RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780659|ref|YP_003065072.1| hypothetical protein CLIBASIA_02730 [Candidatus Liberibacter asiaticus str. psy62] (274 letters) >gnl|CDD|161802 TIGR00282, TIGR00282, metallophosphoesterase, MG_246/BB_0505 family. A member of this family from Mycoplasma Pneumoniae has been crystallized and described as a novel phosphatase. Length = 266 Score = 261 bits (669), Expect = 1e-70 Identities = 107/262 (40%), Positives = 148/262 (56%), Gaps = 5/262 (1%) Query: 1 MRLLFLGDIVGKTGRSIVYEMLPRLIRDFQLDFVIANGENSAGGFGITEKIFCEMMETGI 60 ++ LF+GD+ GK GR IV LP+L +Q D VIANGEN+ G G+T KI+ + ++G+ Sbjct: 1 IKFLFIGDVYGKAGRKIVKNNLPQLKSKYQADLVIANGENTTHGKGLTLKIYEFLKQSGV 60 Query: 61 DVITTGNHVWDKREALVFSQRHCKFLRPANYPPNTPGNGSGLYCAKNGSNVLVANIMGRV 120 + IT GNH W ++ L +RP N+ + G GS L NG+ + V N+ G Sbjct: 61 NYITMGNHTWFQKLILDVVINQKDLVRPLNFDTSFAGKGS-LVFEFNGAKIAVTNLQGTS 119 Query: 121 F-MNPLLDDPFRTADKILATCPLKEQADVIVFDFHAETTSEKQCFAHFVDSRASLVVGTH 179 + +PF+ +++ LK+ D+I DFHAETTSEK F D + VVGTH Sbjct: 120 VNLPFKTTNPFKVLKELINM--LKKDCDLIFVDFHAETTSEKNAFGMAFDGYVTAVVGTH 177 Query: 180 THIPTADAQILDGGTGYITDLGMCGDYNSSIGLDKEEPINRFITQIPRNRFVIANGPATL 239 TH+PTAD +IL GT YITD+GM G + S IG + E+ I F T P RF ++ L Sbjct: 178 THVPTADLRILPKGTAYITDVGMTGPFGSVIGANPEQSIKLFCTGSPE-RFEVSECGTQL 236 Query: 240 CGICAEISDVTGLAEKIAPIRI 261 G+ E+ T A KI IRI Sbjct: 237 NGVFIEVDVKTKKAVKIERIRI 258 >gnl|CDD|150300 pfam09587, PGA_cap, Bacterial capsule synthesis protein PGA_cap. This protein is a putative poly-gamma-glutamate capsule biosynthesis protein found in bacteria. Poly-gamma-glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein. Length = 237 Score = 44.9 bits (107), Expect = 2e-05 Identities = 40/217 (18%), Positives = 63/217 (29%), Gaps = 37/217 (17%) Query: 2 RLLFLGDIVGKTGRSIVYEMLPRLIRDF---------QLDFVIANGENSAGG-------- 44 L F+GD++ GR + P D I N E Sbjct: 1 TLAFVGDVM--LGRGLDQIAPPYDFDYPFADVKPLLRAADLAIGNLETPITDSGEPYSGK 58 Query: 45 --FGITEKIFCEMMETGIDVITTG-NHVWD-KREALVFSQRHCK--FLRPANYPPNTPGN 98 F + + G DV++ NH D E L+ + + A N Sbjct: 59 PAFRAPPENAEALKAAGFDVVSLANNHSLDYGEEGLLDTLDALDRAGIAHAGAGRNLEEA 118 Query: 99 GSGLYCAKNGSNVLVANIMGRVFMNPLLDDPFRTADKILATCP-----LKEQADVIVFDF 153 NG + K++AD+++ Sbjct: 119 RRPAILEVNGIRIAFLAYTYGTNGWGAGPYRPGVNPLDEEKIKADIRRAKKKADIVIVSL 178 Query: 154 HA------ETTSEKQCFAHF-VDSRASLVVGTHTHIP 183 H E T E++ AH +D+ A LV+G H H+ Sbjct: 179 HWGVEYQYEPTPEQRELAHALIDAGADLVIGHHPHVL 215 >gnl|CDD|129087 smart00854, PGA_cap, Bacterial capsule synthesis protein PGA_cap. This protein is a putative poly-gamma-glutamate capsule biosynthesis protein found in bacteria. Poly-gamma-glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein. Length = 239 Score = 44.9 bits (107), Expect = 2e-05 Identities = 52/222 (23%), Positives = 80/222 (36%), Gaps = 45/222 (20%) Query: 2 RLLFLGDI-----VGKTGRSIVYEMLPRLIRDFQLDFVIAN--------GENSAGGFGIT 48 L F+GD+ V K S + + L+R D I N G ++G Sbjct: 1 TLSFVGDVMLGRGVYKADFSPPFAGVKPLLR--AADLAIGNLETPITGSGSPASGKKYPN 58 Query: 49 ----EKIFCEMMETGIDVITTG-NHVWDK-REALVFSQRHCK-----------FLRPANY 91 + + G DV++ NH D E L+ + L A Sbjct: 59 FRAPPENAAALKAAGFDVVSLANNHSLDYGEEGLLDTLAALDAAGIAHVGAGRNLAEARK 118 Query: 92 PP--NTPGNGSGLYCAKNGSNVLVANIMGRVFMNPLLDDPFRTADKILAT-CPLKEQADV 148 P G L G+N A R + L P +KILA +++ADV Sbjct: 119 PAIVEVKGIKIALLAYTYGTNNGWAASKDRPGVALL---PDLDREKILADIARARKKADV 175 Query: 149 IVFDFH------AETTSEKQCFAH-FVDSRASLVVGTHTHIP 183 ++ H E T E++ AH +D+ A +V+G H H+ Sbjct: 176 VIVSLHWGVEYQYEPTDEQRELAHALIDAGADVVIGHHPHVL 217 >gnl|CDD|180168 PRK05621, PRK05621, F0F1 ATP synthase subunit gamma; Validated. Length = 284 Score = 30.5 bits (70), Expect = 0.49 Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 3/20 (15%) Query: 194 TGYI---TDLGMCGDYNSSI 210 GYI +D G+CG YNS+I Sbjct: 75 VGYIVVTSDRGLCGGYNSNI 94 >gnl|CDD|180023 PRK05335, PRK05335, tRNA (uracil-5-)-methyltransferase Gid; Reviewed. Length = 436 Score = 29.3 bits (67), Expect = 1.1 Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 5/47 (10%) Query: 218 INRFITQIPRNRFVIANGPATLCGICAEISDVTG---LA--EKIAPI 259 I +T+IP + +IA GP T + I +TG L + API Sbjct: 118 IREEVTEIPEDITIIATGPLTSDALAEAIKALTGEDYLYFFDAAAPI 164 >gnl|CDD|181944 PRK09549, mtnW, 2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed. Length = 407 Score = 28.1 bits (63), Expect = 2.7 Identities = 12/24 (50%), Positives = 15/24 (62%), Gaps = 4/24 (16%) Query: 21 MLPRLIRDFQLDFVIANGENSAGG 44 ++P LIRDF D VI N+ GG Sbjct: 337 LVPLLIRDFGKDVVI----NAGGG 356 >gnl|CDD|178946 PRK00249, flgH, flagellar basal body L-ring protein; Reviewed. Length = 222 Score = 27.9 bits (63), Expect = 2.8 Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 2/22 (9%) Query: 178 THTHIPTADAQILDGGTGYITD 199 + T I ADA+I GG GYI+D Sbjct: 186 SSTRI--ADARISYGGRGYISD 205 >gnl|CDD|132235 TIGR03191, benz_CoA_bzdO, benzoyl-CoA reductase, bzd-type, O subunit. Members of this family are the O subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene. Length = 430 Score = 28.0 bits (62), Expect = 2.9 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 3/61 (4%) Query: 16 SIVYEMLPRLIRDFQLDFVIANGENSAGGF--GITEKIFCEMMETGIDVITTGNHVWDKR 73 I EM+ + RD+ +D + + G GI E + + GI ++T ++ D+R Sbjct: 347 RIKSEMMLNIARDWNVDGCMLHLNRGCEGLSIGIMENRLA-IAKAGIPIMTFEGNMGDER 405 Query: 74 E 74 E Sbjct: 406 E 406 >gnl|CDD|162225 TIGR01146, ATPsyn_F1gamma, ATP synthase, F1 gamma subunit. This model describes the ATP synthase gamma subunit in bacteria and its equivalents in organelles, namely, mitochondria and chloroplast. F1/F0-ATP synthase is a multisubunit, membrane associated enzyme found in bacteria and organelles of higher eukaryotes, namely, mitochondria and chloroplast. This enzyme is principally involed in the synthesis of ATP from ADP and inorganic phosphate by coupling the energy derived from the proton electrochemical gradient across the biological membrane. A brief description of this multisubunit enzyme complex: F1 and F0 represent two major clusters of subunits. The gamma subunit is the part of F1 cluster. Surrounding the gamma subunit in a cylinder-like structure are three alpha and three subunits in an alternating fashion. This is the central catalytic unit whose different conformations permit the binding of ADP and inorganic phosphate and release of ATP. Length = 287 Score = 27.6 bits (62), Expect = 3.5 Identities = 8/20 (40%), Positives = 13/20 (65%), Gaps = 3/20 (15%) Query: 194 TGYI---TDLGMCGDYNSSI 210 G + +D G+CG YNS++ Sbjct: 76 VGILVITSDRGLCGGYNSNV 95 >gnl|CDD|162183 TIGR01063, gyrA, DNA gyrase, A subunit. This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Length = 800 Score = 26.9 bits (60), Expect = 5.6 Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 6/43 (13%) Query: 7 GDIVGK---TGRSIVYEMLPRLIRDFQLDFVIANGENSAGGFG 46 GD++GK G S +Y+ L R+ +DF L + + +G+ G FG Sbjct: 64 GDVMGKYHPHGDSAIYDTLVRMAQDFSLRYPLVDGQ---GNFG 103 >gnl|CDD|172371 PRK13845, PRK13845, putative glycerol-3-phosphate acyltransferase PlsX; Provisional. Length = 437 Score = 26.7 bits (59), Expect = 5.9 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 5/63 (7%) Query: 69 VWDKREALVFSQRHCKFLRPANYPPNTPGNGSGLYCAKNGSNVLVANIMGRVFMNPLLDD 128 +W +R + V S + A + GN +G + GS V A + + + PL+ D Sbjct: 18 IWYRRNSAVTS-----LVDTAASSASAAGNVAGTVVSSAGSVVSTAGSIAKSTLQPLVFD 72 Query: 129 PFR 131 P R Sbjct: 73 PLR 75 >gnl|CDD|129243 TIGR00137, gid_trmFO, tRNA:m(5)U-54 methyltransferase. This model represents an orthologous set of proteins present in relatively few bacteria but very tightly conserved where it occurs. It is closely related to gidA (glucose-inhibited division protein A), which appears to be present in all complete eubacterial genomes so far and in Saccharomyces cerevisiae. It was designated gid but is now recognized as a tRNA:m(5)U-54 methyltransferase and is now designated trmFO. Length = 433 Score = 26.8 bits (59), Expect = 6.3 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 6/51 (11%) Query: 218 INRFITQIPRNRF-VIANGPATLCGICAEISDVTGLA-----EKIAPIRIG 262 I +T+IP VIA GP T + ++ ++TG+ + API G Sbjct: 116 IREEVTEIPEEGITVIATGPLTSPALSEDLKELTGMDYLYFYDAAAPIVEG 166 >gnl|CDD|181482 PRK08575, PRK08575, 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional. Length = 326 Score = 26.6 bits (59), Expect = 6.5 Identities = 9/24 (37%), Positives = 12/24 (50%) Query: 48 TEKIFCEMMETGIDVITTGNHVWD 71 T++ F + GID T G WD Sbjct: 42 TKRFFELAKDVGIDYTTDGLFRWD 65 >gnl|CDD|182501 PRK10503, PRK10503, multidrug efflux system subunit MdtB; Provisional. Length = 1040 Score = 26.6 bits (59), Expect = 7.0 Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 12/34 (35%) Query: 3 LLFLGDIVGKTGRSIVYEMLPRLIRDFQLDFVIA 36 LLF+GDIVG RL R+F + +A Sbjct: 458 LLFMGDIVG------------RLFREFAVTLAVA 479 >gnl|CDD|132254 TIGR03210, badI, 2-ketocyclohexanecarboxyl-CoA hydrolase. Members of this protein family are 2-ketocyclohexanecarboxyl-CoA hydrolase, a ring-opening enzyme that acts in catabolism of molecules such as benzoyl-CoA and cyclohexane carboxylate. It converts -ketocyclohexanecarboxyl-CoA to pimelyl-CoA. It is not sensitive to oxygen. Length = 256 Score = 26.4 bits (58), Expect = 8.3 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 14/79 (17%) Query: 204 GDYNS--SIGLDKEEPINRFITQIPR------NRFVIANGPATLCGICAEISDVTGLAEK 255 G Y+ +IGL EE ++ I +P+ + I G L IC D+T +EK Sbjct: 71 GGYDGRGTIGLPMEE-LHSAIRDVPKPVIARVQGYAIGGG-NVLVTIC----DLTIASEK 124 Query: 256 IAPIRIGPRLSETRPDFWT 274 ++GP++ P + T Sbjct: 125 AQFGQVGPKVGSVDPGYGT 143 >gnl|CDD|180326 PRK05954, PRK05954, precorrin-8X methylmutase; Provisional. Length = 203 Score = 26.2 bits (58), Expect = 8.5 Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 5/39 (12%) Query: 220 RFITQIPRNRFVIANGPATLCGICAEISDVTGLAEKIAP 258 + Q P +VI N P L +C +I A ++ P Sbjct: 115 KCAQQYPEAIYVIGNAPTALLALCQQIR-----AGRVKP 148 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.323 0.141 0.434 Gapped Lambda K H 0.267 0.0628 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,574,714 Number of extensions: 291498 Number of successful extensions: 520 Number of sequences better than 10.0: 1 Number of HSP's gapped: 516 Number of HSP's successfully gapped: 21 Length of query: 274 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 182 Effective length of database: 4,006,537 Effective search space: 729189734 Effective search space used: 729189734 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 56 (25.6 bits)