Query         gi|254780330|ref|YP_003064743.1| 30S ribosomal protein S18 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 83
No_of_seqs    108 out of 995
Neff          5.3 
Searched_HMMs 33803
Date          Wed Jun  1 12:06:39 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780330.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >2vqe_R 30S ribosomal protein   99.9 1.3E-28 3.7E-33  181.1   6.1   79    4-82      5-83  (88)
  2 >3i1m_R 30S ribosomal protein   99.9 1.1E-28 3.3E-33  181.4   5.1   70   13-82      3-72  (75)
  3 >3bbn_R Ribosomal protein S18;  99.9 2.9E-25 8.7E-30  162.3   0.3   64   19-82     16-79  (103)
  4 >3h0g_A DNA-directed RNA polym  39.5      13 0.00039   18.9   1.4   30   29-58    172-201 (202)
  5 >2waq_C DNA-directed RNA polym  32.8      10 0.00031   19.5  -0.0   22   30-51     84-105 (107)
  6 >1d2v_C Myeloperoxidase; heme-  21.1      53  0.0016   15.5   1.8   18   64-81     16-33  (87)
  7 >1tol_A G3P - TOLA, protein (f  20.3      43  0.0013   16.1   1.2   37   43-79    161-197 (222)
  8 >2ivf_A Ethylbenzene dehydroge  18.4      61  0.0018   15.2   1.6   49   32-80     98-146 (208)
  9 >1q4g_A Prostaglandin G/H synt  13.8   1E+02   0.003   14.0   1.8   45   33-82     24-69  (119)
 10 >2a6h_D DNA-directed RNA polym  12.9      26 0.00078   17.2  -1.4   27   31-57     13-39  (80)

No 1  
>>2vqe_R 30S ribosomal protein S18; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (R:)
Probab=99.95  E-value=1.3e-28  Score=181.10  Aligned_cols=79  Identities=37%  Similarity=0.526  Sum_probs=72.8

Q ss_pred             CCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             6667132277777888854350388511446889999962899848550331748999999999999999704658676
Q gi|254780330|r    4 VAPTPLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus         4 ~~p~p~~~~~~~~~~k~c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      ..+.+...+....+++.|+||.++++.|||||+++|++|||++|+|+||++||+|++|||+|++|||+||+||||||+.
T Consensus         5 ~~~~~~~~~~~~~~~~~c~~~~~~~~~idykn~~lL~~Fis~~GkIlprr~TGl~~k~Qr~l~~aIkrAR~~gLlP~~~   83 (88)
T 2vqe_R            5 NAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGKEQRILAKTIKRARILGLLPFTE   83 (88)
T ss_dssp             -----------CCCSCCTTTSCCCEETTCTTCHHHHGGGBCSSSCBCCHHHHCCCHHHHHHHHHHHHHHHHTTSSCSCC
T ss_pred             CCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
T ss_conf             6464412320887776663333666866765889999876998858177458878999999999999999975453229


No 2  
>>3i1m_R 30S ribosomal protein S18; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_R* 1vs5_R 3i1o_R 3i1q_R 3i1s_R 3i1z_R 3i21_R 2qal_R* 1p6g_R 1p87_R 2aw7_R 2avy_R 2i2u_R 2i2p_R* 2qan_R* 2qb9_R* 2qbb_R* 2qbd_R 2qbf_R 2qbh_R* ... (R:)
Probab=99.95  E-value=1.1e-28  Score=181.43  Aligned_cols=70  Identities=50%  Similarity=0.850  Sum_probs=66.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             7777888854350388511446889999962899848550331748999999999999999704658676
Q gi|254780330|r   13 NVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        13 ~~~~~~k~c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      +...++++|+||.++++++||||+++|++||||+|+|+||++||+|+++||+|++|||+||.||||||++
T Consensus         3 k~~~r~k~c~~~~~~~~~idykn~~lL~~Fis~~GkIl~Rr~TGl~~k~Qrki~~aIkrAR~~gLlP~~~   72 (75)
T 3i1m_R            3 RYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTD   72 (75)
T ss_dssp             -----------------CCSTTCHHHHGGGBCTTCCBCCHHHHCCCHHHHHHHHHHHHHHHTTTSSCSSS
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             6467898897766799857865889999866888728177227868999999999999999843576354


No 3  
>>3bbn_R Ribosomal protein S18; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (R:)
Probab=99.90  E-value=2.9e-25  Score=162.27  Aligned_cols=64  Identities=36%  Similarity=0.664  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             8854350388511446889999962899848550331748999999999999999704658676
Q gi|254780330|r   19 KSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        19 k~c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      +.|+++..+.+.|||||+++|++|||++|+|+||++||+|+++||+|++|||+||+||||||+.
T Consensus        16 ~~~~~~~~~~~~idyknv~lL~~Fis~~GkIlprr~TGl~~k~Qr~l~~aIkrAR~~gLlP~~~   79 (103)
T 3bbn_R           16 RRRLPPIQSGDRIDYRNMSLISRFISEQGKILSRRVNRLTLKQQRLITSAIKQARILSLLPFLN   79 (103)
T ss_dssp             ---------CCSSCCSCHHHHTTTSCSSSSCCCSSSTTCCTTTTTTTHHHHHHHTTTTSSCTTC
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             7778987778867765889999865888868676337769999999999999999961678565


No 4  
>>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (A:794-884,A:1064-1113,A:1337-1397)
Probab=39.51  E-value=13  Score=18.89  Aligned_cols=30  Identities=17%  Similarity=0.489  Sum_probs=26.5

Q ss_pred             CCCCCCCHHHHHHHCCCCCEECCCHHHCCC
Q ss_conf             511446889999962899848550331748
Q gi|254780330|r   29 PRIDYKDIRLLNRFLSQRGKIVPSRISSVS   58 (83)
Q Consensus        29 ~~iDYKn~~lL~~Fis~~GkI~prr~TG~~   58 (83)
                      ..|||++..||..+++-.|.+.|=.+-|+.
T Consensus       172 ~~Vd~rHl~ll~D~mt~~G~~~~~~r~g~~  201 (202)
T 3h0g_A          172 SYVNYRHLALLCDVMTSRGHLMAITRHGIN  201 (202)
T ss_dssp             CCCCHHHHHHHHHHHTSSSSCCCCCTTSCS
T ss_pred             CEECHHHHHHHHHHHCCCCEEEEECHHHCC
T ss_conf             475189999999988359768664677657


No 5  
>>2waq_C DNA-directed RNA polymerase RPO1C subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_C 3hkz_C 2pmz_C (C:64-116,C:277-330)
Probab=32.84  E-value=10  Score=19.48  Aligned_cols=22  Identities=18%  Similarity=0.439  Sum_probs=20.1

Q ss_pred             CCCCCCHHHHHHHCCCCCEECC
Q ss_conf             1144688999996289984855
Q gi|254780330|r   30 RIDYKDIRLLNRFLSQRGKIVP   51 (83)
Q Consensus        30 ~iDYKn~~lL~~Fis~~GkI~p   51 (83)
                      .||+|+++++-++++..|+|.+
T Consensus        84 ~In~kHielIad~Mt~kg~i~~  105 (107)
T 2waq_C           84 DVDMRHILLVADVMTRTGVVRQ  105 (107)
T ss_dssp             CCCHHHHHHHHHHHHSSSSCCC
T ss_pred             CCCHHHHHHHHHHHCCCCEEEE
T ss_conf             0344676555524300361650


No 6  
>>1d2v_C Myeloperoxidase; heme-protein, oxidoreductase, peroxidase- bromide complex; HET: NAG BMA MAN FUC HEM; 1.75A {Homo sapiens} (C:290-376)
Probab=21.12  E-value=53  Score=15.52  Aligned_cols=18  Identities=33%  Similarity=0.349  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHHCCCCCCC
Q ss_conf             999999999970465867
Q gi|254780330|r   64 ELAKAIKRARYLGLIAYV   81 (83)
Q Consensus        64 ~i~~aIKrAR~~gLlPy~   81 (83)
                      .++..|.|+|..||=||.
T Consensus        16 l~al~IqRgRDhGlp~Yn   33 (87)
T 1d2v_C           16 LPALNMQRSRDHGLPGYN   33 (87)
T ss_dssp             HHHHHHHHHHHTTCCCHH
T ss_pred             HHHHHHHHHHHHCCCCHH
T ss_conf             778878999972899789


No 7  
>>1tol_A G3P - TOLA, protein (fusion protein consisting of minor coat protein, glycine rich linker, TOLA,...; bacteriophage M13, phage infection; 1.85A {Enterobacteria phage M13} (A:)
Probab=20.32  E-value=43  Score=16.06  Aligned_cols=37  Identities=14%  Similarity=0.023  Sum_probs=33.7

Q ss_pred             CCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             2899848550331748999999999999999704658
Q gi|254780330|r   43 LSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIA   79 (83)
Q Consensus        43 is~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlP   79 (83)
                      |+..|.|..=.+++-..-.-+..-+||++++..+.+|
T Consensus       161 i~~~G~v~~v~~sSG~~~lD~aA~~av~~~~~~~~~p  197 (222)
T 1tol_A          161 LAPDGMLLDIKPEGGDPALCQAALAAAKLAKIPKPPS  197 (222)
T ss_dssp             ECTTSCEEEEEEEEECHHHHHHHHHHHHHCCCCCCSC
T ss_pred             ECCCCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             8689649863416899999999999998588998986


No 8  
>>2ivf_A Ethylbenzene dehydrogenase alpha-subunit; anaerobic hydrocarbon degradation, MOCO, Fe/S cluster, MO- bismgd enzyme, DMSO reductase family; HET: MES MGD MD1 HEM; 1.88A {Azoarcus SP} (A:221-331,A:412-482,A:781-806)
Probab=18.44  E-value=61  Score=15.20  Aligned_cols=49  Identities=16%  Similarity=0.139  Sum_probs=39.4

Q ss_pred             CCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             4468899999628998485503317489999999999999997046586
Q gi|254780330|r   32 DYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAY   80 (83)
Q Consensus        32 DYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy   80 (83)
                      ++=|.++|.++.+..--=.-..+||+.+.+=++|++.+-.++-+..+.|
T Consensus        98 ~~~D~~fl~~~t~~yTpE~aa~itgvpa~~I~~lAr~~a~~~p~~~~g~  146 (208)
T 2ivf_A           98 KLFDRQFVCEQTDLYTPEKASAKCGVPVSLIRELGRKVAKKRTCSYIGF  146 (208)
T ss_dssp             TCSCHHHHHHHBSTGSHHHHHHHHCCCHHHHHHHHHHHHHSCEEEEECT
T ss_pred             CCCCHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCEEEEEE
T ss_conf             8821899998447569999753406869999999987334653699840


No 9  
>>1q4g_A Prostaglandin G/H synthase 1; cyclooxygenase, non-steroidal anti-inflammatory drug, peroxidase, prostaglandin synthase, EGF-like domain; HET: BOG NAG NDG BMA MAN BFL HEM; 2.00A {Ovis aries} (A:117-157,A:407-484)
Probab=13.83  E-value=1e+02  Score=13.95  Aligned_cols=45  Identities=27%  Similarity=0.315  Sum_probs=30.6

Q ss_pred             CCCHHHHHH-HCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             468899999-62899848550331748999999999999999704658676
Q gi|254780330|r   33 YKDIRLLNR-FLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        33 YKn~~lL~~-Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      .-|.++|++ |+--+-=|.+..-.|+     -..+..|.|+|..||=+|.+
T Consensus        24 ~~~~~~~~~~~~~~~~~~~~~~~~g~-----DL~AlnIqRGRDhGLpsYN~   69 (119)
T 1q4g_A           24 LPDAEFLSRRFLLRRKFIRNIDHHIL-----HVAVDVIKESRVLRLQPFNE   69 (119)
T ss_dssp             CCCHHHHHHHHTBCSSCCSCBCTTTH-----HHHHHHHHHHHHTTCCCHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCCCCHHHH-----HHHHHHHHHHHHCCCCCHHH
T ss_conf             92989999998266886356770688-----88899988777528985899


No 10 
>>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} (D:1-12,D:595-619,D:1437-1479)
Probab=12.95  E-value=26  Score=17.24  Aligned_cols=27  Identities=15%  Similarity=0.135  Sum_probs=22.8

Q ss_pred             CCCCCHHHHHHHCCCCCEECCCHHHCC
Q ss_conf             144688999996289984855033174
Q gi|254780330|r   31 IDYKDIRLLNRFLSQRGKIVPSRISSV   57 (83)
Q Consensus        31 iDYKn~~lL~~Fis~~GkI~prr~TG~   57 (83)
                      =||++..||..++|..|.|.+.-++..
T Consensus        13 ~d~RHl~LlaD~MT~~Gg~~~S~l~~a   39 (80)
T 2a6h_D           13 GSDRPLRSLTDILSGKQGRFRQNLLAA   39 (80)
T ss_dssp             SCCCBCCCHHHHHSTTTCHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHCCCEECCCCHH
T ss_conf             789855308888631045100145683


Done!