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!