Query gi|254780963|ref|YP_003065376.1| hypothetical protein CLIBASIA_04320 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 215 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 03:06:42 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780963.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam05758 Ycf1 Ycf1. The chlor 53.7 7.5 0.00019 19.5 1.6 24 85-108 64-87 (832) 2 pfam09143 AvrPphF-ORF-2 AvrPph 42.3 12 0.00031 18.3 1.2 47 157-206 115-164 (175) 3 cd07079 ALDH_F18-19_ProA-GPR G 35.9 19 0.00049 17.1 1.4 12 45-56 78-89 (406) 4 COG0014 ProA Gamma-glutamyl ph 35.0 15 0.00039 17.7 0.8 32 112-143 353-388 (417) 5 TIGR00407 proA gamma-glutamyl 34.6 14 0.00036 17.9 0.5 34 111-144 361-398 (415) 6 TIGR02909 spore_YkwD uncharact 23.7 26 0.00068 16.3 0.4 80 27-127 22-118 (129) 7 TIGR02014 BchZ chlorophyllide 23.5 23 0.00059 16.7 0.1 37 104-142 279-316 (482) 8 pfam09353 DUF1995 Domain of un 20.0 40 0.001 15.3 0.7 18 139-156 166-183 (205) 9 pfam10783 DUF2599 Protein of u 19.5 38 0.00097 15.4 0.5 18 133-150 5-22 (94) 10 pfam06593 RBDV_coat Raspberry 18.7 32 0.00082 15.8 -0.0 36 79-114 38-77 (274) No 1 >pfam05758 Ycf1 Ycf1. The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Probab=53.70 E-value=7.5 Score=19.45 Aligned_cols=24 Identities=46% Similarity=0.790 Sum_probs=20.2 Q ss_pred HCCCCCHHHHHHHHHHHHHHHCCC Q ss_conf 228000023454566433320477 Q gi|254780963|r 85 IVNPTTMRVLVLPVLSMHKTWNNN 108 (215) Q Consensus 85 ivnpttmrvlvlpvlsmhktwnnn 108 (215) ...|.|+-||+||.|..|=-|||+ T Consensus 64 L~rPHtITvL~lPYllf~ff~~n~ 87 (832) T pfam05758 64 LGRPHTITVLALPYLLFHFFWNNH 87 (832) T ss_pred HCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 745533089999999999974066 No 2 >pfam09143 AvrPphF-ORF-2 AvrPphF-ORF-2. Members of this family of plant pathogenic proteins adopt an elongated structure somewhat reminiscent of a mushroom that can be divided into 'stalk' and 'head' subdomains. The stalk subdomain is composed of the N-terminal helix (alpha1) and beta strands beta3-beta4. An antiparallel beta sheet (beta5, beta7-beta8) forms the base of the head subdomain that interacts with the stalk. A pair of twisted antiparallel beta sheets (beta1 and beta6; beta2 and beta9/9') supported by alpha2 form the dome of the head. The head subdomain possesses weak structural similarity with the catalytic portion of a number of ADP-ribosyltransferase toxins. Probab=42.31 E-value=12 Score=18.30 Aligned_cols=47 Identities=47% Similarity=0.501 Sum_probs=35.9 Q ss_pred EEEEECC--CC-EEEEEEEEEEEEEEECCEEEEECHHHHHHHHHCCCCCCEEE Q ss_conf 0011056--76-79998630137775021001100246566541133432112 Q gi|254780963|r 157 FAIRHAS--SD-VVVCMRYQAKFLITDSIGILYRNVSAVSAAVDKNIGLGVTK 206 (215) Q Consensus 157 fairhas--sd-vvvcmryqakflitdsigilyrnvsavsaavdkniglgvtk 206 (215) -+||+-+ +| |+|-||.- .|| +.-|-.|-..|||++.-|+.+.|-||- T Consensus 115 ~~~r~Ya~~~dhV~v~MrlG-Dfl--e~GGkVy~D~sav~~~gd~~~aLIVTL 164 (175) T pfam09143 115 AGIRGYAHTSDHVVVKMRLG-DFL--EAGGKVYADTSAVSAGGDHTKALIVTL 164 (175) T ss_pred HCCCCCCCCCCEEEEEEEHH-HHH--HCCCEEEEECCCCCCCCCCEEEEEEEC T ss_conf 30423266788179998623-577--628848854222247987315699986 No 3 >cd07079 ALDH_F18-19_ProA-GPR Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19. Gamma-glutamyl phosphate reductase (GPR), a L-proline biosynthetic pathway (PBP) enzyme that catalyzes the NADPH dependent reduction of L-gamma-glutamyl 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The glutamate route of the PBP involves two enzymatic steps catalyzed by gamma-glutamyl kinase (GK, EC 2.7.2.11) and GPR (EC 1.2.1.41). These enzymes are fused into the bifunctional enzyme, ProA or delta(1)-pyrroline-5-carboxylate synthetase (P5CS) in plants and animals, whereas they are separate enzymes in bacteria and yeast. In humans, the P5CS (ALDH18A1), an inner mitochondrial membrane enzyme, is essential to the de novo synthesis of the amino acids proline and arginine. Tomato (Lycopersicon esculentum) has both the prokaryotic-like polycistronic operons encoding GK and GPR (PRO1, ALDH19) and the full-length, bifunctional P5CS (PRO2, ALDH18B1). Probab=35.90 E-value=19 Score=17.10 Aligned_cols=12 Identities=17% Similarity=0.515 Sum_probs=5.6 Q ss_pred HHHHHHCCCCEE Q ss_conf 634420357324 Q gi|254780963|r 45 SREISSYRTPLS 56 (215) Q Consensus 45 sreissyrtpls 56 (215) -|++..-..|+. T Consensus 78 l~~ia~l~DPvG 89 (406) T cd07079 78 LRQVAALPDPVG 89 (406) T ss_pred HHHHHHCCCCCC T ss_conf 999981899666 No 4 >COG0014 ProA Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism] Probab=34.97 E-value=15 Score=17.70 Aligned_cols=32 Identities=44% Similarity=0.680 Sum_probs=22.4 Q ss_pred HHHHHHH---CEEEEEECCCCCCCHH-HHHHCCCEE Q ss_conf 3465342---5013530366752000-012108158 Q gi|254780963|r 112 SYFFKKI---GVGVVASTGFNTGDKW-LGAEMGMSF 143 (215) Q Consensus 112 syffkki---gvgvvastgfntgdkw-lgaemgmsf 143 (215) .+|+..+ .|-|-|||-|..|-.+ +|||+|+|- T Consensus 353 ~~F~~~VDSAaVyvNASTRFtDG~~fG~GaEiGIST 388 (417) T COG0014 353 ERFVNEVDSAAVYVNASTRFTDGGQFGLGAEIGIST 388 (417) T ss_pred HHHHHHCCHHEEEEECCCCCCCCCCCCCCEEEEEEC T ss_conf 999962361148972465545676555754888633 No 5 >TIGR00407 proA gamma-glutamyl phosphate reductase; InterPro: IPR000965 Gamma-glutamyl phosphate reductase (1.2.1.41 from EC) (GPR) is the enzyme that catalyzes the second step in the biosynthesis of proline from glutamate, the NADP-dependent reduction of L-glutamate 5-phosphate into L-glutamate 5-semialdehyde and phosphate. In bacteria (gene proA) and yeast (gene PRO2), GPR is a monofunctional protein, while in plants and mammals, it is a bifunctional enzyme (P5CS) that consists of two domains, an N-terminal glutamate 5-kinase domain (2.7.2.11 from EC) and a C-terminal GPR domain. ; GO: 0004350 glutamate-5-semialdehyde dehydrogenase activity, 0006561 proline biosynthetic process. Probab=34.55 E-value=14 Score=17.89 Aligned_cols=34 Identities=35% Similarity=0.508 Sum_probs=26.8 Q ss_pred HHHHHHHH---CEEEEEECCCCCCCHH-HHHHCCCEEE Q ss_conf 13465342---5013530366752000-0121081588 Q gi|254780963|r 111 DSYFFKKI---GVGVVASTGFNTGDKW-LGAEMGMSFY 144 (215) Q Consensus 111 dsyffkki---gvgvvastgfntgdkw-lgaemgmsfy 144 (215) -.+|.+.+ ||=+-|||-|.-|-++ +|||.|.|-- T Consensus 361 A~~F~~~VDsaaVY~NASTRFtDGf~fG~GAEVgiSTq 398 (415) T TIGR00407 361 AEQFVNEVDSAAVYHNASTRFTDGFRFGFGAEVGISTQ 398 (415) T ss_pred HHHHHHHCCCCCEEECCCCEECCCCCCCCCEEEEEECC T ss_conf 99997310303022255101147762566006621136 No 6 >TIGR02909 spore_YkwD uncharacterized protein, YkwD family; InterPro: IPR014258 This entry represents a subgroup of the SCP-like extracellular domain which is found only in bacteria capable of endospore formation. Proteins in this entry include YkwD of Bacillus subtilis. This domain is generally found at the C-terminal region of these proteins, while the N-terminal region sometimes contains a domain homologous to the spore coat assembly protein SafA (IPR014248 from INTERPRO).. Probab=23.72 E-value=26 Score=16.33 Aligned_cols=80 Identities=30% Similarity=0.453 Sum_probs=44.2 Q ss_pred HCEEEEHHHHHH------HHHHH--HHHHHHHCCCCEEEEECCCEEEEEEEEEEEEE-EEC-HHHHHHH-CCCCCHHHHH Q ss_conf 000100899999------99998--66344203573244302201588864103677-631-5777522-2800002345 Q gi|254780963|r 27 DELKVNFGLMRR------VMIDL--WSREISSYRTPLSLDLDYKHRVYLDTYKSFSI-NLG-FETFNEI-VNPTTMRVLV 95 (215) Q Consensus 27 delkvnfglmrr------vmidl--wsreissyrtplsldldykhrvyldtyksfsi-nlg-fetfnei-vnpttmrvlv 95 (215) .-||+|-.|.|- -|+|. .|.+=..|-.|-++ -|.|-| +-- ---=|=- .|+|.-+ T Consensus 22 ~PLk~d~~L~~vARlKs~DM~d~nYFsH~SPTYGSPF~M------------mk~FGik~Y~W~AGENIA~G~~T~~~--- 86 (129) T TIGR02909 22 KPLKADEELSKVARLKSEDMIDKNYFSHTSPTYGSPFDM------------MKKFGIKSYRWAAGENIAAGNSTVEA--- 86 (129) T ss_pred CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHH------------HHHCCCCCCHHHHHHHHHHCCCCHHH--- T ss_conf 800017477888637468510078998888899971689------------98646643102323543304877889--- Q ss_pred HHHHHHHHHHCC------CCCHHHHHHHHCEEEEEECC Q ss_conf 456643332047------77313465342501353036 Q gi|254780963|r 96 LPVLSMHKTWNN------NFDDSYFFKKIGVGVVASTG 127 (215) Q Consensus 96 lpvlsmhktwnn------nfddsyffkkigvgvvastg 127 (215) .|+.|=| |-=+.. |.+||||+|.+-- T Consensus 87 -----v~~awMNS~GHRaNIL~p~-yt~IGVG~v~~g~ 118 (129) T TIGR02909 87 -----VHQAWMNSPGHRANILNPN-YTEIGVGYVEGGS 118 (129) T ss_pred -----HHHHHCCCHHHHHCCCCCC-CCEEEEEEEECCC T ss_conf -----9853058720222268898-8711257750688 No 7 >TIGR02014 BchZ chlorophyllide reductase subunit Z; InterPro: IPR010244 This entry represents the Z subunit of the three-subunit enzyme, bacteriochlorophyllide reductase , . This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase.; GO: 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0030494 bacteriochlorophyll biosynthetic process. Probab=23.55 E-value=23 Score=16.66 Aligned_cols=37 Identities=30% Similarity=0.575 Sum_probs=29.7 Q ss_pred HHCCCCCHHHHHHHHCEEEEEECCCCCCCH-HHHHHCCCE Q ss_conf 204777313465342501353036675200-001210815 Q gi|254780963|r 104 TWNNNFDDSYFFKKIGVGVVASTGFNTGDK-WLGAEMGMS 142 (215) Q Consensus 104 twnnnfddsyffkkigvgvvastgfntgdk-wlgaemgms 142 (215) -|..- .+-||-.+.-||||+..+..|=| .|+.||||. T Consensus 279 LWRs~--~~~fFgT~~FGivA~~~Ya~Gi~~~L~~elGl~ 316 (482) T TIGR02014 279 LWRSV--TQDFFGTARFGIVASETYARGIRHVLEDELGLP 316 (482) T ss_pred HCCCC--CCCCCCCCEECEEECHHHHHHHHHHHCCCCCCC T ss_conf 12677--633456510011321146676787511024751 No 8 >pfam09353 DUF1995 Domain of unknown function (DUF1995). This family of proteins are functionally uncharacterized. Probab=19.97 E-value=40 Score=15.29 Aligned_cols=18 Identities=39% Similarity=0.947 Sum_probs=15.0 Q ss_pred CCCEEEEECCCEEEEECC Q ss_conf 081588705624777313 Q gi|254780963|r 139 MGMSFYVYPTPWLILQSD 156 (215) Q Consensus 139 mgmsfyvyptpwlilqsd 156 (215) .|.-|..||-||-+..-+ T Consensus 166 ~gal~r~yP~~W~v~~~~ 183 (205) T pfam09353 166 GGALFRCYPGPWQLFKED 183 (205) T ss_pred CEEEEEECCCCCEEEEEE T ss_conf 758999579874799981 No 9 >pfam10783 DUF2599 Protein of unknown function (DUF2599). This family is conserved in Actinobacteria. The function is not known. Probab=19.55 E-value=38 Score=15.43 Aligned_cols=18 Identities=33% Similarity=0.348 Sum_probs=0.0 Q ss_pred HHHHHHCCCEEEEECCCE Q ss_conf 000121081588705624 Q gi|254780963|r 133 KWLGAEMGMSFYVYPTPW 150 (215) Q Consensus 133 kwlgaemgmsfyvyptpw 150 (215) .|.-.+-+.|.-|||||| T Consensus 5 ~W~~~~~~~sL~V~PT~~ 22 (94) T pfam10783 5 TWAQWGDLWSLRVYPTDA 22 (94) T ss_pred EEEECCCCCCEEEECCHH T ss_conf 521227876148825367 No 10 >pfam06593 RBDV_coat Raspberry bushy dwarf virus coat protein. This family consists of several Raspberry bushy dwarf virus coat proteins. Probab=18.71 E-value=32 Score=15.85 Aligned_cols=36 Identities=36% Similarity=0.553 Sum_probs=0.0 Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHH----HHHCCCCCHHHH Q ss_conf 577752228000023454566433----320477731346 Q gi|254780963|r 79 FETFNEIVNPTTMRVLVLPVLSMH----KTWNNNFDDSYF 114 (215) Q Consensus 79 fetfneivnpttmrvlvlpvlsmh----ktwnnnfddsyf 114 (215) |..|.|-.||.|-.-.----.|.. .||-.|||.+|+ T Consensus 38 f~gfse~~~p~tgkp~~dmsmsakvkrvntwlknfdr~yw 77 (274) T pfam06593 38 FVGFSEGSNPATGKPHADMSMSAKVKRVNTWLKNFDREYW 77 (274) T ss_pred EECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCHHHH T ss_conf 0222456786679974321045658888889874357776 Done!