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!