Query gi|254780584|ref|YP_003064997.1| 50S ribosomal protein L28 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 97
No_of_seqs 107 out of 724
Neff 5.3
Searched_HMMs 23785
Date Tue May 31 20:17:57 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780584.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_X 50S ribosomal protein L 99.9 1.1E-28 4.5E-33 191.2 3.6 73 2-75 1-73 (77)
2 3bbo_Y Ribosomal protein L28; 99.9 9.7E-30 4.1E-34 197.4 -3.4 76 1-78 74-149 (151)
3 2jz6_A 50S ribosomal protein L 99.9 9.1E-26 3.8E-30 173.7 3.6 70 1-75 6-75 (77)
4 2j01_1 50S ribosomal protein L 99.9 2.9E-24 1.2E-28 164.7 -1.1 84 1-92 1-98 (98)
5 2zjr_U 50S ribosomal protein L 99.8 9.2E-23 3.9E-27 155.7 -2.0 65 1-67 1-80 (81)
6 2jl6_1 50S ribosomal protein L 99.8 3.9E-22 1.6E-26 152.0 -1.3 60 1-62 1-73 (89)
7 2zkr_o 60S ribosomal protein L 34.7 22 0.00094 15.9 2.7 28 47-74 101-132 (188)
8 1vq8_O 50S ribosomal protein L 31.9 22 0.00093 15.9 2.3 39 36-74 64-108 (116)
9 2uz0_A Esterase, tributyrin es 28.6 31 0.0013 15.1 3.4 25 29-53 3-27 (263)
10 1dvp_A HRS, hepatocyte growth 24.4 36 0.0015 14.6 4.2 59 2-61 161-219 (220)
11 2k5c_A Uncharacterized protein 23.6 15 0.00062 17.0 0.2 11 1-12 8-18 (95)
No 1
>3ofq_X 50S ribosomal protein L28; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 2i2v_X 2wwq_0* 3fik_X 2i2t_X 3ofr_X* 3i1n_X 1vt2_X* 2qao_Z* 2qba_Z* 2qbc_Z* 2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z 2qox_Z 2qoz_Z* 2qp1_Z* 2z4l_Z* 2z4n_Z* ...
Probab=99.94 E-value=1.1e-28 Score=191.19 Aligned_cols=73 Identities=37% Similarity=0.596 Sum_probs=69.9
Q ss_pred CCCCCCCCCCCCCCCCCCHHHCCCCCEECCCEEEEEEEECCCCCEEEEEEEHHHHHHHHHCCCHHHHHHHCCHH
Q ss_conf 85410117855367722332302374255524899998557786899999724530236418877999729844
Q gi|254780584|r 2 SRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKE 75 (97)
Q Consensus 2 sr~C~itGk~~~~Gn~vshs~~kTkR~~~PNlq~~~~~s~~l~~~v~l~vst~~lrtI~K~GGlD~yLl~~~~~ 75 (97)
||+||||||+|++||+||||+++|+|+|.||||++++|+|+++++|+|+|||+|||||+| +|||+||++++++
T Consensus 1 Sr~C~itGK~~~~Gn~vShs~~kTkR~~~pNlq~kr~~~~~~~~~v~lkvst~~LRtI~K-~Gld~~l~~~~~~ 73 (77)
T 3ofq_X 1 SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDK-KGIDTVLAELRAR 73 (77)
T ss_dssp CCCCSSSCCCCCCCBCCCSTTCCCBCCCCCCCCCEEEECSSSCSEEEECCCTTTTTHHHH-TCHHHHHHHHHTT
T ss_pred CCCCCCCCCCCCCCCEECCCCCCCCCEECCCEEEEEEEECCCCEEEEEEEEHHHEEEEHH-CCHHHHHHHHHHC
T ss_conf 988700897445586101025644655526538999998679979999999142316203-4999999998870
No 2
>3bbo_Y Ribosomal protein L28; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Nicotiana tabacum}
Probab=99.94 E-value=9.7e-30 Score=197.41 Aligned_cols=76 Identities=32% Similarity=0.450 Sum_probs=72.3
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHCCCCCEECCCEEEEEEEECCCCCEEEEEEEHHHHHHHHHCCCHHHHHHHCCHHHHH
Q ss_conf 985410117855367722332302374255524899998557786899999724530236418877999729844553
Q gi|254780584|r 1 MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKENLS 78 (97)
Q Consensus 1 Msr~C~itGk~~~~Gn~vshs~~kTkR~~~PNlq~~~~~s~~l~~~v~l~vst~~lrtI~K~GGlD~yLl~~~~~~Ls 78 (97)
|||+|+||||++++||+||||+++|+|+|+||||++++|+|++++||+++|||+||||||| ||||+||.++.. +|+
T Consensus 74 MSr~C~itGK~~~~Gn~VShS~~kTKR~f~pNlq~kri~~~~l~r~VklkVstkaLRTI~K-~Gld~~lkk~~~-~l~ 149 (151)
T 3bbo_Y 74 ARRICPFTGKKSNRANKVSHSNHKTKKLQFVNLQYKRIWWEAGKRYVKLRLSTKAIKTIEK-NGLDAVAKKAGI-DLS 149 (151)
T ss_dssp --CCCCCSCCTTCCCCCCEECCSSSCCEECCCCCCCCBCCCTTSSCCCBCCCSSSTTTTTT-STTTCSCCSSSS-CSS
T ss_pred HCCEEECCCCCCCCCCEEECCCCCCCCCCCCCEEEEEEEECCCCEEEEEEEECHHEEEEEC-CCHHHHHHHCCC-CCC
T ss_conf 4325003687345686232015533450315407999997568958999998430026304-079999997374-436
No 3
>2jz6_A 50S ribosomal protein L28; structure, NESG, ribonucleoprotein, structural genomics, PSI-2, protein structure initiative; NMR {Thermotoga maritima MSB8} SCOP: d.325.1.1
Probab=99.91 E-value=9.1e-26 Score=173.67 Aligned_cols=70 Identities=29% Similarity=0.542 Sum_probs=67.0
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHCCCCCEECCCEEEEEEEECCCCCEEEEEEEHHHHHHHHHCCCHHHHHHHCCHH
Q ss_conf 985410117855367722332302374255524899998557786899999724530236418877999729844
Q gi|254780584|r 1 MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKE 75 (97)
Q Consensus 1 Msr~C~itGk~~~~Gn~vshs~~kTkR~~~PNlq~~~~~s~~l~~~v~l~vst~~lrtI~K~GGlD~yLl~~~~~ 75 (97)
|||+||||||++++||+||||+++|+|+|+||||++++|+|+ |++++|+|||+|||| ||||+|++++++.
T Consensus 6 Mar~C~i~GK~~~~Gn~vShs~~kTkR~~~pNlq~~r~~~~~-g~~vrlkv~t~~lrt----g~i~k~~~~~~~~ 75 (77)
T 2jz6_A 6 MAKRCEVCGKAPRSGNTVSHSDKKSERWFRPNLQKVRVVLPD-GTIKRMRVCTSCLKS----GKVKKYVGQVSEV 75 (77)
T ss_dssp CCCCCTTTCCCCCCCCCCCCSCCCCSSSCBTTEEEEEEEETT-TEEEEEEEEHHHHHH----CCSCCCCCCCCSC
T ss_pred EEEECCCCCCCCCCCCEEEECCCCCCCEECCCEEEEEEEECC-CCEEEEEEEHHHHHH----CCHHHHHHHHHHC
T ss_conf 763344157847669707665862476053752899999439-979999999799543----4788999977664
No 4
>2j01_1 50S ribosomal protein L28; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: d.325.1.1 PDB: 2j03_1 2v47_1 2v49_1 2wdi_1 2wdj_1 2wdl_1 2wdn_1 2wh2_1 2wh4_1 2wrj_1 2wrl_1 2wro_1 2wrr_1 2x9s_1 2x9u_1 3hux_1 3huz_1 3i8f_Z 3i8i_Z 3i9c_Z ...
Probab=99.87 E-value=2.9e-24 Score=164.66 Aligned_cols=84 Identities=23% Similarity=0.444 Sum_probs=74.8
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHC-------------CCCCEECCCEEEEEEEECCCCCEEEEEEEHHHHHHHHHCCCHHH
Q ss_conf 98541011785536772233230-------------23742555248999985577868999997245302364188779
Q gi|254780584|r 1 MSRVCELTKKTVMSGNKVSHANN-------------KTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDR 67 (97)
Q Consensus 1 Msr~C~itGk~~~~Gn~vshs~~-------------kTkR~~~PNlq~~~~~s~~l~~~v~l~vst~~lrtI~K~GGlD~ 67 (97)
|||+|+||||+|++||+||||++ +|+|+|.||||++++|++ +++++++|||+|||||||
T Consensus 1 Msr~C~itGK~~~~Gn~vshsg~akk~GG~g~k~~~kTkR~f~PNlq~~r~~~~--g~~v~~~vst~~LRti~K------ 72 (98)
T 2j01_1 1 MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVA--GQEITFRVAASHIPKVYE------ 72 (98)
T ss_dssp -------CCCSSSCCCCCCCCCEECSCCSSSSCCCEEECCCCCCCCCCCCEEET--TTTEEECCCSSSHHHHHH------
T ss_pred CCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCEEECCCCEEEEEEEC--CEEEEEEEEHHHHHHHHH------
T ss_conf 977622259833358758715631113775322467543166255078999989--998999999799999999------
Q ss_pred HHHHCCHHHHHH-HHHHHHHHHHHHH
Q ss_conf 997298445539-9999999999999
Q gi|254780584|r 68 FLSNSKKENLSA-RMRTLRSQILKKM 92 (97)
Q Consensus 68 yLl~~~~~~Ls~-~~~klk~~i~~~l 92 (97)
|++.+....|+. .+.+++++|+..|
T Consensus 73 ~~~~~~~~kl~~~~~~~~kk~i~k~l 98 (98)
T 2j01_1 73 LVERAKGLKLEGLSPKEIKKELLKLL 98 (98)
T ss_dssp HHSCCCCCCCCSCCHHHHHHHCC---
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf 87875554203223899999998629
No 5
>2zjr_U 50S ribosomal protein L28; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.325.1.1 PDB: 2zjp_U 2zjq_U 3cf5_U* 3dll_U*
Probab=99.83 E-value=9.2e-23 Score=155.70 Aligned_cols=65 Identities=29% Similarity=0.358 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCCCCCCC-------------CHHHCCCCCEECCCEEEEEEEECCCCCEEEEEEEHHHHHHHHH--CCCH
Q ss_conf 985410117855367722-------------3323023742555248999985577868999997245302364--1887
Q gi|254780584|r 1 MSRVCELTKKTVMSGNKV-------------SHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVER--QGGL 65 (97)
Q Consensus 1 Msr~C~itGk~~~~Gn~v-------------shs~~kTkR~~~PNlq~~~~~s~~l~~~v~l~vst~~lrtI~K--~GGl 65 (97)
|||+||+|||+|++||+| |||+++|+|+|+||||++++|+| +++++++|||+|||||+| +.|+
T Consensus 1 Msr~C~i~GK~~~~Gn~v~~~Gkakk~Gg~~shs~~kTkR~f~PNlQ~~~~~~~--g~~v~~kvstk~Lrti~K~~~~~~ 78 (81)
T 2zjr_U 1 MSRECYLTGKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAIREN--GQVKTVWLSANALRTLSKGPYKGI 78 (81)
T ss_dssp -------CCSSSCCCCCCCCCCEESCCCTTTCSCCEECCCCCCCCCCCCCCCCS--SSCCCCCCCHHHHHHHHSSCCSSC
T ss_pred CCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEC--CEEEEEEEEHHHHHEECCCCCCCC
T ss_conf 975724368734338565103411114664130477025366467489999889--998999999578020500345671
Q ss_pred HH
Q ss_conf 79
Q gi|254780584|r 66 DR 67 (97)
Q Consensus 66 D~ 67 (97)
|.
T Consensus 79 ~~ 80 (81)
T 2zjr_U 79 EL 80 (81)
T ss_dssp C-
T ss_pred CC
T ss_conf 13
No 6
>2jl6_1 50S ribosomal protein L28, 50S ribosomal protein L25; methylation, translation, paromomycin, tRNA-binding, tRNA, zinc, mRNA, ribosome, repressor, RNA-binding; 3.45A {Thermus thermophilus} PDB: 2jl8_1
Probab=99.82 E-value=3.9e-22 Score=151.96 Aligned_cols=60 Identities=25% Similarity=0.455 Sum_probs=57.7
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHC-------------CCCCEECCCEEEEEEEECCCCCEEEEEEEHHHHHHHHHC
Q ss_conf 98541011785536772233230-------------237425552489999855778689999972453023641
Q gi|254780584|r 1 MSRVCELTKKTVMSGNKVSHANN-------------KTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQ 62 (97)
Q Consensus 1 Msr~C~itGk~~~~Gn~vshs~~-------------kTkR~~~PNlq~~~~~s~~l~~~v~l~vst~~lrtI~K~ 62 (97)
|||+|+||||+|++||+||||++ +|+|+|+||||++++|+| +++++|+|||+|||||+|.
T Consensus 1 Msr~C~itGK~~~~Gn~vshsgkakk~Gg~g~~~~~kTkR~fkPNLQkkri~~~--g~~vkvrVStkaLRTI~kl 73 (89)
T 2jl6_1 1 MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVA--GQEITFRVAASHIPKVYEL 73 (89)
T ss_dssp --CCCSSSCCCCEEEEEEEEESCCTTTSSSCCEEEEEEEEEECCCBCCBCCEET--TEECCBCCBGGGHHHHHHH
T ss_pred CCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEC--CEEEEEEEEHHHHHHHHHH
T ss_conf 977635679750248868724732213775223578426573368248999989--9999999996996529998
No 7
>2zkr_o 60S ribosomal protein L18; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}
Probab=34.69 E-value=22 Score=15.87 Aligned_cols=28 Identities=32% Similarity=0.472 Sum_probs=24.3
Q ss_pred EEEEEEHHHHHHHHHCCC----HHHHHHHCCH
Q ss_conf 999997245302364188----7799972984
Q gi|254780584|r 47 YQLRISKCALRSVERQGG----LDRFLSNSKK 74 (97)
Q Consensus 47 v~l~vst~~lrtI~K~GG----lD~yLl~~~~ 74 (97)
.-+++|..|-.-|.++|| ||+.++..|.
T Consensus 101 ~AL~fS~~Ar~kI~~aGGk~lT~dqLa~~~P~ 132 (188)
T 2zkr_o 101 CALRVSSRARSRILKAGGKILTFDQLALESPK 132 (188)
T ss_dssp EEEEECHHHHHHHHHHSSCEEEHHHHHHHCTT
T ss_pred EEEEECHHHHHHHHHCCCEEEEHHHHHHHCCC
T ss_conf 99971378999999759879769999987899
No 8
>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} SCOP: c.12.1.1 PDB: 1vq4_O* 1vq5_O* 1vq6_O* 1vq7_O* 1s72_O* 1vq9_O* 1vqk_O* 1vql_O* 1vqm_O* 1vqn_O* 1vqo_O* 1vqp_O* 1yhq_O* 1yi2_O* 1yij_O* 1yit_O* 1yj9_O* 1yjn_O* 1yjw_O* 2otj_O* ...
Probab=31.91 E-value=22 Score=15.90 Aligned_cols=39 Identities=18% Similarity=0.314 Sum_probs=27.9
Q ss_pred EEEEECCCCCEEE---EEEEHHHHHHHHHCCC---HHHHHHHCCH
Q ss_conf 9998557786899---9997245302364188---7799972984
Q gi|254780584|r 36 ITLISDIMEQKYQ---LRISKCALRSVERQGG---LDRFLSNSKK 74 (97)
Q Consensus 36 ~~~~s~~l~~~v~---l~vst~~lrtI~K~GG---lD~yLl~~~~ 74 (97)
+-+-...+...++ +.+|.+|..-|+++|| ||+++.+.|.
T Consensus 64 KVLg~G~l~~k~~V~A~~fS~sA~~kIe~aGg~iti~el~~~nP~ 108 (116)
T 1vq8_O 64 KVLGSGVLQKDVTVAAVDFSGTAETKIDQVGEAVSLEQAIENNPE 108 (116)
T ss_dssp EEECCSCCCSCCEEEEEEECHHHHHHHHHHSEEEEHHHHHHHCTT
T ss_pred EEECCCEECCCEEEEEECCCHHHHHHHHHCCCEEEHHHHHHHCCC
T ss_conf 896787476788999714178999999981988988999987899
No 9
>2uz0_A Esterase, tributyrin esterase; alpha/beta hydrolase, hydrolase, A virulence factor for LUNG infection; HET: MSE; 1.7A {Streptococcus pneumoniae}
Probab=28.56 E-value=31 Score=15.06 Aligned_cols=25 Identities=12% Similarity=0.371 Sum_probs=21.7
Q ss_pred ECCCEEEEEEEECCCCCEEEEEEEH
Q ss_conf 5552489999855778689999972
Q gi|254780584|r 29 FLPNLCRITLISDIMEQKYQLRISK 53 (97)
Q Consensus 29 ~~PNlq~~~~~s~~l~~~v~l~vst 53 (97)
..|.+++..|+|+++++.+.+.|-.
T Consensus 3 ~~p~~~~~~~~S~~~g~~~~~~Vyl 27 (263)
T 2uz0_A 3 MDPAVMKIEYYSQVLDMEWGVNVLY 27 (263)
T ss_dssp TCCEEEEEEEEETTTTEEEEEEEEE
T ss_pred CCCCEEEEEEEECCCCCEEEEEEEE
T ss_conf 8875899999927899888999997
No 10
>1dvp_A HRS, hepatocyte growth factor-regulated tyrosine kinase substrate; VHS, FYVE, zinc finger, superhelix, transferase; HET: CIT; 2.00A {Drosophila melanogaster} SCOP: a.118.9.2 g.50.1.1
Probab=24.45 E-value=36 Score=14.61 Aligned_cols=59 Identities=12% Similarity=0.132 Sum_probs=42.1
Q ss_pred CCCCCCCCCCCCCCCCCCHHHCCCCCEECCCEEEEEEEECCCCCEEEEEEEHHHHHHHHH
Q ss_conf 854101178553677223323023742555248999985577868999997245302364
Q gi|254780584|r 2 SRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVER 61 (97)
Q Consensus 2 sr~C~itGk~~~~Gn~vshs~~kTkR~~~PNlq~~~~~s~~l~~~v~l~vst~~lrtI~K 61 (97)
++.|..|++.-. ..+..|.=+.--+.|..+.-..+...+..+-.-.++||..|...|.|
T Consensus 161 ~~~C~~C~~~F~-~~~r~~~Cr~CG~~~C~~Cs~~~~~~p~~g~~~~~RVC~~C~~~l~r 219 (220)
T 1dvp_A 161 GRVCHRCRVEFT-FTNRKHHCRNCGQVFCGQCTAKQCPLPKYGIEKEVRVCDGCFAALQR 219 (220)
T ss_dssp CSBCTTTCCBCC-SSSCCEECTTTCCEECSTTSCEEEEEGGGTEEEEEEECHHHHHHHHH
T ss_pred CCCCCCCCCCCC-CCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCEECHHHHHHHHC
T ss_conf 885767898111-76537164402788627870896317877899986533988999867
No 11
>2k5c_A Uncharacterized protein PF0385; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Pyrococcus furiosus}
Probab=23.56 E-value=15 Score=16.96 Aligned_cols=11 Identities=18% Similarity=0.676 Sum_probs=6.0
Q ss_pred CCCCCCCCCCCC
Q ss_conf 985410117855
Q gi|254780584|r 1 MSRVCELTKKTV 12 (97)
Q Consensus 1 Msr~C~itGk~~ 12 (97)
||| |.+||+..
T Consensus 8 Mak-CPlCG~~l 18 (95)
T 2k5c_A 8 MAK-CPICGSPL 18 (95)
T ss_dssp CEE-CSSSCCEE
T ss_pred HHC-CCCCCCCC
T ss_conf 423-88678826
Done!