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!