Query         gi|254780668|ref|YP_003065081.1| hypothetical protein CLIBASIA_02775 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 46
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 20:17:07 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780668.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam06754 PhnG Phosphonate met  15.4      83  0.0021   15.0   1.4   11   30-40     61-71  (147)
  2 TIGR03293 PhnG_redo phosphonat  10.2 1.5E+02  0.0039   13.8   1.5   11   30-40     59-69  (144)
  3 PRK02693 apocytochrome f; Revi   7.7 1.8E+02  0.0046   13.4   1.0   11   15-25     93-103 (312)
  4 CHL00037 petA cytochrome f       7.6 1.8E+02  0.0045   13.5   0.9   11   15-25    100-110 (320)
  5 TIGR00720 sda_mono L-serine am   7.5 2.3E+02  0.0058   12.9   1.4   17    5-21    439-458 (463)
  6 TIGR02348 GroEL chaperonin Gro   6.4 2.7E+02  0.0068   12.6   1.5   12   15-26    265-276 (528)
  7 TIGR02154 PhoB phosphate regul   6.3 1.3E+02  0.0034   14.1  -0.3   14    3-16     94-109 (226)
  8 pfam12471 GTP_CH_N GTP cyclohy   6.2 2.7E+02  0.0069   12.6   2.3   32    9-40    137-169 (195)
  9 pfam01916 DS Deoxyhypusine syn   5.7 1.9E+02  0.0048   13.3   0.2   30    5-34    257-286 (297)
 10 PRK01221 putative deoxyhypusin   5.2 1.8E+02  0.0047   13.4  -0.1   29    6-34    273-301 (312)

No 1  
>pfam06754 PhnG Phosphonate metabolism protein PhnG. This family consists of several bacterial phosphonate metabolism protein PhnG sequences. In Escherichia coli, the phn operon encodes proteins responsible for the uptake and breakdown of phosphonates. The exact function of PhnG is unknown, however it is thought likely that along with six other proteins PhnG makes up the the C-P (carbon-phosphorus) lyase.
Probab=15.39  E-value=83  Score=14.98  Aligned_cols=11  Identities=64%  Similarity=0.749  Sum_probs=8.0

Q ss_pred             EEEEEEEEEEE
Q ss_conf             23677533331
Q gi|254780668|r   30 AEVTVTRAAIV   40 (46)
Q Consensus        30 aevtvtraaiv   40 (46)
                      .|+||||+++-
T Consensus        61 GE~TVTRc~Vr   71 (147)
T pfam06754        61 GEMTVTRAAVR   71 (147)
T ss_pred             CCEEEEEEEEE
T ss_conf             63378889999


No 2  
>TIGR03293 PhnG_redo phosphonate C-P lyase system protein PhnG. PhnH is a component of the C-P lyase system (GenProp0232) for the catabolism of phosphonate compounds. The specific function of this component is unknown. This model is based on pfam06754.2, and has been broadened to include sequences missed by that model which are clearly true positive hits based on genome context.
Probab=10.24  E-value=1.5e+02  Score=13.77  Aligned_cols=11  Identities=64%  Similarity=0.794  Sum_probs=7.0

Q ss_pred             EEEEEEEEEEE
Q ss_conf             23677533331
Q gi|254780668|r   30 AEVTVTRAAIV   40 (46)
Q Consensus        30 aevtvtraaiv   40 (46)
                      .|+||||+.+-
T Consensus        59 GE~tvTrc~V~   69 (144)
T TIGR03293        59 GEITVTRAAVR   69 (144)
T ss_pred             CCEEEEEEEEE
T ss_conf             72389999999


No 3  
>PRK02693 apocytochrome f; Reviewed
Probab=7.74  E-value=1.8e+02  Score=13.42  Aligned_cols=11  Identities=64%  Similarity=0.510  Sum_probs=7.4

Q ss_pred             CCCCEEEEEEE
Q ss_conf             04730377898
Q gi|254780668|r   15 SKGKLNVAAVK   25 (46)
Q Consensus        15 skgklnvaavk   25 (46)
                      |||.|||.||-
T Consensus        93 ~kg~LNVGAVl  103 (312)
T PRK02693         93 SKVGLNVGAVV  103 (312)
T ss_pred             CCCCCCEEEEE
T ss_conf             40674135799


No 4  
>CHL00037 petA cytochrome f
Probab=7.58  E-value=1.8e+02  Score=13.45  Aligned_cols=11  Identities=64%  Similarity=0.733  Sum_probs=6.8

Q ss_pred             CCCCEEEEEEE
Q ss_conf             04730377898
Q gi|254780668|r   15 SKGKLNVAAVK   25 (46)
Q Consensus        15 skgklnvaavk   25 (46)
                      +||.|||.||-
T Consensus       100 ~kg~LNVGAVl  110 (320)
T CHL00037        100 KKGGLNVGAVL  110 (320)
T ss_pred             CCCCCCEEEEE
T ss_conf             51675302699


No 5  
>TIGR00720 sda_mono L-serine ammonia-lyase; InterPro: IPR004644 This enzyme is also called serine deaminase. L-serine dehydratase converts serine into pyruvate in the gluconeogenesis pathway from serine. This enzyme is comprised of a single chain in Escherichia coli, Mycobacterium tuberculosis, and several other species, but has separate alpha and beta chains in Bacillus subtilis and related species. The beta and alpha chains are homologous to the N-terminal and C-terminal regions, respectively, but are rather deeply branched in a UPGMA tree. This enzyme requires iron and dithiothreitol for activation in vitro, and is a predicted 4Fe-4S protein. Escherichia coli Pseudomonas aeruginosa have two copies of this protein.; GO: 0003941 L-serine ammonia-lyase activity, 0006094 gluconeogenesis.
Probab=7.47  E-value=2.3e+02  Score=12.94  Aligned_cols=17  Identities=47%  Similarity=0.814  Sum_probs=13.0

Q ss_pred             CCCHHHHHHH---CCCCEEE
Q ss_conf             2220145553---0473037
Q gi|254780668|r    5 ATGADLTEKF---SKGKLNV   21 (46)
Q Consensus         5 atgadltekf---skgklnv   21 (46)
                      +||.|..+||   |.|-|-+
T Consensus       439 ~TGkDMn~KYkETS~GGLA~  458 (463)
T TIGR00720       439 ATGKDMNAKYKETSAGGLAI  458 (463)
T ss_pred             HHHHHHHHHHHHHCCCCCEE
T ss_conf             73055533317657897047


No 6  
>TIGR02348 GroEL chaperonin GroL; InterPro: IPR012723   Partially folded polypeptide chains, either newly made by ribosomes or emerging from mature proteins unfolded by stress, run the risk of aggregating with one another to the detriment of the organism. Folding of newly synthesised polypeptides in the crowded cellular environment requires the assistance of molecular chaperone proteins, such as the large bacterial chaperonins GroEL and GroES.    GroEL and GroES prevent aggregation by encapsulating individual chains within the so-called Anfinsen cage provided by the GroELGroES complex, where they can fold in isolation from one another . GroEL consists of two heptameric rings of identical ATPase subunits stacked back to back, containing a cage in each ring. Each subunit consists of three domains. The equatorial domain contains the nucleotide binding site and is connected by a flexible intermediate domain with the apical domain. The latter presents several hydrophobic amino-acid side chains at the top of the ring, orientated towards the cavity of the cage. These side chains are involved in binding either a partially folded polypeptide chain or a single molecule of GroES.   This family consists of GroEL, found in bacteria, organelles derived from bacteria, and occasionally in archaeal species. The bacterial GroEL/GroES group I chaperonin is replaced by a group II chaperonin, usually called the thermosome in archaeal species, and CCT (chaperone-containing TCP) in eukaryotes. GroEL, thermosome subunits, and CCT subunits all fall under the scope of IPR002423 from INTERPRO.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=6.40  E-value=2.7e+02  Score=12.63  Aligned_cols=12  Identities=58%  Similarity=0.792  Sum_probs=8.1

Q ss_pred             CCCCEEEEEEEE
Q ss_conf             047303778987
Q gi|254780668|r   15 SKGKLNVAAVKC   26 (46)
Q Consensus        15 skgklnvaavkc   26 (46)
                      -+|-|||+|||-
T Consensus       265 lRG~l~v~AVKA  276 (528)
T TIGR02348       265 LRGTLNVCAVKA  276 (528)
T ss_pred             HCCEEEEEEEEC
T ss_conf             166257999845


No 7  
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB; InterPro: IPR011879    PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself . It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006817 phosphate transport.
Probab=6.28  E-value=1.3e+02  Score=14.05  Aligned_cols=14  Identities=57%  Similarity=0.812  Sum_probs=8.2

Q ss_pred             CCCCCHH--HHHHHCC
Q ss_conf             2122201--4555304
Q gi|254780668|r    3 NLATGAD--LTEKFSK   16 (46)
Q Consensus         3 nlatgad--ltekfsk   16 (46)
                      .|.||||  .|.-||-
T Consensus        94 GLetGADDYvtKPFSp  109 (226)
T TIGR02154        94 GLETGADDYVTKPFSP  109 (226)
T ss_pred             CCCCCCCCEEECCCCH
T ss_conf             1136887503678865


No 8  
>pfam12471 GTP_CH_N GTP cyclohydrolase N terminal. This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. This family is the N terminal of GTP cyclohydrolase, the rate limiting enzyme in the synthesis of tetrahydrobiopterin.
Probab=6.23  E-value=2.7e+02  Score=12.58  Aligned_cols=32  Identities=31%  Similarity=0.383  Sum_probs=24.9

Q ss_pred             HHHHHHCCCCEEEEEEEEEE-EEEEEEEEEEEE
Q ss_conf             14555304730377898764-223677533331
Q gi|254780668|r    9 DLTEKFSKGKLNVAAVKCEL-KAEVTVTRAAIV   40 (46)
Q Consensus         9 dltekfskgklnvaavkcel-kaevtvtraaiv   40 (46)
                      .+.|-..+|.|.+-.--|-- ..++.||.+||-
T Consensus       137 Ei~eAv~~GrL~~DG~i~l~~~Gd~~VTK~Ave  169 (195)
T pfam12471       137 ELREAVAKGRLVPDGKIVLNSNGDVAVTKAAVE  169 (195)
T ss_pred             HHHHHHHCCCCCCCCEEEECCCCCEEEEEEEEC
T ss_conf             799999849988887688358986899987632


No 9  
>pfam01916 DS Deoxyhypusine synthase. Eukaryotic initiation factor 5A (eIF-5A) contains an unusual amino acid, hypusine [N epsilon-(4-aminobutyl-2-hydroxy)lysine]. The first step in the post-translational formation of hypusine is catalysed by the enzyme deoxyhypusine synthase (DS) EC:1.1.1.249. The modified version of eIF-5A, and DS, are required for eukaryotic cell proliferation.
Probab=5.71  E-value=1.9e+02  Score=13.33  Aligned_cols=30  Identities=27%  Similarity=0.333  Sum_probs=20.6

Q ss_pred             CCCHHHHHHHCCCCEEEEEEEEEEEEEEEE
Q ss_conf             222014555304730377898764223677
Q gi|254780668|r    5 ATGADLTEKFSKGKLNVAAVKCELKAEVTV   34 (46)
Q Consensus         5 atgadltekfskgklnvaavkcelkaevtv   34 (46)
                      -.||.+.|+-|-||+...+-+-..-++.|+
T Consensus       257 lSGA~p~EaiSWGKi~~~~~~v~V~~DATI  286 (297)
T pfam01916       257 LSGAPPEEAVSWGKIKAGADAVTVYGDATI  286 (297)
T ss_pred             CCCCCHHHHHCCCCCCCCCCEEEEEEEHHH
T ss_conf             668982243016761799973999961668


No 10 
>PRK01221 putative deoxyhypusine synthase; Provisional
Probab=5.25  E-value=1.8e+02  Score=13.38  Aligned_cols=29  Identities=28%  Similarity=0.376  Sum_probs=19.7

Q ss_pred             CCHHHHHHHCCCCEEEEEEEEEEEEEEEE
Q ss_conf             22014555304730377898764223677
Q gi|254780668|r    6 TGADLTEKFSKGKLNVAAVKCELKAEVTV   34 (46)
Q Consensus         6 tgadltekfskgklnvaavkcelkaevtv   34 (46)
                      .||.+.|+-|-||+...+-+-...++.|+
T Consensus       273 SGA~~~EaiSWGKi~~~~~~v~V~~DATI  301 (312)
T PRK01221        273 SGARPREAISWGKVKPSAKSVTIYGDATI  301 (312)
T ss_pred             CCCCCCHHCCCCCCCCCCCEEEEEEEHHH
T ss_conf             68982210026774799871899960768


Done!