Query         gi|254780543|ref|YP_003064956.1| NADH dehydrogenase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 131
No_of_seqs    109 out of 570
Neff          5.1 
Searched_HMMs 33803
Date          Wed Jun  1 16:23:17 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780543.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >3gqh_A Preneck appendage prot  31.1      34   0.001   15.7   2.3   20   39-58      5-24  (109)
  2 >3gqn_A Preneck appendage prot  29.9      38  0.0011   15.4   2.5   40   32-71     66-111 (168)
  3 >3bgv_A MRNA CAP guanine-N7 me  25.3      22 0.00064   16.7   0.5   27   14-40     13-39  (53)
  4 >2r51_A Vacuolar protein sorti  16.3      38  0.0011   15.4   0.2   42    2-43     92-133 (181)
  5 >2k0q_A Putative uncharacteriz  14.0      70  0.0021   14.0   1.0   26   18-43     15-40  (74)
  6 >1d3b_B Protein (small nuclear  13.5      58  0.0017   14.4   0.5   20   24-43     26-45  (91)
  7 >2fau_A Vacuolar protein sorti  12.6      42  0.0012   15.2  -0.4   41    3-43     93-133 (182)
  8 >1m5q_A SMAP3, small nuclear r  12.0      78  0.0023   13.7   0.8   23   24-46     22-44  (67)
  9 >1b34_B Protein (small nuclear  11.2      85  0.0025   13.5   0.8   20   24-43     51-70  (118)
 10 >3bw1_A SMX4 protein, U6 snRNA  11.2      86  0.0025   13.5   0.8   21   23-43     31-51  (96)

No 1  
>>3gqh_A Preneck appendage protein; beta barrel, viral protein; 1.80A {Bacillus phage PHI29} PDB: 3gqk_A* (A:1-109)
Probab=31.12  E-value=34  Score=15.70  Aligned_cols=20  Identities=20%  Similarity=0.135  Sum_probs=8.3

Q ss_pred             EEEECCCCCCCCCEEEEECC
Q ss_conf             65505777777620899478
Q gi|254780543|r   39 YYESRKNINGSSRRWVIYNG   58 (131)
Q Consensus        39 Yye~~~~~~~~~rRwV~Y~~   58 (131)
                      |||+.+......-..|-..+
T Consensus         5 ~FEs~dg~pi~~G~~VTl~g   24 (109)
T 3gqh_A            5 YFESLGGQVIETGYLVTLEK   24 (109)
T ss_dssp             EEEBTTSSCCCTTCEEEEET
T ss_pred             HEECCCCCCCCCCEEEEEEC
T ss_conf             22306899765646999609


No 2  
>>3gqn_A Preneck appendage protein; coiled coil, beta helix, beta barrel, ATP binding, viral protein; HET: ATP; 2.15A {Bacillus phage PHI29} (A:605-772)
Probab=29.94  E-value=38  Score=15.39  Aligned_cols=40  Identities=33%  Similarity=0.464  Sum_probs=25.8

Q ss_pred             EECCCCEEEEECCCCCCCCCEEEEECCCCCC------CCCCCCCCC
Q ss_conf             6665878655057777776208994786675------536865320
Q gi|254780543|r   32 KDEFGNTYYESRKNINGSSRRWVIYNGYTDP------SSIPPMWHG   71 (131)
Q Consensus        32 ~D~~GNkYye~~~~~~~~~rRwV~Y~~~~d~------s~IppeWh~   71 (131)
                      .|+||..-||......+...+-.+-+.++||      ..--||||.
T Consensus        66 ~defG~~~y~~~~~~~g~~~~~P~~NP~~dp~~~Y~sR~eR~EW~~  111 (168)
T 3gqn_A           66 KNEFGGIIYEEVTTEDGVKFKRPLPNPDFDPNKNYIPRSQRREWHV  111 (168)
T ss_dssp             BCTTSCBCEEEEECSSSCEEEEECBCTTCCTTSCCCCTTTCSSEEE
T ss_pred             ECCCCCEEEEEEECCCCCEEECCCCCCCCCCCCCCCCCCCCCCEEE
T ss_conf             6136878999831377967602454889897666505023866223


No 3  
>>3bgv_A MRNA CAP guanine-N7 methyltransferase; alternative splicing, mRNA capping, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: SAH; 2.30A {Homo sapiens} PDB: 3epp_A* (A:158-210)
Probab=25.27  E-value=22  Score=16.72  Aligned_cols=27  Identities=22%  Similarity=0.407  Sum_probs=12.9

Q ss_pred             CCEEHHHHHHHHHCEEEEEECCCCEEE
Q ss_conf             966102143313070436666587865
Q gi|254780543|r   14 GQTLGTRFFTWRFGHIVGKDEFGNTYY   40 (131)
Q Consensus        14 ~~TlgT~l~t~~~g~~VG~D~~GNkYy   40 (131)
                      +.++|..+|..+|...--.-.||++|.
T Consensus        13 ~~~fGN~vY~V~F~~~~~~p~FG~kY~   39 (53)
T 3bgv_A           13 TESFGNEIYTVKFQKKGDYPLFGCKYD   39 (53)
T ss_dssp             SSEEECSSEEEEESCSSCCCSSCCEEE
T ss_pred             HHHHCCCEEEEEECCCCCCCCCCCCCE
T ss_conf             132088027998424456677775412


No 4  
>>2r51_A Vacuolar protein sorting-associated protein 26B; retromer, fibronectin III, arrestin domain, alternative splicing, cytoplasm, membrane; 2.10A {Mus musculus} (A:160-340)
Probab=16.30  E-value=38  Score=15.40  Aligned_cols=42  Identities=17%  Similarity=0.192  Sum_probs=29.1

Q ss_pred             HHHHHHHHHCCCCCEEHHHHHHHHHCEEEEEECCCCEEEEEC
Q ss_conf             667786733147966102143313070436666587865505
Q gi|254780543|r    2 KNFLLQIFTWWNGQTLGTRFFTWRFGHIVGKDEFGNTYYESR   43 (131)
Q Consensus         2 ~~~l~~iftWwn~~TlgT~l~t~~~g~~VG~D~~GNkYye~~   43 (131)
                      ..+|..+|+.=.-.++.-.+-..++=.+|=.|+.|.+||++-
T Consensus        92 rl~L~~l~ltPT~~~v~~~FsV~y~Lnlviided~~ryfk~~  133 (181)
T 2r51_A           92 RLFLAGYELTPTXRDINKKFSVRYYLNLVLIDEEERRYFKQQ  133 (181)
T ss_dssp             EEEGGGSCCCCCEEEETTTEEEEEEEEEEEEETTCCEEEEEE
T ss_pred             EEECCCCCCCCCCCCCCCCEEEEEEEEEEEECCCCCEEEEEE
T ss_conf             997788999995202698499999999999928995799961


No 5  
>>2k0q_A Putative uncharacterized protein COPK; copper, heavy metal resistance, open barrel, plasmid- encoded, metal binding protein; NMR {Cupriavidus metallidurans} PDB: 3dso_A 3dsp_A (A:)
Probab=13.95  E-value=70  Score=13.99  Aligned_cols=26  Identities=15%  Similarity=0.427  Sum_probs=22.5

Q ss_pred             HHHHHHHHHCEEEEEECCCCEEEEEC
Q ss_conf             02143313070436666587865505
Q gi|254780543|r   18 GTRFFTWRFGHIVGKDEFGNTYYESR   43 (131)
Q Consensus        18 gT~l~t~~~g~~VG~D~~GNkYye~~   43 (131)
                      |..+|.|.-|+.-=+|.+|+-++...
T Consensus        15 GstvyiFKDGKM~mEdk~Gra~~m~~   40 (74)
T 2k0q_A           15 GSKVHVFKDGKMGMENKFGKSMNMPE   40 (74)
T ss_dssp             SCEEEEETTSCEEEECTTSCEECCCB
T ss_pred             CCEEEEEECCCCCCHHHCCCEEECCC
T ss_conf             97899971673100010584277468


No 6  
>>1d3b_B Protein (small nuclear ribonucleoprotein associated protein B); snRNP, splicing, core snRNP domain, systemic lupus erythematosus, SLE; HET: CIT; 2.00A {Homo sapiens} (B:)
Probab=13.53  E-value=58  Score=14.44  Aligned_cols=20  Identities=15%  Similarity=-0.027  Sum_probs=16.1

Q ss_pred             HHHCEEEEEECCCCEEEEEC
Q ss_conf             13070436666587865505
Q gi|254780543|r   24 WRFGHIVGKDEFGNTYYESR   43 (131)
Q Consensus        24 ~~~g~~VG~D~~GNkYye~~   43 (131)
                      .+.|+|+|-|.++|-=-++-
T Consensus        26 ~~~G~L~~~D~~~NlvL~d~   45 (91)
T 1d3b_B           26 IFIGTFKAFDKHMNLILCDC   45 (91)
T ss_dssp             EEEEEEEECCTTCCEEEEEE
T ss_pred             EEEEEEEEECCCCCEEEECE
T ss_conf             99999999867578797167


No 7  
>>2fau_A Vacuolar protein sorting 26; arrestin, retromer, protein transport; HET: CAF; 2.10A {Homo sapiens} (A:160-341)
Probab=12.57  E-value=42  Score=15.19  Aligned_cols=41  Identities=20%  Similarity=0.171  Sum_probs=29.7

Q ss_pred             HHHHHHHHCCCCCEEHHHHHHHHHCEEEEEECCCCEEEEEC
Q ss_conf             67786733147966102143313070436666587865505
Q gi|254780543|r    3 NFLLQIFTWWNGQTLGTRFFTWRFGHIVGKDEFGNTYYESR   43 (131)
Q Consensus         3 ~~l~~iftWwn~~TlgT~l~t~~~g~~VG~D~~GNkYye~~   43 (131)
                      .+|..+|++=.-.+..-.+-.-++=.+|=.|+.|.+||++-
T Consensus        93 l~L~~l~l~Pt~~~~~~~FsV~y~lnlviided~~~yfk~~  133 (182)
T 2fau_A           93 LFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQ  133 (182)
T ss_dssp             EESTTTCCCCCEEEEETTEEEEEEEEEEEEETTCCEEEEEE
T ss_pred             EECCCCCCCCCCCCCCCEEEEEEEEEEEEECCCCCEEEECC
T ss_conf             97789999997535797499999999999988886898827


No 8  
>>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} (A:1-67)
Probab=11.99  E-value=78  Score=13.74  Aligned_cols=23  Identities=17%  Similarity=-0.008  Sum_probs=17.9

Q ss_pred             HHHCEEEEEECCCCEEEEECCCC
Q ss_conf             13070436666587865505777
Q gi|254780543|r   24 WRFGHIVGKDEFGNTYYESRKNI   46 (131)
Q Consensus        24 ~~~g~~VG~D~~GNkYye~~~~~   46 (131)
                      .+.|+|+|-|.+.|---++-...
T Consensus        22 ~~~G~L~~~D~~~NlvL~da~E~   44 (67)
T 1m5q_A           22 VYKGVLHAVDNQLNIVLANASNK   44 (67)
T ss_dssp             EEEEEEEEECTTCCEEEEEEECT
T ss_pred             EEEEEEEEECCCCEEEEEEEEEC
T ss_conf             99999999879965699157987


No 9  
>>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemic lupus erythematosus, SLE; 2.50A {Homo sapiens} (B:)
Probab=11.24  E-value=85  Score=13.53  Aligned_cols=20  Identities=20%  Similarity=0.164  Sum_probs=16.3

Q ss_pred             HHHCEEEEEECCCCEEEEEC
Q ss_conf             13070436666587865505
Q gi|254780543|r   24 WRFGHIVGKDEFGNTYYESR   43 (131)
Q Consensus        24 ~~~g~~VG~D~~GNkYye~~   43 (131)
                      .+.|.|+|-|++.|---++-
T Consensus        51 ~~~G~L~~fD~~mNlvL~d~   70 (118)
T 1b34_B           51 KLLGRVKAFDRHCNMVLENV   70 (118)
T ss_dssp             EEEEEEEEECTTCCEEEEEE
T ss_pred             EEEEEEEEECCCCEEEEECE
T ss_conf             99999999710002673030


No 10 
>>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, homomeric, octamer, cytoplasm; 2.50A {Saccharomyces cerevisiae} (A:)
Probab=11.20  E-value=86  Score=13.52  Aligned_cols=21  Identities=14%  Similarity=0.066  Sum_probs=16.6

Q ss_pred             HHHHCEEEEEECCCCEEEEEC
Q ss_conf             313070436666587865505
Q gi|254780543|r   23 TWRFGHIVGKDEFGNTYYESR   43 (131)
Q Consensus        23 t~~~g~~VG~D~~GNkYye~~   43 (131)
                      ..+.|++.|.|.+.|---++-
T Consensus        31 ~~~~G~L~~~D~~mNlvL~d~   51 (96)
T 3bw1_A           31 RTLVGTLQAFDSHCNIVLSDA   51 (96)
T ss_dssp             CEEEEEEEEECTTCCEEEEEE
T ss_pred             CEEEEEEEEECCCCCEEECCE
T ss_conf             199999999889997298848


Done!