----022798999999
Q gi|254780239|r   17 RALCYIHGIGFKSSQDICNKLAIPPERR----VHQLVESEVIQI   56 (122)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~lgId~~~k----v~~Lt~~qi~~l   56 (122)
                      ..|+.|+|||+++|..+- .+||..-.-    ...|++.|..-|
T Consensus        98 ~~l~~I~GvGpk~a~~l~-~~Gi~ti~dL~~~~~kl~~~q~~gl  140 (335)
T 2fmp_A           98 NFLTRVSGIGPSAARKFV-DEGIKTLEDLRKNEDKLNHHQRIGL  140 (335)
T ss_dssp             HHHTTSTTCCHHHHHHHH-HTTCCSHHHHHTCGGGSCHHHHHHH
T ss_pred             HHHHHCCCCCHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             998745687989999999-8188759999877887688999889


No 44 
>2hnh_A DNA polymerase III alpha subunit; DNA replication, nucleotidyltransferase, POL beta, PHP; HET: DNA; 2.30A {Escherichia coli} PDB: 2hqa_A*
Probab=40.95  E-value=12  Score=17.93  Aligned_cols=50  Identities=14%  Similarity=0.148  Sum_probs=32.2

Q ss_pred             CCCCCEEEEEEEEEECCCHHHHHHHHHHC---CC-----CHHHHH--CCCCHHHHHHHHH
Q ss_conf             89985766643120071768999999980---88-----821200--2279899999998
Q gi|254780239|r    9 IPRAKRVVRALCYIHGIGFKSSQDICNKL---AI-----PPERRV--HQLVESEVIQIRQ   58 (122)
Q Consensus         9 i~~~K~i~~aLt~I~GIG~~~A~~Ic~~l---gI-----d~~~kv--~~Lt~~qi~~l~~   58 (122)
                      +.++..|.++|+.|.|||...|..|...=   |.     |-..++  +.++..+++.|.+
T Consensus       825 ~~~~~~i~~gl~~ikgig~~~a~~Iv~~R~~~~~f~s~~Df~~r~~~~~~~~~~~~~Li~  884 (910)
T 2hnh_A          825 VNDDGEIVYGIGAIKGVGEGPIEAIIEARNKGGYFRELFDLCARTDTKKLNRRVLEKLIM  884 (910)
T ss_dssp             ECTTSCEECBGGGSTTCCHHHHHHHHHHHHTTCCCSSHHHHTTSSCSSSSCHHHHHHHHH
T ss_pred             ECCCCEEEECHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             768995983254359989999999999897479989999999870646799999999987


No 45 
>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans}
Probab=39.59  E-value=6.1  Score=19.83  Aligned_cols=45  Identities=18%  Similarity=0.152  Sum_probs=28.8

Q ss_pred             EEEEEEEEEECCCHHHHHHHHHHCCCCHHH-HHCCCCHHHHHHHHHHHCCCC
Q ss_conf             766643120071768999999980888212-002279899999998612456
Q gi|254780239|r   14 RVVRALCYIHGIGFKSSQDICNKLAIPPER-RVHQLVESEVIQIRQAIEQDY   64 (122)
Q Consensus        14 ~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~-kv~~Lt~~qi~~l~~~I~~~~   64 (122)
                      .+.-.|+.|.|||+.+|..++-..-=+|+. .++|+      .|.+.++.-|
T Consensus       135 e~~~~L~~ikGIGpWTA~~illf~lgr~DvfP~~Dl------~l~ra~~~ly  180 (233)
T 2h56_A          135 TVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSVGDV------GLQRGAKWLY  180 (233)
T ss_dssp             HHHHHHHTSTTCCHHHHHHHHHHTTCCSCCCCTTCH------HHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCH------HHHHHHHHHH
T ss_conf             999998806884878999999996899978986379------9999999982


No 46 
>2eo2_A Adult MALE hypothalamus cDNA, riken FULL-length enriched library, clone:A230045M11...; FTHFSDC1, structural genomics, NPPSFA; NMR {Mus musculus}
Probab=39.40  E-value=14  Score=17.55  Aligned_cols=26  Identities=27%  Similarity=0.247  Sum_probs=20.5

Q ss_pred             HHHHCCCCHHHHHCCCCHHHHHHHHHH
Q ss_conf             999808882120022798999999986
Q gi|254780239|r   33 ICNKLAIPPERRVHQLVESEVIQIRQA   59 (122)
Q Consensus        33 Ic~~lgId~~~kv~~Lt~~qi~~l~~~   59 (122)
                      =|++|||++. ...+||++|+.+..-.
T Consensus        36 RL~kLGI~kt-dP~~LT~EE~~~F~RL   61 (71)
T 2eo2_A           36 RLKKLGIHKT-DPSTLTEEEVRKFARL   61 (71)
T ss_dssp             HHHHHTCCCC-STTTCCHHHHHHHHHT
T ss_pred             HHHHCCCCCC-CCCCCCHHHHHHHHEE
T ss_conf             9998398989-9021899998440131


No 47 
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, hydrolase; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*
Probab=38.64  E-value=3.6  Score=21.23  Aligned_cols=28  Identities=18%  Similarity=0.310  Sum_probs=24.4

Q ss_pred             EEEEEEEECCCHHHHHHHHHHCCCCHHH
Q ss_conf             6643120071768999999980888212
Q gi|254780239|r   16 VRALCYIHGIGFKSSQDICNKLAIPPER   43 (122)
Q Consensus        16 ~~aLt~I~GIG~~~A~~Ic~~lgId~~~   43 (122)
                      .|.|..|.|||+..|..|...+|++++.
T Consensus        43 Py~l~~i~gi~f~~aD~ia~~~g~~~~d   70 (574)
T 3e1s_A           43 LFTLTEVEGIGFLTADKLWQARGGALDD   70 (574)
T ss_dssp             -CGGGTSSSCCHHHHHTTC-------CC
T ss_pred             CCEEEECCCCCHHHHHHHHHHCCCCCCC
T ss_conf             9123125889958999999976999899


No 48 
>1im4_A DBH; DNA polymerase PALM, thumb, fingers, helix-hairpin-helix, fidelity, processivity, transferase; 2.30A {Sulfolobus solfataricus} SCOP: e.8.1.7
Probab=37.95  E-value=13  Score=17.83  Aligned_cols=20  Identities=20%  Similarity=0.233  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHHHCCCCCC
Q ss_conf             88999999999973031001
Q gi|254780239|r   70 LRRTVAMNIKRLMDLGCYRG   89 (122)
Q Consensus        70 L~~~~~~~i~rl~~i~syrG   89 (122)
                      +-..++..|.+...+.|-=|
T Consensus       130 ~a~~ir~~I~~~~gl~~siG  149 (221)
T 1im4_A          130 LARKIKQEILEKEKITVTVG  149 (221)
T ss_dssp             HHHHHHHHHHHHHCCCEEEE
T ss_pred             HHHHHHHHHHHHHCCCEEEE
T ss_conf             99999999999869876653


No 49 
>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7
Probab=37.12  E-value=23  Score=16.28  Aligned_cols=42  Identities=21%  Similarity=0.189  Sum_probs=27.2

Q ss_pred             EEEEEECCCHHHHHHHHHHC-------CCCHHHHHCCCCHHHHHHHHHH
Q ss_conf             43120071768999999980-------8882120022798999999986
Q gi|254780239|r   18 ALCYIHGIGFKSSQDICNKL-------AIPPERRVHQLVESEVIQIRQA   59 (122)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~l-------gId~~~kv~~Lt~~qi~~l~~~   59 (122)
                      -|..+.|||+..|..|...-       .++.=.++.-+++..+++|.+.
T Consensus        41 eL~~lpgIg~~~A~~Iv~~R~~~G~f~sledL~~v~Gi~~k~~eki~k~   89 (98)
T 2edu_A           41 DLRSLQRIGPKKAQLIVGWRELHGPFSQVEDLERVEGITGKQMESFLKA   89 (98)
T ss_dssp             HHHHSTTCCHHHHHHHHHHHHHHCCCSSGGGGGGSTTCCHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHC
T ss_conf             9964799899999999999998599288999844899899999999983


No 50 
>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C; HET: DGT; 2.39A {Geobacillus kaustophilus} PDB: 3f2c_A* 3f2d_A*
Probab=36.54  E-value=24  Score=16.14  Aligned_cols=60  Identities=20%  Similarity=0.284  Sum_probs=36.9

Q ss_pred             CCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCH
Q ss_conf             8576664312007176899999998088821200227989999999861245643337889999999999730310012
Q gi|254780239|r   12 AKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGL   90 (122)
Q Consensus        12 ~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~rl~~i~syrG~   90 (122)
                      +..|.++|..|.|+|...|..|...-.=.|.     .|-+++.. +.-      +       -+..++.|+..++..++
T Consensus       962 ~~~I~~gl~aIkGlG~~~a~~Iv~~R~~g~F-----~s~~Df~~-R~~------~-------~k~~le~Li~~Gafd~l 1021 (1041)
T 3f2b_A          962 GNSLIPPFNAIPGLGTNVAQAIVRAREEGEF-----LSKEDLQQ-RGK------L-------SKTLLEYLESRGCLDSL 1021 (1041)
T ss_dssp             TTEEECCGGGSTTCCHHHHHHHHHHHHTSCC-----CSHHHHHH-HHT------C-------CHHHHHHHHHTTTTTTS
T ss_pred             CCEEEECHHHCCCCCHHHHHHHHHHHCCCCC-----CCHHHHHH-HHC------C-------CHHHHHHHHHCCCCCCC
T ss_conf             9949951564389799999999998667999-----99999997-328------9-------99999999977997789


No 51 
>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19
Probab=35.10  E-value=13  Score=17.74  Aligned_cols=29  Identities=21%  Similarity=0.423  Sum_probs=21.3

Q ss_pred             CCCEEEEEEEEEECCCHHHHHHHHHHCCCC
Q ss_conf             985766643120071768999999980888
Q gi|254780239|r   11 RAKRVVRALCYIHGIGFKSSQDICNKLAIP   40 (122)
Q Consensus        11 ~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId   40 (122)
                      ..+.+.-.+++++|||+++|..+ +++||.
T Consensus       109 ~~~~l~~~i~~lkGVGpk~a~~L-~klGI~  137 (780)
T 1gm5_A          109 EEVDLSTDIQYAKGVGPNRKKKL-KKLGIE  137 (780)
T ss_dssp             CCCCSCCCSSSSSSCCHHHHHHH-HTTTCC
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHH-HHCCCC
T ss_conf             77899998601788159999999-976999


No 52 
>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
Probab=34.15  E-value=9.7  Score=18.57  Aligned_cols=33  Identities=18%  Similarity=0.184  Sum_probs=21.2

Q ss_pred             EEEEEEEEECCCHHHHHHHHHHCCCCHHH-HHCCC
Q ss_conf             66643120071768999999980888212-00227
Q gi|254780239|r   15 VVRALCYIHGIGFKSSQDICNKLAIPPER-RVHQL   48 (122)
Q Consensus        15 i~~aLt~I~GIG~~~A~~Ic~~lgId~~~-kv~~L   48 (122)
                      +.-.|+.|.|||+.+|..|+-. +++++. .++|+
T Consensus       208 ~~~~L~~i~GIGpWTA~~ill~-~lg~d~fP~~D~  241 (295)
T 2jhn_A          208 AYEYLTSFKGIGRWTAELVLSI-ALGKNVFPADDL  241 (295)
T ss_dssp             HHHHHHTSTTCCHHHHHHHHHH-TTCCCCCCTTCH
T ss_pred             HHHHHHHCCCCCHHHHHHHHHH-HCCCCCCCCCCH
T ss_conf             8889984599488999999998-169895227459


No 53 
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ...
Probab=32.85  E-value=5.8  Score=19.95  Aligned_cols=30  Identities=20%  Similarity=0.241  Sum_probs=21.0

Q ss_pred             CCCCEEEEEEEEEECCCHHHHHHHHHHCCCC
Q ss_conf             9985766643120071768999999980888
Q gi|254780239|r   10 PRAKRVVRALCYIHGIGFKSSQDICNKLAIP   40 (122)
Q Consensus        10 ~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId   40 (122)
                      ...-++...|+.|+|||+++|..+- .+||.
T Consensus        89 ~~~~p~~~~l~~I~GvGpk~a~~l~-~~Gi~  118 (335)
T 2bcq_A           89 SESVPVLELFSNIWGAGTKTAQMWY-QQGFR  118 (335)
T ss_dssp             CTTHHHHHHHHTSTTCCHHHHHHHH-HTTCC
T ss_pred             HHHCCHHHHHHCCCCCCHHHHHHHH-HCCCC
T ss_conf             6334015665118876889999999-81925


No 54 
>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A
Probab=30.93  E-value=13  Score=17.73  Aligned_cols=28  Identities=14%  Similarity=0.301  Sum_probs=20.5

Q ss_pred             CCCCCCEEEEEEEEEECCCHHHHHHHHHHCC
Q ss_conf             5899857666431200717689999999808
Q gi|254780239|r    8 NIPRAKRVVRALCYIHGIGFKSSQDICNKLA   38 (122)
Q Consensus         8 ~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lg   38 (122)
                      ++|.+   .-.|.++-|||+.+|..|+..+-
T Consensus       103 ~~p~~---~~~L~~LpGVG~kTA~~il~~a~  130 (225)
T 1kg2_A          103 KFPET---FEEVAALPGVGRSTAGAILSLSL  130 (225)
T ss_dssp             SCCCS---HHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             CCCCH---HHHHHHCCCCCHHHHHHHHHHHC
T ss_conf             99742---99997589874789999999852


No 55 
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1
Probab=29.96  E-value=14  Score=17.65  Aligned_cols=22  Identities=27%  Similarity=0.324  Sum_probs=17.8

Q ss_pred             EEEEEEEECCCHHHHHHHHHHC
Q ss_conf             6643120071768999999980
Q gi|254780239|r   16 VRALCYIHGIGFKSSQDICNKL   37 (122)
Q Consensus        16 ~~aLt~I~GIG~~~A~~Ic~~l   37 (122)
                      .-.|..+-|||+.+|..|+..+
T Consensus       108 ~~~L~~LpGVG~kTA~~il~~a  129 (211)
T 2abk_A          108 RAALEALPGVGRKTANVVLNTA  129 (211)
T ss_dssp             HHHHHHSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHH
T ss_conf             9998717887369999999987


No 56 
>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A*
Probab=29.20  E-value=15  Score=17.31  Aligned_cols=27  Identities=22%  Similarity=0.423  Sum_probs=20.9

Q ss_pred             CCCCCCEEEEEEEEEECCCHHHHHHHHHHC
Q ss_conf             589985766643120071768999999980
Q gi|254780239|r    8 NIPRAKRVVRALCYIHGIGFKSSQDICNKL   37 (122)
Q Consensus         8 ~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~l   37 (122)
                      .+|.+   .-.|.++-|||+.+|..|+..+
T Consensus       107 ~vP~~---~~~L~~LpGVG~kTA~~il~~a  133 (226)
T 1orn_A          107 EVPRD---RDELMKLPGVGRKTANVVVSVA  133 (226)
T ss_dssp             SCCSC---HHHHTTSTTCCHHHHHHHHHHH
T ss_pred             CCCCC---HHHHHHCCCCCHHHHHHHHHHH
T ss_conf             79878---9999748775367999999998


No 57 
>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A*
Probab=29.10  E-value=15  Score=17.42  Aligned_cols=28  Identities=11%  Similarity=0.230  Sum_probs=21.5

Q ss_pred             CCCCCCCEEEEEEEEEECCCHHHHHHHHHHC
Q ss_conf             7589985766643120071768999999980
Q gi|254780239|r    7 VNIPRAKRVVRALCYIHGIGFKSSQDICNKL   37 (122)
Q Consensus         7 ~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~l   37 (122)
                      -.+|.+.   -.|..+-|||+.+|.+|+..+
T Consensus       111 g~~P~~~---~~L~~LpGVG~~TA~ail~~a  138 (369)
T 3fsp_A          111 GKVPDDP---DEFSRLKGVGPYTVGAVLSLA  138 (369)
T ss_dssp             TCCCCSH---HHHHTSTTCCHHHHHHHHHHH
T ss_pred             CCCCCCH---HHHHHCCCHHHHHHHHHHHHH
T ss_conf             9999879---998524225889999999986


No 58 
>3doa_A Fibrinogen binding protein; structural genomics, MCSG., PSI-2, protein structure initiative, midwest center for structural genomics; 2.81A {Staphylococcus aureus subsp}
Probab=28.75  E-value=13  Score=17.68  Aligned_cols=36  Identities=8%  Similarity=0.148  Sum_probs=26.8

Q ss_pred             EEEEEEEEE-ECCCHHHHHHHHHHCCCCHHHHHCCCC
Q ss_conf             766643120-071768999999980888212002279
Q gi|254780239|r   14 RVVRALCYI-HGIGFKSSQDICNKLAIPPERRVHQLV   49 (122)
Q Consensus        14 ~i~~aLt~I-~GIG~~~A~~Ic~~lgId~~~kv~~Lt   49 (122)
                      .+.-+|..- -|+|+..|..+|..+|+++...+.+.-
T Consensus       189 ~l~k~L~~~~~g~~~~l~~ei~~ra~~~~~~~~~~~~  225 (288)
T 3doa_A          189 NIAKQLLNQFEGFSPLITNEIVSRRQFMTSSTLPEAF  225 (288)
T ss_dssp             CHHHHHHHHBTTCCHHHHHHHHTTSSSCSTTHHHHHH
T ss_pred             CHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCHHHHH
T ss_conf             1999999863899989999999974999755689999


No 59 
>3mfi_A DNA polymerase ETA; DNA damage, DNA repair, DNA replication, DNA synthesis, NUCL binding, magnesium; HET: DNA DOC TTD DTP; 1.76A {Saccharomyces cerevisiae} PDB: 3mfh_A* 2r8j_A* 2r8k_A* 2wtf_A* 1jih_A*
Probab=27.80  E-value=16  Score=17.29  Aligned_cols=40  Identities=8%  Similarity=0.198  Sum_probs=27.3

Q ss_pred             EEEEEEECCCHHHHHHHHHHCCCCH---HHHHCCC---CHHHHHHH
Q ss_conf             6431200717689999999808882---1200227---98999999
Q gi|254780239|r   17 RALCYIHGIGFKSSQDICNKLAIPP---ERRVHQL---VESEVIQI   56 (122)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~lgId~---~~kv~~L---t~~qi~~l   56 (122)
                      ..++.|.|||..++..++..+++..   =..+++|   +..++.++
T Consensus       307 lpI~~i~GIG~~~~~kL~~~L~~~~~~gI~~i~dl~~~~~~~L~~~  352 (520)
T 3mfi_A          307 FEITSFWTLGGVLGKELIDVLDLPHENSIKHIRETWPDNAGQLKEF  352 (520)
T ss_dssp             CCGGGSTTCSSHHHHHHHHHTTCCSSSHHHHHHHHSCSCHHHHHHH
T ss_pred             CCCCEECCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             9801006747899999999856556685746997743899999988


No 60 
>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} SCOP: a.96.1.2
Probab=27.43  E-value=17  Score=17.00  Aligned_cols=25  Identities=12%  Similarity=0.087  Sum_probs=19.7

Q ss_pred             EEEEEEECCCHHHHHHHHHHCCCCH
Q ss_conf             6431200717689999999808882
Q gi|254780239|r   17 RALCYIHGIGFKSSQDICNKLAIPP   41 (122)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~lgId~   41 (122)
                      -.|..+-|||+.+|..|+..+-=.|
T Consensus       115 ~eL~~LPGVG~ktA~~vl~~a~~~~  139 (221)
T 1kea_A          115 KAILDLPGVGKYTCAAVMCLAFGKK  139 (221)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHTTCCC
T ss_pred             HHHHCCCCCCHHHHHHHHHHHCCCC
T ss_conf             8874489876567999999853887


No 61 
>1zq9_A Probable dimethyladenosine transferase; SGC, structural genomics, structural genomics consortium; HET: SAM; 1.90A {Homo sapiens} SCOP: c.66.1.24
Probab=25.12  E-value=37  Score=14.93  Aligned_cols=32  Identities=13%  Similarity=0.242  Sum_probs=25.1

Q ss_pred             HHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf             999999808882120022798999999986124
Q gi|254780239|r   30 SQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ   62 (122)
Q Consensus        30 A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~   62 (122)
                      ...++..+|+++ .+..+||.+|+.+|.+.+++
T Consensus       248 i~~~l~~~g~~~-~R~E~Ls~~~f~~L~~~l~~  279 (285)
T 1zq9_A          248 IQQILTSTGFSD-KRARSMDIDDFIRLLHGFNA  279 (285)
T ss_dssp             HHHHHHHHTCTT-CBGGGCCHHHHHHHHHHHHT
T ss_pred             HHHHHHHCCCCC-CCHHHCCHHHHHHHHHHHHH
T ss_conf             999998569977-88044999999999999997


No 62 
>3lay_A Zinc resistance-associated protein; salmonella typhimurium LT2, ZRAP, periplasm, structural genomics; 2.70A {Salmonella enterica subsp}
Probab=23.07  E-value=41  Score=14.69  Aligned_cols=58  Identities=9%  Similarity=0.062  Sum_probs=35.6

Q ss_pred             ECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHC-CCCHHH---HHCCCCHHHHHHHHHHHCC
Q ss_conf             167589985766643120071768999999980-888212---0022798999999986124
Q gi|254780239|r    5 AGVNIPRAKRVVRALCYIHGIGFKSSQDICNKL-AIPPER---RVHQLVESEVIQIRQAIEQ   62 (122)
Q Consensus         5 ~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~l-gId~~~---kv~~Lt~~qi~~l~~~I~~   62 (122)
                      -++...-++.+.++|-.+-+++...+..++... |-...+   -..+||++|..++.++.++
T Consensus        21 ~~~~mk~~~~~~~~l~a~~~~~~~s~~a~a~~~~G~g~g~~~~~~~~LT~EQq~~~~~I~~~   82 (175)
T 3lay_A           21 QSNAMKRNNKSAIALIALSLLALSSGAAFAGHHWGNNDGMWQQGGSPLTTEQQATAQKIYDD   82 (175)
T ss_dssp             -----------------------------------------------CCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             55426689999999999999996123888654679889988877888999999999999999


No 63 
>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices, helix-hairpin-helix motif, iron-sulfur cluste hydrolase; 2.30A {Homo sapiens}
Probab=22.96  E-value=22  Score=16.38  Aligned_cols=20  Identities=15%  Similarity=0.165  Sum_probs=16.0

Q ss_pred             EEEEECCCHHHHHHHHHHCC
Q ss_conf             31200717689999999808
Q gi|254780239|r   19 LCYIHGIGFKSSQDICNKLA   38 (122)
Q Consensus        19 Lt~I~GIG~~~A~~Ic~~lg   38 (122)
                      |..+-|||+++|..|+..+-
T Consensus       131 l~~LPGVG~kTA~aIl~~af  150 (287)
T 3n5n_X          131 QQLLPGVGRYTAGAIASIAF  150 (287)
T ss_dssp             HHHSTTCCHHHHHHHHHHHS
T ss_pred             CCCCCCCCHHHHHHHHHHHH
T ss_conf             04688756899999999883


No 64 
>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A
Probab=22.65  E-value=26  Score=15.95  Aligned_cols=80  Identities=25%  Similarity=0.333  Sum_probs=45.9

Q ss_pred             EEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC----CCCCCH-------HHHH--------HHH
Q ss_conf             666431200717689999999808882120022798999999986124----564333-------7889--------999
Q gi|254780239|r   15 VVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ----DYQVEG-------DLRR--------TVA   75 (122)
Q Consensus        15 i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~----~~~i~~-------~L~~--------~~~   75 (122)
                      +.-+|+++=|||+++|..+...+=-.+...+.+|.+.=.+ +.+-|..    ....+.       |-.|        +..
T Consensus        10 LI~~l~kLPGIG~KsA~RlA~~LL~~~~~~~~~La~~i~~-~k~~i~~C~~C~~lse~~~C~IC~D~~Rd~~~iCVVE~~   88 (228)
T 1vdd_A           10 LIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLE-AKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEP   88 (228)
T ss_dssp             HHHHHHTSTTCCHHHHHHHHHHHSSSCHHHHHHHHHHHHH-HHHHCEECSSSCCEESSSSCHHHHCSSSCTTEEEEESSH
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCH
T ss_conf             9999966899988999999999981999999999999999-998188386788716777766435777765458997789


Q ss_pred             HHHHHHHHCCCCCCHHHHCC
Q ss_conf             99999973031001233179
Q gi|254780239|r   76 MNIKRLMDLGCYRGLRHRRG   95 (122)
Q Consensus        76 ~~i~rl~~i~syrG~RH~~g   95 (122)
                      .|+.-+=+.+.|+|.=|..|
T Consensus        89 ~Dl~aIE~tg~y~G~YhVLg  108 (228)
T 1vdd_A           89 GDVIALERSGEYRGLYHVLH  108 (228)
T ss_dssp             HHHHHTTTTSSCCSEEEECS
T ss_pred             HHHHHHHHCCCCCEEEEECC
T ss_conf             99999986081126998668


No 65 
>2r6f_A Excinuclease ABC subunit A; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, ATP-binding cassette, cytoplasm; HET: ADP; 3.20A {Geobacillus stearothermophilus 10}
Probab=22.22  E-value=42  Score=14.58  Aligned_cols=85  Identities=14%  Similarity=0.086  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC-----------------CCCCCHH---HHHHHHHH--HHHHHHC
Q ss_conf             689999999808882120022798999999986124-----------------5643337---88999999--9999730
Q gi|254780239|r   27 FKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ-----------------DYQVEGD---LRRTVAMN--IKRLMDL   84 (122)
Q Consensus        27 ~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~-----------------~~~i~~~---L~~~~~~~--i~rl~~i   84 (122)
                      ...-..+|+..|||+++...+|++++.+.|-.=-+.                 .+..++-   |.+...+.  ...-..+
T Consensus       336 ~~~l~~~a~~~~~~~~~P~~~L~~~~~~~ll~G~~~~~~~~~~~~~~~~~~~~~~~~eGvi~~l~r~~~~~~s~~~r~~l  415 (972)
T 2r6f_A          336 PQLLEAVCRHYGIPMDVPVKDLPKEQLDKILYGSGGEPIYFRYTNDFGQVREQYIAFEGVIPNVERRYRETSSDYIREQM  415 (972)
T ss_dssp             HHHHHHHHHHHCCCSSCBGGGSCHHHHHHHHHCCTTCCCCBCCBCSSSCBCCBCCCCCCHHHHHHHHHHHCCCTTHHHHH
T ss_pred             HHHHHHHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCCEEEEEECCCCCEEECCCCCCCHHHHHHHHHHHCCCHHHHHHH
T ss_conf             99999999985999888846668999999853899751467642367833211456432578999999864278899999


Q ss_pred             CCCCCHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             31001233179878770778776577776
Q gi|254780239|r   85 GCYRGLRHRRGLPVRGQRTHTNARTRKKF  113 (122)
Q Consensus        85 ~syrG~RH~~gLpvRGQRT~tn~rt~k~~  113 (122)
                      ..|++...  =--|.|.|-+..|+..+=.
T Consensus       416 ~~y~~~~~--Cp~C~G~RL~~~al~v~i~  442 (972)
T 2r6f_A          416 EKYMAEQP--CPTCQGYRLKKESLAVLVG  442 (972)
T ss_dssp             GGGEEEEE--CTTTTTSCBCTTTTTEESS
T ss_pred             HHHCCCCC--CCCCCCCCCCHHHHCCCCC
T ss_conf             98536877--6665465577787506117


No 66 
>3hdt_A Putative kinase; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}
Probab=22.03  E-value=43  Score=14.56  Aligned_cols=34  Identities=15%  Similarity=0.162  Sum_probs=26.7

Q ss_pred             CCCCCCCEEEEEEEEEECCCHHH-HHHHHHHCCCC
Q ss_conf             75899857666431200717689-99999980888
Q gi|254780239|r    7 VNIPRAKRVVRALCYIHGIGFKS-SQDICNKLAIP   40 (122)
Q Consensus         7 ~~i~~~K~i~~aLt~I~GIG~~~-A~~Ic~~lgId   40 (122)
                      --+-.++++.++++.-+|-|.++ |..+++.+|+.
T Consensus         7 ~~~m~~~~~iItI~g~~GsGKsTia~~LA~~Lg~~   41 (223)
T 3hdt_A            7 GRFMGNKNLIITIEREYGSGGRIVGKKLAEELGIH   41 (223)
T ss_dssp             -----CCCEEEEEEECTTSCHHHHHHHHHHHHTCE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCC
T ss_conf             75246899799857999899799999999994986


No 67 
>1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} SCOP: a.96.1.2 PDB: 3iho_A
Probab=21.29  E-value=28  Score=15.74  Aligned_cols=19  Identities=21%  Similarity=0.107  Sum_probs=12.8

Q ss_pred             EEEEEECCCHHHHHHHHHH
Q ss_conf             4312007176899999998
Q gi|254780239|r   18 ALCYIHGIGFKSSQDICNK   36 (122)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~   36 (122)
                      .|+.+.|||+.+|..+.--
T Consensus       105 ~l~~LpGVG~ytad~~~if  123 (155)
T 1ngn_A          105 YPIELHGIGKYGNDSYRIF  123 (155)
T ss_dssp             SGGGSTTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHH
T ss_conf             1675898219999999999


Done!