Query         gi|254781129|ref|YP_003065542.1| hypothetical protein CLIBASIA_05155 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 103
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 04:59:44 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781129.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 KOG0188 consensus               37.4     8.8 0.00022   19.8  -0.1   80    7-89    570-655 (895)
  2 TIGR02553 SipD_IpaD_SspD type   37.1     6.8 0.00017   20.4  -0.8   41   29-73    207-247 (377)
  3 COG4908 Uncharacterized protei  31.6     7.3 0.00019   20.3  -1.3   49   52-100    18-66  (439)
  4 TIGR02853 spore_dpaA dipicolin  20.4      39 0.00098   16.6   0.7   45    3-47     40-97  (288)
  5 pfam09475 Dot_icm_IcmQ Dot/Icm  18.1      53  0.0014   15.9   1.0   31   62-92    118-156 (179)
  6 KOG0706 consensus               14.1      69  0.0018   15.3   0.7   38   33-81    395-432 (454)
  7 pfam10909 DUF2682 Protein of u  12.6 1.1E+02  0.0029   14.3   1.4   48   30-79     11-59  (77)
  8 COG4989 Predicted oxidoreducta  11.4      90  0.0023   14.7   0.6   31   20-52    153-183 (298)
  9 pfam05745 CRPA Chlamydia 15 kD  10.4      66  0.0017   15.4  -0.4   29   24-58    117-145 (150)
 10 CHL00076 chlB photochlorophyll  10.0 1.6E+02  0.0042   13.4   1.6   33   56-88    165-202 (510)

No 1  
>KOG0188 consensus
Probab=37.44  E-value=8.8  Score=19.84  Aligned_cols=80  Identities=30%  Similarity=0.351  Sum_probs=59.8

Q ss_pred             HHHHHHCCCCEEEE------EEEECCCHHHHCCCHHHCCCCCHHHHHHCCCCHHHHHHHHEEEEEECCCHHHHHHHHCCC
Q ss_conf             66431001100236------675125834501014434788811211025776552221101001057812356552050
Q gi|254781129|r    7 HKAASNALNFATTQ------VQYSTFTPEKMKLSQDYLGNTNPDAVNQLNLDDQKINNIILSKAMVFPNQSDIASLKEGV   80 (103)
Q Consensus         7 hkaasnalnfattq------vqystftpekmklsqdylgntnpdavnqlnlddqkinniilskamvfpnqsdiaslkegv   80 (103)
                      +..|...||||-.+      -+-|...|+|+++.-.+.+.   -...||..-.+++|..|-+.+-|+-..+..+--|+--
T Consensus       570 nHTaTHlLN~aLr~~l~~t~QkGSlV~pdklRfDf~~k~~---lt~eql~~vE~~~ne~I~~~~~V~~~e~~l~~ak~i~  646 (895)
T KOG0188         570 NHTATHLLNFALRQVLKGTDQKGSLVAPDKLRFDFSTKGA---LTKEQLKKVEDKINEFIQKNAPVYAKELPLAEAKKIP  646 (895)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCCCCCCCHHHEEEECCCCCC---CCHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHCCC
T ss_conf             1409999999999862652456664575670564236777---8999999999999999863885698865788873277


Q ss_pred             EEEEEECCC
Q ss_conf             344540463
Q gi|254781129|r   81 ALNLVKDES   89 (103)
Q Consensus        81 alnlvkdes   89 (103)
                      .|.-|-||.
T Consensus       647 glr~v~~E~  655 (895)
T KOG0188         647 GLRAVFDEV  655 (895)
T ss_pred             CCCCCCCCC
T ss_conf             710025774


No 2  
>TIGR02553 SipD_IpaD_SspD type III effector protein IpaD/SipD/SspD; InterPro: IPR013386    These proteins are encoded within type III secretion operons and have been shown to be secreted by that system .; GO: 0009405 pathogenesis.
Probab=37.11  E-value=6.8  Score=20.42  Aligned_cols=41  Identities=37%  Similarity=0.475  Sum_probs=28.1

Q ss_pred             HHHCCCHHHCCCCCHHHHHHCCCCHHHHHHHHEEEEEECCCHHHH
Q ss_conf             450101443478881121102577655222110100105781235
Q gi|254781129|r   29 EKMKLSQDYLGNTNPDAVNQLNLDDQKINNIILSKAMVFPNQSDI   73 (103)
Q Consensus        29 ekmklsqdylgntnpdavnqlnlddqkinniilskamvfpnqsdi   73 (103)
                      .+|||.-+-|-+.--.-++.+.|.|    |.|-+++..||-||.-
T Consensus       207 ~~vKldv~~lKa~l~~l~~~~~lGd----N~~N~~~VLFPAQSk~  247 (377)
T TIGR02553       207 NKVKLDVGKLKALLEKLIDKLPLGD----NLINKKAVLFPAQSKD  247 (377)
T ss_pred             CEEEECHHHHHHHHHHHHHHCCCCC----CCCCCCEECCCCCCCC
T ss_conf             7153246999999999997547776----6323430105420578


No 3  
>COG4908 Uncharacterized protein containing a NRPS condensation (elongation) domain [General function prediction only]
Probab=31.59  E-value=7.3  Score=20.26  Aligned_cols=49  Identities=35%  Similarity=0.496  Sum_probs=42.3

Q ss_pred             CHHHHHHHHEEEEEECCCHHHHHHHHCCCEEEEEECCCEEEEEECCCHH
Q ss_conf             7655222110100105781235655205034454046323663233200
Q gi|254781129|r   52 DDQKINNIILSKAMVFPNQSDIASLKEGVALNLVKDESLSCVIAEGEKL  100 (103)
Q Consensus        52 ddqkinniilskamvfpnqsdiaslkegvalnlvkdeslscviaegekl  100 (103)
                      +|-+|++-.|--+.+|-+.-+|.-||..|-+-...-.-|+|-.+||++-
T Consensus        18 ~d~~i~~htl~~vi~f~~~fni~~lkkAl~~svka~piL~c~f~eg~~~   66 (439)
T COG4908          18 DDYKINDHTLHYVITFGDKFNIDRLKKALRYSVKAVPILSCKFSEGEKR   66 (439)
T ss_pred             HHCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             3127577648999995884688999999998887665454254312452


No 4  
>TIGR02853 spore_dpaA dipicolinic acid synthetase, A subunit; InterPro: IPR014215   This predicted Rossman fold-containing protein is the A subunit of dipicolinic acid synthetase as found in most, though not all, endospore-forming low-GC Gram-positive bacteria; it is absent in Clostridium. The B subunit is represented by IPR014214 from INTERPRO. This protein is also known as SpoVFA..
Probab=20.45  E-value=39  Score=16.60  Aligned_cols=45  Identities=24%  Similarity=0.343  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHCCCCEEEEE-------------EEECCCHHHHCCCHHHCCCCCHHHHH
Q ss_conf             1355664310011002366-------------75125834501014434788811211
Q gi|254781129|r    3 RDGLHKAASNALNFATTQV-------------QYSTFTPEKMKLSQDYLGNTNPDAVN   47 (103)
Q Consensus         3 rdglhkaasnalnfattqv-------------qystftpekmklsqdylgntnpdavn   47 (103)
                      +-|..+..++.+.|.|++|             -++.|+-|+.+|.+||+-++.+..+=
T Consensus        40 F~G~~~~~~~~~~~~~~DvviLPv~G~~~~G~v~t~f~~~~~~l~~~~~~~~~~~~~~   97 (288)
T TIGR02853        40 FTGVEKLELDELDLSTLDVVILPVQGVSQDGKVATVFSNEKVVLKPELLEETKKHCTI   97 (288)
T ss_pred             CCCHHHHCCCCCCCCCCCEEEECCCCCCCCCEEEEECCCCCEEECHHHHHHCCCCEEE
T ss_conf             1330010134244446667881678859988487411587216466899520794389


No 5  
>pfam09475 Dot_icm_IcmQ Dot/Icm secretion system protein (dot_icm_IcmQ). Proteins in this entry are the IcmQ component of Dot/Icm secretion systems, as found in the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favour calling this the Dot/Icm system. This protein was shown to be essential for translocation.
Probab=18.09  E-value=53  Score=15.89  Aligned_cols=31  Identities=35%  Similarity=0.462  Sum_probs=23.7

Q ss_pred             EEEEECCCHHHHHHH--------HCCCEEEEEECCCEEE
Q ss_conf             100105781235655--------2050344540463236
Q gi|254781129|r   62 SKAMVFPNQSDIASL--------KEGVALNLVKDESLSC   92 (103)
Q Consensus        62 skamvfpnqsdiasl--------kegvalnlvkdeslsc   92 (103)
                      .-..++-||+||-++        |.|-.|--+||.+++-
T Consensus       118 AYV~iyinq~dIl~~~~dk~~~Dk~GkpLltLkd~ai~l  156 (179)
T pfam09475       118 AYVAIYINQSDILSVSPDKTPTDKLGKPLLTLKDRAINL  156 (179)
T ss_pred             EEEEEEECHHHCCCCCCCCCCCCCCCCCCEECCHHHCCH
T ss_conf             689999867870367844476355788201041312053


No 6  
>KOG0706 consensus
Probab=14.06  E-value=69  Score=15.33  Aligned_cols=38  Identities=29%  Similarity=0.421  Sum_probs=22.3

Q ss_pred             CCHHHCCCCCHHHHHHCCCCHHHHHHHHEEEEEECCCHHHHHHHHCCCE
Q ss_conf             0144347888112110257765522211010010578123565520503
Q gi|254781129|r   33 LSQDYLGNTNPDAVNQLNLDDQKINNIILSKAMVFPNQSDIASLKEGVA   81 (103)
Q Consensus        33 lsqdylgntnpdavnqlnlddqkinniilskamvfpnqsdiaslkegva   81 (103)
                      -|-||.|+-.+         ++.-.+.++  -.+|+++.||+++|.++-
T Consensus       395 SSsd~fG~~~~---------~~~~g~~~~--~~~~~a~~di~~~k~~~~  432 (454)
T KOG0706         395 SSSDLFGEGDD---------DHTAGSLAL--RDSFRAAQDIASFKNSAR  432 (454)
T ss_pred             CHHHHCCCCCC---------CCCCCCHHH--CCCCCCCCCHHHHHHHHH
T ss_conf             42754278887---------778651122--023335444899999999


No 7  
>pfam10909 DUF2682 Protein of unknown function (DUF2682). This viral family of proteins has no known function.
Probab=12.65  E-value=1.1e+02  Score=14.25  Aligned_cols=48  Identities=25%  Similarity=0.444  Sum_probs=34.6

Q ss_pred             HHCCCHHHCCCCCHHHHHHCCCCHHHHHHHHEEEEEECC-CHHHHHHHHCC
Q ss_conf             501014434788811211025776552221101001057-81235655205
Q gi|254781129|r   30 KMKLSQDYLGNTNPDAVNQLNLDDQKINNIILSKAMVFP-NQSDIASLKEG   79 (103)
Q Consensus        30 kmklsqdylgntnpdavnqlnlddqkinniilskamvfp-nqsdiaslkeg   79 (103)
                      .|.--+.||.+.+|++..+|  ++.-..-.+-+.|.+|- .|+..-.||..
T Consensus        11 l~~Ev~~fL~~~~p~~~~~l--E~~Ltkll~~~naI~FD~~~~~l~~Lk~N   59 (77)
T pfam10909        11 LASEVDAFLNSDNPTAFDDL--EERLTKLLIRANAIVFDPQQTNLKILKTN   59 (77)
T ss_pred             HHHHHHHHHCCCCCCCHHHH--HHHHHHHHHHHCCEEECCCHHHHHHHHHH
T ss_conf             99999999479996300059--99999999995560468535567999988


No 8  
>COG4989 Predicted oxidoreductase [General function prediction only]
Probab=11.35  E-value=90  Score=14.75  Aligned_cols=31  Identities=35%  Similarity=0.414  Sum_probs=25.1

Q ss_pred             EEEEECCCHHHHCCCHHHCCCCCHHHHHHCCCC
Q ss_conf             667512583450101443478881121102577
Q gi|254781129|r   20 QVQYSTFTPEKMKLSQDYLGNTNPDAVNQLNLD   52 (103)
Q Consensus        20 qvqystftpekmklsqdylgntnpdavnqlnld   52 (103)
                      .+--|.|+|-.+.|-|.|+.++  -+.||+.+.
T Consensus       153 ~fGVSNf~p~Q~~LL~s~l~~~--LvtNQlelS  183 (298)
T COG4989         153 HFGVSNFNPAQFELLQSRLPFT--LVTNQLELS  183 (298)
T ss_pred             EEECCCCCHHHHHHHHHHCCCH--HHHCCEEEC
T ss_conf             5413789888999999763204--332104413


No 9  
>pfam05745 CRPA Chlamydia 15 kDa cysteine-rich outer membrane protein (CRPA). This family consists of several Chlamydia 15 kDa cysteine-rich outer membrane proteins which are associated with differentiation of reticulate bodies (RBs) into elementary bodies (EBs).
Probab=10.36  E-value=66  Score=15.42  Aligned_cols=29  Identities=38%  Similarity=0.536  Sum_probs=21.0

Q ss_pred             ECCCHHHHCCCHHHCCCCCHHHHHHCCCCHHHHHH
Q ss_conf             12583450101443478881121102577655222
Q gi|254781129|r   24 STFTPEKMKLSQDYLGNTNPDAVNQLNLDDQKINN   58 (103)
Q Consensus        24 stftpekmklsqdylgntnpdavnqlnlddqkinn   58 (103)
                      ..-||||.+|-+..|+.+.      --|||-.+||
T Consensus       117 ~~CtpeKw~lckk~l~tsE------DilDDGqlNn  145 (150)
T pfam05745       117 GPCTPEKWRLCKKVLKTSE------DILDDGQLNN  145 (150)
T ss_pred             CCCCHHHHHHHHHHHHHHH------HHHCCCCCCC
T ss_conf             8889899999999986677------6405432166


No 10 
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=10.02  E-value=1.6e+02  Score=13.43  Aligned_cols=33  Identities=39%  Similarity=0.408  Sum_probs=26.1

Q ss_pred             HHHHHEEEEEECCCHHHHHHHHC-----CCEEEEEECC
Q ss_conf             22211010010578123565520-----5034454046
Q gi|254781129|r   56 INNIILSKAMVFPNQSDIASLKE-----GVALNLVKDE   88 (103)
Q Consensus        56 inniilskamvfpnqsdiaslke-----gvalnlvkde   88 (103)
                      --|||=.-..-|-++||++.++.     |+..|+|--.
T Consensus       165 svNIiGpt~lgF~~~~Dl~Ei~RLl~~~Gi~VN~V~P~  202 (510)
T CHL00076        165 SVNIIGIFTLGFHNQHDCRELKRLLQDLGIEINQVIPE  202 (510)
T ss_pred             EEEEECCCCCCCCCHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             47885777566788788999999999759778898149


Done!