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 23785
Date          Tue May 31 20:38:48 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780543.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3gqh_A Preneck appendage prote  24.7      37  0.0015   14.7   2.4   12   32-43     61-72  (163)
  2 2c4b_A Barnase mcoeeti fusion;  23.2      39  0.0016   14.5   3.4   37   21-58     41-91  (143)
  3 3gqn_A Preneck appendage prote  16.8      55  0.0023   13.7   2.5   16   32-47    670-685 (772)
  4 2k0q_A Putative uncharacterize  14.0      49  0.0021   14.0   1.0   26   18-43     15-40  (74)
  5 2kxq_A E3 ubiquitin-protein li  13.8      66  0.0028   13.3   2.3   28   26-56     12-39  (90)
  6 3cw1_G Small nuclear ribonucle  12.6      48   0.002   14.0   0.7   20   24-43     26-45  (76)
  7 1d3b_B Protein (small nuclear   11.1      53  0.0022   13.8   0.5   20   24-43     26-45  (91)
  8 2fwk_A U6 snRNA-associated SM-  10.7      75  0.0032   13.0   1.1   21   24-44     50-70  (121)
  9 3da7_A Barnase circular permut   9.9      75  0.0031   13.0   0.9   21   36-56      2-25  (111)
 10 1p6r_A Penicillinase repressor   9.7      64  0.0027   13.4   0.5   29   12-40     39-67  (82)

No 1  
>3gqh_A Preneck appendage protein; beta barrel, viral protein; 1.80A {Bacillus phage PHI29} PDB: 3gqk_A*
Probab=24.65  E-value=37  Score=14.69  Aligned_cols=12  Identities=50%  Similarity=0.869  Sum_probs=5.8

Q ss_pred             EECCCCEEEEEC
Q ss_conf             666587865505
Q gi|254780543|r   32 KDEFGNTYYESR   43 (131)
Q Consensus        32 ~D~~GNkYye~~   43 (131)
                      .|+||+.=||.-
T Consensus        61 ~DefG~~iye~~   72 (163)
T 3gqh_A           61 KNEFGGIIYEEV   72 (163)
T ss_dssp             BCTTSCBCEEEE
T ss_pred             ECCCCCEEEEEC
T ss_conf             745799998970


No 2  
>2c4b_A Barnase mcoeeti fusion; squash inhibitor, hybrid microprotein, fusion protein, ribonuclease, endonuclease, hydrolase, nuclease; HET: 2PE MES; 1.3A {Bacillus amyloliquefaciens} SCOP: d.1.1.2 g.3.2.1 PDB: 1b3s_A 2kf3_A 2kf4_A 2kf5_A 2kf6_A 1a2p_A 1b27_A 1b2x_A 1bgs_A 1bni_A 1bnj_A 1bnr_A 1brn_L* 1brs_A 1fw7_A 1x1u_A 1x1w_A 1x1x_A 1yvs_A 3kch_A ...
Probab=23.16  E-value=39  Score=14.53  Aligned_cols=37  Identities=27%  Similarity=0.401  Sum_probs=22.9

Q ss_pred             HHHHHHCEEEEEECCCCE-----------EEEECCCCCCC---CCEEEEECC
Q ss_conf             433130704366665878-----------65505777777---620899478
Q gi|254780543|r   21 FFTWRFGHIVGKDEFGNT-----------YYESRKNINGS---SRRWVIYNG   58 (131)
Q Consensus        21 l~t~~~g~~VG~D~~GNk-----------Yye~~~~~~~~---~rRwV~Y~~   58 (131)
                      |--...|+-+|-|.|+|+           |+|--.+..+.   .+|.| |.+
T Consensus        41 L~~v~pGk~IGGd~F~NrE~~LP~~~g~~Y~E~DV~~~gg~RGa~RIV-~s~   91 (143)
T 2c4b_A           41 LADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRIL-YSS   91 (143)
T ss_dssp             HHHHSTTCEEEEEEECCTTCCSCCCTTCCEEEEECSCCSSSCCSCEEE-EET
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCEEE-ECC
T ss_conf             100488752067533478576888889838887648999888987699-869


No 3  
>3gqn_A Preneck appendage protein; coiled coil, beta helix, beta barrel, ATP binding, viral protein; HET: ATP; 2.15A {Bacillus phage PHI29}
Probab=16.79  E-value=55  Score=13.75  Aligned_cols=16  Identities=38%  Similarity=0.654  Sum_probs=7.5

Q ss_pred             EECCCCEEEEECCCCC
Q ss_conf             6665878655057777
Q gi|254780543|r   32 KDEFGNTYYESRKNIN   47 (131)
Q Consensus        32 ~D~~GNkYye~~~~~~   47 (131)
                      +|+||..-||....+.
T Consensus       670 ~~~~g~~~~~~~~~~~  685 (772)
T 3gqn_A          670 KNEFGGIIYEEVTTED  685 (772)
T ss_dssp             BCTTSCBCEEEEECSS
T ss_pred             ECCCCCEEEEEEECCC
T ss_conf             4247878988863167


No 4  
>2k0q_A Putative uncharacterized protein COPK; copper, heavy metal resistance, open barrel, plasmid- encoded, metal binding protein; NMR {Cupriavidus metallidurans} PDB: 2km0_A 3dso_A 3dsp_A
Probab=13.99  E-value=49  Score=14.00  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             CCEEEEECCCCEEHHHHCCCEEECCC
T ss_conf             96899972782110010485077579


No 5  
>2kxq_A E3 ubiquitin-protein ligase smurf2; WW, smurf2, TGF-beta, modular binding, protein BIN; NMR {Homo sapiens}
Probab=13.82  E-value=66  Score=13.31  Aligned_cols=28  Identities=14%  Similarity=0.156  Sum_probs=18.2

Q ss_pred             HCEEEEEECCCCEEEEECCCCCCCCCEEEEE
Q ss_conf             0704366665878655057777776208994
Q gi|254780543|r   26 FGHIVGKDEFGNTYYESRKNINGSSRRWVIY   56 (131)
Q Consensus        26 ~g~~VG~D~~GNkYye~~~~~~~~~rRwV~Y   56 (131)
                      -|--+-.|..|..||-+....   .--|+..
T Consensus        12 ~GWe~~~d~~Gr~YY~n~~T~---~TtW~~P   39 (90)
T 2kxq_A           12 EGYEQRTTQQGQVYFLHTQTG---VSTWHDP   39 (90)
T ss_dssp             SSCEEEEETTTEEEEEETTTT---EEESSCS
T ss_pred             CCCEEEECCCCCEEEEECCCC---EEECCCC
T ss_conf             996898989999998978998---0763589


No 6  
>3cw1_G Small nuclear ribonucleoprotein G; PRE-mRNA splicing, spliceosome, RNA-binding domain, SM fold, zinc finger, RNA recognition motif; 5.49A {Homo sapiens}
Probab=12.63  E-value=48  Score=14.04  Aligned_cols=20  Identities=25%  Similarity=0.205  Sum_probs=16.4

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~~mNlvL~~~   45 (76)
T 3cw1_G           26 HVQGILRGFDPFMNLVIDEC   45 (76)
T ss_pred             EEEEEEEEECCCCCEEECCE
T ss_conf             99999999977235898047


No 7  
>1d3b_B Protein (small nuclear ribonucleoprotein associated protein B); snRNP, splicing, core snRNP domain, systemic lupus erythematosus, SLE; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1
Probab=11.15  E-value=53  Score=13.81  Aligned_cols=20  Identities=15%  Similarity=-0.027  Sum_probs=15.6

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~~~   45 (91)
T 1d3b_B           26 IFIGTFKAFDKHMNLILCDC   45 (91)
T ss_dssp             EEEEEEEECCTTCCEEEEEE
T ss_pred             EEEEEEEEECCCCCEEEECE
T ss_conf             99999999987568885065


No 8  
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1
Probab=10.74  E-value=75  Score=13.01  Aligned_cols=21  Identities=24%  Similarity=0.213  Sum_probs=17.2

Q ss_pred             HHHCEEEEEECCCCEEEEECC
Q ss_conf             130704366665878655057
Q gi|254780543|r   24 WRFGHIVGKDEFGNTYYESRK   44 (131)
Q Consensus        24 ~~~g~~VG~D~~GNkYye~~~   44 (131)
                      .+.|+|+|-|.+.|---++-.
T Consensus        50 ~~~G~L~~fD~~mNLvL~d~~   70 (121)
T 2fwk_A           50 EFSGVLRGFDEYVNMVLDDVQ   70 (121)
T ss_dssp             EECCEEEEECTTCCEEEESCC
T ss_pred             EEEEEEEEECCCCCEEEEEEE
T ss_conf             999999999776885785279


No 9  
>3da7_A Barnase circular permutant; circular permutant, protein-protein complex, endonuclease, cytoplasm, protein binding; 2.25A {Bacillus amyloliquefaciens}
Probab=9.94  E-value=75  Score=13.03  Aligned_cols=21  Identities=29%  Similarity=0.357  Sum_probs=9.0

Q ss_pred             CCEEEEECCCCCCC---CCEEEEE
Q ss_conf             87865505777777---6208994
Q gi|254780543|r   36 GNTYYESRKNINGS---SRRWVIY   56 (131)
Q Consensus        36 GNkYye~~~~~~~~---~rRwV~Y   56 (131)
                      |..|||.-.+..++   ..|.|.=
T Consensus         2 Gr~w~EaDiny~~g~Rga~Rivys   25 (111)
T 3da7_A            2 GRTWREADINYTSGFRNSDRILYS   25 (111)
T ss_dssp             -CCEEEEECSCCSBSCCSCEEEEE
T ss_pred             CCEEEECCCCCCCCCCCCCEEEEE
T ss_conf             857788101666788886368995


No 10 
>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B
Probab=9.67  E-value=64  Score=13.38  Aligned_cols=29  Identities=14%  Similarity=0.296  Sum_probs=0.0

Q ss_pred             CCCCEEHHHHHHHHHCEEEEEECCCCEEE
Q ss_conf             47966102143313070436666587865
Q gi|254780543|r   12 WNGQTLGTRFFTWRFGHIVGKDEFGNTYY   40 (131)
Q Consensus        12 wn~~TlgT~l~t~~~g~~VG~D~~GNkYy   40 (131)
                      |.-.|+-|.|.-...-.+|..+..|+.|+
T Consensus        39 ~~~sTv~T~L~RL~~Kg~l~~~~~gr~~~   67 (82)
T 1p6r_A           39 WSPKTIQTMLLRLIKKGALNHHKEGRVFV   67 (82)
T ss_dssp             CCHHHHHHHHHHHHHTTSEEEEEETTEEE
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEECCCEEE
T ss_conf             72857999999999889868872598389


Done!