Query         gi|254781013|ref|YP_003065426.1| phage-associated protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 302
No_of_seqs    124 out of 144
Neff          3.0 
Searched_HMMs 33803
Date          Wed Jun  1 21:21:54 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781013.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >3k59_A POL II, DNA polymerase  37.5     8.8 0.00026   18.6   0.2   58  162-222     9-66  (116)
  2 >1y1x_A Leishmania major homol  28.0      33 0.00096   15.1   1.8   42  134-175    28-71  (79)
  3 >2vak_A Sigma A; double-strand  26.2      33 0.00099   15.0   1.6   34  116-149    24-57  (162)
  4 >2qac_A Myosin A tail domain i  24.9      45  0.0013   14.2   3.0   42  134-175     6-49  (67)
  5 >1dvp_A HRS, hepatocyte growth  21.6      53  0.0016   13.8   4.3   44   34-87     15-59  (73)
  6 >1zza_A Stannin, AG8_1; helix,  21.5      53  0.0016   13.8   2.5   15  275-289    24-38  (90)
  7 >3khi_A Putative metal-depende  20.6      29 0.00084   15.5   0.3   32   18-51     44-78  (143)
  8 >1bjf_A Neurocalcin delta; cal  18.9      59  0.0018   13.5   1.7   59  137-195    32-95  (96)
  9 >2j69_A Bacterial dynamin-like  18.8      61  0.0018   13.4   2.2   37  260-299   192-230 (300)
 10 >2b4j_C PC4 and SFRS1 interact  18.7      61  0.0018   13.4   2.8   38  167-204    50-87  (98)

No 1  
>>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA repair, DNA-binding; HET: DNA DOC DCP; 1.92A {Escherichia coli k-12} PDB: 3k57_A* 3k58_A* 3k5a_A* 3k5l_A* 3k5m_A* 3k5n_A* 3k5o_A* 1q8i_A* (A:426-541)
Probab=37.54  E-value=8.8  Score=18.64  Aligned_cols=58  Identities=17%  Similarity=0.147  Sum_probs=40.1

Q ss_pred             CCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8789889999853243337742056778999844540795888887764474231246776
Q gi|254781013|r  162 SNISPENVVEQIKKPVRFDSDSEFATLESQLVKGFKSMPPQLTKEFQEAQVQIKKDSAIAR  222 (302)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (302)
                      -|||||.+|.+...+.-.++..++.....   +-.++.-|++.++.-+....+|++---++
T Consensus         9 ~Ni~~~Tiv~~~~~~~~~~~~~~~~~~~~---~~~~gi~p~~l~~l~~~R~~~K~~m~d~~   66 (116)
T 3k59_A            9 FLIDPVGLVEGMAQPDPEHSTEGFLDAWF---SREKHCLPEIVTNIWHGRDEAKRQGNKPL   66 (116)
T ss_dssp             HCCCHHHHHHHHHSCSTTTEEECSTTCEE---ESSCCSHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCEEE---CHHHHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_conf             48997421047767884213345664222---02221369999998852688876502366


No 2  
>>1y1x_A Leishmania major homolog of programmed cell death 6 protein; SGPP, structural genomics, PSI, protein structure initiative; 1.95A {Leishmania major strain friedlin} (A:1-79)
Probab=27.96  E-value=33  Score=15.09  Aligned_cols=42  Identities=14%  Similarity=0.207  Sum_probs=33.5

Q ss_pred             CCHHCCCCCCCCCCCEECHHHHHHHCC--CCCCCHHHHHHHHHC
Q ss_conf             621216877878642021998664115--787898899998532
Q gi|254781013|r  134 TWRRLYDPNDPNTNRTITVEEITKMAD--GSNISPENVVEQIKK  175 (302)
Q Consensus       134 PWkkaYDP~dp~~N~~ItvE~itk~~~--~~~~~~~~~~~~~~~  175 (302)
                      -|++++.--|..++..|+.+++.++..  |..+|++.+-+-++.
T Consensus        28 ~l~~~F~~~D~d~~G~I~~~el~~~l~~~g~~ls~~ei~~~~~~   71 (79)
T 1y1x_A           28 ELMEWFRAVDTDGSGAISVPELNAALSSAGVPFSLATTEKLLHM   71 (79)
T ss_dssp             CHHHHHHHHCTTCSSSBCHHHHHHHHCBTTBCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             99999999779984969799999999985026877776677642


No 3  
>>2vak_A Sigma A; double-stranded RNA binding, RNA, viral protein; 2.34A {Avian orthoreovirus} (A:1-162)
Probab=26.23  E-value=33  Score=15.03  Aligned_cols=34  Identities=21%  Similarity=0.374  Sum_probs=25.7

Q ss_pred             HCCCCHHHHHHHHCCCCCCCHHCCCCCCCCCCCE
Q ss_conf             4489989999965188876212168778786420
Q gi|254781013|r  116 YQSHSTEQLQEIVQEENKTWRRLYDPNDPNTNRT  149 (302)
Q Consensus       116 YG~ySA~qLeeLTHqEnSPWkkaYDP~dp~~N~~  149 (302)
                      +-.....+|++|-..-|+||.+.+++..+-.++-
T Consensus        24 ~lp~n~~qls~LLssSNSpWQ~fls~~~~~~~~~   57 (162)
T 2vak_A           24 GLATNRTQLSSLLSSSNSPWQRFLSSMTPLTAPG   57 (162)
T ss_dssp             BSSCCHHHHHHHSCTTSCSCC-------------
T ss_pred             CCCCCHHHHHHHHHCCCCHHHHHHCCCCCCCCCC
T ss_conf             8885889999998537867677622010146775


No 4  
>>2qac_A Myosin A tail domain interacting protein MTIP; malaria invasion, structural genomics, PSI, protein structure initiative; 1.70A {Plasmodium falciparum 3D7} PDB: 2auc_A (A:80-146)
Probab=24.92  E-value=45  Score=14.19  Aligned_cols=42  Identities=10%  Similarity=0.290  Sum_probs=32.9

Q ss_pred             CCHHCCCCCCCCCCCEECHHHHHHH--CCCCCCCHHHHHHHHHC
Q ss_conf             6212168778786420219986641--15787898899998532
Q gi|254781013|r  134 TWRRLYDPNDPNTNRTITVEEITKM--ADGSNISPENVVEQIKK  175 (302)
Q Consensus       134 PWkkaYDP~dp~~N~~ItvE~itk~--~~~~~~~~~~~~~~~~~  175 (302)
                      -|+++|.--|++.+..|+.+++-++  +-|..++++.+-.-++.
T Consensus         6 ~l~~~F~~~D~d~~G~I~~~el~~~l~~lg~~~~~~e~~~~~~d   49 (67)
T 2qac_A            6 ELIKMFAHFDNNCTGYLTKSQMKNILTTWGDALTDQEAIDALNA   49 (67)
T ss_dssp             HHHHHHHTTCTTCSSEEEHHHHHHHHHHSSSCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             99987656643898776899999999980899999999999996


No 5  
>>1dvp_A HRS, hepatocyte growth factor-regulated tyrosine kinase substrate; VHS, FYVE, zinc finger, superhelix; HET: CIT; 2.00A {Drosophila melanogaster} (A:84-156)
Probab=21.58  E-value=53  Score=13.78  Aligned_cols=44  Identities=11%  Similarity=0.017  Sum_probs=33.5

Q ss_pred             CHHHH-HHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCCCC
Q ss_conf             89999-9999999699999844848867235745688169999998513544442
Q gi|254781013|r   34 DHLKI-QQFIYLTHCDVVLQKKKSMLDEEPQAWKQGPVFVGVYHRFKYFDSHPIE   87 (302)
Q Consensus        34 TnLKL-QKLLYyAQg~~La~~gkpLFdE~fEAW~yGPVvP~VY~~FK~yg~~pI~   87 (302)
                      +|.++ +|+|.+.|.|..+.-+.+=+          +.+.++|+..|.-|...-+
T Consensus        15 ~~~~Vk~kiL~li~~Wa~~f~~~~~l----------~~i~~~Y~~Lk~~G~~FP~   59 (73)
T 1dvp_A           15 PHENVRQKMLELVQTWAYAFRSSDKY----------QAIKDTMTILKAKGHTFPE   59 (73)
T ss_dssp             SCHHHHHHHHHHHHHHHHHTTTCSSC----------CHHHHHHHHHHHTTCCCCC
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCC----------HHHHHHHHHHHHCCCCCCC
T ss_conf             98899999999999999980788440----------8999999999977866665


No 6  
>>1zza_A Stannin, AG8_1; helix, membrane protein; NMR {Homo sapiens} (A:)
Probab=21.50  E-value=53  Score=13.77  Aligned_cols=15  Identities=33%  Similarity=0.844  Sum_probs=11.5

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             998999999999986
Q gi|254781013|r  275 VVSLSAIICGFWAIV  289 (302)
Q Consensus       275 ~~~~~~~~~~~~~~~  289 (302)
                      +..|+|.|||.|...
T Consensus        24 vaalg~li~~cwcyl   38 (90)
T 1zza_A           24 IAALGALILGCWCYL   38 (90)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999889999999999


No 7  
>>3khi_A Putative metal-dependent hydrolase; structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 1.95A {Klebsiella pneumoniae subsp} PDB: 3dl1_A (A:1-143)
Probab=20.57  E-value=29  Score=15.45  Aligned_cols=32  Identities=13%  Similarity=0.117  Sum_probs=15.9

Q ss_pred             HHHHHHH-HHHH--CCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             9999999-6663--59878899999999999699999
Q gi|254781013|r   18 VANFFID-KGVK--YSIPIDHLKIQQFIYLTHCDVVL   51 (302)
Q Consensus        18 VANyFI~-kA~e--~g~~ITnLKLQKLLYyAQg~~La   51 (302)
                      .+..||. |...  .|..+|  --+|++-=||+.-+.
T Consensus        44 ~~~~FL~eK~f~G~~Glevt--demk~~IAAqAclli   78 (143)
T 3khi_A           44 XAARFLQQKRLVALQGLELT--PLHQARIAXLFCLPV   78 (143)
T ss_dssp             HHHHHHHHCEEEECTTCCCC--HHHHHHHHHHHHGGG
T ss_pred             HHHHHHCCCEEECCCCCCCC--HHHHHHHHHHHHHHH
T ss_conf             99998542568356887667--689999999999998


No 8  
>>1bjf_A Neurocalcin delta; calcium-binding, myristoylation, neuronal specific guanylate cyclase activator; 2.40A {Escherichia coli} (A:1-96)
Probab=18.93  E-value=59  Score=13.46  Aligned_cols=59  Identities=12%  Similarity=0.038  Sum_probs=29.6

Q ss_pred             HCCCCCCCCCCCEECHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCC-----CHHHHHHHHHHHH
Q ss_conf             2168778786420219986641157878988999985324333774-----2056778999844
Q gi|254781013|r  137 RLYDPNDPNTNRTITVEEITKMADGSNISPENVVEQIKKPVRFDSD-----SEFATLESQLVKG  195 (302)
Q Consensus       137 kaYDP~dp~~N~~ItvE~itk~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~  195 (302)
                      +.|+..|++..-.+...+.....-+.+.+++-.++++=.-+--|.|     .||...-|.+.+|
T Consensus        32 ~~F~~ld~~~~~~~~~~~~~~~~~~~~~~~~~~~~~if~~~D~d~dG~I~f~EFv~~ls~~~~G   95 (96)
T 1bjf_A           32 KGFLRDCPSGHLSMEEFKKIYGNFFPYGDASKFAEHVFRTFDANGDGTIDFREFIIALSVTSRG   95 (96)
T ss_dssp             HHHHHHSTTSEEEHHHHHHHHTTTSSSSCCHHHHHHHHHHHCSSCSSEEEHHHHHHHHHHHTSS
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             9999778999805999999999846899889999999973046899989599999999997100


No 9  
>>2j69_A Bacterial dynamin-like protein; FZO, FZL, GTPase, hydrolase; 3.0A {Nostoc punctiforme} PDB: 2j68_A (A:358-657)
Probab=18.79  E-value=61  Score=13.41  Aligned_cols=37  Identities=27%  Similarity=0.371  Sum_probs=27.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHCHHHCCCCC
Q ss_conf             04899975223678899899999999--99861102102477
Q gi|254781013|r  260 SNVFAQLCESKYIATVVSLSAIICGF--WAIVGKGLFGVHND  299 (302)
Q Consensus       260 ~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~  299 (302)
                      .++|.++|..--|+.|+.   ++-|.  ||.+|-|++..+.+
T Consensus       192 ~~~~~v~gIg~~i~~v~g---i~lgp~G~aLig~gvg~~qa~  230 (300)
T 2j69_A          192 LNYFTVIGIGGIITAVTG---ILLGPIGFALLGLGVGFLQAD  230 (300)
T ss_dssp             HHHHHTTCSSTTTHHHHH---HHHHHHHHHHHHTTTTSSCHH
T ss_pred             HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH
T ss_conf             889999998788999888---887789999999889999778


No 10 
>>2b4j_C PC4 and SFRS1 interacting protein; HIV, integration, transcription, viral protein, recombination; 2.02A {Homo sapiens} (C:)
Probab=18.66  E-value=61  Score=13.39  Aligned_cols=38  Identities=21%  Similarity=0.218  Sum_probs=30.7

Q ss_pred             HHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             89999853243337742056778999844540795888
Q gi|254781013|r  167 ENVVEQIKKPVRFDSDSEFATLESQLVKGFKSMPPQLT  204 (302)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  204 (302)
                      -.+|+-|||--||-.+.+.-.....+-.+||+|-..-+
T Consensus        50 ~e~V~tikklrry~gn~~Ir~kA~~lY~kfK~lF~~~e   87 (98)
T 2b4j_C           50 TEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFLVGE   87 (98)
T ss_dssp             HHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHC-----
T ss_pred             HHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             49999999999865509999999999999999971742


Done!