Query         gi|254780496|ref|YP_003064909.1| integration host factor subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 114
No_of_seqs    103 out of 2506
Neff          6.4 
Searched_HMMs 33803
Date          Wed Jun  1 18:33:03 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780496.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   2E-25 5.8E-30  177.0  11.2   92    5-96      1-92  (94)
  2 >3c4i_A DNA-binding protein HU  99.9 4.6E-25 1.3E-29  174.8  11.6   96    5-100     1-96  (99)
  3 >1owf_B IHF-beta, integration   99.9 6.5E-25 1.9E-29  173.8  11.2   92    5-96      1-93  (94)
  4 >1mul_A NS2, HU-2, DNA binding  99.9 7.6E-25 2.2E-29  173.4  10.1   90    5-94      1-90  (90)
  5 >2o97_B NS1, HU-1, DNA-binding  99.9 8.4E-25 2.5E-29  173.1   9.3   90    5-94      1-90  (90)
  6 >2iie_A Integration HOST facto  99.9   2E-24 5.9E-29  170.9  10.8  100    1-100    43-142 (204)
  7 >1b8z_A Protein (histonelike p  99.9 7.4E-25 2.2E-29  173.5   8.5   90    5-94      1-90  (90)
  8 >1exe_A Transcription factor 1  99.9 5.1E-25 1.5E-29  174.5   3.6   96    5-100     1-96  (99)
  9 >1hue_A HU protein; DNA-bindin  99.9 7.9E-24 2.3E-28  167.2   8.3   90    5-94      1-90  (90)
 10 >2iie_A Integration HOST facto  99.7   3E-17 8.9E-22  126.9   7.5   70   29-98    127-196 (204)
 11 >1owf_A IHF-alpha, integration  99.6 1.4E-15 4.2E-20  116.6   5.5   55   44-98      1-55  (58)
 12 >2np2_A HBB; protein-DNA compl  99.5   7E-15 2.1E-19  112.3   4.1   53   44-96      1-54  (56)
 13 >1i27_A Transcription factor I  50.0      15 0.00044   18.4   2.9   36    1-36     20-56  (73)
 14 >1aip_C EF-TS, elongation fact  44.6      24 0.00071   17.1   3.3   54    5-58      1-66  (137)
 15 >1z67_A Hypothetical protein S  41.2      29 0.00085   16.6   5.3   40    8-47     57-96  (117)
 16 >2ysk_A Hypothetical protein T  40.6      13 0.00037   18.8   1.4   43    4-46     13-56  (145)
 17 >1nha_A TFIIF-alpha, transcrip  35.7      23 0.00068   17.2   2.1   36    1-36     29-65  (82)
 18 >2hhv_A DNA polymerase I; DNA   32.7      39  0.0012   15.8   3.9   24   12-35     52-75  (76)
 19 >2j37_W Signal recognition par  30.9      42  0.0012   15.6   4.6   32    3-34     67-113 (127)
 20 >3g2b_A Coenzyme PQQ synthesis  30.3      43  0.0013   15.5   6.0   36    3-38     15-50  (56)
 21 >1o17_A Anthranilate PRT, anth  28.3      47  0.0014   15.3   3.5   30    5-34      1-30  (95)
 22 >1w6s_A Methanol dehydrogenase  27.8      26 0.00076   16.9   1.3   17   63-79     56-72  (73)
 23 >1dul_A Signal recognition par  26.4      51  0.0015   15.1   4.2   32    3-34     20-61  (69)
 24 >1brw_A PYNP, protein (pyrimid  26.3      51  0.0015   15.1   3.5   30    5-34      1-30  (191)
 25 >2kfn_A Klenow fragment of DNA  26.3      37  0.0011   16.0   1.8   24   12-35     52-75  (76)
 26 >1tk9_A Phosphoheptose isomera  25.8      40  0.0012   15.8   1.9   48    7-54      3-53  (188)
 27 >2hye_C Cullin-4A, CUL-4A; bet  25.6      52  0.0015   15.0   3.3   33    2-34     34-68  (86)
 28 >2heo_A Z-DNA binding protein   25.2      53  0.0016   15.0   4.1   38   11-56     28-65  (67)
 29 >1qzx_A SRP54, signal recognit  24.0      56  0.0017   14.8   4.0   32    3-34     19-60  (69)
 30 >2do7_A Cullin-4B, CUL-4B; hel  23.4      58  0.0017   14.8   4.4   33    2-34     43-77  (101)
 31 >2ftc_E Mitochondrial ribosoma  22.1      42  0.0012   15.6   1.5   37    6-42     15-52  (72)
 32 >1hq1_A Signal recognition par  22.0      61  0.0018   14.6   4.0   32    3-34     54-95  (105)
 33 >2v3c_C SRP54, signal recognit  21.8      62  0.0018   14.6   4.6   32    3-34     68-109 (123)
 34 >2wvr_C DNA replication factor  21.3      23 0.00068   17.2   0.0   38    3-40    471-510 (546)
 35 >2cp9_A EF-TS, EF-TSMT, elonga  20.8      65  0.0019   14.4   3.2   31    8-38     10-40  (64)
 36 >2e7j_A SEP-tRNA:Cys-tRNA synt  20.8      65  0.0019   14.4   3.4   21   18-38     98-118 (120)
 37 >3dm5_A SRP54, signal recognit  20.5      66   0.002   14.4   4.4   33    3-35     68-110 (131)

No 1  
>>1p71_A DNA-binding protein HU; protein-DNA complex, DNA bending, DNA binding protein/DNA complex; 1.90A {Anabaena SP} (A:)
Probab=99.93  E-value=2e-25  Score=177.03  Aligned_cols=92  Identities=21%  Similarity=0.520  Sum_probs=90.6

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC
Q ss_conf             66999999999971999999999999999999999755996000041699985026764306889888995688537761
Q gi|254780496|r    5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK   84 (114)
Q Consensus         5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk   84 (114)
                      |||+|||+.||+++++++.+++.++++|+++|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.||++++|+|+
T Consensus         1 MtK~eli~~ia~~~~ls~~~v~~~i~~~~~~i~~~L~~~~~V~l~~fG~F~v~~~~~r~~~Np~Tge~i~i~~~~~v~Fk   80 (94)
T 1p71_A            1 MNKGELVDAVAEKASVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREGRNPKTNEKMEIPATRVPAFS   80 (94)
T ss_dssp             CBHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEEE
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCEECCEEEEEEEEECCCEEECCCCCCEEEECCCCCEEEE
T ss_conf             98899999999845979999999999999999999864886050352699999836723289799978996487408995


Q ss_pred             CCHHHHHHHHHH
Q ss_conf             698999997311
Q gi|254780496|r   85 ASSILKKRIMDD   96 (114)
Q Consensus        85 psk~Lk~~in~~   96 (114)
                      ||+.|+++||+.
T Consensus        81 psk~lk~~in~~   92 (94)
T 1p71_A           81 AGKLFREKVAPP   92 (94)
T ss_dssp             ECHHHHHHHSCC
T ss_pred             CCHHHHHHHCCC
T ss_conf             498999975778


No 2  
>>3c4i_A DNA-binding protein HU homolog; dimerization by four helix bundle interaction, DNA condensation; 2.04A {Mycobacterium tuberculosis} (A:)
Probab=99.92  E-value=4.6e-25  Score=174.78  Aligned_cols=96  Identities=23%  Similarity=0.508  Sum_probs=93.0

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC
Q ss_conf             66999999999971999999999999999999999755996000041699985026764306889888995688537761
Q gi|254780496|r    5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK   84 (114)
Q Consensus         5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk   84 (114)
                      |||+|||..||+++|+++.++..+|++|+++|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.||++++|+|+
T Consensus         1 Mtk~eli~~ia~~~~~s~~~v~~~i~~~~~~i~~~L~~g~~V~l~~fG~F~~~~~~~r~~~np~T~e~i~i~~k~~v~Fk   80 (99)
T 3c4i_A            1 MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFR   80 (99)
T ss_dssp             CBHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECSEEEECTTTCCEEEECCEEEEEEE
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCEECCCEEEEEEEEECCEEEECCCCCCEEEECCCCEEEEE
T ss_conf             97899999999874989999999999999999999964996131556899998756811068599988986387228996


Q ss_pred             CCHHHHHHHHHHHCCC
Q ss_conf             6989999973111013
Q gi|254780496|r   85 ASSILKKRIMDDMRGR  100 (114)
Q Consensus        85 psk~Lk~~in~~~~~~  100 (114)
                      ||+.|++.||......
T Consensus        81 psk~Lk~~in~~~~~~   96 (99)
T 3c4i_A           81 PGAQFKAVVSGAQRLP   96 (99)
T ss_dssp             ECHHHHHHHHTSSCCC
T ss_pred             CCHHHHHHHCCCCCCC
T ss_conf             2989999866666899


No 3  
>>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=6.5e-25  Score=173.83  Aligned_cols=92  Identities=24%  Similarity=0.437  Sum_probs=89.8

Q ss_pred             CCHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEE
Q ss_conf             6699999999997-199999999999999999999975599600004169998502676430688988899568853776
Q gi|254780496|r    5 ITRSDLVKSISKE-FGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVF   83 (114)
Q Consensus         5 mtK~eli~~ia~~-~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~F   83 (114)
                      |||+|||+.|+++ +++++.+++.++++|+++|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.||++++|+|
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             CCCHHHHHHHHHH
Q ss_conf             1698999997311
Q gi|254780496|r   84 KASSILKKRIMDD   96 (114)
Q Consensus        84 kpsk~Lk~~in~~   96 (114)
                      +||+.||+.||..
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 4  
>>1mul_A NS2, HU-2, DNA binding protein HU-alpha; histone-like; HET: DNA; 2.30A {Escherichia coli} (A:)
Probab=99.92  E-value=7.6e-25  Score=173.42  Aligned_cols=90  Identities=28%  Similarity=0.506  Sum_probs=88.6

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC
Q ss_conf             66999999999971999999999999999999999755996000041699985026764306889888995688537761
Q gi|254780496|r    5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK   84 (114)
Q Consensus         5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk   84 (114)
                      |||+|||+.|++++|+++.+++.+|++|+++|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.||+|++|+|+
T Consensus         1 Mtk~eli~~ia~~~~~s~~~v~~~v~~~~~~i~~~L~~~~~v~l~~fG~F~v~~r~~r~~~Np~Tge~i~ip~k~~v~Fr   80 (90)
T 1mul_A            1 MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFV   80 (90)
T ss_dssp             CCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECC--------------CCEEEEEEE
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCEEEECCCCCCEEEECCCCCEEEE
T ss_conf             97899999999704969999999999999999999971998772036999998628843089399978997487408997


Q ss_pred             CCHHHHHHHH
Q ss_conf             6989999973
Q gi|254780496|r   85 ASSILKKRIM   94 (114)
Q Consensus        85 psk~Lk~~in   94 (114)
                      ||+.|++.|.
T Consensus        81 p~k~lk~~i~   90 (90)
T 1mul_A           81 SGKALKDAVK   90 (90)
T ss_dssp             ECHHHHHHHC
T ss_pred             CCHHHHHHHC
T ss_conf             2989998639


No 5  
>>2o97_B NS1, HU-1, DNA-binding protein HU-beta; heterodimer, DNA structure, DNA supercoiling, E. coli; 2.45A {Escherichia coli} (B:)
Probab=99.92  E-value=8.4e-25  Score=173.14  Aligned_cols=90  Identities=28%  Similarity=0.517  Sum_probs=89.3

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC
Q ss_conf             66999999999971999999999999999999999755996000041699985026764306889888995688537761
Q gi|254780496|r    5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK   84 (114)
Q Consensus         5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk   84 (114)
                      |||+|||+.|++++++++++++.++++|++.|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.||+|++|+|+
T Consensus         1 Mtk~eli~~ia~~~~~t~~~v~~~v~~~~~~i~~~L~~~~~V~l~~fG~F~v~~~~~r~~~np~tge~~~i~~k~~v~Fk   80 (90)
T 2o97_B            1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFR   80 (90)
T ss_dssp             CBHHHHHHHHHHTTC-CHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEECCC------------------CEEEEE
T ss_pred             CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCEEECCCCCCEEEECCCCEEEEE
T ss_conf             97899999999720999999999999999999999980764445505899998405640288999978995386228996


Q ss_pred             CCHHHHHHHH
Q ss_conf             6989999973
Q gi|254780496|r   85 ASSILKKRIM   94 (114)
Q Consensus        85 psk~Lk~~in   94 (114)
                      ||+.|++.||
T Consensus        81 p~k~lk~~iN   90 (90)
T 2o97_B           81 AGKALKDAVN   90 (90)
T ss_dssp             ECHHHHHHCC
T ss_pred             CCHHHHHHHC
T ss_conf             3989997629


No 6  
>>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=99.91  E-value=2e-24  Score=170.86  Aligned_cols=100  Identities=32%  Similarity=0.583  Sum_probs=90.7

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCE
Q ss_conf             98766699999999997199999999999999999999975599600004169998502676430688988899568853
Q gi|254780496|r    1 MSKTITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRV   80 (114)
Q Consensus         1 m~~~mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~   80 (114)
                      |.++|||+|||+.||+++|+++++++.+|++|+++|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.+|++++
T Consensus        43 ~~~~MtK~eLi~~ia~~~glskk~a~~ii~~~~~~I~e~L~~g~~V~l~gfGtF~v~~r~~R~~rNP~Tge~i~i~~kk~  122 (204)
T 2iie_A           43 GSGGLTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRV  122 (204)
T ss_dssp             CSSSBCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHTTCEEEETTTEEEEEEEECCBCCBCTTTCCBCCBCCEEE
T ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEEEECCCCCCCCCCCCEEEECCCCC
T ss_conf             56883599999999998697999999999999999999996699256511589999876471123889998898648651


Q ss_pred             EEECCCHHHHHHHHHHHCCC
Q ss_conf             77616989999973111013
Q gi|254780496|r   81 VVFKASSILKKRIMDDMRGR  100 (114)
Q Consensus        81 v~Fkpsk~Lk~~in~~~~~~  100 (114)
                      |+|+||+.|+..++....+.
T Consensus       123 vkFk~~k~LK~iveaL~~ge  142 (204)
T 2iie_A          123 VTFRPGQKLKSRVENAGGGE  142 (204)
T ss_dssp             EEEEECHHHHHHHHHHCCCC
T ss_pred             EEEEECHHHHHHHHCCCCCC
T ss_conf             79995479998864134465


No 7  
>>1b8z_A Protein (histonelike protein HU); thermostable DNA binding protein; 1.60A {Thermotoga maritima} (A:)
Probab=99.91  E-value=7.4e-25  Score=173.50  Aligned_cols=90  Identities=28%  Similarity=0.556  Sum_probs=89.3

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC
Q ss_conf             66999999999971999999999999999999999755996000041699985026764306889888995688537761
Q gi|254780496|r    5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK   84 (114)
Q Consensus         5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk   84 (114)
                      |||+|||..|++++++++++++.++++|++.|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.||++++|+|+
T Consensus         1 Mtk~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~~~~~V~l~~fG~F~v~~~~~r~~~np~tge~i~i~~k~~v~Fk   80 (90)
T 1b8z_A            1 MNKKELIDRVAKKAGAKKKDVKLILDTILETITEALAKGEKVQIVGFGSFEVRKAAARKGVNPQTRKPITIPERKVPKFK   80 (90)
T ss_dssp             CCHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEC-----------------------CCEEE
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCEECCEEEEEEECCCCEEEECCCCCCEEEECCCCEEEEE
T ss_conf             97899999999854989999999999999999999872886374665789886135444457999988986387218997


Q ss_pred             CCHHHHHHHH
Q ss_conf             6989999973
Q gi|254780496|r   85 ASSILKKRIM   94 (114)
Q Consensus        85 psk~Lk~~in   94 (114)
                      ||+.||+.||
T Consensus        81 ~sk~Lk~~in   90 (90)
T 1b8z_A           81 PGKALKEKVK   90 (90)
T ss_dssp             ECHHHHHHHC
T ss_pred             ECHHHHHHHC
T ss_conf             3899998639


No 8  
>>1exe_A Transcription factor 1; beta ribbon ARMS, DNA-binding, DNA-bending protein; NMR {Bacillus phage SPO1} (A:)
Probab=99.90  E-value=5.1e-25  Score=174.47  Aligned_cols=96  Identities=21%  Similarity=0.381  Sum_probs=92.8

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC
Q ss_conf             66999999999971999999999999999999999755996000041699985026764306889888995688537761
Q gi|254780496|r    5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK   84 (114)
Q Consensus         5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk   84 (114)
                      |||+|||..|++++++++.+++.++++|+++|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.||++++|+|+
T Consensus         1 Mtk~eli~~ia~~~~~s~~~v~~~i~~~~~~i~~~L~~g~~V~l~gfG~F~v~~~~~r~~~np~Tge~i~i~~k~~v~Fk   80 (99)
T 1exe_A            1 MNKTELIKAIAQDTGLTQVSVSKMLASFEKIITETVAKGDKVQLTGFLNIKPVARQARKGFNPQTQEALEIAPSVGVSVK   80 (99)
T ss_dssp             CCTTHHHHHHHHHHCSCCTTHHHHHHHHHHHHHHHHHHTCCCCBTTTBCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCC
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEEEEECCCCCCCCCCCCEEEECCCCCEEEE
T ss_conf             98899999999986969999999999999999999968995997367899987555734478999988984285347993


Q ss_pred             CCHHHHHHHHHHHCCC
Q ss_conf             6989999973111013
Q gi|254780496|r   85 ASSILKKRIMDDMRGR  100 (114)
Q Consensus        85 psk~Lk~~in~~~~~~  100 (114)
                      ||+.||+.||......
T Consensus        81 psk~LK~~in~~~~~~   96 (99)
T 1exe_A           81 PGESLKKAAEGLKYED   96 (99)
T ss_dssp             CCHHHHHHHHHHTHHH
T ss_pred             CCHHHHHHHCCCCHHH
T ss_conf             4989999882898544


No 9  
>>1hue_A HU protein; DNA-binding; NMR {Geobacillus stearothermophilus} (A:)
Probab=99.90  E-value=7.9e-24  Score=167.19  Aligned_cols=90  Identities=30%  Similarity=0.628  Sum_probs=88.5

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC
Q ss_conf             66999999999971999999999999999999999755996000041699985026764306889888995688537761
Q gi|254780496|r    5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK   84 (114)
Q Consensus         5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk   84 (114)
                      |||+|||..|++++++++.+++.++++|++.|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.+|++++|+|+
T Consensus         1 Mtk~~li~~i~~~~~~s~~~v~~~i~~~~~~i~~~L~~~~~v~l~~fG~F~v~~~~~r~~~Np~Tge~~~i~~k~~vkFr   80 (90)
T 1hue_A            1 MNKTELINAVAETSGLSKKDATKAVDAVFDSITEALRKGDKVQLIGFGNFEVRERAARKGRNPQTGEEMEIPASKVPAFK   80 (90)
T ss_dssp             CBSHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHTCCCCBTTTBEECCCCCCCCEEECSSSSSEEECCCCCCCCEE
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECCEEEEEEEECCCCCCCCCCCCEEEECCCCEEEEE
T ss_conf             97899999999854989999999999999999999965982884024399998616844558399988995487418981


Q ss_pred             CCHHHHHHHH
Q ss_conf             6989999973
Q gi|254780496|r   85 ASSILKKRIM   94 (114)
Q Consensus        85 psk~Lk~~in   94 (114)
                      ||+.|++.|.
T Consensus        81 ~sk~lk~~ik   90 (90)
T 1hue_A           81 PGKALKDAVK   90 (90)
T ss_dssp             CTTHHHHHTC
T ss_pred             CCHHHHHHHC
T ss_conf             3989998639


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=99.70  E-value=3e-17  Score=126.85  Aligned_cols=70  Identities=26%  Similarity=0.361  Sum_probs=65.5

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEECCCHHHHHHHHHHHC
Q ss_conf             9999999999975599600004169998502676430688988899568853776169899999731110
Q gi|254780496|r   29 VTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFKASSILKKRIMDDMR   98 (114)
Q Consensus        29 v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fkpsk~Lk~~in~~~~   98 (114)
                      ...+++.+.+++..++.|.|+|||+|+++.+++|.||||+|||.|.||++++|+|+||+.||++||....
T Consensus       127 ~~k~LK~iveaL~~ge~V~i~~fG~F~~~~r~~R~grNP~Tge~i~Ipa~~~~~Fk~~k~lk~~vn~~~~  196 (204)
T 2iie_A          127 PGQKLKSRVENAGGGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYGG  196 (204)
T ss_dssp             ECHHHHHHHHHHCCCCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEEEECHHHHHHHCSSCC
T ss_pred             ECHHHHHHHHCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEECCCCCEEECCCHHHHHHHCCCCC
T ss_conf             5479998864134465422265688998740673561929999888659753687878899998757999


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=99.59  E-value=1.4e-15  Score=116.60  Aligned_cols=55  Identities=36%  Similarity=0.657  Sum_probs=52.1

Q ss_pred             CCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEECCCHHHHHHHHHHHC
Q ss_conf             9600004169998502676430688988899568853776169899999731110
Q gi|254780496|r   44 EAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFKASSILKKRIMDDMR   98 (114)
Q Consensus        44 ~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fkpsk~Lk~~in~~~~   98 (114)
                      ++|.|+|||+|+++.+++|.||||+|||.|.||++++|+|+||+.|+++||+...
T Consensus         1 ekV~l~gfGtF~~~~r~~R~grNP~Tge~i~I~ak~~v~Fk~sk~Lk~~vn~~~~   55 (58)
T 1owf_A            1 EQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASP   55 (58)
T ss_dssp             CCEEETTTEEEEEEEECCEEEECSSSCCEEEECCEEEEEEEECHHHHHHHHTCCC
T ss_pred             CEEEECCEEEEEEEEECCCCCCCCCCCCEEEECCCCEEEEEECHHHHHHHHCCCC
T ss_conf             9799511379999876682125889998899538722899749999999807896


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=99.52  E-value=7e-15  Score=112.33  Aligned_cols=53  Identities=34%  Similarity=0.484  Sum_probs=50.2

Q ss_pred             CCCCCCCCEEEEEEECCCC-CCCCCCCCCEEEECCCCEEEECCCHHHHHHHHHH
Q ss_conf             9600004169998502676-4306889888995688537761698999997311
Q gi|254780496|r   44 EAIKISSFATFHVKQKGSR-VGRNLQTNQEVKIDPRRVVVFKASSILKKRIMDD   96 (114)
Q Consensus        44 ~~V~l~gfGtF~~~~~~~R-~~rNP~Tge~i~ip~k~~v~Fkpsk~Lk~~in~~   96 (114)
                      ++|.|+|||+|+++.+++| .||||+|||.|.||++++|+|+||+.||++||+.
T Consensus         1 d~V~l~gFGtF~~~~r~~R~~grNP~Tge~i~I~a~~v~~Fk~~k~lk~~vn~~   54 (56)
T 2np2_A            1 NVIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGI   54 (56)
T ss_dssp             CEEEETTTEEEEEEEECCBSSCBCTTTCCBCCBCCEEEEEEEECHHHHHHHHSC
T ss_pred             CEEEEEEEEEEEEEEECCCCCCCCCCCCCEEEECCCCCEEECCCHHHHHHHHCC
T ss_conf             969984468999973047655538899988985387567874898999997067


No 13 
>>1i27_A Transcription factor IIF; general transcription factor, RAP74, RAP30, TFIIF, RNA polymerase II, winged-helix domain; 1.02A {Homo sapiens} (A:)
Probab=50.05  E-value=15  Score=18.40  Aligned_cols=36  Identities=25%  Similarity=0.486  Sum_probs=26.9

Q ss_pred             CCCCCCHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHH
Q ss_conf             987666999999999-971999999999999999999
Q gi|254780496|r    1 MSKTITRSDLVKSIS-KEFGLSRKDSTRFVTTLFNEI   36 (114)
Q Consensus         1 m~~~mtK~eli~~ia-~~~g~s~~~~~~~v~~~~~~i   36 (114)
                      |.+-||-.||+.... .++|++..+...++..++.-|
T Consensus        20 ~rKP~TT~eLl~KFk~k~t~l~~~e~v~~~a~ILkkI   56 (73)
T 1i27_A           20 TRKPMTTKDLLKKFQTKKTGLSSEQTVNVLAQILKRL   56 (73)
T ss_dssp             HHSCBCHHHHHHTSCHHHHCCCHHHHHHHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf             3188728999999853244774488899999999972


No 14 
>>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=44.57  E-value=24  Score=17.11  Aligned_cols=54  Identities=11%  Similarity=0.131  Sum_probs=37.4

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH------------HHHCCCCCCCCCCEEEEEEE
Q ss_conf             6699999999997199999999999999999999------------97559960000416999850
Q gi|254780496|r    5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICD------------SAVRGEAIKISSFATFHVKQ   58 (114)
Q Consensus         5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~------------~L~~g~~V~l~gfGtF~~~~   58 (114)
                      |...++|+.|-++||.+..++++.++..-.-+..            +-....++.-.|+....+..
T Consensus         1 mis~e~IK~LR~~Tgagi~dCKkAL~es~gDiekAi~~Lrk~G~~kA~Kk~~r~t~eG~v~~~v~~   66 (137)
T 1aip_C            1 MSQMELIKKLREATGAGMMDVKRALEDAGWDEEKAVQLLRERGAMKAAKKADREAREGIIGHYIHH   66 (137)
T ss_dssp             -CHHHHHHHHHHHHCCCHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHTTSCCCCCEEEEEECT
T ss_pred             CCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEC
T ss_conf             984799999999869889999999998499899999999987776777877799874100047854


No 15 
>>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=41.18  E-value=29  Score=16.61  Aligned_cols=40  Identities=10%  Similarity=0.315  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             9999999997199999999999999999999975599600
Q gi|254780496|r    8 SDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIK   47 (114)
Q Consensus         8 ~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~   47 (114)
                      .|-+..+|.++|++..++...+..++=.+.+.+.-+++|.
T Consensus        57 ~d~i~~lA~k~Gl~~~~~~~~La~~LP~~VD~lTP~G~~p   96 (117)
T 1z67_A           57 TNAVSDLGQKLGVDTSTASSLLAEQLPKIIDALSPQGEVS   96 (117)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHTCTTSCC-
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             5999999999891999999999999779997119899899


No 16 
>>2ysk_A Hypothetical protein TTHA1432; conserved hypothetical, NPPSFA, national project on protein structural and functional analyses; 1.90A {Thermus thermophilus HB8} (A:)
Probab=40.57  E-value=13  Score=18.80  Aligned_cols=43  Identities=16%  Similarity=0.220  Sum_probs=32.5

Q ss_pred             CCCHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             66699999999997199-99999999999999999997559960
Q gi|254780496|r    4 TITRSDLVKSISKEFGL-SRKDSTRFVTTLFNEICDSAVRGEAI   46 (114)
Q Consensus         4 ~mtK~eli~~ia~~~g~-s~~~~~~~v~~~~~~i~~~L~~g~~V   46 (114)
                      .|...++++.+.++.|+ +..++..++.+.+.++.+.|..++..
T Consensus        13 ~~~~~~fl~~V~~~~~~~~~~~A~~a~raVL~~Lr~RL~~~ea~   56 (145)
T 2ysk_A           13 LHKTHAWLKAIMEELGTEDRHKAYLALRAVLHALRDRLTVEEVA   56 (145)
T ss_dssp             HHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHTTSCHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCHHHHH
T ss_conf             99999999999998389988999999999999999877867899


No 17 
>>1nha_A TFIIF-alpha, transcription initiation factor IIF, alpha subunit; transcription factor, human general transcription factor TFIIF, RAP74; NMR {Homo sapiens} (A:)
Probab=35.67  E-value=23  Score=17.20  Aligned_cols=36  Identities=22%  Similarity=0.457  Sum_probs=26.7

Q ss_pred             CCCCCCHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHH
Q ss_conf             98766699999999997-1999999999999999999
Q gi|254780496|r    1 MSKTITRSDLVKSISKE-FGLSRKDSTRFVTTLFNEI   36 (114)
Q Consensus         1 m~~~mtK~eli~~ia~~-~g~s~~~~~~~v~~~~~~i   36 (114)
                      |.+-||-.||+.....+ +|++..+...++..++.-|
T Consensus        29 ~rkP~Tt~eLl~KFk~k~t~l~~~e~v~~~a~ILkkI   65 (82)
T 1nha_A           29 TRKPMTTKDLLKKFQTKKTGLSSEQTVNVLAQILKRL   65 (82)
T ss_dssp             HHSCBCHHHHHHHTTSSCCSSCHHHHHHHHHHHHHHH
T ss_pred             HHCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHC
T ss_conf             7189739999999986246788599999999999970


No 18 
>>2hhv_A DNA polymerase I; DNA replication, klenow fragment, protein- DNA complex, O6-methyl-guanine, transferase/DNA complex; HET: DNA 6OG SUC; 1.55A {Geobacillus stearothermophilus} (A:372-447)
Probab=32.72  E-value=39  Score=15.78  Aligned_cols=24  Identities=21%  Similarity=0.592  Sum_probs=21.1

Q ss_pred             HHHHHHCCCCHHHHHHHHHHHHHH
Q ss_conf             999997199999999999999999
Q gi|254780496|r   12 KSISKEFGLSRKDSTRFVTTLFNE   35 (114)
Q Consensus        12 ~~ia~~~g~s~~~~~~~v~~~~~~   35 (114)
                      ..|+++.|++..++..+++.|+..
T Consensus        52 ~~La~~lgis~~eA~~~i~~f~~~   75 (76)
T 2hhv_A           52 YGLAQNLNISRKEAAEFIERYFES   75 (76)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHCCCHHHHHHHHHHHHHH
T ss_conf             444502023388888888778777


No 19 
>>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A (W:314-440)
Probab=30.94  E-value=42  Score=15.60  Aligned_cols=32  Identities=16%  Similarity=0.432  Sum_probs=26.4

Q ss_pred             CCCCHHHH---------------HHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             76669999---------------999999719999999999999999
Q gi|254780496|r    3 KTITRSDL---------------VKSISKEFGLSRKDSTRFVTTLFN   34 (114)
Q Consensus         3 ~~mtK~el---------------i~~ia~~~g~s~~~~~~~v~~~~~   34 (114)
                      .+||..|+               +.+||.-+|.+..+|..++..|..
T Consensus        67 ~SMT~~Er~~P~~i~~~~~~~SR~~RIA~GSG~~~~eV~~Ll~~~~~  113 (127)
T 2j37_W           67 DSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQELLTQYTK  113 (127)
T ss_dssp             TTSCHHHHHCTTHHHHHHHCTHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HCCCHHHHCCCCHHHHCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             51698774396301111567018888556699999999999999999


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=30.31  E-value=43  Score=15.53  Aligned_cols=36  Identities=14%  Similarity=0.216  Sum_probs=31.5

Q ss_pred             CCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             766699999999997199999999999999999999
Q gi|254780496|r    3 KTITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICD   38 (114)
Q Consensus         3 ~~mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~   38 (114)
                      ..-|-.+|+..++++.+....+++.-|..|+..+.+
T Consensus        15 g~~tv~~I~~~L~~~y~~~~~~~~~dv~~fl~~L~~   50 (56)
T 3g2b_A           15 GTQSLAQIAQTLAAEFDADASEIETDVIELTTTLHQ   50 (56)
T ss_dssp             SSSCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             986599999999999698888999999999999998


No 21 
>>1o17_A Anthranilate PRT, anthranilate phosphoribosyltransferase, TRPD; nucleoside-phosphorylases; 2.05A {Sulfolobus solfataricus} (A:1-74,A:156-176)
Probab=28.32  E-value=47  Score=15.32  Aligned_cols=30  Identities=7%  Similarity=0.290  Sum_probs=25.0

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             669999999999719999999999999999
Q gi|254780496|r    5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFN   34 (114)
Q Consensus         5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~   34 (114)
                      |+=++++..+...-.+|.+++..+++.+++
T Consensus         1 M~~k~iL~kl~~g~~LT~eE~~~~~~~il~   30 (95)
T 1o17_A            1 MNINEILKKLINKSDLEINEAEELAKAIIR   30 (95)
T ss_dssp             CCHHHHHHHHHTTCCCCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHCCCCCCHHHHHHHHHHHHC
T ss_conf             988999999866999699999999999987


No 22 
>>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=27.81  E-value=26  Score=16.90  Aligned_cols=17  Identities=24%  Similarity=0.155  Sum_probs=14.3

Q ss_pred             CCCCCCCCCEEEECCCC
Q ss_conf             43068898889956885
Q gi|254780496|r   63 VGRNLQTNQEVKIDPRR   79 (114)
Q Consensus        63 ~~rNP~Tge~i~ip~k~   79 (114)
                      .+.+|+||.+|+.|++.
T Consensus        56 ~gid~ktGrPi~~p~~~   72 (73)
T 1w6s_A           56 KSVDLKTGQPVRDPEYG   72 (73)
T ss_dssp             EEECTTTCCEEECGGGC
T ss_pred             CCCCCCCCCCCCCCCCC
T ss_conf             54221244321173002


No 23 
>>1dul_A Signal recognition particle protein (fifty-four homolog); protein-RNA complex, double helix, tetraloop, internal loop, SRP, ribonucleoprotein; HET: CCC; 1.80A {Escherichia coli} (A:)
Probab=26.36  E-value=51  Score=15.11  Aligned_cols=32  Identities=16%  Similarity=0.273  Sum_probs=26.6

Q ss_pred             CCCCHHHH----------HHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             76669999----------999999719999999999999999
Q gi|254780496|r    3 KTITRSDL----------VKSISKEFGLSRKDSTRFVTTLFN   34 (114)
Q Consensus         3 ~~mtK~el----------i~~ia~~~g~s~~~~~~~v~~~~~   34 (114)
                      .+||..|+          +..||.-+|.+..+|..++..|..
T Consensus        20 ~SMT~~Er~~p~~l~~sR~~RIArGSG~~~~eV~~Ll~q~~~   61 (69)
T 1dul_A           20 NSXTXKERAKPEIIKGSRKRRIAAGSGXQVQDVNRLLKQFDD   61 (69)
T ss_dssp             HTSCHHHHHCGGGCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHCHHHHCHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             818999984926302159999982589989999999999999


No 24 
>>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=26.31  E-value=51  Score=15.10  Aligned_cols=30  Identities=17%  Similarity=0.213  Sum_probs=24.8

Q ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             669999999999719999999999999999
Q gi|254780496|r    5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFN   34 (114)
Q Consensus         5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~   34 (114)
                      |+-+++++.+.....|+.+++..+++.+++
T Consensus         1 M~i~eli~kl~~G~~Ls~eEa~~~i~~il~   30 (191)
T 1brw_A            1 MRMVDLIAKKRDGKALTKEEIEWIVRGYTN   30 (191)
T ss_dssp             CCHHHHHHHHHTTCCCCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHCCCCCCHHHHHHHHHHHHC
T ss_conf             987999999877999699999999999986


No 25 
>>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} (A:397-472)
Probab=26.29  E-value=37  Score=15.97  Aligned_cols=24  Identities=13%  Similarity=0.544  Sum_probs=20.5

Q ss_pred             HHHHHHCCCCHHHHHHHHHHHHHH
Q ss_conf             999997199999999999999999
Q gi|254780496|r   12 KSISKEFGLSRKDSTRFVTTLFNE   35 (114)
Q Consensus        12 ~~ia~~~g~s~~~~~~~v~~~~~~   35 (114)
                      ..|+++.|++..+++.+++.|+..
T Consensus        52 ~~La~~lgis~~eA~~~i~~f~~~   75 (76)
T 2kfn_A           52 FGLARQLNIPRKEAQKYMDLYFER   75 (76)
T ss_dssp             THHHHHHTCCTTTHHHHHHHHHHH
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             789988397999999999999865


No 26 
>>1tk9_A Phosphoheptose isomerase 1; lipopolysaccharide biosynthesis, structural genomics, NYSGXRC, LPC1_camje, PSI, protein structure initiative; 2.10A {Campylobacter jejuni} (A:)
Probab=25.82  E-value=40  Score=15.77  Aligned_cols=48  Identities=17%  Similarity=0.114  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHH---HHHHHHHHHHHCCCCCCCCCCEEE
Q ss_conf             999999999971999999999999---999999999755996000041699
Q gi|254780496|r    7 RSDLVKSISKEFGLSRKDSTRFVT---TLFNEICDSAVRGEAIKISSFATF   54 (114)
Q Consensus         7 K~eli~~ia~~~g~s~~~~~~~v~---~~~~~i~~~L~~g~~V~l~gfGtF   54 (114)
                      -.++++.+.+...-....++..++   ..++.+.+.|.++++|.+-|.|.=
T Consensus         3 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~rI~~~G~G~S   53 (188)
T 1tk9_A            3 LINLVEKEWQEHQKIVQASEILKGQIAKVGELLCECLKKGGKILICGNGGS   53 (188)
T ss_dssp             HHHHHHHHHHHHHHHHHHGGGGHHHHHHHHHHHHHHHHTTCCEEEEESTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCC
T ss_conf             699999999999999999887199999999999999985998999916887


No 27 
>>2hye_C Cullin-4A, CUL-4A; beta propeller, ring finger, zinc finger, propeller cluster, helical repeats, cullin repeats, protein binding; HET: DNA; 3.10A {Homo sapiens} (C:674-759)
Probab=25.60  E-value=52  Score=15.02  Aligned_cols=33  Identities=18%  Similarity=0.310  Sum_probs=27.5

Q ss_pred             CCCCCHHHHHHHHHHHCC--CCHHHHHHHHHHHHH
Q ss_conf             876669999999999719--999999999999999
Q gi|254780496|r    2 SKTITRSDLVKSISKEFG--LSRKDSTRFVTTLFN   34 (114)
Q Consensus         2 ~~~mtK~eli~~ia~~~g--~s~~~~~~~v~~~~~   34 (114)
                      .++|+-.||+..+.....  .+..+++..++.|++
T Consensus        34 ~k~l~~~eL~~~v~~~l~f~p~~~~iK~~Ie~LIe   68 (86)
T 2hye_C           34 RKTLGHNLLVSELYNQLKFPVKPGDLKKRIESLID   68 (86)
T ss_dssp             SSEEETHHHHHHHHHHSSSCCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             58888999999999982799999999999999970


No 28 
>>2heo_A Z-DNA binding protein 1; protein DLM1/Z-DNA complex, immune system/DNA complex; 1.70A {Mus musculus} PDB: 1j75_A (A:)
Probab=25.24  E-value=53  Score=14.98  Aligned_cols=38  Identities=8%  Similarity=0.157  Sum_probs=28.7

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEE
Q ss_conf             9999997199999999999999999999975599600004169998
Q gi|254780496|r   11 VKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHV   56 (114)
Q Consensus        11 i~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~   56 (114)
                      ...|++.+|++++++.+++..        |...+.|..+.=+.|.+
T Consensus        28 a~~Iae~lgv~kkeV~k~L~~--------Lkkeg~I~~~~r~~w~l   65 (67)
T 2heo_A           28 IFQLVKKCQVPKKTLNQVLYR--------LKKEDRVSSPSPKYWSI   65 (67)
T ss_dssp             HHHHHHHHCSCHHHHHHHHHH--------HHHTTSEEEEETTEEEE
T ss_pred             HHHHHHHHCCCHHHHHHHHHH--------HHHCCCCCCCCCCCCCC
T ss_conf             999999978888999999999--------98774805899862047


No 29 
>>1qzx_A SRP54, signal recognition 54 kDa protein; signal recognition particle, protein targeting, signaling protein; 4.00A {Sulfolobus solfataricus} (A:372-440)
Probab=24.03  E-value=56  Score=14.84  Aligned_cols=32  Identities=19%  Similarity=0.334  Sum_probs=26.5

Q ss_pred             CCCCHHHH----------HHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             76669999----------999999719999999999999999
Q gi|254780496|r    3 KTITRSDL----------VKSISKEFGLSRKDSTRFVTTLFN   34 (114)
Q Consensus         3 ~~mtK~el----------i~~ia~~~g~s~~~~~~~v~~~~~   34 (114)
                      .+||..|+          +..||.-+|.+..+|..++..|..
T Consensus        19 dSMT~~Er~~p~ll~~sR~~RIA~GSG~~~~eV~~Ll~q~~~   60 (69)
T 1qzx_A           19 NSMTYKELENPNIIDKSRMRRIAEGSGLEVEEVRELLEWYNN   60 (69)
T ss_dssp             HSCBHHHHHCGGGCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHCCHHHCHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             738999872934114479999775599999999999999999


No 30 
>>2do7_A Cullin-4B, CUL-4B; helix-turn-helix motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:)
Probab=23.42  E-value=58  Score=14.77  Aligned_cols=33  Identities=18%  Similarity=0.348  Sum_probs=27.4

Q ss_pred             CCCCCHHHHHHHHHHHCCC--CHHHHHHHHHHHHH
Q ss_conf             8766699999999997199--99999999999999
Q gi|254780496|r    2 SKTITRSDLVKSISKEFGL--SRKDSTRFVTTLFN   34 (114)
Q Consensus         2 ~~~mtK~eli~~ia~~~g~--s~~~~~~~v~~~~~   34 (114)
                      .++|+-.||+..+.....+  +..+++..++.|++
T Consensus        43 ~K~l~~~eL~~~V~~~l~F~p~~~~iKk~Ie~LIe   77 (101)
T 2do7_A           43 RKTLSHNLLVSEVYNQLKFPVKPADLKKRIESLID   77 (101)
T ss_dssp             SSEEEHHHHHHHHHHHCSSCCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             06475999999999985699999999999999981


No 31 
>>2ftc_E Mitochondrial ribosomal protein L7/12, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} (E:66-137)
Probab=22.06  E-value=42  Score=15.61  Aligned_cols=37  Identities=22%  Similarity=0.364  Sum_probs=30.0

Q ss_pred             CHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             69999999999-71999999999999999999999755
Q gi|254780496|r    6 TRSDLVKSISK-EFGLSRKDSTRFVTTLFNEICDSAVR   42 (114)
Q Consensus         6 tK~eli~~ia~-~~g~s~~~~~~~v~~~~~~i~~~L~~   42 (114)
                      +|-.+|+.|-. -+|++-.++..+++.+=..|.+.+..
T Consensus        15 kKi~vIK~vr~~~tglgL~eAK~lVe~~P~~ike~v~k   52 (72)
T 2ftc_E           15 DKVKLIKEIKNYVQGINLVQAKKLVESLPQEIKANVAK   52 (72)
T ss_pred             CHHHHHHHHHHHCCCCCHHHHHHHHHHCCHHHHCCCCH
T ss_conf             14579999998717998799999987088888708999


No 32 
>>1hq1_A Signal recognition particle protein; protein-RNA complex, double helix, tetraloop, internal loop, SRP, ribonucleoprotein; HET: CCC; 1.52A {Escherichia coli} (A:)
Probab=22.00  E-value=61  Score=14.59  Aligned_cols=32  Identities=16%  Similarity=0.311  Sum_probs=26.1

Q ss_pred             CCCCHHHH----------HHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             76669999----------999999719999999999999999
Q gi|254780496|r    3 KTITRSDL----------VKSISKEFGLSRKDSTRFVTTLFN   34 (114)
Q Consensus         3 ~~mtK~el----------i~~ia~~~g~s~~~~~~~v~~~~~   34 (114)
                      .+||+.|+          +.+||.-+|.+..+|..++..|-.
T Consensus        54 ~SMT~~Er~~p~ll~~sR~~RIA~GSG~~~~eV~~Ll~q~~~   95 (105)
T 1hq1_A           54 NSMTMKERAKPEIIKGSRKRRIAAGSGMQVQDVNRLLKQFDD   95 (105)
T ss_dssp             HTSCHHHHHCGGGCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHCCHHHHCCCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             867999880952366344678764489899999999999999


No 33 
>>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} (C:310-432)
Probab=21.77  E-value=62  Score=14.56  Aligned_cols=32  Identities=13%  Similarity=0.294  Sum_probs=26.6

Q ss_pred             CCCCHHHH----------HHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             76669999----------999999719999999999999999
Q gi|254780496|r    3 KTITRSDL----------VKSISKEFGLSRKDSTRFVTTLFN   34 (114)
Q Consensus         3 ~~mtK~el----------i~~ia~~~g~s~~~~~~~v~~~~~   34 (114)
                      ++||..|+          +.+||.-+|.+..+|..++..|-.
T Consensus        68 ~SMT~~Er~~P~ll~~SR~~RIA~GSG~~~~eVn~Llkq~~~  109 (123)
T 2v3c_C           68 SSMTKEERENPKIIKASRIRRIARGSGTTENDVREVLRYYET  109 (123)
T ss_dssp             TTSCHHHHSSCTTCCHHHHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             728999873940014689989774599999999999999999


No 34 
>>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=21.27  E-value=23  Score=17.20  Aligned_cols=38  Identities=8%  Similarity=-0.010  Sum_probs=30.2

Q ss_pred             CCCCHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             7666999999999971--9999999999999999999997
Q gi|254780496|r    3 KTITRSDLVKSISKEF--GLSRKDSTRFVTTLFNEICDSA   40 (114)
Q Consensus         3 ~~mtK~eli~~ia~~~--g~s~~~~~~~v~~~~~~i~~~L   40 (114)
                      ..|+..+|+..|.+..  .++..|+++.|+.|.+++-+-|
T Consensus       471 ~~~~~~~~~~~i~~s~~~~~~~~e~~~~l~~l~~~~p~~~  510 (546)
T 2wvr_C          471 PALSMEVACARMVGSCCTIMSPGEMEKHLLLLSELLPDWL  510 (546)
T ss_dssp             ----------------------------------------
T ss_pred             CCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCE
T ss_conf             7507999999999854576999999999999998687206


No 35 
>>2cp9_A EF-TS, EF-TSMT, elongation factor TS, mitochondrial; UBA, structural genomics, human, NPPSFA; NMR {Homo sapiens} (A:)
Probab=20.82  E-value=65  Score=14.44  Aligned_cols=31  Identities=13%  Similarity=0.215  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             9999999997199999999999999999999
Q gi|254780496|r    8 SDLVKSISKEFGLSRKDSTRFVTTLFNEICD   38 (114)
Q Consensus         8 ~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~   38 (114)
                      .++|+.|-++||.+..++.+.+...-.-|..
T Consensus        10 ~~~ik~LR~~Tga~~~dCKkAL~e~~gD~~~   40 (64)
T 2cp9_A           10 KELLMKLRRKTGYSFVNCKKALETCGGDLKQ   40 (64)
T ss_dssp             CHHHHHHHHHHCCCHHHHHHHHHHHTSCHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHCCCCHHH
T ss_conf             9999999999698899999999993899999


No 36 
>>2e7j_A SEP-tRNA:Cys-tRNA synthase; seven-stranded BETE-strand, lyase, structural genomics, NPPSFA; HET: PLP; 2.40A {Archaeoglobus fulgidus} (A:1-18,A:270-371)
Probab=20.80  E-value=65  Score=14.44  Aligned_cols=21  Identities=19%  Similarity=0.320  Sum_probs=17.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q ss_conf             199999999999999999999
Q gi|254780496|r   18 FGLSRKDSTRFVTTLFNEICD   38 (114)
Q Consensus        18 ~g~s~~~~~~~v~~~~~~i~~   38 (114)
                      .|++.++++.++|+|.+++.+
T Consensus        98 YGl~~eqv~yv~daF~EIaek  118 (120)
T 2e7j_A           98 YGLSDEEVDYVLNAFKEIIEK  118 (120)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHH
T ss_conf             789999999999999999998


No 37 
>>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus} (A:313-443)
Probab=20.54  E-value=66  Score=14.41  Aligned_cols=33  Identities=24%  Similarity=0.391  Sum_probs=26.8

Q ss_pred             CCCCHHHH----------HHHHHHHCCCCHHHHHHHHHHHHHH
Q ss_conf             76669999----------9999997199999999999999999
Q gi|254780496|r    3 KTITRSDL----------VKSISKEFGLSRKDSTRFVTTLFNE   35 (114)
Q Consensus         3 ~~mtK~el----------i~~ia~~~g~s~~~~~~~v~~~~~~   35 (114)
                      ++||..|+          +.+||.-+|.+..+|..++..|-..
T Consensus        68 ~SMT~~Er~~p~ll~~sR~~RIA~GSG~~~~dVn~Llk~~~~~  110 (131)
T 3dm5_A           68 DSMTEEELLNPEIINYSRIKRIARGSGTSTKDVKELLDQYRQM  110 (131)
T ss_dssp             TTSCHHHHHCGGGCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf             7399998739401366899998753898999999999999999


Done!