Query         gi|254780256|ref|YP_003064669.1| 50S ribosomal protein L22 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 131
No_of_seqs    114 out of 1450
Neff          5.6 
Searched_HMMs 23785
Date          Tue May 24 08:43:49 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780256.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 2zjr_P 50S ribosomal protein L 100.0 2.2E-42       0  269.3  10.9  123    5-127    12-134 (134)
  2 1i4j_A 50S ribosomal protein L 100.0 3.5E-40 1.5E-44  256.3  11.8  110   15-127     1-110 (110)
  3 3bbo_U Ribosomal protein L22;  100.0 5.8E-42       0  266.8   0.9  115   14-128    29-143 (199)
  4 2ftc_M Mitochondrial ribosomal 100.0 1.6E-39 6.9E-44  252.4  11.8  107   21-127     3-110 (110)
  5 3ofq_S 50S ribosomal protein L 100.0 7.1E-41 2.8E-45  260.4   2.8  110   15-124     1-110 (110)
  6 1vq8_R 50S ribosomal protein L 100.0 1.1E-37 4.6E-42  241.6   9.7  118   10-128     8-155 (155)
  7 2zkr_r 60S ribosomal protein L 100.0   2E-36 8.3E-41  234.2  12.4  116   11-127     9-156 (184)
  8 2wwb_I 60S ribosomal protein L 100.0 7.5E-37 3.2E-41  236.7   9.0  119    8-127     6-156 (184)
  9 1su0_B NIFU like protein ISCU;  58.9     9.1 0.00038   17.9   3.8   66   17-82     58-152 (159)
 10 2z7e_A ISCU protein, NIFU-like  50.6      13 0.00055   17.0   4.1   63   16-78     55-128 (157)
 11 3lvl_A NIFU-like protein; prot  27.6      31  0.0013   14.8   6.2   60   17-76     57-126 (129)
 12 3ka5_A Ribosome-associated pro  26.3      22 0.00092   15.7   1.5   17   38-54     10-26  (65)
 13 3k2t_A LMO2511 protein; lister  24.3      26  0.0011   15.2   1.6   18   38-55     10-27  (57)
 14 3lyv_A Ribosome-associated fac  22.8      24   0.001   15.5   1.1   18   38-55     11-28  (66)

No 1  
>2zjr_P 50S ribosomal protein L22; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.55.1.1 PDB: 1j5a_L* 1jzy_L* 1jzz_L* 1k01_L* 1nkw_Q 1nwx_Q* 1nwy_Q* 1ond_Q* 1sm1_Q* 1xbp_Q* 2zjp_P* 2zjq_P 1jzx_L 3cf5_P* 3dll_P* 1pnu_Q 1pny_Q 1vor_T 1vou_T 1vow_T ...
Probab=100.00  E-value=2.2e-42  Score=269.27  Aligned_cols=123  Identities=36%  Similarity=0.432  Sum_probs=114.6

Q ss_pred             HHHHHHHHHHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEE
Q ss_conf             35767421011231121487508899999999847986999998886582024799999999999999840599823369
Q gi|254780256|r    5 RSVSKRRMGDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLI   84 (131)
Q Consensus         5 ~~~~~~~~~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~   84 (131)
                      +...+....+++..|+++|+|+||+|+++|+++|||++|+||+.||+|+|+++|.+|+|+|.||++||++|+|+|+|+||
T Consensus        12 k~~~~~~~~~~~~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kkaA~~i~K~L~SA~aNA~~~~~~d~~~L~   91 (134)
T 2zjr_P           12 KQRKQQVKLRKPGFAVAKYVRMSPRKVRLVVDVIRGKSVQDAEDLLRFIPRSASEPVAKVLNSAKANALHNDEMLEDRLF   91 (134)
T ss_dssp             HHHHHHCCCCCTTEEEEEEESSCHHHHHHHHHHSTTSBHHHHHHHHHHCCCTTHHHHHHHHTTTHHHHTTTTCCCGGGEE
T ss_pred             HHHHHHHHCCCHHHHHHCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHEE
T ss_conf             99888761203456745627448899999999986990999999980197879999999999999999985399889958


Q ss_pred             EEEEEECCCCEEEEEEECCCCCCCCEECCCCEEEEEEEECCCC
Q ss_conf             9999988981142010256666372017850089999851723
Q gi|254780256|r   85 VSEAYVGKSVFMKRFHCRGRQRIGRIVRPFSRLTVIVREVSDE  127 (131)
Q Consensus        85 I~~~~v~~G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~~~  127 (131)
                      |+++|||+||++|||+||||||++++++|+|||+|+|+|..++
T Consensus        92 I~~~~v~~G~~~KR~~prArGRa~~i~k~~sHI~VvL~ek~~~  134 (134)
T 2zjr_P           92 VKEAYVDAGPTLKRLIPRARGSANIIKKRTSHITIIVAEKGNK  134 (134)
T ss_dssp             EEEEEEEECCCEEEEEECSTTCEEEEEECCEEEEEEEEECCCC
T ss_pred             EEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCC
T ss_conf             8999989997054769875888876137840489999746889


No 2  
>1i4j_A 50S ribosomal protein L22; mutant, erythromycin resistance, RNA binding, RNA binding protein; 1.80A {Thermus thermophilus} SCOP: d.55.1.1 PDB: 1bxe_A 1giy_S 1ml5_s* 1vsa_Q 1vsp_Q 1yl3_S 2b66_W 2b9n_W 2b9p_W 2hgj_V 2hgq_V 2hgu_V 2j01_W 2j03_W 2jl6_W 2jl8_W 2v47_W 2v49_W 2wdi_W 2wdj_W ...
Probab=100.00  E-value=3.5e-40  Score=256.29  Aligned_cols=110  Identities=44%  Similarity=0.494  Sum_probs=106.0

Q ss_pred             HEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCC
Q ss_conf             12311214875088999999998479869999988865820247999999999999998405998233699999988981
Q gi|254780256|r   15 NEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSV   94 (131)
Q Consensus        15 ~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~   94 (131)
                      +|++|.+||+++||+|+|+|+++|||++|++|+.||+|+|+++|.+|+|+|+||++||++++|+|+|+|||+++|||+||
T Consensus         1 Me~~A~~r~ir~Sp~K~r~va~~IRG~~v~~Al~~L~f~~kk~A~~i~k~L~SA~aNA~~~~~~d~~~L~I~~~~v~~Gp   80 (110)
T 1i4j_A            1 MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKVLESAAANAVNNHDALEDRLYVKAAYVDEGP   80 (110)
T ss_dssp             CCEEEEEEEESSCHHHHHHHHHHHTTCBHHHHHHHHHHCCCTTHHHHHHHHHHHHHHHHHTSCCCGGGEEEEEEEEEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCC
T ss_conf             90798818653288999999999869919999999821871219999999999999999854998102699999989997


Q ss_pred             EEEEEEECCCCCCCCEECCCCEEEEEEEECCCC
Q ss_conf             142010256666372017850089999851723
Q gi|254780256|r   95 FMKRFHCRGRQRIGRIVRPFSRLTVIVREVSDE  127 (131)
Q Consensus        95 ~~KR~~prarGRa~~i~k~~sHi~VvL~e~~~~  127 (131)
                      ++   +||||||+++|+||+|||+|+|+|.+.+
T Consensus        81 ~~---kprarGRa~~i~k~~sHi~vvL~e~~~k  110 (110)
T 1i4j_A           81 AV---LPRARGRADIIKKRTSHITVILGEKHGK  110 (110)
T ss_dssp             EE---CSCSSSCCCSCCEEEEEEEEEEEESSCC
T ss_pred             EE---CCCCCCCCCCCCCCCCCEEEEEECCCCC
T ss_conf             48---8267898886068877789999336789


No 3  
>3bbo_U Ribosomal protein L22; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Probab=100.00  E-value=5.8e-42  Score=266.83  Aligned_cols=115  Identities=29%  Similarity=0.379  Sum_probs=110.5

Q ss_pred             HHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCC
Q ss_conf             11231121487508899999999847986999998886582024799999999999999840599823369999998898
Q gi|254780256|r   14 DNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKS   93 (131)
Q Consensus        14 ~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G   93 (131)
                      ..|+.|.++||++||+|+|+|+|+|||++|++|+.||+|+|+++|.+|.++|.||++||++|+|+|+|+|||++||||+|
T Consensus        29 ~~ev~a~~~~IriSpkK~R~VadlIRGk~V~eAl~~L~fspkKaA~~I~KlL~SAvaNA~~n~~ld~d~L~I~ea~V~~G  108 (199)
T 3bbo_U           29 CDEITTRGYSISMSVDKARRVIDQIRGRSYAETLMILELMPYRACYPIFKLIYSAAANASHNKQFNKANLIISKAEVNKG  108 (199)
T ss_dssp             -CCBCCCCSCCSSCSSSSSTTHHHHTTCBTTTTTTTGGGCCCTTHHHHHHHHHHHTTHHHHTSSCCSSSCEEEECCCCBC
T ss_pred             CCEEEEECCEEEECHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCC
T ss_conf             71379987852048799999999986992999999974696768999999999999998730156644449999998899


Q ss_pred             CEEEEEEECCCCCCCCEECCCCEEEEEEEECCCCC
Q ss_conf             11420102566663720178500899998517233
Q gi|254780256|r   94 VFMKRFHCRGRQRIGRIVRPFSRLTVIVREVSDEG  128 (131)
Q Consensus        94 ~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~~~~  128 (131)
                      |++||++||||||+++|++|+|||||||+|.+..+
T Consensus       109 p~lKR~rpRARGRa~~I~krtsHItIVL~E~s~~~  143 (199)
T 3bbo_U          109 ITLKKVKPRARGRSYMILRPTCHITIVLRDITHFD  143 (199)
T ss_dssp             CCCCCCCCSSSSCSCCCCCCCBCCCCEEECCCCCC
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHH
T ss_conf             74448798757888875688634899998677146


No 4  
>2ftc_M Mitochondrial ribosomal protein L22 isoform A; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_M
Probab=100.00  E-value=1.6e-39  Score=252.35  Aligned_cols=107  Identities=27%  Similarity=0.421  Sum_probs=103.6

Q ss_pred             CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCC-HHHEEEEEEEECCCCEEEEE
Q ss_conf             14875088999999998479869999988865820247999999999999998405998-23369999998898114201
Q gi|254780256|r   21 ASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLD-VDRLIVSEAYVGKSVFMKRF   99 (131)
Q Consensus        21 ~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld-~~~L~I~~~~v~~G~~~KR~   99 (131)
                      .+++++||+|+|+|+++|||++|+||++||+|+|+|+|..|.|+|+||++||++|+|+| +|+|||+++|||+||++|||
T Consensus         3 ~r~ir~SpkK~r~v~~~IrG~~v~~A~~~L~f~~kkaA~~i~k~l~sA~aNA~~~~~~~~~~~L~I~~~~v~~G~~~KR~   82 (110)
T 2ftc_M            3 RRQIKYSKDKMWYLAKLIRGMSIDQALAQLEFNDKKGAKIIKEVLLEAQDMAVRDHNVEFRSNLYIAESTSGRGQCLKRI   82 (110)
T ss_pred             CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCCCCC
T ss_conf             56474487999999999869919999999811881008999999999999999861999767579999998999705476


Q ss_pred             EECCCCCCCCEECCCCEEEEEEEECCCC
Q ss_conf             0256666372017850089999851723
Q gi|254780256|r  100 HCRGRQRIGRIVRPFSRLTVIVREVSDE  127 (131)
Q Consensus       100 ~prarGRa~~i~k~~sHi~VvL~e~~~~  127 (131)
                      +||||||+++|+||+|||+|+|+|.+++
T Consensus        83 ~prarGRa~~i~k~~sHi~vvL~E~~~p  110 (110)
T 2ftc_M           83 RYHGRGRFGIMEKVYCHYFVKLVEGPPP  110 (110)
T ss_pred             CCCCCCCCCCCCCCCCCEEEEEEECCCC
T ss_conf             9875888886468731189999827999


No 5  
>3ofq_S 50S ribosomal protein L22; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_Q 1p86_Q 1vs8_S 1vs6_S 2aw4_S 2awb_S 1vt2_S 2i2v_S 2j28_S 2i2t_S* 2qao_S* 2qba_S* 2qbc_S* 2qbe_S 2qbg_S 2qbi_S* 2qbk_S* 2qov_S 2qox_S 2qoz_S* ...
Probab=100.00  E-value=7.1e-41  Score=260.38  Aligned_cols=110  Identities=42%  Similarity=0.523  Sum_probs=107.9

Q ss_pred             HEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCC
Q ss_conf             12311214875088999999998479869999988865820247999999999999998405998233699999988981
Q gi|254780256|r   15 NEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSV   94 (131)
Q Consensus        15 ~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~   94 (131)
                      +|++|.++|+|+||+|+|+|+++|||++|+||++||+|+|+++|..|.|+|+||++||++++|+|+|+|||.++|||+||
T Consensus         1 me~~A~~k~~r~SpkK~r~va~~IRG~~v~~Al~~L~f~~~k~a~~i~k~l~sA~anA~~~~~~d~~~L~I~~~~v~~G~   80 (110)
T 3ofq_S            1 METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGP   80 (110)
T ss_dssp             CCCEEEESSCSSCHHHHHHHHTTSSSSCSSSTTTTTTTCCSGGGGTTHHHHHHHHHHHHSSSCCCGGGCCCCCEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCC
T ss_conf             95899838863287999999999869929999999865871108999999999999877512477030199999979986


Q ss_pred             EEEEEEECCCCCCCCEECCCCEEEEEEEEC
Q ss_conf             142010256666372017850089999851
Q gi|254780256|r   95 FMKRFHCRGRQRIGRIVRPFSRLTVIVREV  124 (131)
Q Consensus        95 ~~KR~~prarGRa~~i~k~~sHi~VvL~e~  124 (131)
                      ++|||+||||||++++++|+|||+|+|+|.
T Consensus        81 ~~KR~~prarGRa~~i~k~~sHi~vvL~Ek  110 (110)
T 3ofq_S           81 SMKRIMPRAKGRADRILKRTSHITVVVSDR  110 (110)
T ss_dssp             CEECCEECGGGCEECCEECCCEEEEECCCC
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEEEECC
T ss_conf             304768962588885237861489999269


No 6  
>1vq8_R 50S ribosomal protein L22P; 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: d.55.1.1 PDB: 1vq4_R* 1vq5_R* 1vq6_R* 1vq7_R* 1s72_R* 1vq9_R* 1vqk_R* 1vql_R* 1vqm_R* 1vqn_R* 1vqo_R* 1vqp_R* 1yhq_R* 1yi2_R* 1yij_R* 1yit_R* 1yjn_R* 1yjw_R* 2otj_R* 2otl_R* ...
Probab=100.00  E-value=1.1e-37  Score=241.57  Aligned_cols=118  Identities=20%  Similarity=0.180  Sum_probs=112.1

Q ss_pred             HHHHHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHH------------------------------HCCCHHHH
Q ss_conf             421011231121487508899999999847986999998886------------------------------58202479
Q gi|254780256|r   10 RRMGDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLE------------------------------FSRKRIAG   59 (131)
Q Consensus        10 ~~~~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~------------------------------f~~kk~A~   59 (131)
                      ...++++++|.++++++||+|++.|+++|||+++++|+.+|+                              |+|+++|+
T Consensus         8 ~~~~~~~akA~~~~~riS~kk~~~v~~~Irg~~v~~A~~~L~~v~~kk~~vpf~r~~~~v~~~~~~~~~~~g~~P~kaa~   87 (155)
T 1vq8_R            8 EADPDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFKQHNSGVGHKSKVDGWDAGRYPEKASK   87 (155)
T ss_dssp             CCCGGGEEEEEEEEECSCHHHHHHHHHHHTTSBHHHHHHHHHHHHHTSSCEECSSSCTTCCBCTTCSSSSBEECCHHHHH
T ss_pred             CCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHH
T ss_conf             89998148998488755689999999997698999999999998865466677644466243224357676658067899


Q ss_pred             HHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEEEEECCCCCCCCEECCCCEEEEEEEECCCCC
Q ss_conf             999999999999984059982336999999889811420102566663720178500899998517233
Q gi|254780256|r   60 EVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKRFHCRGRQRIGRIVRPFSRLTVIVREVSDEG  128 (131)
Q Consensus        60 ~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~~~~  128 (131)
                      +|.|+|+||.+||+++ ++|+|+|||++||||+||++||++|||+||++++++++|||+|||+|.+.|+
T Consensus        88 ~i~kllksa~aNA~~~-~~d~~~l~I~~~~v~kg~~~kr~~pRA~GRa~~~~k~~~hi~Ivl~E~~~ee  155 (155)
T 1vq8_R           88 AFLDLLENAVGNADHQ-GFDGEAMTIKHVAAHKVGEQQGRKPRAMGRASAWNSPQVDVELILEEPEVED  155 (155)
T ss_dssp             HHHHHHHHHHHHHHHT-TSCGGGSEEEEEEEEEEEEECCEEECGGGCEEECCEEEEEEEEEEECC----
T ss_pred             HHHHHHHHHHHHHHHC-CCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCC
T ss_conf             9999999999999854-8885561899999899872356675547788870489712899997068779


No 7  
>2zkr_r 60S ribosomal protein L17; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}
Probab=100.00  E-value=2e-36  Score=234.19  Aligned_cols=116  Identities=26%  Similarity=0.256  Sum_probs=109.3

Q ss_pred             HHHHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHC--------------------------------CCHHH
Q ss_conf             2101123112148750889999999984798699999888658--------------------------------20247
Q gi|254780256|r   11 RMGDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFS--------------------------------RKRIA   58 (131)
Q Consensus        11 ~~~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~--------------------------------~kk~A   58 (131)
                      ..+++.++|.++++++||+|+++||++||||++++|+.+|+|+                                |+++|
T Consensus         9 ~~~~k~akA~~~~~riS~Kk~r~va~~IrG~~v~~A~~~L~~v~~kk~~vp~kr~~~~v~~~~~~~~~~~~~gr~P~kaa   88 (184)
T 2zkr_r            9 ENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPFRRYNGGVGRCAQAKQWGWTQGRWPKKSA   88 (184)
T ss_dssp             SCTTTEEEEEECSCCSCHHHHHHHHHHHTTSBHHHHHHHHHHHHHTSSCEECSSSCTTCCBCCSTTSCSCSBEECCHHHH
T ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHH
T ss_conf             89984268966877476799999999987990999999999888567431056652001136563024766454758999


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEEEEECCCCCCCCEECCCCEEEEEEEECCCC
Q ss_conf             999999999999998405998233699999988981142010256666372017850089999851723
Q gi|254780256|r   59 GEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKRFHCRGRQRIGRIVRPFSRLTVIVREVSDE  127 (131)
Q Consensus        59 ~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~~~  127 (131)
                      ..|.++|+||.+||+++ |+|+|+|||+++|||+||++||++|||+||++++++++|||+|||+|.++.
T Consensus        89 ~~i~klL~sa~aNA~~~-~ld~~~L~I~~i~v~~G~~~kR~~pRArGRa~~i~k~~shI~vvl~E~~~~  156 (184)
T 2zkr_r           89 EFLLHMLKNAESNAELK-GLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKEQI  156 (184)
T ss_dssp             HHHHHHHHHHHHHHHHH-TSCTTTCEEEEEEEC-CCCEEEEEEETTTEEEEEEEC-CCEEEEEECC---
T ss_pred             HHHHHHHHHHHHHHHHC-CCCHHHEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCC
T ss_conf             99999999999878734-998033499999979886046776166888787317984589999507745


No 8  
>2wwb_I 60S ribosomal protein L17-A; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 2wwa_I 2ww9_I 1s1i_N
Probab=100.00  E-value=7.5e-37  Score=236.65  Aligned_cols=119  Identities=28%  Similarity=0.254  Sum_probs=111.2

Q ss_pred             HHHHHHHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHH--------------------------------HCCC
Q ss_conf             67421011231121487508899999999847986999998886--------------------------------5820
Q gi|254780256|r    8 SKRRMGDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLE--------------------------------FSRK   55 (131)
Q Consensus         8 ~~~~~~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~--------------------------------f~~k   55 (131)
                      .....+++.++|.++|+|+||+|+++||++||||++++|+.+|+                                |.|+
T Consensus         6 ~~~~~~~k~akA~~~~lriS~Kk~r~va~~IrG~~v~~A~~~L~~V~~kK~~Vpf~r~~~~vg~~~~~~~~g~~~gr~P~   85 (184)
T 2wwb_I            6 ATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPA   85 (184)
T ss_dssp             SCCCCGGGEEEEEEEEESSCHHHHHHHHHHSCSSCHHHHHHHHHHHHHTSCSCCCSSCCCCSSCCCCSCCSSCCCCCCCT
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHEEEEEEEECCCCCCHHHHHHCCCCCCCCCH
T ss_conf             68789981289954887246699999999987984999999999987500420367761765634566641887774857


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEEEEECCCCCCCCEECCCCEEEEEEEECCCC
Q ss_conf             247999999999999998405998233699999988981142010256666372017850089999851723
Q gi|254780256|r   56 RIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKRFHCRGRQRIGRIVRPFSRLTVIVREVSDE  127 (131)
Q Consensus        56 k~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~~~  127 (131)
                      ++|.+|.|+|+||.+||++ .|+|+|+|||+++|||+||++||++|||+||++++++++|||+|||+|.++.
T Consensus        86 kaa~~i~KlL~sa~aNA~~-~~ld~~~L~I~~i~v~~G~~~KR~~pRA~GRa~~i~k~~~HI~ivl~e~~~~  156 (184)
T 2wwb_I           86 KSVKFVQGLLQNAAANAEA-KGLDATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVTEKEEA  156 (184)
T ss_dssp             HHHHHHHHHHHHHHHHTTS-SCCCSSCCCEEEEEEECCCCEEEEEEEETTEEEEEEECCEEEEEEEECC---
T ss_pred             HHHHHHHHHHHHHHHHHHH-CCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCC
T ss_conf             8999999999999987651-1367324399999988885336767123568886038974489999737644


No 9  
>1su0_B NIFU like protein ISCU; structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; 2.30A {Streptococcus pyogenes} SCOP: d.224.1.2
Probab=58.91  E-value=9.1  Score=17.94  Aligned_cols=66  Identities=17%  Similarity=0.187  Sum_probs=46.9

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHH----------------------H-------CCCHHHHHHHHHHHH
Q ss_conf             31121487508899999999847986999998886----------------------5-------820247999999999
Q gi|254780256|r   17 ANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLE----------------------F-------SRKRIAGEVRKTLCS   67 (131)
Q Consensus        17 ~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~----------------------f-------~~kk~A~~i~k~L~S   67 (131)
                      ++-.++.--+|-==+..++.+|.|+++++|.....                      |       +..+.|.+-.++|+.
T Consensus        58 i~f~~~GCai~~ASasi~~e~i~Gk~~~e~~~l~~~~~~~l~~~~~~~~~~l~~l~~l~~v~~~p~R~~Ca~L~~~Al~~  137 (159)
T 1su0_B           58 IAFAGNGCTISTASSSMMTDAVIGKSKEEALALADIFSEMVQGQENPAQKELGEAELLAGVAKFPQRIKCSTLAWNALKE  137 (159)
T ss_dssp             EEEEEECCHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCGGGGGGGGGGGGGGGGGCHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             89997177898999999999984998999999999999998367787322235788740756686222999879999999


Q ss_pred             HHHHHHHCCCCCHHH
Q ss_conf             999998405998233
Q gi|254780256|r   68 AVANAENNHDLDVDR   82 (131)
Q Consensus        68 A~aNA~~n~~ld~~~   82 (131)
                      |+.++.++.....++
T Consensus       138 al~~~~~~~~~~~~~  152 (159)
T 1su0_B          138 AIKRSANAQHLTDQN  152 (159)
T ss_dssp             HHTC-----------
T ss_pred             HHHHHHHCCCCCHHC
T ss_conf             999787433332102


No 10 
>2z7e_A ISCU protein, NIFU-like protein; iron-sulfur cluster, iron, biosynthesis, [2Fe-2S], asymmetric trimer, three conserved Cys; 2.30A {Aquifex aeolicus}
Probab=50.64  E-value=13  Score=17.03  Aligned_cols=63  Identities=13%  Similarity=0.055  Sum_probs=46.4

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHH---------HH--CCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             23112148750889999999984798699999888---------65--82024799999999999999840599
Q gi|254780256|r   16 EANAIASMLRVSPQKLNLVAAMIRGKRVSDALADL---------EF--SRKRIAGEVRKTLCSAVANAENNHDL   78 (131)
Q Consensus        16 e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L---------~f--~~kk~A~~i~k~L~SA~aNA~~n~~l   78 (131)
                      +++-....--+|-==+-.++++|+|+++++|+.+-         .+  ...+.|.+-..+|+.|+.+...+.|-
T Consensus        55 di~f~~~GCais~AsaSil~e~i~Gktl~ea~~I~~~~i~e~Lg~lpp~R~~CA~La~~Al~~Al~dy~~k~g~  128 (157)
T 2z7e_A           55 DVRFKTFGCGSAIAVSSMLTEMVKGKPIQYALNLTYKDIFEELGGLPPQKIHCTNLGLETLHVAIKDYLMKQGR  128 (157)
T ss_dssp             EEEEEEESCTTHHHHHHHHHHHHTTSBHHHHHHCCHHHHHHHHTCCCCSSCCTTCCHHHHHHHHHHHHHHTTTC
T ss_pred             EEEEEECCCHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             88999768756678999999997699599998512589999866999531429999999999999999974588


No 11 
>3lvl_A NIFU-like protein; protein-protein complex, structural genomics, montreal-kings bacterial structural genomics initiative, BSGI; HET: PLP; 3.00A {Escherichia coli} PDB: 1q48_A 1r9p_A 1wfz_A
Probab=27.60  E-value=31  Score=14.82  Aligned_cols=60  Identities=18%  Similarity=0.172  Sum_probs=42.3

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHH--------HHH--CCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             311214875088999999998479869999988--------865--820247999999999999998405
Q gi|254780256|r   17 ANAIASMLRVSPQKLNLVAAMIRGKRVSDALAD--------LEF--SRKRIAGEVRKTLCSAVANAENNH   76 (131)
Q Consensus        17 ~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~--------L~f--~~kk~A~~i~k~L~SA~aNA~~n~   76 (131)
                      ++-.+..--+|-==.-.++.+|+|+++++|..+        |..  +..+.|.+...+|+.|+.+.+.++
T Consensus        57 i~F~~~GC~is~Asas~~~e~i~Gkt~~ea~~i~~~~i~~~l~~~p~r~~Ca~L~~~al~~al~~y~~k~  126 (129)
T 3lvl_A           57 ARFKTYGCGSAIASSSLVTEWVKGKSLDEAQAIKNTDIAEELELPPVKIHCSILAEDAIKAAIADYKSKR  126 (129)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHTTCCHHHHHTCCHHHHHHHHTCCGGGGHHHHHHHHHHHHHHHHHHHSC
T ss_pred             EEEEECCCHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8777358889999999999998599699998653689998733787512099999999999999999875


No 12 
>3ka5_A Ribosome-associated protein Y (PSRP-1); structural genomics, PSI-2, protein structure initiative; 1.80A {Clostridium acetobutylicum}
Probab=26.25  E-value=22  Score=15.69  Aligned_cols=17  Identities=18%  Similarity=0.305  Sum_probs=13.5

Q ss_pred             HCCCCHHHHHHHHHHCC
Q ss_conf             47986999998886582
Q gi|254780256|r   38 IRGKRVSDALADLEFSR   54 (131)
Q Consensus        38 IrG~~v~eAl~~L~f~~   54 (131)
                      ++-|+++||+.||..+.
T Consensus        10 ~kpmsveEAv~qmel~~   26 (65)
T 3ka5_A           10 IKPMSEEEAVLEMELLG   26 (65)
T ss_dssp             CSCBCHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHCCC
T ss_conf             78899999999975489


No 13 
>3k2t_A LMO2511 protein; listeria monocytogenes,binding, structural genomics, PSI-2, protein structure initiative; 2.40A {Listeria monocytogenes}
Probab=24.34  E-value=26  Score=15.23  Aligned_cols=18  Identities=6%  Similarity=0.209  Sum_probs=14.1

Q ss_pred             HCCCCHHHHHHHHHHCCC
Q ss_conf             479869999988865820
Q gi|254780256|r   38 IRGKRVSDALADLEFSRK   55 (131)
Q Consensus        38 IrG~~v~eAl~~L~f~~k   55 (131)
                      ++-|+++||+.||..+..
T Consensus        10 ~kpmsveEAv~~mel~~~   27 (57)
T 3k2t_A           10 LKPMDSEEAVLQMNLLGH   27 (57)
T ss_dssp             -CCBCHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHCCCC
T ss_conf             788999999999754799


No 14 
>3lyv_A Ribosome-associated factor Y; ribosomal protein S30AE family, structural genomics, PSI-2, structure initiative; 2.70A {Streptococcus pyogenes}
Probab=22.81  E-value=24  Score=15.48  Aligned_cols=18  Identities=17%  Similarity=0.266  Sum_probs=13.4

Q ss_pred             HCCCCHHHHHHHHHHCCC
Q ss_conf             479869999988865820
Q gi|254780256|r   38 IRGKRVSDALADLEFSRK   55 (131)
Q Consensus        38 IrG~~v~eAl~~L~f~~k   55 (131)
                      ++-|+++||+.||+.+..
T Consensus        11 ~kpmsveEAv~qmel~~~   28 (66)
T 3lyv_A           11 LKPMDVEEARLQMELLGH   28 (66)
T ss_dssp             CCEECHHHHHHHHHTTTC
T ss_pred             CCCCCHHHHHHHHHCCCC
T ss_conf             788999999998744799


Done!