Query         gi|254781010|ref|YP_003065423.1| hypothetical protein CLIBASIA_04560 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 195
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 03:54:52 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781010.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 KOG3802 consensus               23.5      54  0.0014   14.0   1.9   27   29-55    295-321 (398)
  2 PRK01712 carbon storage regula  22.4      58  0.0015   13.8   2.0   29   51-79     35-63  (64)
  3 PHA00407 phage lambda Rz1-like  20.8      30 0.00077   15.5   0.2   14   10-23     37-50  (84)
  4 pfam06253 MTTB Trimethylamine   20.3      22 0.00057   16.3  -0.6   32  161-192   427-458 (505)
  5 PRK03002 prsA peptidylprolyl i  20.0      17 0.00043   17.0  -1.2   23    1-24      1-23  (285)
  6 TIGR00187 ribE riboflavin synt  18.6      29 0.00074   15.6  -0.3   13   19-31     39-51  (225)
  7 COG5598 Trimethylamine:corrino  17.2      25 0.00063   16.0  -0.9   32  161-192   444-475 (526)
  8 PRK13731 conjugal transfer sur  16.7      34 0.00086   15.2  -0.3   33    1-34      1-33  (243)
  9 TIGR01357 aroB 3-dehydroquinat  16.5      46  0.0012   14.4   0.3   15  170-184   141-155 (361)
 10 TIGR02026 BchE magnesium-proto  16.1      54  0.0014   14.0   0.6   18  105-122     5-22  (506)

No 1  
>KOG3802 consensus
Probab=23.46  E-value=54  Score=13.99  Aligned_cols=27  Identities=26%  Similarity=0.485  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             654224567799999999861488751
Q gi|254781010|r   29 AKKRNTIGNTIKKSINRVIQENNKPRN   55 (195)
Q Consensus        29 akkrntigntikksinrviqennkprn   55 (195)
                      -|||..|-..++-..+.-.++|.||--
T Consensus       295 RKKRTSie~~vr~aLE~~F~~npKPt~  321 (398)
T KOG3802         295 RKKRTSIEVNVRGALEKHFLKNPKPTS  321 (398)
T ss_pred             CCCCCCEEHHHHHHHHHHHHHCCCCCH
T ss_conf             443452108899999999986889988


No 2  
>PRK01712 carbon storage regulator; Provisional
Probab=22.36  E-value=58  Score=13.81  Aligned_cols=29  Identities=21%  Similarity=0.521  Sum_probs=21.7

Q ss_pred             CCCCCEEEEHHHHHHHHHHHHHCCHHHHC
Q ss_conf             88751266426777876676412313320
Q gi|254781010|r   51 NKPRNMTIFKTEVKRDIRRASRLSLEEKS   79 (195)
Q Consensus        51 nkprnmtifktevkrdirrasrlsleeks   79 (195)
                      .-|+++.|+..|+-..|+...+-..+..|
T Consensus        35 ~AP~~v~I~R~Eiy~~I~~eN~~A~~~s~   63 (64)
T PRK01712         35 NAPKEVSVHREEIYQRIQEENSAALQQSS   63 (64)
T ss_pred             ECCCCCCEEHHHHHHHHHHHHHHHHHHCC
T ss_conf             88999819099999999999999987515


No 3  
>PHA00407 phage lambda Rz1-like protein
Probab=20.80  E-value=30  Score=15.53  Aligned_cols=14  Identities=50%  Similarity=0.997  Sum_probs=10.2

Q ss_pred             HHHHHHHHCCCCCC
Q ss_conf             21474352024353
Q gi|254781010|r   10 STLVICVLSISSCD   23 (195)
Q Consensus        10 stlvicvlsisscd   23 (195)
                      .-|.|||..||.|.
T Consensus        37 Glllicv~tISGCa   50 (84)
T PHA00407         37 GLLLICVATISGCA   50 (84)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999976665


No 4  
>pfam06253 MTTB Trimethylamine methyltransferase (MTTB). This family consists of several trimethylamine methyltransferase (MTTB) (EC:2.1.1.-) proteins from numerous Rhizobium and Methanosarcina species.
Probab=20.33  E-value=22  Score=16.31  Aligned_cols=32  Identities=31%  Similarity=0.635  Sum_probs=22.2

Q ss_pred             CCCCCCCCCHHHCCCCCCCCCCCCCCCEEEEE
Q ss_conf             32012233221101221143100368414643
Q gi|254781010|r  161 DHQVDRNHTLSNLRGACYQPSLVSNSSLKLWD  192 (195)
Q Consensus       161 dhqvdrnhtlsnlrgacyqpslvsnsslklwd  192 (195)
                      .|-....||+.+.|.+-|+|.|...++..-|.
T Consensus       427 GhfLg~~hT~~~~~~~~~~P~l~dr~~~e~W~  458 (505)
T pfam06253       427 GHFLGTEHTLARYQTAFYQPALSDWNNFEQWN  458 (505)
T ss_pred             CCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHH
T ss_conf             87679789999974352588664535987898


No 5  
>PRK03002 prsA peptidylprolyl isomerase; Reviewed
Probab=20.02  E-value=17  Score=17.02  Aligned_cols=23  Identities=35%  Similarity=0.793  Sum_probs=18.0

Q ss_pred             CCCCCEEEEHHHHHHHHCCCCCCC
Q ss_conf             987616830214743520243532
Q gi|254781010|r    1 MKSKNILIVSTLVICVLSISSCDL   24 (195)
Q Consensus         1 mksknilivstlvicvlsisscdl   24 (195)
                      ||.|.|++.++ +++|++++.|.-
T Consensus         1 mkkK~i~~~~~-~~svl~LaaC~~   23 (285)
T PRK03002          1 MRGKHIFIITA-LISILMLSACGQ   23 (285)
T ss_pred             CCHHHHHHHHH-HHHHHHHHHHCC
T ss_conf             96018999999-999999998457


No 6  
>TIGR00187 ribE riboflavin synthase, alpha subunit; InterPro: IPR001783   The following proteins have been shown ,  to be structurally and evolutionary related:  Riboflavin synthase alpha chain (2.5.1.9 from EC) (RS-alpha) (gene ribC in Escherichia coli, ribB in Bacillus subtilis and Photobacterium leiognathi, RIB5 in yeast. This enzyme synthesises riboflavin from two moles of 6,7- dimethyl-8-(1'-D-ribityl)lumazine (Lum), a pteridine-derivative. Photobacterium phosphoreum lumazine protein (LumP) (gene luxL). LumP is a protein that modulates the colour of the bioluminescence emission of bacterial luciferase. In the presence of LumP, light emission is shifted to higher energy values (shorter wavelength). LumP binds non-covalently to 6,7-dimethyl-8-(1'-D-ribityl)lumazine. Vibrio fischeri yellow fluorescent protein (YFP) (gene luxY). Like LumP, YFP modulates light emission but towards a longer wavelength. YFP binds non-covalently to FMN.    These proteins seem to have evolved from the duplication of a domain of about 100 residues. In its C-terminal section, this domain contains a conserved motif [KR]-V-N-[LI]-E which has been proposed to be the binding site for lumazine (Lum) and some of its derivatives. RS-alpha which binds two molecules of Lum has two perfect copies of this motif, while LumP which binds one molecule of Lum, has a Glu instead of Lys/Arg in the first position of the second copy of the motif. Similarly, YFP, which binds to one molecule of FMN, also seems to have a potentially dysfunctional binding site by substitution of Gly for Glu in the last position of the first copy of the motif. .
Probab=18.56  E-value=29  Score=15.61  Aligned_cols=13  Identities=46%  Similarity=0.652  Sum_probs=9.7

Q ss_pred             CCCCCCCHHHHHH
Q ss_conf             2435320256654
Q gi|254781010|r   19 ISSCDLGDSIAKK   31 (195)
Q Consensus        19 isscdlgdsiakk   31 (195)
                      ...|.||||||--
T Consensus        39 L~D~~lGdSIA~N   51 (225)
T TIGR00187        39 LEDLHLGDSIAVN   51 (225)
T ss_pred             HCCCCCCCEEEEC
T ss_conf             4025204541236


No 7  
>COG5598 Trimethylamine:corrinoid methyltransferase [Coenzyme metabolism]
Probab=17.16  E-value=25  Score=16.02  Aligned_cols=32  Identities=31%  Similarity=0.544  Sum_probs=20.7

Q ss_pred             CCCCCCCCCHHHCCCCCCCCCCCCCCCEEEEE
Q ss_conf             32012233221101221143100368414643
Q gi|254781010|r  161 DHQVDRNHTLSNLRGACYQPSLVSNSSLKLWD  192 (195)
Q Consensus       161 dhqvdrnhtlsnlrgacyqpslvsnsslklwd  192 (195)
                      .|-..-.||+.+..-|.|+|.+-.+.|.+-|.
T Consensus       444 gHflG~~hT~~~~qTaf~~p~l~D~~~~e~W~  475 (526)
T COG5598         444 GHFLGCPHTLALYQTAFYDPMLADRRSFEQWA  475 (526)
T ss_pred             CCCCCCHHHHHHHHHHHCCHHHCCCCCHHHHH
T ss_conf             86257778999987641040430544878898


No 8  
>PRK13731 conjugal transfer surface exclusion protein TraT; Provisional
Probab=16.71  E-value=34  Score=15.23  Aligned_cols=33  Identities=39%  Similarity=0.629  Sum_probs=23.5

Q ss_pred             CCCCCEEEEHHHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             9876168302147435202435320256654224
Q gi|254781010|r    1 MKSKNILIVSTLVICVLSISSCDLGDSIAKKRNT   34 (195)
Q Consensus         1 mksknilivstlvicvlsisscdlgdsiakkrnt   34 (195)
                      ||.|.++++ .++..+|.+|+|.--...-+|||-
T Consensus         1 m~~kk~~~~-~~~~~~l~lsGC~a~~tai~krnL   33 (243)
T PRK13731          1 MKTKKLMMV-ALVSSTLALSGCGAMSTAIKKRNL   33 (243)
T ss_pred             CCHHHHHHH-HHHHHHHHHCCHHHHHHHHHHCCC
T ss_conf             933775799-999999997156876778773575


No 9  
>TIGR01357 aroB 3-dehydroquinate synthase; InterPro: IPR016037   The 3-dehydroquinate synthase (4.2.3.4 from EC) domain is present in isolation in various bacterial 3-dehydroquinate synthases and also present as a domain in the pentafunctional AROM polypeptide (P07547 from SWISSPROT) . 3-dehydroquinate (DHQ) synthase catalyses the formation of dehydroquinate (DHQ) and orthophosphate from 3-deoxy-D-arabino heptulosonic 7 phosphate . This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids.; GO: 0003856 3-dehydroquinate synthase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=16.52  E-value=46  Score=14.44  Aligned_cols=15  Identities=53%  Similarity=0.614  Sum_probs=11.4

Q ss_pred             HHHCCCCCCCCCCCC
Q ss_conf             211012211431003
Q gi|254781010|r  170 LSNLRGACYQPSLVS  184 (195)
Q Consensus       170 lsnlrgacyqpslvs  184 (195)
                      .-|+=||-|||.+|-
T Consensus       141 gKNlIGaFy~P~~V~  155 (361)
T TIGR01357       141 GKNLIGAFYQPKAVL  155 (361)
T ss_pred             CCCCEEEEECCCCEE
T ss_conf             863042113774026


No 10 
>TIGR02026 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase; InterPro: IPR011772    This entry respresents the cobalamin-dependent oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under anaerobic conditions . This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under anaerobic conditions (a separate enzyme, AcsF, acts under aerobic conditions). This entry identifies two clades of sequences, one from photosynthetic, non-cyanobacterial bacteria and another including Synechocystis and several non-photosynthetic bacteria. The function of the Synechocystis gene is supported by gene clustering with other photosynthetic genes, so the purpose of the gene in the non-photosynthetic bacteria is uncertain. Note that homologues of this gene are not found in plants which rely solely on the aerobic cyclase.; GO: 0016709 oxidoreductase activity acting on paired donors with incorporation or reduction of molecular oxygen NADH or NADPH as one donor and incorporation of one atom of oxygen, 0050661 NADP binding, 0015995 chlorophyll biosynthetic process.
Probab=16.15  E-value=54  Score=14.02  Aligned_cols=18  Identities=50%  Similarity=0.652  Sum_probs=0.0

Q ss_pred             CCCCCCCCEEEEEECCCC
Q ss_conf             788763222335310373
Q gi|254781010|r  105 LNPNHQASEIDIAIENLP  122 (195)
Q Consensus       105 lnpnhqaseidiaienlp  122 (195)
                      ++|||.|.--.||-|++|
T Consensus         5 ~~PnyhagGa~Iage~~P   22 (506)
T TIGR02026         5 LNPNYHAGGAEIAGEQWP   22 (506)
T ss_pred             ECCCCCCCCCCCCCCCCC
T ss_conf             338788666607766676


Done!