Query         gi|254780345|ref|YP_003064758.1| transcription antitermination protein NusB [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 170
No_of_seqs    111 out of 2231
Neff          7.9 
Searched_HMMs 23785
Date          Mon May 30 09:21:21 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780345.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3d3b_A Protein NUSB, N utiliza 100.0 2.4E-34   1E-38  225.3  14.4  138   10-161     3-140 (141)
  2 1eyv_A NUSB protein, N-utilizi 100.0 4.5E-34 1.9E-38  223.7  13.3  148   11-167     5-152 (156)
  3 2jr0_A Protein NUSB, N utiliza 100.0 1.7E-33 7.3E-38  220.2  15.0  138   13-161     1-138 (148)
  4 1tzv_A NUSB protein, N utiliza 100.0 1.3E-32 5.6E-37  214.8  13.4  138   12-161     1-138 (142)
  5 1q8c_A Hypothetical protein Mg 100.0   1E-29 4.4E-34  197.4   7.9  135    8-153     6-150 (151)
  6 1sqg_A SUN protein, FMU protei  99.9 1.9E-20 7.9E-25  141.6  13.9  128   15-158     3-130 (429)
  7 2yxl_A PH0851 protein, 450AA l  99.7   2E-15 8.2E-20  111.3  13.4   96   60-159    44-139 (450)
  8 1v54_E Cytochrome C oxidase po  43.5      14  0.0006   15.6   3.8   52  103-154    24-76  (109)
  9 1qgp_A Protein (double strande  41.0      15 0.00065   15.4   2.8   33  130-164    34-66  (77)
 10 1xmk_A Double-stranded RNA-spe  40.8      16 0.00066   15.4   2.7   55  106-167    10-64  (79)
 11 2zc2_A DNAD-like replication p  38.6      17 0.00071   15.1   3.8   51  100-156    18-68  (78)
 12 2i5u_A DNAD domain protein; st  34.8      19 0.00082   14.8   3.8   59   97-156    13-73  (83)
 13 1qbj_A Protein (double-strande  26.7      27  0.0011   13.9   2.8   32  130-163    30-61  (81)

No 1  
>3d3b_A Protein NUSB, N utilization substance protein B; NUSB, NUSE, NUT site, phage lambda, lambdan antitermination; HET: NHE; 1.30A {Escherichia coli K12} PDB: 3d3c_A 3imq_A 1ey1_A
Probab=100.00  E-value=2.4e-34  Score=225.32  Aligned_cols=138  Identities=28%  Similarity=0.363  Sum_probs=125.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98132346999999999999995699989999999985310013221120144343999999999999989999999997
Q gi|254780345|r   10 LKLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISS   89 (170)
Q Consensus        10 ~~~~~~r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~   89 (170)
                      |++ ..|+.||+.|+|+||++++++.+.++++.+|...           ......|..|+++++.|+.++...+|.+|.+
T Consensus         3 m~~-~~R~~aR~~a~q~Ly~~~~~~~~~~~~~~~~~~~-----------~~~~~~d~~~~~~lv~gv~~~~~~ld~~I~~   70 (141)
T 3d3b_A            3 MEP-AARRRARECAVQALYSWQLSQNDIADVEYQFLAE-----------QDVKDVDVLYFRELLAGVATNTAYLDGLMKP   70 (141)
T ss_dssp             CCC-HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH-----------SCCTTSCHHHHHHHHHHHHHTHHHHHHHHGG
T ss_pred             CCC-CHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH-----------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             998-4799999999999999984699999999999884-----------4444357999999999899739999999999


Q ss_pred             HHCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             410357633235348999999999986435578103398899999983387723149999999995233320
Q gi|254780345|r   90 CLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKR  161 (170)
Q Consensus        90 ~l~~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~  161 (170)
                      ++  +|+++|+++++++|||+|+||+++.+++|++|+|||||+|||.|++++++||||||||+++|+.+.++
T Consensus        71 ~l--~~~~~rl~~~~~~ILrla~~El~~~~~~p~~vvInE~VelAK~~~~~~~~~fVNaVL~~i~k~~r~~e  140 (141)
T 3d3b_A           71 YL--SRLLEELGQVEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPNK  140 (141)
T ss_dssp             GG--TTCSSCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHSCTTHHHHHHHHHHHHHHHHCTTC
T ss_pred             HH--HHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             76--75598637989999999999998665899702199999999996899720338999999999847357


No 2  
>1eyv_A NUSB protein, N-utilizing substance protein B homolog; helical bundle, structural genomics, PSI, protein structure initiative; 1.60A {Mycobacterium tuberculosis} SCOP: a.79.1.1
Probab=100.00  E-value=4.5e-34  Score=223.71  Aligned_cols=148  Identities=28%  Similarity=0.399  Sum_probs=129.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             81323469999999999999956999899999999853100132211201443439999999999999899999999974
Q gi|254780345|r   11 KLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSC   90 (170)
Q Consensus        11 ~~~~~r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~   90 (170)
                      ++.+.|+.||+.|+|+||++++++.+++++++.+.....        .......|..|+++|+.|+.+++..||.+|.++
T Consensus         5 k~~~~R~~aR~~a~q~Ly~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~lv~g~~~~~~~id~~I~~~   76 (156)
T 1eyv_A            5 KPVRGRHQARKRAVALLFEAEVRGISAAEVVDTRAALAE--------AKPDIARLHPYTAAVARGVSEHAAHIDDLITAH   76 (156)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHH--------HCTTSCCCCHHHHHHHHHHHHTHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH--------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             976458999999999999999609987888999999864--------030148899999999999999899999999986


Q ss_pred             HCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             10357633235348999999999986435578103398899999983387723149999999995233320378763
Q gi|254780345|r   91 LTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRSGCVSA  167 (170)
Q Consensus        91 l~~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~~~~~~~  167 (170)
                      + ++|+++|+++++++|||+|+||+++++++|++|+|||||+|||.|++++++||||||||+++|..+..+....++
T Consensus        77 l-~~~~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~~~~~~~~~fVNgVL~~i~r~~~~l~~~~~~~  152 (156)
T 1eyv_A           77 L-RGWTLDRLPAVDRAILRVSVWELLHAADVPEPVVVDEAVQLAKELSTDDSPGFVNGVLGQVMLVTPQLRAAAQAV  152 (156)
T ss_dssp             S-TTCCGGGSCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHSCTTHHHHHHHHHHHHC-------------
T ss_pred             H-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             3-124787612888999999999998343799734159999999996898744216999999998446666666423


No 3  
>2jr0_A Protein NUSB, N utilization substance protein B homolog; antiterminator, transcription; NMR {Aquifex aeolicus}
Probab=100.00  E-value=1.7e-33  Score=220.16  Aligned_cols=138  Identities=24%  Similarity=0.311  Sum_probs=124.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             32346999999999999995699989999999985310013221120144343999999999999989999999997410
Q gi|254780345|r   13 SHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLT   92 (170)
Q Consensus        13 ~~~r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~   92 (170)
                      ++.|+.||..|+|+||++++++.+..+++.+|.+..          ......+..|++.|+.|+.++...+|.+|..++ 
T Consensus         1 m~~R~~aR~~a~q~Ly~~~~~~~~~~~~l~~~~~~~----------~~~~~~~~~~~~~lv~g~~~~~~~id~~i~~~l-   69 (148)
T 2jr0_A            1 MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEK----------NIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHL-   69 (148)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHT----------TCCCHHHHHHHHHHHHHHHTSHHHHHHHHHTTT-
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHC----------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_conf             963899999999999999800959999999999871----------657667999999999999984999999999875-


Q ss_pred             CCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             357633235348999999999986435578103398899999983387723149999999995233320
Q gi|254780345|r   93 EKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKR  161 (170)
Q Consensus        93 ~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~  161 (170)
                      ++|+++|+++++++|||+|+||+++++++|++|||||||+|||.|++++++||||||||+++|+.....
T Consensus        70 ~~~~~~rl~~~~~~ILr~ai~El~~~~~~p~~~vInE~v~lak~~~~~~s~~FVNaVL~~i~r~~~~~~  138 (148)
T 2jr0_A           70 KGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSS  138 (148)
T ss_dssp             TTCCTTSSCHHHHHHHHHHHHHHTTTCCSSHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHH
T ss_conf             328688876899999999999998678899622899999999986899743229999999998624213


No 4  
>1tzv_A NUSB protein, N utilization substance protein B homolog; RNA-protein interaction, transcriptional antitermination, transcription regulation; 1.35A {Thermotoga maritima} SCOP: a.79.1.1 PDB: 1tzu_A 1tzt_A 1tzw_A 1tzx_A*
Probab=100.00  E-value=1.3e-32  Score=214.85  Aligned_cols=138  Identities=32%  Similarity=0.433  Sum_probs=120.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             13234699999999999999569998999999998531001322112014434399999999999998999999999741
Q gi|254780345|r   12 LSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCL   91 (170)
Q Consensus        12 ~~~~r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l   91 (170)
                      |..+|+.+|+.|+|+||++++++.+..+.+..+..           .......|..|++.++.|+.++...+|.+|.+++
T Consensus         1 m~~pR~~aR~~avq~Ly~~~~~~~~~~~~~~~~~~-----------~~~~~~~d~~~~~~lv~g~~~~~~~id~~I~~~l   69 (142)
T 1tzv_A            1 MKTPRRRMRLAVFKALFQHEFRRDEDLEQILEEIL-----------DETYDKKAKEDARRYIRGIKENLSMIDDLISRYL   69 (142)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTTCTTSCHHHHHHHHC-----------CTTSCHHHHHHHHHHHHHHHHTHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH-----------HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99736999999999999998728985999999998-----------6557767799999999999985999999999864


Q ss_pred             CCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             0357633235348999999999986435578103398899999983387723149999999995233320
Q gi|254780345|r   92 TEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKR  161 (170)
Q Consensus        92 ~~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~  161 (170)
                       ++|+++++++++++|||+|+||+++.+++|++|||||||+|||.|++++++||||||||+++|+.+..+
T Consensus        70 -~~~~~~~l~~~~~~ILr~a~~El~~~~~~p~~vvInE~v~lak~~~~~~~~~fiNavL~~i~r~~~~~~  138 (142)
T 1tzv_A           70 -EKWSLNRLSVVDRNVLRLATYELLFEKDIPIEVTIDEAIEIAKRYGTENSGKFVNGILDRIAKEHAPKE  138 (142)
T ss_dssp             -SSSCGGGSCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHCCGG
T ss_pred             -CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCHH
T ss_conf             -248888885899999999999998653576038999999999986898643208999999998729301


No 5  
>1q8c_A Hypothetical protein Mg027; structural genomics, NUSB, GI 3844637, BSGC structure funded by NIH, protein structure initiative, PSI; 2.00A {Mycoplasma genitalium} SCOP: a.79.1.2
Probab=99.96  E-value=1e-29  Score=197.40  Aligned_cols=135  Identities=21%  Similarity=0.217  Sum_probs=106.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             79981323469999999999999956999899999999853100132211201443439999999999999899999999
Q gi|254780345|r    8 KDLKLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLI   87 (170)
Q Consensus         8 ~~~~~~~~r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I   87 (170)
                      +++.....|+.+|+.|+|+|||+++++.+..+.+..+.....          .....+..|.+.++.++..+...++..+
T Consensus         6 k~~~~k~tR~~aRe~avQ~Lyq~~~~~~~~~e~i~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~i~~~i   75 (151)
T 1q8c_A            6 KGLTNKLTRTQRRIAVVEFIFSLLFFLPKEAEVIQADFLEYD----------TKERQLNEWQKLIVKAFSENIFSFQKKI   75 (151)
T ss_dssp             ------CCHHHHHHHHHHHHHHHGGGCCCCHHHHHHHHHHTC----------CTTTCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH----------CCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             545545249999999999999988288424889999998610----------0012567899998999999999999986


Q ss_pred             HHH----------HCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf             974----------103576332353489999999999864355781033988999999833877231499999999
Q gi|254780345|r   88 SSC----------LTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKV  153 (170)
Q Consensus        88 ~~~----------l~~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki  153 (170)
                      ..+          +..+|+++|+++++++|||+|+||+.+ .++|++|+|||||+|||.|+++++++|||||||++
T Consensus        76 ~~~~~~~~~~i~~~~~~w~~~Ri~~vd~aILrla~~El~~-~d~p~~v~InEavelak~f~~~~~~kfiNgvLdki  150 (151)
T 1q8c_A           76 EEQQLKNQLEIQTKYNKISGKKIDLLTTAVVLCALSEQKA-HNTDKPLLISEALLIMDHYSQGAEKKQTHALLDKL  150 (151)
T ss_dssp             HHHHHHCCCSCCCC--------CCHHHHHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHTTCCCTTSCSCTTTSCC
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC-CCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             7777888999988752797877349999999999999843-69996412999999999868885177999999851


No 6  
>1sqg_A SUN protein, FMU protein; rossmann-fold, mixed beta sheet, methyltransferase-fold, RNA-binding domain; 1.65A {Escherichia coli} SCOP: a.79.1.3 c.66.1.38 PDB: 1sqf_A
Probab=99.85  E-value=1.9e-20  Score=141.56  Aligned_cols=128  Identities=20%  Similarity=0.255  Sum_probs=113.8

Q ss_pred             CHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             34699999999999999569998999999998531001322112014434399999999999998999999999741035
Q gi|254780345|r   15 RRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEK   94 (170)
Q Consensus        15 ~r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~   94 (170)
                      +++.+|..|.++|++....+..++.++....             ..++..|++|++++++|++|++..+|.+|++++++ 
T Consensus         3 ~~~~~R~~A~~~L~~v~~~g~~~~~~L~~~~-------------~~l~~~Dr~~i~~Lv~g~lR~~~~Ld~il~~~~~k-   68 (429)
T 1sqg_A            3 KQRNLRSMAAQAVEQVVEQGQSLSNILPPLQ-------------QKVSDKDKALLQELCFGVLRTLSQLDWLINKLMAR-   68 (429)
T ss_dssp             --CCHHHHHHHHHHHHHHHCCCHHHHHHHHH-------------TTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSS-
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHH-------------HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-
T ss_conf             8877999999999999985987999999998-------------52999899999999999998799999999986489-


Q ss_pred             CCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             7633235348999999999986435578103398899999983387723149999999995233
Q gi|254780345|r   95 WSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEE  158 (170)
Q Consensus        95 w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~  158 (170)
                       +++..++..+.+||+|+||++++ .+|++++|||+|+++|.+......+||||||+++.++..
T Consensus        69 -~~~~~~~~v~~lL~i~~~qll~~-~~p~~a~v~e~V~~ak~~~~~~~~~lvNavLR~~~r~~~  130 (429)
T 1sqg_A           69 -PMTGKQRTVHYLIMVGLYQLLYT-RIPPHAALAETVEGAIAIKRPQLKGLINGVLRQFQRQQE  130 (429)
T ss_dssp             -CCCGGGHHHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHH
T ss_pred             -CCCCCCHHHHHHHHHHHHHHHHC-CCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
T ss_conf             -98643689999999999999727-898521158899999863241102221034443223333


No 7  
>2yxl_A PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog, methyltransferase, structural genomics, NPPSFA; HET: SFG; 2.55A {Pyrococcus horikoshii OT3}
Probab=99.66  E-value=2e-15  Score=111.28  Aligned_cols=96  Identities=19%  Similarity=0.097  Sum_probs=85.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             14434399999999999998999999999741035763323534899999999998643557810339889999998338
Q gi|254780345|r   60 VYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFY  139 (170)
Q Consensus        60 ~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~  139 (170)
                      .....|+.++++||+|++|++..||.+|.+++.+  +...+++..+++||+|+||++|+ + |++++|+++|++|+.+..
T Consensus        44 ~~~~~dr~~~t~lvygvlR~~~~Ld~~l~~~~~~--~~~~~~~~vr~~Lrlg~yqllfl-~-p~~aav~~~v~~a~~~~~  119 (450)
T 2yxl_A           44 VEEAWLNRVLTMIFYDIMKKQGLIDKVIKEIVGV--TPLILDPWLRAALRVAVDIALFH-D-PSSQTIKNLRWKASDFIS  119 (450)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS--CGGGSCHHHHHHHHHHHHHHHHS-C-BCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CHHHCCHHHHHHHHHHHHHHHHC-C-CHHHHHHHHHHHHHHHHC
T ss_conf             6671578999999999998599999999987089--91336999999999999999864-9-517899999999876512


Q ss_pred             CCCCCHHHHHHHHHHHHHHH
Q ss_conf             77231499999999952333
Q gi|254780345|r  140 GDEPKFINAVLDKVSRKEEI  159 (170)
Q Consensus       140 ~~~~~fVNaVL~ki~k~~~~  159 (170)
                      ....+||||||+++.|+...
T Consensus       120 ~~~~~~vnavlr~vlr~~~~  139 (450)
T 2yxl_A          120 SRTHPYVGMYFWDLLDKIFE  139 (450)
T ss_dssp             HHSCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHHCC
T ss_conf             23247667998730133202


No 8  
>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* 3ag3_E* ...
Probab=43.54  E-value=14  Score=15.61  Aligned_cols=52  Identities=23%  Similarity=0.241  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC-CCCCCHHHHHHHHHH
Q ss_conf             4899999999998643557810339889999998338-772314999999999
Q gi|254780345|r  103 ILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFY-GDEPKFINAVLDKVS  154 (170)
Q Consensus       103 ~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~-~~~~~fVNaVL~ki~  154 (170)
                      +|..-+|-|+-.+.-..-+|.+.||..++.-++...+ .-+.+|.-||=+|..
T Consensus        24 iD~we~rr~mN~l~~~DlVP~P~ii~aALkAcRRvND~alAVR~lE~vK~K~~   76 (109)
T 1v54_E           24 IDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAG   76 (109)
T ss_dssp             CCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             52999999999984367789919999999999884006999999999999844


No 9  
>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19
Probab=41.04  E-value=15  Score=15.37  Aligned_cols=33  Identities=18%  Similarity=0.159  Sum_probs=27.0

Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99999983387723149999999995233320378
Q gi|254780345|r  130 YVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRSGC  164 (170)
Q Consensus       130 ~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~~~~  164 (170)
                      +.+|||.++-++  +=||-+|=++.++.+..+.+.
T Consensus        34 A~~LAk~lg~~K--k~vN~~LY~L~k~g~v~~~~~   66 (77)
T 1qgp_A           34 AHDLSGKLGTPK--KEINRVLYSLAKKGKLQKEAG   66 (77)
T ss_dssp             HHHHHHHHCCCH--HHHHHHHHHHHHHTSEEEECS
T ss_pred             HHHHHHHHCCCH--HHHHHHHHHHHHCCCEEECCC
T ss_conf             999999969888--888999999998789530699


No 10 
>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19
Probab=40.84  E-value=16  Score=15.35  Aligned_cols=55  Identities=18%  Similarity=0.235  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             99999999986435578103398899999983387723149999999995233320378763
Q gi|254780345|r  106 SILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRSGCVSA  167 (170)
Q Consensus       106 ~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~~~~~~~  167 (170)
                      +=+---+|+.++..  ++    ..++.|||.++-++ .+=||.+|=.+.|..+..+.+.--|
T Consensus        10 ~~~~ekI~~~L~~~--~~----stAl~iAk~LGl~k-akeVN~~LY~L~k~g~v~k~~~tPP   64 (79)
T 1xmk_A           10 AEIKEKICDYLFNV--SD----SSALNLAKNIGLTK-ARDINAVLIDMERQGDVYRQGTTPP   64 (79)
T ss_dssp             HHHHHHHHHHHHHT--CC----EEHHHHHHHHCGGG-HHHHHHHHHHHHHTTSEEEECSSSC
T ss_pred             HHHHHHHHHHHHHC--CC----CHHHHHHHHHCCCC-HHHHHHHHHHHHHCCCEECCCCCCC
T ss_conf             78999999999966--99----53999999929972-6777499999997678122799899


No 11 
>2zc2_A DNAD-like replication protein; GI 24377835, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Streptococcus mutans UA159}
Probab=38.57  E-value=17  Score=15.14  Aligned_cols=51  Identities=14%  Similarity=-0.004  Sum_probs=33.4

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf             353489999999999864355781033988999999833877231499999999952
Q gi|254780345|r  100 LDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRK  156 (170)
Q Consensus       100 l~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~  156 (170)
                      +++.+...|.--+-+.    ..| .-+|-++++.|..- +..+.++|+|||.+-.++
T Consensus        18 ls~~e~e~i~~w~~~~----~~~-~elI~~A~~~a~~~-~~~s~~Yi~~IL~~W~~~   68 (78)
T 2zc2_A           18 LSPFELEDLQKTVSDD----KTD-PDLVRSALREAVFN-GKTNWNYIQAILRNWRHE   68 (78)
T ss_dssp             CCHHHHHHHHHHHTTT----CCC-HHHHHHHHHHHHHH-TCCCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHH----CCC-HHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHC
T ss_conf             9999999999999881----999-99999999999994-999899999999999994


No 12 
>2i5u_A DNAD domain protein; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.50A {Enterococcus faecalis V583} SCOP: a.275.1.1
Probab=34.80  E-value=19  Score=14.77  Aligned_cols=59  Identities=17%  Similarity=0.198  Sum_probs=37.5

Q ss_pred             HHHCCCHHHHHHHHHHHHHHH--CCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf             332353489999999999864--355781033988999999833877231499999999952
Q gi|254780345|r   97 FSRLDMILCSILRAGVLELIE--CHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRK  156 (170)
Q Consensus        97 ~~rl~~~~~~iLr~a~~El~~--~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~  156 (170)
                      +-++++.+.--|.-=+-++-.  ..+-=+.-+|-+|++.|-.- +....++||+||++=.++
T Consensus        13 fG~lsp~e~e~i~~W~dd~~~~~~~~~~~~elI~~A~~~av~~-~~~n~~Yi~~IL~~W~~~   73 (83)
T 2i5u_A           13 FGLMSSKTMTDFDYWISDFEKIGASQKEAEQLIVKAIEIAIDA-NARNYNYINAILKDWEQR   73 (83)
T ss_dssp             SCSCCHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHH-TCCSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHC
T ss_conf             7778889999999999997500123359999999999999995-999879999999999995


No 13 
>1qbj_A Protein (double-stranded RNA specific adenosine deaminase (ADAR1)); protein/Z-DNA complex, hydrolase/DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A
Probab=26.74  E-value=27  Score=13.94  Aligned_cols=32  Identities=19%  Similarity=0.173  Sum_probs=25.8

Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999998338772314999999999523332037
Q gi|254780345|r  130 YVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRSG  163 (170)
Q Consensus       130 ~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~~~  163 (170)
                      +.+|||.++-+  .+=||-+|=++.++.+..+.+
T Consensus        30 A~~LAk~lg~~--Kk~vN~~LY~L~k~g~v~~~~   61 (81)
T 1qbj_A           30 AHDLSGKLGTP--KKEINRVLYSLAKKGKLQKEA   61 (81)
T ss_dssp             HHHHHHHHTCC--HHHHHHHHHHHHHTTSEEEES
T ss_pred             HHHHHHHHCCC--HHHHHHHHHHHHHCCCEEECC
T ss_conf             99999996988--889899999999879864069


Done!