Query         gi|254780518|ref|YP_003064931.1| hypothetical protein CLIBASIA_02025 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 48
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 23:43:47 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780518.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam04056 Ssl1 Ssl1-like. Ssl1  37.3      17 0.00044   18.6   1.3   30    2-31     89-121 (250)
  2 cd01453 vWA_transcription_fact  23.7      48  0.0012   16.5   1.7   29    2-30     40-71  (183)
  3 PHA02107 hypothetical protein   17.6      73  0.0019   15.6   1.6   29   14-42     54-82  (216)
  4 PRK02963 hypothetical protein;  11.9 1.5E+02  0.0038   14.2   1.9   30   18-48    109-138 (316)
  5 TIGR01925 spIIAB anti-sigma F   10.6      61  0.0015   16.0  -0.5   14   31-44     10-23  (137)
  6 PTZ00221 cyclophilin; Provisio  10.4 1.5E+02  0.0039   14.1   1.5   29   12-43     86-114 (249)
  7 KOG1106 consensus               10.2   1E+02  0.0026   15.0   0.5   33    8-40     22-57  (177)
  8 pfam08943 CsiD CsiD. This fami   9.8 1.9E+02  0.0049   13.7   1.9   30   18-48     96-125 (297)
  9 KOG2448 consensus                6.9 1.6E+02  0.0041   14.0   0.4    7   25-31     80-86  (596)
 10 TIGR01757 Malate-DH_plant mala   6.6 1.7E+02  0.0043   13.9   0.4    8   26-33    171-178 (390)

No 1  
>pfam04056 Ssl1 Ssl1-like. Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.
Probab=37.33  E-value=17  Score=18.55  Aligned_cols=30  Identities=20%  Similarity=0.556  Sum_probs=24.0

Q ss_pred             CCCCCCEEEEEEEEECC---CCCHHCCCCCCCC
Q ss_conf             01476114788886244---3600016984210
Q gi|254780518|r    2 YYNSNTVSKLSVACTSE---TGISKLSGNPCNL   31 (48)
Q Consensus         2 yynsntvsklsvactse---tgisklsgnpcnl   31 (48)
                      ||..|..|.|++-.+..   .-++.++|||-..
T Consensus        89 fFdqNPiSQlgii~~rn~~a~~ls~lsgnp~~h  121 (250)
T pfam04056        89 FFDQNPISQIGLITCKDGRAHRLTDLTGNPRVH  121 (250)
T ss_pred             HHHCCCCCCEEEEEEECCEEEEEEECCCCHHHH
T ss_conf             874398302279999657137833257998999


No 2  
>cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.
Probab=23.71  E-value=48  Score=16.46  Aligned_cols=29  Identities=24%  Similarity=0.635  Sum_probs=22.9

Q ss_pred             CCCCCCEEEEEEEEECCC---CCHHCCCCCCC
Q ss_conf             014761147888862443---60001698421
Q gi|254780518|r    2 YYNSNTVSKLSVACTSET---GISKLSGNPCN   30 (48)
Q Consensus         2 yynsntvsklsvactset---gisklsgnpcn   30 (48)
                      |+..|..|.+++..+..-   -++.++|||-.
T Consensus        40 ffdqNPisqlGii~~rn~~a~~ls~lsgn~~~   71 (183)
T cd01453          40 FFDQNPISQLGIISIKNGRAEKLTDLTGNPRK   71 (183)
T ss_pred             HHCCCCCCEEEEEEEECCEEEEEEECCCCHHH
T ss_conf             87079740489999946816997646899899


No 3  
>PHA02107 hypothetical protein
Probab=17.63  E-value=73  Score=15.60  Aligned_cols=29  Identities=38%  Similarity=0.332  Sum_probs=23.3

Q ss_pred             EEECCCCCHHCCCCCCCCHHCCCCCEEEE
Q ss_conf             86244360001698421011037531557
Q gi|254780518|r   14 ACTSETGISKLSGNPCNLAASRGVSFARV   42 (48)
Q Consensus        14 actsetgisklsgnpcnlaasrgvsfarv   42 (48)
                      +-.+.-||+|.+-|--|++|...++....
T Consensus        54 s~G~~~GI~KI~PN~~N~~A~~~~sV~G~   82 (216)
T PHA02107         54 SFGSRFGIAKISPNHINLAAVGTHSVCGT   82 (216)
T ss_pred             HHCCCCCCCCCCCCEEEEECCCCEEEEEE
T ss_conf             31134683313777044411133688778


No 4  
>PRK02963 hypothetical protein; Validated
Probab=11.88  E-value=1.5e+02  Score=14.18  Aligned_cols=30  Identities=33%  Similarity=0.464  Sum_probs=23.7

Q ss_pred             CCCCHHCCCCCCCCHHCCCCCEEEEEEEECC
Q ss_conf             4360001698421011037531557876429
Q gi|254780518|r   18 ETGISKLSGNPCNLAASRGVSFARVLVFLSD   48 (48)
Q Consensus        18 etgisklsgnpcnlaasrgvsfarvlvflsd   48 (48)
                      -|+++.|-|+| |.-|--|--+||-.|--.|
T Consensus       109 STAvaHLIG~p-N~DsMsGkYYARF~VKh~D  138 (316)
T PRK02963        109 ATAVAHLIGRS-NFDAMSGQYYARFVVKNVD  138 (316)
T ss_pred             HHHHHHHCCCC-CCCCCCCCEEEEEEEECCC
T ss_conf             66789872898-7212477427999994587


No 5  
>TIGR01925 spIIAB anti-sigma F factor; InterPro: IPR010194   This entry describes the SpoIIAB anti-sigma F factor. Sigma F regulates spore development in B subtilis. SpoIIAB binds to sigma F, preventing formation of the transcription complex at the promoter . SpoIIAA (anti-anti-sigma F factor) binds to SpoIIAB to inhibit association with sigma F, however SpoIIAB can phosphorylate SpoIIAA, causing disassociation of the SpoIIAA/B complex . The SpoIIE phosphatase dephosphorylates SpoIIAA.; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0016989 sigma factor antagonist activity, 0006468 protein amino acid phosphorylation, 0030435 sporulation, 0045892 negative regulation of transcription DNA-dependent.
Probab=10.55  E-value=61  Score=16.00  Aligned_cols=14  Identities=64%  Similarity=0.688  Sum_probs=10.7

Q ss_pred             CHHCCCCCEEEEEE
Q ss_conf             01103753155787
Q gi|254780518|r   31 LAASRGVSFARVLV   44 (48)
Q Consensus        31 laasrgvsfarvlv   44 (48)
                      +|.|..-|||||-|
T Consensus        10 ~A~S~NEsFARVtV   23 (137)
T TIGR01925        10 LAKSENESFARVTV   23 (137)
T ss_pred             EEECCCCCCHHHHH
T ss_conf             31016764013445


No 6  
>PTZ00221 cyclophilin; Provisional
Probab=10.44  E-value=1.5e+02  Score=14.12  Aligned_cols=29  Identities=17%  Similarity=0.093  Sum_probs=22.4

Q ss_pred             EEEEECCCCCHHCCCCCCCCHHCCCCCEEEEE
Q ss_conf             88862443600016984210110375315578
Q gi|254780518|r   12 SVACTSETGISKLSGNPCNLAASRGVSFARVL   43 (48)
Q Consensus        12 svactsetgisklsgnpcnlaasrgvsfarvl   43 (48)
                      -.-||.|.|+.+.+|.|-..   .|-.|-||.
T Consensus        86 RaLCTGEkG~~~~~G~~L~Y---kgs~FHRVi  114 (249)
T PTZ00221         86 RALITGSCGIDTNTGVKLDY---LYTPVHHVD  114 (249)
T ss_pred             HHHHCCCCCCCCCCCCCCCC---CCCEEEEEE
T ss_conf             98853788778888985351---697160783


No 7  
>KOG1106 consensus
Probab=10.19  E-value=1e+02  Score=14.95  Aligned_cols=33  Identities=36%  Similarity=0.508  Sum_probs=24.9

Q ss_pred             EEEEEEEEECCCCCHHCC---CCCCCCHHCCCCCEE
Q ss_conf             147888862443600016---984210110375315
Q gi|254780518|r    8 VSKLSVACTSETGISKLS---GNPCNLAASRGVSFA   40 (48)
Q Consensus         8 vsklsvactsetgiskls---gnpcnlaasrgvsfa   40 (48)
                      .+.-++.||.||+|-.|.   --|-.+++.++|...
T Consensus        22 a~~~ki~ct~e~~i~~lgfl~~~~~~~~~g~kVelP   57 (177)
T KOG1106          22 ASGEKIPCTFETKIPNLGFLQAPPRELPAGRKVELP   57 (177)
T ss_pred             HCCCCCCCEEEECCCCCCCCCCCCCCCCCCCEECCH
T ss_conf             079744654650588877567886638999720532


No 8  
>pfam08943 CsiD CsiD. This family consists of various bacterial proteins pertaining to the non-haem Fe(II)-dependent oxygenase family. Exact function is unknown, but a putative role includes involvement in the control of utilisation of gamma-aminobutyric acid.
Probab=9.77  E-value=1.9e+02  Score=13.66  Aligned_cols=30  Identities=37%  Similarity=0.557  Sum_probs=23.3

Q ss_pred             CCCCHHCCCCCCCCHHCCCCCEEEEEEEECC
Q ss_conf             4360001698421011037531557876429
Q gi|254780518|r   18 ETGISKLSGNPCNLAASRGVSFARVLVFLSD   48 (48)
Q Consensus        18 etgisklsgnpcnlaasrgvsfarvlvflsd   48 (48)
                      -|.|+.|-|+| |..+--|--+||-.|--.|
T Consensus        96 STAi~hLiG~P-N~DsM~GKYYARF~VKh~D  125 (297)
T pfam08943        96 STAVAHLIGRP-NFDAMSGKYYARFVVKNED  125 (297)
T ss_pred             HHHHHHHHCCC-CHHHCCCCEEEEEEEECCC
T ss_conf             76679871898-7112056237999996587


No 9  
>KOG2448 consensus
Probab=6.86  E-value=1.6e+02  Score=14.00  Aligned_cols=7  Identities=71%  Similarity=1.725  Sum_probs=0.0

Q ss_pred             CCCCCCC
Q ss_conf             6984210
Q gi|254780518|r   25 SGNPCNL   31 (48)
Q Consensus        25 sgnpcnl   31 (48)
                      +|||||.
T Consensus        80 egnpcnm   86 (596)
T KOG2448          80 EGNPCNM   86 (596)
T ss_pred             CCCCCCH
T ss_conf             4886521


No 10 
>TIGR01757 Malate-DH_plant malate dehydrogenase, NADP-dependent; InterPro: IPR011273   This entry represents the NADP-dependent malate dehydrogenase found in plants, mosses and green algae and localised to the chloroplast. Malate dehydrogenase converts oxaloacetate into malate, a critical step in the C4 cycle which allows circumvention of the effects of photorespiration. Malate is subsequently transported from the chloroplast to the cytoplasm (and then to the bundle sheath cells in C4 plants). The plant and moss enzymes are light regulated via cysteine diisulphide bonds. The enzyme from sorghum has been crystallised .; GO: 0046554 malate dehydrogenase (NADP+) activity, 0006108 malate metabolic process.
Probab=6.61  E-value=1.7e+02  Score=13.94  Aligned_cols=8  Identities=75%  Similarity=1.419  Sum_probs=0.0

Q ss_pred             CCCCCCHH
Q ss_conf             98421011
Q gi|254780518|r   26 GNPCNLAA   33 (48)
Q Consensus        26 gnpcnlaa   33 (48)
                      |||||-.|
T Consensus       171 GnPCntna  178 (390)
T TIGR01757       171 GNPCNTNA  178 (390)
T ss_pred             CCCCCHHH
T ss_conf             28754146


Done!