Query         gi|254780331|ref|YP_003064744.1| 50S ribosomal protein L9 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 179
No_of_seqs    119 out of 1863
Neff          6.4 
Searched_HMMs 23785
Date          Mon May 30 08:30:23 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780331.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 1div_A Ribosomal protein L9; r 100.0       0       0  320.3  13.4  148   14-161     1-149 (149)
  2 3bbo_J Ribosomal protein L9; l 100.0       0       0  322.5   2.6  159    1-160    37-197 (197)
  3 1nkw_F 50S ribosomal protein L 100.0 2.8E-45       0  304.9  14.4  145   14-160     1-145 (146)
  4 2j01_I 50S ribosomal protein L 100.0 2.8E-45       0  305.4   6.2  147   14-161     1-148 (148)
  5 3ofq_H 50S ribosomal protein L 100.0       0       0  316.0  -8.2  147   14-160     1-149 (149)
  6 2hba_A BL17, 50S ribosomal pro  99.8 2.1E-20   9E-25  147.8   2.7   51   14-64      1-51  (52)
  7 3fbi_A Mediator of RNA polymer  37.5      20 0.00083   15.7   2.8   22   48-69     20-41  (84)
  8 3fio_A A cystathionine beta-sy  32.2      12  0.0005   17.1   0.9   25   98-122    30-54  (70)
  9 3k2v_A Putative D-arabinose 5-  31.1      25  0.0011   15.0   3.3   55   78-132    49-105 (149)
 10 2yzi_A Hypothetical protein PH  28.2      29  0.0012   14.7   2.8   25   96-120    44-68  (138)
 11 2yvy_A MGTE, Mg2+ transporter   26.7      30  0.0012   14.6   2.2   16   97-112   178-193 (278)
 12 3gby_A Uncharacterized protein  26.7      25   0.001   15.1   1.8   21   97-117   106-126 (128)
 13 3kpb_A Uncharacterized protein  26.5      31  0.0013   14.5   3.0   24   96-119    38-61  (122)
 14 1yav_A Hypothetical protein BS  23.7      35  0.0015   14.1   2.7   22   96-117   121-142 (159)
 15 1m2d_A [2Fe-2S] ferredoxin; th  23.5      29  0.0012   14.6   1.7   30   96-125    67-99  (110)
 16 2auv_A Potential NAD-reducing   22.9      25  0.0011   15.0   1.3   20   98-117    65-84  (85)
 17 2oux_A Magnesium transporter;   22.0      37  0.0016   13.9   3.2   40   78-117   220-259 (286)
 18 2ef7_A Hypothetical protein ST  21.7      38  0.0016   13.9   3.2   21   97-117   105-125 (133)
 19 2nyc_A Nuclear protein SNF4; b  21.4      38  0.0016   13.9   3.0   21   97-117    49-69  (144)
 20 2ahq_A Sigma-54, RNA polymeras  21.3      38  0.0016   13.8   2.4   23  105-127    37-59  (76)
 21 3kxr_A Magnesium transporter,   20.8      40  0.0017   13.8   3.0   39   79-117   136-174 (205)
 22 2uv4_A 5'-AMP-activated protei  20.5      40  0.0017   13.7   3.0   22   97-118    59-80  (152)

No 1  
>1div_A Ribosomal protein L9; rRNA-binding; 2.60A {Geobacillus stearothermophilus} SCOP: d.99.1.1 d.100.1.1 PDB: 1giy_K 1yl3_K 2b66_I 2b9n_I 2b9p_I 487d_K
Probab=100.00  E-value=0  Score=320.26  Aligned_cols=148  Identities=30%  Similarity=0.537  Sum_probs=144.3

Q ss_pred             EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             33465201117587783888277632110143787301220146888778999998422346789999887654321000
Q gi|254780331|r   14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEKKAKYEGISKDLAKKNFSLI   93 (179)
Q Consensus        14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~i~   93 (179)
                      |||||++||++||+.||+|+|+||||||||||+|+|++||++|+++++.+++..+++..+..+.|+.++++|++..++|.
T Consensus         1 MkVIL~~dv~~lG~~GdvV~Vk~GyaRNyLiP~g~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~~~~i~i~   80 (149)
T 1div_A            1 MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQKEQRQAAEELANAKKLKEQLEKLTVTIP   80 (149)
T ss_dssp             CEEEECSBSSSBGGGTEEEECCTTHHHHTTTTTTSEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CEEEEECCCCCCCCCCCEEEECCCCHHHHHCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             97999044114798899999877014566155682455588889999999999999888887778889999730557999


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHH-CCCCCCHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECH
Q ss_conf             255654310034107899999986-08876866630265643205499999963972999999997251
Q gi|254780331|r   94 RAAGDTGYLYGSVSSRDIADLLIE-EGFDVNRGQINLKSPIKSVGIHNIMISLHADVSTTITLNVARST  161 (179)
Q Consensus        94 ~k~~e~gkLfGsVt~~dI~~~L~~-~gi~I~k~~I~l~~pIk~~G~y~V~I~L~~~V~a~i~V~V~~~~  161 (179)
                      +++|++|+||||||+.||+++|.+ .|++|++++|.|++|||++|+|+|+|+||++|+++|+|+|++++
T Consensus        81 ~k~~~~gklfGsVt~~~I~~~l~~~~gi~i~k~~i~l~~~Ik~~G~y~v~i~l~~~v~~~i~v~V~~ek  149 (149)
T 1div_A           81 AKAGEGGRLFGSITSKQIAESLQAQHGLKLDKRKIELADAIRALGYTNVPVKLHPEVTATLKVHVTEQK  149 (149)
T ss_dssp             ECBCGGGEEEEEECHHHHHHHHHHHHCCCCCGGGBCCCSCEEESEEEEEEEEEETTEEEEEEEEEEECC
T ss_pred             EEECCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCEEEEEEEEECCCEEEEEEEEEEECC
T ss_conf             974699975022489999999998519821743422445752546689999953997999999999578


No 2  
>3bbo_J Ribosomal protein L9; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana} SCOP: i.1.1.1
Probab=100.00  E-value=0  Score=322.50  Aligned_cols=159  Identities=27%  Similarity=0.450  Sum_probs=152.3

Q ss_pred             CCEEECCCCCCCCEEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             93132121024303346520111758778388827763211014378730122014688877899999842234678999
Q gi|254780331|r    1 MYDTQKNKKGKKIMEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEKKAKYEG   80 (179)
Q Consensus         1 ~~~~~~~kk~~~~mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~   80 (179)
                      .|.++++||.+++|||||++||++||++||+|+|++|||||||||+|+|++||++|+++++.+++.+++...+..++++.
T Consensus        37 ~~~~~a~kk~kk~~kVIL~~dV~~lGk~GdvV~Vk~GyaRNfLiP~g~A~~aT~~nl~~~~~~~~~~~~~~~~~~~~a~~  116 (197)
T 3bbo_J           37 NFEVVSQKKAKKLRKVILKEDVTDLGKQGQLLDVKAGFFRNFLLPTGKAQLMTPLLLKELKMEDERIEAEKQRVKEEAQQ  116 (197)
T ss_dssp             -------------CCCCCCSCSSSSCSSCCCSCCCSSSCCCCCTTTTCCCCCCHHHHHHHHTTTHHHHGGGTTTTHHHHT
T ss_pred             EEEEEEECCCCCEEEEEEECCCCCCCCCCCEEEECCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             17999861457405899905412489999999987733440143677265624999999999999999888887767999


Q ss_pred             HHHHHHHH-HHHHCCCCCCCCCCCCCCCHHHHHHHHHHC-CCCCCHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEE
Q ss_conf             98876543-210002556543100341078999999860-8876866630265643205499999963972999999997
Q gi|254780331|r   81 ISKDLAKK-NFSLIRAAGDTGYLYGSVSSRDIADLLIEE-GFDVNRGQINLKSPIKSVGIHNIMISLHADVSTTITLNVA  158 (179)
Q Consensus        81 ~~~~L~~~-~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~-gi~I~k~~I~l~~pIk~~G~y~V~I~L~~~V~a~i~V~V~  158 (179)
                      ++.+|+++ .+.+.++++++|+||||||+.||+++|.++ |++|++++|.|+ ||+++|+|+|+|+||+||+++|+|+|+
T Consensus       117 l~~~l~~~~~~~i~~~~~~~g~LfGSVT~~dI~~~L~~q~g~~V~k~~I~l~-~IK~lG~y~V~V~Lh~eV~a~ikV~Vv  195 (197)
T 3bbo_J          117 LAMVFQTVGAFKVKRKGGKGKLIFGSVTAQDLVDIIKSQLQKDIDKRLVSLP-EIRETGEYIAELKLHPDVTARVKINVF  195 (197)
T ss_dssp             HHHHSSSCCCCBCCCCBCTTSSBSSCCSSHHHHGGGTSSSSCCCCSTTCCSC-CCSSSSCEEECCCCBTTBCCCEEEBCC
T ss_pred             HHHHHHCCCEEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHEECCC-CCCCCEEEEEEEEECCCEEEEEEEEEE
T ss_conf             9998730002443431254544555769999999998733982265026363-453458689999944996999999999


Q ss_pred             EC
Q ss_conf             25
Q gi|254780331|r  159 RS  160 (179)
Q Consensus       159 ~~  160 (179)
                      ++
T Consensus       196 A~  197 (197)
T 3bbo_J          196 AN  197 (197)
T ss_dssp             CC
T ss_pred             EC
T ss_conf             69


No 3  
>1nkw_F 50S ribosomal protein L9; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB: 1nwx_F* 1nwy_F* 1sm1_F* 1xbp_F* 1pnu_F 1pny_F 1vor_I 1vou_I 1vow_I 1voy_I 1vp0_I
Probab=100.00  E-value=2.8e-45  Score=304.88  Aligned_cols=145  Identities=37%  Similarity=0.586  Sum_probs=141.4

Q ss_pred             EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             33465201117587783888277632110143787301220146888778999998422346789999887654321000
Q gi|254780331|r   14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEKKAKYEGISKDLAKKNFSLI   93 (179)
Q Consensus        14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~i~   93 (179)
                      |+|||++|+ +||+.||+|+|++|||||||||+|+|+|||++|+++++.++...+++..+..+.|+.++++|++..+++.
T Consensus         1 MkvIL~~~~-~lG~~GdiV~Vk~GyaRN~LiP~~~A~~at~~nl~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~~l~~~   79 (146)
T 1nkw_F            1 MQVILLEPS-RLGKTGEVVSVKDGYARNWLIPQGLAVSATRTNMKTLEAQLRSIEKRQAQEKAVAEDLASRLNGVAVELS   79 (146)
T ss_pred             CEEEEEECC-CCCCCCCEEEECCHHHHHHHCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             979998447-7898899899876103244066670666789999999999999999999989999999998640455554


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEEC
Q ss_conf             2556543100341078999999860887686663026564320549999996397299999999725
Q gi|254780331|r   94 RAAGDTGYLYGSVSSRDIADLLIEEGFDVNRGQINLKSPIKSVGIHNIMISLHADVSTTITLNVARS  160 (179)
Q Consensus        94 ~k~~e~gkLfGsVt~~dI~~~L~~~gi~I~k~~I~l~~pIk~~G~y~V~I~L~~~V~a~i~V~V~~~  160 (179)
                      +++++ |+||||||+.||+++|.+.|++|++++|.||+||+++|+|+|+|+||++|+++++|+|+++
T Consensus        80 ~~~~~-g~LfGsVt~~dI~~~l~~~g~~I~k~~I~l~~~Ik~~G~y~V~v~l~~~V~~~l~v~V~a~  145 (146)
T 1nkw_F           80 VRAGE-GKIYGAVTHQDVANSLDQLGFDVDRRKIDMPKTVKEVGEYDIAYRAHPEVTIPMKLVVHAA  145 (146)
T ss_pred             HCCCC-CCCCCCCCHHHHHHHHHHCCCEECHHHCCCCCCCCCCEEEEEEEEECCCEEEEEEEEEEEC
T ss_conf             21345-4465546899999999984980169993599721364899999993498799999999978


No 4  
>2j01_I 50S ribosomal protein L9; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: d.99.1.1 d.100.1.1 PDB: 2j03_I 2jl6_I 2jl8_I 2v47_I 2v49_I 2wdi_I 2wdj_I 2wdl_I 2wdn_I 2wh2_I 2x9s_I 2x9u_I 2xg0_I 2xg2_I 3hux_I 3huz_I 3i8f_K 3i8i_K 3i9c_K 3i9e_K ...
Probab=100.00  E-value=2.8e-45  Score=305.43  Aligned_cols=147  Identities=34%  Similarity=0.537  Sum_probs=141.7

Q ss_pred             EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             33465201117587783888277632110143787301220146888778999998422346789999887654321000
Q gi|254780331|r   14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEKKAKYEGISKDLAKKNFSLI   93 (179)
Q Consensus        14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~i~   93 (179)
                      |||||++||++||+.||+|+|+||||||||||+|+|+|||++|+++++.+++..+.+..+..+.+..++..+++..+.+.
T Consensus         1 MkVIL~~dv~~lG~~Gdvv~Vk~GyarN~LiP~~~A~~at~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   80 (148)
T 2j01_I            1 MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAERKAEAERLKEILENLTLTIP   80 (148)
T ss_dssp             CEEEECSCCSSSCSTTCEEECCHHHHHHTTTTTTSEEECCHHHHHHHHHHHHHHHHHSSSTTTTTHHHHHHHTTCBCCCC
T ss_pred             CEEEEECCCCCCCCCCCEEEECCCCHHHHHCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEE
T ss_conf             97999144103798899999877222355165571555799999999999999876656678999999987532204778


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHC-CCCCCHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECH
Q ss_conf             2556543100341078999999860-8876866630265643205499999963972999999997251
Q gi|254780331|r   94 RAAGDTGYLYGSVSSRDIADLLIEE-GFDVNRGQINLKSPIKSVGIHNIMISLHADVSTTITLNVARST  161 (179)
Q Consensus        94 ~k~~e~gkLfGsVt~~dI~~~L~~~-gi~I~k~~I~l~~pIk~~G~y~V~I~L~~~V~a~i~V~V~~~~  161 (179)
                      ++++ +|+||||||+.+|+++|.++ |++|++++|.|++||+++|+|+|+|+||++|+++|+|+|++++
T Consensus        81 ~k~~-~g~LfGsVt~~~I~~~l~~~~~i~I~~~~I~l~~pIk~~G~y~V~v~l~~~v~~~i~v~Vv~~e  148 (148)
T 2j01_I           81 VRAG-ETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPIKELGEYVLTYKPHPEVPIQLKVSVVAQE  148 (148)
T ss_dssp             CCBC-SSSBSSCCCHHHHHHHHHTTTCCCCCTTTTCCSSCCCSCEEEECCCSSSSCCCCEEEECCC---
T ss_pred             EECC-CCCCCCCCCHHHHHHHHHHHCCCEECHHHEECCCCHHCCEEEEEEEEECCCEEEEEEEEEEECC
T ss_conf             6046-6423156489999999998549765499951788210138889999954988999999999688


No 5  
>3ofq_H 50S ribosomal protein L9; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_F 1p86_F 1vs8_H 1vs6_H 2aw4_H 2awb_H 2gya_F 2gyc_F 1vt2_H 2i2v_H 2j28_H 2i2t_H* 2qao_H* 2qba_H* 2qbc_H* 2qbe_H 2qbg_H 2qbi_H* 2qbk_H* 2qov_H ...
Probab=100.00  E-value=0  Score=316.05  Aligned_cols=147  Identities=37%  Similarity=0.632  Sum_probs=142.6

Q ss_pred             EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHH
Q ss_conf             334652011175877838882776321101437873012201468887789999984223467899998876543-2100
Q gi|254780331|r   14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEKKAKYEGISKDLAKK-NFSL   92 (179)
Q Consensus        14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~-~l~i   92 (179)
                      |||||++||++||+.||+|+|++|||||||||+|+|++||++|+++++.+++..+++..+....|+.++++|+++ .++|
T Consensus         1 MkVIL~~dV~~lG~~GdiV~Vk~GyARN~LiP~~~Av~at~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~l~~~~i   80 (149)
T 3ofq_H            1 MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTI   80 (149)
T ss_dssp             CCCEESSCCSSSCCSSCCCCCCTTTTTTTTTTTTSEECCCSHHHHHHHHHHHHHHHHHHTTTTTCCCCCSTTSSCCCCCS
T ss_pred             CEEEECCCCCCCCCCCCEEEECCHHHHHHHCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             97999144115798999999873434776165684444458889999999999987767887789999986402217987


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHCCC-CCCCCEEEEEEEEEECCCEEEEEEEEEEEC
Q ss_conf             02556543100341078999999860887686663026-564320549999996397299999999725
Q gi|254780331|r   93 IRAAGDTGYLYGSVSSRDIADLLIEEGFDVNRGQINLK-SPIKSVGIHNIMISLHADVSTTITLNVARS  160 (179)
Q Consensus        93 ~~k~~e~gkLfGsVt~~dI~~~L~~~gi~I~k~~I~l~-~pIk~~G~y~V~I~L~~~V~a~i~V~V~~~  160 (179)
                      .+++|++|+||||||+.||+++|+++|++|++++|.+| +|||++|+|+|+|+||++|+++++|+|+++
T Consensus        81 ~~k~~e~gkLfGsVt~~~I~~~l~~~g~~i~k~~i~l~~~pIK~~G~~~V~v~L~~~V~a~i~v~V~~e  149 (149)
T 3ofq_H           81 ASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE  149 (149)
T ss_dssp             CCCCCTTSSCCSCCCSCCSCCSSSCSSSCCCSCCSCCSSSSCCCSSCCCCCCCSSSSCCCCCCCCCCCC
T ss_pred             EEEECCCCCCCCCCCHHHHHHHHHHCCCCCCHHHEECCCCCCCCCEEEEEEEEECCCEEEEEEEEEEEC
T ss_conf             764189984457426999999999859911589811788552063778999996599199999999979


No 6  
>2hba_A BL17, 50S ribosomal protein L9; NTL9, K12M, RNA binding protein; 1.25A {Geobacillus stearothermophilus} SCOP: d.100.1.1 PDB: 1cqu_A 2hbb_A 2hvf_A
Probab=99.79  E-value=2.1e-20  Score=147.83  Aligned_cols=51  Identities=37%  Similarity=0.651  Sum_probs=49.4

Q ss_pred             EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHH
Q ss_conf             334652011175877838882776321101437873012201468887789
Q gi|254780331|r   14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQR   64 (179)
Q Consensus        14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~   64 (179)
                      |||||++||++||+.||+|+|+||||||||||+|+|++||++|+++++.++
T Consensus         1 MkVIL~~dV~~lG~~Gdiv~Vk~GyaRN~Lip~~~A~~at~~~~~~~~~~k   51 (52)
T 2hba_A            1 MKVIFLKDVKGMGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQK   51 (52)
T ss_dssp             CEEEESSCBTTTBCTTCEEECCHHHHHHTTTTTTSEEECCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCCCCCCEEEECCHHHHHHHCCCCCCHHCCHHHHHHHHHHH
T ss_conf             979990532157878989998540056660667851337999999999860


No 7  
>3fbi_A Mediator of RNA polymerase II transcription subunit 7; proline-rich stretches, right-handed four-helix bundle, protein-protein complex; 2.80A {Saccharomyces cerevisiae} PDB: 3fbn_A
Probab=37.53  E-value=20  Score=15.68  Aligned_cols=22  Identities=9%  Similarity=-0.135  Sum_probs=15.7

Q ss_pred             CEECCCCHHHHHHHHHHHHHHH
Q ss_conf             7301220146888778999998
Q gi|254780331|r   48 KALRANKENKILFESQRSVLEA   69 (179)
Q Consensus        48 ~A~~aT~~n~~~~~~~~~~~~~   69 (179)
                      +=..-|++|++.++..++....
T Consensus        20 f~K~FT~ENl~kL~e~k~~~~~   41 (84)
T 3fbi_A           20 YVKFFTQSNLEKLPKYKEKKAA   41 (84)
T ss_dssp             GGGGCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHCCHHHHHHHHHHHHHHHH
T ss_conf             8885699999999999987643


No 8  
>3fio_A A cystathionine beta-synthase domain protein fused to A Zn-ribbon-like domain; PF1953,APC40009,cystathionine beta-synthase domain protein; 1.81A {Pyrococcus furiosus} PDB: 3ghd_A
Probab=32.23  E-value=12  Score=17.06  Aligned_cols=25  Identities=28%  Similarity=0.496  Sum_probs=19.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf             5431003410789999998608876
Q gi|254780331|r   98 DTGYLYGSVSSRDIADLLIEEGFDV  122 (179)
Q Consensus        98 e~gkLfGsVt~~dI~~~L~~~gi~I  122 (179)
                      ++|+++|-+|..||...+...+...
T Consensus        30 d~~~lvGIvT~~Di~~~~~~~~~~~   54 (70)
T 3fio_A           30 EGDEILGVVTERDILDKVVAKGKNP   54 (70)
T ss_dssp             ETTEEEEEEEHHHHHHHTTTTTCCG
T ss_pred             ECCEEEEEEEHHHHHHHHHHCCCCC
T ss_conf             8998627986999999998569981


No 9  
>3k2v_A Putative D-arabinose 5-phosphate isomerase; KPSF-like protein, CBS domain, , structural genomics, PSI-2; HET: MSE CMK; 1.95A {Klebsiella pneumoniae subsp} PDB: 3fna_A*
Probab=31.13  E-value=25  Score=14.98  Aligned_cols=55  Identities=11%  Similarity=0.171  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCC--CCCCHHHHCCCCC
Q ss_conf             999988765432100025565431003410789999998608--8768666302656
Q gi|254780331|r   78 YEGISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIEEG--FDVNRGQINLKSP  132 (179)
Q Consensus        78 a~~~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~g--i~I~k~~I~l~~p  132 (179)
                      ..+....+....+..-.=++++|+|.|-||..||...+....  ....-+.|--..|
T Consensus        49 l~~a~~~m~~~~~~~~~Vvd~~~~l~GiiT~~Di~r~~~~~~~~~~~~V~~imt~~p  105 (149)
T 3k2v_A           49 LRDALLEITRKNLGMTAICDDDMNIIGIFTDGDLRRVFDTGVDMRDASIADVMTRGG  105 (149)
T ss_dssp             HHHHHHHHHHHTSSEEEEECTTCBEEEEEEHHHHHHHHCSSSCCTTCBHHHHSEESC
T ss_pred             HHHHHHHHHHHCCCEEEEEECCCCEEEEEECHHHHHHHHHCCCCCCCEEEECCCCCE
T ss_conf             999999855746988999958993999997005654333122344305640454450


No 10 
>2yzi_A Hypothetical protein PH0107; sheet/helix/sheet/sheet/helix, structural genomics, unknown function, NPPSFA; 2.25A {Pyrococcus horikoshii} SCOP: d.37.1.1
Probab=28.16  E-value=29  Score=14.66  Aligned_cols=25  Identities=28%  Similarity=0.440  Sum_probs=16.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCC
Q ss_conf             5654310034107899999986088
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIEEGF  120 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~~gi  120 (179)
                      ++++|+++|-||..||...+...+.
T Consensus        44 vd~~~~~~Giit~~Di~~~~~~~~~   68 (138)
T 2yzi_A           44 INDDGNVVGFFTKSDIIRRVIVPGL   68 (138)
T ss_dssp             ECTTSCEEEEEEHHHHHHHTTTTCC
T ss_pred             EECCCEEEEEEEHHHHHHHHHHCCC
T ss_conf             9389839999877898887764044


No 11 
>2yvy_A MGTE, Mg2+ transporter MGTE; membrane protein, transport protein; 2.30A {Thermus thermophilus HB8} PDB: 2yvz_A
Probab=26.71  E-value=30  Score=14.57  Aligned_cols=16  Identities=38%  Similarity=0.594  Sum_probs=7.8

Q ss_pred             CCCCCCCCCCCHHHHH
Q ss_conf             6543100341078999
Q gi|254780331|r   97 GDTGYLYGSVSSRDIA  112 (179)
Q Consensus        97 ~e~gkLfGsVt~~dI~  112 (179)
                      .++|+|-|.|+..++.
T Consensus       178 d~~~~l~G~v~~~dLl  193 (278)
T 2yvy_A          178 DEKGRLKGVLSLRDLI  193 (278)
T ss_dssp             CTTCBEEEEEEHHHHH
T ss_pred             CCCCCEECCCCHHHHH
T ss_conf             7655641013199998


No 12 
>3gby_A Uncharacterized protein CT1051; CBS domain, structural genomics, PSI-2, protein structure initiative; HET: EPE; 1.66A {Chlorobium tepidum tls}
Probab=26.66  E-value=25  Score=15.07  Aligned_cols=21  Identities=33%  Similarity=0.477  Sum_probs=11.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHH
Q ss_conf             654310034107899999986
Q gi|254780331|r   97 GDTGYLYGSVSSRDIADLLIE  117 (179)
Q Consensus        97 ~e~gkLfGsVt~~dI~~~L~~  117 (179)
                      +++|++.|=||..||...|.+
T Consensus       106 d~~g~~~Giit~~dil~~l~~  126 (128)
T 3gby_A          106 DEDGRYEGVVSRKRILGFLAE  126 (128)
T ss_dssp             CTTCBEEEEEEHHHHHHHHHT
T ss_pred             CCCCEEEEEEEHHHHHHHHHH
T ss_conf             689969999999999999982


No 13 
>3kpb_A Uncharacterized protein MJ0100; CBS domain, S-adenosylmethionine, conformational change, unknown function; HET: SAM; 1.60A {Methanocaldococcus jannaschii} PDB: 3kpd_A* 3kpc_A*
Probab=26.47  E-value=31  Score=14.47  Aligned_cols=24  Identities=33%  Similarity=0.489  Sum_probs=15.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCC
Q ss_conf             565431003410789999998608
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIEEG  119 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~~g  119 (179)
                      ++++|++.|-||..|+...+....
T Consensus        38 vd~~~~~~G~it~~dl~~~~~~~~   61 (122)
T 3kpb_A           38 VDEHGKLVGIITSWDIAKALAQNK   61 (122)
T ss_dssp             ECTTSBEEEEECHHHHHHHHHTTC
T ss_pred             EECCCCEEEEEEHHHHHHHHCCCC
T ss_conf             908992999988999987650389


No 14 
>1yav_A Hypothetical protein BSU14130; cystathionine beta synthase (CBS) domain, structural genomics, protein structure initiative, PSI; 2.10A {Bacillus subtilis} SCOP: d.37.1.1
Probab=23.69  E-value=35  Score=14.14  Aligned_cols=22  Identities=18%  Similarity=0.187  Sum_probs=11.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             5654310034107899999986
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIE  117 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~  117 (179)
                      ++++|++-|=||..||.+++..
T Consensus       121 Vde~g~~~GIIT~~Dil~~l~~  142 (159)
T 1yav_A          121 ENDEQVFEGIFTRRVVLKELNK  142 (159)
T ss_dssp             ECTTCBEEEEEEHHHHHHHHHH
T ss_pred             EECCCEEEEEEEHHHHHHHHHH
T ss_conf             9449979999889999999999


No 15 
>1m2d_A [2Fe-2S] ferredoxin; thioredoxin-like fold, [2Fe-2S] cluster, Cys59Ser variant, electron transport; 1.05A {Aquifex aeolicus} SCOP: c.47.1.11 PDB: 1m2a_A 1f37_A 1m2b_A
Probab=23.52  E-value=29  Score=14.57  Aligned_cols=30  Identities=27%  Similarity=0.439  Sum_probs=23.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHC---CCCCCHH
Q ss_conf             56543100341078999999860---8876866
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIEE---GFDVNRG  125 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~~---gi~I~k~  125 (179)
                      +.++|..|+-||+.+|.+.+.++   |-.+++-
T Consensus        67 I~P~g~~Y~~v~p~~v~~Iv~~hl~~g~pv~~l   99 (110)
T 1m2d_A           67 VYPDGVWYGQVKPEDVDEIVEKHLKGGEPVERL   99 (110)
T ss_dssp             EETTTEEECSCCGGGHHHHHHHTTTTSCCCGGG
T ss_pred             EECCCCEEECCCHHHHHHHHHHHHHCCCEEEEE
T ss_conf             907977781599999999999999799470356


No 16 
>2auv_A Potential NAD-reducing hydrogenase subunit; thioredoxin, thiordoxin-like, oxidoreductase; NMR {Desulfovibrio fructosovorans}
Probab=22.89  E-value=25  Score=14.99  Aligned_cols=20  Identities=25%  Similarity=0.471  Sum_probs=16.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHH
Q ss_conf             54310034107899999986
Q gi|254780331|r   98 DTGYLYGSVSSRDIADLLIE  117 (179)
Q Consensus        98 e~gkLfGsVt~~dI~~~L~~  117 (179)
                      =||++|+.+|+.++.+.|.+
T Consensus        65 id~~~y~~vt~e~v~~il~~   84 (85)
T 2auv_A           65 VGEKVYGNVTPGQVKKILAE   84 (85)
T ss_dssp             EGGGCCCCSSSSHHHHHHHH
T ss_pred             ECCEEECCCCHHHHHHHHHH
T ss_conf             99998778899999999971


No 17 
>2oux_A Magnesium transporter; 10001B, structural genomics, PSI-2, protein structure initiative, nysgxrc; 2.16A {Enterococcus faecalis V583} SCOP: a.118.26.1 d.37.1.1
Probab=22.00  E-value=37  Score=13.93  Aligned_cols=40  Identities=20%  Similarity=0.341  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             9999887654321000255654310034107899999986
Q gi|254780331|r   78 YEGISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIE  117 (179)
Q Consensus        78 a~~~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~  117 (179)
                      .+..++.+....+..--=+.++|+|-|-||..||.+.+.+
T Consensus       220 ~eeaa~~~~~~~l~~lPVVD~~g~LvGiIT~~Dii~~i~e  259 (286)
T 2oux_A          220 QEDVAQTIRDYDFLAVPVTDYDDHLLGIVTVDDIIDVIDD  259 (286)
T ss_dssp             HHHHHHHHHHHTCSEEEEECTTCBEEEEEEHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCEEEEECCCCEEEEEEEHHHHHHHHHH
T ss_conf             9999999997399766188579969999789999999999


No 18 
>2ef7_A Hypothetical protein ST2348; CBS-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.10A {Sulfolobus tokodaii} SCOP: d.37.1.1
Probab=21.70  E-value=38  Score=13.89  Aligned_cols=21  Identities=38%  Similarity=0.548  Sum_probs=11.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHH
Q ss_conf             654310034107899999986
Q gi|254780331|r   97 GDTGYLYGSVSSRDIADLLIE  117 (179)
Q Consensus        97 ~e~gkLfGsVt~~dI~~~L~~  117 (179)
                      +++|++.|=||..||..++.+
T Consensus       105 d~~~~~~Giit~~Di~~~l~~  125 (133)
T 2ef7_A          105 DDKGNLKGIISIRDITRAIDD  125 (133)
T ss_dssp             CTTSCEEEEEEHHHHHHHHHH
T ss_pred             ECCCEEEEEEEHHHHHHHHHH
T ss_conf             489969999999999999978


No 19 
>2nyc_A Nuclear protein SNF4; bateman2 domain, AMP kinase, protein binding; 1.90A {Saccharomyces cerevisiae} SCOP: d.37.1.1 PDB: 2nye_A
Probab=21.39  E-value=38  Score=13.85  Aligned_cols=21  Identities=24%  Similarity=0.468  Sum_probs=12.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHH
Q ss_conf             654310034107899999986
Q gi|254780331|r   97 GDTGYLYGSVSSRDIADLLIE  117 (179)
Q Consensus        97 ~e~gkLfGsVt~~dI~~~L~~  117 (179)
                      .++|++.|-||..||...+..
T Consensus        49 d~~~~~iGiis~~Di~~~l~~   69 (144)
T 2nyc_A           49 DENGYLINVYEAYDVLGLIKG   69 (144)
T ss_dssp             CTTCBEEEEEEHHHHHHHHHT
T ss_pred             ECCCEEEEEEEECHHHHHHHC
T ss_conf             279929999986020134322


No 20 
>2ahq_A Sigma-54, RNA polymerase sigma factor RPON; sigma-54,sigma factors, solution structure, transcription; NMR {Aquifex aeolicus} PDB: 2o8k_A 2o9l_A
Probab=21.34  E-value=38  Score=13.85  Aligned_cols=23  Identities=39%  Similarity=0.700  Sum_probs=19.9

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHH
Q ss_conf             41078999999860887686663
Q gi|254780331|r  105 SVSSRDIADLLIEEGFDVNRGQI  127 (179)
Q Consensus       105 sVt~~dI~~~L~~~gi~I~k~~I  127 (179)
                      +.+-..|++.|.+.|+.|.++-|
T Consensus        37 PlSD~~i~~~L~~~Gi~IaRRTV   59 (76)
T 2ahq_A           37 PYSDQEIANILKEKGFKVARRTV   59 (76)
T ss_dssp             CCCHHHHHHHHTTTSSCCCHHHH
T ss_pred             CCCHHHHHHHHHHCCCCEEHHHH
T ss_conf             97699999999986995531619


No 21 
>3kxr_A Magnesium transporter, putative; cystathionine beta-synthase, Mg2+ transporter, structural genomics, PSI-2; 2.41A {Shewanella oneidensis mr-1}
Probab=20.76  E-value=40  Score=13.77  Aligned_cols=39  Identities=21%  Similarity=0.239  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             999887654321000255654310034107899999986
Q gi|254780331|r   79 EGISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIE  117 (179)
Q Consensus        79 ~~~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~  117 (179)
                      ...+..+....+..--=++++|+|-|-||..||.+.+.+
T Consensus       136 ~ea~~~~~~~~~~~lPVVD~~g~lvGiIt~~Dil~~i~e  174 (205)
T 3kxr_A          136 LDAAEAIEHSREIELPVIDDAGELIGRVTLRAATALVRE  174 (205)
T ss_dssp             HHHHHHHHTSSCSEEEEECTTSBEEEEEEHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCEEEEECCCCEEEEEEEHHHHHHHHHH
T ss_conf             999999997697365388759989999889999999999


No 22 
>2uv4_A 5'-AMP-activated protein kinase subunit gamma-1; transferase, CBS domain, lipid synthesis, fatty acid biosynthesis; HET: AMP; 1.33A {Homo sapiens} PDB: 2uv5_A* 2uv6_A* 2uv7_A*
Probab=20.49  E-value=40  Score=13.74  Aligned_cols=22  Identities=23%  Similarity=0.315  Sum_probs=15.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             6543100341078999999860
Q gi|254780331|r   97 GDTGYLYGSVSSRDIADLLIEE  118 (179)
Q Consensus        97 ~e~gkLfGsVt~~dI~~~L~~~  118 (179)
                      +++|++.|-||..||...+...
T Consensus        59 d~~~~lvGiit~~di~~~~~~~   80 (152)
T 2uv4_A           59 DEKGRVVDIYSKFDVINLAAEK   80 (152)
T ss_dssp             CTTSBEEEEEEHHHHHHHHHCS
T ss_pred             CCCCCEEEEEEHHHHHHHHHCC
T ss_conf             0898199999623226676505


Done!