Query         gi|254781209|ref|YP_003065622.1| hypothetical protein CLIBASIA_05580 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 175
No_of_seqs    109 out of 402
Neff          7.9 
Searched_HMMs 39220
Date          Mon May 30 08:15:32 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781209.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PHA00662 hypothetical protein  100.0       0       0  295.4  16.3  170    2-174     3-195 (215)
  2 PHA00428 tail tubular protein  100.0 3.8E-31 9.8E-36  202.2  15.8  162    1-167     9-177 (193)
  3 PRK05446 imidazole glycerol-ph  22.0      57  0.0014   13.6   2.7   56  116-171   295-352 (354)
  4 smart00040 CSF2 Granulocyte-ma  18.6      52  0.0013   13.8   1.0   41    3-44     15-55  (121)
  5 pfam06426 SATase_N Serine acet  17.1      73  0.0019   12.9   4.6   45  119-163    31-77  (105)
  6 pfam02945 Endonuclease_7 Recom  16.7      49  0.0013   13.9   0.5   15   41-55     16-30  (81)
  7 KOG3028 consensus               16.6      45  0.0011   14.2   0.3   72    5-81    145-217 (313)
  8 cd01256 PH_dynamin Dynamin ple  16.5      56  0.0014   13.6   0.7   59   66-124    39-104 (110)
  9 KOG0428 consensus               15.8      79   0.002   12.7   3.3   46   47-93     40-89  (314)
 10 cd02851 Galactose_oxidase_C_te  14.6      85  0.0022   12.5   1.9   32   45-77     42-73  (101)

No 1  
>PHA00662 hypothetical protein
Probab=100.00  E-value=0  Score=295.40  Aligned_cols=170  Identities=25%  Similarity=0.365  Sum_probs=149.3

Q ss_pred             CHHHHHHHHHHHCCC-CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCC-CCCCCCEEEECCCCCEE
Q ss_conf             889999999997182-1124336889789999999679999886404775111100003456-77676504654855000
Q gi|254781209|r    2 TELEICNWALLKLGQ-RPLENWNERSLKADYCRLLLPPIHKGLLRSFSWSFATQSMDLLPLY-FTYNGELKYYIPLKCLK   79 (175)
Q Consensus         2 T~l~i~N~aL~~iG~-~~I~sl~e~t~~A~~~~~~y~~~r~~~L~~~~W~Fa~~r~~L~~~~-~~~~~~~~y~lP~D~lr   79 (175)
                      |+|+|||+||.+||+ .+|+||+|+|++|++|+++|+++|+++|++|+||||++|++|+.++ ++++|.|+|+||+||||
T Consensus         3 S~v~Icn~AL~~lG~~~~I~s~~e~s~~A~~c~~~Y~~~r~~~L~~~~W~fA~~r~~La~~~~~p~~~~~ay~lP~DcLr   82 (215)
T PHA00662          3 SEVDICNRALAYIGDERTIASLNEGSKQAEYCARFYDFARDALLELHTWGFATKRAQLAAMGISPPEWRYAYAQPADAIR   82 (215)
T ss_pred             CHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEEECCCHHHHEE
T ss_conf             48999999999857788614777899899999988899999999739745465433343047899876442338157156


Q ss_pred             EEECCCCCC------------------CCCCEEEECCCCCCEEEEEEEECCCH-HHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             232045663------------------12312543047877089999971786-67559999999999999995775296
Q gi|254781209|r   80 VLNTSEETQ------------------LRGRCIVARGDTPRPLSLKYIGEVPL-SDCDPLYQEAFALKLAGELCPPLIMD  140 (175)
Q Consensus        80 v~~v~~~~~------------------~~~~~~~~~~~~~~~~~~~yv~~~~~-~~~p~~f~~~i~~~lA~~~A~~itg~  140 (175)
                      |+.|.++..                  ..|+++++   +.++++++||+++++ +.||++|+++|+++||+++|++||||
T Consensus        83 v~~v~~~~~~~~~~~~~~~~~~~~e~~~~G~~I~t---d~~~~~l~Yi~rvtD~~~fd~~F~~aLa~~LAa~lA~piT~s  159 (215)
T PHA00662         83 IVAVLPHGAANIEAGIDNAQPFSCEIDNTGDIILT---NQVNAVARYISRVTDTNKFDALFVEALAWRLAAMLAGPLTGS  159 (215)
T ss_pred             EEEEECCCCCCCCCCCCCCCCEEEEECCCCCEEEE---CCCCCEEEEEEECCCHHHCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             66772388655543334565224430566886882---698618999984588033889999999999999988876198


Q ss_pred             HHHHHHHHHHHHHH--HHHHHHHHCCCCCCCCCCCC
Q ss_conf             89999999999999--99999832217873344337
Q gi|254781209|r  141 DQMRSYLKGESERV--LAVAMDMDGVEIPEDRGYHN  174 (175)
Q Consensus       141 ~~l~~~l~q~~~~~--l~~A~~~Da~q~~~~~~~~~  174 (175)
                      .++.+.+++++++.  +++|+..|++|++++++...
T Consensus       160 ~~l~~~~~~~~~~~~~~A~A~~~Da~e~~~~~~~~~  195 (215)
T PHA00662        160 AGAAESARCVGAMQIYLAQAMVSNANQRPTKPAHMD  195 (215)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             799999999999999998876424556888877756


No 2  
>PHA00428 tail tubular protein A
Probab=99.98  E-value=3.8e-31  Score=202.19  Aligned_cols=162  Identities=19%  Similarity=0.275  Sum_probs=140.1

Q ss_pred             CCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEE-EECCCCCCCCCCCEEEECCCCCEE
Q ss_conf             9889999999997182112433688978999999967999988640477511110-000345677676504654855000
Q gi|254781209|r    1 MTELEICNWALLKLGQRPLENWNERSLKADYCRLLLPPIHKGLLRSFSWSFATQS-MDLLPLYFTYNGELKYYIPLKCLK   79 (175)
Q Consensus         1 ~T~l~i~N~aL~~iG~~~I~sl~e~t~~A~~~~~~y~~~r~~~L~~~~W~Fa~~r-~~L~~~~~~~~~~~~y~lP~D~lr   79 (175)
                      ||+|++||.+|+.|||+||+||+++++++.+|.++++++.+++ ++.||+||+++ ..|.|+...    ..+.+|+|+|+
T Consensus         9 ~teL~AVN~iL~~IGeaPV~sLd~~npd~~~A~~~L~ev~r~V-QseGW~FNTE~~~~ltpd~~~----~~I~vP~n~L~   83 (193)
T PHA00428          9 LTELDAVNDILASIGEPPVTTLDDTNPDVANARRILNDINRQV-QSEGWTFNIEEGATLTPDPFT----GRINLPSDYLS   83 (193)
T ss_pred             CCHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH-HHCCCEECCCCCEEEEECCCC----CEEECCCCEEE
T ss_conf             3348999999997187876435678967999999999998999-860524222325574126999----95935654899


Q ss_pred             EEECCCCC--CCCCCEEEEC----CCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             23204566--3123125430----47877089999971786675599999999999999957752968999999999999
Q gi|254781209|r   80 VLNTSEET--QLRGRCIVAR----GDTPRPLSLKYIGEVPLSDCDPLYQEAFALKLAGELCPPLIMDDQMRSYLKGESER  153 (175)
Q Consensus        80 v~~v~~~~--~~~~~~~~~~----~~~~~~~~~~yv~~~~~~~~p~~f~~~i~~~lA~~~A~~itg~~~l~~~l~q~~~~  153 (175)
                      +......+  ..+|++++..    ....+++++++|+..+|+++|+.|++||++|+|++++.+++|++++.+.+.+++++
T Consensus        84 vd~~~~~~d~v~Rg~~LYDr~n~T~~f~~~i~~dvv~~l~fedlPe~~q~yIt~rAAr~f~~r~vG~~~l~q~l~~dE~~  163 (193)
T PHA00428         84 FYPDSGDTQYVNRGGYVYDRSTGTDRFGSPVTVRLVLLREFDEMPECFRRYIVTKAARQFNTRFFGAPETAQVLAEEEQE  163 (193)
T ss_pred             EECCCCCCEEEEECCEEEECCCCCEECCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             97689952479766899985889667289727879998134548899999999999999999853869999999999999


Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             99999983221787
Q gi|254781209|r  154 VLAVAMDMDGVEIP  167 (175)
Q Consensus       154 ~l~~A~~~Da~q~~  167 (175)
                      +.+.+++++++|+.
T Consensus       164 Ara~l~e~e~~q~d  177 (193)
T PHA00428        164 ARAEVSEYETDQGD  177 (193)
T ss_pred             HHHHHHHHHHHCCC
T ss_conf             99999999984578


No 3  
>PRK05446 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional
Probab=22.02  E-value=57  Score=13.57  Aligned_cols=56  Identities=14%  Similarity=0.169  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHH--HHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             755999999999999999577529689--99999999999999999832217873344
Q gi|254781209|r  116 DCDPLYQEAFALKLAGELCPPLIMDDQ--MRSYLKGESERVLAVAMDMDGVEIPEDRG  171 (175)
Q Consensus       116 ~~p~~f~~~i~~~lA~~~A~~itg~~~--l~~~l~q~~~~~l~~A~~~Da~q~~~~~~  171 (175)
                      ++-+-|.+.++..+..-+-..+.|.+.  +.+.+-.-...+|++|...|+.+-|+..+
T Consensus       295 el~~~Ff~s~a~~~~~tlHi~~~G~n~HH~~Ea~FKa~a~Al~~A~~~~~~~vpSTKG  352 (354)
T PRK05446        295 EMVEHFFRSLSDAMGCTLHLKTKGKNDHHKVESLFKAFGRALRQAIRVEGNTLPSSKG  352 (354)
T ss_pred             HHHHHHHHHHHHHCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             7799999999960788899984138708899999999999999985638998989886


No 4  
>smart00040 CSF2 Granulocyte-macrophage colony-simulating factor (GM-CSF). GM-CSF stimulates the development of and the cytotoxic  activity of white blood cells.
Probab=18.63  E-value=52  Score=13.77  Aligned_cols=41  Identities=10%  Similarity=-0.033  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             899999999971821124336889789999999679999886
Q gi|254781209|r    3 ELEICNWALLKLGQRPLENWNERSLKADYCRLLLPPIHKGLL   44 (175)
Q Consensus         3 ~l~i~N~aL~~iG~~~I~sl~e~t~~A~~~~~~y~~~r~~~L   44 (175)
                      -||++.-||+.+...+-+. .+-+....+.+.+++.-.-.+|
T Consensus        15 HVdAIkEAlsLLn~s~d~~-a~mnE~VeVVSe~Fd~qeptCl   55 (121)
T smart00040       15 HVDAIKEALSLLNDSRDTA-AVMNETVEVVSEMFDLQEPTCL   55 (121)
T ss_pred             HHHHHHHHHHHHHCCCCHH-HHHCCHHHHHHHHCCCCCCCHH
T ss_conf             9999999999985488337-6742148999870487787289


No 5  
>pfam06426 SATase_N Serine acetyltransferase, N-terminal. The N-terminal domain of serine acetyltransferase has a sequence that is conserved in plants and bacteria.
Probab=17.06  E-value=73  Score=12.92  Aligned_cols=45  Identities=20%  Similarity=0.247  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH--HHHHHHHHHC
Q ss_conf             99999999999999957752968999999999999--9999998322
Q gi|254781209|r  119 PLYQEAFALKLAGELCPPLIMDDQMRSYLKGESER--VLAVAMDMDG  163 (175)
Q Consensus       119 ~~f~~~i~~~lA~~~A~~itg~~~l~~~l~q~~~~--~l~~A~~~Da  163 (175)
                      +.|.+++++++|.+++.+......+.....+-+..  .+.++...|-
T Consensus        31 ~sl~~ALs~~La~kL~~~~~~~~~l~~~~~~a~~~~p~i~~~a~~Dl   77 (105)
T pfam06426        31 DSLESALAYRLANKLASSTMSADTLRELFDEAYAADPEIVEAARADL   77 (105)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             87999999999998389857899999999999982969999999999


No 6  
>pfam02945 Endonuclease_7 Recombination endonuclease VII.
Probab=16.72  E-value=49  Score=13.94  Aligned_cols=15  Identities=7%  Similarity=-0.137  Sum_probs=10.5

Q ss_pred             HHHHHHCCCCCEEEE
Q ss_conf             988640477511110
Q gi|254781209|r   41 KGLLRSFSWSFATQS   55 (175)
Q Consensus        41 ~~~L~~~~W~Fa~~r   55 (175)
                      ++++...++.||+=.
T Consensus        16 ~~ll~~Q~g~CaiC~   30 (81)
T pfam02945        16 WAIYEAQGGRCAICQ   30 (81)
T ss_pred             HHHHHHHCCCCCCCC
T ss_conf             999999399887889


No 7  
>KOG3028 consensus
Probab=16.57  E-value=45  Score=14.16  Aligned_cols=72  Identities=22%  Similarity=0.216  Sum_probs=43.2

Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCC-CCEEEECCCCCEEEE
Q ss_conf             99999999718211243368897899999996799998864047751111000034567767-650465485500023
Q gi|254781209|r    5 EICNWALLKLGQRPLENWNERSLKADYCRLLLPPIHKGLLRSFSWSFATQSMDLLPLYFTYN-GELKYYIPLKCLKVL   81 (175)
Q Consensus         5 ~i~N~aL~~iG~~~I~sl~e~t~~A~~~~~~y~~~r~~~L~~~~W~Fa~~r~~L~~~~~~~~-~~~~y~lP~D~lrv~   81 (175)
                      +|+|+....+|+.+    ..+...-..++..|+.... .|.+.-|=|+-+-..|......+- .-++..||.|.+++.
T Consensus       145 qAk~rl~l~~g~~~----~~e~~i~~~Aska~~~LS~-~Lgs~kffFgd~psslDa~lfs~la~~~~~~Lp~~~Lq~~  217 (313)
T KOG3028         145 QAKERLQLTLGELT----EREDQIYKDASKALNLLST-LLGSKKFFFGDKPSSLDALLFSYLAILLQVALPNDSLQVH  217 (313)
T ss_pred             HHHHHHHHHHCCCH----HHHHHHHHHHHHHHHHHHH-HHCCCEEEECCCCCHHHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             99999999848860----5678999999999999999-8467617637987368899999999997444871258999


No 8  
>cd01256 PH_dynamin Dynamin pleckstrin homology (PH) domain. Dynamin is a GTPase that regulates endocytic vesicle formation. It has an N-terminal GTPase domain, followed by a PH domain, a GTPase effector domain and a C-terminal proline arginine rich domain.  Dynamin-like proteins, which are found in metazoa, plants and yeast have the same domain architecture as dynamin, but lack the PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding.  Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=16.45  E-value=56  Score=13.62  Aligned_cols=59  Identities=20%  Similarity=0.164  Sum_probs=31.9

Q ss_pred             CCCEEEECCCCCEEEEECCCCCCCCCCEEEECCCCCCEEEEEE-----EECC-CH-HHHHHHHHHH
Q ss_conf             7650465485500023204566312312543047877089999-----9717-86-6755999999
Q gi|254781209|r   66 NGELKYYIPLKCLKVLNTSEETQLRGRCIVARGDTPRPLSLKY-----IGEV-PL-SDCDPLYQEA  124 (175)
Q Consensus        66 ~~~~~y~lP~D~lrv~~v~~~~~~~~~~~~~~~~~~~~~~~~y-----v~~~-~~-~~~p~~f~~~  124 (175)
                      +-...|.||-|.|+++++..+.............+...+|-+|     ..+. ++ +.|-..|.++
T Consensus        39 ekekky~l~ld~lklrd~E~gfms~~~~falF~~~~rNvyKD~kqlEL~~~sqe~vdsWKASfLRA  104 (110)
T cd01256          39 EKEKKYMLPLDGLKLRDIEGGFMSRNHKFALFYPDGRNVYKDYKQLELGCETLEEVDSWKASFLRA  104 (110)
T ss_pred             HHHHCCCCCCCCCCCCHHHHCCCCCCCEEEEECCCCHHHHHHHHHHEECCCCHHHHHHHHHHHHHC
T ss_conf             654332003477320100102345671488866764124530233100368588898999998863


No 9  
>KOG0428 consensus
Probab=15.78  E-value=79  Score=12.73  Aligned_cols=46  Identities=9%  Similarity=0.085  Sum_probs=26.0

Q ss_pred             CCCCCEEEEEECCCCCCCCCCCEEEECCCCCEE----EEECCCCCCCCCCE
Q ss_conf             477511110000345677676504654855000----23204566312312
Q gi|254781209|r   47 FSWSFATQSMDLLPLYFTYNGELKYYIPLKCLK----VLNTSEETQLRGRC   93 (175)
Q Consensus        47 ~~W~Fa~~r~~L~~~~~~~~~~~~y~lP~D~lr----v~~v~~~~~~~~~~   93 (175)
                      +.|+|+.+- .+..+-.++-|-..++||+|.-.    ++-..+.++++..+
T Consensus        40 FEWhFtiRG-p~dtdFeGGiYHGRI~lPadYPmKPPs~iLLTpNGRFE~nk   89 (314)
T KOG0428          40 FEWHFTIRG-PPDTDFEGGIYHGRIVLPADYPMKPPSIILLTPNGRFEVNK   89 (314)
T ss_pred             EEEEEEEEC-CCCCCCCCCEEEEEEECCCCCCCCCCEEEEECCCCCEEECC
T ss_conf             147888537-99877657414435856877898998079976887334076


No 10 
>cd02851 Galactose_oxidase_C_term Galactose oxidase C-terminus domain. Galactose oxidase is an extracellular monomeric enzyme which catalyses the stereospecific oxidation of a broad range of primary alcohol substrates and possesses a unique mononuclear copper site essential for catalysing a two-electron transfer reaction during the oxidation of primary alcohols to corresponding aldehydes. The second redox active center necessary for the reaction was found to be situated at a tyrosine residue.  The C-terminus of galactose oxidase may be related to the immunoglobulin and/or fibronectin type III superfamilies.  These domains are associated with different types of catalytic domains at  either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions.  Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=14.61  E-value=85  Score=12.55  Aligned_cols=32  Identities=9%  Similarity=0.055  Sum_probs=21.7

Q ss_pred             HHCCCCCEEEEEECCCCCCCCCCCEEEECCCCC
Q ss_conf             404775111100003456776765046548550
Q gi|254781209|r   45 RSFSWSFATQSMDLLPLYFTYNGELKYYIPLKC   77 (175)
Q Consensus        45 ~~~~W~Fa~~r~~L~~~~~~~~~~~~y~lP~D~   77 (175)
                      -.|.+|+..|++.|.- ....+..+...+|.|-
T Consensus        42 ~THs~n~~QR~v~L~~-~~~~~~~~~v~~P~~~   73 (101)
T cd02851          42 ATHTVNTDQRRIPLTL-FSVGGNSYSVQIPSDP   73 (101)
T ss_pred             CCCCCCCCCCEEECCC-EECCCCEEEEEECCCC
T ss_conf             4306578876886540-8358998999838998


Done!