Query         gi|254780437|ref|YP_003064850.1| 30S ribosomal protein S21 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 95
No_of_seqs    109 out of 269
Neff          3.9 
Searched_HMMs 33803
Date          Wed Jun  1 13:03:43 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780437.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >3i1m_U 30S ribosomal protein   99.5 8.9E-17 2.6E-21  114.4  -6.6   66   19-84      1-67  (71)
  2 >3bbn_U Ribosomal protein S21;  99.5 2.4E-16   7E-21  112.0  -7.1   68   17-84     95-162 (190)
  3 >3kfv_A Tight junction protein  41.3      20 0.00059   17.3   2.5   23   21-43    125-147 (150)
  4 >2hfv_A Hypothetical protein R  33.3      29 0.00084   16.4   2.3   23   15-37     63-85  (97)
  5 >1udx_A The GTP-binding protei  29.4      30 0.00089   16.3   1.8   25   28-52     37-61  (82)
  6 >3f6g_B Alpha-isopropylmalate   22.1      54  0.0016   14.9   2.0   22   24-45     36-57  (57)
  7 >2gw1_A Mitochondrial precurso  20.9      36  0.0011   15.9   0.9   30   21-50     10-39  (67)
  8 >3fp2_A TPR repeat-containing   20.4      26 0.00078   16.6   0.1   33   19-51     38-70  (107)
  9 >2cp9_A EF-TS, EF-TSMT, elonga  18.7      72  0.0021   14.2   2.2   17   25-41     34-50  (64)
 10 >1xb2_B EF-TS, elongation fact  18.4      74  0.0022   14.1   2.5   16   25-40     29-44  (45)

No 1  
>>3i1m_U 30S ribosomal protein S21; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_U* 2avy_U 2aw7_U 2vho_U 2vhp_U 3df1_U* 3df3_U* 3e1a_Q 3e1c_Q 1vs5_U 3i1o_U 3i1q_U 3i1s_U 3i1z_U 3i21_U 2qal_U* 2i2u_U 2i2p_U* 2qan_U* 2qb9_U* ... (U:)
Probab=99.50  E-value=8.9e-17  Score=114.38  Aligned_cols=66  Identities=35%  Similarity=0.559  Sum_probs=60.0

Q ss_pred             EEEEEEECCC-HHHHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             0688872795-89999999999964344999874351269558999999999888999999999850
Q gi|254780437|r   19 AVYVLVRDNN-VEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQRE   84 (95)
Q Consensus        19 ~i~V~V~~nn-vE~AlR~lKrkv~~eGi~~elR~R~~YEKPsekRrRkk~ea~kR~~K~~rK~~~~~   84 (95)
                      +++|.|.+|+ +|.||+.||++|+++||++|+|.|+||||||++++++..+|.++..+..++.....
T Consensus         1 M~~V~v~enE~~e~ALrRFKr~~~k~Gil~E~R~R~~yEkPs~~rkrk~~~a~kr~~k~~r~~~~~~   67 (71)
T 3i1m_U            1 MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARR   67 (71)
T ss_dssp             ---CEEECCSSCCSCCCTTTTSSSTHHHHTTSSSCCCSSSHHHHHHHHHHTSCC-------------
T ss_pred             CCEEECCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9843618999899999999999998466999987760258389999999999999999999974201


No 2  
>>3bbn_U Ribosomal protein S21; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Cucumis sativus} (U:)
Probab=99.46  E-value=2.4e-16  Score=111.99  Aligned_cols=68  Identities=22%  Similarity=0.312  Sum_probs=59.3

Q ss_pred             CCEEEEEEECCCHHHHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             31068887279589999999999964344999874351269558999999999888999999999850
Q gi|254780437|r   17 ISAVYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQRE   84 (95)
Q Consensus        17 ~~~i~V~V~~nnvE~AlR~lKrkv~~eGi~~elR~R~~YEKPsekRrRkk~ea~kR~~K~~rK~~~~~   84 (95)
                      .+...+.|.|++||+|||+||++|+++||++|+|+++||||||++|+|+.+++++|.++...++....
T Consensus        95 ~~~~v~~~~ne~ie~alr~~k~~~~~~g~~~e~k~~~~yekps~kr~r~~~~~~~r~~~~~~~~~~~~  162 (190)
T 3bbn_U           95 YNVQVVVDDNEPEERLLNRFRREVMRAGVIQECKRRRFFENTQDVRKRKTREAAKRNRRRRPQARFTP  162 (190)
T ss_dssp             --CCCCCCCCSSCCCCCCSSSTTTTTTHHHHSSSSCCCTTTTTTHHHHHHHHTTC-------------
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             02799858999999999999999998262999975124578379999999999999999765303787


No 3  
>>3kfv_A Tight junction protein ZO-3; structural genomics consortium, SGC, cell junction, cell membrane, membrane, SH3 domain; 2.80A {Homo sapiens} (A:144-293)
Probab=41.28  E-value=20  Score=17.31  Aligned_cols=23  Identities=9%  Similarity=0.104  Sum_probs=18.3

Q ss_pred             EEEEECCCHHHHHHHHHHHHHHC
Q ss_conf             88872795899999999999643
Q gi|254780437|r   21 YVLVRDNNVEQALRVLKKKMQGE   43 (95)
Q Consensus        21 ~V~V~~nnvE~AlR~lKrkv~~e   43 (95)
                      .|.|.|+|+|.|+..|+..+..+
T Consensus       125 ~vIv~n~~le~a~~~l~~iI~~e  147 (150)
T 3kfv_A          125 ATIPLNGTSDTWYQELKAIIREQ  147 (150)
T ss_dssp             EEEEECSSSTHHHHHHHHHHHHH
T ss_pred             EEEECCCCHHHHHHHHHHHHHHH
T ss_conf             89978988999999999999984


No 4  
>>2hfv_A Hypothetical protein RPA1041; NESG, GFT-alpha+beta, structural genomics, PSI-2, protein structure initiative; NMR {Pseudomonas aeruginosa} (A:)
Probab=33.32  E-value=29  Score=16.44  Aligned_cols=23  Identities=26%  Similarity=0.362  Sum_probs=19.2

Q ss_pred             CCCCEEEEEEECCCHHHHHHHHH
Q ss_conf             43310688872795899999999
Q gi|254780437|r   15 REISAVYVLVRDNNVEQALRVLK   37 (95)
Q Consensus        15 k~~~~i~V~V~~nnvE~AlR~lK   37 (95)
                      -.+.++.|+|.+.+.+.|.+.|.
T Consensus        63 igi~p~Ri~V~e~D~~~Ar~iL~   85 (97)
T 2hfv_A           63 LGVIPRRVLVHEDDLAGARRLLT   85 (97)
T ss_dssp             SSSSCEEEEEEGGGHHHHHHHHH
T ss_pred             CCCCEEEEEECHHHHHHHHHHHH
T ss_conf             35513789974758999999999


No 5  
>>1udx_A The GTP-binding protein OBG; TGS domain, riken structural genomics/proteomics initiative, RSGI, structural genomics, protein binding; 2.07A {Thermus thermophilus HB8} (A:335-416)
Probab=29.37  E-value=30  Score=16.30  Aligned_cols=25  Identities=20%  Similarity=0.360  Sum_probs=21.4

Q ss_pred             CHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             5899999999999643449998743
Q gi|254780437|r   28 NVEQALRVLKKKMQGEGVLRELKMR   52 (95)
Q Consensus        28 nvE~AlR~lKrkv~~eGi~~elR~R   52 (95)
                      |-+.|+..|.+.|.+.||...|+..
T Consensus        37 ~~~es~~~f~~~L~~~Gv~~~L~~~   61 (82)
T 1udx_A           37 DLMEAAGYLQEVFRRQGVEAALRAK   61 (82)
T ss_dssp             CTGGGHHHHHHHHHHTTHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHC
T ss_conf             8789999999999987806999965


No 6  
>>3f6g_B Alpha-isopropylmalate synthase; licmsc, allosteric regulation, feedback inhibition, selectivity, specificity, transferase; 2.00A {Leptospira interrogans} PDB: 3f6h_A (B:1-57)
Probab=22.12  E-value=54  Score=14.87  Aligned_cols=22  Identities=18%  Similarity=0.246  Sum_probs=18.6

Q ss_pred             EECCCHHHHHHHHHHHHHHCCH
Q ss_conf             7279589999999999964344
Q gi|254780437|r   24 VRDNNVEQALRVLKKKMQGEGV   45 (95)
Q Consensus        24 V~~nnvE~AlR~lKrkv~~eGi   45 (95)
                      ..||-||.+++.+++.+..+||
T Consensus        36 ~G~GPVDA~~~AI~~i~~~~~i   57 (57)
T 3f6g_B           36 EGDGGYDAFMNALTKITNRLGI   57 (57)
T ss_dssp             ECSSHHHHHHHHHHHHHHHHTC
T ss_pred             ECCCCHHHHHHHHHHHHCCCCC
T ss_conf             1798789999999987462576


No 7  
>>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae} (A:448-514)
Probab=20.88  E-value=36  Score=15.89  Aligned_cols=30  Identities=7%  Similarity=0.238  Sum_probs=24.1

Q ss_pred             EEEEECCCHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             888727958999999999996434499987
Q gi|254780437|r   21 YVLVRDNNVEQALRVLKKKMQGEGVLRELK   50 (95)
Q Consensus        21 ~V~V~~nnvE~AlR~lKrkv~~eGi~~elR   50 (95)
                      ++.|.-||++.|+.-|.+...=+--..|+=
T Consensus        10 ql~lQ~g~~~eAi~lFekA~~lARte~El~   39 (67)
T 2gw1_A           10 QMKLQQEDIDEAITLFEESADLARTMEEKL   39 (67)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCSSHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHCCCCHHHH
T ss_conf             999985999999999999987689919999


No 8  
>>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric regulation, phosphoprotein, TPR repeat; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A (A:127-156,A:461-537)
Probab=20.43  E-value=26  Score=16.63  Aligned_cols=33  Identities=6%  Similarity=0.108  Sum_probs=26.4

Q ss_pred             EEEEEEECCCHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             068887279589999999999964344999874
Q gi|254780437|r   19 AVYVLVRDNNVEQALRVLKKKMQGEGVLRELKM   51 (95)
Q Consensus        19 ~i~V~V~~nnvE~AlR~lKrkv~~eGi~~elR~   51 (95)
                      .-++.|+-||+|.|+.-|.+...=+.-..|+=.
T Consensus        38 LaqlelQqgn~~eAIelFEkAa~LARTe~El~~   70 (107)
T 3fp2_A           38 LAQLKLQMEKIDEAIELFEDSAILARTMDEKLQ   70 (107)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--CHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             999999859999999999999740999699999


No 9  
>>2cp9_A EF-TS, EF-TSMT, elongation factor TS, mitochondrial; UBA, structural genomics, human, NPPSFA; NMR {Homo sapiens} (A:)
Probab=18.71  E-value=72  Score=14.17  Aligned_cols=17  Identities=29%  Similarity=0.233  Sum_probs=13.2

Q ss_pred             ECCCHHHHHHHHHHHHH
Q ss_conf             27958999999999996
Q gi|254780437|r   25 RDNNVEQALRVLKKKMQ   41 (95)
Q Consensus        25 ~~nnvE~AlR~lKrkv~   41 (95)
                      -|||+|.|+..|+++-.
T Consensus        34 ~~gD~~~A~~~Lrk~G~   50 (64)
T 2cp9_A           34 CGGDLKQAEIWLHKEAQ   50 (64)
T ss_dssp             HTSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH
T ss_conf             38999999999999888


No 10 
>>1xb2_B EF-TS, elongation factor TS, mitochondrial, EF-TSMT; protein-protein complex, translation; HET: MSE; 2.20A {Bos taurus} (B:1-45)
Probab=18.43  E-value=74  Score=14.13  Aligned_cols=16  Identities=25%  Similarity=0.243  Sum_probs=12.1

Q ss_pred             ECCCHHHHHHHHHHHH
Q ss_conf             2795899999999999
Q gi|254780437|r   25 RDNNVEQALRVLKKKM   40 (95)
Q Consensus        25 ~~nnvE~AlR~lKrkv   40 (95)
                      -|||+|.|+-.|+++-
T Consensus        29 ~~gD~~kA~e~Lr~~G   44 (45)
T 1xb2_B           29 CGGDLKQAESWLHKQA   44 (45)
T ss_dssp             TTTCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH
T ss_conf             4898999999999864


Done!