RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780434|ref|YP_003064847.1| dihydroorotate dehydrogenase 2 [Candidatus Liberibacter asiaticus str. psy62] (362 letters) >gnl|CDD|73400 cd04738, DHOD_2_like, Dihydroorotate dehydrogenase (DHOD) class 2. 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, their cellular location and their natural electron acceptor used to reoxidize the flavin group. Members of class 1 are cytosolic enzymes and multimers, while class 2 enzymes are membrane associated, monomeric and use respiratory quinones as their physiological electron acceptors.. Length = 327 Score = 412 bits (1061), Expect = e-116 Identities = 174/328 (53%), Positives = 223/328 (67%), Gaps = 10/328 (3%) Query: 13 LTHLDPEIAHHLSIVALKSGLLSFFP---VHSDPRLNTKVAGISLSNPLGMAAGYDKNAE 69 L LDPE AH L+I ALK GL V+ DPRL +V G++ NP+G+AAG+DKNAE Sbjct: 4 LFLLDPETAHRLAIRALKLGLGPPLLLLLVYDDPRLEVEVFGLTFPNPVGLAAGFDKNAE 63 Query: 70 VPIELLKLGFGFVEIGTVTPHPQAGNPRPRVFRLTKDRAIINKLGFNNAGYHTVFSRLSK 129 LL LGFGFVE+GTVTP PQ GNP+PR+FRL +D A+IN++GFNN G V RL K Sbjct: 64 AIDALLALGFGFVEVGTVTPRPQPGNPKPRLFRLPEDEALINRMGFNNDGADAVAKRLKK 123 Query: 130 IQP-TSPIGINLGANKDSK--DFILDYVSGIRLFFTIASYFTINISSPNTPGLRSLQKKK 186 +P P+G+N+G NKD+ D + DYV G+R A Y +N+SSPNTPGLR LQ K+ Sbjct: 124 RRPRGGPLGVNIGKNKDTPLEDAVEDYVIGVRKLGPYADYLVVNVSSPNTPGLRDLQGKE 183 Query: 187 NLERLLIHVMQTREEEKIKTGKFVPIFLKISPDLSEEELDDIAVEVLSHKVEGIIVSNTT 246 L LL V EE+ K GK VP+ +KI+PDLS+EEL+DIA L H V+GII +NTT Sbjct: 184 ALRELLTAVK----EERNKLGKKVPLLVKIAPDLSDEELEDIADVALEHGVDGIIATNTT 239 Query: 247 LSRKGVQCSDNHEQDGGLSGSPLFLKSTIALAKIRQRVGPKIAIIGTGGISSTKDALDKI 306 +SR G+ S + GGLSG+PL +ST L ++ + G KI IIG GGISS +DA +KI Sbjct: 240 ISRPGLLRSPLANETGGLSGAPLKERSTEVLRELYKLTGGKIPIIGVGGISSGEDAYEKI 299 Query: 307 MAGANLIQLYSAMIYEGISLPKRIIQGL 334 AGA+L+QLY+ ++YEG L KRI + L Sbjct: 300 RAGASLVQLYTGLVYEGPGLVKRIKREL 327 >gnl|CDD|36649 KOG1436, KOG1436, KOG1436, Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]. Length = 398 Score = 323 bits (828), Expect = 6e-89 Identities = 169/344 (49%), Positives = 225/344 (65%), Gaps = 9/344 (2%) Query: 16 LDPEIAHHLSIVALKSGLLSFFPVHSDPRLNTKVAGISLSNPLGMAAGYDKNAEVPIELL 75 LDPE +H L+++A GLL V D L TKV G SNP+G+AAG+DKNAE L Sbjct: 55 LDPEFSHRLAVLAASWGLLPRDRVADDASLETKVLGRKFSNPIGLAAGFDKNAEAIDGLA 114 Query: 76 KLGFGFVEIGTVTPHPQAGNPRPRVFRLTKDRAIINKLGFNNAGYHTVFSRLSKI----- 130 GFGF+EIG+VTP PQ GNP+PRVFRL +D A+IN+ GFN+ G V RL Sbjct: 115 NSGFGFIEIGSVTPKPQEGNPKPRVFRLPEDLAVINRYGFNSEGIDAVLQRLRAKRQAKY 174 Query: 131 -QPTSPIGINLGANKDSKDFILDYVSGIRLFFTIASYFTINISSPNTPGLRSLQKKKNLE 189 + + +G+NLG NK S+D ILDYV G+R+F A Y IN+SSPNTPGLRSLQKK +L Sbjct: 175 PEAPAKLGVNLGKNKTSEDAILDYVEGVRVFGPFADYLVINVSSPNTPGLRSLQKKSDLR 234 Query: 190 RLLIHVMQTREEEKIKTGKFVPIFLKISPDLSEEELDDIAVEVLSHKVEGIIVSNTTLSR 249 +LL V+Q R +K+ GK P+ +KI+PDLSE+EL DIA+ V ++G+IVSNTT+SR Sbjct: 235 KLLTKVVQAR--DKLPLGKKPPVLVKIAPDLSEKELKDIALVVKKLNIDGLIVSNTTVSR 292 Query: 250 -KGVQCSDNHEQDGGLSGSPLFLKSTIALAKIRQRVGPKIAIIGTGGISSTKDALDKIMA 308 K + E+ GGLSG PL ST + + KI IIG GG+SS KDA +KI A Sbjct: 293 PKASLVNKLKEETGGLSGPPLKPISTNTVRAMYTLTRGKIPIIGCGGVSSGKDAYEKIRA 352 Query: 309 GANLIQLYSAMIYEGISLPKRIIQGLSDFLNKENEVNFENIRGS 352 GA+L+QLY+A++YEG ++ ++I + LS L + + ++ G Sbjct: 353 GASLVQLYTALVYEGPAIIEKIKRELSALLKAKGFTSVDDAIGK 396 >gnl|CDD|30516 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]. Length = 310 Score = 279 bits (714), Expect = 1e-75 Identities = 121/318 (38%), Positives = 182/318 (57%), Gaps = 21/318 (6%) Query: 44 RLNTKVAGISLSNPLGMAAGYD-KNAEVPIELLKLGFGFVEIGTVTPHPQAGNPRPRVFR 102 L+T++ G+ NPLG+AAG+D KN E L LGFG + TVTP PQ GNP+PR+FR Sbjct: 1 DLSTEILGLKFPNPLGLAAGFDGKNGEELDALAALGFGAIVTKTVTPEPQEGNPKPRLFR 60 Query: 103 LTKDRAIINKLGFNNAGYHTVFSRLSKIQPT-SPIGINLGANKD--SKDFILDYVSGIRL 159 L +D +IN++GFNN G L + PIG+N+G NK S++ DY + Sbjct: 61 LPEDEGLINRMGFNNPGADAFLEELKLAKYEGKPIGVNIGKNKGGPSEEAWADYARLLEE 120 Query: 160 FFTIASYFTINISSPNTPGLRSLQKKKN-LERLLIHVMQTREEEKIKTGKFVPIFLKISP 218 A +NIS PNTPG R+L + LE+LL E +K VP+F+K++P Sbjct: 121 AGD-ADAIELNISCPNTPGGRALGQDPELLEKLL---------EAVKAATKVPVFVKLAP 170 Query: 219 DLSEEELDDIAVEVLSHKVEGIIVSNTTLSR----KGVQCSDNHEQDGGLSGSPLFLKST 274 + ++D+IA +G+I NTT S + + GGLSG PL + Sbjct: 171 N--ITDIDEIAKAAEEAGADGLIAINTTKSGMKIDLETKKPVLANETGGLSGPPLKPIAL 228 Query: 275 IALAKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMIYEGISLPKRIIQGL 334 +A++ +R+G I IIG GGI + +DAL+ I+AGA+ +Q+ +A+IY+G + K II+GL Sbjct: 229 RVVAELYKRLGGDIPIIGVGGIETGEDALEFILAGASAVQVGTALIYKGPGIVKEIIKGL 288 Query: 335 SDFLNKENEVNFENIRGS 352 + +L ++ + ++I GS Sbjct: 289 ARWLEEKGFESIQDIIGS 306 >gnl|CDD|144683 pfam01180, DHO_dh, Dihydroorotate dehydrogenase. Length = 290 Score = 251 bits (643), Expect = 2e-67 Identities = 116/306 (37%), Positives = 170/306 (55%), Gaps = 27/306 (8%) Query: 44 RLNTKVAGISLSNPLGMAAGYDKNAEVPIELLKLG-FGFVEIGTVTPHPQAGNPRPRVFR 102 L K+ G+ NP+G+A+G+DK E ++ L LG FG +EI +VTP PQ GNP PRVFR Sbjct: 1 MLAVKIPGLKFKNPIGLASGFDKFGEEALKWLALGKFGAIEIKSVTPEPQPGNPTPRVFR 60 Query: 103 LTKDRAIINKLGFNNAGYHTVFSRLSKIQP--TSPIGINLGANKDSKDFILDYVSGIRLF 160 L + ++N +G NN G V L K + P+GI L + + DYV R Sbjct: 61 LPEG--VLNAMGLNNPGLDAVLEELLKRRKEYPRPLGIILSKAGSTVE---DYVEVARKI 115 Query: 161 FTIASYFTINISSPNTPGLRSLQKKKNLERLLIHVMQTREEEKIKTGKFVPIFLKISPDL 220 A Y +N+S PNTPGLR+LQ L +L+ V++ + VP+ +K++PDL Sbjct: 116 GPFADYLELNVSCPNTPGLRALQTDPELAAILLKVVKEVSK--------VPVLVKLAPDL 167 Query: 221 SEEELDDIAVEVLS-HKVEGIIVSNTTLSR--KGVQCSDNHEQD--GGLSGSPLFLKSTI 275 ++ + DIA + GI +NTT+ ++ + GGLSG + I Sbjct: 168 TDIVIIDIADVAAGEDGLTGINATNTTVRGMRIDLKTESPILANGTGGLSGPAI---KPI 224 Query: 276 ALAKIR---QRVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMIYEGISLPKRIIQ 332 AL IR QRVGP+I IIG GGI + +DAL+KI+AGA+ +Q+ +A+I+ G + +II Sbjct: 225 ALKVIRELYQRVGPEIPIIGVGGIFTGEDALEKILAGASAVQIGTALIFGGPFIFPKIID 284 Query: 333 GLSDFL 338 L + L Sbjct: 285 ELPELL 290 >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 = 165 bits (420), Expect = 1e-41 Identities = 86/302 (28%), Positives = 140/302 (46%), Gaps = 28/302 (9%) Query: 47 TKVAGISLSNPLGMAAGYDKNAEVPIELL-KLGFGFVEIGTVTPHPQAGNPRPRVFRLTK 105 G+ L NP G+AAG I GFG V TVT HP+ GNP PRV RL Sbjct: 1 VNFLGLKLKNPFGVAAGPLLKTGELIARAAAAGFGAVVYKTVTLHPRPGNPLPRVARLPP 60 Query: 106 DR-------AIINKLGFNNAGYHTVFSRLSKIQ---PTSPIGINLGANKDSKDFILDYVS 155 + I+N G N G ++K + P P+ ++G + SK+ ++ Sbjct: 61 EGESYPEQLGILNSFGLPNLGLDVWLQDIAKAKKEFPGQPLIASVGGS--SKEDYVELAR 118 Query: 156 GIRLFFTIASYFTINISSPNTPGLRSL-QKKKNLERLLIHVMQTREEEKIKTGKFVPIFL 214 I A +N+S PN G R L Q + + LL + +K +P+ + Sbjct: 119 KIERAG--AKALELNLSCPNVGGGRQLGQDPEAVANLL---------KAVKAAVDIPLLV 167 Query: 215 KISPDLSEEELDDIAVEVLSHKVEGIIVSNTTLSRKGVQCSD---NHEQDGGLSGSPLFL 271 K+SP E++ ++A +G+ NT R + GGLSG+P+ Sbjct: 168 KLSPYFDLEDIVELAKAAERAGADGLTAINTISGRVVDLKTVGPGPKRGTGGLSGAPIRP 227 Query: 272 KSTIALAKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMIYEGISLPKRII 331 + +A++ R+ I IIG GGI S +D L+ +MAGA+ +Q+ +A++++G + ++I Sbjct: 228 LALRWVARLAARLQLDIPIIGVGGIDSGEDVLEMLMAGASAVQVATALMWDGPDVIRKIK 287 Query: 332 QG 333 + Sbjct: 288 KE 289 >gnl|CDD|73402 cd04740, DHOD_1B_like, Dihydroorotate dehydrogenase (DHOD) class 1B 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.. Length = 296 Score = 109 bits (273), Expect = 1e-24 Identities = 78/320 (24%), Positives = 144/320 (45%), Gaps = 40/320 (12%) Query: 47 TKVAGISLSNPLGMAAG-YDKNAEVPIELLKLGFGFVEIGTVTPHPQAGNPRPRVFRLTK 105 ++AG+ L NP+ +A+G + E+ G + ++T P+ GNP PRV Sbjct: 2 VELAGLRLKNPVILASGTFGFGEELSRVADLGKLGAIVTKSITLEPREGNPPPRVVETP- 60 Query: 106 DRAIINKLGFNNAGYHTVFSRLS--KIQPTSPIGINLGANKDSKDFILDYVSGIRLFFTI 163 ++N +G N G L + +P+ ++ + + ++V Sbjct: 61 -GGMLNAIGLQNPGVEAFLEELLPWLREFGTPVIASIAG--STVE---EFVEVAEKLADA 114 Query: 164 -ASYFTINISSPNTP--GLRSLQKKKNLERLLIHVMQTREEEKIKTGKFVPIFLKISPDL 220 A +NIS PN G+ + + ++ + +K VP+ +K++P++ Sbjct: 115 GADAIELNISCPNVKGGGMAFGTDPEAVAEIV---------KAVKKATDVPVIVKLTPNV 165 Query: 221 SEEELDDIAVEVLSHKVEGIIVSNTTL-------SRKGVQCSDNHEQDGGLSGSPLFLKS 273 ++ + +IA +G+ + NT +RK + + GGLSG + Sbjct: 166 TD--IVEIARAAEEAGADGLTLINTLKGMAIDIETRKPILGNVT----GGLSGPAIK--- 216 Query: 274 TIALAKIRQ-RVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMIYEGISLPKRIIQ 332 IAL + Q +I IIG GGI+S +DAL+ +MAGA+ +Q+ +A + K II+ Sbjct: 217 PIALRMVYQVYKAVEIPIIGVGGIASGEDALEFLMAGASAVQVGTA-NFVDPEAFKEIIE 275 Query: 333 GLSDFLNKENEVNFENIRGS 352 GL +L++E + E + G Sbjct: 276 GLEAYLDEEGIKSIEELVGL 295 >gnl|CDD|37010 KOG1799, KOG1799, KOG1799, Dihydropyrimidine dehydrogenase [Nucleotide transport and metabolism]. Length = 471 Score = 76.7 bits (188), Expect = 9e-15 Identities = 71/362 (19%), Positives = 137/362 (37%), Gaps = 38/362 (10%) Query: 23 HLSIVALKSGLLSFFPVHSDPRLNTKVAGISLSNPLGMAAG-YDKNAEVPIELLKLGFGF 81 +++ +GL + + S L G +NP + AE+ G+G+ Sbjct: 82 DFTVIEDYTGLKALLYLKSIEELVD-WDGQKPANPFHQKSKPPPTIAELMDRAFPSGWGY 140 Query: 82 VEIGTVT-PHPQAGNPRPRVFRLTKDRA----------IINKLGFNNAGYH-TVFSRLSK 129 +E T + N PRV R R+ I + A + F L Sbjct: 141 LEQKTKILDENKVRNVEPRVARSPTKRSCFIPKRPIPTNIELISDRKAEQYLGTFGELKN 200 Query: 130 IQPTSPIGINLGANKDSKDFILDYVSGIRLFFTIASYFTINISSPNTPGLRSLQKKKNLE 189 ++P + + + K ++ SG + N+S P+ R + Sbjct: 201 VEPVVIMIASEMCIYNKKCWMELNDSGEQ---AGQDDLETNLSCPHGMCERGMGLALGQC 257 Query: 190 RLLIHVMQTREEEKIKTGKFVPIFLKISPDLSEEELDDIAVEVLSHKVEGIIVSNTTLSR 249 ++ + K +P+ K++P++ + ++A V EGI NT +S Sbjct: 258 PIVDCEVCGWINAKAT----IPMVSKMTPNI--TDKREVARSVNPVGCEGIAAINTIMSV 311 Query: 250 KGVQ--------CSDNHEQDGGLSGS---PLFLKSTIALAKIRQRVGPKIAIIGTGGISS 298 G+ C + + GG S P+ L + +AK+ + + ++ G GG+ + Sbjct: 312 MGIDMKTLRPEPCVEGYSTPGGYSYKAVRPIALAKVMNIAKMMK----EFSLSGIGGVET 367 Query: 299 TKDALDKIMAGANLIQLYSAMIYEGISLPKRIIQGLSDFLNKENEVNFENIRGSYTEYWA 358 DA + I+ G+N +Q+ + ++ G K + L DF+ + N E RG +Y+ Sbjct: 368 GYDAAEFILLGSNTVQVCTGVMMHGYGHVKTLCAELKDFMKQHNFSTIEEFRGHSLQYFT 427 Query: 359 KK 360 Sbjct: 428 TH 429 >gnl|CDD|73403 cd04741, DHOD_1A_like, Dihydroorotate dehydrogenase (DHOD) class 1A 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.. Length = 294 Score = 76.5 bits (188), Expect = 1e-14 Identities = 75/312 (24%), Positives = 120/312 (38%), Gaps = 42/312 (13%) Query: 47 TKVAGISLSNPLGMAAG-YDKNAEVPIELLKLGFGFVEIGTVTPHPQAGNPRPRVFRLTK 105 G+++S PL AAG + E +EL G V + T + GNP PR + Sbjct: 1 VTPPGLTISPPLMNAAGPWCTTLEDLLELAASSTGAVTTRSSTLAGRPGNPEPRYYAFPL 60 Query: 106 DRAIINKLGFNNAGYHTVFSRLSKIQPTSPIGINLGANKDSKDFIL-------DYVSGIR 158 IN LG N G + I G +K F + D + + Sbjct: 61 --GSINSLGLPNLGLDYYLEYIRTISD--------GLPGSAKPFFISVTGSAEDIAAMYK 110 Query: 159 LFFTIASYFT----INISSPNTPGLRSLQKKKNLERLLIHVMQTREEEKIKTGKFVPIFL 214 F +N+S PN PG + + L ++ +K +P+ + Sbjct: 111 KIAAHQKQFPLAMELNLSCPNVPG--KPPPAYDFDATLEYL------TAVKAAYSIPVGV 162 Query: 215 KISPDLSEEELDDIAVEVLSHKVEGI--IVSNTTLSRKGVQCSDNHEQD--------GGL 264 K P + D +A E L+ I I + TL G+ E GGL Sbjct: 163 KTPPYTDPAQFDTLA-EALNAFACPISFITATNTLG-NGLVLDPERETVVLKPKTGFGGL 220 Query: 265 SGSPLFLKSTIALAKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMIYEGI 324 +G+ L + + R+ + +I IIG GG+ + A +AGA+ +Q+ +A+ EG Sbjct: 221 AGAYLHPLALGNVRTFRRLLPSEIQIIGVGGVLDGRGAFRMRLAGASAVQVGTALGKEGP 280 Query: 325 SLPKRIIQGLSD 336 + RI + L D Sbjct: 281 KVFARIEKELED 292 >gnl|CDD|73382 cd02940, DHPD_FMN, Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. 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 the dimer interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.. Length = 299 Score = 73.0 bits (179), Expect = 1e-13 Identities = 68/314 (21%), Positives = 125/314 (39%), Gaps = 40/314 (12%) Query: 45 LNTKVAGISLSNPLGMAAG-YDKNAEVPIELLKLGFGFVEIGTVTP-HPQAGNPRPRVFR 102 L+ GI NP G+A+ + + + G+G T+ N PR+ R Sbjct: 2 LSVTFCGIKFPNPFGLASAPPTTSYPMIRRAFEAGWGGAVTKTLGLDKDIVTNVSPRIAR 61 Query: 103 LTKDRAIINKLGFNN---------AGYHTVFSRLSKIQPTSPI--GINLGANKDSKDFIL 151 L ++GFNN + L K P + I NK+ + Sbjct: 62 LRTSGR--GQIGFNNIELISEKPLEYWLKEIRELKKDFPDKILIASIMCEYNKEDWTELA 119 Query: 152 DYVSGIRLFFTIASYFTINISSPNTPGLRSLQKKKNLERLLIHVMQTREEEKIKTGKFVP 211 V A +N S P+ R + + L+ R ++ +P Sbjct: 120 KLVEE-----AGADALELNFSCPHGMPERGMGAAVGQDPELVE-EICRW---VREAVKIP 170 Query: 212 IFLKISPDLSEEELDDIAVEVLSHKVEGIIVSNTTLSRKGVQ--------CSDNHEQDGG 263 + K++P++++ + +IA +G+ NT S GV + GG Sbjct: 171 VIAKLTPNITD--IREIARAAKEGGADGVSAINTVNSLMGVDLDGTPPAPGVEGKTTYGG 228 Query: 264 LSGS---PLFLKSTIALAKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMI 320 SG P+ L+ A+++I + P + I G GGI S +DA + ++ GA+++Q+ +A++ Sbjct: 229 YSGPAVKPIALR---AVSQIARAPEPGLPISGIGGIESWEDAAEFLLLGASVVQVCTAVM 285 Query: 321 YEGISLPKRIIQGL 334 +G ++ + GL Sbjct: 286 NQGFTIVDDMCTGL 299 >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 = 47.1 bits (112), Expect = 8e-06 Identities = 32/153 (20%), Positives = 67/153 (43%), Gaps = 24/153 (15%) Query: 210 VPIFLKISPDLSEEELDDIAVEVLSHKVEGIIVSN---------TTLS-RKGVQCSDNHE 259 +P+ +K+SP S L +A ++ + +G+++ N TL + S E Sbjct: 164 IPVAVKLSPFFSA--LAHMAKQLDAAGADGLVLFNRFYQPDIDLETLEVVPNLLLSSPAE 221 Query: 260 QDGGLSGSPLFLKSTIALAKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAM 319 L +A + RV +A +GG+ +D + ++AGA+++ SA+ Sbjct: 222 IRLPLRW----------IAILSGRVKASLAA--SGGVHDAEDVVKYLLAGADVVMTTSAL 269 Query: 320 IYEGISLPKRIIQGLSDFLNKENEVNFENIRGS 352 + G ++ GL ++ + + + +RGS Sbjct: 270 LRHGPDYIGTLLAGLEAWMEEHGYESVQQLRGS 302 >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 = 41.6 bits (98), Expect = 3e-04 Identities = 28/96 (29%), Positives = 43/96 (44%), Gaps = 23/96 (23%) Query: 229 AVEVLSHKVEGIIVSNTTLSRKGVQCSDNHEQDGG--LSGSPLFLKSTI-ALAKIRQRVG 285 A+ + +GI+VSN H GG L G+P +TI AL +I VG Sbjct: 186 ALRAVDAGADGIVVSN-------------H---GGRQLDGAP----ATIDALPEIVAAVG 225 Query: 286 PKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMIY 321 +I ++ GGI D L + GA+ + + +Y Sbjct: 226 GRIEVLLDGGIRRGTDVLKALALGADAVLIGRPFLY 261 >gnl|CDD|144604 pfam01070, FMN_dh, FMN-dependent dehydrogenase. Length = 301 Score = 41.3 bits (98), Expect = 5e-04 Identities = 38/118 (32%), Positives = 54/118 (45%), Gaps = 35/118 (29%) Query: 210 VPIFLK--ISPDLSEEELDDIAVEVLSHKVEGIIVSNTTLSRKGVQCSDNHEQDGG--LS 265 P+ LK +SP+ D A + V+GI+VSN H GG L Sbjct: 170 GPLVLKGILSPE-------D-AKRAVEAGVDGIVVSN-------------H---GGRQLD 205 Query: 266 GSPLFLKSTI-ALAKIRQRVGPKIAIIGTGGISSTKDALDKIMA-GANLIQLYSAMIY 321 G+P +TI AL +I VG +I ++ GGI D L K +A GA+ + L +Y Sbjct: 206 GAP----ATIDALPEIVAAVGGRIPVLVDGGIRRGTDVL-KALALGADAVLLGRPFLY 258 >gnl|CDD|31495 COG1304, LldD, L-lactate dehydrogenase (FMN-dependent) and related alpha-hydroxy acid dehydrogenases [Energy production and conversion]. Length = 360 Score = 36.8 bits (85), Expect = 0.009 Identities = 26/114 (22%), Positives = 46/114 (40%), Gaps = 14/114 (12%) Query: 222 EEELDDIAVEVLSHKVEGIIVSNTT--LSRKGVQCSDNHEQDGGLSGSPLFLK------- 272 E + ++V V+S + I L KG+ ++ GG + + Sbjct: 194 AEYVSALSVPVISKEDGAGISKEWAGPLVLKGILAPEDAAGAGGTGADGIEVSNHGGRQL 253 Query: 273 ----STI-ALAKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMIY 321 ST +L +I + VG +I +I GGI S D + GA+ + + +Y Sbjct: 254 DWGISTADSLPEIVEAVGDRIEVIADGGIRSGLDVAKALALGADAVGIGRPFLY 307 >gnl|CDD|32253 COG2070, COG2070, Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]. Length = 336 Score = 34.2 bits (78), Expect = 0.061 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 2/61 (3%) Query: 262 GGLSGSPLFLKSTIAL-AKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMI 320 GG G ST AL ++ V I +I GGI+ + + GA+ +Q+ + + Sbjct: 159 GGHRGGVDLEVSTFALVPEVVDAV-DGIPVIAAGGIADGRGIAAALALGADGVQMGTRFL 217 Query: 321 Y 321 Sbjct: 218 A 218 >gnl|CDD|30622 COG0274, DeoC, Deoxyribose-phosphate aldolase [Nucleotide transport and metabolism]. Length = 228 Score = 32.1 bits (73), Expect = 0.23 Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 9/55 (16%) Query: 280 IRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMIYEGISLPKRIIQGL 334 +++ VG ++ + +GGI + +DA I AGA I G S I++GL Sbjct: 176 MKETVGGRVGVKASGGIRTAEDAKAMIEAGATRI---------GTSSGVAILEGL 221 >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 = 32.1 bits (73), Expect = 0.26 Identities = 26/102 (25%), Positives = 44/102 (43%), Gaps = 27/102 (26%) Query: 211 PIFLK--ISPDLSEEELDDIAVEVLSHKVEGIIVSNTTLSRKGVQCSDNHEQDGGLSGSP 268 PI LK + PD D A + V+G++VSN G Q DG ++ Sbjct: 255 PIVLKGILHPD-------D-ARRAVEAGVDGVVVSN----HGGRQ------VDGSIA--- 293 Query: 269 LFLKSTIALAKIRQRVGPKIAIIGTGGISSTKDALDKIMAGA 310 + AL +I + VG ++ ++ G+ + D + + GA Sbjct: 294 ----ALDALPEIVEAVGDRLTVLFDSGVRTGADIMKALALGA 331 >gnl|CDD|107273 cd06278, PBP1_LacI_like_2, Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Length = 266 Score = 31.4 bits (72), Expect = 0.42 Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 4/51 (7%) Query: 209 FVPIFLKISPDLSEEELDDIAVEVLSHKVEGIIVSNTTLSRKGV-QCSDNH 258 + P+ + D E+LD ++L ++V+G+IV++ TLS + +C N Sbjct: 30 YQPLLINTDDD---EDLDAALRQLLQYRVDGVIVTSGTLSSELAEECRRNG 77 >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 = 31.3 bits (71), Expect = 0.44 Identities = 30/161 (18%), Positives = 58/161 (36%), Gaps = 40/161 (24%) Query: 171 ISSPNTPGLRSLQKKKNLERLLIHVMQTREEEKIKTGKFVPIFLKISPDLSEEELDDIAV 230 IS P + S+ E L + RE PI +K+ + DIA Sbjct: 187 ISPPPHHDIYSI------EDLAQLIEDLREA-----TGGKPIGVKLV---AGHGEGDIAA 232 Query: 231 EVLSHKVEGIIVSNTTLSRKGVQCSDNHEQDGGLSGSPLFLK------STIALAKIRQR- 283 V + + I + +GG +PL + + LA+ Q Sbjct: 233 GVAAAGADFITIDG---------------AEGGTGAAPLTFIDHVGLPTELGLARAHQAL 277 Query: 284 ----VGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMI 320 + ++++I +GG+ + D + GA+ + + +A + Sbjct: 278 VKNGLRDRVSLIASGGLRTGADVAKALALGADAVGIGTAAL 318 >gnl|CDD|73397 cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.. Length = 353 Score = 30.9 bits (70), Expect = 0.57 Identities = 10/43 (23%), Positives = 27/43 (62%) Query: 280 IRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMIYE 322 +++R+ ++ +I G I++ DAL+ + GA+L+ + ++ + Sbjct: 277 VKERIAGRLPLIAVGSINTPDDALEALETGADLVAIGRGLLVD 319 >gnl|CDD|29952 cd00959, DeoC, 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family. DERA belongs to the class I aldolases and catalyzes a reversible aldol reaction between acetaldehyde and glyceraldehyde 3-phosphate to generate 2-deoxyribose 5-phosphate. DERA is unique in catalyzing the aldol reaction between two aldehydes, and its broad substrate specificity confers considerable utility as a biocatalyst, offering an environmentally benign alternative to chiral transition metal catalysis of the asymmetric aldol reaction.. Length = 203 Score = 30.5 bits (69), Expect = 0.65 Identities = 13/34 (38%), Positives = 21/34 (61%) Query: 280 IRQRVGPKIAIIGTGGISSTKDALDKIMAGANLI 313 +++ VG ++ + GGI + +DAL I AGA I Sbjct: 167 MKEAVGGRVGVKAAGGIRTLEDALAMIEAGATRI 200 >gnl|CDD|29940 cd00945, Aldolase_Class_I, Class I aldolases. The class I aldolases use an active-site lysine which stablilzes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin.. Length = 201 Score = 30.3 bits (68), Expect = 0.79 Identities = 13/38 (34%), Positives = 23/38 (60%) Query: 276 ALAKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLI 313 + +++ VG ++ + GGI + +DAL I AGA+ I Sbjct: 161 DVKLMKEAVGGRVGVKAAGGIKTLEDALAAIEAGADGI 198 >gnl|CDD|73384 cd04722, TIM_phosphate_binding, TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.. Length = 200 Score = 30.2 bits (67), Expect = 0.84 Identities = 15/55 (27%), Positives = 26/55 (47%) Query: 261 DGGLSGSPLFLKSTIALAKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQL 315 +GG G L I + G K+ +I GGI+ +DA + + GA+ + + Sbjct: 144 NGGGGGGGRDAVPIADLLLILAKRGSKVPVIAGGGINDPEDAAEALALGADGVIV 198 >gnl|CDD|73392 cd04730, NPD_like, 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN.. Length = 236 Score = 29.7 bits (67), Expect = 1.3 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 5/60 (8%) Query: 262 GGLSGSPLFLKSTIAL-AKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMI 320 GG G+ F T AL ++R V I +I GGI+ + + GA+ +Q+ + + Sbjct: 134 GGHRGT--FDIGTFALVPEVRDAV--DIPVIAAGGIADGRGIAAALALGADGVQMGTRFL 189 >gnl|CDD|39161 KOG3958, KOG3958, KOG3958, Putative dynamitin [Cytoskeleton]. Length = 371 Score = 29.3 bits (65), Expect = 1.6 Identities = 29/134 (21%), Positives = 61/134 (45%), Gaps = 13/134 (9%) Query: 186 KNLERLLIHVMQ-TREEEKIKTGKFVPIFLKISPDLSEEELDDIAVEVLSHKVEGIIVSN 244 + +RLL V + T E EKIKT K K++P L + L + ++++ +E ++ + Sbjct: 94 QKYQRLLHEVQELTTEVEKIKTDKESATEEKLTPVLLAKVLAALKKQLVALHLEQLLGKD 153 Query: 245 TT----LSRKGVQCSDNHEQDGGLSGSP---LFLKSTIALAKIRQRVGPKIAIIGTGGIS 297 T L ++ + + + G +G+P +A++ +R+ ++G Sbjct: 154 ATPDGALVKRLLLQLEATKNSGKTTGTPRPEQDFSQAAKVAELEKRLTELETVVG----- 208 Query: 298 STKDALDKIMAGAN 311 +DA + + AG Sbjct: 209 CDQDAQNPLSAGLQ 222 >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 = 29.4 bits (66), Expect = 1.7 Identities = 30/115 (26%), Positives = 46/115 (40%), Gaps = 24/115 (20%) Query: 229 AVEVLSHKVEGIIVSNTTLSRKGVQCSDNHEQDGG--LSGSPLFLKSTIALAKIRQRVGP 286 AV + V+GI++SN H GG L +P ++ + + K V Sbjct: 227 AVLAAEYGVDGIVLSN-------------H---GGRQLDTAPAPIEVLLEIRKHCPEVFD 270 Query: 287 KIAIIGTGGISSTKDALDKIMAGANLIQ-----LYSAMIYEGISLPKRIIQGLSD 336 KI + GG+ D L + GA + LY A+ G ++ IQ L D Sbjct: 271 KIEVYVDGGVRRGTDVLKALCLGAKAVGLGRPFLY-ALSAYGEEGVEKAIQILKD 324 >gnl|CDD|29938 cd00452, KDPG_aldolase, KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources.. Length = 190 Score = 29.0 bits (65), Expect = 2.1 Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 2/38 (5%) Query: 276 ALAKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLI 313 A+ +R+ A+IG G + + + A I AGA I Sbjct: 45 AIRALRKEFPE--ALIGAGTVLTPEQADAAIAAGAQFI 80 >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 = 28.9 bits (65), Expect = 2.4 Identities = 9/32 (28%), Positives = 17/32 (53%) Query: 282 QRVGPKIAIIGTGGISSTKDALDKIMAGANLI 313 + P + +I +GGI + D + GA+L+ Sbjct: 250 RSALPDLPLIASGGIRNGLDIAKALALGADLV 281 >gnl|CDD|35758 KOG0538, KOG0538, KOG0538, Glycolate oxidase [Energy production and conversion]. Length = 363 Score = 27.9 bits (62), Expect = 4.0 Identities = 23/95 (24%), Positives = 38/95 (40%), Gaps = 21/95 (22%) Query: 229 AVEVLSHKVEGIIVSNTTLSRKGVQCSDNHEQDGG--LSGSPLFLKSTIALAKIRQRVGP 286 A + + V GIIVS NH GG L P + AL ++ + V Sbjct: 237 ARKAVEAGVAGIIVS-------------NH---GGRQLDYVP---ATIEALPEVVKAVEG 277 Query: 287 KIAIIGTGGISSTKDALDKIMAGANLIQLYSAMIY 321 +I + GG+ D L + GA + + +++ Sbjct: 278 RIPVFLDGGVRRGTDVLKALALGAKGVFIGRPIVW 312 >gnl|CDD|31292 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription]. Length = 183 Score = 27.9 bits (62), Expect = 4.1 Identities = 9/30 (30%), Positives = 15/30 (50%) Query: 215 KISPDLSEEELDDIAVEVLSHKVEGIIVSN 244 +I P E+L++ E L K EG + + Sbjct: 12 RIPPSYFGEDLEEAVKEELKEKYEGKLDGD 41 >gnl|CDD|32083 COG1899, DYS1, Deoxyhypusine synthase [Posttranslational modification, protein turnover, chaperones]. Length = 318 Score = 27.9 bits (62), Expect = 5.2 Identities = 22/81 (27%), Positives = 31/81 (38%), Gaps = 17/81 (20%) Query: 214 LKISPDLSEEELDDIAVEVLSHKVEGIIVS---------NTTLSRKG----VQCSDNHEQ 260 LKI EL+DI + K II+ L R G VQ + Sbjct: 212 LKIDIVEDVHELNDIVFN--AEKTGAIILGGGVPKHHIIQANLFRGGLDYAVQITTARPY 269 Query: 261 DGGLSGSPLFLKSTIALAKIR 281 DG LSG+ + ++ KI+ Sbjct: 270 DGSLSGAT--PEEAVSWGKIK 288 >gnl|CDD|111754 pfam02900, LigB, Catalytic LigB subunit of aromatic ring-opening dioxygenase. Length = 265 Score = 27.3 bits (61), Expect = 6.6 Identities = 10/22 (45%), Positives = 18/22 (81%) Query: 276 ALAKIRQRVGPKIAIIGTGGIS 297 ALAK R+++ ++ +IG+GG+S Sbjct: 158 ALAKAREKLPERVLVIGSGGLS 179 >gnl|CDD|29637 cd00537, MTHFR, Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of methylenetetrahydrofolate and the acceptor is free FAD. The family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from prokaryotes and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The bacterial enzyme is a homotetramer and NADH is the preferred reductant while the eukaryotic enzyme is a homodimer and NADPH is the preferred reductant. In humans, there are several clinically significant mutations in MTHFR that result in hyperhomocysteinemia, which is a risk factor for the development of cardiovascular disease.. Length = 274 Score = 27.2 bits (60), Expect = 6.8 Identities = 19/84 (22%), Positives = 29/84 (34%), Gaps = 9/84 (10%) Query: 62 AGYDKNAEVPIELLKL----GFGFVEIGTVTPHPQAGNPRPRVFRLTKD-----RAIINK 112 A +EL++ GF HP+A + + RL + II + Sbjct: 108 PVGFVYAVDLVELIRKENGGGFSIGVAAYPEGHPEAPSLEEDIKRLKRKVDAGADFIITQ 167 Query: 113 LGFNNAGYHTVFSRLSKIQPTSPI 136 L F+N + R T PI Sbjct: 168 LFFDNDAFLRFVDRCRAAGITVPI 191 >gnl|CDD|73375 cd02911, arch_FMN, Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent flavin oxidoreductase (oxidored) FMN-binding family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN. The specific function of this group is unknown.. Length = 233 Score = 27.2 bits (60), Expect = 7.6 Identities = 10/39 (25%), Positives = 22/39 (56%), Gaps = 1/39 (2%) Query: 277 LAKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQL 315 L KIR + ++ IIG +++ + A + GA+++ + Sbjct: 182 LKKIR-DISTELFIIGNNSVTTIESAKEMFSYGADMVSV 219 >gnl|CDD|112389 pfam03569, Peptidase_C8, Peptidase family C8. Length = 213 Score = 26.9 bits (59), Expect = 7.9 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 3/58 (5%) Query: 105 KDRAIINKLGFNNAGYHTVFSRLSKIQPTSPIGINLGANKDSKDFILDYVSGIRLFFT 162 + + + G N GYH + +RL + + +GA + I DYV F Sbjct: 114 EAGCVHCEPGDNFRGYHEIKARLEECEGIDEEPCLVGAEEGK---IADYVGAAGHFLF 168 >gnl|CDD|38831 KOG3625, KOG3625, KOG3625, Alpha amylase [Carbohydrate transport and metabolism]. Length = 1521 Score = 26.9 bits (59), Expect = 8.5 Identities = 12/39 (30%), Positives = 22/39 (56%) Query: 118 AGYHTVFSRLSKIQPTSPIGINLGANKDSKDFILDYVSG 156 G + S L++I+P + +G L N D+++DY+S Sbjct: 925 CGLQGLVSVLAEIRPKNDLGHPLCNNLRDGDWMIDYISN 963 >gnl|CDD|30455 COG0106, HisA, Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]. Length = 241 Score = 26.7 bits (59), Expect = 9.2 Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 20/81 (24%) Query: 221 SEEELDDIAVEVLSHKVEGIIVSNTTLSRKGVQCSDNHEQDGGLSGSPLFLKSTIALAKI 280 S EL+++A + + I+ T +SR DG LSG + L + ++ Sbjct: 145 SGVELEELAKRLEEVGLAHILY--TDISR-----------DGTLSGPNVDL-----VKEL 186 Query: 281 RQRVGPKIAIIGTGGISSTKD 301 + V I +I +GG+SS D Sbjct: 187 AEAV--DIPVIASGGVSSLDD 205 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 0.318 0.137 0.388 Gapped Lambda K H 0.267 0.0540 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,325,812 Number of extensions: 233606 Number of successful extensions: 757 Number of sequences better than 10.0: 1 Number of HSP's gapped: 722 Number of HSP's successfully gapped: 49 Length of query: 362 Length of database: 6,263,737 Length adjustment: 95 Effective length of query: 267 Effective length of database: 4,210,882 Effective search space: 1124305494 Effective search space used: 1124305494 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 58 (26.6 bits)