Query         gi|254780748|ref|YP_003065161.1| integration host factor, beta subunit [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 100
No_of_seqs    101 out of 3065
Neff          6.7 
Searched_HMMs 33803
Date          Wed Jun  1 14:10:04 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780748.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1p71_A DNA-binding protein HU  99.9 6.6E-25   2E-29  179.4  10.9   94    1-95      1-94  (94)
  2 >1owf_B IHF-beta, integration   99.9 8.2E-25 2.4E-29  178.8  11.2   93    1-93      1-93  (94)
  3 >3c4i_A DNA-binding protein HU  99.9 6.7E-24   2E-28  173.0  10.8   97    1-98      1-97  (99)
  4 >2o97_B NS1, HU-1, DNA-binding  99.9 3.7E-24 1.1E-28  174.6   8.7   90    1-91      1-90  (90)
  5 >1mul_A NS2, HU-2, DNA binding  99.9 5.1E-24 1.5E-28  173.8   9.0   90    1-91      1-90  (90)
  6 >1b8z_A Protein (histonelike p  99.9 4.2E-24 1.2E-28  174.3   7.8   90    1-91      1-90  (90)
  7 >1hue_A HU protein; DNA-bindin  99.9   6E-23 1.8E-27  166.9   8.6   90    1-91      1-90  (90)
  8 >1exe_A Transcription factor 1  99.9 7.6E-24 2.3E-28  172.6   3.6   94    1-95      1-94  (99)
  9 >2iie_A Integration HOST facto  99.9 1.4E-22 4.2E-27  164.6   7.7   92    1-93     47-138 (204)
 10 >2iie_A Integration HOST facto  99.7 8.3E-17 2.5E-21  128.0   6.6   71   26-96    127-197 (204)
 11 >1owf_A IHF-alpha, integration  99.5 4.2E-15 1.2E-19  117.2   4.6   56   41-96      1-56  (58)
 12 >2np2_A HBB; protein-DNA compl  99.5 7.4E-15 2.2E-19  115.6   2.8   54   41-94      1-55  (56)
 13 >1jeo_A MJ1247, hypothetical p  37.8      21 0.00062   17.6   2.2   51    1-51      1-51  (180)
 14 >1w6s_A Methanol dehydrogenase  37.7      17  0.0005   18.1   1.7   19   59-77     55-73  (73)
 15 >1i27_A Transcription factor I  33.1      29 0.00085   16.7   2.3   33    1-33     24-56  (73)
 16 >1z67_A Hypothetical protein S  32.2      40  0.0012   15.8   5.1   40    4-44     57-96  (117)
 17 >2ysk_A Hypothetical protein T  31.5      16 0.00048   18.3   0.8   41    1-42     14-55  (145)
 18 >1o17_A Anthranilate PRT, anth  31.3      42  0.0012   15.7   3.6   30    1-31      1-30  (95)
 19 >1nha_A TFIIF-alpha, transcrip  31.2      42  0.0012   15.7   2.8   33    1-33     33-65  (82)
 20 >3g2b_A Coenzyme PQQ synthesis  28.0      48  0.0014   15.3   5.4   33    2-35     18-50  (56)
 21 >2yva_A DNAA initiator-associa  27.0      39  0.0012   15.8   2.1   34   18-51     19-52  (196)
 22 >2wvr_C DNA replication factor  25.7      17  0.0005   18.2   0.0   37    1-37    473-510 (546)
 23 >1whu_A Polynucleotide phospho  25.4      53  0.0016   15.0   5.0   45    3-47     52-96  (104)
 24 >1aip_C EF-TS, elongation fact  24.4      55  0.0016   14.9   4.0   54    1-55      1-66  (137)
 25 >1brw_A PYNP, protein (pyrimid  23.4      58  0.0017   14.8   3.6   30    1-31      1-30  (191)
 26 >1tk9_A Phosphoheptose isomera  22.0      48  0.0014   15.3   1.7   48    3-51      3-53  (188)
 27 >2i7t_A Cleavage and polyadeny  21.8      62  0.0018   14.6   3.0   28   23-50      6-33  (186)
 28 >2elc_A Trp D, anthranilate ph  21.2      63  0.0019   14.5   2.2   26    5-31      2-27  (89)
 29 >3cdi_A Polynucleotide phospho  20.8      65  0.0019   14.4   5.8   43    3-45     41-83  (85)

No 1  
>>1p71_A DNA-binding protein HU; protein-DNA complex, DNA bending, DNA binding protein/DNA complex; 1.90A {Anabaena SP} (A:)
Probab=99.92  E-value=6.6e-25  Score=179.38  Aligned_cols=94  Identities=31%  Similarity=0.592  Sum_probs=91.5

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf             98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF   80 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F   80 (100)
                      |||+|||+.||+++ ++++++++.++|+|++.|.++|.+|+.|+|+|||+|+++.+++|.|+||+|||.+.||++++|+|
T Consensus         1 MtK~eli~~ia~~~-~ls~~~v~~~i~~~~~~i~~~L~~~~~V~l~~fG~F~v~~~~~r~~~Np~Tge~i~i~~~~~v~F   79 (94)
T 1p71_A            1 MNKGELVDAVAEKA-SVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREGRNPKTNEKMEIPATRVPAF   79 (94)
T ss_dssp             CBHHHHHHHHHHHH-TCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEE
T ss_pred             CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCCCEECCEEEEEEEEECCCEEECCCCCCEEEECCCCCEEE
T ss_conf             98899999999845-97999999999999999999986488605035269999983672328979997899648740899


Q ss_pred             CCCHHHHHHHCCCCC
Q ss_conf             269899997078610
Q gi|254780748|r   81 RAGKNLKERLNSPDS   95 (100)
Q Consensus        81 k~sk~lk~~iN~~~~   95 (100)
                      +||+.|+++||+..+
T Consensus        80 kpsk~lk~~in~~~a   94 (94)
T 1p71_A           80 SAGKLFREKVAPPKA   94 (94)
T ss_dssp             EECHHHHHHHSCCCC
T ss_pred             ECCHHHHHHHCCCCC
T ss_conf             549899997577899


No 2  
>>1owf_B IHF-beta, integration HOST factor beta-subunit; protein-DNA recognition, indirect readout, DNA bending, minor groove; 1.95A {Escherichia coli} (B:)
Probab=99.92  E-value=8.2e-25  Score=178.77  Aligned_cols=93  Identities=42%  Similarity=0.669  Sum_probs=91.2

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf             98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF   80 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F   80 (100)
                      |||+|||+.||++++++++++++.++|+|++.|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.||++++|+|
T Consensus         1 MtK~eli~~ia~~~~~~sk~~~~~~v~~~~~~i~~~L~~~~~V~l~gfG~F~~~~r~~r~~~nP~Tge~~~ip~k~~v~F   80 (94)
T 1owf_B            1 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIAIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHF   80 (94)
T ss_dssp             CBHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEE
T ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEEEEECCCCCCCCCCCCEEEECCCCCEEE
T ss_conf             97899999999876999999999999999999999997699599657379999860683333849999898648631898


Q ss_pred             CCCHHHHHHHCCC
Q ss_conf             2698999970786
Q gi|254780748|r   81 RAGKNLKERLNSP   93 (100)
Q Consensus        81 k~sk~lk~~iN~~   93 (100)
                      +||+.|++.||+.
T Consensus        81 kpsk~lk~~vn~~   93 (94)
T 1owf_B           81 KPGKELRDRANIY   93 (94)
T ss_dssp             EECHHHHHHHCCC
T ss_pred             ECCHHHHHHHCCC
T ss_conf             1698999987559


No 3  
>>3c4i_A DNA-binding protein HU homolog; dimerization by four helix bundle interaction, DNA condensation; 2.04A {Mycobacterium tuberculosis} (A:)
Probab=99.91  E-value=6.7e-24  Score=172.98  Aligned_cols=97  Identities=30%  Similarity=0.507  Sum_probs=93.3

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf             98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF   80 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F   80 (100)
                      |||+|||..||+++ ++|+.++..++|+|++.|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.+|++++|+|
T Consensus         1 Mtk~eli~~ia~~~-~~s~~~v~~~i~~~~~~i~~~L~~g~~V~l~~fG~F~~~~~~~r~~~np~T~e~i~i~~k~~v~F   79 (99)
T 3c4i_A            1 MNKAELIDVLTQKL-GSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAF   79 (99)
T ss_dssp             CBHHHHHHHHHHHH-TCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECSEEEECTTTCCEEEECCEEEEEE
T ss_pred             CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCCEECCCEEEEEEEEECCEEEECCCCCCEEEECCCCEEEE
T ss_conf             97899999999874-98999999999999999999996499613155689999875681106859998898638722899


Q ss_pred             CCCHHHHHHHCCCCCCCC
Q ss_conf             269899997078610012
Q gi|254780748|r   81 RAGKNLKERLNSPDSTLS   98 (100)
Q Consensus        81 k~sk~lk~~iN~~~~~~~   98 (100)
                      +||+.|++.||.......
T Consensus        80 kpsk~Lk~~in~~~~~~~   97 (99)
T 3c4i_A           80 RPGAQFKAVVSGAQRLPA   97 (99)
T ss_dssp             EECHHHHHHHHTSSCCCC
T ss_pred             ECCHHHHHHHCCCCCCCC
T ss_conf             629899998666668999


No 4  
>>2o97_B NS1, HU-1, DNA-binding protein HU-beta; heterodimer, DNA structure, DNA supercoiling, E. coli; 2.45A {Escherichia coli} (B:)
Probab=99.91  E-value=3.7e-24  Score=174.64  Aligned_cols=90  Identities=38%  Similarity=0.627  Sum_probs=88.7

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf             98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF   80 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F   80 (100)
                      |||+|||+.||+++ ++++++++.++|+|++.|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.+|++++|+|
T Consensus         1 Mtk~eli~~ia~~~-~~t~~~v~~~v~~~~~~i~~~L~~~~~V~l~~fG~F~v~~~~~r~~~np~tge~~~i~~k~~v~F   79 (90)
T 2o97_B            1 MNKSQLIDKIAAGA-DISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSF   79 (90)
T ss_dssp             CBHHHHHHHHHHTT-C-CHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEECCC------------------CEEEE
T ss_pred             CCHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCEEECCCCCCEEEECCCCEEEE
T ss_conf             97899999999720-99999999999999999999998076444550589999840564028899997899538622899


Q ss_pred             CCCHHHHHHHC
Q ss_conf             26989999707
Q gi|254780748|r   81 RAGKNLKERLN   91 (100)
Q Consensus        81 k~sk~lk~~iN   91 (100)
                      +||+.|++.||
T Consensus        80 kp~k~lk~~iN   90 (90)
T 2o97_B           80 RAGKALKDAVN   90 (90)
T ss_dssp             EECHHHHHHCC
T ss_pred             ECCHHHHHHHC
T ss_conf             63989997629


No 5  
>>1mul_A NS2, HU-2, DNA binding protein HU-alpha; histone-like; HET: DNA; 2.30A {Escherichia coli} (A:)
Probab=99.90  E-value=5.1e-24  Score=173.76  Aligned_cols=90  Identities=36%  Similarity=0.573  Sum_probs=87.9

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf             98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF   80 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F   80 (100)
                      |||+|||+.||+++ ++++++++.++|+|++.|.++|.+|+.|.|+|||+|+++.+++|.++||+|||.+.||++++|+|
T Consensus         1 Mtk~eli~~ia~~~-~~s~~~v~~~v~~~~~~i~~~L~~~~~v~l~~fG~F~v~~r~~r~~~Np~Tge~i~ip~k~~v~F   79 (90)
T 1mul_A            1 MNKTQLIDVIAEKA-ELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAF   79 (90)
T ss_dssp             CCHHHHHHHHHHHT-TCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECC--------------CCEEEEEE
T ss_pred             CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCEEEECCCCCCEEEECCCCCEEE
T ss_conf             97899999999704-96999999999999999999997199877203699999862884308939997899748740899


Q ss_pred             CCCHHHHHHHC
Q ss_conf             26989999707
Q gi|254780748|r   81 RAGKNLKERLN   91 (100)
Q Consensus        81 k~sk~lk~~iN   91 (100)
                      +||+.|+++|.
T Consensus        80 rp~k~lk~~i~   90 (90)
T 1mul_A           80 VSGKALKDAVK   90 (90)
T ss_dssp             EECHHHHHHHC
T ss_pred             ECCHHHHHHHC
T ss_conf             72989998639


No 6  
>>1b8z_A Protein (histonelike protein HU); thermostable DNA binding protein; 1.60A {Thermotoga maritima} (A:)
Probab=99.90  E-value=4.2e-24  Score=174.30  Aligned_cols=90  Identities=47%  Similarity=0.707  Sum_probs=88.8

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf             98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF   80 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F   80 (100)
                      |||+|||+.|++++ ++++++++.++|+|++.|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.+|++++|+|
T Consensus         1 Mtk~eli~~ia~~~-~~s~~~~~~~v~~~~~~i~~~L~~~~~V~l~~fG~F~v~~~~~r~~~np~tge~i~i~~k~~v~F   79 (90)
T 1b8z_A            1 MNKKELIDRVAKKA-GAKKKDVKLILDTILETITEALAKGEKVQIVGFGSFEVRKAAARKGVNPQTRKPITIPERKVPKF   79 (90)
T ss_dssp             CCHHHHHHHHHHHH-TCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEC-----------------------CCEE
T ss_pred             CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHCCCCEECCEEEEEEECCCCEEEECCCCCCEEEECCCCEEEE
T ss_conf             97899999999854-98999999999999999999987288637466578988613544445799998898638721899


Q ss_pred             CCCHHHHHHHC
Q ss_conf             26989999707
Q gi|254780748|r   81 RAGKNLKERLN   91 (100)
Q Consensus        81 k~sk~lk~~iN   91 (100)
                      +||+.|++.||
T Consensus        80 k~sk~Lk~~in   90 (90)
T 1b8z_A           80 KPGKALKEKVK   90 (90)
T ss_dssp             EECHHHHHHHC
T ss_pred             EECHHHHHHHC
T ss_conf             73899998639


No 7  
>>1hue_A HU protein; DNA-binding; NMR {Geobacillus stearothermophilus} (A:)
Probab=99.88  E-value=6e-23  Score=166.93  Aligned_cols=90  Identities=37%  Similarity=0.655  Sum_probs=88.0

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf             98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF   80 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F   80 (100)
                      |||+|||..|++++ ++++++++.++|+|++.|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.+||+++|+|
T Consensus         1 Mtk~~li~~i~~~~-~~s~~~v~~~i~~~~~~i~~~L~~~~~v~l~~fG~F~v~~~~~r~~~Np~Tge~~~i~~k~~vkF   79 (90)
T 1hue_A            1 MNKTELINAVAETS-GLSKKDATKAVDAVFDSITEALRKGDKVQLIGFGNFEVRERAARKGRNPQTGEEMEIPASKVPAF   79 (90)
T ss_dssp             CBSHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHTCCCCBTTTBEECCCCCCCCEEECSSSSSEEECCCCCCCCE
T ss_pred             CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECCEEEEEEEECCCCCCCCCCCCEEEECCCCEEEE
T ss_conf             97899999999854-98999999999999999999996598288402439999861684455839998899548741898


Q ss_pred             CCCHHHHHHHC
Q ss_conf             26989999707
Q gi|254780748|r   81 RAGKNLKERLN   91 (100)
Q Consensus        81 k~sk~lk~~iN   91 (100)
                      +||+.|+++|.
T Consensus        80 r~sk~lk~~ik   90 (90)
T 1hue_A           80 KPGKALKDAVK   90 (90)
T ss_dssp             ECTTHHHHHTC
T ss_pred             ECCHHHHHHHC
T ss_conf             13989998639


No 8  
>>1exe_A Transcription factor 1; beta ribbon ARMS, DNA-binding, DNA-bending protein; NMR {Bacillus phage SPO1} (A:)
Probab=99.88  E-value=7.6e-24  Score=172.63  Aligned_cols=94  Identities=24%  Similarity=0.354  Sum_probs=91.2

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf             98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF   80 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F   80 (100)
                      |||+|||+.||+++ ++++++++.++|+|+++|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.||++++|+|
T Consensus         1 Mtk~eli~~ia~~~-~~s~~~v~~~i~~~~~~i~~~L~~g~~V~l~gfG~F~v~~~~~r~~~np~Tge~i~i~~k~~v~F   79 (99)
T 1exe_A            1 MNKTELIKAIAQDT-GLTQVSVSKMLASFEKIITETVAKGDKVQLTGFLNIKPVARQARKGFNPQTQEALEIAPSVGVSV   79 (99)
T ss_dssp             CCTTHHHHHHHHHH-CSCCTTHHHHHHHHHHHHHHHHHHTCCCCBTTTBCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCC
T ss_pred             CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEEEEECCCCCCCCCCCCEEEECCCCCEEE
T ss_conf             98899999999986-96999999999999999999996899599736789998755573447899998898428534799


Q ss_pred             CCCHHHHHHHCCCCC
Q ss_conf             269899997078610
Q gi|254780748|r   81 RAGKNLKERLNSPDS   95 (100)
Q Consensus        81 k~sk~lk~~iN~~~~   95 (100)
                      +||+.|+++||....
T Consensus        80 kpsk~LK~~in~~~~   94 (99)
T 1exe_A           80 KPGESLKKAAEGLKY   94 (99)
T ss_dssp             CCCHHHHHHHHHHTH
T ss_pred             ECCHHHHHHHCCCCH
T ss_conf             349899998828985


No 9  
>>2iie_A Integration HOST factor; DNA kinking, bending, U-turn, intercalation, divalent, metal, recombination/DNA complex; HET: DNA; 2.41A {Escherichia coli} PDB: 2iif_A* (A:)
Probab=99.87  E-value=1.4e-22  Score=164.58  Aligned_cols=92  Identities=30%  Similarity=0.578  Sum_probs=75.1

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf             98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF   80 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F   80 (100)
                      |||+|||+.||+++ ++++++++.++|+|++.|.++|.+|+.|.|+|||+|+++.+++|.++||+|||.+.+|++++|+|
T Consensus        47 MtK~eLi~~ia~~~-glskk~a~~ii~~~~~~I~e~L~~g~~V~l~gfGtF~v~~r~~R~~rNP~Tge~i~i~~kk~vkF  125 (204)
T 2iie_A           47 LTKAEMSEYLFDKL-GLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTF  125 (204)
T ss_dssp             BCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHTTCEEEETTTEEEEEEEECCBCCBCTTTCCBCCBCCEEEEEE
T ss_pred             CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEEEECCCCCCCCCCCCEEEECCCCCEEE
T ss_conf             35999999999986-97999999999999999999996699256511589999876471123889998898648651799


Q ss_pred             CCCHHHHHHHCCC
Q ss_conf             2698999970786
Q gi|254780748|r   81 RAGKNLKERLNSP   93 (100)
Q Consensus        81 k~sk~lk~~iN~~   93 (100)
                      +||+.|+..+|..
T Consensus       126 k~~k~LK~iveaL  138 (204)
T 2iie_A          126 RPGQKLKSRVENA  138 (204)
T ss_dssp             EECHHHHHHHHHH
T ss_pred             EECHHHHHHHHCC
T ss_conf             9547999886413


No 10 
>>2iie_A Integration HOST factor; DNA kinking, bending, U-turn, intercalation, divalent, metal, recombination/DNA complex; HET: DNA; 2.41A {Escherichia coli} PDB: 2iif_A* (A:)
Probab=99.67  E-value=8.3e-17  Score=127.97  Aligned_cols=71  Identities=38%  Similarity=0.630  Sum_probs=67.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEECCCHHHHHHHCCCCCC
Q ss_conf             99999999999864985120345788862146541025889888994687346762698999970786100
Q gi|254780748|r   26 VNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPDST   96 (100)
Q Consensus        26 vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~Fk~sk~lk~~iN~~~~~   96 (100)
                      .+.+++.+.++|..++.|+|+|||+|+++.+++|.||||+|||.|.||++++|+|+||+.|+++||+....
T Consensus       127 ~~k~LK~iveaL~~ge~V~i~~fG~F~~~~r~~R~grNP~Tge~i~Ipa~~~~~Fk~~k~lk~~vn~~~~~  197 (204)
T 2iie_A          127 PGQKLKSRVENAGGGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYGGS  197 (204)
T ss_dssp             ECHHHHHHHHHHCCCCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEEEECHHHHHHHCSSCCS
T ss_pred             ECHHHHHHHHCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEECCCCCEEECCCHHHHHHHCCCCCC
T ss_conf             54799988641344654222656889987406735619299998886597536878788999987579998


No 11 
>>1owf_A IHF-alpha, integration HOST factor alpha-subunit; protein-DNA recognition, indirect readout, DNA bending, minor groove; 1.95A {Escherichia coli} (A:42-99)
Probab=99.54  E-value=4.2e-15  Score=117.17  Aligned_cols=56  Identities=30%  Similarity=0.608  Sum_probs=53.4

Q ss_pred             CCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEECCCHHHHHHHCCCCCC
Q ss_conf             85120345788862146541025889888994687346762698999970786100
Q gi|254780748|r   41 GRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPDST   96 (100)
Q Consensus        41 ~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~Fk~sk~lk~~iN~~~~~   96 (100)
                      ++|.|+|||+|+++.+++|.|+||+|||.|.||++++|+|+||+.|+++||+....
T Consensus         1 ekV~l~gfGtF~~~~r~~R~grNP~Tge~i~I~ak~~v~Fk~sk~Lk~~vn~~~~~   56 (58)
T 1owf_A            1 EQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPK   56 (58)
T ss_dssp             CCEEETTTEEEEEEEECCEEEECSSSCCEEEECCEEEEEEEECHHHHHHHHTCCCC
T ss_pred             CEEEECCEEEEEEEEECCCCCCCCCCCCEEEECCCCEEEEEECHHHHHHHHCCCCC
T ss_conf             97995113799998766821258899988995387228997499999998078968


No 12 
>>2np2_A HBB; protein-DNA complex, DNA-binding protein, DNA-bending protein, dnabii family, HU/IHF family, DNA binding protein/DNA complex; 3.02A {Borrelia burgdorferi} (A:53-108)
Probab=99.50  E-value=7.4e-15  Score=115.59  Aligned_cols=54  Identities=43%  Similarity=0.706  Sum_probs=51.5

Q ss_pred             CCCCCEEEEEEEEECCCCC-CEECCCCCCEEEECCCCEEEECCCHHHHHHHCCCC
Q ss_conf             8512034578886214654-10258898889946873467626989999707861
Q gi|254780748|r   41 GRVEIRGFGSFSVRKRAAR-LARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPD   94 (100)
Q Consensus        41 ~~V~i~gfGtF~~~~~~~r-~~rNP~Tge~i~i~~~~~v~Fk~sk~lk~~iN~~~   94 (100)
                      ++|.|+|||+|+++.+++| .||||+|||.|.||++++|+|+||+.|+++||+..
T Consensus         1 d~V~l~gFGtF~~~~r~~R~~grNP~Tge~i~I~a~~v~~Fk~~k~lk~~vn~~~   55 (56)
T 2np2_A            1 NVIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGIK   55 (56)
T ss_dssp             CEEEETTTEEEEEEEECCBSSCBCTTTCCBCCBCCEEEEEEEECHHHHHHHHSCC
T ss_pred             CEEEEEEEEEEEEEEECCCCCCCCCCCCCEEEECCCCCEEECCCHHHHHHHHCCC
T ss_conf             9699844689999730476555388999889853875678748989999970679


No 13 
>>1jeo_A MJ1247, hypothetical protein MJ1247; RUMP pathway, phosphosugar, 3-hexulose-6-phosphate isomerase, PHI, structural genomics; HET: CME CIT; 2.00A {Methanocaldococcus jannaschii} (A:)
Probab=37.84  E-value=21  Score=17.58  Aligned_cols=51  Identities=14%  Similarity=0.109  Sum_probs=37.3

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEE
Q ss_conf             988999999999738999899999999999999999864985120345788
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSF   51 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF   51 (100)
                      |+..|.+..+.+.....-....+.+-...++.+.+.+.+.++|.+-|.|.=
T Consensus         1 mse~~~~~~i~~~~~~~i~~~~~~~~~~~~~~~~~~l~~a~~i~i~g~G~S   51 (180)
T 1jeo_A            1 MSKLEELDIVSNNILILKKFYTNDEWKNKLDSLIDRIIKAKKIFIFGVGRS   51 (180)
T ss_dssp             ---CHHHHHHHHHHHGGGHHHHCHHHHHHHHHHHHHHHHCSSEEEECCHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHCCCEEEEEECCHH
T ss_conf             982258999999999999987242889999999999978993999977889


No 14 
>>1w6s_A Methanol dehydrogenase subunit 1; anisotropic, electron transfer, oxidoreductase, calcium- binding, methanol utilization, PQQ; HET: PQQ; 1.2A {Methylobacterium extorquens} (A:304-376)
Probab=37.66  E-value=17  Score=18.14  Aligned_cols=19  Identities=5%  Similarity=-0.244  Sum_probs=16.2

Q ss_pred             CCEECCCCCCEEEECCCCE
Q ss_conf             4102588988899468734
Q gi|254780748|r   59 RLARAPLAQKVISVEEKMV   77 (100)
Q Consensus        59 r~~rNP~Tge~i~i~~~~~   77 (100)
                      -.+.+|+||.++..|++.+
T Consensus        55 a~gid~ktGrPi~~p~~~t   73 (73)
T 1w6s_A           55 FKSVDLKTGQPVRDPEYGT   73 (73)
T ss_dssp             EEEECTTTCCEEECGGGCC
T ss_pred             CCCCCCCCCCCCCCCCCCC
T ss_conf             5542212443211730023


No 15 
>>1i27_A Transcription factor IIF; general transcription factor, RAP74, RAP30, TFIIF, RNA polymerase II, winged-helix domain; 1.02A {Homo sapiens} (A:)
Probab=33.09  E-value=29  Score=16.68  Aligned_cols=33  Identities=15%  Similarity=0.339  Sum_probs=24.8

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Q ss_conf             988999999999738999899999999999999
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEM   33 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i   33 (100)
                      ||-+||+.++-.+..+++..+...++-.++.-|
T Consensus        24 ~TT~eLl~KFk~k~t~l~~~e~v~~~a~ILkkI   56 (73)
T 1i27_A           24 MTTKDLLKKFQTKKTGLSSEQTVNVLAQILKRL   56 (73)
T ss_dssp             BCHHHHHHTSCHHHHCCCHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf             728999999853244774488899999999972


No 16 
>>1z67_A Hypothetical protein S4005; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 1.45A {Shigella flexneri 2a str} (A:19-135)
Probab=32.25  E-value=40  Score=15.76  Aligned_cols=40  Identities=15%  Similarity=0.299  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             99999999973899989999999999999999986498512
Q gi|254780748|r    4 SSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVE   44 (100)
Q Consensus         4 ~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~   44 (100)
                      .|-|..+|+++ +++..++...+-.++=.+.+.+.-+++|.
T Consensus        57 ~d~i~~lA~k~-Gl~~~~~~~~La~~LP~~VD~lTP~G~~p   96 (117)
T 1z67_A           57 TNAVSDLGQKL-GVDTSTASSLLAEQLPKIIDALSPQGEVS   96 (117)
T ss_dssp             HHHHHHHHHHH-TCCHHHHHHHHHHHHHHHHHHTCTTSCC-
T ss_pred             HHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             59999999998-91999999999999779997119899899


No 17 
>>2ysk_A Hypothetical protein TTHA1432; conserved hypothetical, NPPSFA, national project on protein structural and functional analyses; 1.90A {Thermus thermophilus HB8} (A:)
Probab=31.51  E-value=16  Score=18.25  Aligned_cols=41  Identities=7%  Similarity=0.046  Sum_probs=25.7

Q ss_pred             CCHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             98899999999973899-9899999999999999999864985
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKL-NYQDVEKIVNMLLEEMTQALANGGR   42 (100)
Q Consensus         1 MtK~eli~~ia~~~~~l-s~~~~~~~vd~~~~~i~~~L~~~~~   42 (100)
                      |...++++.+.++. ++ ++.++..++.+++.++.+-|.-++.
T Consensus        14 ~~~~~fl~~V~~~~-~~~~~~~A~~a~raVL~~Lr~RL~~~ea   55 (145)
T 2ysk_A           14 HKTHAWLKAIMEEL-GTEDRHKAYLALRAVLHALRDRLTVEEV   55 (145)
T ss_dssp             HHHHHHHHHHHHHH-TCCCHHHHHHHHHHHHHHHHTTSCHHHH
T ss_pred             HHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHCCHHHH
T ss_conf             99999999999983-8998899999999999999987786789


No 18 
>>1o17_A Anthranilate PRT, anthranilate phosphoribosyltransferase, TRPD; nucleoside-phosphorylases; 2.05A {Sulfolobus solfataricus} (A:1-74,A:156-176)
Probab=31.25  E-value=42  Score=15.66  Aligned_cols=30  Identities=13%  Similarity=0.374  Sum_probs=25.2

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             9889999999997389998999999999999
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLE   31 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~   31 (100)
                      |+=++++.++.+. .+||..++..+++.+++
T Consensus         1 M~~k~iL~kl~~g-~~LT~eE~~~~~~~il~   30 (95)
T 1o17_A            1 MNINEILKKLINK-SDLEINEAEELAKAIIR   30 (95)
T ss_dssp             CCHHHHHHHHHTT-CCCCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHCC-CCCCHHHHHHHHHHHHC
T ss_conf             9889999998669-99699999999999987


No 19 
>>1nha_A TFIIF-alpha, transcription initiation factor IIF, alpha subunit; transcription factor, human general transcription factor TFIIF, RAP74; NMR {Homo sapiens} (A:)
Probab=31.22  E-value=42  Score=15.66  Aligned_cols=33  Identities=15%  Similarity=0.339  Sum_probs=24.4

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Q ss_conf             988999999999738999899999999999999
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEM   33 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i   33 (100)
                      ||-.||+..+-.+..+++..+...++-.++.-|
T Consensus        33 ~Tt~eLl~KFk~k~t~l~~~e~v~~~a~ILkkI   65 (82)
T 1nha_A           33 MTTKDLLKKFQTKKTGLSSEQTVNVLAQILKRL   65 (82)
T ss_dssp             BCHHHHHHHTTSSCCSSCHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHC
T ss_conf             739999999986246788599999999999970


No 20 
>>3g2b_A Coenzyme PQQ synthesis protein D; helix-turn-helix, PQQ biosynthesis, biosynthetic protein; 1.66A {Xanthomonas campestris PV} (A:40-95)
Probab=27.95  E-value=48  Score=15.30  Aligned_cols=33  Identities=18%  Similarity=0.157  Sum_probs=28.1

Q ss_pred             CHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             8899999999973899989999999999999999
Q gi|254780748|r    2 IKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQ   35 (100)
Q Consensus         2 tK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~   35 (100)
                      |-.++++.+++++ +....++..-+..|+..+.+
T Consensus        18 tv~~I~~~L~~~y-~~~~~~~~~dv~~fl~~L~~   50 (56)
T 3g2b_A           18 SLAQIAQTLAAEF-DADASEIETDVIELTTTLHQ   50 (56)
T ss_dssp             CHHHHHHHHHHHT-TCCHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
T ss_conf             5999999999996-98888999999999999998


No 21 
>>2yva_A DNAA initiator-associating protein DIAA; intermolecular disulfide bonding, putative phosphosugar binding protein, DNAA binding protein; 1.85A {Escherichia coli} (A:)
Probab=27.02  E-value=39  Score=15.84  Aligned_cols=34  Identities=18%  Similarity=0.261  Sum_probs=26.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEE
Q ss_conf             9899999999999999999864985120345788
Q gi|254780748|r   18 NYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSF   51 (100)
Q Consensus        18 s~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF   51 (100)
                      ........++..++.+.+.|.+.++|.+-|.|+=
T Consensus        19 ~~~~~~~~~~~~~~~~~~~l~~~~~I~i~G~G~S   52 (196)
T 2yva_A           19 AAEALPDAISRAAMTLVQSLLNGNKILCCGNGTS   52 (196)
T ss_dssp             HHHHSHHHHHHHHHHHHHHHHTTCCEEEEESTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCH
T ss_conf             9986499999999999999987997999978801


No 22 
>>2wvr_C DNA replication factor CDT1; DNA replication license, DNA replication inhibitor, phosphoprotein, UBL conjugation, DNA-binding, polymorphism; HET: DNA; 3.30A {Homo sapiens} PDB: 2klo_A* (C:)
Probab=25.70  E-value=17  Score=18.18  Aligned_cols=37  Identities=14%  Similarity=0.078  Sum_probs=28.2

Q ss_pred             CCHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             988999999999738-9998999999999999999998
Q gi|254780748|r    1 MIKSSLIGTIAKKNP-KLNYQDVEKIVNMLLEEMTQAL   37 (100)
Q Consensus         1 MtK~eli~~ia~~~~-~ls~~~~~~~vd~~~~~i~~~L   37 (100)
                      |+..+|+..|.+.+. .++..++++.|+.+.+++-+-|
T Consensus       473 ~~~~~~~~~i~~s~~~~~~~~e~~~~l~~l~~~~p~~~  510 (546)
T 2wvr_C          473 LSMEVACARMVGSCCTIMSPGEMEKHLLLLSELLPDWL  510 (546)
T ss_dssp             --------------------------------------
T ss_pred             CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCE
T ss_conf             07999999999854576999999999999998687206


No 23 
>>1whu_A Polynucleotide phosphorylase; 3'-5' RNA exonuclease; pnpase, alpha-helical domain, structural genomics; NMR {Mus musculus} (A:)
Probab=25.42  E-value=53  Score=15.01  Aligned_cols=45  Identities=11%  Similarity=0.189  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             899999999973899989999999999999999986498512034
Q gi|254780748|r    3 KSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRG   47 (100)
Q Consensus         3 K~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~g   47 (100)
                      +.++++.++..+.+.+..++..+++.+...+...+.-.+.+.+-|
T Consensus        52 k~~v~e~~~e~~~~~~~~~i~~a~~~l~k~ivR~~Il~~g~R~DG   96 (104)
T 1whu_A           52 RLDTEEHLKEKFPEVDQFEIIESFNIVAKEVFRSIILNEYKRCDG   96 (104)
T ss_dssp             HHHHHHHHTTTCSSSCHHHHHHHHHHHHHHHHHHHHTTSSCSCCC
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             999999986311314799999999999999999999857986899


No 24 
>>1aip_C EF-TS, elongation factor TS; nucleotide exchange, GTP-binding, complex of two elongation factors; 3.00A {Thermus thermophilus} (C:1-104,C:164-196)
Probab=24.40  E-value=55  Score=14.89  Aligned_cols=54  Identities=15%  Similarity=0.139  Sum_probs=36.7

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH------------HHHHCCCCCCCEEEEEEEEEC
Q ss_conf             9889999999997389998999999999999999------------998649851203457888621
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMT------------QALANGGRVEIRGFGSFSVRK   55 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~------------~~L~~~~~V~i~gfGtF~~~~   55 (100)
                      |...++|+.|-+++ +.+..+++++++..-.-+.            .+-+..+++.-.|+....+..
T Consensus         1 mis~e~IK~LR~~T-gagi~dCKkAL~es~gDiekAi~~Lrk~G~~kA~Kk~~r~t~eG~v~~~v~~   66 (137)
T 1aip_C            1 MSQMELIKKLREAT-GAGMMDVKRALEDAGWDEEKAVQLLRERGAMKAAKKADREAREGIIGHYIHH   66 (137)
T ss_dssp             -CHHHHHHHHHHHH-CCCHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHTTSCCCCCEEEEEECT
T ss_pred             CCCHHHHHHHHHHH-CCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEC
T ss_conf             98479999999986-9889999999998499899999999987776777877799874100047854


No 25 
>>1brw_A PYNP, protein (pyrimidine nucleoside phosphorylase); domain movement; HET: MES; 2.10A {Bacillus stearothermophilus} (A:1-94,A:156-242,A:424-433)
Probab=23.37  E-value=58  Score=14.77  Aligned_cols=30  Identities=23%  Similarity=0.203  Sum_probs=24.8

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             9889999999997389998999999999999
Q gi|254780748|r    1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLE   31 (100)
Q Consensus         1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~   31 (100)
                      |+=.+++.++.+. ..||+.++..+++.+++
T Consensus         1 M~i~eli~kl~~G-~~Ls~eEa~~~i~~il~   30 (191)
T 1brw_A            1 MRMVDLIAKKRDG-KALTKEEIEWIVRGYTN   30 (191)
T ss_dssp             CCHHHHHHHHHTT-CCCCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHCC-CCCCHHHHHHHHHHHHC
T ss_conf             9879999998779-99699999999999986


No 26 
>>1tk9_A Phosphoheptose isomerase 1; lipopolysaccharide biosynthesis, structural genomics, NYSGXRC, LPC1_camje, PSI, protein structure initiative; 2.10A {Campylobacter jejuni} (A:)
Probab=21.98  E-value=48  Score=15.30  Aligned_cols=48  Identities=21%  Similarity=0.226  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHH---HHHHHHHHHHHCCCCCCCEEEEEE
Q ss_conf             8999999999738999899999999---999999999864985120345788
Q gi|254780748|r    3 KSSLIGTIAKKNPKLNYQDVEKIVN---MLLEEMTQALANGGRVEIRGFGSF   51 (100)
Q Consensus         3 K~eli~~ia~~~~~ls~~~~~~~vd---~~~~~i~~~L~~~~~V~i~gfGtF   51 (100)
                      -.++++.+.+.. .-....++..++   ..++.+.+.|.+.++|.+-|.|.=
T Consensus         3 ~~~~~~~i~~~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~~~rI~~~G~G~S   53 (188)
T 1tk9_A            3 LINLVEKEWQEH-QKIVQASEILKGQIAKVGELLCECLKKGGKILICGNGGS   53 (188)
T ss_dssp             HHHHHHHHHHHH-HHHHHHGGGGHHHHHHHHHHHHHHHHTTCCEEEEESTHH
T ss_pred             HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCC
T ss_conf             699999999999-999999887199999999999999985998999916887


No 27 
>>2i7t_A Cleavage and polyadenylation specificity factor 73 kDa subunit; metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J recombination; 2.10A {Homo sapiens} (A:211-396)
Probab=21.80  E-value=62  Score=14.57  Aligned_cols=28  Identities=21%  Similarity=0.240  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             9999999999999986498512034578
Q gi|254780748|r   23 EKIVNMLLEEMTQALANGGRVEIRGFGS   50 (100)
Q Consensus        23 ~~~vd~~~~~i~~~L~~~~~V~i~gfGt   50 (100)
                      ++..+.|.+.|.++|.+|++|-||-|..
T Consensus         6 ~~~~~~l~~~I~~tl~~gG~VLIP~fa~   33 (186)
T 2i7t_A            6 EEREARFCNTVHDIVNRGGRGLIPVFAL   33 (186)
T ss_dssp             HHHHHHHHHHHHHHHHTTCEEEEECCSS
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEECCH
T ss_conf             4677888899999985698289995222


No 28 
>>2elc_A Trp D, anthranilate phosphoribosyltransferase; structural genomics, NPPSFA; 1.55A {Thermus thermophilus HB8} (A:1-67,A:156-177)
Probab=21.25  E-value=63  Score=14.52  Aligned_cols=26  Identities=8%  Similarity=0.139  Sum_probs=20.4

Q ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             999999997389998999999999999
Q gi|254780748|r    5 SLIGTIAKKNPKLNYQDVEKIVNMLLE   31 (100)
Q Consensus         5 eli~~ia~~~~~ls~~~~~~~vd~~~~   31 (100)
                      |+|+++.+. .+||..++..+++.+++
T Consensus         2 eiL~kl~~G-~~Ls~eEa~~~~~~i~~   27 (89)
T 2elc_A            2 DAVKKAILG-EVLEEEEAYEVMRALMA   27 (89)
T ss_dssp             CHHHHHHTT-CCCCHHHHHHHHHHHHT
T ss_pred             HHHHHHHCC-CCCCHHHHHHHHHHHHC
T ss_conf             689998779-99799999999999987


No 29 
>>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A (A:240-324)
Probab=20.77  E-value=65  Score=14.44  Aligned_cols=43  Identities=19%  Similarity=0.329  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             8999999999738999899999999999999999864985120
Q gi|254780748|r    3 KSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEI   45 (100)
Q Consensus         3 K~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i   45 (100)
                      +.++++.++..+++.+..++..+++.+...+...+.-.+...+
T Consensus        41 k~~v~e~~~ee~~~~~~~~i~~~~~~l~k~~vR~~Il~~~~R~   83 (85)
T 3cdi_A           41 KSETIATLLAEDETLDENELGEILHAIEKNVVRSRVLAGEPRI   83 (85)
T ss_dssp             HHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHHTTCCCT
T ss_pred             HHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             9998877503466889999999999999999999987368577


Done!