Query         gi|254781186|ref|YP_003065599.1| hypothetical protein CLIBASIA_05465 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 45
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 05:43:33 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781186.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01582 FDH-beta formate deh  47.3     8.6 0.00022   20.7   1.1   13    6-18    117-129 (293)
  2 TIGR01111 mtrA tetrahydrometha  42.0     5.5 0.00014   21.6  -0.6   31   12-42     97-136 (246)
  3 PTZ00205 DNA polymerase kappa;  21.2      67  0.0017   16.2   2.0   31   13-43    313-343 (571)
  4 TIGR01368 CPSaseIIsmall carbam  18.3      63  0.0016   16.3   1.4   19    3-22    234-253 (383)
  5 PRK04943 consensus              15.7      73  0.0019   16.0   1.2   19   25-43    267-285 (288)
  6 COG2168 DsrH Uncharacterized c  14.5      76  0.0019   15.9   1.0   29    6-34     24-54  (96)
  7 TIGR02278 PaaN-DH phenylacetic  13.3      44  0.0011   17.1  -0.5   15   16-30    615-630 (690)
  8 TIGR02236 recomb_radA DNA repa  12.6 1.1E+02  0.0028   15.1   1.4   23   15-37      6-28  (333)
  9 PRK06580 putative monovalent c  12.5 1.2E+02  0.0029   15.0   1.5   21    2-22     47-71  (106)
 10 PRK01726 consensus              11.2 1.2E+02   0.003   14.9   1.2   18   26-43    284-301 (312)

No 1  
>TIGR01582 FDH-beta formate dehydrogenase, beta subunit; InterPro: IPR006470   The sequences in this group represent the beta subunit of the gamma-proteobacterial formate dehydrogenase. This subunit contains four 4Fe-4S clusters and is involved in transmitting electrons from the alpha subunit (IPR006443 from INTERPRO) at the periplasmic space to the gamma subunit which spans the cytoplasmic membrane . In addition to the gamma proteobacteria, a sequence from Aquifex aolicus falls within this group. This appears to be the case for the alpha, gamma and epsilon (accessory protein IPR006452 from INTERPRO) chains as well. ; GO: 0008863 formate dehydrogenase activity, 0045333 cellular respiration, 0016021 integral to membrane.
Probab=47.34  E-value=8.6  Score=20.69  Aligned_cols=13  Identities=54%  Similarity=0.871  Sum_probs=11.3

Q ss_pred             CCCEEEEEECCCH
Q ss_conf             6877999834601
Q gi|254781186|r    6 NPDAIVLYANGIG   18 (45)
Q Consensus         6 npdaivlyangig   18 (45)
                      .|-|||-|+|||-
T Consensus       117 aPGAiiQY~NGiV  129 (293)
T TIGR01582       117 APGAIIQYQNGIV  129 (293)
T ss_pred             CCCCEEEECCCEE
T ss_conf             6784575048637


No 2  
>TIGR01111 mtrA tetrahydromethanopterin S-methyltransferase, subunit A; InterPro: IPR005778    This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit A in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump.  5-methyl-5,6,7,8-tetrahydromethanopterin + 2-mercaptoethanesulphonate = 5,6,7,8-tetrahydromethanopterin + 2-(methylthio)ethanesulphonate.  Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0006814 sodium ion transport, 0005737 cytoplasm, 0012506 vesicle membrane.
Probab=41.98  E-value=5.5  Score=21.64  Aligned_cols=31  Identities=42%  Similarity=0.573  Sum_probs=22.3

Q ss_pred             EEECCC--------HHHHH-HHHHCCCCCHHHHHHCCHHH
Q ss_conf             983460--------12237-67640882479998300232
Q gi|254781186|r   12 LYANGI--------GAVTA-NYLENLNYSPIEKILGQRSS   42 (45)
Q Consensus        12 lyangi--------gavta-nylenlnyspiekilgqrss   42 (45)
                      ||+||+        ||.-| -||||+|-.-||+.-.|--.
T Consensus        97 Lh~NGv~PD~~~IiGA~GAIPY~EN~n~eAveRF~~Q~Ve  136 (246)
T TIGR01111        97 LHENGVDPDDGRIIGAKGAIPYLENINEEAVERFRKQIVE  136 (246)
T ss_pred             HHHCCCCCCCCCEECCCCCCCCEECCCHHHHHHHHHHHHH
T ss_conf             9827888788853023367651016876788998641310


No 3  
>PTZ00205 DNA polymerase kappa; Provisional
Probab=21.19  E-value=67  Score=16.19  Aligned_cols=31  Identities=26%  Similarity=0.483  Sum_probs=26.4

Q ss_pred             EECCCHHHHHHHHHCCCCCHHHHHHCCHHHC
Q ss_conf             8346012237676408824799983002321
Q gi|254781186|r   13 YANGIGAVTANYLENLNYSPIEKILGQRSSV   43 (45)
Q Consensus        13 yangigavtanylenlnyspiekilgqrssv   43 (45)
                      --+|||.||+.-|+.+.-.....|+-+|.-+
T Consensus       313 KIpGIGkVte~~L~alGI~TCgDiy~~R~~L  343 (571)
T PTZ00205        313 SVPGVGKVTEALLKGLGITTLSDIYNRRVEL  343 (571)
T ss_pred             CCCCCCHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             6897568889999875975099999867799


No 4  
>TIGR01368 CPSaseIIsmall carbamoyl-phosphate synthase, small subunit; InterPro: IPR006274   Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC).   Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain.   Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains .    This entry represents the small subunit of the glutamine-dependent form (6.3.5.5 from EC) of carbamoyl phosphate synthase, CPSase II. The small subunit catalyses the hydrolysis of glutamine to ammonia, which in turn used by the large chain to synthesize carbamoyl phosphate. The C-terminal domain of the small subunit of CPSase has glutamine amidotransferase activity. Note that the sequence from the mammalian urea cycle form has lost the active site Cys, resulting in an ammonia-dependent form, CPSase I (6.3.4.16 from EC). CPSases of pyrimidine biosynthesis, arginine biosynthesis, and the urea cycle may be encoded by one or by several genes, depending on the species. ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=18.29  E-value=63  Score=16.32  Aligned_cols=19  Identities=53%  Similarity=0.894  Sum_probs=13.7

Q ss_pred             CCCCCCEEEEEECCCHHH-HH
Q ss_conf             443687799983460122-37
Q gi|254781186|r    3 HQYNPDAIVLYANGIGAV-TA   22 (45)
Q Consensus         3 hqynpdaivlyangigav-ta   22 (45)
                      -+||||.|.| .||=|-- .+
T Consensus       234 ~~~~PDGifl-SNGPGDPH~~  253 (383)
T TIGR01368       234 KKYNPDGIFL-SNGPGDPHAA  253 (383)
T ss_pred             HHHCCCEEEE-ECCCCCCHHH
T ss_conf             8657888999-0879880567


No 5  
>PRK04943 consensus
Probab=15.68  E-value=73  Score=16.00  Aligned_cols=19  Identities=26%  Similarity=0.392  Sum_probs=13.5

Q ss_pred             HHCCCCCHHHHHHCCHHHC
Q ss_conf             6408824799983002321
Q gi|254781186|r   25 LENLNYSPIEKILGQRSSV   43 (45)
Q Consensus        25 lenlnyspiekilgqrssv   43 (45)
                      .+.|||||+.+.|.|-.|.
T Consensus       267 ~kgl~~spl~~~~~~~~~~  285 (288)
T PRK04943        267 AQGRNISPLKETLADYQSA  285 (288)
T ss_pred             ECCCCCCHHHHHHHHHHHH
T ss_conf             3688768689999987765


No 6  
>COG2168 DsrH Uncharacterized conserved protein involved in oxidation of intracellular sulfur [Inorganic ion transport and metabolism]
Probab=14.52  E-value=76  Score=15.89  Aligned_cols=29  Identities=38%  Similarity=0.615  Sum_probs=21.9

Q ss_pred             CCCEEEEEECCCHHHH--HHHHHCCCCCHHH
Q ss_conf             6877999834601223--7676408824799
Q gi|254781186|r    6 NPDAIVLYANGIGAVT--ANYLENLNYSPIE   34 (45)
Q Consensus         6 npdaivlyangigavt--anylenlnyspie   34 (45)
                      .-|+++|..||+-+.-  ..|++.++-+|++
T Consensus        24 ~~D~vlL~qdGV~aAl~~~~~~~sl~~~p~~   54 (96)
T COG2168          24 EGDAVLLLQDGVYAALKGNRYLASLRESPIK   54 (96)
T ss_pred             CCCEEEEECCCCHHHHCCCHHHHHHHCCCCC
T ss_conf             6686999725004665086789998659612


No 7  
>TIGR02278 PaaN-DH phenylacetic acid degradation protein paaN; InterPro: IPR011966    This enzyme is proposed to act in the ring-opening step of phenylacetic acid degradation  which follows ligation of the acid with coenzyme A (by PaaF) and hydroxylation by a multicomponent non-heme iron hydroxylase complex (PaaGHIJK). Gene symbols have been standardised in . This enzyme is related to aldehyde dehydrogenases..
Probab=13.27  E-value=44  Score=17.09  Aligned_cols=15  Identities=60%  Similarity=0.926  Sum_probs=10.7

Q ss_pred             CCHHHHHHH-HHCCCC
Q ss_conf             601223767-640882
Q gi|254781186|r   16 GIGAVTANY-LENLNY   30 (45)
Q Consensus        16 gigavtany-lenlny   30 (45)
                      +.|-|-||| ||||-+
T Consensus       615 ~pGPvLANYGLe~LRF  630 (690)
T TIGR02278       615 APGPVLANYGLENLRF  630 (690)
T ss_pred             CCCCEEEECCCCCCCC
T ss_conf             8985473136776630


No 8  
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938   This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=12.63  E-value=1.1e+02  Score=15.08  Aligned_cols=23  Identities=35%  Similarity=0.598  Sum_probs=20.5

Q ss_pred             CCCHHHHHHHHHCCCCCHHHHHH
Q ss_conf             46012237676408824799983
Q gi|254781186|r   15 NGIGAVTANYLENLNYSPIEKIL   37 (45)
Q Consensus        15 ngigavtanylenlnyspiekil   37 (45)
                      .|+|..||.-|..--|+.+++|-
T Consensus         6 PGVGp~TA~KL~EaGy~t~~~iA   28 (333)
T TIGR02236         6 PGVGPATAEKLREAGYDTLEAIA   28 (333)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             89757688998861078899984


No 9  
>PRK06580 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=12.50  E-value=1.2e+02  Score=14.99  Aligned_cols=21  Identities=33%  Similarity=0.485  Sum_probs=15.5

Q ss_pred             CCCCCCCEEEEEECCC----HHHHH
Q ss_conf             8443687799983460----12237
Q gi|254781186|r    2 AHQYNPDAIVLYANGI----GAVTA   22 (45)
Q Consensus         2 ahqynpdaivlyangi----gavta   22 (45)
                      +.|-++-+.|.|||.|    |.||.
T Consensus        47 a~~kt~~g~v~yANSITLTPGTvTv   71 (106)
T PRK06580         47 AEGLEEIGEIIYGNSITLTPGTVTL   71 (106)
T ss_pred             CCCCCCCCEEEEEEEEEECCCEEEE
T ss_conf             4457753258885148716975999


No 10 
>PRK01726 consensus
Probab=11.24  E-value=1.2e+02  Score=14.95  Aligned_cols=18  Identities=44%  Similarity=0.578  Sum_probs=13.3

Q ss_pred             HCCCCCHHHHHHCCHHHC
Q ss_conf             408824799983002321
Q gi|254781186|r   26 ENLNYSPIEKILGQRSSV   43 (45)
Q Consensus        26 enlnyspiekilgqrssv   43 (45)
                      ..||+||+..++-|-||.
T Consensus       284 k~l~~spl~~~~~~~~~~  301 (312)
T PRK01726        284 KGLNVSPLHAMLKQLSST  301 (312)
T ss_pred             CCCCCCHHHHHHHHHHHC
T ss_conf             688768799999986300


Done!