Query         gi|254780963|ref|YP_003065376.1| hypothetical protein CLIBASIA_04320 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 215
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 03:06:42 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780963.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam05758 Ycf1 Ycf1. The chlor  53.7     7.5 0.00019   19.5   1.6   24   85-108    64-87  (832)
  2 pfam09143 AvrPphF-ORF-2 AvrPph  42.3      12 0.00031   18.3   1.2   47  157-206   115-164 (175)
  3 cd07079 ALDH_F18-19_ProA-GPR G  35.9      19 0.00049   17.1   1.4   12   45-56     78-89  (406)
  4 COG0014 ProA Gamma-glutamyl ph  35.0      15 0.00039   17.7   0.8   32  112-143   353-388 (417)
  5 TIGR00407 proA gamma-glutamyl   34.6      14 0.00036   17.9   0.5   34  111-144   361-398 (415)
  6 TIGR02909 spore_YkwD uncharact  23.7      26 0.00068   16.3   0.4   80   27-127    22-118 (129)
  7 TIGR02014 BchZ chlorophyllide   23.5      23 0.00059   16.7   0.1   37  104-142   279-316 (482)
  8 pfam09353 DUF1995 Domain of un  20.0      40   0.001   15.3   0.7   18  139-156   166-183 (205)
  9 pfam10783 DUF2599 Protein of u  19.5      38 0.00097   15.4   0.5   18  133-150     5-22  (94)
 10 pfam06593 RBDV_coat Raspberry   18.7      32 0.00082   15.8  -0.0   36   79-114    38-77  (274)

No 1  
>pfam05758 Ycf1 Ycf1. The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene.
Probab=53.70  E-value=7.5  Score=19.45  Aligned_cols=24  Identities=46%  Similarity=0.790  Sum_probs=20.2

Q ss_pred             HCCCCCHHHHHHHHHHHHHHHCCC
Q ss_conf             228000023454566433320477
Q gi|254780963|r   85 IVNPTTMRVLVLPVLSMHKTWNNN  108 (215)
Q Consensus        85 ivnpttmrvlvlpvlsmhktwnnn  108 (215)
                      ...|.|+-||+||.|..|=-|||+
T Consensus        64 L~rPHtITvL~lPYllf~ff~~n~   87 (832)
T pfam05758        64 LGRPHTITVLALPYLLFHFFWNNH   87 (832)
T ss_pred             HCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             745533089999999999974066


No 2  
>pfam09143 AvrPphF-ORF-2 AvrPphF-ORF-2. Members of this family of plant pathogenic proteins adopt an elongated structure somewhat reminiscent of a mushroom that can be divided into 'stalk' and 'head' subdomains. The stalk subdomain is composed of the N-terminal helix (alpha1) and beta strands beta3-beta4. An antiparallel beta sheet (beta5, beta7-beta8) forms the base of the head subdomain that interacts with the stalk. A pair of twisted antiparallel beta sheets (beta1 and beta6; beta2 and beta9/9') supported by alpha2 form the dome of the head. The head subdomain possesses weak structural similarity with the catalytic portion of a number of ADP-ribosyltransferase toxins.
Probab=42.31  E-value=12  Score=18.30  Aligned_cols=47  Identities=47%  Similarity=0.501  Sum_probs=35.9

Q ss_pred             EEEEECC--CC-EEEEEEEEEEEEEEECCEEEEECHHHHHHHHHCCCCCCEEE
Q ss_conf             0011056--76-79998630137775021001100246566541133432112
Q gi|254780963|r  157 FAIRHAS--SD-VVVCMRYQAKFLITDSIGILYRNVSAVSAAVDKNIGLGVTK  206 (215)
Q Consensus       157 fairhas--sd-vvvcmryqakflitdsigilyrnvsavsaavdkniglgvtk  206 (215)
                      -+||+-+  +| |+|-||.- .||  +.-|-.|-..|||++.-|+.+.|-||-
T Consensus       115 ~~~r~Ya~~~dhV~v~MrlG-Dfl--e~GGkVy~D~sav~~~gd~~~aLIVTL  164 (175)
T pfam09143       115 AGIRGYAHTSDHVVVKMRLG-DFL--EAGGKVYADTSAVSAGGDHTKALIVTL  164 (175)
T ss_pred             HCCCCCCCCCCEEEEEEEHH-HHH--HCCCEEEEECCCCCCCCCCEEEEEEEC
T ss_conf             30423266788179998623-577--628848854222247987315699986


No 3  
>cd07079 ALDH_F18-19_ProA-GPR Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19. Gamma-glutamyl phosphate reductase (GPR), a L-proline biosynthetic pathway (PBP) enzyme that catalyzes the NADPH dependent reduction of L-gamma-glutamyl  5-phosphate into L-glutamate 5-semialdehyde and phosphate. The glutamate route of the PBP involves two enzymatic steps catalyzed by gamma-glutamyl kinase (GK, EC 2.7.2.11) and GPR (EC 1.2.1.41). These enzymes are fused into the bifunctional enzyme, ProA or delta(1)-pyrroline-5-carboxylate synthetase (P5CS) in plants and animals, whereas they are separate enzymes in bacteria and yeast. In humans, the P5CS (ALDH18A1), an inner mitochondrial membrane enzyme, is essential to the de novo synthesis of the amino acids proline and arginine. Tomato (Lycopersicon esculentum) has both the prokaryotic-like polycistronic operons encoding GK and GPR (PRO1, ALDH19) and the full-length, bifunctional P5CS (PRO2, ALDH18B1).
Probab=35.90  E-value=19  Score=17.10  Aligned_cols=12  Identities=17%  Similarity=0.515  Sum_probs=5.6

Q ss_pred             HHHHHHCCCCEE
Q ss_conf             634420357324
Q gi|254780963|r   45 SREISSYRTPLS   56 (215)
Q Consensus        45 sreissyrtpls   56 (215)
                      -|++..-..|+.
T Consensus        78 l~~ia~l~DPvG   89 (406)
T cd07079          78 LRQVAALPDPVG   89 (406)
T ss_pred             HHHHHHCCCCCC
T ss_conf             999981899666


No 4  
>COG0014 ProA Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism]
Probab=34.97  E-value=15  Score=17.70  Aligned_cols=32  Identities=44%  Similarity=0.680  Sum_probs=22.4

Q ss_pred             HHHHHHH---CEEEEEECCCCCCCHH-HHHHCCCEE
Q ss_conf             3465342---5013530366752000-012108158
Q gi|254780963|r  112 SYFFKKI---GVGVVASTGFNTGDKW-LGAEMGMSF  143 (215)
Q Consensus       112 syffkki---gvgvvastgfntgdkw-lgaemgmsf  143 (215)
                      .+|+..+   .|-|-|||-|..|-.+ +|||+|+|-
T Consensus       353 ~~F~~~VDSAaVyvNASTRFtDG~~fG~GaEiGIST  388 (417)
T COG0014         353 ERFVNEVDSAAVYVNASTRFTDGGQFGLGAEIGIST  388 (417)
T ss_pred             HHHHHHCCHHEEEEECCCCCCCCCCCCCCEEEEEEC
T ss_conf             999962361148972465545676555754888633


No 5  
>TIGR00407 proA gamma-glutamyl phosphate reductase; InterPro: IPR000965   Gamma-glutamyl phosphate reductase (1.2.1.41 from EC) (GPR) is the enzyme that catalyzes the second step in the biosynthesis of proline from glutamate, the NADP-dependent reduction of L-glutamate 5-phosphate into L-glutamate 5-semialdehyde and phosphate. In bacteria (gene proA) and yeast  (gene PRO2), GPR is a monofunctional protein, while in plants and mammals, it is a bifunctional enzyme (P5CS)  that consists of two domains, an N-terminal glutamate 5-kinase domain (2.7.2.11 from EC) and a C-terminal GPR domain. ; GO: 0004350 glutamate-5-semialdehyde dehydrogenase activity, 0006561 proline biosynthetic process.
Probab=34.55  E-value=14  Score=17.89  Aligned_cols=34  Identities=35%  Similarity=0.508  Sum_probs=26.8

Q ss_pred             HHHHHHHH---CEEEEEECCCCCCCHH-HHHHCCCEEE
Q ss_conf             13465342---5013530366752000-0121081588
Q gi|254780963|r  111 DSYFFKKI---GVGVVASTGFNTGDKW-LGAEMGMSFY  144 (215)
Q Consensus       111 dsyffkki---gvgvvastgfntgdkw-lgaemgmsfy  144 (215)
                      -.+|.+.+   ||=+-|||-|.-|-++ +|||.|.|--
T Consensus       361 A~~F~~~VDsaaVY~NASTRFtDGf~fG~GAEVgiSTq  398 (415)
T TIGR00407       361 AEQFVNEVDSAAVYHNASTRFTDGFRFGFGAEVGISTQ  398 (415)
T ss_pred             HHHHHHHCCCCCEEECCCCEECCCCCCCCCEEEEEECC
T ss_conf             99997310303022255101147762566006621136


No 6  
>TIGR02909 spore_YkwD uncharacterized protein, YkwD family; InterPro: IPR014258   This entry represents a subgroup of the SCP-like extracellular domain which is found only in bacteria capable of endospore formation. Proteins in this entry include YkwD of Bacillus subtilis. This domain is generally found at the C-terminal region of these proteins, while the N-terminal region sometimes contains a domain homologous to the spore coat assembly protein SafA (IPR014248 from INTERPRO)..
Probab=23.72  E-value=26  Score=16.33  Aligned_cols=80  Identities=30%  Similarity=0.453  Sum_probs=44.2

Q ss_pred             HCEEEEHHHHHH------HHHHH--HHHHHHHCCCCEEEEECCCEEEEEEEEEEEEE-EEC-HHHHHHH-CCCCCHHHHH
Q ss_conf             000100899999------99998--66344203573244302201588864103677-631-5777522-2800002345
Q gi|254780963|r   27 DELKVNFGLMRR------VMIDL--WSREISSYRTPLSLDLDYKHRVYLDTYKSFSI-NLG-FETFNEI-VNPTTMRVLV   95 (215)
Q Consensus        27 delkvnfglmrr------vmidl--wsreissyrtplsldldykhrvyldtyksfsi-nlg-fetfnei-vnpttmrvlv   95 (215)
                      .-||+|-.|.|-      -|+|.  .|.+=..|-.|-++            -|.|-| +-- ---=|=- .|+|.-+   
T Consensus        22 ~PLk~d~~L~~vARlKs~DM~d~nYFsH~SPTYGSPF~M------------mk~FGik~Y~W~AGENIA~G~~T~~~---   86 (129)
T TIGR02909        22 KPLKADEELSKVARLKSEDMIDKNYFSHTSPTYGSPFDM------------MKKFGIKSYRWAAGENIAAGNSTVEA---   86 (129)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHH------------HHHCCCCCCHHHHHHHHHHCCCCHHH---
T ss_conf             800017477888637468510078998888899971689------------98646643102323543304877889---


Q ss_pred             HHHHHHHHHHCC------CCCHHHHHHHHCEEEEEECC
Q ss_conf             456643332047------77313465342501353036
Q gi|254780963|r   96 LPVLSMHKTWNN------NFDDSYFFKKIGVGVVASTG  127 (215)
Q Consensus        96 lpvlsmhktwnn------nfddsyffkkigvgvvastg  127 (215)
                           .|+.|=|      |-=+.. |.+||||+|.+--
T Consensus        87 -----v~~awMNS~GHRaNIL~p~-yt~IGVG~v~~g~  118 (129)
T TIGR02909        87 -----VHQAWMNSPGHRANILNPN-YTEIGVGYVEGGS  118 (129)
T ss_pred             -----HHHHHCCCHHHHHCCCCCC-CCEEEEEEEECCC
T ss_conf             -----9853058720222268898-8711257750688


No 7  
>TIGR02014 BchZ chlorophyllide reductase subunit Z; InterPro: IPR010244   This entry represents the Z subunit of the three-subunit enzyme, bacteriochlorophyllide reductase , . This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase.; GO: 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0030494 bacteriochlorophyll biosynthetic process.
Probab=23.55  E-value=23  Score=16.66  Aligned_cols=37  Identities=30%  Similarity=0.575  Sum_probs=29.7

Q ss_pred             HHCCCCCHHHHHHHHCEEEEEECCCCCCCH-HHHHHCCCE
Q ss_conf             204777313465342501353036675200-001210815
Q gi|254780963|r  104 TWNNNFDDSYFFKKIGVGVVASTGFNTGDK-WLGAEMGMS  142 (215)
Q Consensus       104 twnnnfddsyffkkigvgvvastgfntgdk-wlgaemgms  142 (215)
                      -|..-  .+-||-.+.-||||+..+..|=| .|+.||||.
T Consensus       279 LWRs~--~~~fFgT~~FGivA~~~Ya~Gi~~~L~~elGl~  316 (482)
T TIGR02014       279 LWRSV--TQDFFGTARFGIVASETYARGIRHVLEDELGLP  316 (482)
T ss_pred             HCCCC--CCCCCCCCEECEEECHHHHHHHHHHHCCCCCCC
T ss_conf             12677--633456510011321146676787511024751


No 8  
>pfam09353 DUF1995 Domain of unknown function (DUF1995). This family of proteins are functionally uncharacterized.
Probab=19.97  E-value=40  Score=15.29  Aligned_cols=18  Identities=39%  Similarity=0.947  Sum_probs=15.0

Q ss_pred             CCCEEEEECCCEEEEECC
Q ss_conf             081588705624777313
Q gi|254780963|r  139 MGMSFYVYPTPWLILQSD  156 (215)
Q Consensus       139 mgmsfyvyptpwlilqsd  156 (215)
                      .|.-|..||-||-+..-+
T Consensus       166 ~gal~r~yP~~W~v~~~~  183 (205)
T pfam09353       166 GGALFRCYPGPWQLFKED  183 (205)
T ss_pred             CEEEEEECCCCCEEEEEE
T ss_conf             758999579874799981


No 9  
>pfam10783 DUF2599 Protein of unknown function (DUF2599). This family is conserved in Actinobacteria. The function is not known.
Probab=19.55  E-value=38  Score=15.43  Aligned_cols=18  Identities=33%  Similarity=0.348  Sum_probs=0.0

Q ss_pred             HHHHHHCCCEEEEECCCE
Q ss_conf             000121081588705624
Q gi|254780963|r  133 KWLGAEMGMSFYVYPTPW  150 (215)
Q Consensus       133 kwlgaemgmsfyvyptpw  150 (215)
                      .|.-.+-+.|.-||||||
T Consensus         5 ~W~~~~~~~sL~V~PT~~   22 (94)
T pfam10783         5 TWAQWGDLWSLRVYPTDA   22 (94)
T ss_pred             EEEECCCCCCEEEECCHH
T ss_conf             521227876148825367


No 10 
>pfam06593 RBDV_coat Raspberry bushy dwarf virus coat protein. This family consists of several Raspberry bushy dwarf virus coat proteins.
Probab=18.71  E-value=32  Score=15.85  Aligned_cols=36  Identities=36%  Similarity=0.553  Sum_probs=0.0

Q ss_pred             HHHHHHHCCCCCHHHHHHHHHHHH----HHHCCCCCHHHH
Q ss_conf             577752228000023454566433----320477731346
Q gi|254780963|r   79 FETFNEIVNPTTMRVLVLPVLSMH----KTWNNNFDDSYF  114 (215)
Q Consensus        79 fetfneivnpttmrvlvlpvlsmh----ktwnnnfddsyf  114 (215)
                      |..|.|-.||.|-.-.----.|..    .||-.|||.+|+
T Consensus        38 f~gfse~~~p~tgkp~~dmsmsakvkrvntwlknfdr~yw   77 (274)
T pfam06593        38 FVGFSEGSNPATGKPHADMSMSAKVKRVNTWLKNFDREYW   77 (274)
T ss_pred             EECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCHHHH
T ss_conf             0222456786679974321045658888889874357776


Done!