Query         gi|254780248|ref|YP_003064661.1| 30S ribosomal protein S14 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 101
No_of_seqs    107 out of 1176
Neff          5.4 
Searched_HMMs 23785
Date          Tue May 24 05:31:09 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780248.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3ofo_N 30S ribosomal protein S 100.0   4E-42       0  275.8   1.2  100    2-101     1-100 (100)
  2 3bbn_N Ribosomal protein S14;  100.0 1.1E-41       0  273.2  -6.0  100    1-101     1-100 (100)
  3 2vqe_N 30S ribosomal protein S  99.9 9.4E-24 3.9E-28  164.0   1.8   54   46-101     8-61  (61)
  4 2zkq_n 40S ribosomal protein S  91.8   0.036 1.5E-06   32.7   0.8   30   61-90     18-49  (56)
  5 3jyv_N 40S ribosomal protein S  91.5   0.042 1.8E-06   32.3   0.9   29   62-90     15-45  (50)
  6 1y6u_A XIS, excisionase from t  38.9      12 0.00052   17.3   1.9   23   74-96     23-45  (70)
  7 1z4h_A TORI, TOR inhibition pr  20.5      22 0.00092   15.8   0.5   26   70-95     13-38  (66)
  8 1l8d_A DNA double-strand break  11.8      48   0.002   13.8   0.4   25   38-71     33-57  (112)
  9 2ko6_A Uncharacterized protein  10.8      77  0.0033   12.5   1.5   22   78-99     50-71  (89)
 10 2zqe_A MUTS2 protein; alpha/be  10.1      82  0.0035   12.3   1.3   35   42-76     15-49  (83)

No 1  
>3ofo_N 30S ribosomal protein S14; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 1p6g_N 1p87_N 2aw7_N 2avy_N 2i2u_N 2i2p_N* 2qan_N* 2qb9_N* 2qbb_N* 2qbd_N 2qbf_N 2qbh_N* 2qbj_N* 2qou_N* 2qow_N* 2qoy_N* 2qp0_N* 2vho_N 2vhp_N 2z4k_N* ...
Probab=100.00  E-value=4e-42  Score=275.78  Aligned_cols=100  Identities=44%  Similarity=0.714  Sum_probs=99.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHHH
Q ss_conf             12689999999999999999999999998348798989999999997208604432444022143566411440425629
Q gi|254780248|r    2 AKVSAVERNKRRLRVVAKQASKRLALKKIVMDKSVTLEERFDAMLQLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLSR   81 (101)
Q Consensus         2 akks~i~rd~kRr~l~~k~~~kR~~lk~~~~~~~l~~~~r~~a~~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lSR   81 (101)
                      ||+|+|+||.+|++++++|+.+|.+||+++.|+++|++++++|+.+|++||+|||||||+|||++||||||||++|||||
T Consensus         1 AK~s~i~R~~kR~~l~~k~~~kR~~Lk~i~~~~~l~~~~r~~a~~kL~~LPrnSs~~RirNRC~~TGR~Rgv~r~f~lsR   80 (100)
T 3ofo_N            1 AKQSMKAREVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGLSR   80 (100)
T ss_dssp             CCHHHHHHHHHHHHHHHHSTTTGGGTTTTTTSSCC----CCTHHHHSCCCCSSCSGGGCCCCCTTTCCCSSEETTTTEEH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCHHHCCCHHCCCCCCCCCCCCCCHH
T ss_conf             90489999999999999999999999999847799999999999999847834200154046023796652213425439


Q ss_pred             HHHHHHHHCCCCCCCCCCCC
Q ss_conf             99999996589998321469
Q gi|254780248|r   82 LALRELGGVGKIPGIIKSSW  101 (101)
Q Consensus        82 i~fRela~~G~ipGv~KaSW  101 (101)
                      |+|||||+.|+||||+||||
T Consensus        81 i~fRela~~G~ipGv~KaSW  100 (100)
T 3ofo_N           81 IKVREAAMRGEIPGLKKASW  100 (100)
T ss_dssp             HHHHHHHTTSCSTTEEECCC
T ss_pred             HHHHHHHHCCCCCCEECCCC
T ss_conf             99999997697888431679


No 2  
>3bbn_N Ribosomal protein S14; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}
Probab=100.00  E-value=1.1e-41  Score=273.24  Aligned_cols=100  Identities=33%  Similarity=0.525  Sum_probs=97.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHH
Q ss_conf             91268999999999999999999999999834879898999999999720860443244402214356641144042562
Q gi|254780248|r    1 MAKVSAVERNKRRLRVVAKQASKRLALKKIVMDKSVTLEERFDAMLQLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLS   80 (101)
Q Consensus         1 Makks~i~rd~kRr~l~~k~~~kR~~lk~~~~~~~l~~~~r~~a~~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lS   80 (101)
                      |||||+|+||.+|++++++||.+|.+|+++++|. ++++++++|+.+|++||+||||||++|||++||||||||++||||
T Consensus         1 Makks~I~rd~kRr~l~~k~~~~R~~lk~~i~~~-~~~~~r~~~~~kL~~lprnss~~Ri~NRC~~TGR~Rg~~r~f~lS   79 (100)
T 3bbn_N            1 MARKSLIQREKKRRNLEQKYHLIRRSSKQEIRKV-TSLSDKWEIHGKLQSPPRNSAPARLHRRCFLTGRPRANIRDFGLS   79 (100)
T ss_dssp             -CCTTHHHHHHTTTSSTTTTSSSTTTTTTTTSSC-CSSSCCCSHHHHSCCSCSSCCGGGCCCCCSSSCCSSSBCTTTCSB
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCCCCCCCCH
T ss_conf             9568999999999999999999999999988056-887799999999874775446589966355689976224554645


Q ss_pred             HHHHHHHHHCCCCCCCCCCCC
Q ss_conf             999999996589998321469
Q gi|254780248|r   81 RLALRELGGVGKIPGIIKSSW  101 (101)
Q Consensus        81 Ri~fRela~~G~ipGv~KaSW  101 (101)
                      ||+|||||+.|+||||+||||
T Consensus        80 Ri~fR~lA~~G~ipGv~KaSW  100 (100)
T 3bbn_N           80 GHILREMVHTCLLPGATRSSW  100 (100)
T ss_dssp             TTHHHHHHTTTCSSSCEECCC
T ss_pred             HHHHHHHHHCCCCCCEECCCC
T ss_conf             999999998698888522779


No 3  
>2vqe_N 30S ribosomal protein S14 type Z; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: g.39.1.7 PDB: 1gix_Q* 1hnw_N* 1hnx_N* 1hnz_N* 1hr0_N 1ibk_N* 1ibl_N* 1ibm_N 1jgo_Q* 1jgp_Q* 1jgq_Q* 1ml5_Q* 1xmo_N* 1xmq_N* 1xnq_N* 1xnr_N* 1yl4_Q 2b64_N* 2b9m_N* 2b9o_N* ...
Probab=99.87  E-value=9.4e-24  Score=164.05  Aligned_cols=54  Identities=44%  Similarity=0.799  Sum_probs=50.1

Q ss_pred             HHHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             99720860443244402214356641144042562999999996589998321469
Q gi|254780248|r   46 LQLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLSRLALRELGGVGKIPGIIKSSW  101 (101)
Q Consensus        46 ~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lSRi~fRela~~G~ipGv~KaSW  101 (101)
                      .+++++|++  +||++|||++||||||||++||||||+|||+|+.|+||||+||||
T Consensus         8 ~k~~~~pk~--~tR~~nRC~~tGR~Rg~~r~f~lsRi~fR~la~~G~iPGv~KaSW   61 (61)
T 2vqe_N            8 EKAKRTPKF--KVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW   61 (61)
T ss_dssp             GGCCSCCSS--GGGCCCCCTTTCCCTTCCTTTSSCHHHHHHHHHHTCSSSCEECCC
T ss_pred             HHHHCCCCC--CCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEECCC
T ss_conf             997718998--763302125789976202452617999999997598888360679


No 4  
>2zkq_n 40S ribosomal protein S29E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_N
Probab=91.81  E-value=0.036  Score=32.73  Aligned_cols=30  Identities=17%  Similarity=0.495  Sum_probs=26.4

Q ss_pred             CCCCCCCCCCCHHHHHHC--HHHHHHHHHHHC
Q ss_conf             022143566411440425--629999999965
Q gi|254780248|r   61 RNRCEISGRSRGVYRDFR--LSRLALRELGGV   90 (101)
Q Consensus        61 ~NRC~~TGR~Rgv~r~f~--lSRi~fRela~~   90 (101)
                      -+.|.++|+..|++++||  |||-+|||.|..
T Consensus        18 sr~Cr~Cg~~~glIrKYgL~~CRqCFre~A~d   49 (56)
T 2zkq_n           18 SRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKD   49 (56)
T ss_dssp             CCCCSSSCCSTTCCTTTCCCSCHHHHHHTTTT
T ss_pred             CCEEEECCCCCCEEEEECCCHHHHHHHHHHHH
T ss_conf             76236779974311001732288899988785


No 5  
>3jyv_N 40S ribosomal protein S29(A); eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus}
Probab=91.54  E-value=0.042  Score=32.31  Aligned_cols=29  Identities=21%  Similarity=0.537  Sum_probs=26.2

Q ss_pred             CCCCCCCCCCHHHHHHC--HHHHHHHHHHHC
Q ss_conf             22143566411440425--629999999965
Q gi|254780248|r   62 NRCEISGRSRGVYRDFR--LSRLALRELGGV   90 (101)
Q Consensus        62 NRC~~TGR~Rgv~r~f~--lSRi~fRela~~   90 (101)
                      +.|.++|+..|++++||  +||-+|||.|..
T Consensus        15 r~CrvCg~~~glIrKYgL~~CRqCFre~A~d   45 (50)
T 3jyv_N           15 RQCRVCSSHTGLVRKYDLNICRQCFREKAND   45 (50)
T ss_dssp             CCCSSSCCCSSCCSSCSCSSSSHHHHHHHHH
T ss_pred             CEEEECCCCCCEEEECCCCHHHHHHHHHHHH
T ss_conf             7027779984553122763067799998986


No 6  
>1y6u_A XIS, excisionase from transposon TN916; structure, DNA architectural protein, tyrosine recombinase, winged-helix protein; NMR {Enterococcus faecalis}
Probab=38.89  E-value=12  Score=17.32  Aligned_cols=23  Identities=26%  Similarity=0.299  Sum_probs=19.2

Q ss_pred             HHHHCHHHHHHHHHHHCCCCCCC
Q ss_conf             40425629999999965899983
Q gi|254780248|r   74 YRDFRLSRLALRELGGVGKIPGI   96 (101)
Q Consensus        74 ~r~f~lSRi~fRela~~G~ipGv   96 (101)
                      -..||+++-.+|+|++.+..|+.
T Consensus        23 a~Y~gIg~~klr~L~~e~~~~~f   45 (70)
T 1y6u_A           23 SKYFRIGENKLRRLAEENKNANW   45 (70)
T ss_dssp             HHHTCSCHHHHHHHHHHCTTCSS
T ss_pred             HHHHCCCHHHHHHHHHHCCCCCC
T ss_conf             99969279999999984889997


No 7  
>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}
Probab=20.48  E-value=22  Score=15.80  Aligned_cols=26  Identities=12%  Similarity=0.156  Sum_probs=20.9

Q ss_pred             CCHHHHHHCHHHHHHHHHHHCCCCCC
Q ss_conf             41144042562999999996589998
Q gi|254780248|r   70 SRGVYRDFRLSRLALRELGGVGKIPG   95 (101)
Q Consensus        70 ~Rgv~r~f~lSRi~fRela~~G~ipG   95 (101)
                      -.-|....|+||-.+..++..|.+|=
T Consensus        13 ~keV~~~~glsrstiy~~i~~G~FP~   38 (66)
T 1z4h_A           13 LKFIMADTGFGKTFIYDRIKSGDLPK   38 (66)
T ss_dssp             HHHHHHHHSSCHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf             99999998979999999998799999


No 8  
>1l8d_A DNA double-strand break repair RAD50 ATPase; zinc finger, DNA repair, recombination, HOOK motif, replication; HET: DNA CIT; 2.20A {Pyrococcus furiosus} SCOP: h.4.12.1
Probab=11.76  E-value=48  Score=13.75  Aligned_cols=25  Identities=20%  Similarity=0.473  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCC
Q ss_conf             8999999999720860443244402214356641
Q gi|254780248|r   38 LEERFDAMLQLGSLPRDGSRVRVRNRCEISGRSR   71 (101)
Q Consensus        38 ~~~r~~a~~kL~~Lprnss~tRi~NRC~~TGR~R   71 (101)
                      ..+.-.|...|.+         ..-+|-+||||=
T Consensus        33 i~elkKal~ELk~---------a~GkCPvCgreL   57 (112)
T 1l8d_A           33 IGDLKTAIEELKK---------AKGKCPVCGREL   57 (112)
T ss_dssp             HHHHHHHHHHHTT---------CSEECTTTCCEE
T ss_pred             HHHHHHHHHHHHH---------HCCCCCCCCCCC
T ss_conf             9999999999997---------478799889937


No 9  
>2ko6_A Uncharacterized protein YIHD; alpha protein, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}
Probab=10.79  E-value=77  Score=12.46  Aligned_cols=22  Identities=27%  Similarity=0.442  Sum_probs=15.9

Q ss_pred             CHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             5629999999965899983214
Q gi|254780248|r   78 RLSRLALRELGGVGKIPGIIKS   99 (101)
Q Consensus        78 ~lSRi~fRela~~G~ipGv~Ka   99 (101)
                      =+-....|.-...-.|||++|-
T Consensus        50 lIYhLKMr~s~k~e~IPGlkKD   71 (89)
T 2ko6_A           50 LIYHLKMRDSAKDAVIPGLQKD   71 (89)
T ss_dssp             HHHHHHHHHHTTSSSCSSCCCC
T ss_pred             EEEEHEECCCCCCCCCCCCCHH
T ss_conf             0000000488766758861022


No 10 
>2zqe_A MUTS2 protein; alpha/beta, ATP-binding, DNA-binding, nucleotide-binding, DNA binding protein; 1.70A {Thermus thermophilus HB8}
Probab=10.05  E-value=82  Score=12.30  Aligned_cols=35  Identities=14%  Similarity=0.314  Sum_probs=21.9

Q ss_pred             HHHHHHHHHCCHHHHHHHHCCCCCCCCCCCHHHHH
Q ss_conf             99999972086044324440221435664114404
Q gi|254780248|r   42 FDAMLQLGSLPRDGSRVRVRNRCEISGRSRGVYRD   76 (101)
Q Consensus        42 ~~a~~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~   76 (101)
                      .+|...|.+.=-++-...++.-+++||...|+.+.
T Consensus        15 ~eA~~~l~~~i~~a~~~~~~~v~IIHGkG~gvLk~   49 (83)
T 2zqe_A           15 AEALLEVDQALEEARALGLSTLRLLHGKGTGALRQ   49 (83)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSEEEEECCSTTSHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHH
T ss_conf             99999999999999985993899994478823899


Done!