Query         gi|254781131|ref|YP_003065544.1| hypothetical protein CLIBASIA_05165 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 150
No_of_seqs    117 out of 1622
Neff          7.6 
Searched_HMMs 39220
Date          Mon May 30 06:37:52 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781131.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 KOG3661 consensus               99.4 1.3E-13 3.3E-18   94.3   3.5   75   71-146   481-574 (1019)
  2 pfam02689 Herpes_Helicase Heli  48.4      20 0.00051   17.4   3.1   41   89-129   652-693 (801)
  3 TIGR01127 ilvA_1Cterm threonin  44.5     2.8 7.1E-05   22.0  -1.8   13   75-87     15-28  (381)
  4 TIGR02653 Lon_rel_chp conserve  35.0      25 0.00063   16.8   1.8   36   71-106   441-481 (677)
  5 KOG3046 consensus               20.7      30 0.00076   16.4   0.1   16  105-120   116-131 (147)
  6 PRK13765 ATP-dependent proteas  18.4      32 0.00082   16.2  -0.1   41  102-142   322-377 (637)
  7 pfam10702 DUF2507 Protein of u  14.4      42  0.0011   15.6  -0.3   18  102-119    89-109 (124)
  8 pfam02341 RcbX RbcX protein. T  14.3      38 0.00097   15.8  -0.6   17  105-121    75-91  (108)
  9 PTZ00274 cytochrome b5 reducta  13.4      84  0.0021   14.0   1.0   19  100-118   240-259 (325)
 10 TIGR02179 PorD_KorD 2-oxoacid:  13.4 1.1E+02  0.0029   13.3   1.6   17  116-132    38-59  (84)

No 1  
>KOG3661 consensus
Probab=99.40  E-value=1.3e-13  Score=94.26  Aligned_cols=75  Identities=29%  Similarity=0.337  Sum_probs=60.0

Q ss_pred             CCCCCCHHHCCCCCCCC---------CEEEEEEEECCC----------CCEEEEECHHHHHHHCCCEEEECCCCEEEEEH
Q ss_conf             10013513105511245---------322279787189----------85699775678885378018437984688862
Q gi|254781131|r   71 APLVSDRRMKCNVKPVA---------NLYQYRYLSDPK----------NVQRIGVIAQEISKIRPDTVVENNQGIKSVDY  131 (150)
Q Consensus        71 ~~~~SD~RLK~NI~~I~---------~l~~~~y~~~~~----------~~~~~GvIAQEVe~v~Pe~V~~~~dg~~~VdY  131 (150)
                      .-..||.|||++|+.++         .||-+.|.+|++          ..+..|||||||++|+||||.+.. .|++||=
T Consensus       481 ~m~PSDiRlKe~itE~~t~ealenl~klR~VdYrYKPEvA~~wGl~e~qr~rTGvIAQEl~avLPdAVkD~G-dyLtvne  559 (1019)
T KOG3661         481 LMHPSDIRLKEHITEVDTTEALENLSKLRLVDYRYKPEVAASWGLEETQRPRTGVIAQELKAVLPDAVKDTG-DYLTVNE  559 (1019)
T ss_pred             ECCHHHHHHHHHHCHHHHHHHHHHHHHHEEEEEEECHHHHHHCCCCCCCCCCCCHHHHHHHHHCHHHHHCCC-CEEEECC
T ss_conf             326222006664000028999987664253345307034433175500265523689999886657664025-6468614


Q ss_pred             HCHHHHHHHHHHHHH
Q ss_conf             023679999998865
Q gi|254781131|r  132 GRLFNIGQIQTKQKK  146 (150)
Q Consensus       132 ~~L~~l~~~~~~~~~  146 (150)
                      +++.=--.+|+||+-
T Consensus       560 ~RvFyEtV~AtqeLC  574 (1019)
T KOG3661         560 ERVFYETVGATQELC  574 (1019)
T ss_pred             CCHHHHHHHHHHHHH
T ss_conf             300166778899998


No 2  
>pfam02689 Herpes_Helicase Helicase. This family consists of Helicases from the Herpes viruses. Helicases are responsible for the unwinding of DNA and are essential for replication and completion of the viral life cycle.
Probab=48.43  E-value=20  Score=17.36  Aligned_cols=41  Identities=27%  Similarity=0.321  Sum_probs=27.3

Q ss_pred             EEEEEEEECCCCCEEEEECHHHH-HHHCCCEEEECCCCEEEE
Q ss_conf             22279787189856997756788-853780184379846888
Q gi|254781131|r   89 LYQYRYLSDPKNVQRIGVIAQEI-SKIRPDTVVENNQGIKSV  129 (150)
Q Consensus        89 l~~~~y~~~~~~~~~~GvIAQEV-e~v~Pe~V~~~~dg~~~V  129 (150)
                      |.+|+|..-.-......-+++++ +.-+|-+|..|..|+.+|
T Consensus       652 L~GYT~~~V~~~~~~~~r~~~~~~~~~mP~lVv~D~~GFis~  693 (801)
T pfam02689       652 LEGYTFAPVPFGAEDLQRTASLLLSLKLPRLVVRDQMGFISV  693 (801)
T ss_pred             EEEEEECCCCCCCCCHHHHHHHHHHCCCCCEEEECCCCEEEE
T ss_conf             830560464246730111047887449994899837770430


No 3  
>TIGR01127 ilvA_1Cterm threonine dehydratase; InterPro: IPR005789    Serine and threonine dehydratases ,  are functionally and structurally related pyridoxal-phosphate dependent enzymes. L-serine dehydratase () and D-serine dehydratase () catalyze the dehydratation of L-serine (respectively D-serine) into ammonia and pyruvate. Threonine dehydratase () (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism. Threonine synthase () is also a pyridoxal-phosphate enzyme, it catalyzes the transformation of homoserine-phosphate into threonine. It has been shown  that threonine synthase is distantly related to the serine/threonine dehydratases. In all these enzymes, the pyridoxal-phosphate group is attached to a lysine residue.    A form of threonine dehydratase with two copies of the C-terminal domain  is described by . This model describes a phylogenetically distinct which branches with the catabolic threonine dehydratase of E. coli; many members are designated as catabolic for this reason. However, the catabolic form lacks any  domain. Many members of this model are found in species with other isoleucine biosynthetic enzymes.; GO: 0004794 L-threonine ammonia-lyase activity.
Probab=44.49  E-value=2.8  Score=21.99  Aligned_cols=13  Identities=15%  Similarity=0.258  Sum_probs=5.9

Q ss_pred             CCHHHC-CCCCCCC
Q ss_conf             351310-5511245
Q gi|254781131|r   75 SDRRMK-CNVKPVA   87 (150)
Q Consensus        75 SD~RLK-~NI~~I~   87 (150)
                      ||.||| ||.++=+
T Consensus        15 ~E~YlKlENlQkTG   28 (381)
T TIGR01127        15 AEVYLKLENLQKTG   28 (381)
T ss_pred             HHCCHHHHHCCCCC
T ss_conf             00002113110127


No 4  
>TIGR02653 Lon_rel_chp conserved hypothetical protein; InterPro: IPR013473    This entry describes a protein family of unknown function, about 690 residues in length, in which some members show C-terminal sequence similarity to IPR008269 from INTERPRO, which is the Lon protease C-terminal proteolytic domain, from MEROPS family S16. However, the annotated catalytic sites of Escherichia coli Lon protease are not conserved in members of this family. Members have a motif GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif GxxGxGK[ST]..
Probab=34.96  E-value=25  Score=16.84  Aligned_cols=36  Identities=22%  Similarity=0.364  Sum_probs=25.3

Q ss_pred             CCCCCCHHHCCCCCCCCCEE----EEEEEECCC-CCEEEEE
Q ss_conf             10013513105511245322----279787189-8569977
Q gi|254781131|r   71 APLVSDRRMKCNVKPVANLY----QYRYLSDPK-NVQRIGV  106 (150)
Q Consensus        71 ~~~~SD~RLK~NI~~I~~l~----~~~y~~~~~-~~~~~Gv  106 (150)
                      ++.-.=||.||-.+|++.+-    .|.|++++. .+.+++|
T Consensus       441 yalegRRRVKEQLKK~Gg~Effdv~FSYiDNe~leE~fv~V  481 (677)
T TIGR02653       441 YALEGRRRVKEQLKKLGGLEFFDVNFSYIDNESLEEFFVSV  481 (677)
T ss_pred             HHHCCCCHHHHHHHHHCCCEEEECEEEEEECCCCCEEEEEC
T ss_conf             76235620366664306730662204672078731227745


No 5  
>KOG3046 consensus
Probab=20.73  E-value=30  Score=16.39  Aligned_cols=16  Identities=31%  Similarity=0.366  Sum_probs=13.9

Q ss_pred             EECHHHHHHHCCCEEE
Q ss_conf             7756788853780184
Q gi|254781131|r  105 GVIAQEISKIRPDTVV  120 (150)
Q Consensus       105 GvIAQEVe~v~Pe~V~  120 (150)
                      --+|+|+.+.|||+|.
T Consensus       116 ~~l~eEl~q~fPe~~~  131 (147)
T KOG3046         116 KHLAEELSQEFPELVD  131 (147)
T ss_pred             HHHHHHHHHHCHHHHH
T ss_conf             9999999997747789


No 6  
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=18.39  E-value=32  Score=16.23  Aligned_cols=41  Identities=17%  Similarity=0.281  Sum_probs=30.8

Q ss_pred             EEEEECHHHHHHH--CC----CEEE---------ECCCCEEEEEHHCHHHHHHHHH
Q ss_conf             6997756788853--78----0184---------3798468886202367999999
Q gi|254781131|r  102 QRIGVIAQEISKI--RP----DTVV---------ENNQGIKSVDYGRLFNIGQIQT  142 (150)
Q Consensus       102 ~~~GvIAQEVe~v--~P----e~V~---------~~~dg~~~VdY~~L~~l~~~~~  142 (150)
                      +..-||||||++-  +|    ++|.         -...+.++.....|..|+.||=
T Consensus       322 k~arfiaqev~~dg~iPhfdr~AVaeII~eA~R~AG~k~kLTLrLReL~~LIReAg  377 (637)
T PRK13765        322 KLVRFVAQEVKRDGKIPHFDREAVEEIIREARRRAGRKGHLTLKLRDLGGLVRVAG  377 (637)
T ss_pred             HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             99999999997438889999899999999999740545663052898874999988


No 7  
>pfam10702 DUF2507 Protein of unknown function (DUF2507). This family is conserved in Firmicutes. The function is not known.
Probab=14.39  E-value=42  Score=15.60  Aligned_cols=18  Identities=17%  Similarity=0.327  Sum_probs=13.0

Q ss_pred             EEEEECHHHHHHH---CCCEE
Q ss_conf             6997756788853---78018
Q gi|254781131|r  102 QRIGVIAQEISKI---RPDTV  119 (150)
Q Consensus       102 ~~~GvIAQEVe~v---~Pe~V  119 (150)
                      --.|||||++|..   .-|+.
T Consensus        89 LEAGFlAe~iq~q~~~~aEa~  109 (124)
T pfam10702        89 LEAGFLAEQIQQQLGVVAEAY  109 (124)
T ss_pred             EEHHHHHHHHHHHHCCCEEEE
T ss_conf             633799999999869726888


No 8  
>pfam02341 RcbX RbcX protein. The RBCX protein has been identified as having a possible chaperone-like function. The rbcX gene is juxtaposed to and cotranscribed with rbcL and rbcS encoding RuBisCO in Anabaena sp. CA. RbcX has been shown to possess a chaperone-like function assisting correct folding of RuBisCO in E. coli expression studies and is needed for RuBisCO to reach its maximal activity.
Probab=14.26  E-value=38  Score=15.81  Aligned_cols=17  Identities=24%  Similarity=0.436  Sum_probs=13.9

Q ss_pred             EECHHHHHHHCCCEEEE
Q ss_conf             77567888537801843
Q gi|254781131|r  105 GVIAQEISKIRPDTVVE  121 (150)
Q Consensus       105 GvIAQEVe~v~Pe~V~~  121 (150)
                      =-+|+||.+.+||.|..
T Consensus        75 eHlae~v~~flpemvr~   91 (108)
T pfam02341        75 EHLAEEVADFLPEMVRT   91 (108)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             99999999885999999


No 9  
>PTZ00274 cytochrome b5 reductase; Provisional
Probab=13.41  E-value=84  Score=13.95  Aligned_cols=19  Identities=16%  Similarity=0.342  Sum_probs=14.5

Q ss_pred             CCEEEEECHHHH-HHHCCCE
Q ss_conf             856997756788-8537801
Q gi|254781131|r  100 NVQRIGVIAQEI-SKIRPDT  118 (150)
Q Consensus       100 ~~~~~GvIAQEV-e~v~Pe~  118 (150)
                      +....|+|-.|+ ++.+|.-
T Consensus       240 W~g~~G~ITkEmik~~lP~P  259 (325)
T PTZ00274        240 WNHFLGYVTKEMVRRTMPAP  259 (325)
T ss_pred             CCCCCCEECHHHHHHHCCCC
T ss_conf             85776764899999768799


No 10 
>TIGR02179 PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family; InterPro: IPR011898    A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This entry describes the delta subunits, representing mostly pyruvate, 2-ketoisovalerate, and 2-oxoglutarate specific enzymes. The delta subunit is the smallest and resembles ferredoxins.; GO: 0016625 oxidoreductase activity acting on the aldehyde or oxo group of donors iron-sulfur protein as acceptor, 0051539 4 iron 4 sulfur cluster binding, 0006118 electron transport.
Probab=13.39  E-value=1.1e+02  Score=13.27  Aligned_cols=17  Identities=29%  Similarity=0.722  Sum_probs=0.0

Q ss_pred             CCE-EE-ECCCC---EEEEEHH
Q ss_conf             801-84-37984---6888620
Q gi|254781131|r  116 PDT-VV-ENNQG---IKSVDYG  132 (150)
Q Consensus       116 Pe~-V~-~~~dg---~~~VdY~  132 (150)
                      ||. +. .++++   +..|||+
T Consensus        38 Pe~~~I~~~e~~~~~~~~iDYd   59 (84)
T TIGR02179        38 PEGAAIQEDEGGDEKKVEIDYD   59 (84)
T ss_pred             CCCCEEECCCCCEEEEEEECCC
T ss_conf             9974776158932677676487


Done!