RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781020|ref|YP_003065433.1| isopentenyl pyrophosphate isomerase [Candidatus Liberibacter asiaticus str. psy62] (337 letters) >gnl|CDD|73373 cd02811, IDI-2_FMN, Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal, FMN and NADPH. IDI-2 catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the mevalonate pathway.. Length = 326 Score = 393 bits (1011), Expect = e-110 Identities = 150/326 (46%), Positives = 211/326 (64%), Gaps = 5/326 (1%) Query: 5 RKIDHINIVCKDPGIDRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSM 64 RK +H+ + ++ FDD L+H ALPE+ D++D S EFLGK+LS PLLIS+M Sbjct: 1 RKDEHLELCLEENVESGGSTGFDDVRLVHNALPELDLDDIDLSTEFLGKRLSAPLLISAM 60 Query: 65 TGGNNKMIERINRNLAIAAEKTKVAMAVGSQRVMFSDHNAIKSFEL-RQYAPHTVLISNL 123 TGG+ K + INRNLA AAE+ +AM VGSQR D +SF + R+ P+ LI+NL Sbjct: 61 TGGSEK-AKEINRNLAEAAEELGIAMGVGSQRAALEDPELAESFTVVREAPPNGPLIANL 119 Query: 124 GAVQLNYDFGVQKAHQAVHVLGADGLFLHLNPLQEIIQPNGNTNFADLSSKIALLSSAMD 183 GAVQLN +GV++A +AV ++ AD L +HLNPLQE +QP G+ +F +I L A+ Sbjct: 120 GAVQLN-GYGVEEARRAVEMIEADALAIHLNPLQEAVQPEGDRDFRGWLERIEELVKALS 178 Query: 184 VPLLLKEVGCGLSSMDIELGLKSGIRYFDIAGRGGTSWSRIESHR--DLESDIGIVFQDW 241 VP+++KEVG G+S + +G++ D+AG GGTSW+R+E++R D + + F DW Sbjct: 179 VPVIVKEVGFGISRETAKRLADAGVKAIDVAGAGGTSWARVENYRAKDSDQRLAEYFADW 238 Query: 242 GIPTPLSLEMARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLASPFLKPAMDSSDAV 301 GIPT SL R + IASGG+RNG+DI K++ LGA L G+A PFLK A++ +AV Sbjct: 239 GIPTAASLLEVRSALPDLPLIASGGIRNGLDIAKALALGADLVGMAGPFLKAALEGEEAV 298 Query: 302 VAAIESLRKEFIVSMFLLGTKRVQEL 327 + IE + +E +MFL G K + EL Sbjct: 299 IETIEQIIEELRTAMFLTGAKNLAEL 324 >gnl|CDD|31495 COG1304, LldD, L-lactate dehydrogenase (FMN-dependent) and related alpha-hydroxy acid dehydrogenases [Energy production and conversion]. Length = 360 Score = 230 bits (587), Expect = 6e-61 Identities = 120/340 (35%), Positives = 170/340 (50%), Gaps = 26/340 (7%) Query: 5 RKIDHINIVCKDPGID--RNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLIS 62 K H + + RN++ F+D L R LPE+ D++D S FLG+KLS P++I+ Sbjct: 13 PKAFHYIDGGAEDEVTLRRNREAFEDIALRPRVLPEV--DDIDLSTTFLGQKLSAPIIIA 70 Query: 63 SMTGGN--NKMIERINRNLAIAAEKTKVAMAVGSQRVMFSDHNAIKSFEL-----RQYAP 115 MTGG + E IN LA AA + + VGSQR+ + A F+L R++AP Sbjct: 71 PMTGGGLAHPEGEVINAKLAAAAGEPFILSTVGSQRI--EEVAAAPPFQLYFSKDREFAP 128 Query: 116 HTV-LISNLGAVQLNY----DFGVQKAHQAVHVLGADGLFLHLNPLQEIIQPNGNTNFAD 170 + V +N GA QL G ++ AV+ + A L +HLN LQE QP G+ + Sbjct: 129 NLVDRAANAGAKQLVLTVDSPVGGERERDAVNGISAPALAIHLNVLQEATQPEGDRDGKG 188 Query: 171 LSSKIALLSSAMDVPLLLKEVGCGLSSMDIELGLKSGIRY-FDIAGRGGTSWSRIESHRD 229 IA SA+ VP++ KE G G+S + GI D AG GGT IE Sbjct: 189 GLDSIAEYVSALSVPVISKEDGAGISKEWAGPLVLKGILAPEDAAGAGGTGADGIEVSNH 248 Query: 230 LESDIGIVFQDWGIPTPLSL-EMARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLAS 288 G DWGI T SL E+ + + IA GG+R+G+D+ K++ LGA G+ Sbjct: 249 -----GGRQLDWGISTADSLPEIVEAVGDRIEVIADGGIRSGLDVAKALALGADAVGIGR 303 Query: 289 PFLKPAMDS-SDAVVAAIESLRKEFIVSMFLLGTKRVQEL 327 PFL V +E +RKE ++M L G K ++EL Sbjct: 304 PFLYGLAAGGEAGVERVLEIIRKELKIAMALTGAKNIEEL 343 >gnl|CDD|144604 pfam01070, FMN_dh, FMN-dependent dehydrogenase. Length = 301 Score = 87.9 bits (219), Expect = 3e-18 Identities = 78/313 (24%), Positives = 119/313 (38%), Gaps = 46/313 (14%) Query: 20 DRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSMTGGNNKMIERINRNL 79 RN+ FD L R L ++S + D S LG++LS P I+ G L Sbjct: 23 RRNRAAFDRIRLRPRVLRDVS--DRDTSTTLLGQRLSLPFGIAPT-GMQGLAHPDGELAL 79 Query: 80 AIAAEKTKVAMAVGSQRVMFSDHNAIKSFE-LRQYAPHTVL--ISNLGAVQLNYDFGVQK 136 A AA + + + A S E + A + + +L D +++ Sbjct: 80 ARAAAAAGIPFVLST--------VASTSLEEVAAAAGGPLWFQLYVPKDRELTEDL-LER 130 Query: 137 AHQAVHVLGADGLFLHLNPLQEIIQPNGNTNFADLSSKIALLSSAMDVPLLLKEVGCGLS 196 A A G L L ++ + N D +A L PL+LK + LS Sbjct: 131 AEAA----GYKALVLTVDTPVLGNRERDLRNGDD----LAWLRDQWKGPLVLKGI---LS 179 Query: 197 SMDIELGLKSGIRYFDIAGRGGTSWSRIESHRDLESDIGIVFQDWGIPTPLSL-EMARPY 255 D + +++G+ ++ GG R L D T +L E+ Sbjct: 180 PEDAKRAVEAGVDGIVVSNHGG---------RQL---------DGAPATIDALPEIVAAV 221 Query: 256 CNEAQFIASGGLRNGVDILKSIILGASLGGLASPFLKP-AMDSSDAVVAAIESLRKEFIV 314 + GG+R G D+LK++ LGA L PFL A V A+E LR E Sbjct: 222 GGRIPVLVDGGIRRGTDVLKALALGADAVLLGRPFLYGLAAGGEAGVAHALEILRDELER 281 Query: 315 SMFLLGTKRVQEL 327 +M LLG + +L Sbjct: 282 TMALLGCTSIADL 294 >gnl|CDD|73371 cd02809, alpha_hydroxyacid_oxid_FMN, Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO). In green plants, glycolate oxidase is one of the key enzymes in photorespiration where it oxidizes glycolate to glyoxylate. LMO catalyzes the oxidation of L-lactate to acetate and carbon dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate. It is an enzyme in the mandelate pathway that occurs in several strains of Pseudomonas which converts (R)-mandelate to benzoate.. Length = 299 Score = 64.7 bits (158), Expect = 3e-11 Identities = 74/318 (23%), Positives = 114/318 (35%), Gaps = 62/318 (19%) Query: 21 RNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSMTGGNNKMIERINRNLA 80 RN+ FD L R L ++S + D S LG+KL+ P I+ TG A Sbjct: 31 RNRAAFDRIRLRPRVLRDVS--KRDTSTTLLGQKLAMPFGIAP-TGLQGLAHPDGELATA 87 Query: 81 IAAEKTKVAMAVGSQRVMFSDHNAIKSFELRQYAPHTVLISNLGAVQLNYDFG------- 133 AA + + + + S E + A QL Y Sbjct: 88 RAAAAAGIPFTLSTV--------STTSLE--EVAAAA---PGPRWFQL-YVPRDREITED 133 Query: 134 -VQKAHQAVHVLGADGLFLHLNPLQEIIQPNGNTNFADLSSKIALLSSAMDVPLLLKEVG 192 +++A A G L L + + + D +A L S PL+LK + Sbjct: 134 LLRRAEAA----GYKALVLTV----DTPVLGRRLTWDD----LAWLRSQWKGPLILKGI- 180 Query: 193 CGLSSMDIELGLKSGIRYFDIAGRGGTSWSRIESHRDLESDIGIVFQDWGIPTPLSL--E 250 L+ D + +G ++ GG R L+ G P + E Sbjct: 181 --LTPEDALRAVDAGADGIVVSNHGG---------RQLD----------GAPATIDALPE 219 Query: 251 MARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLASPFLKP-AMDSSDAVVAAIESLR 309 + + + GG+R G D+LK++ LGA + PFL A V +E LR Sbjct: 220 IVAAVGGRIEVLLDGGIRRGTDVLKALALGADAVLIGRPFLYGLAAGGEAGVAHVLEILR 279 Query: 310 KEFIVSMFLLGTKRVQEL 327 E +M LLG + +L Sbjct: 280 DELERAMALLGCASLADL 297 >gnl|CDD|73376 cd02922, FCB2_FMN, Flavocytochrome b2 (FCB2) FMN-binding domain. FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a respiratory enzyme located in the intermembrane space of fungal mitochondria which catalyzes the oxidation of L-lactate to pyruvate. FCB2 also participates in a short electron-transport chain involving cytochrome c and cytochrome oxidase which ultimately directs the reducing equivalents gained from L-lactate oxidation to oxygen, yielding one molecule of ATP for every L-lactate molecule consumed. FCB2 is composed of 2 domains: a C-terminal flavin-binding domain, which includes the active site for lacate oxidation, and an N-terminal b2-cytochrome domain, required for efficient cytochrome c reduction. FCB2 is a homotetramer and contains two noncovalently bound cofactors, FMN and heme per subunit.. Length = 344 Score = 63.7 bits (155), Expect = 7e-11 Identities = 83/351 (23%), Positives = 124/351 (35%), Gaps = 80/351 (22%) Query: 20 DRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLIS--SMTGGNNKMIERINR 77 N + F R L ++ +VD S LG K+S P IS ++ + E Sbjct: 30 RENLEAFQRIRFRPRVLRDVE--KVDTSTTILGHKVSLPFFISPAALAKLAHPDGEL--- 84 Query: 78 NLAIAAEKTKVAMAVGSQRVMFSDHNAIKSFE--LRQYAPHTVL---------------- 119 NLA AA K + + + NA S E + P L Sbjct: 85 NLARAAGKHGILQMIST--------NASCSLEEIVDARPPDQPLFFQLYVNKDRTKTEEL 136 Query: 120 ---ISNLG--AVQLNYDFGV---------QKAHQAVHVLGADGLFLHLNPLQEIIQPNGN 165 LG A+ L D V KA +AV A + Sbjct: 137 LKRAEKLGAKAIFLTVDAPVLGKRERDERLKAEEAVSDGPAGKK--TKAKGGGAGRAMSG 194 Query: 166 TNFADLS-SKIALLSSAMDVPLLLKEVGCGLSSMDIELGLKSGIRYFDIAGRGGTSWSRI 224 L+ I L +P++LK V D L + G+ ++ GG Sbjct: 195 FIDPTLTWDDIKWLRKHTKLPIVLKGVQTV---EDAVLAAEYGVDGIVLSNHGG------ 245 Query: 225 ESHRDLESDIGIVFQDWGIPTPLS--LEMARPYC----NEAQFIASGGLRNGVDILKSII 278 R L+ P P+ LE+ R +C ++ + GG+R G D+LK++ Sbjct: 246 ---RQLD----------TAPAPIEVLLEI-RKHCPEVFDKIEVYVDGGVRRGTDVLKALC 291 Query: 279 LGASLGGLASPFL-KPAMDSSDAVVAAIESLRKEFIVSMFLLGTKRVQELY 328 LGA GL PFL + + V AI+ L+ E +M LLG + +L Sbjct: 292 LGAKAVGLGRPFLYALSAYGEEGVEKAIQILKDEIETTMRLLGVTSLDQLG 342 >gnl|CDD|35758 KOG0538, KOG0538, KOG0538, Glycolate oxidase [Energy production and conversion]. Length = 363 Score = 59.1 bits (143), Expect = 2e-09 Identities = 73/348 (20%), Positives = 127/348 (36%), Gaps = 59/348 (16%) Query: 20 DRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSMTGGNNKMIE-RINRN 78 D N F R L ++S ++D S LG+K+S P++I+ KM Sbjct: 34 DENINAFRRILFRPRILRDVS--KIDTSTTVLGQKISAPIMIAPT--AMQKMAHPDGELA 89 Query: 79 LAIAAEKTKVAMAVGS------QRVMFSDHNAIKSFELRQYAPHTVLIS--------NLG 124 A AA+ M + S + + + I+ F+L Y + Sbjct: 90 TARAAQAAGTIMILSSWATCSVEDIASAAPPGIRWFQLYVYKDRDITEQLVKRAEKAGFK 149 Query: 125 AVQLNYD---FGVQKAHQAVHVLGADGLFLH--LNPLQEIIQPNGNTNFADLSSK----- 174 A+ L D G +++ L L ++ G++ A S Sbjct: 150 ALVLTVDTPRLGRRESDIKNKFSLPKNLTLKNFEGLKLTEVEEAGDSGLAAYVSSQIDPS 209 Query: 175 -----IALLSSAMDVPLLLKEVGCGLSSMDIELGLKSGIRYFDIAGRGGTSWSRIESHRD 229 I L S +P+++K V L+ D +++G+ ++ GG R Sbjct: 210 LSWKDIKWLRSITKLPIVVKGV---LTGEDARKAVEAGVAGIIVSNHGG---------RQ 257 Query: 230 LESDIGIVFQDWGIPTPLSL--EMARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLA 287 L+ +P + E+ + GG+R G D+LK++ LGA + Sbjct: 258 LD----------YVPATIEALPEVVKAVEGRIPVFLDGGVRRGTDVLKALALGAKGVFIG 307 Query: 288 SPFL-KPAMDSSDAVVAAIESLRKEFIVSMFLLGTKRVQELYLNTALI 334 P + A V ++ LR EF ++M L G + V+E+ N L Sbjct: 308 RPIVWGLAAKGEAGVKKVLDILRDEFELTMALSGCRSVKEITRNHVLT 355 >gnl|CDD|73383 cd03332, LMO_FMN, L-Lactate 2-monooxygenase (LMO) FMN-binding domain. LMO is a FMN-containing enzyme that catalyzes the conversion of L-lactate and oxygen to acetate, carbon dioxide, and water. LMO is a member of the family of alpha-hydroxy acid oxidases. It is thought to be a homooctamer with two- and four- fold axes in the center of the octamer.. Length = 383 Score = 48.7 bits (116), Expect = 2e-06 Identities = 74/352 (21%), Positives = 122/352 (34%), Gaps = 66/352 (18%) Query: 19 IDRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLL------ISSMTGGNNKMI 72 N+ F W ++ R L E D SVE G+ L+ PLL Sbjct: 50 ARANRDAFSRWRIVPRML--RGVTERDLSVELFGRTLAAPLLLAPIGVQELFHPDAELAT 107 Query: 73 ERINRNLAI------AAEKT--KVAMAVGSQRVMF-----SDHNAIKSFELR-QYAPHTV 118 R L + A+ + VA A G F D + +S R + A + V Sbjct: 108 ARAAAELGVPYILSTASSSSIEDVAAAAGDAPRWFQLYWPKDDDLTESLLRRAEKAGYRV 167 Query: 119 LISNLGAVQLNY-----DFGV--QKAHQAVHVLGADGLFLHL--NPLQEIIQPNGNTN-- 167 L+ L L + D G + +D +F P+ E + Sbjct: 168 LVVTLDTWSLGWRPRDLDLGYLPFLRGIGIANYFSDPVFRKKLAEPVGEDPEAPPPMEAA 227 Query: 168 ---FADLSS-------KIALLSSAMDVPLLLKEVGCGLSSMDIELGLKSGIRYFDIAGRG 217 F + S +A L D+P++LK + L D +++G+ ++ G Sbjct: 228 VARFVSVFSGPSLTWEDLAFLREWTDLPIVLKGI---LHPDDARRAVEAGVDGVVVSNHG 284 Query: 218 GTSWSRIESHRDLESDIGIVFQDWGIPTPLSL-EMARPYCNEAQFIASGGLRNGVDILKS 276 G D I +L E+ + + G+R G DI+K+ Sbjct: 285 GRQ------------------VDGSIAALDALPEIVEAVGDRLTVLFDSGVRTGADIMKA 326 Query: 277 IILGASLGGLASPFLKP-AMDSSDAVVAAIESLRKEFIVSMFLLGTKRVQEL 327 + LGA + P+ A+ D V + +L E ++M L G + + EL Sbjct: 327 LALGAKAVLIGRPYAYGLALGGEDGVEHVLRNLLAELDLTMGLAGIRSIAEL 378 >gnl|CDD|73370 cd02808, GltS_FMN, Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast and bacterial pathway for ammonia assimilation. It is a multifunctional enzyme that functions through three distinct active centers, carrying out L-glutamine hydrolysis, conversion of 2-oxoglutarate into L-glutamate, and electron uptake from an electron donor.. Length = 392 Score = 45.6 bits (108), Expect = 2e-05 Identities = 68/308 (22%), Positives = 108/308 (35%), Gaps = 40/308 (12%) Query: 8 DHINIVCKDPGIDRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGK--KLSFPLLISSMT 65 N + G R+ F H P+ D+ K KL P IS+M+ Sbjct: 27 RAGNSRGRPFGTLRDLLEFGAQLAKHPLEPDEEVDDRVTIGPNAEKPLKLDSPFNISAMS 86 Query: 66 GGNNKMIERINRNLAIAAEKTKVAMAVGSQRVMFSDHNAIKSFELRQYAP-----HTVLI 120 G + + LAI A A G + + ++Q A + Sbjct: 87 FG--ALSKEAKEALAIGAALAGTASNTG-EGGELPEEREGGGDIIKQVASGRFGVRPEYL 143 Query: 121 SNLGAVQLNYDFGVQKAHQAVHVLGAD-----GLFLHLNPLQEIIQPNGNTNF---ADLS 172 + A+++ G + H+ G + P ++I P + + DL+ Sbjct: 144 NKADAIEIKIGQGAKPGEGG-HLPGEKVTEEIAKIRGIPPGVDLISPPPHHDIYSIEDLA 202 Query: 173 SKIALLSSAMD-VPLLLKEVGCGLSSMDIELGLKSG-IRYFDIAGR-GGTSWSRIESHRD 229 I L A P+ +K + G DI G+ + + I G GGT + + D Sbjct: 203 QLIEDLREATGGKPIGVK-LVAGHGEGDIAAGVAAAGADFITIDGAEGGTGAAPLTF-ID 260 Query: 230 LESDIGIVFQDWGIPTPLSLEMARPYCNEA------QFIASGGLRNGVDILKSIILGASL 283 G+PT L L A + IASGGLR G D+ K++ LGA Sbjct: 261 ----------HVGLPTELGLARAHQALVKNGLRDRVSLIASGGLRTGADVAKALALGADA 310 Query: 284 GGLASPFL 291 G+ + L Sbjct: 311 VGIGTAAL 318 >gnl|CDD|30418 COG0069, GltB, Glutamate synthase domain 2 [Amino acid transport and metabolism]. Length = 485 Score = 39.9 bits (93), Expect = 0.001 Identities = 35/134 (26%), Positives = 49/134 (36%), Gaps = 19/134 (14%) Query: 166 TNFADLSSKIALLSSAMDVPLLLKEVGCGLSSMDIELG-LKSGIRYFDIAG-RGGTSWSR 223 + DL+ I L A + ++ I G K+G I G GGT S Sbjct: 285 YSIEDLAQLIKDLKEANPWAKISVKLVAEHGVGTIAAGVAKAGADVITIDGADGGTGASP 344 Query: 224 IESHRDLESDIGIVFQDWGIPTPLSL----EMARPYC--NEAQFIASGGLRNGVDILKSI 277 + S GIP L L + ++ + IA GGLR G D+ K+ Sbjct: 345 LTSIDH-----------AGIPWELGLAETHQTLVLNGLRDKVKLIADGGLRTGADVAKAA 393 Query: 278 ILGASLGGLASPFL 291 LGA G + L Sbjct: 394 ALGADAVGFGTAAL 407 >gnl|CDD|73399 cd04737, LOX_like_FMN, L-Lactate oxidase (LOX) FMN-binding domain. LOX is a member of the family of FMN-containing alpha-hydroxyacid oxidases and catalyzes the oxidation of l-lactate using molecular oxygen to generate pyruvate and H2O2. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO).. Length = 351 Score = 39.9 bits (93), Expect = 0.001 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 1/67 (1%) Query: 262 IASGGLRNGVDILKSIILGASLGGLASPFLKP-AMDSSDAVVAAIESLRKEFIVSMFLLG 320 I G+R G + K++ GA + P L A+ + V + +E L KE + M L G Sbjct: 280 IFDSGVRRGEHVFKALASGADAVAVGRPVLYGLALGGAQGVASVLEHLNKELKIVMQLAG 339 Query: 321 TKRVQEL 327 T+ ++++ Sbjct: 340 TRTIEDV 346 Score = 30.7 bits (69), Expect = 0.68 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 2/43 (4%) Query: 22 NKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSM 64 N + F+ ++ R L + + D S E LG KL P++++ + Sbjct: 40 NTRAFNHKQIVPRVLQGV--ESPDTSTELLGIKLKTPIIMAPI 80 >gnl|CDD|110632 pfam01645, Glu_synthase, Conserved region in glutamate synthase. This family represents a region of the glutamate synthase protein. This region is expressed as a separate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. The aligned region of these proteins contains a putative FMN binding site and Fe-S cluster. Length = 367 Score = 39.2 bits (92), Expect = 0.001 Identities = 34/117 (29%), Positives = 46/117 (39%), Gaps = 13/117 (11%) Query: 170 DLSSKIALLSSA-MDVPLLLKEVGCGLSSMDIELGL-KSGIRYFDIAG-RGGTSWSRIES 226 DL+ I L P+ +K + G I G+ K+G I G GGT S S Sbjct: 188 DLAQLIYDLKEINPKAPISVK-LVSGHGVGTIAAGVAKAGADIILIDGHDGGTGASPKTS 246 Query: 227 --HRDLESDIGIVFQDWGIPTPLSLEMARPYCNEAQFIASGGLRNGVDILKSIILGA 281 H L ++ + L R + IA GGLR G D+ K+ LGA Sbjct: 247 IKHAGLPWELALAEVH----QTLVENGLR---DRVSLIADGGLRTGADVAKAAALGA 296 >gnl|CDD|73398 cd04736, MDH_FMN, Mandelate dehydrogenase (MDH)-like FMN-binding domain. MDH is part of a widespread family of homologous FMN-dependent a-hydroxy acid oxidizing enzymes that oxidizes (S)-mandelate to phenylglyoxalate. MDH is an enzyme in the mandelate pathway that occurs in several strains of Pseudomonas which converts (R)-mandelate to benzoate. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO).. Length = 361 Score = 36.9 bits (85), Expect = 0.008 Identities = 26/81 (32%), Positives = 37/81 (45%), Gaps = 3/81 (3%) Query: 18 GIDRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSMTGGNNKMIERINR 77 G+ N+ FD W I R L ++S + D S GK S PL+I+ TG N + Sbjct: 28 GLRHNRDAFDRWRFIPRRLVDVS--KRDISASLFGKVWSAPLVIAP-TGLNGAFWPNGDL 84 Query: 78 NLAIAAEKTKVAMAVGSQRVM 98 LA AA K + + + M Sbjct: 85 ALARAAAKAGIPFVLSTASNM 105 >gnl|CDD|144171 pfam00478, IMPDH, IMP dehydrogenase / GMP reductase domain. This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel structure. In the inosine monophosphate dehydrogenases 2 CBS domains pfam00571 are inserted in the TIM barrel. This family is a member of the common phosphate binding site TIM barrel family. Length = 467 Score = 32.2 bits (74), Expect = 0.18 Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 3/28 (10%) Query: 262 IASGGLRNGVDILKSIILGAS---LGGL 286 IA GG+R DI K++ GAS LG L Sbjct: 330 IADGGIRYSGDIAKALAAGASAVMLGSL 357 >gnl|CDD|72988 cd03229, ABC_Class3, This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 178 Score = 30.5 bits (69), Expect = 0.61 Identities = 23/105 (21%), Positives = 44/105 (41%), Gaps = 11/105 (10%) Query: 217 GGTSWSRIE-SHRDLESDIGIVFQDWGIPTPLSLEMARPYCNEAQFIASGGLRNGVDILK 275 G + +E L IG+VFQD+ + L++ SGG + V + + Sbjct: 60 DGEDLTDLEDELPPLRRRIGMVFQDFALFPHLTVL------ENIALGLSGGQQQRVALAR 113 Query: 276 SIILGASLGGLASPF--LKPAMDSSDAVVAAIESLRKEFIVSMFL 318 ++ + + L P L P V A ++SL+ + +++ L Sbjct: 114 ALAMDPDVLLLDEPTSALDPITRRE--VRALLKSLQAQLGITVVL 156 >gnl|CDD|73364 cd00381, IMPDH, IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine nucleotides. There is often a CBS domain inserted in the middle of this domain, which is proposed to play a regulatory role. IMPDH is a key enzyme in the regulation of cell proliferation and differentiation. It has been identified as an attractive target for developing chemotherapeutic agents.. Length = 325 Score = 30.5 bits (69), Expect = 0.74 Identities = 12/29 (41%), Positives = 16/29 (55%) Query: 262 IASGGLRNGVDILKSIILGASLGGLASPF 290 IA GG+R DI+K++ GA L S Sbjct: 201 IADGGIRTSGDIVKALAAGADAVMLGSLL 229 >gnl|CDD|32253 COG2070, COG2070, Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]. Length = 336 Score = 30.3 bits (68), Expect = 0.81 Identities = 11/40 (27%), Positives = 19/40 (47%) Query: 252 ARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLASPFL 291 + IA+GG+ +G I ++ LGA + + FL Sbjct: 178 VVDAVDGIPVIAAGGIADGRGIAAALALGADGVQMGTRFL 217 >gnl|CDD|73401 cd04739, DHOD_like, Dihydroorotate dehydrogenase (DHOD) like proteins. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. This subgroup has the conserved FMN binding site, but lacks some catalytic residues and may therefore be inactive.. Length = 325 Score = 30.2 bits (68), Expect = 0.95 Identities = 14/50 (28%), Positives = 27/50 (54%) Query: 258 EAQFIASGGLRNGVDILKSIILGASLGGLASPFLKPAMDSSDAVVAAIES 307 +A ASGG+ + D++K ++ GA + S L+ D ++A +E+ Sbjct: 237 KASLAASGGVHDAEDVVKYLLAGADVVMTTSALLRHGPDYIGTLLAGLEA 286 >gnl|CDD|176716 cd09014, BphC-JF8_C_like, C-terminal, catalytic, domain of BphC_JF8, (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Bacillus sp. JF8 and similar proteins. 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, a key step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). BphC belongs to the type I extradiol dioxygenase family, which requires a metal ion in the active site in its catalytic mechanism. Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of BphCs. This subfamily of BphC is represented by the enzyme purified from the thermophilic biphenyl and naphthalene degrader, Bacillus sp. JF8. The members in this family of BphC enzymes may use either Mn(II) or Fe(II) as cofactors. The enzyme purified from Bacillus sp. JF8 is Mn(II)-dependent, however, the enzyme from Rhodococcus jostii RHAI has Fe(II) bound to it. BphC_JF8 is thermostable and its optimum activity is at 85 degrees C. The enzymes in this family have an internal duplication. This family represents the C-terminal repeat. Length = 166 Score = 28.8 bits (65), Expect = 2.0 Identities = 9/27 (33%), Positives = 17/27 (62%), Gaps = 2/27 (7%) Query: 2 VNDRKIDHINIVCKDPGIDRNKKFFDD 28 V R++DH+N++ D D N+ F ++ Sbjct: 2 VGVRRLDHVNLLASDV--DANRDFMEE 26 >gnl|CDD|73372 cd02810, DHOD_DHPD_FMN, Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.. Length = 289 Score = 28.7 bits (64), Expect = 2.1 Identities = 38/191 (19%), Positives = 74/191 (38%), Gaps = 19/191 (9%) Query: 109 ELRQYAPHTVLISNLGAVQLN-YDFGVQKAHQAVHVLGADGLFLHLNPLQEIIQPNGNTN 167 + ++ P LI+++G Y +K +A GA L L+L+ + Sbjct: 91 KAKKEFPGQPLIASVGGSSKEDYVELARKIERA----GAKALELNLSCPNVGGGRQLGQD 146 Query: 168 FADLSSKIALLSSAMDVPLLLKEVGCGLSSMDIELGLKS----GIRYF----DIAGRGGT 219 +++ + + +A+D+PLL+K + DI K+ G I+GR Sbjct: 147 PEAVANLLKAVKAAVDIPLLVK-LSPYFDLEDIVELAKAAERAGADGLTAINTISGRVVD 205 Query: 220 SWSRIESHRDLESDIGIVFQDWGIPTPLSL--EMARPYCNEAQFIASGGLRNGVDILKSI 277 + + + P L +A + I GG+ +G D+L+ + Sbjct: 206 LKTVGPGPKRGTGGLS---GAPIRPLALRWVARLAARLQLDIPIIGVGGIDSGEDVLEML 262 Query: 278 ILGASLGGLAS 288 + GAS +A+ Sbjct: 263 MAGASAVQVAT 273 >gnl|CDD|153133 cd01583, IPMI, 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate. Aconatase-like catalytic domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-isopropylmalate. IPMI is involved in fungal and bacterial leucine biosynthesis and is also found in eukaryotes. Length = 382 Score = 27.9 bits (63), Expect = 4.3 Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 6/51 (11%) Query: 195 LSSMDIELGLKSGIRYFD------IAGRGGTSWSRIESHRDLESDIGIVFQ 239 L +M IE G K+GI D + GRG W ++S D E D + Sbjct: 183 LCNMAIEAGAKAGIVAPDETTFEYLKGRGKAYWKELKSDEDAEYDKVVEID 233 >gnl|CDD|176555 cd08616, PI-PLCXD1c, Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing 1. This subfamily corresponds to the catalytic domain present in a group of phosphatidylinositol-specific phospholipase C X domain containing 1 (PI-PLCXD1), 2 (PI-PLCXD2) and 3 (PI-PLCXD3), which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs found in vertebrates. The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, members in this group contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of eukaryotic PI-PLCXDs still remains unclear, it may distinct from that of typical eukaryotic PI-PLCs. Length = 290 Score = 27.6 bits (62), Expect = 4.5 Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 10/41 (24%) Query: 197 SMDIELGLKSGIRYFDIAGRGGTSWSRIESHRDLESDIGIV 237 S+ I L++GIRYFD+ RI + + ++D+ V Sbjct: 61 SLTITEQLEAGIRYFDL---------RI-ATKPKDNDLYFV 91 >gnl|CDD|176528 cd08586, PI-PLCc_BcPLC_like, Catalytic domain of Bacillus cereus phosphatidylinositol-specific phospholipases C and similar proteins. This subfamily corresponds to the catalytic domain present in Bacillus cereus phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) and its sequence homologs found in bacteria and eukaryota. Bacterial PI-PLCs participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although their precise physiological function remains unclear, bacterial PI-PLCs may function as virulence factors in some pathogenic bacteria. Bacterial PI-PLCs contain a single TIM-barrel type catalytic domain. Their catalytic mechanism is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This family also includes some uncharacterized eukaryotic homologs, which contains a single TIM-barrel type catalytic domain, X domain. They are similar to bacterial PI-PLCs, and distinct from typical eukaryotic PI-PLCs, which have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains, and strictly require Ca2+ for their catalytic activities. The prototype of this family is Bacillus cereus PI-PLC, which has a moderate thermal stability and is active as a monomer. Length = 279 Score = 27.6 bits (62), Expect = 5.4 Identities = 7/17 (41%), Positives = 9/17 (52%) Query: 197 SMDIELGLKSGIRYFDI 213 I L +GIR+ DI Sbjct: 36 DWSIAEQLNAGIRFLDI 52 >gnl|CDD|30516 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]. Length = 310 Score = 27.1 bits (60), Expect = 6.8 Identities = 11/43 (25%), Positives = 20/43 (46%) Query: 250 EMARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLASPFLK 292 E+ + + I GG+ G D L+ I+ GAS + + + Sbjct: 233 ELYKRLGGDIPIIGVGGIETGEDALEFILAGASAVQVGTALIY 275 >gnl|CDD|176529 cd08587, PI-PLCXDc_like, Catalytic domain of phosphatidylinositol-specific phospholipase C X domain containing and similar proteins. This family corresponds to the catalytic domain present in phosphatidylinositol-specific phospholipase C X domain containing proteins (PI-PLCXD) which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs mainly found in eukaryota. The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, eukaryotic PI-PLCXDs and their bacterial homologs contain a single TIM-barrel type catalytic domain, X domain, which is more closely related to that of bacterial PI-PLCs. Although the biological function of eukaryotic PI-PLCXDs still remains unclear, it may be distinct from that of typical eukaryotic PI-PLCs. Length = 288 Score = 26.9 bits (60), Expect = 7.3 Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 9/31 (29%) Query: 204 LKSGIRYFDIAGRGGTSWSRIESHRDLESDI 234 L++GIRYFD+ R+ D E+ + Sbjct: 61 LEAGIRYFDL---------RVAYKPDSENKL 82 >gnl|CDD|30622 COG0274, DeoC, Deoxyribose-phosphate aldolase [Nucleotide transport and metabolism]. Length = 228 Score = 26.7 bits (59), Expect = 8.4 Identities = 12/38 (31%), Positives = 15/38 (39%) Query: 251 MARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLAS 288 M ASGG+R D I GA+ G +S Sbjct: 176 MKETVGGRVGVKASGGIRTAEDAKAMIEAGATRIGTSS 213 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.321 0.138 0.400 Gapped Lambda K H 0.267 0.0731 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,063,342 Number of extensions: 217808 Number of successful extensions: 538 Number of sequences better than 10.0: 1 Number of HSP's gapped: 520 Number of HSP's successfully gapped: 39 Length of query: 337 Length of database: 6,263,737 Length adjustment: 94 Effective length of query: 243 Effective length of database: 4,232,491 Effective search space: 1028495313 Effective search space used: 1028495313 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 (21.8 bits) S2: 58 (26.1 bits)