Query         gi|254780147|ref|YP_003064560.1| 50S ribosomal protein L11 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 142
No_of_seqs    113 out of 1395
Neff          5.5 
Searched_HMMs 23785
Date          Sun May 22 14:59:32 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780147.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3bbo_K Ribosomal protein L11;  100.0       0       0  365.6  10.1  140    1-141    72-211 (224)
  2 1mms_A Protein (ribosomal prot 100.0       0       0  358.9  15.4  140    2-142     1-140 (140)
  3 2ftc_G L11MT, MRP-L11, 39S rib 100.0       0       0  350.1  16.1  141    2-142     1-145 (145)
  4 3egv_B 50S ribosomal protein L 100.0       0       0  352.3   9.8  138    3-141     1-138 (146)
  5 1vq8_I 50S ribosomal protein L 100.0       0       0  351.7   7.5  137    5-142     1-137 (162)
  6 3ofq_I 50S ribosomal protein L 100.0       0       0  365.5 -15.0  141    2-142     1-141 (141)
  7 2zkr_i 60S ribosomal protein L 100.0       0       0  330.2   5.3  139    1-142     1-145 (165)
  8 3cjs_B 50S ribosomal protein L 100.0 2.9E-29 1.2E-33  192.3  10.2   71    3-74      2-72  (72)
  9 1wib_A 60S ribosomal protein L 100.0   2E-29 8.3E-34  193.3   3.4   78    5-85     15-92  (92)
 10 1hc8_A Ribosomal protein L11;   99.9 3.2E-28 1.3E-32  186.2   5.7   76   67-142     1-76  (76)
 11 1qa6_A Ribosomal protein L11;   99.9 3.9E-24 1.6E-28  162.0   5.3   67   72-138     1-67  (67)
 12 1no4_A Late, head morphogenesi  29.2      14 0.00058   17.2   0.9   25   26-50     26-50  (97)
 13 2vqe_M 30S ribosomal protein S  27.6      32  0.0014   15.0   3.2   52   73-130    26-78  (126)
 14 2k53_A A3DK08 protein; NESG, C  25.3      36  0.0015   14.8   4.2   37   13-49     30-66  (76)
 15 1hh2_P NUSA, N utilization sub  21.0      44  0.0018   14.3   5.2   69    9-78    233-316 (344)

No 1  
>3bbo_K Ribosomal protein L11; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Probab=100.00  E-value=0  Score=365.61  Aligned_cols=140  Identities=46%  Similarity=0.795  Sum_probs=138.0

Q ss_pred             CCCCEEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHH
Q ss_conf             98423689999994455668970446866429998999999999977543797513899983895299998597489999
Q gi|254780147|r    1 MAKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFL   80 (142)
Q Consensus         1 M~k~v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~li   80 (142)
                      |+|+++++|||+|+||+|+|+|||||+|||+|||+|+||+|||++|++|+ |++|||+|++|+||+|+|++++||+||||
T Consensus        72 ~aKkvv~~IKL~V~AGkA~PaPPlGPaLGp~GINi~~Fck~fN~~Tk~~k-G~~VpV~ItV~~Dksf~f~iktPptS~Li  150 (224)
T 3bbo_K           72 KAKKVIGVIKLALEAGKATPAPPVGPALGSKGVNIMAFCKDYNARTADKP-GFVIPVEITVFDDKSFTFILKTPPASVLL  150 (224)
T ss_dssp             CCCCCSSEEEECCBTTBCCCSTTTTTTTTTTSSCTTSSHHHHHHHGGGSC-SSBCCEEEEECSSSCEEEEECCCCTTHHH
T ss_pred             CCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC-CCCCCEEEEEECCCCEEEEECCCCHHHHH
T ss_conf             87347899999985474168998751013469899999999999973458-97443699997686279998699678998


Q ss_pred             HHHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEE
Q ss_conf             9633766678899963010125999999999988540678789999997743021452893
Q gi|254780147|r   81 KKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVV  141 (142)
Q Consensus        81 kk~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~  141 (142)
                      ++++|+++||++|+++++|+||++|+||||+.|++|+++.+|+++||+|+|||+||||+||
T Consensus       151 kkaagi~kGS~~p~~~~vG~ITl~qv~eIAk~K~~dlna~~L~aavK~VlGTArSMGI~Vd  211 (224)
T 3bbo_K          151 LKASGAEKGSKDPQMEKVGKITIDQLRGIATEKLPDLNCTTIESAMRIIAGTAANMGIDID  211 (224)
T ss_dssp             HHHHTCSSCCSSTTTSCCEEECHHHHHHHHHHTCTTSCCSSHHHHHHHHHHHHTTTTEEEC
T ss_pred             HHHCCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHEECEEEEE
T ss_conf             8643776678899861645763999999999987763652599999996822625868997


No 2  
>1mms_A Protein (ribosomal protein L11); RNA-protein complex, RNA, ribosome, translocation, thiostrepton; 2.57A {Thermotoga maritima} SCOP: a.4.7.1 d.47.1.1 PDB: 1mvr_L 1oln_A* 1giy_L 1mj1_L* 1ml5_l* 1yl3_L 2b66_K 2b9n_K 2b9p_K 2jq7_A* 2k3f_A 1eg0_K 1jqm_A 1jqs_A 1jqt_A 1r2w_A 1r2x_A 487d_L 1pn8_L 1pn7_L
Probab=100.00  E-value=0  Score=358.91  Aligned_cols=140  Identities=51%  Similarity=0.884  Sum_probs=137.8

Q ss_pred             CCCEEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHHH
Q ss_conf             84236899999944556689704468664299989999999999775437975138999838952999985974899999
Q gi|254780147|r    2 AKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLK   81 (142)
Q Consensus         2 ~k~v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~lik   81 (142)
                      ||++++.|+|+++||+|+|+|||||+|||+|||+|+||+|||++|++|+ |++|||+|++|+||+|+|++++||+||||+
T Consensus         1 aK~v~~~ikl~v~aG~A~p~Pplgp~LG~~Gin~~~f~k~fN~~T~~~~-g~~v~V~i~v~~dksf~~~v~~P~~s~li~   79 (140)
T 1mms_A            1 AKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKA-GMILPVVITVYEDKSFTFIIKTPPASFLLK   79 (140)
T ss_dssp             ------CEEEEEETTCCCCTTTTTHHHHTTTCCHHHHHHHHHHHTTTSC-SSEEEEEEEECTTSCEEEEECCCCHHHHHH
T ss_pred             CCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC-CCCEEEEEEEECCCCEEEEECCCCHHHHHH
T ss_conf             9716899999976575079998641013579898999999999986216-982138999957972799986997799998


Q ss_pred             HHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEEC
Q ss_conf             6337666788999630101259999999999885406787899999977430214528939
Q gi|254780147|r   82 KEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVVD  142 (142)
Q Consensus        82 k~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~~  142 (142)
                      +++|+++||++|+++++|+||++|+||||+.|++|+++++|+++||+|+||||||||+|||
T Consensus        80 k~~g~~kgs~~p~~~~vG~it~~~v~eIAk~K~~~~~~~~l~~~vk~VlGTa~SmGi~V~~  140 (140)
T 1mms_A           80 KAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVVD  140 (140)
T ss_dssp             HHHTCSSCCSSTTTSCCEEECHHHHHHHHHHHGGGCCCSSHHHHHHHHHHHHTTTTEEEC-
T ss_pred             HHCCCCCCCCCCCCCCCCEEEHHHHHHHHHHHHHHCCCCCHHHHHHHHHEEHEECEEEEEC
T ss_conf             7026667767999841518709999999999887607788999999534113457489989


No 3  
>2ftc_G L11MT, MRP-L11, 39S ribosomal protein L11, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_G
Probab=100.00  E-value=0  Score=350.07  Aligned_cols=141  Identities=38%  Similarity=0.746  Sum_probs=137.4

Q ss_pred             CCCEEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHHH
Q ss_conf             84236899999944556689704468664299989999999999775437975138999838952999985974899999
Q gi|254780147|r    2 AKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLK   81 (142)
Q Consensus         2 ~k~v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~lik   81 (142)
                      .|++.++|||+|+||+|+|+|||||+|||+|||+++||++||++|++|++|+++||+|++|+||+|+|++++||+||||+
T Consensus         1 k~~i~~vikl~v~aG~A~p~PplGp~LG~~Gin~~~f~k~fN~~Tk~~~~g~~v~v~i~v~~dksf~~~v~~P~~s~ll~   80 (145)
T 2ftc_G            1 KPEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDIKEGIPLPTKILVKPDRTFEIKIGQPTVSYFLK   80 (145)
T ss_pred             CCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCEEEEEECCCCHHHHHH
T ss_conf             97504999999856752789987521245698989999999998776439970679999947970999987998799999


Q ss_pred             HHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHH----CCCCCHHHHHHHHHHHEEECCEEEEC
Q ss_conf             63376667889996301012599999999998854----06787899999977430214528939
Q gi|254780147|r   82 KEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQD----MGAIDIEGAMRMVEGSACSMGISVVD  142 (142)
Q Consensus        82 k~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d----~~~~~l~~~vk~VlGTa~SmGi~V~~  142 (142)
                      +++|+++||++|+++++|+||++|+||||+.|++|    |++.+|+++||+|+||||||||+|+.
T Consensus        81 k~~g~~kgs~~p~~~~vG~it~~~v~eIAk~K~~d~~~~l~~~~l~~~vk~VlGTa~SmGi~V~k  145 (145)
T 2ftc_G           81 AAAGIEKGARQTGKEVAGLVTLKHVYEIARIKAQDEAFALQDVPLSSVVRSIIGSARSLGIRVVK  145 (145)
T ss_pred             HHCCCCCCCCCCCCEEEEEECHHHHHHHHHHHCCCCHHHCCCCCHHHHHHHHHHHHEECEEEEEC
T ss_conf             86288877555687676136399999999987706332335878999999988004347589979


No 4  
>3egv_B 50S ribosomal protein L11, ribosomal protein L11 methyltransferase; post-translational modification, multiple methyltransferase, cytoplasm; HET: SAH 4MM; 1.75A {Thermus thermophilus} SCOP: d.47.1.1 PDB: 2e34_A 2e35_A 2e36_A 2h8w_A 2hgj_L 2hgq_L 2hgu_L 2j01_K 2j03_K 2jl6_K 2jl8_K 2klm_A 2nxn_B 2wh2_K 2wh4_K 2wrj_K 2wrl_K 2x9s_K 2x9u_K 3cjt_B* ...
Probab=100.00  E-value=0  Score=352.29  Aligned_cols=138  Identities=49%  Similarity=0.842  Sum_probs=135.8

Q ss_pred             CCEEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHHHH
Q ss_conf             42368999999445566897044686642999899999999997754379751389998389529999859748999996
Q gi|254780147|r    3 KVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLKK   82 (142)
Q Consensus         3 k~v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~likk   82 (142)
                      |+++++|||+++||+|+|+|||||+|||+|||+|+||++||++|++|+ |.++||+|++|+||+|+|++++||+||||++
T Consensus         1 K~v~~~ikl~v~aG~A~p~PplGP~LG~~Gini~~f~k~fN~~T~~~~-g~~vpV~i~v~~dksf~~~i~~P~~s~ll~k   79 (146)
T 3egv_B            1 KKVVAVVKLQLPAGAATPAPPVGPALGQHGANIMEFVKAFNAATANMG-DAIVPVEITIYADRSFTFVTKTPPASYLIRK   79 (146)
T ss_dssp             CCEEEEEEEEEETTCCCSSTTHHHHHHTTTCCHHHHHHHHHHHTTTST-TCEEEEEEEEETTSCEEEEECCCCHHHHC--
T ss_pred             CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC-CCCCEEEEEECCCCCEEEEECCCCHHHHHHH
T ss_conf             937899999977574379998630003579898999999999975216-9954069997289628999869966999997


Q ss_pred             HCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEE
Q ss_conf             33766678899963010125999999999988540678789999997743021452893
Q gi|254780147|r   83 EVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVV  141 (142)
Q Consensus        83 ~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~  141 (142)
                      ++|+++||++|+++++|+||++|+||||+.|++||++.+|+++||+|+||||||||+|+
T Consensus        80 ~~g~~kgs~~~~~~~~g~it~~~v~eIAk~K~~dl~~~~l~~~vk~VlGTa~SmGi~V~  138 (146)
T 3egv_B           80 AAGLEKGAHKPGREKVGRITWEQVLEIAKQKMPDLNTTDLEAAARMIAGSARSMGVEVV  138 (146)
T ss_dssp             -----------------------------------------------------------
T ss_pred             HHCCCCCCCCCCCEEEEEEEHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHEECEEEEE
T ss_conf             43214566789972512788999999999987765552499999985600435768999


No 5  
>1vq8_I 50S ribosomal protein L11P; 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: a.4.7.1 PDB: 1vq4_I* 1vq5_I* 1vq6_I* 1vq7_I* 1s72_I* 1vq9_I* 1vqk_I* 1vql_I* 1vqm_I* 1vqn_I* 1vqo_I* 1vqp_I* 1yhq_I* 1yi2_I* 1yij_I* 1yit_I* 1yj9_I* 1yjn_I* 1yjw_I* 2otl_I* ...
Probab=100.00  E-value=0  Score=351.69  Aligned_cols=137  Identities=26%  Similarity=0.561  Sum_probs=133.7

Q ss_pred             EEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHHHHHC
Q ss_conf             36899999944556689704468664299989999999999775437975138999838952999985974899999633
Q gi|254780147|r    5 VSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLKKEV   84 (142)
Q Consensus         5 v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~likk~~   84 (142)
                      +.++|||+|+||+|+|+|||||+|||+|||+|+||++||++|++|+ |++|||+|++|+||+|+|++++||+||||++++
T Consensus         1 ~~~~ikl~v~aG~A~p~Pplgp~LG~~Gini~~f~k~fN~~T~~~~-g~~v~V~i~v~~dksf~~~v~~Pp~s~llkkaa   79 (162)
T 1vq8_I            1 MAGTIEVLVPGGEANPGPPLGPELGPTPVDVQAVVQEINDQTAAFD-GTEVPVTVKYDDDGSFEIEVGVPPTAELIKDEA   79 (162)
T ss_dssp             -------------------------------------------------------------------CCCCHHHHHHHTT
T ss_pred             CCEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC-CCEEEEEEEEECCCCEEEEECCCCHHHHHHHHH
T ss_conf             9469999987686179998640003579898999999999987538-976669999974885689985898799999972


Q ss_pred             CCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEEC
Q ss_conf             7666788999630101259999999999885406787899999977430214528939
Q gi|254780147|r   85 GIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVVD  142 (142)
Q Consensus        85 g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~~  142 (142)
                      |+++||++|+++++|+||++|+||||+.|++|+++.+|+++||+|+||||||||+|+.
T Consensus        80 gi~kgs~~p~~~~vG~It~~qv~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~g  137 (162)
T 1vq8_I           80 GFETGSGEPQEDFVADLSVDQVKQIAEQKHPDLLSYDLTNAAKEVVGTCTSLGVTIEG  137 (162)
T ss_dssp             SCCSCCSSTTTSCCEEECHHHHHHHHHHTTTTCCCSSHHHHHHHHHHHTTTTTEEEC-
T ss_pred             CCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCEEEEEC
T ss_conf             6677789999754660649999999999714015589999999999826325599977


No 6  
>3ofq_I 50S ribosomal protein L11; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_G 1p86_G 2awb_I 2aw4_I 2i2v_I 2j28_I 2i2t_I* 2qao_I* 2qba_I* 2qbc_I* 2qbe_I 2qbg_I 2qbi_I* 2qbk_I* 2qov_I 2qox_I 2qoz_I* 2qp1_I* 2rdo_I 2vhm_I ...
Probab=100.00  E-value=0  Score=365.46  Aligned_cols=141  Identities=55%  Similarity=0.901  Sum_probs=139.3

Q ss_pred             CCCEEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHHH
Q ss_conf             84236899999944556689704468664299989999999999775437975138999838952999985974899999
Q gi|254780147|r    2 AKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLK   81 (142)
Q Consensus         2 ~k~v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~lik   81 (142)
                      ||++.++|||+++||+|+|+|||||+|||+|||+|+||++||++|++|+.|+++||+|++|+||+|+|++++||+||||+
T Consensus         1 aK~v~~~ikl~v~aG~A~p~PplGP~LG~~Gini~~f~k~fN~~T~~~k~g~~vpV~Itv~~dksf~~~i~~Pp~s~li~   80 (141)
T 3ofq_I            1 AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFTFVTKTPPAAVLLK   80 (141)
T ss_dssp             CCCCCCCCCCCCCTTCCSSSSSSSTTTCSSSCCSSTTTSTTSSTTTTTCSSSCCCCCCCCCSSSCCCCCCCCCCSTTTGG
T ss_pred             CCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCEEEEEECCCCHHHHHH
T ss_conf             97247999999755852799987511135698989999999998763107964778999957952999977997599998


Q ss_pred             HHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEEC
Q ss_conf             6337666788999630101259999999999885406787899999977430214528939
Q gi|254780147|r   82 KEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVVD  142 (142)
Q Consensus        82 k~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~~  142 (142)
                      +++|+++||++|+++++|+||++|+||||+.|++||++.+|+++||+|+||||||||+|+|
T Consensus        81 k~~g~~kgs~~p~~~~vG~it~~~v~eIAk~K~~dl~~~~l~~~vk~V~GTa~SmGi~V~~  141 (141)
T 3ofq_I           81 KAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRSIEGTARSMGLVVED  141 (141)
T ss_dssp             GSSSCSSCCSSSSSSCCCCCCTTSTTTSSSSSSSSSSCCSTTSSSHHHHTTTTTTSCCCCC
T ss_pred             HHCCCCCCCCCCCCCCCCEEEHHHHHHHHHHHHHHHCCCCHHHHHHHHHEEEEECEEEEEC
T ss_conf             7427764468998642564719999999999888766788999999845312447589879


No 7  
>2zkr_i 60S ribosomal protein L12; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 3jyw_K 1s1i_K
Probab=100.00  E-value=0  Score=330.22  Aligned_cols=139  Identities=22%  Similarity=0.300  Sum_probs=126.3

Q ss_pred             CCCCE----EEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCH
Q ss_conf             98423----68999999445566897044686642999899999999997754379751389998389529999859748
Q gi|254780147|r    1 MAKVV----SRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPV   76 (142)
Q Consensus         1 M~k~v----~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~   76 (142)
                      |.+++    +++|+|+|+||+|+|+|||||+|||+|||+|+||++||++|++|+ |++|||+|++|+|++|.+.+  ||+
T Consensus         1 m~~k~~~~~v~~ikl~v~~G~A~P~PplGpaLG~~GiNi~~f~k~fN~~T~~~~-G~~VpV~Itv~~d~~~~~~~--p~~   77 (165)
T 2zkr_i            1 MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWK-GLRITVKLTIQNRQAQIEVV--PSA   77 (165)
T ss_dssp             -----------------------------------------------------------------------CCCC--CCH
T ss_pred             CCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC-CCEEEEEEEEECCEEEEEEC--CCC
T ss_conf             969988880699999972575489997652114568789999999999875337-94565899994564799973--880


Q ss_pred             HHHHHHHC--CCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEEC
Q ss_conf             99999633--7666788999630101259999999999885406787899999977430214528939
Q gi|254780147|r   77 SFFLKKEV--GIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVVD  142 (142)
Q Consensus        77 s~likk~~--g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~~  142 (142)
                      |+++++++  +..+|+..++++++|+||++|+||||+.|++||++++|+++||+|+||||||||+||.
T Consensus        78 s~~~lk~~~~~~~~gs~~~~~e~vG~It~~qv~eIAk~K~~dl~~~~l~~a~k~V~GTArSMGI~VeG  145 (165)
T 2zkr_i           78 SALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVGCNVDG  145 (165)
T ss_dssp             HHHHHHHHTCSSCCSSTTTCSSCSEEECHHHHHHHHHHHTTTCCCSSHHHHHHHHHHHHHHHTEEEC-
T ss_pred             HHHHHHHHCCCCCCCCCCCCCEEEEEECHHHHHHHHHHHHHHHCCCCHHHHHHHHHEEHEEEEEEEEC
T ss_conf             69999986677556788875405513539999999995441014799999999855566034689857


No 8  
>3cjs_B 50S ribosomal protein L11, ribosomal protein L11 methyltransferase; S-adenosyl-L-methionine dependent methyltransferase; 1.37A {Thermus thermophilus} SCOP: d.47.1.1 PDB: 3cju_B* 2bcw_A
Probab=99.96  E-value=2.9e-29  Score=192.29  Aligned_cols=71  Identities=54%  Similarity=0.881  Sum_probs=67.9

Q ss_pred             CCEEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCC
Q ss_conf             423689999994455668970446866429998999999999977543797513899983895299998597
Q gi|254780147|r    3 KVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQP   74 (142)
Q Consensus         3 k~v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P   74 (142)
                      |++.++|||+++||+|+|+|||||+|||+|||+|+||++||++|++++ |..+||+|++|+||||+|++++|
T Consensus         2 Kkv~~~ikl~i~aG~A~P~PPvGpaLGq~GiNi~~Fck~fN~~T~~~~-g~~vpv~I~v~~Dksf~f~ik~P   72 (72)
T 3cjs_B            2 KKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMG-DAIVPVEITIYADRSFTFVTKTP   72 (72)
T ss_dssp             CCEEEEEEEEEETTCCCSSTTHHHHHHTTTCCHHHHHHHHHHHHGGGC-SCEEEEEEEEETTSCEEEEECCC
T ss_pred             CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC-CCCEEEEEEEECCCCEEEEECCC
T ss_conf             643589999986677788999775101258788999999999876435-99367999997798389996088


No 9  
>1wib_A 60S ribosomal protein L12; N-terminal domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Mus musculus} SCOP: d.47.1.1
Probab=99.95  E-value=2e-29  Score=193.28  Aligned_cols=78  Identities=19%  Similarity=0.333  Sum_probs=74.9

Q ss_pred             EEEEEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCHHHHHHHHC
Q ss_conf             36899999944556689704468664299989999999999775437975138999838952999985974899999633
Q gi|254780147|r    5 VSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLKKEV   84 (142)
Q Consensus         5 v~~~ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~~~g~~v~V~i~v~~dksf~~~i~~P~~s~likk~~   84 (142)
                      .+++|+|+|+||+|+|+|||||+|||+|||+|+||++||++|++|+ |++|||+|+| +||+|+|++ +||+|+||++++
T Consensus        15 ~v~~Ikl~v~gG~A~p~PplgPaLG~~Gini~~f~k~fN~~T~~~k-G~~VpV~ItV-~dR~f~~~v-~Pp~S~L~~~aa   91 (92)
T 1wib_A           15 EVKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWK-GLRITVKLTI-QNRQAQIEV-VPSASALSGPSS   91 (92)
T ss_dssp             SCEEEEEEEETTCCCCSSCSHHHHTTTCSCHHHHHHHHHHHTTTTT-TSEEEEEEEE-ETTEEECCB-CSCCCCCCCCSC
T ss_pred             CEEEEEEEEECCCCCCCCCCCCHHCCCCCCHHHHHHHHHHHHHHCC-CCEEEEEEEE-ECCEEEEEE-ECCHHHHHHHHC
T ss_conf             0799999984575378997650003568779999999999863316-9875699999-486589999-388999988741


Q ss_pred             C
Q ss_conf             7
Q gi|254780147|r   85 G   85 (142)
Q Consensus        85 g   85 (142)
                      |
T Consensus        92 G   92 (92)
T 1wib_A           92 G   92 (92)
T ss_dssp             C
T ss_pred             C
T ss_conf             9


No 10 
>1hc8_A Ribosomal protein L11; ribosome, ribosomal RNA, tertiary structure, RNA-protein; HET: GTP; 2.8A {Bacillus stearothermophilus} SCOP: a.4.7.1 PDB: 1y39_A* 1aci_A 1fow_A 1fox_A 1foy_A 2fow_A
Probab=99.94  E-value=3.2e-28  Score=186.17  Aligned_cols=76  Identities=50%  Similarity=0.817  Sum_probs=75.1

Q ss_pred             EEEEECCCCHHHHHHHHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCEEEEC
Q ss_conf             9999859748999996337666788999630101259999999999885406787899999977430214528939
Q gi|254780147|r   67 FTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGISVVD  142 (142)
Q Consensus        67 f~~~i~~P~~s~likk~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~~  142 (142)
                      |+|++++||+||||++++|+++||++|+++.+|+||++|+||||+.|++||++.+|+++||+|+||||||||+|||
T Consensus         1 F~f~~ktPP~s~llkkaagi~kGs~~p~~~~vG~it~~qv~eIAk~K~~dl~~~~l~~a~k~V~GTarSmGI~Ved   76 (76)
T 1hc8_A            1 FTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGIVVEN   76 (76)
T ss_dssp             -CCCCCCCCHHHHHHHHHTCSCCCSSTTTCCCEEECHHHHHHHHHHSGGGCCCSSHHHHHHHHHHHHHHHTEEEC-
T ss_pred             CEEEECCCCHHHHHHHHHCCCCCCCCCCCEEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHEECEEEEEC
T ss_conf             9489758988999999978887789988715565669999999998750238989999999978105016689769


No 11 
>1qa6_A Ribosomal protein L11; ribosomal RNA, tertiary structur,E RNA-protein interaction, minor groove binding, antibiotic binding; 2.80A {Geobacillus stearothermophilus} SCOP: a.4.7.1 PDB: 1c04_C
Probab=99.89  E-value=3.9e-24  Score=162.03  Aligned_cols=67  Identities=51%  Similarity=0.837  Sum_probs=66.1

Q ss_pred             CCCCHHHHHHHHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEECCE
Q ss_conf             5974899999633766678899963010125999999999988540678789999997743021452
Q gi|254780147|r   72 SQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSACSMGI  138 (142)
Q Consensus        72 ~~P~~s~likk~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d~~~~~l~~~vk~VlGTa~SmGi  138 (142)
                      ++||+||||++++|+++||++|+++++|+||++|+||||+.|++|||+.+++++||+|+||||||||
T Consensus         1 KtPP~s~llkkaagi~kGs~~p~~~~vG~it~~qv~eIAk~K~~dl~~~~l~~a~k~v~GtArSMGI   67 (67)
T 1qa6_A            1 KTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGI   67 (67)
T ss_dssp             CCSCHHHHHHHHHTCSCCCCTTSSCCCCCCTTTHHHHHHHHHGGGCCCSSHHHHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             9898899999997889788999983220126999999999875103899999999999988983489


No 12 
>1no4_A Late, head morphogenesis protein; coiled-coil, viral protein; 2.20A {Bacillus phage PHI29} SCOP: h.1.24.1 PDB: 1noh_A
Probab=29.22  E-value=14  Score=17.21  Aligned_cols=25  Identities=24%  Similarity=0.324  Sum_probs=21.5

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf             6866429998999999999977543
Q gi|254780147|r   26 PAIGQAGIPIMAFCKAFNAATEGME   50 (142)
Q Consensus        26 p~LG~~Gini~~f~k~fN~~T~~~~   50 (142)
                      -+|.|+.+|-..|.-+||+.|+...
T Consensus        26 e~lqqlr~~ygs~vse~~dlt~~~e   50 (97)
T 1no4_A           26 EALQQLRVNYGSFVSEYNDLTKSHE   50 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999887679999888878899


No 13 
>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ...
Probab=27.63  E-value=32  Score=15.04  Aligned_cols=52  Identities=6%  Similarity=0.022  Sum_probs=36.7

Q ss_pred             CCCHHHHHHHHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHH-CCCCCHHHHHHHHH
Q ss_conf             97489999963376667889996301012599999999998854-06787899999977
Q gi|254780147|r   73 QPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQD-MGAIDIEGAMRMVE  130 (142)
Q Consensus        73 ~P~~s~likk~~g~~kgs~~p~~~~~g~it~~~i~eIAk~K~~d-~~~~~l~~~vk~Vl  130 (142)
                      .+..|..|.+.+|++.      ...+|++|-+|+.+|......+ +...+|+..+++=+
T Consensus        26 G~~~A~~Ic~~lGId~------~~kvg~Lt~~qi~~l~~~i~~~~~i~~~L~~~~~~~i   78 (126)
T 2vqe_M           26 GKARAKEALEKTGINP------ATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANI   78 (126)
T ss_dssp             CSHHHHHHTTTTTCCT------TSBGGGCCHHHHHHHHHHHHTTSCCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHCCCCC------CCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             8999999999859796------6301639999999999998314511478999999989


No 14 
>2k53_A A3DK08 protein; NESG, CMR9, structural genomics, PSI-2, protein structure initiative; NMR {Clostridium thermocellum atcc 27405}
Probab=25.32  E-value=36  Score=14.79  Aligned_cols=37  Identities=16%  Similarity=0.079  Sum_probs=30.1

Q ss_pred             EECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH
Q ss_conf             9445566897044686642999899999999997754
Q gi|254780147|r   13 IESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGM   49 (142)
Q Consensus        13 v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T~~~   49 (142)
                      ..++..++.-+|..+.--+|+|+-.|.++.|+..++-
T Consensus        30 C~gc~~a~~~tL~eaa~~~gid~~~ll~eLn~~i~~~   66 (76)
T 2k53_A           30 CLGCPSSMGESIEDACAVHGIDADKLVKELNEYFEKK   66 (76)
T ss_dssp             CCSSCCCCCSBHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             8578776667099999994979999999999999977


No 15 
>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A
Probab=20.97  E-value=44  Score=14.27  Aligned_cols=69  Identities=19%  Similarity=0.337  Sum_probs=44.6

Q ss_pred             EEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH---------------HHHHCCCCCEEEEEEECCCEEEEEECC
Q ss_conf             99999445566897044686642999899999999997---------------754379751389998389529999859
Q gi|254780147|r    9 VKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAAT---------------EGMEKGIPIPTTVTCYKDKSFTFTMSQ   73 (142)
Q Consensus         9 ikl~v~aG~A~p~PplGp~LG~~Gini~~f~k~fN~~T---------------~~~~~g~~v~V~i~v~~dksf~~~i~~   73 (142)
                      -|+-|.+-..+- -|+|-..|+.|.++..+.++.|..-               ..+.+-..+.|.+.-..++++...+..
T Consensus       233 tKvAV~s~d~~i-DpvGa~vG~~G~ri~~i~~el~ge~idii~~s~d~~~fi~nal~Pa~v~~v~~~~~~~~~~~v~v~~  311 (344)
T 1hh2_P          233 TKVAVASNDPNV-DPIGACIGEGGSRIAAILKELKGEKLDVLKWSDDPKQLIANALAPATVIEVEILDKENKAARVLVPP  311 (344)
T ss_dssp             EEEEEEESSTTS-CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECCSSHHHHHHHHTCSSCCSEEEEEETTTTEEEEEECT
T ss_pred             EEEEEEECCCCC-CCCEEEECCCCCHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCEEEEEEECCCCCEEEEEECH
T ss_conf             469999348875-5101456589717999999857993589966899999999844956301899973888779999880


Q ss_pred             CCHHH
Q ss_conf             74899
Q gi|254780147|r   74 PPVSF   78 (142)
Q Consensus        74 P~~s~   78 (142)
                      -.-|.
T Consensus       312 ~~~~~  316 (344)
T 1hh2_P          312 TQLSL  316 (344)
T ss_dssp             TSHHH
T ss_pred             HHHHH
T ss_conf             24026


Done!