Query gi|254780990|ref|YP_003065403.1| hypothetical protein CLIBASIA_04455 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 66 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 02:40:11 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780990.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK06813 homoserine dehydrogen 49.2 24 0.00061 18.1 3.6 63 4-66 241-307 (341) 2 KOG2130 consensus 36.1 16 0.00042 18.9 1.1 21 6-26 157-177 (407) 3 pfam07991 IlvN Acetohydroxy ac 33.1 50 0.0013 16.4 3.2 41 1-42 65-105 (165) 4 PRK06270 homoserine dehydrogen 22.6 82 0.0021 15.4 3.1 62 4-66 244-306 (342) 5 TIGR01437 selA_rel pyridoxal p 17.6 55 0.0014 16.2 0.9 22 13-34 195-216 (391) 6 KOG3175 consensus 16.4 9.7 0.00025 20.1 -3.2 51 12-62 64-114 (366) 7 pfam08304 consensus 12.8 80 0.002 15.4 0.7 23 9-31 180-202 (378) 8 TIGR01501 MthylAspMutase methy 12.5 1.2E+02 0.003 14.6 1.5 26 23-50 51-76 (134) 9 TIGR02974 phageshock_pspF psp 11.6 53 0.0013 16.3 -0.5 20 28-47 43-62 (349) 10 pfam08411 Exonuc_X-T_C Exonucl 11.0 1.4E+02 0.0036 14.1 1.5 33 22-54 13-45 (268) No 1 >PRK06813 homoserine dehydrogenase; Validated Probab=49.20 E-value=24 Score=18.10 Aligned_cols=63 Identities=14% Similarity=0.300 Sum_probs=48.4 Q ss_pred CCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCEEE----EEEEEHHHHHCCCCCCCCCCCCEEEEEC Q ss_conf 45643456777554541389521898650222134----5441052210076520002463465429 Q gi|254780990|r 4 VPDDGIDDLFEEDLFQYDANKSELVLISSLWSIDF----FEINCALLRRRHPINKYEKTDNFFALYT 66 (66) Q Consensus 4 vpddgiddlfeedlfqydankselvlisslwsidf----feincallrrrhpinkyektdnffalyt 66 (66) |+-.||+.+..+|+-+-.+....+-|+.+..-.+- ..+.-.++.+-||+..-+-++|.+.++| T Consensus 241 v~~~GI~~i~~~di~~A~~~g~~iklva~~~~~~~g~~~~~V~p~~v~~~~pla~v~g~~N~v~i~t 307 (341) T PRK06813 241 IHIKGIEHVTKQQIRNAKEQNKIIKLIASAYKDNEGNVNLNVEPYKIEKNHPLANVNGTEKGITFFT 307 (341) T ss_pred CCCCCHHHHCHHHHHHHHHCCCEEEEEEEEEECCCCEEEEEEEEEEECCCCCCEECCCCCEEEEEEE T ss_conf 0116722309999999997799699999999726974999999999589995520579847999971 No 2 >KOG2130 consensus Probab=36.13 E-value=16 Score=18.94 Aligned_cols=21 Identities=33% Similarity=0.640 Sum_probs=16.2 Q ss_pred CCCHHHHHHHHHHHHCCCCCE Q ss_conf 643456777554541389521 Q gi|254780990|r 6 DDGIDDLFEEDLFQYDANKSE 26 (66) Q Consensus 6 ddgiddlfeedlfqydankse 26 (66) |-.+-.+|++|||||-.+++. T Consensus 157 dY~VPk~F~dDlF~y~g~e~R 177 (407) T KOG2130 157 DYSVPKYFRDDLFQYLGEERR 177 (407) T ss_pred HCCCCHHHHHHHHHHCCCCCC T ss_conf 047533456779986074669 No 3 >pfam07991 IlvN Acetohydroxy acid isomeroreductase, catalytic domain. Acetohydroxy acid isomeroreductase catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine. Probab=33.10 E-value=50 Score=16.44 Aligned_cols=41 Identities=22% Similarity=0.413 Sum_probs=31.2 Q ss_pred CEECCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEEE Q ss_conf 933456434567775545413895218986502221345441 Q gi|254780990|r 1 MFLVPDDGIDDLFEEDLFQYDANKSELVLISSLWSIDFFEIN 42 (66) Q Consensus 1 mflvpddgiddlfeedlfqydankselvlisslwsidffein 42 (66) |+|+||...-++++++...+-...+-| ..+.=.+|.|-.|. T Consensus 65 m~L~PD~~q~~iy~~~I~p~lk~G~~L-~FaHGFnI~y~~I~ 105 (165) T pfam07991 65 MILLPDEVQAEVYEKEIAPNLKEGAAL-AFAHGFNIHFGQIK 105 (165) T ss_pred EEECCCHHHHHHHHHHHHHHCCCCCEE-EECCCCEEEECCEE T ss_conf 983797778999999898657899779-97157577741076 No 4 >PRK06270 homoserine dehydrogenase; Provisional Probab=22.55 E-value=82 Score=15.38 Aligned_cols=62 Identities=21% Similarity=0.174 Sum_probs=44.0 Q ss_pred CCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCE-EEEEEEEHHHHHCCCCCCCCCCCCEEEEEC Q ss_conf 456434567775545413895218986502221-345441052210076520002463465429 Q gi|254780990|r 4 VPDDGIDDLFEEDLFQYDANKSELVLISSLWSI-DFFEINCALLRRRHPINKYEKTDNFFALYT 66 (66) Q Consensus 4 vpddgiddlfeedlfqydankselvlisslwsi-dffeincallrrrhpinkyektdnffalyt 66 (66) |+-.||+++..+|+-+-.....-+-+|.+.-.- .-.++.-.++...||+. -.-++|.+.++| T Consensus 244 v~~~gI~~i~~~di~~A~~~G~~iklva~~~~~~~~~~V~p~~v~~~~pla-v~g~~N~i~i~t 306 (342) T PRK06270 244 VEVTGITRITPEAIRLAAKEGYRIKLIGEVSREADKLSVSPRLVPIGHPLA-VSGTLNAATFET 306 (342) T ss_pred CCCCCCCCCCHHHHHHHHHCCCEEEEEEEEECCCCEEEEEEEEECCCCCEE-ECCCCEEEEEEE T ss_conf 034785659999999999879969999999978988999989988999324-789857999984 No 5 >TIGR01437 selA_rel pyridoxal phosphate-dependent enzyme, putative; InterPro: IPR006337 Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy . PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic . This entry represents a group of proteins that are related to a number of pyridoxal phosphate-dependent enzymes, and in particular to selenocysteine synthase (SelA), which converts Ser to selenocysteine on its tRNA. While resembling SelA, this protein is found only in species that have a better candidate SelA or else lack the other genes (selB, selC, and selD) required for selenocysteine incorporation. . Probab=17.56 E-value=55 Score=16.24 Aligned_cols=22 Identities=36% Similarity=0.374 Sum_probs=18.8 Q ss_pred HHHHHHHHCCCCCEEEEEEECC Q ss_conf 7755454138952189865022 Q gi|254780990|r 13 FEEDLFQYDANKSELVLISSLW 34 (66) Q Consensus 13 feedlfqydankselvlisslw 34 (66) -||||+.|-+.-+.||+-|.-- T Consensus 195 P~edL~~y~~~GaDlViYSGaK 216 (391) T TIGR01437 195 PEEDLTRYLKAGADLVIYSGAK 216 (391) T ss_pred CHHHHHHHHHHCCCEEEECCHH T ss_conf 8014689997168755532034 No 6 >KOG3175 consensus Probab=16.44 E-value=9.7 Score=20.08 Aligned_cols=51 Identities=22% Similarity=0.167 Sum_probs=37.4 Q ss_pred HHHHHHHHHCCCCCEEEEEEECCCEEEEEEEEHHHHHCCCCCCCCCCCCEE Q ss_conf 777554541389521898650222134544105221007652000246346 Q gi|254780990|r 12 LFEEDLFQYDANKSELVLISSLWSIDFFEINCALLRRRHPINKYEKTDNFF 62 (66) Q Consensus 12 lfeedlfqydankselvlisslwsidffeincallrrrhpinkyektdnff 62 (66) --.+|.|||+.-|+.+.-|-.+|.+--|-+.--+----||-..|+++|.|. T Consensus 64 ~pn~d~~~y~~~k~~~~~~~~~~n~~~~t~~~~~e~li~p~~nv~~~dk~~ 114 (366) T KOG3175 64 NPNVDYIPYDEMKERILKIVTGFNGIPFTIQRLCELLIDPRRNVTGTDKFL 114 (366) T ss_pred CCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHH T ss_conf 998772127889876622424303788899998787427222657214666 No 7 >pfam08304 consensus Probab=12.82 E-value=80 Score=15.42 Aligned_cols=23 Identities=39% Similarity=0.622 Sum_probs=19.0 Q ss_pred HHHHHHHHHHHHCCCCCEEEEEE Q ss_conf 45677755454138952189865 Q gi|254780990|r 9 IDDLFEEDLFQYDANKSELVLIS 31 (66) Q Consensus 9 iddlfeedlfqydankselvlis 31 (66) -||-|||....|+..++-|-|-. T Consensus 180 CDD~FEEHVL~Y~~~~aGLyLHG 202 (378) T pfam08304 180 CDDSFEEHILPYPKDKAGLYLHG 202 (378) T ss_pred CCCCHHHHHCCCCHHHCCEEEEC T ss_conf 07517765347890104234301 No 8 >TIGR01501 MthylAspMutase methylaspartate mutase, S subunit; InterPro: IPR006394 These sequences represent the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation. ; GO: 0016866 intramolecular transferase activity, 0019670 anaerobic glutamate catabolic process. Probab=12.54 E-value=1.2e+02 Score=14.59 Aligned_cols=26 Identities=38% Similarity=0.621 Sum_probs=20.7 Q ss_pred CCCEEEEEEECCCEEEEEEEEHHHHHCC Q ss_conf 9521898650222134544105221007 Q gi|254780990|r 23 NKSELVLISSLWSIDFFEINCALLRRRH 50 (66) Q Consensus 23 nkselvlisslwsidffeincallrrrh 50 (66) .+..-+|+|||+-- =+|.|+=||.|- T Consensus 51 t~ADAilvSSlYGh--g~~DC~Glr~~c 76 (134) T TIGR01501 51 TDADAILVSSLYGH--GEIDCAGLRDKC 76 (134) T ss_pred CCCCEEEEECCCCC--CCCCHHHHHHHH T ss_conf 89988998302078--000124578999 No 9 >TIGR02974 phageshock_pspF psp operon transcriptional activator PspF; InterPro: IPR014317 Members of this protein are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, found in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol and filamentous phage infection.. Probab=11.63 E-value=53 Score=16.35 Aligned_cols=20 Identities=30% Similarity=0.652 Sum_probs=16.8 Q ss_pred EEEEECCCEEEEEEEEHHHH Q ss_conf 98650222134544105221 Q gi|254780990|r 28 VLISSLWSIDFFEINCALLR 47 (66) Q Consensus 28 vlisslwsidffeincallr 47 (66) -..|+=|.-.|...|||-|- T Consensus 43 HyLS~RW~~Plv~LNCAALs 62 (349) T TIGR02974 43 HYLSKRWQQPLVKLNCAALS 62 (349) T ss_pred HHHHHHHCCCCEEEECCCCC T ss_conf 33246554886266101278 No 10 >pfam08411 Exonuc_X-T_C Exonuclease C-terminal. This bacterial domain is found at the C-terminus of Exodeoxyribonuclease I/Exonuclease I (pfam00929), which is a single-strand specific DNA nuclease affecting recombination and expression pathways. The exonuclease I protein in E. coli is associated with DNA deoxyribophosphodiesterase (dRPase). Probab=11.00 E-value=1.4e+02 Score=14.14 Aligned_cols=33 Identities=24% Similarity=0.236 Sum_probs=0.0 Q ss_pred CCCCEEEEEEECCCEEEEEEEEHHHHHCCCCCC Q ss_conf 895218986502221345441052210076520 Q gi|254780990|r 22 ANKSELVLISSLWSIDFFEINCALLRRRHPINK 54 (66) Q Consensus 22 ankselvlisslwsidffeincallrrrhpink 54 (66) .+..-+|.||+..+-...-+.+.+---.||.|| T Consensus 13 ~~~~P~vhvSg~~~a~~~~~s~v~Pla~HP~N~ 45 (268) T pfam08411 13 VAMKPLVHVSGMFGAERGCTSWVLPLAWHPTNK 45 (268) T ss_pred CCCCCEEEECCCCCCCCCCEEEEEECCCCCCCC T ss_conf 789966987686641148837887513589998 Done!