Query         gi|254780907|ref|YP_003065320.1| hypothetical protein CLIBASIA_04030 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 88
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 00:23:49 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780907.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00059 L17 ribosomal protei  54.4       3 7.6E-05   22.2  -0.4   14    1-14     84-97  (125)
  2 TIGR01804 BADH betaine aldehyd  44.1       9 0.00023   19.7   0.8   25    6-38    155-179 (471)
  3 pfam03346 consensus             26.7      61  0.0016   15.4   3.1   52   13-68     12-70  (369)
  4 TIGR02123 TRAP_fused TRAP tran  18.9      24 0.00061   17.5  -0.7   12   30-45    537-548 (681)
  5 pfam07078 FYTT Forty-two-three  18.8      70  0.0018   15.1   1.7   19   68-86     25-43  (316)
  6 pfam10231 DUF2315 Uncharacteri  18.0      48  0.0012   15.9   0.7   27   20-52      1-27  (127)
  7 TIGR01481 ccpA catabolite cont  15.7      77   0.002   14.9   1.3   41   36-76    137-177 (332)
  8 TIGR02408 ectoine_ThpD ectoine  11.9   1E+02  0.0027   14.2   1.1   17   28-44    230-246 (278)
  9 pfam10668 Phage_terminase Phag  10.7      80   0.002   14.8   0.2   17   54-70      2-18  (60)
 10 pfam07771 TSGP1 Tick salivary    8.8 1.5E+02  0.0039   13.3   1.0   33   27-59     86-118 (120)

No 1  
>TIGR00059 L17 ribosomal protein L17; InterPro: IPR000456   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   Ribosomal protein L17 is one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is colinear with the sequence of L17 from Escherichia coli.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=54.38  E-value=3  Score=22.22  Aligned_cols=14  Identities=50%  Similarity=0.819  Sum_probs=11.3

Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             93246543046542
Q gi|254780907|r    1 MKLLFSKIAPVFAM   14 (88)
Q Consensus         1 mkllfskiapvfam   14 (88)
                      |.-||++|||.|+-
T Consensus        84 ~~kLF~~iaPry~~   97 (125)
T TIGR00059        84 LNKLFSEIAPRYAQ   97 (125)
T ss_pred             HHHHHHHHCCCCCC
T ss_conf             99876530553234


No 2  
>TIGR01804 BADH betaine aldehyde dehydrogenase; InterPro: IPR011264   Under osmotic stress, betaine aldehyde dehydrogenase oxidises glycine betaine aldehyde into the osmoprotectant glycine betaine, via the second of two oxidation steps from exogenously supplied choline or betaine aldehyde. This choline-glycine betaine synthesis pathway can be found in Gram-positive and Gram-negative bacteria. In Escherichia coli, betaine aldehyde dehydrogenase (betB) is osmotically co-induced with choline dehydrogenase (betA) in the presence of choline. These dehydrogenases are located in a betaine gene cluster with the upstream choline transporter (betT) and transcriptional regulator (betI) . Similar to E. coli, betaine synthesis in Staphylococcus xylosus is also influenced by osmotic stress and the presence of choline with genes localised in a functionally equivalent gene cluster . Organisation of the betaine gene cluster in Sinorhizobium meliloti and Bacillus subtilis differs from that of E. coli by the absence of upstream choline transporter and transcriptional regulator homologues , . Additionally, Bacillus subtilis co-expresses a type II alcohol dehydrogenase with betaine aldehyde dehydrogenase instead of choline dehydrogenase as in E. coli, Staphylococcus xylosus, and Sinorhizobium meliloti . Betaine aldehyde dehydrogenase is a member of the aldehyde dehydrogenase family.  ; GO: 0008802 betaine-aldehyde dehydrogenase activity, 0006578 betaine biosynthetic process.
Probab=44.06  E-value=9  Score=19.72  Aligned_cols=25  Identities=48%  Similarity=0.650  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHHHEECCCCCCCHHHCCCCCCCC
Q ss_conf             543046542001023156668022147754787
Q gi|254780907|r    6 SKIAPVFAMGTALISCDSASDPAKKSNITPIPP   38 (88)
Q Consensus         6 skiapvfamgtaliscdsasdpakksnitpipp   38 (88)
                      -|+||-.|+|.++|-        |-|.+||+.-
T Consensus       155 WK~APALa~Gna~v~--------KPSE~TPLta  179 (471)
T TIGR01804       155 WKSAPALAAGNALVF--------KPSEITPLTA  179 (471)
T ss_pred             HHCCHHHHHCCCEEE--------CCCCCCHHHH
T ss_conf             401457770582553--------5888773689


No 3  
>pfam03346 consensus
Probab=26.68  E-value=61  Score=15.39  Aligned_cols=52  Identities=38%  Similarity=0.634  Sum_probs=28.4

Q ss_pred             HHHHHHEECC----CCCCCHHHCCCCCCCCCCEEECCCCC---CCCCCCCCCCCCCCHHHHEE
Q ss_conf             4200102315----66680221477547876431026887---54326543234500012000
Q gi|254780907|r   13 AMGTALISCD----SASDPAKKSNITPIPPAPVALAAPPK---NKTEAPKTESSNKDKAKEIT   68 (88)
Q Consensus        13 amgtaliscd----sasdpakksnitpippapvalaappk---nkteapktessnkdkakeit   68 (88)
                      .-|..|..|.    |.|.|--.|..||-    |-.+||--   .|.|||+.+++.-++.|++.
T Consensus        12 vaglvltacsgggssgss~kpnse~tpk----vDmsAPkAeqPKkEeaPqAd~pKae~PK~~A   70 (369)
T pfam03346        12 VAGLVLTACSGGGSSGSSPKPNSESTPK----VDMSAPKAEQPKKEEAPQADSPKAEKPKSIA   70 (369)
T ss_pred             HHHHEEEECCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHC
T ss_conf             7644255114788888899998777875----4555765668642226656686333750007


No 4  
>TIGR02123 TRAP_fused TRAP transporter, 4TM/12TM fusion protein; InterPro: IPR011853    In some species, the 12-transmembrane spanning and 4-transmembrane spanning components of tripartite ATP-independent periplasmic (TRAP)-type transporters are fused. This entry describes such transporters, found in the archaea and in bacteria..
Probab=18.94  E-value=24  Score=17.52  Aligned_cols=12  Identities=75%  Similarity=1.041  Sum_probs=7.0

Q ss_pred             HCCCCCCCCCCEEECC
Q ss_conf             1477547876431026
Q gi|254780907|r   30 KSNITPIPPAPVALAA   45 (88)
Q Consensus        30 ksnitpippapvalaa   45 (88)
                      -|||||    ||||||
T Consensus       537 ~a~iTP----PVALAA  548 (681)
T TIGR02123       537 LADITP----PVALAA  548 (681)
T ss_pred             HHCCCC----CHHHHH
T ss_conf             604884----179999


No 5  
>pfam07078 FYTT Forty-two-three protein. This family consists of several mammalian proteins of around 320 residues in length called 40-2-3 proteins. The function of this family is unknown.
Probab=18.83  E-value=70  Score=15.10  Aligned_cols=19  Identities=42%  Similarity=0.646  Sum_probs=9.6

Q ss_pred             EHHHHHHHHHHHHHHHHHC
Q ss_conf             0132201035530003420
Q gi|254780907|r   68 TLDIIDLGIDLLTKEDKKE   86 (88)
Q Consensus        68 tldiidlgidlltkedkke   86 (88)
                      ++|-||...|-.-|-.|||
T Consensus        25 ~~dKiDMSLDDIIkLNKkE   43 (316)
T pfam07078        25 NLDKIDMSLDDIIKLNRKE   43 (316)
T ss_pred             CHHHHCCCHHHHHHHHHHH
T ss_conf             1444215689998753676


No 6  
>pfam10231 DUF2315 Uncharacterized conserved protein (DUF2315). This is a family of small conserved proteins found from worms to humans. The function is not known.
Probab=18.03  E-value=48  Score=15.93  Aligned_cols=27  Identities=37%  Similarity=0.469  Sum_probs=19.8

Q ss_pred             ECCCCCCCHHHCCCCCCCCCCEEECCCCCCCCC
Q ss_conf             315666802214775478764310268875432
Q gi|254780907|r   20 SCDSASDPAKKSNITPIPPAPVALAAPPKNKTE   52 (88)
Q Consensus        20 scdsasdpakksnitpippapvalaappknkte   52 (88)
                      |||-..-|-..|||-||--.      .|.|.|+
T Consensus         1 s~D~igPPd~~SNlRPi~~~------~~~nEt~   27 (127)
T pfam10231         1 SHDWIGPPDPQSNLRPIVLH------IPENETP   27 (127)
T ss_pred             CCCCCCCCCCCCCCCCEECC------CCCCCCH
T ss_conf             98867999941246531102------7999988


No 7  
>TIGR01481 ccpA catabolite control protein A; InterPro: IPR006377   Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [e.g. acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription.
Probab=15.70  E-value=77  Score=14.88  Aligned_cols=41  Identities=29%  Similarity=0.432  Sum_probs=31.9

Q ss_pred             CCCCCEEECCCCCCCCCCCCCCCCCCCHHHHEEHHHHHHHH
Q ss_conf             78764310268875432654323450001200013220103
Q gi|254780907|r   36 IPPAPVALAAPPKNKTEAPKTESSNKDKAKEITLDIIDLGI   76 (88)
Q Consensus        36 ippapvalaappknkteapktessnkdkakeitldiidlgi   76 (88)
                      --|+||-||+---.+.+-|--.---+.-+||++...|+-|-
T Consensus       137 rs~~PVVLAGt~D~~~~~pSVNIDy~~A~kEav~~l~~~Gh  177 (332)
T TIGR01481       137 RSPVPVVLAGTVDKENELPSVNIDYKQATKEAVKELIAKGH  177 (332)
T ss_pred             CCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             28998899535486546773101678999999999863358


No 8  
>TIGR02408 ectoine_ThpD ectoine hydroxylase; InterPro: IPR012774    Both ectoine and hydroxyectoine are compatible solvents that serve as protectants against osmotic and thermal stresses. A number of genomes synthesize ectoine. This enzyme allows conversion of ectoine to hydroxyectoine, which may be more effective for some purposes, and is found in a subset of ectoine-producing organisms.; GO: 0016725 oxidoreductase activity acting on CH or CH2 groups.
Probab=11.95  E-value=1e+02  Score=14.18  Aligned_cols=17  Identities=47%  Similarity=0.608  Sum_probs=13.3

Q ss_pred             HHHCCCCCCCCCCEEEC
Q ss_conf             22147754787643102
Q gi|254780907|r   28 AKKSNITPIPPAPVALA   44 (88)
Q Consensus        28 akksnitpippapvala   44 (88)
                      .-.|||||.|-+-|-+.
T Consensus       230 GSgsNItP~pRsNVF~V  246 (278)
T TIGR02408       230 GSGSNITPYPRSNVFLV  246 (278)
T ss_pred             CCCCCCCCCCCCCEEEE
T ss_conf             78888887543452678


No 9  
>pfam10668 Phage_terminase Phage terminase small subunit. This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.
Probab=10.72  E-value=80  Score=14.80  Aligned_cols=17  Identities=35%  Similarity=0.542  Sum_probs=13.0

Q ss_pred             CCCCCCCCCHHHHEEHH
Q ss_conf             54323450001200013
Q gi|254780907|r   54 PKTESSNKDKAKEITLD   70 (88)
Q Consensus        54 pktessnkdkakeitld   70 (88)
                      |...|.|.|+|+||-++
T Consensus         2 aR~RsP~RDkA~eiy~~   18 (60)
T pfam10668         2 ARQRSPDRDKAKEMWKE   18 (60)
T ss_pred             CCCCCCCHHHHHHHHHH
T ss_conf             88889578899999998


No 10 
>pfam07771 TSGP1 Tick salivary peptide group 1. This contains a group of peptides derived from a salivary gland cDNA library of the tick Ixodes scapularis. Also present are peptides from a related tick species, Ixodes ricinus. They are characterized by a putative signal peptide indicative of secretion and conserved cysteine residues.
Probab=8.81  E-value=1.5e+02  Score=13.32  Aligned_cols=33  Identities=24%  Similarity=0.363  Sum_probs=13.6

Q ss_pred             CHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCC
Q ss_conf             022147754787643102688754326543234
Q gi|254780907|r   27 PAKKSNITPIPPAPVALAAPPKNKTEAPKTESS   59 (88)
Q Consensus        27 pakksnitpippapvalaappknkteapktess   59 (88)
                      |..-..-+|-|+...--..--..|++.||++|.
T Consensus        86 P~~~~d~~~~pte~~k~kkkK~~k~k~~k~~s~  118 (120)
T pfam07771        86 PSHPDDHPPEPTEKPKKKKKKSKKTKKPKKSSK  118 (120)
T ss_pred             CCCCCCCCCCCCCCHHHHHHCHHHHHCCCHHHC
T ss_conf             888243888887652333303344312202223


Done!