RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781167|ref|YP_003065580.1| tRNA-dihydrouridine synthase A [Candidatus Liberibacter asiaticus str. psy62] (322 letters) >gnl|CDD|183323 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional. Length = 333 Score = 470 bits (1212), Expect = e-133 Identities = 162/321 (50%), Positives = 215/321 (66%), Gaps = 11/321 (3%) Query: 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60 M+DWTDRH R+F RLL+ +ALLYTEM+ AI+ GD++ +L F +E P+ALQ+GG+D + Sbjct: 18 MMDWTDRHCRYFHRLLSRHALLYTEMVTTGAIIHGDRERLLAFDPEEHPVALQLGGSDPA 77 Query: 61 KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120 L EAAK+ ED+GY+EINLNVGCPS RV G FGACLM P++V DC+ AM A+SIPVT Sbjct: 78 DLAEAAKLAEDWGYDEINLNVGCPSDRVQNGRFGACLMAEPELVADCVKAMKDAVSIPVT 137 Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180 VK RIG+DDQ L + V ++ ++G + +HARKA LKGLSPK+NR+IP LDYD VY Sbjct: 138 VKHRIGIDDQDSYEFLCDFVDTVAEAGCDTFIVHARKAWLKGLSPKENREIPPLDYDRVY 197 Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239 +K++ P L I +NGG++ + +A + L VDGVMIGRAAY N +L VD E F P Sbjct: 198 RLKRDFPHLTIEINGGIKTLEEAKEHLQHVDGVMIGRAAYHNPYLLAEVDRELFGEP--- 254 Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299 +P +R + + +M Y RHL GG+L ITRHM+GLF G P +R R L+ Sbjct: 255 -APPLSRSE------VLEAMLPYIERHLAQGGRLNHITRHMLGLFQGLPGARAWRRYLSE 307 Query: 300 EAGASTATHHIIETAFNLMIE 320 A A ++E A L+ E Sbjct: 308 NAHKPGAGIEVLEEALALVEE 328 >gnl|CDD|129825 TIGR00742, yjbN, tRNA dihydrouridine synthase A. Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. Length = 318 Score = 349 bits (896), Expect = 7e-97 Identities = 154/320 (48%), Positives = 206/320 (64%), Gaps = 9/320 (2%) Query: 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60 M+DWTDRH+R+F RLL+ + LLYTEMI A AI+ GDKK+IL FS +E P+ALQ+GG+D + Sbjct: 8 MLDWTDRHFRYFLRLLSKHTLLYTEMITAKAIIHGDKKDILKFSPEESPVALQLGGSDPN 67 Query: 61 KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120 L + AKI E GY+EINLNVGCPS RV G+FGACLM N D+V DC+ AM +A++IPVT Sbjct: 68 DLAKCAKIAEKRGYDEINLNVGCPSDRVQNGNFGACLMGNADLVADCVKAMQEAVNIPVT 127 Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180 VK RIG+D L + V+ + G +HARKA L GLSPK+NR+IP L Y+ VY Sbjct: 128 VKHRIGIDPLDSYEFLCDFVEIVSGKGCQNFIVHARKAWLSGLSPKENREIPPLRYERVY 187 Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240 ++KK+ P L I +NGG+++ Q + L VDGVM+GR AY+N +L VD N + Sbjct: 188 QLKKDFPHLTIEINGGIKNSEQIKQHLSHVDGVMVGREAYENPYLLANVDREIFNE---T 244 Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300 I TR + I M Y +L G L ITRH++GLF G P +++ R L+ Sbjct: 245 DEILTRKE------IVEQMLPYIEEYLSQGLSLNHITRHLLGLFQGKPGAKQWRRYLSEN 298 Query: 301 AGASTATHHIIETAFNLMIE 320 A + A ++ETA + E Sbjct: 299 APKAGAGIEVLETALETVPE 318 >gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family. Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. Length = 319 Score = 122 bits (307), Expect = 2e-28 Identities = 81/302 (26%), Positives = 138/302 (45%), Gaps = 29/302 (9%) Query: 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58 M TD +R L EM+ ++AI+ ++ +L + E P+++Q+ G+D Sbjct: 15 MAGVTDSPFRRLVAEY-GAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQLFGSD 73 Query: 59 ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118 + EAAKI E+ G + I++N+GCP ++ + G+ L+ +PD++G + A+ A+ IP Sbjct: 74 PDTMAEAAKINEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIP 133 Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175 VTVK RIG DD A N + + +G + +H R +G S + N Sbjct: 134 VTVKIRIGWDD-----AHINAVEAARIAEDAGAQAVTLHGRTRA-QGYSGEAN------- 180 Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233 +DI+ +K+ IG NG + A +L + DGVMIGR A N + +++Y Sbjct: 181 WDIIARVKQAVRIPVIG-NGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLFRQIEQYL 239 Query: 234 -SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292 + ++D R + Y L+ +H+ GFP + Sbjct: 240 TTGKYKPPPTFAEKLDA-ILRHLQLLADYYGESKG-----LRIARKHIAWYLKGFPGNAA 293 Query: 293 CR 294 R Sbjct: 294 LR 295 >gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional. Length = 321 Score = 75.8 bits (186), Expect = 1e-14 Identities = 61/228 (26%), Positives = 106/228 (46%), Gaps = 26/228 (11%) Query: 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58 M TDR +R + L +EM+ ++ + DK + E + +QI G+D Sbjct: 17 MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 75 Query: 59 ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118 ++ +AA+I + G I++N+GCP+ +V+ G+ L+ PD+V + + A+ +P Sbjct: 76 PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVP 135 Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173 VT+K R G + RN V+ + G+ + IH R + G Sbjct: 136 VTLKIRTGWAPE-----HRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180 Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219 +YD + +K++ I NG + D +A +L D +MIGRAA Sbjct: 181 AEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAA 227 >gnl|CDD|182540 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional. Length = 312 Score = 52.9 bits (127), Expect = 1e-07 Identities = 47/163 (28%), Positives = 84/163 (51%), Gaps = 24/163 (14%) Query: 65 AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVK 122 AA+ VE G ++LN GCPS V+ GA L+ +P+++ AM +A+ +PVTVK Sbjct: 81 AARAVE-LGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHLPVTVK 139 Query: 123 CRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180 R+G D ++ +A +++++G + +H R + +D + ++++ + Sbjct: 140 VRLGWDSGERKFEIA-----DAVQQAGATELVVHGR-------TKEDGYRAEHINWQAIG 187 Query: 181 EIKKENPDLFIGL--NGGLEDM--SQALKILPSVDGVMIGRAA 219 EI++ L I + NG + D +Q + D VMIGR A Sbjct: 188 EIRQR---LTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGA 227 >gnl|CDD|180909 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed. Length = 301 Score = 45.1 bits (108), Expect = 2e-05 Identities = 32/129 (24%), Positives = 55/129 (42%), Gaps = 30/129 (23%) Query: 54 IGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEG--SFGACLMLNPDIVGDCIAA 110 + G+ + E A+ + + I LN+ CP+ V G +FG +P++ + + A Sbjct: 98 VAGSTEEEYAEVAEKLSKAPNVDAIELNISCPN--VKHGGMAFGT----DPELAYEVVKA 151 Query: 111 MCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVNGIWIHARKAI 159 + + + +PV VK V D + ++L N +K + I I RK I Sbjct: 152 VKEVVKVPVIVKLTPNVTDIVEIAKAAEEAGADGLSLINTLKGMA------IDIKTRKPI 205 Query: 160 LK----GLS 164 L GLS Sbjct: 206 LANVTGGLS 214 >gnl|CDD|130109 TIGR01037, pyrD_sub1_fam, dihydroorotate dehydrogenase (subfamily 1) family protein. This family includes subfamily 1 dihydroorotate dehydrogenases while excluding the closely related subfamily 2 (TIGR01036). This family also includes a number of uncharacterized proteins and a domain of dihydropyrimidine dehydrogenase. The uncharacterized proteins might all be dihydroorotate dehydrogenase. Length = 300 Score = 44.7 bits (106), Expect = 3e-05 Identities = 44/190 (23%), Positives = 76/190 (40%), Gaps = 32/190 (16%) Query: 49 PLALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106 PL + G+ + + E A+ +E + LN+ CP + + G +P++ D Sbjct: 92 PLIASVYGSSVEEFAEVAEKLEKAPPYVDAYELNLSCPHVKGGGIAIG----QDPELSAD 147 Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155 + A+ +PV K V D + K+ +++G +G I I Sbjct: 148 VVKAVKDKTDVPVFAKLSPNVTDIT------EIAKAAEEAGADGLTLINTLRGMKIDIKT 201 Query: 156 RKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210 K IL GLS I + +VY++ K IG+ GG+ AL+ ++ Sbjct: 202 GKPILANKTGGLSGP---AIKPIALRMVYDVYKMVDIPIIGV-GGITSFEDALEFLMAGA 257 Query: 211 DGVMIGRAAY 220 V +G A Y Sbjct: 258 SAVQVGTAVY 267 >gnl|CDD|181383 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B; Validated. Length = 420 Score = 34.5 bits (80), Expect = 0.041 Identities = 29/98 (29%), Positives = 41/98 (41%), Gaps = 26/98 (26%) Query: 64 EAAKIVEDFGYNEINLNVGCPSARVH---EGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120 E A +VE+ G + I LN GCP H E G+ + P++V + + +PV Sbjct: 117 EIAPLVEETGADGIELNFGCP----HGMSERGMGSAVGQVPELVEMYTRWVKRGSRLPVI 172 Query: 121 VKC---------------RIGVDDQIPAVALRNLVKSI 143 VK R G D AV+L N + SI Sbjct: 173 VKLTPNITDIREPARAAKRGGAD----AVSLINTINSI 206 >gnl|CDD|129443 TIGR00343, TIGR00343, pyridoxal 5'-phosphate synthase, synthase subunit Pdx1. This protein had been believed to be a singlet oxygen resistance protein. Subsequent work showed that it is a protein of pyridoxine (vitamin B6) biosynthesis, and that pyridoxine quenches the highly toxic singlet form of oxygen produced by light in the presence of certain chemicals. Length = 287 Score = 30.9 bits (70), Expect = 0.47 Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 4/33 (12%) Query: 94 GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126 G M +P ++ + + A+SIPV K RIG Sbjct: 49 GVARMSDPKMIKEIM----DAVSIPVMAKVRIG 77 >gnl|CDD|179769 PRK04180, PRK04180, pyridoxal biosynthesis lyase PdxS; Provisional. Length = 293 Score = 30.5 bits (70), Expect = 0.53 Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 4/29 (13%) Query: 98 MLNPDIVGDCIAAMCKALSIPVTVKCRIG 126 M +P ++ + + A+SIPV K RIG Sbjct: 60 MADPKMIEEIM----DAVSIPVMAKARIG 84 >gnl|CDD|151243 pfam10788, DUF2603, Protein of unknown function (DUF2603). This family is conserved in Epsilon-proteobacteria. The function is not known. Length = 133 Score = 30.0 bits (68), Expect = 0.81 Identities = 14/30 (46%), Positives = 21/30 (70%), Gaps = 1/30 (3%) Query: 166 KDNRKIPNLDYD-IVYEIKKENPDLFIGLN 194 K K N+D D +V +IKKE+P+LF+ L+ Sbjct: 104 KLAAKDSNIDLDRLVKKIKKEHPNLFVDLD 133 >gnl|CDD|178325 PLN02724, PLN02724, Molybdenum cofactor sulfurase. Length = 805 Score = 29.1 bits (65), Expect = 1.5 Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 10/91 (10%) Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283 + L Y+ P G PI +F R D+A L+S +L+ Sbjct: 3 SFLKEFGGYYGYP-DGPKPIDELRATEFARLKGVVYLDHAGATLYSESQLEAALADFSSN 61 Query: 284 FHGFPNSRRCRHILTVEAGASTATHHIIETA 314 +G P+S ++ +S + IE+A Sbjct: 62 VYGNPHS---------QSDSSMRSSDTIESA 83 >gnl|CDD|184625 PRK14328, PRK14328, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional. Length = 439 Score = 27.6 bits (62), Expect = 4.0 Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 4/55 (7%) Query: 181 EIKKENPDLFIGLNGGL---EDMSQAL-KILPSVDGVMIGRAAYKNSAMLTTVDE 231 ++K++NP+L IG+ G + + M++ + K P VD + +K L V E Sbjct: 66 KLKEKNPNLIIGVCGCMMQQKGMAEKIKKKFPFVDIIFGTHNIHKFPEYLNRVKE 120 >gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 470 Score = 27.8 bits (62), Expect = 4.2 Identities = 5/27 (18%), Positives = 11/27 (40%) Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHIL 297 G+ + + + NS CR ++ Sbjct: 348 GQQRTYKLKLYEMMEYCLNSSTCRRLI 374 >gnl|CDD|184898 PRK14905, PRK14905, triosephosphate isomerase/PTS system glucose/sucrose-specific transporter subunit IIB; Provisional. Length = 355 Score = 27.3 bits (60), Expect = 5.2 Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 7/68 (10%) Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233 +++ E K+ P L+ GG ++ A +++ P +DG+ IGR+A+ + + Sbjct: 204 FELFAEESKKIPVLY----GGSVNLENANELIMKPHIDGLFIGRSAWDAQCFHALIADAL 259 Query: 234 SNPLTGSS 241 L GS Sbjct: 260 -KALAGSK 266 >gnl|CDD|179249 PRK01213, PRK01213, phosphoribosylformylglycinamidine synthase II; Provisional. Length = 724 Score = 27.0 bits (61), Expect = 6.2 Identities = 6/13 (46%), Positives = 8/13 (61%) Query: 108 IAAMCKALSIPVT 120 +A C+AL PV Sbjct: 507 LADACRALGTPVV 519 >gnl|CDD|183341 PRK11858, aksA, trans-homoaconitate synthase; Reviewed. Length = 378 Score = 27.1 bits (61), Expect = 7.3 Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 17/69 (24%) Query: 57 ADISKLVEAAKIVEDFGYNEINL--NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114 D+ L+E AK E+ G + + VG L+P + + + + +A Sbjct: 142 TDLDFLIEFAKAAEEAGADRVRFCDTVGI---------------LDPFTMYELVKELVEA 186 Query: 115 LSIPVTVKC 123 + IP+ V C Sbjct: 187 VDIPIEVHC 195 >gnl|CDD|179108 PRK00748, PRK00748, 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Validated. Length = 233 Score = 27.0 bits (61), Expect = 7.7 Identities = 13/28 (46%), Positives = 20/28 (71%), Gaps = 2/28 (7%) Query: 195 GGLEDMS--QALKILPSVDGVMIGRAAY 220 GG+ + +ALK L +V+GV++GRA Y Sbjct: 197 GGVSSLDDIKALKGLGAVEGVIVGRALY 224 >gnl|CDD|178886 PRK00130, truB, tRNA pseudouridine synthase B; Provisional. Length = 290 Score = 26.8 bits (60), Expect = 8.2 Identities = 12/37 (32%), Positives = 22/37 (59%), Gaps = 1/37 (2%) Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193 K +L G+ KD R + N++ + +Y + E + FIG+ Sbjct: 240 KLLLNGVKIKDRRLLDNIEENKLYRVYDEE-NKFIGI 275 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 0.322 0.137 0.408 Gapped Lambda K H 0.267 0.0752 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,338,187 Number of extensions: 346282 Number of successful extensions: 703 Number of sequences better than 10.0: 1 Number of HSP's gapped: 694 Number of HSP's successfully gapped: 28 Length of query: 322 Length of database: 5,994,473 Length adjustment: 94 Effective length of query: 228 Effective length of database: 3,963,321 Effective search space: 903637188 Effective search space used: 903637188 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 57 (25.7 bits)