Query         gi|254780356|ref|YP_003064769.1| hypothetical protein CLIBASIA_01205 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 120
No_of_seqs    107 out of 144
Neff          5.5 
Searched_HMMs 39220
Date          Sun May 29 15:43:14 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780356.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK11539 hypothetical protein;  93.9     0.4   1E-05   25.0   9.0   63   34-103     6-68  (754)
  2 PRK10404 hypothetical protein;  75.9       5 0.00013   19.3   4.3   46    3-48     51-96  (101)
  3 COG4575 ElaB Uncharacterized c  75.3     4.9 0.00012   19.4   4.1   47    2-48     53-99  (104)
  4 pfam11833 DUF3353 Protein of u  64.2      11 0.00027   17.6   9.1   82   25-108    87-169 (193)
  5 PRK10132 hypothetical protein;  50.6      19 0.00047   16.4   3.6   44    3-47     58-101 (108)
  6 COG3851 UhpB Signal transducti  39.9      28 0.00071   15.5   7.4   56   27-82    178-233 (497)
  7 pfam09925 DUF2157 Predicted me  39.9      28 0.00071   15.5   7.2   66   30-95     34-106 (144)
  8 PRK13743 conjugal transfer pro  38.4      28 0.00072   15.4   2.6   91    2-102    12-110 (140)
  9 pfam05957 DUF883 Bacterial pro  35.8      33 0.00083   15.1   4.5   45    3-47     44-88  (94)
 10 pfam08105 Antimicrobial10 Metc  23.7      45  0.0012   14.4   1.6   29   83-111     6-38  (52)
 11 COG5548 Small integral membran  21.7      60  0.0015   13.7   4.4   59   36-94     13-71  (105)

No 1  
>PRK11539 hypothetical protein; Provisional
Probab=93.89  E-value=0.4  Score=24.96  Aligned_cols=63  Identities=10%  Similarity=0.159  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999996201457879999999999999999714743599999999999999999999999863
Q gi|254780356|r   34 IPVFLAFGAIFWFVYSPEIPIWGIVLSILIIAIISLRIRYSHPHILLIVKTLTYFLTRMILAAIEITRNP  103 (120)
Q Consensus        34 ~PV~lg~GI~~YF~L~~EP~~~~~~~~~~~~~~~~~~~r~~~~~~~~l~~~l~~~~~Gf~~A~~Rt~~va  103 (120)
                      +-+++.+|+....-+|+.|+.|....++..++.+.+..++.   .+.    +++.++||..+.+.++..-
T Consensus         6 ~a~a~~~G~l~l~~lp~lP~~~~~~~l~~~~~~l~~~~~~~---~~~----l~l~ll~f~wa~~~~~~~l   68 (754)
T PRK11539          6 VAVCIICGILPLLILPQLPGTWILAFLLLLACLLAFIPVRY---CRY----LALTLLFFLWGILAANQIL   68 (754)
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH---HHH----HHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999996013893589999999999999987658---999----9999999999999999999


No 2  
>PRK10404 hypothetical protein; Provisional
Probab=75.88  E-value=5  Score=19.31  Aligned_cols=46  Identities=9%  Similarity=-0.028  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             4564007999999999999989855982779999999999999620
Q gi|254780356|r    3 QKKISNPLCNIIQHVKYLIQLEQEYGGFFLFIPVFLAFGAIFWFVY   48 (120)
Q Consensus         3 ~~~~~~~~~~i~~~i~~~l~~E~~~G~lflW~PV~lg~GI~~YF~L   48 (120)
                      |.|++.+..++..+.+.....--+|=|=-||--|..++|+|+...+
T Consensus        51 r~rl~~~~~~~~~~aK~aa~~aD~YVhdnPW~aVGiaA~vGlvlGl   96 (101)
T PRK10404         51 KKRVSQASDSYYYRAKQAVYRADDYVHEKPWQGIGVGAAVGLVLGL   96 (101)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             9999988999999999999989999984972999999999999999


No 3  
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=75.32  E-value=4.9  Score=19.38  Aligned_cols=47  Identities=11%  Similarity=0.019  Sum_probs=40.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             14564007999999999999989855982779999999999999620
Q gi|254780356|r    2 LQKKISNPLCNIIQHVKYLIQLEQEYGGFFLFIPVFLAFGAIFWFVY   48 (120)
Q Consensus         2 ~~~~~~~~~~~i~~~i~~~l~~E~~~G~lflW~PV~lg~GI~~YF~L   48 (120)
                      .|.|++..--++.++-++.+..--+|=|=-||--|..+++||+...+
T Consensus        53 ~r~rl~~~~d~v~~~sk~a~~~tD~yV~e~PWq~VGvaAaVGlllGl   99 (104)
T COG4575          53 ARDRLGDTGDAVVQRSKAAADATDDYVRENPWQGVGVAAAVGLLLGL   99 (104)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             99999761378999999999879999872883388999999999999


No 4  
>pfam11833 DUF3353 Protein of unknown function (DUF3353). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 205 to 258 amino acids in length.
Probab=64.17  E-value=11  Score=17.64  Aligned_cols=82  Identities=15%  Similarity=0.048  Sum_probs=51.2

Q ss_pred             HHCCCCHHHHHHH-HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8559827799999-999999996201457879999999999999999714743599999999999999999999999863
Q gi|254780356|r   25 QEYGGFFLFIPVF-LAFGAIFWFVYSPEIPIWGIVLSILIIAIISLRIRYSHPHILLIVKTLTYFLTRMILAAIEITRNP  103 (120)
Q Consensus        25 ~~~G~lflW~PV~-lg~GI~~YF~L~~EP~~~~~~~~~~~~~~~~~~~r~~~~~~~~l~~~l~~~~~Gf~~A~~Rt~~va  103 (120)
                      .-.+....|--+. .+.+...+|.-+.+.  ..+.+.++..+...+..|+.+...+.+.+.+..+..|..+...=.....
T Consensus        87 ~Ps~~~l~~~~~~f~~L~~~~l~~~~~~~--~~l~LAls~~~~iyfl~rk~~~~~rA~~~tl~~L~~G~~~Gs~l~~~l~  164 (193)
T pfam11833        87 LPSGQGLLIRLVLFGLLALLLLLQGAESG--PQLQLALSTGACIYFLNRKGRRFGRALLWSLGGLVVGLLLGSLLAVLLP  164 (193)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCCCCC--CHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             89955018999999999999986068887--3189999999999988885031789999999999999999999987502


Q ss_pred             CCCCC
Q ss_conf             42207
Q gi|254780356|r  104 TTILS  108 (120)
Q Consensus       104 apVL~  108 (120)
                      .+++.
T Consensus       165 ~~~~~  169 (193)
T pfam11833       165 PFILP  169 (193)
T ss_pred             CCCCC
T ss_conf             22467


No 5  
>PRK10132 hypothetical protein; Provisional
Probab=50.55  E-value=19  Score=16.38  Aligned_cols=44  Identities=7%  Similarity=-0.019  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             456400799999999999998985598277999999999999962
Q gi|254780356|r    3 QKKISNPLCNIIQHVKYLIQLEQEYGGFFLFIPVFLAFGAIFWFV   47 (120)
Q Consensus         3 ~~~~~~~~~~i~~~i~~~l~~E~~~G~lflW~PV~lg~GI~~YF~   47 (120)
                      |.|+++ -..+.++-+.....--+|=|=-||.-|..|+++|+...
T Consensus        58 R~rL~~-~~~v~~~ar~aa~~AD~YVrenPW~sVGigAAVGvvlG  101 (108)
T PRK10132         58 RARMHG-RTRVQQAARDAVGCADTFVRERPWCSVGTAAAVGIFIG  101 (108)
T ss_pred             HHHHCC-CHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             998745-46999999999986888886489504769999999999


No 6  
>COG3851 UhpB Signal transduction histidine kinase, glucose-6-phosphate specific [Signal transduction mechanisms]
Probab=39.95  E-value=28  Score=15.48  Aligned_cols=56  Identities=9%  Similarity=0.220  Sum_probs=42.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             59827799999999999996201457879999999999999999714743599999
Q gi|254780356|r   27 YGGFFLFIPVFLAFGAIFWFVYSPEIPIWGIVLSILIIAIISLRIRYSHPHILLIV   82 (120)
Q Consensus        27 ~G~lflW~PV~lg~GI~~YF~L~~EP~~~~~~~~~~~~~~~~~~~r~~~~~~~~l~   82 (120)
                      |+....|.-.+|.+|+..-..+|+|-+...+..++.-....++...+.......+.
T Consensus       178 r~k~lvw~~L~fiigll~ql~L~de~~rf~l~~l~lP~I~lA~~yGWQG~llasll  233 (497)
T COG3851         178 RGKHLVWYLLLFIIGLLLQLGLPDELSRFTLFCLALPIIALAWHYGWQGALLASLL  233 (497)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             54026999999999999981480766568899999999999999611078999999


No 7  
>pfam09925 DUF2157 Predicted membrane protein (DUF2157). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=39.91  E-value=28  Score=15.47  Aligned_cols=66  Identities=20%  Similarity=0.157  Sum_probs=32.2

Q ss_pred             CHHHH-HHHHHHHHHHHHHHCCCC--CHHHHHHHH----HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             27799-999999999996201457--879999999----9999999997147435999999999999999999
Q gi|254780356|r   30 FFLFI-PVFLAFGAIFWFVYSPEI--PIWGIVLSI----LIIAIISLRIRYSHPHILLIVKTLTYFLTRMILA   95 (120)
Q Consensus        30 lflW~-PV~lg~GI~~YF~L~~EP--~~~~~~~~~----~~~~~~~~~~r~~~~~~~~l~~~l~~~~~Gf~~A   95 (120)
                      .+.++ -+++|+|+..+|+...|-  ...-+....    .......+..++.++...-.+..+..+..|...+
T Consensus        34 il~~lGalllg~gvi~fvAaNW~~i~r~~k~~l~~~~~~~~~~~~~~~~~~~~~~~~~all~l~~~~~Ga~ia  106 (144)
T pfam09925        34 ILLWLGALLLGAGVIFFVAANWEEIPRFAKFGLLLALLVGLALGGFWLWRRGKPRLGEALLLLGALLFGALLA  106 (144)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999829874688999999999999999999999347963999999999999999999


No 8  
>PRK13743 conjugal transfer protein TrbF; Provisional
Probab=38.39  E-value=28  Score=15.44  Aligned_cols=91  Identities=18%  Similarity=0.192  Sum_probs=48.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHC----CCCHH
Q ss_conf             14564007999999999999989855982779999999999999620145787999999999999999971----47435
Q gi|254780356|r    2 LQKKISNPLCNIIQHVKYLIQLEQEYGGFFLFIPVFLAFGAIFWFVYSPEIPIWGIVLSILIIAIISLRIR----YSHPH   77 (120)
Q Consensus         2 ~~~~~~~~~~~i~~~i~~~l~~E~~~G~lflW~PV~lg~GI~~YF~L~~EP~~~~~~~~~~~~~~~~~~~r----~~~~~   77 (120)
                      ++.+.++|-..|-|-=+.-.-.++..++-|-..-|++.+||.+|--...          .--+++-.|.+-    +.+-.
T Consensus        12 mke~~~~~e~kIrq~~rd~~y~~r~~~~Y~~LfiVFltAG~vLw~vM~~----------iFd~cIDsWkAdpeLnn~rym   81 (140)
T PRK13743         12 MKEKKNDAELKIRQTKRDYKYISRISDIYFDLFIVFLTAGIVLWVVMHI----------IFDACIDSWKADPELNNFRYM   81 (140)
T ss_pred             HHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHCCHHHHHHHHH
T ss_conf             8752368440045578777774204657787999999843999999999----------999888845338745219999


Q ss_pred             HHHHH----HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999----99999999999999999986
Q gi|254780356|r   78 ILLIV----KTLTYFLTRMILAAIEITRN  102 (120)
Q Consensus        78 ~~~l~----~~l~~~~~Gf~~A~~Rt~~v  102 (120)
                      |..+.    ..+-+++.||.++..+..-.
T Consensus        82 WNilMYaIPytL~AlaaGFlv~~~~~p~~  110 (140)
T PRK13743         82 WNILMYAIPYTLWALAAGFLVAGVRNPLC  110 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999974174443133589


No 9  
>pfam05957 DUF883 Bacterial protein of unknown function (DUF883). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=35.83  E-value=33  Score=15.12  Aligned_cols=45  Identities=9%  Similarity=0.058  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             456400799999999999998985598277999999999999962
Q gi|254780356|r    3 QKKISNPLCNIIQHVKYLIQLEQEYGGFFLFIPVFLAFGAIFWFV   47 (120)
Q Consensus         3 ~~~~~~~~~~i~~~i~~~l~~E~~~G~lflW~PV~lg~GI~~YF~   47 (120)
                      |++.++..-....+.+.....-.++=|--||--|..++|+|+-.+
T Consensus        44 r~~~~~~~~~~~~~~~~~~~~~d~yV~~~Pw~svgiAagvG~llG   88 (94)
T pfam05957        44 RERLGDAADAAAERARDAADAADDYVHENPWQAVGIAAGVGLLLG   88 (94)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
T ss_conf             999999999999999999998999998792999999999999999


No 10 
>pfam08105 Antimicrobial10 Metchnikowin family. This family consists of the metchnikowin family of antimicrobial peptides from Drosophila. metchnikowin is a proline-rich peptide whose expression is immune-inducible. Induction of the metchnikowin gene expression can be mediated either by the TOLL pathway or by the imd gene product. The metchnikowin peptide is unique among the Drosophila antimicrobial peptides in that it is active against both bacteria and fungi.
Probab=23.72  E-value=45  Score=14.38  Aligned_cols=29  Identities=17%  Similarity=0.159  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHH----HHHHHHHCCCCCCCE
Q ss_conf             99999999999999----999986342207837
Q gi|254780356|r   83 KTLTYFLTRMILAA----IEITRNPTTILSQSI  111 (120)
Q Consensus        83 ~~l~~~~~Gf~~A~----~Rt~~vaapVL~~~~  111 (120)
                      .++++.++|..+++    -+.++-.+|+.|.|-
T Consensus         6 GAifLalL~~~a~~~~v~~e~~~~qGPIFDTRP   38 (52)
T pfam08105         6 GAIFLALLGVMATATSVLAEPHRHQGPIFDTRP   38 (52)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf             799999999998256666751003588656788


No 11 
>COG5548 Small integral membrane protein [Function unknown]
Probab=21.70  E-value=60  Score=13.74  Aligned_cols=59  Identities=14%  Similarity=0.120  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999996201457879999999999999999714743599999999999999999
Q gi|254780356|r   36 VFLAFGAIFWFVYSPEIPIWGIVLSILIIAIISLRIRYSHPHILLIVKTLTYFLTRMIL   94 (120)
Q Consensus        36 V~lg~GI~~YF~L~~EP~~~~~~~~~~~~~~~~~~~r~~~~~~~~l~~~l~~~~~Gf~~   94 (120)
                      ....-|+..||--...|+...-....+....+..+.-+++..-..+.......+++|..
T Consensus        13 L~tiGGliGY~rk~S~vSL~sG~~~G~~~~~A~yL~~~g~~~Gl~~A~~~s~~Ll~~~~   71 (105)
T COG5548          13 LATIGGLIGYFRKNSQVSLLSGVFSGLLLFVAAYLQLQGQTWGLILATVVSAALLVFFA   71 (105)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEHHHHHHHHHHHHCC
T ss_conf             99963578887538800237888986799999999981866585049999999999621


Done!