Query         gi|254781001|ref|YP_003065414.1| hypothetical protein CLIBASIA_04510 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 93
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 03:09:59 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781001.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK12862 malic enzyme; Reviewe  32.4      35 0.00089   16.8   2.2   59   22-80    383-453 (761)
  2 KOG4268 consensus               27.8      47  0.0012   16.1   2.3   14    4-17     95-108 (189)
  3 cd01453 vWA_transcription_fact  22.3      52  0.0013   15.9   1.7   85    4-90     84-178 (183)
  4 PRK07232 malic enzyme; Reviewe  21.8      71  0.0018   15.2   2.2   59   22-80    377-447 (753)
  5 pfam11355 DUF3157 Protein of u  17.6      44  0.0011   16.3   0.4   16   28-43    147-162 (199)
  6 PRK00556 minC septum formation  16.3      10 0.00026   19.6  -3.1   28   40-67    126-153 (195)
  7 COG3232 HpaF 5-carboxymethyl-2  15.7      61  0.0016   15.5   0.8   34   40-73      1-34  (127)
  8 KOG3181 consensus               15.0 1.2E+02  0.0029   14.1   2.2   34   36-72     75-108 (244)
  9 pfam05344 DUF746 Domain of Unk  14.9 1.2E+02   0.003   14.1   2.4   41   19-59     18-64  (65)
 10 pfam04056 Ssl1 Ssl1-like. Ssl1  14.4      95  0.0024   14.5   1.5   52    5-58    136-187 (250)

No 1  
>PRK12862 malic enzyme; Reviewed
Probab=32.39  E-value=35  Score=16.81  Aligned_cols=59  Identities=27%  Similarity=0.407  Sum_probs=40.8

Q ss_pred             HHHCCCHHHHHHHHHHH----HCCCCC----E----EHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCH
Q ss_conf             84086311543153665----077886----2----03556777641263788889987641100002532
Q gi|254781001|r   22 FIEGPTKAIVIIWLSIF----SMPSGS----I----EYRDTLDERVANSGLYMIVKKALVRSKKRKIAVPS   80 (93)
Q Consensus        22 fiegptkaiviiwlsif----smpsgs----i----eyrdtldervansglymivkkalvrskkrkiavps   80 (93)
                      .|-.|-..-+|.|.+--    .|-||-    |    .||+.|..|+..|+..|-.--.-.|..+++|..|.
T Consensus       383 iip~pfdprl~~~v~~ava~aa~~sgva~~~i~d~~~y~~~L~~~~~~s~~~mr~I~erAK~~PKRIVFaE  453 (761)
T PRK12862        383 LIPKPFDPRLILKIAPAVAQAAMDSGVATRPIEDMDAYREQLNQFVYHSGLIMKPVFAAAKAAPKRVVFAE  453 (761)
T ss_pred             ECCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCEEEECC
T ss_conf             52789897426565399999998628876885679999999998867308899999999974886698358


No 2  
>KOG4268 consensus
Probab=27.82  E-value=47  Score=16.11  Aligned_cols=14  Identities=57%  Similarity=1.018  Sum_probs=10.3

Q ss_pred             CCCCHHHHHHHHHH
Q ss_conf             67256677889999
Q gi|254781001|r    4 SSPSLSDYLKIEHY   17 (93)
Q Consensus         4 sspslsdylkiehy   17 (93)
                      .+||++||+..+||
T Consensus        95 t~pS~l~~~t~DiY  108 (189)
T KOG4268          95 TSPSLLDYLTMDIY  108 (189)
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             78678888753241


No 3  
>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=22.31  E-value=52  Score=15.88  Aligned_cols=85  Identities=21%  Similarity=0.323  Sum_probs=53.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCEEHHHHHHHHHHCC------C--HHHHHHHHHHHHHHHH
Q ss_conf             6725667788999999998408631154315366507788620355677764126------3--7888899876411000
Q gi|254781001|r    4 SSPSLSDYLKIEHYMLHSFIEGPTKAIVIIWLSIFSMPSGSIEYRDTLDERVANS------G--LYMIVKKALVRSKKRK   75 (93)
Q Consensus         4 sspslsdylkiehymlhsfiegptkaiviiwlsifsmpsgsieyrdtldervans------g--lymivkkalvrskkrk   75 (93)
                      .+|||.+-|...+-+|.+-----+|.|++|+-|+.+--.|.|.  +|++.-+.+.      |  --+-+-|.+.+...-.
T Consensus        84 G~~SLqN~Le~A~~~L~~~P~~~sREILiI~~Sl~t~DpgdI~--~ti~~lk~~~IrvsvI~l~aEv~I~k~l~~~TgG~  161 (183)
T cd01453          84 GEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIY--ETIDKLKKENIRVSVIGLSAEMHICKEICKATNGT  161 (183)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCHH--HHHHHHHHCCCEEEEEEECHHHHHHHHHHHHHCCE
T ss_conf             9813999999999998208987844899997565347976499--99999998397899997427899999999983997


Q ss_pred             CCCC--HHHHHHHHHHH
Q ss_conf             0253--25788898751
Q gi|254781001|r   76 IAVP--SRQVTDLYKET   90 (93)
Q Consensus        76 iavp--srqvtdlyket   90 (93)
                      -.|+  ..+..++.-+.
T Consensus       162 y~V~lde~H~~~ll~~~  178 (183)
T cd01453         162 YKVILDETHLKELLLEH  178 (183)
T ss_pred             EEEECCHHHHHHHHHHC
T ss_conf             68753999999999956


No 4  
>PRK07232 malic enzyme; Reviewed
Probab=21.81  E-value=71  Score=15.20  Aligned_cols=59  Identities=25%  Similarity=0.386  Sum_probs=40.4

Q ss_pred             HHHCCCHHHHHHHHHH----HHCCCC----CE----EHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCH
Q ss_conf             8408631154315366----507788----62----03556777641263788889987641100002532
Q gi|254781001|r   22 FIEGPTKAIVIIWLSI----FSMPSG----SI----EYRDTLDERVANSGLYMIVKKALVRSKKRKIAVPS   80 (93)
Q Consensus        22 fiegptkaiviiwlsi----fsmpsg----si----eyrdtldervansglymivkkalvrskkrkiavps   80 (93)
                      .|-.|-..-+|.|.+-    -.|-||    .|    .||+.|..|+..|+..|-.--.-.|...++|..|.
T Consensus       377 ~ip~pfd~r~~~~v~~ava~aa~~~gva~~~i~d~~~Y~~~L~~rl~~s~~~mr~I~erAK~~pKRIVFpE  447 (753)
T PRK07232        377 IIPKPFDPRLIVKIAPAVAKAAMDSGVATRPIADMDAYREKLEAFVYRTGLVMKPIFAKAKKDPKRVVFAE  447 (753)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCEEEECC
T ss_conf             26889897315354299999999748887885559999999998767408899999999974886698258


No 5  
>pfam11355 DUF3157 Protein of unknown function (DUF3157). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=17.55  E-value=44  Score=16.28  Aligned_cols=16  Identities=38%  Similarity=0.617  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHCCCC
Q ss_conf             1154315366507788
Q gi|254781001|r   28 KAIVIIWLSIFSMPSG   43 (93)
Q Consensus        28 kaiviiwlsifsmpsg   43 (93)
                      +.-|-+|-|||.||.-
T Consensus       147 ~e~v~vWqsIkRMpdT  162 (199)
T pfam11355       147 TEEVTVWQSIKRMPET  162 (199)
T ss_pred             EEEEHHHHHHHHCHHH
T ss_conf             5003276655328342


No 6  
>PRK00556 minC septum formation inhibitor; Reviewed
Probab=16.33  E-value=10  Score=19.61  Aligned_cols=28  Identities=25%  Similarity=0.444  Sum_probs=24.6

Q ss_pred             CCCCCEEHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             7788620355677764126378888998
Q gi|254781001|r   40 MPSGSIEYRDTLDERVANSGLYMIVKKA   67 (93)
Q Consensus        40 mpsgsieyrdtldervansglymivkka   67 (93)
                      +..|+|.-..+++-+|--.|-|||+++-
T Consensus       126 ~A~Gni~v~G~~~G~v~C~GeYmIlk~i  153 (195)
T PRK00556        126 ISEGNVSVLGVCEGAIECFGEYMILKKV  153 (195)
T ss_pred             EECCCEEEEEECCEEEEECCEEEEECCC
T ss_conf             8288589998624079987718997356


No 7  
>COG3232 HpaF 5-carboxymethyl-2-hydroxymuconate isomerase [Amino acid transport and metabolism]
Probab=15.66  E-value=61  Score=15.52  Aligned_cols=34  Identities=38%  Similarity=0.467  Sum_probs=27.6

Q ss_pred             CCCCCEEHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             7788620355677764126378888998764110
Q gi|254781001|r   40 MPSGSIEYRDTLDERVANSGLYMIVKKALVRSKK   73 (93)
Q Consensus        40 mpsgsieyrdtldervansglymivkkalvrskk   73 (93)
                      ||.=-+||.|.+++++.-.||.--|..+|.-|--
T Consensus         1 MPHli~EyT~Nl~~~~~~~~L~~~vn~~l~asG~   34 (127)
T COG3232           1 MPHLIMEYTDNLREEADLPGLLEKVNAALIASGL   34 (127)
T ss_pred             CCCEEHHHHCCCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             9846020202766447808999999999986388


No 8  
>KOG3181 consensus
Probab=15.02  E-value=1.2e+02  Score=14.08  Aligned_cols=34  Identities=41%  Similarity=0.642  Sum_probs=25.8

Q ss_pred             HHHHCCCCCEEHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             6650778862035567776412637888899876411
Q gi|254781001|r   36 SIFSMPSGSIEYRDTLDERVANSGLYMIVKKALVRSK   72 (93)
Q Consensus        36 sifsmpsgsieyrdtldervansglymivkkalvrsk   72 (93)
                      .-|..|.||+|.   ..|+|+|.||.-+..-.-.|-|
T Consensus        75 kRf~f~~~svel---yaEkV~~rGLcAiaQaeslryK  108 (244)
T KOG3181          75 KRFKFPEGSVEL---YAEKVANRGLCAIAQAESLRYK  108 (244)
T ss_pred             HHCCCCCCCEEE---EHHHHHCCCHHHHHHHHHHHHH
T ss_conf             871899874787---4664311442487877789999


No 9  
>pfam05344 DUF746 Domain of Unknown Function (DUF746). This is a short conserved region found in some transposons.
Probab=14.92  E-value=1.2e+02  Score=14.07  Aligned_cols=41  Identities=29%  Similarity=0.427  Sum_probs=32.1

Q ss_pred             HHHHHHCCCHHHHHHHHHHHH------CCCCCEEHHHHHHHHHHCCC
Q ss_conf             999840863115431536650------77886203556777641263
Q gi|254781001|r   19 LHSFIEGPTKAIVIIWLSIFS------MPSGSIEYRDTLDERVANSG   59 (93)
Q Consensus        19 lhsfiegptkaiviiwlsifs------mpsgsieyrdtldervansg   59 (93)
                      --+.+-|-...++..|+..|.      -|||+.|-|--|.-|.++..
T Consensus        18 qaa~~lg~~~~~i~~wv~~fr~~ll~LDPSG~~e~RVRLG~rpa~~~   64 (65)
T pfam05344        18 QAADQLGTDEGIIRKWVRMFRRWLLQLDPSGHLERRIRLGGRPAAAT   64 (65)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCC
T ss_conf             99999787888999999999999986198877188765277756679


No 10 
>pfam04056 Ssl1 Ssl1-like. Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.
Probab=14.41  E-value=95  Score=14.51  Aligned_cols=52  Identities=23%  Similarity=0.340  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCEEHHHHHHHHHHCC
Q ss_conf             725667788999999998408631154315366507788620355677764126
Q gi|254781001|r    5 SPSLSDYLKIEHYMLHSFIEGPTKAIVIIWLSIFSMPSGSIEYRDTLDERVANS   58 (93)
Q Consensus         5 spslsdylkiehymlhsfiegptkaiviiwlsifsmpsgsieyrdtldervans   58 (93)
                      .|||-.-|..-+-.|...----|+-|+||+-|+.+--.|.|.  +|++.-+.+.
T Consensus       136 ~pSLqN~Le~a~~~L~~~P~~~sREILii~gSL~T~DPgdI~--~tI~~l~~~~  187 (250)
T pfam04056       136 DPSLQNALELARASLKHVPSHGSREVLIIFGSLSTCDPGDIY--STIDTLKKEK  187 (250)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCHH--HHHHHHHHCC
T ss_conf             920899999999887508987854899998204445886599--9999999759


Done!