Query         gi|254780242|ref|YP_003064655.1| 50S ribosomal protein L15 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 151
No_of_seqs    152 out of 2062
Neff          6.3 
Searched_HMMs 33803
Date          Tue May 24 02:47:12 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780242.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >3i1n_L 50S ribosomal protein  100.0       0       0  311.8   9.5  142    1-149     1-143 (144)
  2 >3bbo_N Ribosomal protein L15; 100.0       0       0  318.3   2.0  147    1-151    65-220 (257)
  3 >2j01_P 50S ribosomal protein  100.0       0       0  311.0   6.4  146    1-151     1-148 (150)
  4 >2zjr_I 50S ribosomal protein  100.0       0       0  311.2   6.1  142    1-151     1-143 (156)
  5 >1vq8_L 50S ribosomal protein  100.0       0       0  260.3   8.9  136   11-151     2-144 (165)
  6 >2zkr_l 60S ribosomal protein  100.0 2.4E-42       0  240.8   8.4  135   12-151     3-147 (148)
  7 >3jyw_O 60S ribosomal protein   99.9 9.5E-30 2.8E-34  175.2  -3.2   88   47-151    15-104 (121)
  8 >3jyw_V 60S ribosomal protein   99.9 8.3E-25 2.5E-29  149.4   3.6   92   59-151     1-94  (94)
  9 >1vq8_O 50S ribosomal protein   99.5 6.8E-15   2E-19   97.8   4.8   62   71-151     1-62  (78)
 10 >2zkr_o 60S ribosomal protein   98.4 3.1E-07 9.3E-12   57.8   4.4   64   72-150     2-67  (133)
 11 >2j01_F 50S ribosomal protein   33.6      16 0.00048   17.6   1.0   36  109-144   168-205 (210)
 12 >3i1m_P 30S ribosomal protein   24.3      55  0.0016   14.9   3.4   58   40-106     7-80  (82)
 13 >3cuq_A Vacuolar-sorting prote  23.1      34   0.001   16.0   1.1   40   75-120    34-73  (91)
 14 >3bn0_A 30S ribosomal protein   21.8      34   0.001   15.9   1.0   45   63-109    37-81  (112)
 15 >2ftc_E Mitochondrial ribosoma  21.6      63  0.0019   14.6   2.6   16  135-150    56-71  (72)
 16 >1m0s_A Ribose-5-phosphate iso  20.7      66  0.0019   14.5   3.3   28  123-150     4-32  (77)
 17 >1dd3_A 50S ribosomal protein   20.2      68   0.002   14.4   2.8   16  135-150    55-70  (71)

No 1  
>>3i1n_L 50S ribosomal protein L15; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_J 1p86_J 1vs8_L 2aw4_L 2awb_L 1vs6_L 2i2v_L 2j28_L 2i2t_L* 2qao_L* 2qba_L* 2qbc_L* 2qbe_L 2qbg_L 2qbi_L* 2qbk_L* 2qov_L 2qox_L 2qoz_L* 2qp1_L* ... (L:)
Probab=100.00  E-value=0  Score=311.82  Aligned_cols=142  Identities=43%  Similarity=0.634  Sum_probs=138.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEECCCCCCCCCCCCCEEEEEHH
Q ss_conf             97666888999876761020315789898578776676423689866-44431685301167635546565521477511
Q gi|254780242|r    1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVR-GFEGGQMPLYRRLPKRGFVNIAGSDFVTISLG   79 (151)
Q Consensus         1 m~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~-gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL~   79 (151)
                      |+||||+|+||++++++|+|||+|||+|||||||||||++|+|...+ +|||||||+|+|+||+||+++++.+|.+|||+
T Consensus         1 ~~L~~l~~~~g~~~~k~R~gRg~gsG~gkt~grg~kg~~~r~g~~~~~gfeggq~p~~~~~pK~Gf~~~~~~~~~~inl~   80 (144)
T 3i1n_L            1 MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLS   80 (144)
T ss_dssp             -CTTSCCCCTTTSCCCCCCSSCSTTSSCSTTSSCSSSTTSSSSCCCCTTCCTTSCCHHHHSCCCCCCCSTGGGEEECCST
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCEEECCCCCCEEEEEEEEH
T ss_conf             96365878988841640467878899997888888998776798868664567555521165340121231058776600


Q ss_pred             HHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEE
Q ss_conf             2045430245553322335555430862544332046304431441489999826999999997498899
Q gi|254780242|r   80 LLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVI  149 (151)
Q Consensus        80 ~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~  149 (151)
                      +|+.+++       ++||.+.|.+.+++......+|||++|+|+.||+|+|++||++|+|+||+|||+|+
T Consensus        81 ~l~~~~~-------~~i~~~~l~~~~i~~~~~~~~KlLg~G~l~~~l~Ikv~~~S~~A~ekIe~aGG~v~  143 (144)
T 3i1n_L           81 DLAKVEG-------GVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIE  143 (144)
T ss_dssp             TTTTSSS-------SEECTTTTTTTTSSCTTCCEEECCCCCCCCSCCEEESSBCCHHHHHHHHHTTCEEE
T ss_pred             HHHHHHC-------CCCHHHHHHHCCEEECCCEEEEEECCCCCCCCEEEEEEEECHHHHHHHHHHCCEEE
T ss_conf             1223230-------34103454432656401000178606831677799999858999999998198552


No 2  
>>3bbo_N Ribosomal protein L15; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Pisum sativum} (N:)
Probab=100.00  E-value=0  Score=318.26  Aligned_cols=147  Identities=38%  Similarity=0.620  Sum_probs=134.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEECCC----CCCCCCCCCCEEE
Q ss_conf             97666888999876761020315789898578776676423689866-444316853011676----3554656552147
Q gi|254780242|r    1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVR-GFEGGQMPLYRRLPK----RGFVNIAGSDFVT   75 (151)
Q Consensus         1 m~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~-gfEGGQ~Pl~rrlPK----rGF~~~~~~~~~~   75 (151)
                      |+||||+|++|++++++|+|||++||+|||||||||||++|+|...+ ||||||||||+|+||    +||.++++.+|.+
T Consensus        65 ~~L~nL~~~~garkkkkR~gRG~gsG~Gkt~GrG~KGQk~R~G~~~~~gFeGGqtpl~rr~PK~~~~~gf~~~~~~~~~~  144 (257)
T 3bbo_N           65 FRLDNLGPQPGSRKRPKRKGRGIAAGQGASCGFGMRGQKSRSGPGIMRGFEGGQMPLYRRLPKLRGIAGGMHAGLPKYVN  144 (257)
T ss_dssp             CCCSSSCCCCCCCSCCCCCSSCCCCSCSSSCSSSCCCCGGGTSSCSSTTCCSSCSSTTSCCCCCSSCCCCCSSCCSSSSC
T ss_pred             EECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCEEEEEE
T ss_conf             67477889999855763101677889984278888888888899988662578850178226536634755442368885


Q ss_pred             EEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCC----CCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEC
Q ss_conf             751120454302455533223355554308625----4433204630443144148999982699999999749889989
Q gi|254780242|r   76 ISLGLLQAYIDKDRLDCSSEIDASVLVASGLVR----RSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIVI  151 (151)
Q Consensus        76 iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~----~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ii  151 (151)
                      |||++|++|+|.+..+    +|++.|++.+++.    ...++|||||+|+|+.|++|+|++||++|+++||+|||+|+++
T Consensus       145 iNL~~L~~~i~~~~~~----i~~~~l~~~~~~~~~~~~~~~~vKlLg~G~~~~~i~I~v~~aS~sAi~kIE~aGG~v~~~  220 (257)
T 3bbo_N          145 VNLTDIENAGFQDGEE----VSLETLKAKRVINPSGRERKLPLKILADGELSKKLTIKAGAFSTSAKEKLEYAGCSLIVL  220 (257)
T ss_dssp             SCSSCCSCSSTTTTTT----TCCSSCCSSSCSSSSCCCCSCCCCCCCSSCCCSSCCCCSSCCTGGGTTSSTTTTCCEECC
T ss_pred             ECCHHHHHHCCCCCCH----HHHHHHHHCCCCCCCCCCCCCCEEEECCCEECCCEEEEEEEECHHHHHHHHHCCCEEEEE
T ss_conf             1110133321353110----105568766763010002443248851770644679999985899999999849979995


No 3  
>>2j01_P 50S ribosomal protein L15; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (P:)
Probab=100.00  E-value=0  Score=310.98  Aligned_cols=146  Identities=36%  Similarity=0.515  Sum_probs=134.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CC-CCCCCCCCEEEECCCCCCCCCCCCCEEEEEH
Q ss_conf             976668889998767610203157898985787766764236898-66-4443168530116763554656552147751
Q gi|254780242|r    1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVS-VR-GFEGGQMPLYRRLPKRGFVNIAGSDFVTISL   78 (151)
Q Consensus         1 m~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~-~~-gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL   78 (151)
                      |+||||+|+||++++++|+|||+|||+|||||||||||++|+|.. .+ +|||||||||||+||+||+++++..|.++||
T Consensus         1 m~l~~L~~~~g~k~~kkR~gRg~gsG~Gkt~grG~kGq~~r~g~~~~~~~feggq~Pl~rr~pK~Gf~~~~~~~~~~~~l   80 (150)
T 2j01_P            1 MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLMRLPKRGMQGQVPGEIKRPRY   80 (150)
T ss_dssp             ----CCSSSCCCSSCCCCCCCCSCSSSSSCTTCSSCCSSSCSSCCCCSSSCCSSSCTTCCSCCCCCSCCCSSCSCCCCCE
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCEEHHCCCCCCEEEEEE
T ss_conf             96355888989863763666788899896699999898888888767741137887654147600010345542111343


Q ss_pred             HHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEC
Q ss_conf             1204543024555332233555543086254433204630443144148999982699999999749889989
Q gi|254780242|r   79 GLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIVI  151 (151)
Q Consensus        79 ~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ii  151 (151)
                      ..|+.+++.+.+   ++||++.|+++++++... .+|||++|++ .||+|+|++||++|+|+||+|||+|++|
T Consensus        81 ~~l~~~~~~~~~---~~i~~~~l~~~~~v~~~~-~vKlLg~G~~-~ki~i~v~~~S~~A~~kIe~aGG~v~~v  148 (150)
T 2j01_P           81 QGVNLKDLARFE---GEVTPELLVRAGLLKKGY-RLKILGEGEA-KPLKVVAHAFSKSALEKLKAAGGEPVLL  148 (150)
T ss_dssp             EEEETTTTTTSC---SCCCTTTTTTSSSCSSCC-EEEEECSSCC-CSSCCCCSBCCHHHHHHHHTSCCCCCCC
T ss_pred             EHHHHHHHHCCC---CCCCHHHHHHCCCCCCCC-CEEEECCCCE-EEEEEEEEECCHHHHHHHHHCCCEEEEE
T ss_conf             044566653344---335699999708655587-1788648857-6579998861899999999869989996


No 4  
>>2zjr_I 50S ribosomal protein L15; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (I:)
Probab=100.00  E-value=0  Score=311.23  Aligned_cols=142  Identities=46%  Similarity=0.700  Sum_probs=135.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEECCCCCCCCCCCCCEEEEEHH
Q ss_conf             97666888999876761020315789898578776676423689866-44431685301167635546565521477511
Q gi|254780242|r    1 MKLNEISYDKGSCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVR-GFEGGQMPLYRRLPKRGFVNIAGSDFVTISLG   79 (151)
Q Consensus         1 m~L~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~-gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL~   79 (151)
                      |+||||+|++||+++++|+|||++| .|+|||||||||+||+|..++ +|||||||||||+||+||++ ++..|.+|||+
T Consensus         1 m~L~~l~~~~g~~~~k~R~gRG~~s-~Gkt~grg~kGqk~R~G~~~~~gfeggq~pl~r~~PK~Gf~~-~~~~~~~inl~   78 (156)
T 2zjr_I            1 MKLHDLKPTPGSRKDRKRVGRGPGG-TDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARLPKRGFNN-VGTTYEVVKLS   78 (156)
T ss_dssp             ---CCCCCCSSTTTCCCCSSSCCCC-CCSCSSSCCCCSSSSSCCSCCCSCSCCSSSSTTTSCCCCCCC-CCCCCCEECHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCC-CCCEEEHHHHH
T ss_conf             9625488898985577425788999-998889988887778898988761468677201145357676-54243302087


Q ss_pred             HHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEC
Q ss_conf             204543024555332233555543086254433204630443144148999982699999999749889989
Q gi|254780242|r   80 LLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIVI  151 (151)
Q Consensus        80 ~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ii  151 (151)
                      +|+.+++       ++||+++|++.+|+.....++|||++|+|+.||+|+|++||++|+++||+|||+|+++
T Consensus        79 ~L~~~~~-------~~i~~~~l~~~~l~~~~~~~~Kllg~G~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~~~  143 (156)
T 2zjr_I           79 QLQDLED-------TTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTVHVDAASAAAIKAVEAAGGRVVLP  143 (156)
T ss_dssp             HHTTSCC-------CCCCTTTTHHHHHCCCCSSCCEECCCCCCCCCCCCCCSEECHHHHHHHGGGSCCCCCC
T ss_pred             HHHHHHC-------CCCHHHHHHHHCEECCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEE
T ss_conf             6542110-------1201445555150101466457752884557678999980999999999869989996


No 5  
>>1vq8_L 50S ribosomal protein L15P; 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} (L:)
Probab=100.00  E-value=0  Score=260.32  Aligned_cols=136  Identities=21%  Similarity=0.219  Sum_probs=125.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCEEEEEHHHHHHHHCCCC
Q ss_conf             987676102031578989857-8776676423689866444316853011676355465655214775112045430245
Q gi|254780242|r   11 GSCKVKKRVARGIGSGTGKTA-GRGVKGQKSRSGVSVRGFEGGQMPLYRRLPKRGFVNIAGSDFVTISLGLLQAYIDKDR   89 (151)
Q Consensus        11 g~~~~~kR~GRG~gsg~Gkt~-GrG~kGqk~Rsg~~~~gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL~~L~~~i~~~~   89 (151)
                      .++++++|+|||+|||+|+|+ ||||+||++|+     ||||||||||+|+||+||.+++...|.++||+.|+.|++.+.
T Consensus         2 ~s~~~k~R~gRg~gsG~gk~~~g~G~kG~~~r~-----Gfeggq~p~~~r~pK~Gf~~~~~~~~~~v~l~~l~~~~~~~~   76 (165)
T 1vq8_L            2 TSKKKRQRGSRTHGGGSHKNRRGAGHRGGRGDA-----GRDKHEFHNHEPLGKSGFKRPQKVQEEAATIDVREIDENVTL   76 (165)
T ss_dssp             CCHHHHCTTCSSTTCSSTTSSCSGGGGTSSTTT-----TTTTTTCTTSCCSCCCCCCCCGGGCCCEEEEEHHHHHHTTGG
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHHHH
T ss_conf             886366366757367999888989798888776-----988788714557422367677866534666315458888876


Q ss_pred             C------CCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEC
Q ss_conf             5------5332233555543086254433204630443144148999982699999999749889989
Q gi|254780242|r   90 L------DCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIVI  151 (151)
Q Consensus        90 ~------~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~ii  151 (151)
                      +      +...+++.+.|...+++.....++||||+|+|+.||+|+|++||++|+++||+|||+|+++
T Consensus        77 ~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~KvLg~G~l~~~i~I~~~~~S~~A~~kIE~aGG~v~~~  144 (165)
T 1vq8_L           77 LAADDVAEVEDGGFRVDVRDVVEEADDADYVKVLGAGQVRHELTLIADDFSEGAREKVEGAGGSVELT  144 (165)
T ss_dssp             GTTSCCCC-----CEEEGGGTCTTCTTSSEEEEECCSCCCSCCEEEESEECHHHHHHHHHTTCEEEEC
T ss_pred             HCCCCCCCCCCCHHHHHHHHHCCCCCCCCCEEEECCCCCCCCEEEEEEECCHHHHHHHHHCCCEEEEE
T ss_conf             30123101123301677887411334565279947883287879999972989999999859989994


No 6  
>>2zkr_l 60S ribosomal protein L27A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} (l:)
Probab=100.00  E-value=2.4e-42  Score=240.78  Aligned_cols=135  Identities=21%  Similarity=0.196  Sum_probs=113.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEECC----CCCCCCC----CCCCEEEEEHHHHH
Q ss_conf             876761020315789898578776676423689866-44431685301167----6355465----65521477511204
Q gi|254780242|r   12 SCKVKKRVARGIGSGTGKTAGRGVKGQKSRSGVSVR-GFEGGQMPLYRRLP----KRGFVNI----AGSDFVTISLGLLQ   82 (151)
Q Consensus        12 ~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~Rsg~~~~-gfEGGQ~Pl~rrlP----KrGF~~~----~~~~~~~iNL~~L~   82 (151)
                      ++++++|+|||++||.|+   +|||||++|+|...+ +|||||||||||+|    |+||+++    ++.+|.+|||++|+
T Consensus         3 s~k~k~R~gRG~~sg~gg---~g~kgqk~r~g~~~~~gfeggq~p~~rr~Pk~~gk~Gf~~~~~~~~~~~~~~inl~~l~   79 (148)
T 2zkr_l            3 SRLRKTRKLRGHVSHGHG---RIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMKHYHLKRNQSFCPTVNLDKPW   79 (148)
T ss_dssp             ---CHHHHTTTTSCSSCC---SCSCC--CCSCSSSTTTTTTTCSSCTTTC------------------CCCCEEETHHHH
T ss_pred             CCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHH
T ss_conf             887654657888786889---89898988989888786557643344668663256897788557765060057799998


Q ss_pred             HHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCC-CCEEEEEEEECHHHHHHHHHCCCEEEEC
Q ss_conf             54302455533223355554308625443320463044314-4148999982699999999749889989
Q gi|254780242|r   83 AYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLK-AKVVLRVSGASASAVEKVEKLGGQVIVI  151 (151)
Q Consensus        83 ~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~-~ki~I~v~~~S~sA~ekIE~aGG~v~ii  151 (151)
                      +|+|.+++|+...++...+  ..+.......+|||++|++. .||+|+|++||++|+++||+|||+|++|
T Consensus        80 ~l~~~~~~~~~~~~~~~~~--~~~~~~~~~~~Kvlg~G~~~k~~i~I~v~~~S~~A~~~IE~aGG~v~~v  147 (148)
T 2zkr_l           80 TLVSEQTRVNAAKNKTGVA--PIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKSVGGACVLV  147 (148)
T ss_dssp             HHTTTTTSSCTTTTEEEHH--HHSTTCSSSCCEEECCSCCCSSCCEEEESEECHHHHHHHHHTTCEEEEC
T ss_pred             HHCCCCCEEHHHHHHCCCC--CCCCCCCCCEEEECCCCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEEE
T ss_conf             6421341203344320542--1110000121576147740574689998861999999999869989995


No 7  
>>3jyw_O 60S ribosomal protein L18(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_O (O:)
Probab=99.94  E-value=9.5e-30  Score=175.17  Aligned_cols=88  Identities=16%  Similarity=0.181  Sum_probs=76.6

Q ss_pred             CCCCCCCCCEEEECCCCCCCCCCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCC--
Q ss_conf             644431685301167635546565521477511204543024555332233555543086254433204630443144--
Q gi|254780242|r   47 RGFEGGQMPLYRRLPKRGFVNIAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKA--  124 (151)
Q Consensus        47 ~gfEGGQ~Pl~rrlPKrGF~~~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~--  124 (151)
                      .||||||||||||||||||+|  +++|.+|||+.|+.+++.+.+      |.+.+...         +|||++|+++.  
T Consensus        15 ~gfEggQ~Pl~rrlpKrgf~~--~~~~~~vnl~~i~~~~~~~~v------~~~~lv~~---------gKVL~~G~l~~~~   77 (121)
T 3jyw_O           15 FLARRTDAPFNKVVLKALFLS--KINRPPVSVSRIARALKQEGA------ANKTVVVV---------GTVTDDARIFEFP   77 (121)
T ss_dssp             HHHTTSCCHHHHHHHHTTTSC--STTSCCBCHHHHHHHTTTTSC------SSSEEEES---------SCBCCCSCCCSSS
T ss_pred             HHHHHHCCHHHHHHHHHHHCC--CCCCCCCCHHHHHHHHHCCCC------CCCEEEEE---------EEECCCCEEECCC
T ss_conf             998864768899999997144--446897359999998644578------89889997---------3471883141278


Q ss_pred             CEEEEEEEECHHHHHHHHHCCCEEEEC
Q ss_conf             148999982699999999749889989
Q gi|254780242|r  125 KVVLRVSGASASAVEKVEKLGGQVIVI  151 (151)
Q Consensus       125 ki~I~v~~~S~sA~ekIE~aGG~v~ii  151 (151)
                      |++|++++||++|+++||+|||+|+.+
T Consensus        78 ki~I~a~~~S~sA~~kIe~AGG~v~~~  104 (121)
T 3jyw_O           78 KTTVAALRFTAGARAKIVKAGGECITL  104 (121)
T ss_dssp             CCCEECSSBCTTTTTHHHHHTCCBCCS
T ss_pred             CEEEEEEECCHHHHHHHHHCCCEEEEH
T ss_conf             717999971478999999759979889


No 8  
>>3jyw_V 60S ribosomal protein L28; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_V (V:49-142)
Probab=99.90  E-value=8.3e-25  Score=149.41  Aligned_cols=92  Identities=22%  Similarity=0.150  Sum_probs=74.8

Q ss_pred             ECCCCCCCC-CCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCC-CCCEEEEEEEECHH
Q ss_conf             167635546-5655214775112045430245553322335555430862544332046304431-44148999982699
Q gi|254780242|r   59 RLPKRGFVN-IAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDL-KAKVVLRVSGASAS  136 (151)
Q Consensus        59 rlPKrGF~~-~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel-~~ki~I~v~~~S~s  136 (151)
                      |||||||++ +++.+|.+|||++|+.|++.+++++.+.++.+.+...... ....++||||+|++ +.|++|+|++||++
T Consensus         1 RlPKrGF~~~~~~~~~~~inl~~L~~~~~~~~~~~~~~l~~~~~~~~~~~-~~~~~vKvLg~G~~~k~~i~I~a~~~S~~   79 (94)
T 3jyw_V            1 KVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPVIDT-LAAGYGKILGKGRIPNVPVIVKARFVSKL   79 (94)
T ss_dssp             CCSCCCSSSSTTCCCCCCCCHHHHHTTTTTCCSSBTTTTBCCSTTTCCST-TTSSCCCCCCCSCCCSCCCCEECSSCCHH
T ss_pred             CCCCCCCCCCCCCCEEEEEEHHHHHHHHHCCCCCHHHHHHHCCCCCCCCC-CCCCCEEECCCCCCCCCCEEEEEEECCHH
T ss_conf             58988887576530532587899997644034203343321033321221-10020588558413666389998843989


Q ss_pred             HHHHHHHCCCEEEEC
Q ss_conf             999999749889989
Q gi|254780242|r  137 AVEKVEKLGGQVIVI  151 (151)
Q Consensus       137 A~ekIE~aGG~v~ii  151 (151)
                      |+++||+|||+|+++
T Consensus        80 A~~~Ie~aGG~v~~v   94 (94)
T 3jyw_V           80 AEEKIRAAGGVVELI   94 (94)
T ss_dssp             HHHHHHHHTCCEECC
T ss_pred             HHHHHHHCCCEEEEC
T ss_conf             999999849989969


No 9  
>>1vq8_O 50S ribosomal protein L18E; 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} (O:39-116)
Probab=99.53  E-value=6.8e-15  Score=97.78  Aligned_cols=62  Identities=21%  Similarity=0.330  Sum_probs=53.6

Q ss_pred             CCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEEEECHHHHHHHHHCCCEEEE
Q ss_conf             52147751120454302455533223355554308625443320463044314414899998269999999974988998
Q gi|254780242|r   71 SDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKAKVVLRVSGASASAVEKVEKLGGQVIV  150 (151)
Q Consensus        71 ~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~ki~I~v~~~S~sA~ekIE~aGG~v~i  150 (151)
                      ++|.+|||++|+.+.+.+.+.                   ..++||||+|+++.+++|.+++||++|+|+||+|||+|++
T Consensus         1 K~~~~VNL~~L~~~~~~~~~~-------------------~~~~KvLg~G~l~~~l~V~A~~fS~sA~ekIe~aGG~v~~   61 (78)
T 1vq8_O            1 RTHAEVNLGRIERYAQEDETV-------------------VVPGKVLGSGVLQKDVTVAAVDFSGTAETKIDQVGEAVSL   61 (78)
T ss_dssp             TTSEEEEHHHHHHHCCTTSEE-------------------EEEEEEECCSCCCSCCEEEEEEECHHHHHHHHHHSEEEEH
T ss_pred             CCCCCCCHHHHHHHCCCCCEE-------------------EEEEEEECCCEECCCEEEEEEECCHHHHHHHHHCCCEEEH
T ss_conf             468762099999646699989-------------------9966796678676887999863278899999980987988


Q ss_pred             C
Q ss_conf             9
Q gi|254780242|r  151 I  151 (151)
Q Consensus       151 i  151 (151)
                      +
T Consensus        62 ~   62 (78)
T 1vq8_O           62 E   62 (78)
T ss_dssp             H
T ss_pred             H
T ss_conf             9


No 10 
>>2zkr_o 60S ribosomal protein L18; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} (o:56-188)
Probab=98.39  E-value=3.1e-07  Score=57.82  Aligned_cols=64  Identities=16%  Similarity=0.145  Sum_probs=48.1

Q ss_pred             CEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCCCCC--CEEEEEEEECHHHHHHHHHCCCEEE
Q ss_conf             21477511204543024555332233555543086254433204630443144--1489999826999999997498899
Q gi|254780242|r   72 DFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDGDLKA--KVVLRVSGASASAVEKVEKLGGQVI  149 (151)
Q Consensus        72 ~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~Gel~~--ki~I~v~~~S~sA~ekIE~aGG~v~  149 (151)
                      ++.+|||+.|+.+.....- +++++         +|     .=+||+++.|..  +++|-+..||++|+++|++|||+|.
T Consensus         2 nr~~vslskI~r~~k~~~~-e~~~v---------VV-----vGkVldd~rl~~vPkltV~AL~fS~~Ar~kI~~aGG~~l   66 (133)
T 2zkr_o            2 NRPPLSLSRMIRKMKLPGR-ENKTA---------VV-----VGTVTDDVRILEVPKLKVCALRVSSRARSRILKAGGKIL   66 (133)
T ss_dssp             TSCEEEHHHHHSCSSSCCS-TTSEE---------EE-----EEEEECSSCCCCCSSCCEEEEEECHHHHHHHHHHSSCEE
T ss_pred             CCCCCCHHHHHHHHHCCCC-CCCEE---------EE-----EEEECCCCEEECCCCEEEEEEEECHHHHHHHHHCCCEEE
T ss_conf             5766439999998314466-79858---------99-----755648703521575599999732789999997599796


Q ss_pred             E
Q ss_conf             8
Q gi|254780242|r  150 V  150 (151)
Q Consensus       150 i  150 (151)
                      .
T Consensus        67 t   67 (133)
T 2zkr_o           67 T   67 (133)
T ss_dssp             E
T ss_pred             E
T ss_conf             4


No 11 
>>2j01_F 50S ribosomal protein L4; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (F:)
Probab=33.63  E-value=16  Score=17.65  Aligned_cols=36  Identities=17%  Similarity=0.006  Sum_probs=24.4

Q ss_pred             CCCCCEEEECCCCCCC--CEEEEEEEECHHHHHHHHHC
Q ss_conf             4433204630443144--14899998269999999974
Q gi|254780242|r  109 RSQRGIRILSDGDLKA--KVVLRVSGASASAVEKVEKL  144 (151)
Q Consensus       109 ~~~~~vKiLg~Gel~~--ki~I~v~~~S~sA~ekIE~a  144 (151)
                      .+...|.++..-+|+.  =+.-..--+|++|.+.||..
T Consensus       168 rNi~~v~v~~~~~lnv~dll~~~~ivit~~Al~~l~e~  205 (210)
T 2j01_F          168 RNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR  205 (210)
T ss_dssp             TTCTTEEEECGGGCCHHHHHHSSEEEEEHHHHHHHHHT
T ss_pred             HCCCCCEEEECCCCCHHHHHCCCCEEEEHHHHHHHHHH
T ss_conf             47689678633881299986689499878999999999


No 12 
>>3i1m_P 30S ribosomal protein S16; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1p6g_P 1p87_P* 1vs7_P* 2avy_P 2aw7_P 1vs5_P 2i2u_P 2i2p_P* 2qan_P* 2qb9_P* 2qbb_P* 2qbd_P 2qbf_P 2qbh_P* 2qbj_P* 2qou_P* 2qow_P* 2qoy_P* 2qp0_P* 2vho_P ... (P:)
Probab=24.27  E-value=55  Score=14.86  Aligned_cols=58  Identities=21%  Similarity=0.399  Sum_probs=33.7

Q ss_pred             CCCCCCCCCCCCCCCCEEE------ECCC-------CCCCCCCC---CCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHH
Q ss_conf             2368986644431685301------1676-------35546565---521477511204543024555332233555543
Q gi|254780242|r   40 SRSGVSVRGFEGGQMPLYR------RLPK-------RGFVNIAG---SDFVTISLGLLQAYIDKDRLDCSSEIDASVLVA  103 (151)
Q Consensus        40 ~Rsg~~~~gfEGGQ~Pl~r------rlPK-------rGF~~~~~---~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~  103 (151)
                      +|.|...+       |+||      |-|.       -||.++..   .+...+|.+.+..|+..+--- .+++ ...|..
T Consensus         7 ~r~G~k~~-------P~YrIVv~d~r~~RdGk~iE~lG~Y~P~~~~~~~~i~l~~eri~~Wl~~GAqp-t~~V-~~ll~~   77 (82)
T 3i1m_P            7 ARHGAKKR-------PFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATI-SDRV-AALIKE   77 (82)
T ss_dssp             EECSCTTS-------CCEEEEEEETTSCTTSCCSEECEEECSCCCSSSCCEEECHHHHHHHHHTCCEE-CTTH-HHHHTT
T ss_pred             CCCCCCCC-------CEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEECHHHHHHHHHCCCCC-CHHH-HHHHHH
T ss_conf             13899899-------85899996678888985711253788877898434566799999999975977-8999-999999


Q ss_pred             CCC
Q ss_conf             086
Q gi|254780242|r  104 SGL  106 (151)
Q Consensus       104 ~gl  106 (151)
                      +|+
T Consensus        78 ~gi   80 (82)
T 3i1m_P           78 VNK   80 (82)
T ss_dssp             SCS
T ss_pred             HHH
T ss_conf             863


No 13 
>>3cuq_A Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, alternative splicing, coiled coil, cytoplasm, nucleus, protein transport; 2.61A {Homo sapiens} PDB: 2zme_A (A:61-151)
Probab=23.07  E-value=34  Score=15.97  Aligned_cols=40  Identities=20%  Similarity=0.321  Sum_probs=28.4

Q ss_pred             EEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCC
Q ss_conf             7751120454302455533223355554308625443320463044
Q gi|254780242|r   75 TISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRRSQRGIRILSDG  120 (151)
Q Consensus        75 ~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~~~~~vKiLg~G  120 (151)
                      .|.|++|...+.+.+-....+|+.+++..+      ...+|+||+|
T Consensus        34 li~l~el~~~l~k~r~~~~~~Is~dDi~rA------i~~L~~LG~G   73 (91)
T 3cuq_A           34 LITLEELHQQVLKGRGKFAQDVSQDDLIRA------IKKLKALGTG   73 (91)
T ss_dssp             EEEHHHHHHHHHHTTTTCCSSCCHHHHHHH------HHHHGGGBTT
T ss_pred             EEEHHHHHHHHHHHCCCCCCCCCHHHHHHH------HHHHHHCCCC
T ss_conf             658999999999855776676699999999------9999984998


No 14 
>>3bn0_A 30S ribosomal protein S16; ribonucleoprotein, ribosome; 2.00A {Aquifex aeolicus} (A:)
Probab=21.84  E-value=34  Score=15.93  Aligned_cols=45  Identities=11%  Similarity=0.166  Sum_probs=33.1

Q ss_pred             CCCCCCCCCCEEEEEHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCC
Q ss_conf             35546565521477511204543024555332233555543086254
Q gi|254780242|r   63 RGFVNIAGSDFVTISLGLLQAYIDKDRLDCSSEIDASVLVASGLVRR  109 (151)
Q Consensus        63 rGF~~~~~~~~~~iNL~~L~~~i~~~~~~~~~~Id~~~L~~~gli~~  109 (151)
                      -||.++...+...||.+.|..|+..+-- +.+++ ...|..+|++..
T Consensus        37 iG~YdP~~~k~~~l~~~ri~~Wl~~GAq-pt~~V-~~ll~~~gi~~~   81 (112)
T 3bn0_A           37 LGTYDPKRKVLINVYPEKVKEWVLKGVE-LSHRA-KAILWNHGILKE   81 (112)
T ss_dssp             EEEEETTTTEEEEECHHHHHHHHHTTCE-EEHHH-HHHHHHTTHHHH
T ss_pred             EEEECCCCCCCEEECHHHHHHHHHCCCC-CCHHH-HHHHHHCCCCCC
T ss_conf             5562799975423689999999997498-47999-999997697400


No 15 
>>2ftc_E Mitochondrial ribosomal protein L7/12, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} (E:66-137)
Probab=21.60  E-value=63  Score=14.56  Aligned_cols=16  Identities=25%  Similarity=0.532  Sum_probs=13.2

Q ss_pred             HHHHHHHHHCCCEEEE
Q ss_conf             9999999974988998
Q gi|254780242|r  135 ASAVEKVEKLGGQVIV  150 (151)
Q Consensus       135 ~sA~ekIE~aGG~v~i  150 (151)
                      +.+++++|.+|++|++
T Consensus        56 E~ik~~Le~aGA~Vel   71 (72)
T 2ftc_E           56 EKIKAALEAVGGTVVL   71 (72)
T ss_pred             HHHHHHHHHCCCEEEE
T ss_conf             9999999985997973


No 16 
>>1m0s_A Ribose-5-phosphate isomerase A; D-ribose 5-phosphate isomerase, northeast structural genomics consortium, IR21, structural genomics, PSI; HET: CIT; 1.90A {Haemophilus influenzae} (A:126-202)
Probab=20.70  E-value=66  Score=14.46  Aligned_cols=28  Identities=18%  Similarity=0.157  Sum_probs=15.5

Q ss_pred             CCCEEEEEEEECH-HHHHHHHHCCCEEEE
Q ss_conf             4414899998269-999999974988998
Q gi|254780242|r  123 KAKVVLRVSGASA-SAVEKVEKLGGQVIV  150 (151)
Q Consensus       123 ~~ki~I~v~~~S~-sA~ekIE~aGG~v~i  150 (151)
                      +.|+-|||.-++- ...+.+++.|++.++
T Consensus         4 ~~piPvEV~P~a~~~v~~~l~~lG~~~~l   32 (77)
T 1m0s_A            4 TFPLPVEVIPMARSQVGRKLAALGGSPEY   32 (77)
T ss_dssp             SSCEEEEECGGGHHHHHHHHHHTTCEEEE
T ss_pred             CCCEEEEEEHHHHHHHHHHHHHCCCCCCC
T ss_conf             99778998167889999999982899523


No 17 
>>1dd3_A 50S ribosomal protein L7/L12; dimer formation, flexibility, hinge region, four-helix- bundle, five-helix- bundle, alpha-beta structure; 2.00A {Thermotoga maritima} (A:58-128)
Probab=20.17  E-value=68  Score=14.40  Aligned_cols=16  Identities=25%  Similarity=0.393  Sum_probs=13.3

Q ss_pred             HHHHHHHHHCCCEEEE
Q ss_conf             9999999974988998
Q gi|254780242|r  135 ASAVEKVEKLGGQVIV  150 (151)
Q Consensus       135 ~sA~ekIE~aGG~v~i  150 (151)
                      +..++++|.+|++|++
T Consensus        55 E~iK~~Le~aGA~Vei   70 (71)
T 1dd3_A           55 EEIKKKLEEAGAEVEL   70 (71)
T ss_dssp             HHHHHHHHHTTCEEEE
T ss_pred             HHHHHHHHHCCCEEEE
T ss_conf             9999999985997973


Done!