Query         gi|254780261|ref|YP_003064674.1| 50S ribosomal protein L3 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 221
No_of_seqs    143 out of 1792
Neff          5.6 
Searched_HMMs 23785
Date          Tue May 24 08:23:15 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780261.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3ofq_D 50S ribosomal protein L 100.0       0       0  581.5  15.6  209    2-212     1-209 (209)
  2 2ftc_C L3MT, MRP-L3, mitochond 100.0       0       0  563.2  20.1  209    2-213     1-211 (211)
  3 3bbo_F Ribosomal protein L3; l 100.0       0       0  580.0   4.3  211    1-214    42-254 (259)
  4 2zjr_B 50S ribosomal protein L 100.0       0       0  557.9  16.5  210    2-218     1-210 (211)
  5 2j01_E 50S ribosomal protein L 100.0       0       0  559.0   7.9  205    2-213     1-205 (206)
  6 1vq8_B 50S ribosomal protein L 100.0       0       0  500.7  14.7  214    2-217    39-323 (338)
  7 3jyw_C 60S ribosomal protein L 100.0       0       0  478.6  13.0  211    2-216    39-344 (362)
  8 2zkr_b 60S ribosomal protein L 100.0       0       0  475.4  12.3  209    2-214    43-355 (403)
  9 3kh0_A Ralgds, ralgef, RAL gua  29.6      15 0.00065   16.3   1.2   43   29-75     21-65  (140)
 10 1rax_A Protein (RA-domain of R  28.2      24   0.001   15.2   2.0   48   21-68     16-65  (115)
 11 1ef5_A RGL; RAS-binding domain  23.7      21 0.00088   15.6   1.0   49   23-75      8-58  (103)

No 1  
>3ofq_D 50S ribosomal protein L3; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_B 1p86_B 1vs8_D 1vs6_D 2aw4_D 2awb_D 2gya_B 2gyc_B 1vt2_D 2i2v_D 2j28_D 2i2t_D* 2qao_D* 2qba_D* 2qbc_D* 2qbe_D 2qbg_D 2qbi_D* 2qbk_D* 2qov_D ...
Probab=100.00  E-value=0  Score=581.55  Aligned_cols=209  Identities=45%  Similarity=0.741  Sum_probs=203.4

Q ss_pred             CCCEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCEEE
Q ss_conf             44268996584516988987922689991797899997067788612564055556431571011257640356341036
Q gi|254780261|r    2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLF   81 (221)
Q Consensus         2 r~Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~l~   81 (221)
                      +.||||+|+||||+||+||+++||||||++||+|+|+||.|+|||+|+|+++++.++++++||++|||++++++|+++++
T Consensus         1 m~Glig~KvGMT~v~~~~G~~vPVTVie~~p~~V~~~kt~ekdgY~a~q~g~~~~~~k~~~Kp~~g~~~k~~~~~~~~l~   80 (209)
T 3ofq_D            1 MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLW   80 (209)
T ss_dssp             CCCEEEEECCCBCCCCSSCCCCCEEEEECCCBEEEECCCSSSSSCCEEEEECSCCCTTTCCHHHHHHHHHSCCCCCSCCE
T ss_pred             CCEEEEEECCCCEEECCCCEEEEEEEEEECCCEEEEEEEECCCCCEEEEEEEEECCCCCCCHHHHCCHHHCCCCCCCEEE
T ss_conf             91598997688448899990998799996598999998566789676898230012331685362563231667550489


Q ss_pred             EEECCCCHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCC
Q ss_conf             53206511211003410001230253265789875343364057504421233357745434666555556752242267
Q gi|254780261|r   82 EFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNK  161 (221)
Q Consensus        82 Efrv~~~~~~~~vG~~i~~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGk  161 (221)
                      |||+++++ .+++|++|++|+|++||+|||+|+||||||||+||||||+++|+|||+|++||+|||||++|+|||||||+
T Consensus        81 e~~~~~~~-~~~~G~~~~~~~F~~Gq~VDV~g~tkGKGFqGv~KR~gf~g~p~sHg~s~~hR~~Gs~G~~~~PgrV~kgk  159 (209)
T 3ofq_D           81 EFRLAEGE-EFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGK  159 (209)
T ss_dssp             EEECSSCC-CCSSCCCBCGGGGSSCCCCCCEECCCCCBSCCTTTSSCCCCCCSSSSCCSCSSCCCCSSCSTTTCSCCTTC
T ss_pred             EEECCCHH-HCCCCCEEEEEEECCCCEEEEEEEECCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             97137655-41477632112244897689999981643444067644467985568985465887766789897388897


Q ss_pred             CCCCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEEECCCC
Q ss_conf             666523773336516589998076898999715745888709999603146
Q gi|254780261|r  162 KMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKS  212 (221)
Q Consensus       162 km~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir~a~k~  212 (221)
                      |||||||++++|++||+|++||+|+|||||||||||| ++++|+||+|+|+
T Consensus       160 kmaG~mG~~~~T~~Nl~Vv~id~e~n~i~vkGsVPG~-~~~~V~ir~aik~  209 (209)
T 3ofq_D          160 KMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGA-TGSDLIVKPAVKA  209 (209)
T ss_dssp             CCCCCBSCCCCCCTTCEEEEEETTTTEEEEESCCSSC-TTCEEEECCCSCC
T ss_pred             CCCCCCCCCEEEEECCEEEEEECCCCEEEEEECCCCC-CCCEEEEEECCCC
T ss_conf             2487458734987357999995889999997478789-9999998746359


No 2  
>2ftc_C L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus}
Probab=100.00  E-value=0  Score=563.21  Aligned_cols=209  Identities=33%  Similarity=0.547  Sum_probs=197.8

Q ss_pred             CCCEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCEEEEECCCCCC--CCCCCCCHHHHHHHHCCCCCCE
Q ss_conf             44268996584516988987922689991797899997067788612564055556--4315710112576403563410
Q gi|254780261|r    2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAK--VKNVSKPMRGFFSSVNVSPKKK   79 (221)
Q Consensus         2 r~Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~~k--~k~~~Kp~~G~fkK~g~~pk~~   79 (221)
                      |+||||+|+||||+|||||.++||||||++||.|++++|.|+|+|.++||+++..+  ..+.+++.++||+|++++|+++
T Consensus         1 R~Glig~KiGMT~if~~~G~~vpVTVlev~p~~Vv~~kt~e~~~~~~~~v~~g~~~~~~~~k~k~~~g~~~k~~~~~k~~   80 (211)
T 2ftc_C            1 RVGLIALKLGMMPLWTKDGQKHVVTLLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQT   80 (211)
T ss_pred             CEEEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEEEECCCCCEEEEEECCEECCCCCCCCHHCCCHHHCCCCCCEE
T ss_conf             91899996587077889996988899996288899998640458716777307500100012200104054507887603


Q ss_pred             EEEEECCCCHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC
Q ss_conf             36532065112110034100012302532657898753433640575044212333577454346665555567522422
Q gi|254780261|r   80 LFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFK  159 (221)
Q Consensus        80 l~Efrv~~~~~~~~vG~~i~~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~k  159 (221)
                      ++|||++++ +.+++|++|++|+|++||+|||+|+||||||||+||||||+++|+|||+|++||+|||||+ ++||||||
T Consensus        81 l~Efrv~~~-~~~~~G~~i~v~~F~~Gq~VdVtg~SKGKGFqGvmKRh~F~g~~~sHG~s~~hR~~GSiG~-~~pgRV~k  158 (211)
T 2ftc_C           81 VKIFNITDN-AAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRPGAVAT-GDIGRVWP  158 (211)
T ss_pred             EEEEECCCC-CCCCCCCEEECHHHCCCCEEEEEEEECCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCC
T ss_conf             799963764-0102676078453448853898998758644650545676657743467765757851345-65887885


Q ss_pred             CCCCCCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEEECCCCC
Q ss_conf             676665237733365165899980768989997157458887099996031467
Q gi|254780261|r  160 NKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSA  213 (221)
Q Consensus       160 Gkkm~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir~a~k~~  213 (221)
                      |+|||||||++++|++||+|++||+|+|||||||||||| ++++|+||+|++++
T Consensus       159 GkkM~G~mG~~~~T~~nl~vv~id~e~n~i~vkGsVPG~-~~~~V~ir~a~~pa  211 (211)
T 2ftc_C          159 GTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGH-KNCLVKVKDSKLPA  211 (211)
T ss_pred             CCCCCCCCCCCEEEEECCEEEEEECCCCEEEEEECCCCC-CCCEEEEEECCCCC
T ss_conf             773477437725988288999995878989994168689-99899997366589


No 3  
>3bbo_F Ribosomal protein L3; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Nicotiana tabacum}
Probab=100.00  E-value=0  Score=580.02  Aligned_cols=211  Identities=39%  Similarity=0.666  Sum_probs=201.0

Q ss_pred             CCCCEEEEECCCCEEECCCCCEEEEEEEEECCCEEE-EEEECCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCE
Q ss_conf             944268996584516988987922689991797899-9970677886125640555564315710112576403563410
Q gi|254780261|r    1 MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVV-VHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKK   79 (221)
Q Consensus         1 mr~Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv-~~kt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~   79 (221)
                      +++||||+|+||||+||+||.++||||||++||.|+ |+||.|+|||+|+||||++.++++++||++|||+|++++|+++
T Consensus        42 ~~iGliG~KvGMT~if~~~G~~vPVTViev~p~~VV~qvkt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~f~ka~~~pk~~  121 (259)
T 3bbo_F           42 AGVGVMATKLGMMSFFEESGTVVPVTVVGFREGNIVTQIKTEATDGYNAVQVGYRRVRDRKLTKPEMGHLEKSGIIPLRH  121 (259)
T ss_dssp             ---------------------------------------------------------CCSSCCHHHHTTCSSCCCCCSSC
T ss_pred             CCEEEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEECCCCCCCCEEEEEEEEECCCCCCCHHHHCCHHHCCCCCCEE
T ss_conf             36379999668847888999299779999579969988545455894489999987355235966836702202251014


Q ss_pred             EEEEECCCCHHHHHCCCCEEE-EEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE
Q ss_conf             365320651121100341000-1230253265789875343364057504421233357745434666555556752242
Q gi|254780261|r   80 LFEFRVQKDDDLLPVGSVFSP-SYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVF  158 (221)
Q Consensus        80 l~Efrv~~~~~~~~vG~~i~~-~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~  158 (221)
                      +.||+++++++ +++|++|++ |+|++||+|||+|+|||||||||||||||+|+|+||| |++||+|||||+||+|||||
T Consensus       122 ~~ef~~~~~~~-~~~G~~i~v~~~F~~Gq~VDVtg~SKGKGFqGvmKRhgF~g~pasHG-~~~hR~~GSiG~~~~PgRV~  199 (259)
T 3bbo_F          122 LQEFRLQSIDG-FEVTQKLDFGELFKEGDLVDVSGTTIGKGFQGGIKRHNFKRGQMTHG-SKSHRQLGSIGAGTTPGRVY  199 (259)
T ss_dssp             CCCCCSCCCCT-TTTCCCCSSCSSSCSSSCCCCCCBCCCCSSCCSSSSSCCCCCCSSSC-SSTTTSCCCCSCSSCCTTTT
T ss_pred             EEEEECCCCHH-CCCCCEECHHHHCCCCCEEEEEEEEECCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCCCCCEEC
T ss_conf             44442023000-03565442899435887788799981753665235636456675678-98786688647788898581


Q ss_pred             CCCCCCCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEEECCCCCC
Q ss_conf             26766652377333651658999807689899971574588870999960314677
Q gi|254780261|r  159 KNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAV  214 (221)
Q Consensus       159 kGkkm~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir~a~k~~~  214 (221)
                      ||+|||||||++++|++||+|++||+|+|||||||||||+ +|++|+||||++...
T Consensus       200 kGkkMaG~mG~~~~Tv~Nl~Vv~Id~e~nlilVkGsVPG~-~g~~V~Ir~a~~~~k  254 (259)
T 3bbo_F          200 KGKKMPGRMGGTKRKIRKLKIVKIDDQLNIIMIKGALPGK-PGNLLRIAPAKIVGK  254 (259)
T ss_dssp             TTSCCCCCCCCCBCCCCCCCEEEEETTTTEEEECSCCSSC-SSSCCCCCCCCCC--
T ss_pred             CCCCCCCCCCCCEEEEECCEEEEECCCCCEEEEEECCCCC-CCCEEEEEECCCCCC
T ss_conf             5876687618853898556999982889989993168789-998899976775688


No 4  
>2zjr_B 50S ribosomal protein L3; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.43.3.2 PDB: 1nwx_B* 1nwy_B* 1sm1_B* 1xbp_B* 2ogm_B* 2ogn_B* 2ogo_B* 2zjp_B* 2zjq_B 1nkw_B 3cf5_B* 3dll_B* 1pnu_B 1pny_B 1vor_E 1vou_E 1vow_E 1voy_E 1vp0_E
Probab=100.00  E-value=0  Score=557.86  Aligned_cols=210  Identities=43%  Similarity=0.710  Sum_probs=200.1

Q ss_pred             CCCEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCEEE
Q ss_conf             44268996584516988987922689991797899997067788612564055556431571011257640356341036
Q gi|254780261|r    2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLF   81 (221)
Q Consensus         2 r~Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~l~   81 (221)
                      +.||||+|+||||+||+ |.++||||||++||.|+++||.|+|||+|+||+|++.++++++||+++||+|++++|++++.
T Consensus         1 m~Glig~KiGMT~i~~~-g~~vpVTVlev~~~~Vv~~kt~ekdGY~avqvg~~~~~~k~~~K~~~g~~~k~~~~~~~~~~   79 (211)
T 2zjr_B            1 MKGILGTKIGMTQIWKN-DRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILR   79 (211)
T ss_dssp             CCEEEEEEEEEEEEEET-TEEEEEEEEECCCEEEEEEECTTTTSSCEEEEECSCCCGGGCCHHHHHHHHTTTCCCCSCEE
T ss_pred             CCEEEEEECCCEEEEEC-CCEEEEEEEEECCCEEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCEEECCCCCCCCEE
T ss_conf             94697994467048848-99898899995798899988114479720003576423323364214644313877420001


Q ss_pred             EEECCCCHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCC
Q ss_conf             53206511211003410001230253265789875343364057504421233357745434666555556752242267
Q gi|254780261|r   82 EFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNK  161 (221)
Q Consensus        82 Efrv~~~~~~~~vG~~i~~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGk  161 (221)
                      |||+.     ++.|+++++++|++||+|||+|+|||||||||||||||+++|+|||+|++||+|||||++++|||||||+
T Consensus        80 ef~~~-----~~~g~~~~~~~F~~Gq~VDV~g~SKGKGFqGv~KRhgf~g~p~sHG~s~~hR~~GsiG~~~~PgRV~kgk  154 (211)
T 2zjr_B           80 EFRGF-----APDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGK  154 (211)
T ss_dssp             EETTC-----CCSSEECSTTTSCTTCEEEEEEECCEEEEECHHHHHCCCCCCSSSSCSSCSCSCCCCCCSSTTCSCCTTC
T ss_pred             ECCCC-----CCCCCEEEHHHCCCCCEEEEEEEEECCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCC
T ss_conf             00124-----4678798114616998899999861541233067615577886578984354687668889887087788


Q ss_pred             CCCCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEEECCCCCCCCCC
Q ss_conf             666523773336516589998076898999715745888709999603146778532
Q gi|254780261|r  162 KMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCKG  218 (221)
Q Consensus       162 km~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir~a~k~~~~~k~  218 (221)
                      |||||||++++|++||+|++||+|+|||||||||||| ++++|+||||+|+..+..+
T Consensus       155 kMaG~mG~~~~T~~nl~V~~id~~~n~i~vkGsVPG~-~~~~v~ir~a~k~~~~k~~  210 (211)
T 2zjr_B          155 RMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGA-NGGLVVLRSAAKASAAKGG  210 (211)
T ss_dssp             CCCEEEECCEEEEEEEEEEEEETTTTEEEEESCCSSC-TTCEEEEEBCSSCC-----
T ss_pred             CCCCCCCCCEEEECCCEEEEEECCCCEEEEECCCCCC-CCCEEEEEECCCCCCCCCC
T ss_conf             4477447603887187899995889989995067689-9989999845467767668


No 5  
>2j01_E 50S ribosomal protein L3; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: b.43.3.2 PDB: 1vsp_C 2hgj_E 2hgq_E 2hgu_E 1vsa_C 2j03_E 2jl6_E 2jl8_E 2v47_E 2v49_E 2wdi_E 2wdj_E 2wdl_E 2wdn_E 2wh2_E 2wh4_E 2wrj_E 2wrl_E 2wro_E 2wrr_E ...
Probab=100.00  E-value=0  Score=559.02  Aligned_cols=205  Identities=45%  Similarity=0.745  Sum_probs=197.3

Q ss_pred             CCCEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCEEE
Q ss_conf             44268996584516988987922689991797899997067788612564055556431571011257640356341036
Q gi|254780261|r    2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLF   81 (221)
Q Consensus         2 r~Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~l~   81 (221)
                      +.||||+|+||||+|| ||.++||||||++||+|+++||.|+|||+|+||+|++.++++++||++|||+|++++|++++.
T Consensus         1 m~Glig~KiGMT~if~-~g~~vpVTVlev~p~~V~~~kt~ekdGY~avqlg~~~~k~~~~~K~~~g~~~k~~~~~~~~~~   79 (206)
T 2j01_E            1 MKGILGVKVGMTRIFR-DDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVNRPLKGHFAKAGVEPVRILR   79 (206)
T ss_dssp             CCCCEEEEEEEEEEEE-TTEEEEEEEEEECCBCCCCBCCTTTTSSCCBCCCCCCCCCSTTCSCCCCCSGGGSSCCSSCCC
T ss_pred             CCEEEEEECCCEEEEE-CCCEEEEEEEEECCCEEEEEEEECCCCCEEEEEEEEECCCCCCCHHHCCCCCCCCCCCCEEEE
T ss_conf             9458699448844983-899896899995797899988102689421677453302331485232642226898526788


Q ss_pred             EEECCCCHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCC
Q ss_conf             53206511211003410001230253265789875343364057504421233357745434666555556752242267
Q gi|254780261|r   82 EFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNK  161 (221)
Q Consensus        82 Efrv~~~~~~~~vG~~i~~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGk  161 (221)
                      |||...     +.|++|++|+|++||+|||+|+||||||||+||||||+++|+|||+|++||+|||||+|++|||||||+
T Consensus        80 e~~~~~-----~~~~~i~~~~F~~G~~VDV~g~skGKGFqGv~KR~gf~g~p~sHG~s~~hR~~GsiG~~~~PgRV~kgk  154 (206)
T 2j01_E           80 EIRDFN-----PEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGK  154 (206)
T ss_dssp             CCTTCC-----CCSSCBCSTTCCTTCEECCEEECCCCCEECTTTSSCCCCCCSSSSCSSCSSCCCCCCCSTTTCSCCTTC
T ss_pred             EEECCC-----CCCCEEEEHHCCCCCEEEEEEEEECCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             730355-----777698603306886268888882553556355167778986568995376677777788786276898


Q ss_pred             CCCCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEEECCCCC
Q ss_conf             6665237733365165899980768989997157458887099996031467
Q gi|254780261|r  162 KMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSA  213 (221)
Q Consensus       162 km~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir~a~k~~  213 (221)
                      |||||||++++|++||+|++||+|+|||||||||||| ++++|+||||+|+.
T Consensus       155 kMaG~mG~~~~T~~nl~V~~id~e~nli~vkGsVPG~-~~~~V~ir~a~k~~  205 (206)
T 2j01_E          155 KMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGP-NGGLVIVRETKKAA  205 (206)
T ss_dssp             CCSEECSSCEEECCCEECCCCCTTTTCEECCSCCCSC-SSEEEECCCCCCC-
T ss_pred             CCCCCCCCEEEEECCCEEEEEECCCCEEEEEECCCCC-CCCEEEEEECEECC
T ss_conf             7688758802887188999996879999996167689-99899998443247


No 6  
>1vq8_B 50S ribosomal protein L3P; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: b.43.3.2 PDB: 1vq4_B* 1vq5_B* 1vq6_B* 1vq7_B* 1s72_B* 1vq9_B* 1vqk_B* 1vql_B* 1vqm_B* 1vqn_B* 1vqo_B* 1vqp_B* 1yhq_B* 1yi2_B* 1yij_B* 1yit_B* 1yj9_B* 1yjn_B* 1yjw_B* 2otj_B* ...
Probab=100.00  E-value=0  Score=500.67  Aligned_cols=214  Identities=24%  Similarity=0.321  Sum_probs=188.8

Q ss_pred             CCCEEEEECCCCEEECCCCC----------EEEEEEEEECCCEEEEEEECCCCCCEEEEECCC------CCCCCCCCCCH
Q ss_conf             44268996584516988987----------922689991797899997067788612564055------55643157101
Q gi|254780261|r    2 RSGVVARKLGMTCVYNIEGR----------RIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAG------EAKVKNVSKPM   65 (221)
Q Consensus         2 r~Glig~KiGMT~if~e~G~----------~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~------~~k~k~~~Kp~   65 (221)
                      ..||||+|+||||+|++||.          .+||||||++||.|+|+||+|+|||.|+|||+.      +...+++++|+
T Consensus        39 l~G~iG~KvGMT~v~~~d~~~~s~~~g~~i~vPVTVIe~~P~~Vv~ikt~~kdgy~avqlg~~~~~~~~~~~~r~~~~~~  118 (338)
T 1vq8_B           39 VQGFAGYKAGMTHVVLVNDEPNSPREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRPLTEVWTDEFHSELDRTLDVPE  118 (338)
T ss_dssp             ECCEEEEEEEEEEEEEECCCTTCTTTTSEEEEEEEEEECCCEEEEEEEEEEEETTEEEEEEEEECSCCCTTGGGTSCCCS
T ss_pred             EEEEEEECCCCEEEEEECCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEEECCCCCEEEEEEEEECCCCHHHHHCCCHHH
T ss_conf             37886870374599972797577545751577679998388389999736227983399999860244424310366333


Q ss_pred             HHHHHHHCC----------------------------C-CCCEEEEEECCCC---------HHHHHCCCCEEE-EEECCC
Q ss_conf             125764035----------------------------6-3410365320651---------121100341000-123025
Q gi|254780261|r   66 RGFFSSVNV----------------------------S-PKKKLFEFRVQKD---------DDLLPVGSVFSP-SYFTVG  106 (221)
Q Consensus        66 ~G~fkK~g~----------------------------~-pk~~l~Efrv~~~---------~~~~~vG~~i~~-~~F~~G  106 (221)
                      .++++++..                            + .+.++.||++...         .+.+++|++|.+ |+|++|
T Consensus       119 ~~~~k~~~~~~k~~~e~~~~~~irvi~~t~p~~~~~~~~Kk~~i~E~~v~G~~~~~k~~~~~~~~~~G~ei~v~dvF~~G  198 (338)
T 1vq8_B          119 DHDPDAAEEQIRDAHEAGDLGDLRLITHTVPDAVPSVPKKKPDVMETRVGGGSVSDRLDHALDIVEDGGEHAMNDIFRAG  198 (338)
T ss_dssp             SCCHHHHHHHHHHHHHHTCEEEEEEEEECCGGGCTTSCCCSCCEEEEEEECSCHHHHHHHHHHHHHHTCEECSTTTCCTT
T ss_pred             CCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCHHEEEECCCCCHHHHHHHHHHHCCCCCEEEEEEEEECC
T ss_conf             45633301567655552464048988410642023424467201256316885334222334320357468844123089


Q ss_pred             CEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEEEEECCCEEEEE----
Q ss_conf             3265789875343364057504421233357745434666555556752242267666523773336516589998----
Q gi|254780261|r  107 QLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSV----  182 (221)
Q Consensus       107 q~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGkkm~G~mG~~~~T~~nl~i~~i----  182 (221)
                      |+|||+|+||||||||+||||||+++|+|||++++||++||||+ |+|+|||||++|||||||++||++||+|++|    
T Consensus       199 ~~VDV~g~TKGKGFqGv~KR~gf~g~p~sHg~~~~hR~~GsiG~-~~PgRV~kg~kmaGqmG~~~rT~~Nl~Iv~I~~~~  277 (338)
T 1vq8_B          199 EYADVAGVTKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNLGP-WNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGEGD  277 (338)
T ss_dssp             CEEEEEEECCCCCEECHHHHHCCCCCCGGGGSSSCSSCCSCSCC-SSSSSCCTTSCCCEECSCCEEEEEEEEEEEEEEES
T ss_pred             CEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCEEEECCEEEEECCCC
T ss_conf             88999998605555201787021356865688887868834788-88985747886698868863798343999972765


Q ss_pred             ------------ECCCCEEEEECCCCCCCCCEEEEEEECCCCCCCCC
Q ss_conf             ------------07689899971574588870999960314677853
Q gi|254780261|r  183 ------------DDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCK  217 (221)
Q Consensus       183 ------------d~e~n~i~vkGsVPG~~~~~~v~ir~a~k~~~~~k  217 (221)
                                  |.|+|||||||||||| ++++|+||+|+|+....+
T Consensus       278 ~~n~~gGf~~ygd~e~n~ilVKGsVPG~-~~~~v~ir~a~k~~~~~~  323 (338)
T 1vq8_B          278 EPTVDGGFVNYGEVDGPYTLVKGSVPGP-DKRLVRFRPAVRPNDQPR  323 (338)
T ss_dssp             SSCCTTCBTTTBCCCEEEEEEESCCSSC-TTCEEEEEECSSCSSCCC
T ss_pred             CCCCCCCCEEEEECCCCEEEEEECCCCC-CCCEEEEECCCCCCCCCC
T ss_conf             5445677203313138889998456588-994899930236787666


No 7  
>3jyw_C 60S ribosomal protein L3; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_C
Probab=100.00  E-value=0  Score=478.56  Aligned_cols=211  Identities=21%  Similarity=0.201  Sum_probs=175.0

Q ss_pred             CCCEEEEECCCCEEECCC----------CCEEEEEEEEECCCEEEEEEECCCCCCEEEEECC--CCCCC-----------
Q ss_conf             442689965845169889----------8792268999179789999706778861256405--55564-----------
Q gi|254780261|r    2 RSGVVARKLGMTCVYNIE----------GRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGA--GEAKV-----------   58 (221)
Q Consensus         2 r~Glig~KiGMT~if~e~----------G~~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~--~~~k~-----------   58 (221)
                      ..||||+|+||||+|++|          |.++||||||++||.|+|+||+|+|||.|+||+.  .+..+           
T Consensus        39 l~G~iG~KvGMTqVf~~d~r~~s~~~g~g~~vPVTVIe~~P~~V~~vkt~e~dgY~avqlg~v~~~~~~~~~~r~~~~~~  118 (362)
T 3jyw_C           39 LTSFLGYKAGMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKNW  118 (362)
T ss_dssp             ESBCCEECCCBCCCCBCCSSTTCTTTTCCBCCCCEEEECCCCEEEEEECCBCCSSSSCCSCEEECSSCCSTTTTTSSCCC
T ss_pred             EEEEEEECCCCEEEEEECCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEEEECCCCCEEEEEEECCCCCHHHHHHHCCCC
T ss_conf             57886881474499971687787557861488778998589689999737606985478789860026445542212322


Q ss_pred             -----CCCCCC------HHHHHHHHCCCCCCEEEEEEC-----------------------CCC-------HHHHHCCCC
Q ss_conf             -----315710------112576403563410365320-----------------------651-------121100341
Q gi|254780261|r   59 -----KNVSKP------MRGFFSSVNVSPKKKLFEFRV-----------------------QKD-------DDLLPVGSV   97 (221)
Q Consensus        59 -----k~~~Kp------~~G~fkK~g~~pk~~l~Efrv-----------------------~~~-------~~~~~vG~~   97 (221)
                           +..+++      ..+++.+...++++++.|||+                       ...       .....+|++
T Consensus       119 ~~~~~~~~~k~~~~~~~~~~~~~k~~~~~k~~~~e~Rvi~~tqp~~~~~~kKkp~~~E~~v~G~~~~e~~~~a~~~lg~e  198 (362)
T 3jyw_C          119 YKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEKT  198 (362)
T ss_dssp             SSSCCCCSCCSCCSCSCTTHHHHHHHTTTTSCBCCCEEEEECCCTTSSCCCCSCCEEEEEEEESSTTHHHHGGGTTTTSB
T ss_pred             CCCHHHHCCCHHCCCCCCCCHHHHHHHHHHHCCEEEEEEEECCHHHCCCCCCCCCCEEEECCCCCHHHHHHHHHHHCCCE
T ss_conf             10002320310002221122166766655312206888851241003654357520011026754555566677622760


Q ss_pred             EEE-EEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEEEEECC
Q ss_conf             000-1230253265789875343364057504421233357745434666555556752242267666523773336516
Q gi|254780261|r   98 FSP-SYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKN  176 (221)
Q Consensus        98 i~~-~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGkkm~G~mG~~~~T~~n  176 (221)
                      |.+ |+|++||+|||+|+||||||||+||||||+++|++|  |++||++||||++ +|||||||++||||||+++||++|
T Consensus       199 i~v~dvF~~G~~VDV~GvTKGKGFqGvvKR~gf~~~~~~H--~k~hR~~GSiG~~-~PgrV~kgkkmaGqmG~~~rTv~N  275 (362)
T 3jyw_C          199 VAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKT--HRGLRKVACIGAW-HPAHVMWSVARAGQRGYHSRTSIN  275 (362)
T ss_dssp             CCSTTTCCTTSCEEEEEECCBCCSCCHHHHTCCCCCSSCC--SSCSSCCSCSSCS-SSSCCCTTCCCCCCCBCSEEEEEE
T ss_pred             EEEEEECCCCCEEEEEEEECCCCCCCCEEECCCCCCCCCC--CCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCEEEEEEC
T ss_conf             5642001699889999875475554325664657899877--8888889866899-997377898348776983698843


Q ss_pred             CEEEEEECC------------------------------CCEEEEECCCCCCCCCEEEEEEECCCCCCCC
Q ss_conf             589998076------------------------------8989997157458887099996031467785
Q gi|254780261|r  177 LEVVSVDDK------------------------------RGLILVKGCVPGAKKNSWILVRDSFKSAVNC  216 (221)
Q Consensus       177 l~i~~id~e------------------------------~n~i~vkGsVPG~~~~~~v~ir~a~k~~~~~  216 (221)
                      |+|++||.+                              +|||||||||||| ++++|+||+|+++....
T Consensus       276 l~v~~i~~~~~~~~~~~~~d~~~~~i~p~ggf~~YG~V~~n~ilvkGsvpG~-~~~~v~~r~~~~~~~~~  344 (362)
T 3jyw_C          276 HKIYRVGKGDDEANGATSFDRTKKTITPMGGFVHYGEIKNDFIMVKGCIPGN-RKRIVTLRKSLYTNTSR  344 (362)
T ss_dssp             ECEEEEESSSCCCCCCSSCSSCSCBSSSSSCCSSSCCCCSCEEEESSCCSCC-SSCEECCEECSSCCSCC
T ss_pred             CEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCEEEEEECCCCC-CCCEEEECHHCCCCCCC
T ss_conf             3999977855555543222333421134777543541427889998246578-89479981000567764


No 8  
>2zkr_b 60S ribosomal protein L3; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}
Probab=100.00  E-value=0  Score=475.41  Aligned_cols=209  Identities=21%  Similarity=0.249  Sum_probs=176.1

Q ss_pred             CCCEEEEECCCCEEECCCCC----------EEEEEEEEECCCEEEEEEECCCCCCEEEEECCCC--------------CC
Q ss_conf             44268996584516988987----------9226899917978999970677886125640555--------------56
Q gi|254780261|r    2 RSGVVARKLGMTCVYNIEGR----------RIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGE--------------AK   57 (221)
Q Consensus         2 r~Glig~KiGMT~if~e~G~----------~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~--------------~k   57 (221)
                      ..||||+|+||||+|++|++          ++||||||++||.|+|+||+|+|||.|+|||+.+              ..
T Consensus        43 l~GfiG~K~GMThVf~~d~r~~S~~~gkgi~vPVTVIE~pP~~V~~vktye~dgY~a~qlg~v~a~~~~~~~~rr~~k~~  122 (403)
T 2zkr_b           43 LTAFLGYKAGMTHIVREVDRPGSKVNKKEVVEAVTIVETPPMVIVGIVGYVETPRGLRTFKTIFAEHISDECKRRFYKNW  122 (403)
T ss_dssp             GGSCEEEEEEEEEEEEECCCTTSTTCSCEEEEEEEEEECCCBEEEEEEEEEEETTEEEEEEEEECSCCCGGGGCCCCCCS
T ss_pred             EEEEEEEECCCEEEEEECCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHCCC
T ss_conf             57886880374389963687687557875699789998788589999746406985479899860015346543320000


Q ss_pred             CCCCCCCHHHHHHHHC----------------------------------CC-CCCEEEEEECCCCH--H-----HHHCC
Q ss_conf             4315710112576403----------------------------------56-34103653206511--2-----11003
Q gi|254780261|r   58 VKNVSKPMRGFFSSVN----------------------------------VS-PKKKLFEFRVQKDD--D-----LLPVG   95 (221)
Q Consensus        58 ~k~~~Kp~~G~fkK~g----------------------------------~~-pk~~l~Efrv~~~~--~-----~~~vG   95 (221)
                      .++.+++..+++++..                                  ++ .+.+|.||++...+  +     ...+|
T Consensus       123 ~~~~~k~~~k~~kk~~~~~g~~~~e~~~~~~k~~~~~~rvi~~T~p~~~~~~kKk~~l~E~~v~Gg~~~e~~~~a~~~~g  202 (403)
T 2zkr_b          123 HKSKKKAFTKYCKKWQDADGKKQLERDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEVQVNGGTVAEKLDWARERLE  202 (403)
T ss_dssp             SCCSCCCCCCCCCCCCCHHHHHHHHHHHHHHSCCCSSCEEEEECCGGGSSCSCCCCCCEEEEBCSSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHCCEEEEEEEEECCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             00000233100023344310345667666542010278887511431146666776427997378877776556764047


Q ss_pred             CCEEE-EEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEEEEE
Q ss_conf             41000-12302532657898753433640575044212333577454346665555567522422676665237733365
Q gi|254780261|r   96 SVFSP-SYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTV  174 (221)
Q Consensus        96 ~~i~~-~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGkkm~G~mG~~~~T~  174 (221)
                      ++|.+ |+|++||+|||+|+||||||||+||||||+++|  |++|++||++||||+ |+|+|||||++||||||+++||+
T Consensus       203 kei~v~dvF~~Ge~VDV~GvTKGKGFqGvVKR~Gf~~~p--hk~sk~hR~~GSiG~-~~P~RV~kg~kmaGqmG~~~rT~  279 (403)
T 2zkr_b          203 QQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP--RKTHRGLRKVACIGA-WHPARVAFSVARAGQKGYHHRTE  279 (403)
T ss_dssp             SCBCSTTTCCSSCCCCEEEECCEEEEECHHHHHCCCCCC--SSTTTTTTCCSCSSC-SSSCSCCTTSCCCEEEECCEEEE
T ss_pred             CEEEEEEEECCCCEEEEEEEEECCCCCCCEEECCCCCCC--CCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCEEEE
T ss_conf             536534542289879999876035544426743505688--778987727886579-99986436875577779965888


Q ss_pred             CCCEEEEEEC-------------------------------------CCCEEEEECCCCCCCCCEEEEEEECCCCCC
Q ss_conf             1658999807-------------------------------------689899971574588870999960314677
Q gi|254780261|r  175 KNLEVVSVDD-------------------------------------KRGLILVKGCVPGAKKNSWILVRDSFKSAV  214 (221)
Q Consensus       175 ~nl~i~~id~-------------------------------------e~n~i~vkGsVPG~~~~~~v~ir~a~k~~~  214 (221)
                      +||+|++||.                                     ++||||||||||||.+ .+|.||+|+++..
T Consensus       280 ~Nl~IvkIg~~~~~~~~~~~~~~~~t~~d~~~~~i~p~GGf~~YG~V~~~~ilvKGsVPGp~k-r~v~lR~avr~~~  355 (403)
T 2zkr_b          280 INKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKK-RVLTLRKSLLVQT  355 (403)
T ss_dssp             SCCCEEEEECCCCCCSSCCCCCTTCCCCCCSSCSCCSCCCBTTTBCCCSCEEEEESCCSSCTT-CEEECCCCC----
T ss_pred             ECCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCEEEEEECCCCCCC-CEEEECHHHCCCC
T ss_conf             423899977844444442234555433345554114578866563154878999703568788-2699733305676


No 9  
>3kh0_A Ralgds, ralgef, RAL guanine nucleotide dissociation stimulator; structural genomics consortium, SGC, RAS-association domain, alternative splicing; 2.10A {Homo sapiens} PDB: 2rgf_A 1lxd_A
Probab=29.56  E-value=15  Score=16.34  Aligned_cols=43  Identities=19%  Similarity=0.329  Sum_probs=29.8

Q ss_pred             EECCCEEEEEEECCCCC--CEEEEECCCCCCCCCCCCCHHHHHHHHCCC
Q ss_conf             91797899997067788--612564055556431571011257640356
Q gi|254780261|r   29 HLDNCQVVVHRTLDKNG--YMAVQVGAGEAKVKNVSKPMRGFFSSVNVS   75 (221)
Q Consensus        29 ev~~~~Vv~~kt~ekdG--Y~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~   75 (221)
                      |+++|.|+.+.-...+|  |.++.|...++.+.-+.++..    |.+++
T Consensus        21 Q~~d~~IIRVs~d~~~gnlYKSIllTsqDktP~VI~rAl~----Khnle   65 (140)
T 3kh0_A           21 QVGDCCIIRVSLDVDNGNMYKSILVTSQDKAPAVIRKAMD----KHNLE   65 (140)
T ss_dssp             SSSCEEEEEEEEECSSSEEEEEEEEETTCBHHHHHHHHHH----HTTCT
T ss_pred             CCCCEEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHH----HHCCC
T ss_conf             1797289999996699848988998428867799999999----82899


No 10 
>1rax_A Protein (RA-domain of RAL guanosine dissociation stimulator); RAS-binding domain, ralgef, ralgds, RAS; NMR {Homo sapiens} SCOP: d.15.1.5
Probab=28.21  E-value=24  Score=15.21  Aligned_cols=48  Identities=17%  Similarity=0.299  Sum_probs=34.6

Q ss_pred             CEEEEEEEEECCCEEEEEEECCCCC--CEEEEECCCCCCCCCCCCCHHHH
Q ss_conf             7922689991797899997067788--61256405555643157101125
Q gi|254780261|r   21 RRIPVTVLHLDNCQVVVHRTLDKNG--YMAVQVGAGEAKVKNVSKPMRGF   68 (221)
Q Consensus        21 ~~vpVTViev~~~~Vv~~kt~ekdG--Y~Avqvg~~~~k~k~~~Kp~~G~   68 (221)
                      ...|+---++++|.|+.+.-...+|  |.++.|...++.+.-+.+++..|
T Consensus        16 ~~~P~~nqq~~d~~IIRVs~d~~ngnlYKSIlltsqDktP~VI~rAl~Kh   65 (115)
T 1rax_A           16 SALPLYNQQVGDCCIIRVSLDVDNGNMYKSILVTSQDKAPAVIRKAMDKH   65 (115)
T ss_dssp             -------CCSSCEEEEEEEESSSSCCCCEEEEEETTCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHH
T ss_conf             77752356489708999998458984788899852886779999999980


No 11 
>1ef5_A RGL; RAS-binding domain, RAS, RBD, RA, riken structural genomics/proteomics initiative, RSGI, structural genomics, signaling protein; NMR {Mus musculus} SCOP: d.15.1.5
Probab=23.72  E-value=21  Score=15.57  Aligned_cols=49  Identities=16%  Similarity=0.277  Sum_probs=33.9

Q ss_pred             EEEEEEEECCCEEEEEEECCCCC--CEEEEECCCCCCCCCCCCCHHHHHHHHCCC
Q ss_conf             22689991797899997067788--612564055556431571011257640356
Q gi|254780261|r   23 IPVTVLHLDNCQVVVHRTLDKNG--YMAVQVGAGEAKVKNVSKPMRGFFSSVNVS   75 (221)
Q Consensus        23 vpVTViev~~~~Vv~~kt~ekdG--Y~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~   75 (221)
                      .|+--=|+++|.|+.+.-...+|  |.++.|...++.+.-+.++..    |.+++
T Consensus         8 ~p~~~qq~~d~~IIRVs~d~~~gn~YKSIlltsqDktP~VI~rAl~----Khnl~   58 (103)
T 1ef5_A            8 PPVYNQQNEDTCIIRISVEDNNGNMYKSIMLTSQDKTPAVIQRAMS----KHNLE   58 (103)
T ss_dssp             --------CCCCCEEEEESSCSSCCCCCBCCSSCCCTHHHHHHHTT----TTTCC
T ss_pred             CCCCCCCCCCCEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHH----HHCCC
T ss_conf             7510265898389999973699858888998528857799999999----81899


Done!