Query         gi|254780213|ref|YP_003064626.1| hypothetical protein CLIBASIA_00490 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 63
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 23 17:51:26 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780213.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 KOG3348 consensus               58.6     3.3 8.4E-05   22.6   0.4   19   12-30     53-71  (85)
  2 TIGR00232 tktlase_bact transke  48.3      11 0.00028   19.8   1.7   38   11-48    573-610 (675)
  3 pfam04487 CITED CITED. CITED,   36.0      27 0.00068   17.8   2.1   21   35-55    155-176 (206)
  4 cd01647 RT_LTR RT_LTR: Reverse  26.3      38 0.00098   17.0   1.6   29    1-29     98-134 (177)
  5 pfam07038 DUF1324 Protein of u  24.1      23 0.00059   18.1   0.1   22   26-59     38-59  (59)
  6 TIGR00542 hxl6Piso_put hexulos  20.9      68  0.0017   15.7   2.0   27    4-30    183-209 (290)
  7 TIGR00683 nanA N-acetylneurami  18.6      62  0.0016   15.9   1.4   36   16-51    250-286 (294)
  8 pfam06837 Fijivirus_P9-2 Fijiv  15.8      33 0.00083   17.3  -0.6   56    7-62     20-76  (214)
  9 pfam04792 LcrV V antigen (LcrV  12.0 1.4E+02  0.0035   14.0   1.8   40   13-52     34-79  (326)
 10 TIGR01524 ATPase-IIIB_Mg magne  11.7      48  0.0012   16.5  -0.7   26   17-46    725-750 (892)

No 1  
>KOG3348 consensus
Probab=58.61  E-value=3.3  Score=22.65  Aligned_cols=19  Identities=47%  Similarity=0.635  Sum_probs=15.1

Q ss_pred             EEHHHHHHHHCCCCEEEEE
Q ss_conf             0178887742025217775
Q gi|254780213|r   12 IEVNSILKEEIDDISVVSL   30 (63)
Q Consensus        12 ievnsilkeeiddisvvsl   30 (63)
                      --||++|+|||.+|.-.++
T Consensus        53 RlVN~~L~Eeik~iHalt~   71 (85)
T KOG3348          53 RLVNSILAEEIKEIHALTI   71 (85)
T ss_pred             HHHHHHHHHHHHHHHHHEE
T ss_conf             9999999999998765333


No 2  
>TIGR00232 tktlase_bact transketolase; InterPro: IPR005478     Transketolase (EC 2.2.1.1) (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor.    This group includes two proteins from the yeast Saccharomyces cerevisiae but excludes dihydroxyactetone synthases (formaldehyde transketolases) from various yeasts and the even more distant mammalian transketolases. Among the family of thiamine diphosphate-dependent enzymes that includes transketolases, dihydroxyacetone synthases, pyruvate dehydrogenase E1-beta subunits, and deoxyxylulose-5-phosphate synthases, mammalian and bacterial transketolases seem not to be orthologous. ; GO: 0004802 transketolase activity.
Probab=48.29  E-value=11  Score=19.85  Aligned_cols=38  Identities=34%  Similarity=0.355  Sum_probs=32.3

Q ss_pred             EEEHHHHHHHHCCCCEEEEEECCCCCCEECHHHHHHHH
Q ss_conf             00178887742025217775405777301599999999
Q gi|254780213|r   11 DIEVNSILKEEIDDISVVSLPLSDDNMTIDEEYLEKLV   48 (63)
Q Consensus        11 dievnsilkeeiddisvvslplsddnmtideeyleklv   48 (63)
                      -||....|..|--+..|||+|--+-=..-|++|++.+.
T Consensus       573 a~~a~~~L~~~~~kvrVVS~P~~~~f~~Qd~~Y~~svl  610 (675)
T TIGR00232       573 AVEAAKKLAAENIKVRVVSMPSFDLFDKQDEEYRESVL  610 (675)
T ss_pred             HHHHHHHHHHCCCCEEEEECCCHHHHHHCCHHHHHHHC
T ss_conf             99999999854985799965864666612289887307


No 3  
>pfam04487 CITED CITED. CITED, CBP/p300-interacting transactivator with ED-rich tail, are characterized by a conserved 32-amino acid sequence at the C-terminus. CITED proteins do not bind DNA directly and are thought to function as transcriptional co-activators.
Probab=36.04  E-value=27  Score=17.82  Aligned_cols=21  Identities=57%  Similarity=0.689  Sum_probs=17.1

Q ss_pred             CCCEECHHHHHHHHHH-HHHHH
Q ss_conf             7730159999999999-62322
Q gi|254780213|r   35 DNMTIDEEYLEKLVVE-SLDRS   55 (63)
Q Consensus        35 dnmtideeyleklvve-sldrs   55 (63)
                      |.--||||-|-.||+| .|||-
T Consensus       155 D~d~IDEEvL~SLv~ElGLdRv  176 (206)
T pfam04487       155 DTDLIDEEVLMSLVLELGLDRV  176 (206)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHH
T ss_conf             4431059999999999704776


No 4  
>cd01647 RT_LTR RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.
Probab=26.27  E-value=38  Score=16.97  Aligned_cols=29  Identities=31%  Similarity=0.447  Sum_probs=20.9

Q ss_pred             CCCCCCCCCEEEEHHHHHHHH--------CCCCEEEE
Q ss_conf             940101000000178887742--------02521777
Q gi|254780213|r    1 MGFITSLSKWDIEVNSILKEE--------IDDISVVS   29 (63)
Q Consensus         1 mgfitslskwdievnsilkee--------iddisvvs   29 (63)
                      ||+..|-+-|.--++.++.+.        +|||.+.|
T Consensus        98 ~Gl~~sp~~fq~~~~~~l~~~~~~~~~~Y~DDili~s  134 (177)
T cd01647          98 FGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYS  134 (177)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEC
T ss_conf             6565858999999999999876332024554289956


No 5  
>pfam07038 DUF1324 Protein of unknown function (DUF1324). This family consists of several Circovirus proteins of around 60 residues in length. The function of this family is unknown.
Probab=24.10  E-value=23  Score=18.13  Aligned_cols=22  Identities=50%  Similarity=0.952  Sum_probs=15.7

Q ss_pred             EEEEEECCCCCCEECHHHHHHHHHHHHHHHCCCC
Q ss_conf             1777540577730159999999999623220156
Q gi|254780213|r   26 SVVSLPLSDDNMTIDEEYLEKLVVESLDRSLRCN   59 (63)
Q Consensus        26 svvslplsddnmtideeyleklvvesldrslrcn   59 (63)
                      .|...|||..            |....||||||.
T Consensus        38 tvtriplsnk------------vltavdrslrcp   59 (59)
T pfam07038        38 TVTRIPLSNK------------VLTAVDRSLRCP   59 (59)
T ss_pred             EEEEEECCCH------------HHHHHHHCCCCC
T ss_conf             9887223422------------443530103597


No 6  
>TIGR00542 hxl6Piso_put hexulose-6-phosphate isomerase, putative; InterPro: IPR004560 This family shows similarity to other isomerases. Putative identification as hexulose-6-phosphate isomerase has been reported. This family is conserved at better than 40 0dentity among the four known examples from three species: Escherichia coli (SgbU and SgaU), Haemophilus influenzae, and Mycoplasma pneumoniae. The rarity of the family, high level of conservation, and proposed catabolic role suggests lateral transfer may be a part of the evolutionary history of this protein.; GO: 0016861 intramolecular oxidoreductase activity interconverting aldoses and ketoses, 0005975 carbohydrate metabolic process.
Probab=20.86  E-value=68  Score=15.65  Aligned_cols=27  Identities=37%  Similarity=0.562  Sum_probs=24.1

Q ss_pred             CCCCCCEEEEHHHHHHHHCCCCEEEEE
Q ss_conf             101000000178887742025217775
Q gi|254780213|r    4 ITSLSKWDIEVNSILKEEIDDISVVSL   30 (63)
Q Consensus         4 itslskwdievnsilkeeiddisvvsl   30 (63)
                      |-.||.|+-.|..=|+--||.|+-+.+
T Consensus       183 iGNLSaw~n~v~~El~lGid~I~a~H~  209 (290)
T TIGR00542       183 IGNLSAWSNDVEDELALGIDKIVAIHL  209 (290)
T ss_pred             CCCHHHCCCCHHHHHHHCCCCEEEEEE
T ss_conf             444101151069999718871888874


No 7  
>TIGR00683 nanA N-acetylneuraminate lyase; InterPro: IPR005264    N-acetylneuraminate lyase catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetyl-D-mannosamine. The enzyme plays an important role in the regulation of sialic acid metabolism in bacteria..
Probab=18.62  E-value=62  Score=15.88  Aligned_cols=36  Identities=33%  Similarity=0.445  Sum_probs=28.9

Q ss_pred             HHHHHHCCCCEEEEEECCCCCCE-ECHHHHHHHHHHH
Q ss_conf             88774202521777540577730-1599999999996
Q gi|254780213|r   16 SILKEEIDDISVVSLPLSDDNMT-IDEEYLEKLVVES   51 (63)
Q Consensus        16 silkeeiddisvvslplsddnmt-ideeyleklvves   51 (63)
                      .-+|+-..-+.+|+.|+...-|| +|+.|++.+....
T Consensus       250 ~~~K~~L~yl~~V~~~~CR~P~~Pvd~K~~~E~~A~A  286 (294)
T TIGR00683       250 LTLKELLKYLDVVDVGLCRKPFTPVDEKALEELKAKA  286 (294)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCHHHCCHHHHHHH
T ss_conf             8999999885124667678999852011147889999


No 8  
>pfam06837 Fijivirus_P9-2 Fijivirus P9-2 protein. This family consists of several Fijivirus specific P9-2 proteins from Rice black streaked dwarf virus (RBSDV) and Fiji disease virus. The function of this family is unknown.
Probab=15.76  E-value=33  Score=17.34  Aligned_cols=56  Identities=20%  Similarity=0.251  Sum_probs=38.2

Q ss_pred             CCCEEEEH-HHHHHHHCCCCEEEEEECCCCCCEECHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             00000017-888774202521777540577730159999999999623220156335
Q gi|254780213|r    7 LSKWDIEV-NSILKEEIDDISVVSLPLSDDNMTIDEEYLEKLVVESLDRSLRCNYEK   62 (63)
Q Consensus         7 lskwdiev-nsilkeeiddisvvslplsddnmtideeyleklvvesldrslrcnyek   62 (63)
                      |.|-.++. ..++.+--+..++...|+||....---|-||--|.+..|.-+|-+|.|
T Consensus        20 laKi~~~~~~~~m~~~snf~~ife~~~SDSelDd~vd~lE~~ve~~~~pl~~r~ygk   76 (214)
T pfam06837        20 LAKIRLQNIQNAMNEVTNFMVVFDVNFSDSELDDIVDTLETAVEDTPTPLFKRAYGK   76 (214)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHCCC
T ss_conf             889999864478875202588853567703677788888676772876888875267


No 9  
>pfam04792 LcrV V antigen (LcrV) protein. Yersinia pestis, the aetiologic agent of plague, secretes a set of environmentally regulated, plasmid pCD1-encoded virulence proteins termed Yops and V antigen (LcrV) by a type III secretion mechanism. LcrV is a multifunctional protein that has been shown to act at the level of secretion control by binding the Ysc inner-gate protein LcrG and to modulate the host immune response by altering cytokine production. LcrV is also necessary for full induction of low-calcium response (LCR) stimulon virulence gene transcription. Family members are not confined to Yersinia pestis.
Probab=12.02  E-value=1.4e+02  Score=14.00  Aligned_cols=40  Identities=38%  Similarity=0.442  Sum_probs=30.4

Q ss_pred             EHHHHHHHHCCCCEEEEEECCCCC------CEECHHHHHHHHHHHH
Q ss_conf             178887742025217775405777------3015999999999962
Q gi|254780213|r   13 EVNSILKEEIDDISVVSLPLSDDN------MTIDEEYLEKLVVESL   52 (63)
Q Consensus        13 evnsilkeeiddisvvslplsddn------mtideeyleklvvesl   52 (63)
                      |.-..|++++-+|+...-|++|.+      .|-+.+.|+|+..--|
T Consensus        34 eLv~Ll~~k~i~i~~~~dp~~d~~vf~~~vit~~~~LLkKllAyfl   79 (326)
T pfam04792        34 ELLALLKDENIDIAHAGDPLKDAEVFANRVITDDIELLKKILAYFL   79 (326)
T ss_pred             HHHHHHHCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             9999986167565126886432222113543124999999999857


No 10 
>TIGR01524 ATPase-IIIB_Mg magnesium-translocating P-type ATPase; InterPro: IPR006415   This group describes the magnesium translocating P-type ATPase found in a limited number of bacterial species and best described in Salmonella typhimurium, which contains two isoforms . These transporters are active in low external Mg2+ concentrations and pump the ion into the cytoplasm. The magnesium ATPases have been classified as type IIIB by a phylogenetic analysis .; GO: 0015444 magnesium-importing ATPase activity, 0015693 magnesium ion transport, 0016021 integral to membrane.
Probab=11.66  E-value=48  Score=16.46  Aligned_cols=26  Identities=38%  Similarity=0.773  Sum_probs=16.0

Q ss_pred             HHHHHCCCCEEEEEECCCCCCEECHHHHHH
Q ss_conf             877420252177754057773015999999
Q gi|254780213|r   17 ILKEEIDDISVVSLPLSDDNMTIDEEYLEK   46 (63)
Q Consensus        17 ilkeeiddisvvslplsddnmtideeylek   46 (63)
                      .+..=.-|+|-++||.  |||  |+|+|.|
T Consensus       725 LiQNLlYD~SQl~lPw--Dk~--D~efl~K  750 (892)
T TIGR01524       725 LIQNLLYDVSQLALPW--DKM--DKEFLKK  750 (892)
T ss_pred             HHHHHHHHHHHHCCCC--CCC--CHHHCCC
T ss_conf             9998887676530773--225--7886248


Done!