RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780363|ref|YP_003064776.1| ferredoxin-NADP+ reductase protein [Candidatus Liberibacter asiaticus str. psy62] (264 letters) >gnl|CDD|99792 cd06195, FNR1, Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 241 Score = 275 bits (707), Expect = 6e-75 Identities = 103/250 (41%), Positives = 149/250 (59%), Gaps = 15/250 (6%) Query: 17 VISIKHYTDRLFRFCITRPKSFRFRSGEFVMLGLMVN-GRRISRAYSMASPCWDDKLEFF 75 V+ + +TD LF F +TR FRF++G+F LGL + G+ + RAYS+AS +++ LEF+ Sbjct: 2 VLKRRDWTDDLFSFRVTRDIPFRFQAGQFTKLGLPNDDGKLVRRAYSIASAPYEENLEFY 61 Query: 76 SIKVEQGPLTTHLQNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIR 135 I V GPLT L ++PGDTI + KK TG L LD + PG RL+L +TGTGIAPF+S++R Sbjct: 62 IILVPDGPLTPRLFKLKPGDTIYVGKKPTGFLTLDEVPPGKRLWLLATGTGIAPFLSMLR 121 Query: 136 DPGTYEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEI--LKDLIGQKLKFYRTVTQEDY 193 D +E+FD++++ R EL Y QDEI L K ++ V++E Sbjct: 122 DLEIWERFDKIVLVHGVRYAEELAY---------QDEIEALAKQYNGKFRYVPIVSREKE 172 Query: 194 --LYKGRITNHILSGEFYRNMDLSPLNPDTDRIMICGSPTMIVDMKDLLIAKKFREGSNS 251 GRI + I SGE + L PL+P+T +M+CG+P MI D ++LL K F + Sbjct: 173 NGALTGRIPDLIESGELEEHAGL-PLDPETSHVMLCGNPQMIDDTQELLKEKGFSKNHRR 231 Query: 252 RPGTFVVERA 261 +PG VE+ Sbjct: 232 KPGNITVEKY 241 >gnl|CDD|31221 COG1018, Hmp, Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]. Length = 266 Score = 151 bits (382), Expect = 2e-37 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 17/260 (6%) Query: 17 VISIKHYTDRLFRFCITRPKSFR--FRSGEFVMLGLMVNGRRISRAYSMASPCWDDKLEF 74 V S++ TD +F F + P R F G+++ +GL G + RAYS++S +D L Sbjct: 10 VTSVEPETDDVFSFTLEPPDGLRLDFEPGQYITVGLPNGGEPLLRAYSLSSAPDEDSLYR 69 Query: 75 FSIKVE-QGPLTTHLQ-NIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVS 132 S+K E G + L +++ GDT+ + G VLD L P +L L + G GI PF+S Sbjct: 70 ISVKREDGGGGSNWLHDHLKVGDTLEV-SAPAGDFVLDDL-PERKLLLLAGGIGITPFLS 127 Query: 133 VIRDPGTYEKFDEVIVTQTCRQVVELQYG--IDVMHEISQDEILKDLIGQ-KLKFYRTVT 189 ++R +V++ R +L + +++ E+ +L + KL+ V+ Sbjct: 128 MLRTLLDRGP-ADVVLVHAARTPADLAFRDELELAAELPNALLLGLYTERGKLQGRIDVS 186 Query: 190 QEDYLY--KGRITNHILSGEFYRNMD--LSPLNPDTDRIMICGSPTMIVDMKDLLIAKKF 245 + GR G F + + L L DR+ + G M+ D LL Sbjct: 187 RLLSAAPDGGREVYLCGPGPFMQAVRLALEALGVPDDRVHLEGFGPMLKDTAALLPFTTL 246 Query: 246 -REGS--NSRPGTFVVERAF 262 R G PG ++E A Sbjct: 247 ARSGKEVRVPPGQTLLEAAE 266 >gnl|CDD|99778 cd00322, FNR_like, Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H).. Length = 223 Score = 92.9 bits (231), Expect = 9e-20 Identities = 55/237 (23%), Positives = 97/237 (40%), Gaps = 25/237 (10%) Query: 18 ISIKHYTDRLFRFCITRPKSFRFRSGEFVMLGLMVNGRRISRAYSMASPCWDDK--LEFF 75 ++ + TD + F + P F F+ G++V L L +GR + RAYS+AS D++ LE Sbjct: 1 VATEDVTDDVRLFRLQLPNGFSFKPGQYVDLHLPGDGRGLRRAYSIASS-PDEEGELELT 59 Query: 76 SIKVEQGPLTTHLQNIQPGDTI-LLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVI 134 V GP + L +++PGD + + L L+ + L + G GI PF S++ Sbjct: 60 VKIVPGGPFSAWLHDLKPGDEVEVSGPGGDFFLPLE---ESGPVVLIAGGIGITPFRSML 116 Query: 135 RD-PGTYEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLI--GQKLKFYRTVTQE 191 R + ++ R +L + DE L++L G + +++E Sbjct: 117 RHLAADKPGGEITLLYG-ARTPADLLF---------LDE-LEELAKEGPNFRLVLALSRE 165 Query: 192 DYLYKGRITNHILSGEFYRNMDLSPLNPDTDRIMICGSPTMIVDMKDLLIAKKFREG 248 G E + + ICG P M +++ L++ E Sbjct: 166 SEAKLGPGGRIDREAEI----LALLPDDSGALVYICGPPAMAKAVREALVSLGVPEE 218 >gnl|CDD|99784 cd06187, O2ase_reductase_like, The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate, while mono-oxygenases (aka mixed oxygenases) add one atom to the substrate and one atom to water. In dioxygenases, Class I enzymes are 2 component, containing a reductase with Rieske type [2Fe-2S] redox centers and an oxygenase. Class II are 3 component, having discrete flavin and ferredoxin proteins and an oxygenase. Class III have 2 [2Fe-2S] centers, one fused to the flavin domain and the other separate.. Length = 224 Score = 77.2 bits (191), Expect = 4e-15 Identities = 51/231 (22%), Positives = 95/231 (41%), Gaps = 25/231 (10%) Query: 17 VISIKHYTDRLFRFCITRPKSFRFRSGEFVMLGLMVNGRRISRAYSMASPCWDD-KLEFF 75 V+S++ T + + + F +G++V + + R RAYS A+P +D ++EF Sbjct: 1 VVSVERLTHDIAVVRLQLDQPLPFWAGQYVNVT-VPGRPRTWRAYSPANPPNEDGEIEFH 59 Query: 76 SIKVEQGPLTTHL-QNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVI 134 V G ++ L ++ GD + L GT L L + + GTG+AP +++ Sbjct: 60 VRAVPGGRVSNALHDELKVGDRVRL-SGPYGTFYLRRDHDRPVLCI-AGGTGLAPLRAIV 117 Query: 135 RDPGTYEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLIGQKLKFYRTVTQED-- 192 D + V + R +L Y ++ + ++ L+ V+ E+ Sbjct: 118 EDALRRGEPRPVHLFFGARTERDL-YDLEGLLALAARH-------PWLRVVPVVSHEEGA 169 Query: 193 -YLYKGRITNHILSGEFYRNMDLSPLNPDTDRIMICGSPTMIVDMKDLLIA 242 +G +T+ + G + I ICG P M+ D L+A Sbjct: 170 WTGRRGLVTDVV--GRDG-------PDWADHDIYICGPPAMVDATVDALLA 211 >gnl|CDD|99780 cd06183, cyt_b5_reduct_like, Cytochrome b5 reductase catalyzes the reduction of 2 molecules of cytochrome b5 using NADH as an electron donor. Like ferredoxin reductases, these proteins have an N-terminal FAD binding subdomain and a C-terminal NADH binding subdomain, separated by a cleft, which accepts FAD. The NADH-binding moiety interacts with part of the FAD and resembles a Rossmann fold. However, NAD is bound differently than in canonical Rossmann fold proteins. Nitrate reductases, flavoproteins similar to pyridine nucleotide cytochrome reductases, catalyze the reduction of nitrate to nitrite. The enzyme can be divided into three functional fragments that bind the cofactors molybdopterin, heme-iron, and FAD/NADH.. Length = 234 Score = 68.7 bits (169), Expect = 1e-12 Identities = 54/243 (22%), Positives = 96/243 (39%), Gaps = 44/243 (18%) Query: 16 SVISIKHYTDRLFRFCITRPKS-FRFRSGEFVMLGLMVNGRRISRAYSMASPCWD-DKLE 73 S I H R+FRF + P G+ V L +G ++ R Y+ SP D + Sbjct: 5 SKEDISH-DTRIFRFELPSPDQVLGLPVGQHVELKAPDDGEQVVRPYTPISPDDDKGYFD 63 Query: 74 FFSIKV-EQGPLTTHLQNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVS 132 IK+ G ++ +L +++PGDT+ + + G + + + GTGI P + Sbjct: 64 LL-IKIYPGGKMSQYLHSLKPGDTVEI-RGPFGKFEYKPNGKVKHIGMIAGGTGITPMLQ 121 Query: 133 VIR----DPGTYEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLI-------GQK 181 +IR DP K + L Y + +D +L++ + + Sbjct: 122 LIRAILKDPEDKTK-------------ISLLYA----NRTEEDILLREELDELAKKHPDR 164 Query: 182 LKFYRTVTQEDY---LYKGRITNHILSGEFYRNMDLSPLNPDTDRIMICGSPTMI-VDMK 237 K + +++ G IT ++ L P + +++CG P MI +K Sbjct: 165 FKVHYVLSRPPEGWKGGVGFITKEMIK------EHLPPPPSEDTLVLVCGPPPMIEGAVK 218 Query: 238 DLL 240 LL Sbjct: 219 GLL 221 >gnl|CDD|99811 cd06215, FNR_iron_sulfur_binding_1, Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal portion of the FAD/NAD binding domain contains most of the NADP(H) binding residues and the N-terminal sub-domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. In this ferredoxin like sub-group, the FAD/NAD sub-domains is typically fused to a C-terminal iron-sulfur binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins which act as electron carriers in photosynthesis and ferredoxins which participate in redox chains from bacteria to mammals. Ferredoxin reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 231 Score = 66.8 bits (164), Expect = 5e-12 Identities = 55/232 (23%), Positives = 97/232 (41%), Gaps = 40/232 (17%) Query: 28 FRFCITRPKSFRFRSGEFVMLGLMVNGRRISRAYSMAS-PCWDDKLEFFSIK-VEQGPLT 85 FRF F ++ G+F+ L L ++G + RAY+++S P D L ++K V G ++ Sbjct: 16 FRFAAPDGSLFAYKPGQFLTLELEIDGETVYRAYTLSSSPSRPDSLS-ITVKRVPGGLVS 74 Query: 86 THL-QNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIR-----DPGT 139 L N++ GD + + G L P ++L L S G+GI P +S+ R P Sbjct: 75 NWLHDNLKVGDELWASGPA-GEFTLID-HPADKLLLLSAGSGITPMMSMARWLLDTRPDA 132 Query: 140 YEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLIGQ----KLKFYRTVTQEDYL- 194 +++ + R ++ I DE L++L + +L Sbjct: 133 -----DIVFIHSARSPADI---------IFADE-LEELARRHPNFRLHLILEQPAPGAWG 177 Query: 195 -YKGRITNHILSGEFYRNMDLSPLNPDTDRIMICGSPTMIVDMKDLLIAKKF 245 Y+GR+ +L+ L P + + +CG + +K LL F Sbjct: 178 GYRGRLNAELLA-------LLVPDLKERT-VFVCGPAGFMKAVKSLLAELGF 221 >gnl|CDD|99788 cd06191, FNR_iron_sulfur_binding, Iron-sulfur binding Ferredoxin Reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with a C-terminal iron-sulfur binding cluster domain. FNR was intially identified as a chloroplast reductase activity catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methnae assimilation in a variety of organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H).. Length = 231 Score = 64.5 bits (157), Expect = 3e-11 Identities = 51/221 (23%), Positives = 87/221 (39%), Gaps = 20/221 (9%) Query: 26 RLFRFCITRPKSFRFRSGEFVMLGLMVNGRRISRAYSMASPCWDDKLEFFSIKVEQGPLT 85 F + P + FR G+ V L L +G + R YS+ S D++ +V G ++ Sbjct: 14 VTIVFAVPGPLQYGFRPGQHVTLKLDFDGEELRRCYSLCSSPAPDEISITVKRVPGGRVS 73 Query: 86 THL-QNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIRDPGTYEKFD 144 +L ++IQPG T+ + G V PG R L + G+GI P +++IR Sbjct: 74 NYLREHIQPGMTVEV-MGPQGHFVYQPQPPG-RYLLVAAGSGITPLMAMIRATLQTAPES 131 Query: 145 EVIVTQTCRQVVELQYGIDVMHEISQDEILKDLIGQKLKFYRTVTQED---YLYKGRITN 201 + + + R ++ + + E++ Q+L+ T+E L GRI Sbjct: 132 DFTLIHSARTPADMIFA-QELRELADKP-------QRLRLLCIFTRETLDSDLLHGRIDG 183 Query: 202 HILSGEFYRNMDLSPLNPDTDRIMICGSPTMIVDMKDLLIA 242 G L ICG M+ ++ L Sbjct: 184 EQSLGAALIPDRL------EREAFICGPAGMMDAVETALKE 218 >gnl|CDD|30889 COG0543, UbiB, 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases [Coenzyme metabolism / Energy production and conversion]. Length = 252 Score = 62.0 bits (150), Expect = 2e-10 Identities = 52/249 (20%), Positives = 97/249 (38%), Gaps = 28/249 (11%) Query: 17 VISIKHYTDRLFRFCIT-RPKSFRFRSGEFVMLGLMVNGRRISRAYSMASPCWDDKLEFF 75 V+ + + F + + F+ G+FVML + RR YS+AS D Sbjct: 12 VVEKEEISPDTFLLRLRLPFVALTFKPGQFVMLRVPGGVRR---PYSLASAPDDKGELEL 68 Query: 76 SIKV-EQGPLTTHLQNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVI 134 I+V E G +T ++ ++ GD I + + G L I G + L + GTGIAP ++ Sbjct: 69 HIRVYEVGKVTKYIFGLKEGDKIRV-RGPLGNGFLREKI-GKPVLLIAGGTGIAPLYAIA 126 Query: 135 RDPGTYEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLIGQKLKFYRTVTQEDYL 194 ++ ++V + R +L +D + E++ + + + Sbjct: 127 KELKEKGDANKVTLLYGARTAKDL-LLLDELEELA-----------EKEVHPVTDDGWKG 174 Query: 195 YKGRITNHILSGEFYRNMDLSPLNPDTDRIMICGSPTMIVDMKDLLIAKKFREGSNSRPG 254 KG +T +L L+ + D + ICG P M+ +++ L ++ Sbjct: 175 RKGFVTTDVLKEL---------LDLEVDDVYICGPPAMVKAVREKLKEYGVPISASLVSI 225 Query: 255 TFVVERAFS 263 V Sbjct: 226 MCRVSVDGG 234 >gnl|CDD|99806 cd06210, MMO_FAD_NAD_binding, Methane monooxygenase (MMO) reductase of methanotrophs catalyzes the NADH-dependent hydroxylation of methane to methanol. This multicomponent enzyme mediates electron transfer via a hydroxylase (MMOH), a coupling protein, and a reductase which is comprised of an N-terminal [2Fe-2S] ferredoxin domain, an FAD binding subdomain, and an NADH binding subdomain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. Dioxygenases add both atom of oxygen to the substrate, while mono-oxygenases add one atom to the substrate and one atom to water.. Length = 236 Score = 61.6 bits (150), Expect = 2e-10 Identities = 49/205 (23%), Positives = 85/205 (41%), Gaps = 23/205 (11%) Query: 33 TRPKSFRFRSGEFVMLGLMVNGRRISRAYSMAS-PCWDDKLEFFSIKVEQGPLTTHLQN- 90 + F G+FV + + G R+YS+A+ P WD +LEF + G +T+L+ Sbjct: 28 GAGIAAEFVPGQFV--EIEIPGTDTRRSYSLANTPNWDGRLEFLIRLLPGGAFSTYLETR 85 Query: 91 IQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIRDPGTYEKFDEVIVTQ 150 + G + L + G L R + + GTG+AP +S++R + + Q Sbjct: 86 AKVGQRLNL-RGPLGAFGLRENGLRPR-WFVAGGTGLAPLLSMLRRMAEWGE------PQ 137 Query: 151 TCRQVVELQYGIDVMHEISQDEILKDLIGQ--KLKFYRTVTQEDYLYKGRITNHILSGEF 208 R L +G++ E+ + LK L L V + ++G + Sbjct: 138 EAR----LFFGVNTEAELFYLDELKRLADSLPNLTVRICVWRPGGEWEGYRGTVV--DAL 191 Query: 209 YRNMDLSPLNPDTDRIMICGSPTMI 233 ++ S PD I +CG P M+ Sbjct: 192 REDLASSDAKPD---IYLCGPPGMV 213 >gnl|CDD|99805 cd06209, BenDO_FAD_NAD, Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal ferredoxin at the end fused to an FAD/NADP(P) domain. In dioxygenase FAD/NAD(P) binding domain, the reductase transfers 2 electrons from NAD(P)H to the oxygenase which insert into an aromatic substrate, an initial step in microbial aerobic degradation of aromatic rings. Flavin oxidoreductases use flavins as substrates, unlike flavoenzymes which have a flavin prosthetic group.. Length = 228 Score = 61.5 bits (150), Expect = 2e-10 Identities = 57/203 (28%), Positives = 95/203 (46%), Gaps = 33/203 (16%) Query: 38 FRFRSGEFVMLGLMVNGRRISRAYSMASPCWDDKLEFFSIKVEQGPLTTHLQN-IQPGDT 96 F G++V L V G +R+YS +S D +LEF + G ++++L++ QPGD Sbjct: 29 LAFLPGQYV--NLQVPGTDETRSYSFSSAPGDPRLEFLIRLLPGGAMSSYLRDRAQPGDR 86 Query: 97 ILLHKKSTGTLVLDALIPGNRLYLF-STGTGIAPFVSVIRDPGTYEKFDEVIVTQTCRQV 155 + L TG L L R L + GTG+APF+S++ +V+ Sbjct: 87 LTL----TGPLGSFYLREVKRPLLMLAGGTGLAPFLSML----------DVLAEDGSAHP 132 Query: 156 VELQYGIDVMHEISQDEILKDLIGQKLKF-YRTVTQED---YLYKGRITNHILSGEFYRN 211 V L YG+ ++ + + L+ L + F +RTV + + KG +T+H Sbjct: 133 VHLVYGVTRDADLVELDRLEALAERLPGFSFRTVVADPDSWHPRKGYVTDH--------- 183 Query: 212 MDLSPLN-PDTDRIMICGSPTMI 233 ++ LN D D + +CG P M+ Sbjct: 184 LEAEDLNDGDVD-VYLCGPPPMV 205 >gnl|CDD|99810 cd06214, PA_degradation_oxidoreductase_like, NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like domain with an iron-sulfur binding cluster domain. Ferredoxins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal portion may contain a flavin prosthetic group, as in flavoenzymes, or use flavin as a substrate. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria and participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 241 Score = 61.0 bits (149), Expect = 3e-10 Identities = 50/219 (22%), Positives = 93/219 (42%), Gaps = 30/219 (13%) Query: 38 FRFRSGEFVMLGLMVNGRRISRAYSMASPCWDDKLEFFSIK-VEQGPLTTHL-QNIQPGD 95 FR+R G+F+ L + ++G + R+YS+ S DD+L ++K V G + ++ GD Sbjct: 31 FRYRPGQFLTLRVPIDGEEVRRSYSICSSPGDDELR-ITVKRVPGGRFSNWANDELKAGD 89 Query: 96 TILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIRDPGTYEKFDEVIVTQTCRQV 155 T+ + G L L LF+ G+GI P +S+++ + + +V Sbjct: 90 TLEVM-PPAGRFTLPPLPGARHYVLFAAGSGITPVLSILKT---------ALAREPASRV 139 Query: 156 VELQYG----IDVM--HEISQDEILKDLIGQKLKFYRTVTQEDY---LYKGRITNHILSG 206 L YG V+ E++ LK +L +++E L +GR+ L+ Sbjct: 140 T-LVYGNRTEASVIFREELAD---LKARYPDRLTVIHVLSREQGDPDLLRGRLDAAKLNA 195 Query: 207 EFYRNMDLSPLNPDTDRIMICGSPTMIVDMKDLLIAKKF 245 +D + D +CG M+ ++ L+ Sbjct: 196 LLKNLLDA----TEFDEAFLCGPEPMMDAVEAALLELGV 230 >gnl|CDD|35754 KOG0534, KOG0534, KOG0534, NADH-cytochrome b-5 reductase [Coenzyme transport and metabolism, Energy production and conversion]. Length = 286 Score = 60.3 bits (146), Expect = 5e-10 Identities = 50/227 (22%), Positives = 89/227 (39%), Gaps = 34/227 (14%) Query: 19 SIKHYTDRLFRFCITRPKS-FRFRSGEFVMLGLMVNGRRISRAYSMASPCWDDKLEF--- 74 + H T LFRF + G+ V+L + G+ + R Y+ P D + Sbjct: 61 ELSHDT-SLFRFVLPSADHVLGLPIGQHVVLKAPIGGKLVVRPYT---PVSLDDDKGYFD 116 Query: 75 FSIKV-EQGPLTTHLQNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSV 133 +KV +G ++ HL +++ GDT+ + G D L + + GTGI P + + Sbjct: 117 LVVKVYPKGKMSQHLDSLKIGDTVEF-RGPIGEFKYDPQ-KAKHLGMIAGGTGITPMLQL 174 Query: 134 IR----DPGTYEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLIGQKLKFYRTVT 189 IR DP K + +T ++ ++ S+ ++ K + V Sbjct: 175 IRAILKDPEDTTKISLLYANKTED---DILLREELEELASKYP-------ERFKVWYVVD 224 Query: 190 QEDYLY---KGRITNHILSGEFYRNMDLSPLNPDTDRIMICGSPTMI 233 Q ++ G IT ++ + L ++ICG P MI Sbjct: 225 QPPEIWDGSVGFITKDLIKEHLPPPKEGETL------VLICGPPPMI 265 >gnl|CDD|99817 cd06221, sulfite_reductase_like, Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is linked to ferredoxin and reduces NH2OH and SeO3 at a lesser rate than it's normal substate SO3(2-). Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+.. Length = 253 Score = 59.5 bits (145), Expect = 8e-10 Identities = 53/219 (24%), Positives = 90/219 (41%), Gaps = 32/219 (14%) Query: 20 IKHYTDRLFRFCITRPKSFRFRSGEFVMLGLMVNGRRISRAYSMAS-PCWDDKLEFFSIK 78 IK +T R + F F+ G+FVML L G S++S P LE + Sbjct: 11 IKTFT---LRLEDDDEELFTFKPGQFVMLSLPGVGE---APISISSDPTRRGPLELTIRR 64 Query: 79 VEQGPLTTHLQNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIRDPG 138 V G +T L ++PGDT+ L + G + G L L + G G+AP S+I Sbjct: 65 V--GRVTEALHELKPGDTVGL-RGPFGNGFPVEEMKGKDLLLVAGGLGLAPLRSLINYIL 121 Query: 139 T-YEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLIGQKLKFYRTVTQEDYLYK- 196 E + +V + R +L + ++E+ + ++ TV + + + Sbjct: 122 DNREDYGKVTLLYGARTPEDLLF---------KEELKEWAKRSDVEVILTVDRAEEGWTG 172 Query: 197 --GRITNHILSGEFYRNMDLSPLNPDTDRIMICGSPTMI 233 G +T+ + L+PD ++CG P M+ Sbjct: 173 NVGLVTDLL---------PELTLDPDNTVAIVCGPPIMM 202 >gnl|CDD|99812 cd06216, FNR_iron_sulfur_binding_2, Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 243 Score = 59.5 bits (145), Expect = 9e-10 Identities = 60/217 (27%), Positives = 93/217 (42%), Gaps = 35/217 (16%) Query: 34 RP--KSFRFRSGEFVMLGLMVNGRRISRAYSMASPCWDDKLEFFSI---KVEQGPLTTHL 88 RP R+G+ V LG+ ++G R R+YS++S + ++ G ++ L Sbjct: 38 RPNRGWPGHRAGQHVRLGVEIDGVRHWRSYSLSSS-PTQEDGTITLTVKAQPDGLVSNWL 96 Query: 89 -QNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIRDPGTYEKFDEVI 147 ++ PGD + L + G VL +P RL L + G+GI P +S++R T Sbjct: 97 VNHLAPGDVVEL-SQPQGDFVLPDPLPP-RLLLIAAGSGITPVMSMLR---TLLA----- 146 Query: 148 VTQTCRQVVELQYGIDVMHEISQDEILKDLIGQ--KLKFYRTVTQEDYLYKGRITNHILS 205 VV L Y I DE L+ L Q L+ + T+E+ GR LS Sbjct: 147 -RGPTADVVLLYYARTREDVIFADE-LRALAAQHPNLRLHLLYTREE--LDGR-----LS 197 Query: 206 GEFYRNMDLSPLNPD-TDR-IMICGSPTMIVDMKDLL 240 L + PD DR + CG P + ++LL Sbjct: 198 AA-----HLDAVVPDLADRQVYACGPPGFLDAAEELL 229 >gnl|CDD|99813 cd06217, FNR_iron_sulfur_binding_3, Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap between the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 235 Score = 58.8 bits (143), Expect = 1e-09 Identities = 56/228 (24%), Positives = 98/228 (42%), Gaps = 33/228 (14%) Query: 26 RLFRFCITRPKSFRFRSGEFVMLGL-MVNGRRISRAYSMAS-PCWDDKLEFFSIKVEQGP 83 + FR + F +G+ V L L ++G R+YS+AS P ++E +V G Sbjct: 17 KTFRLAVPDGVPPPFLAGQHVDLRLTAIDGYTAQRSYSIASSPTQRGRVELTVKRVPGGE 76 Query: 84 LTTHL-QNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIRDPGTYEK 142 ++ +L ++ GD + + + GT + L G+ + L + G+GI P +S+IR Sbjct: 77 VSPYLHDEVKVGDLLEV-RGPIGTFTWNPL-HGDPVVLLAGGSGIVPLMSMIRY------ 128 Query: 143 FDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLIGQK--LKFYRTVTQE---DYL-YK 196 ++ R + + DV I +DE L+ L + L +T+ D+L Sbjct: 129 RRDLGWPVPFRLLYSARTAEDV---IFRDE-LEQLARRHPNLHVTEALTRAAPADWLGPA 184 Query: 197 GRITNHILSGEFYRNMDLSPLNPDTD--RIMICGSPTMIVDMKDLLIA 242 GRIT ++ L P R+ +CG P + LL+ Sbjct: 185 GRIT----------ADLIAELVPPLAGRRVYVCGPPAFVEAATRLLLE 222 >gnl|CDD|99786 cd06189, flavin_oxioreductase, NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN, or riboflavin via NAD(P)H. Flavin is used as a substrate, rather than a tightly bound prosthetic group as in flavoenzymes; weaker binding is due to the absence of a binding site for the AMP moeity of FAD.. Length = 224 Score = 57.2 bits (139), Expect = 4e-09 Identities = 52/242 (21%), Positives = 99/242 (40%), Gaps = 37/242 (15%) Query: 16 SVISIKHYTDRLFRFCITRPKSFRFRSGEFVMLGLMVNGRRISRAYSMAS-PCWDDKLEF 74 V SI+ D ++R + P F +G+++ L L+ +G + R +S+AS P D ++E Sbjct: 2 KVESIEPLNDDVYRVRLKPPAPLDFLAGQYLDL-LLDDGDK--RPFSIASAPHEDGEIEL 58 Query: 75 FSIKVEQGPLTTH-LQNIQPGDTILL---HKKSTGTLVLDALIPGNRLYLFSTGTGIAPF 130 V G + + + ++ + + G L L L + GTG AP Sbjct: 59 HIRAVPGGSFSDYVFEELKENGLVRIEGPL----GDFFLRED-SDRPLILIAGGTGFAPI 113 Query: 131 VSVIRDPGTYEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLIGQKLKFYRT--V 188 S++ + ++ + R + L +G ++ DE+L+ F + Sbjct: 114 KSIL---------EHLLAQGSKRPIH-LYWGARTEEDLYLDELLEAWAEAHPNFTYVPVL 163 Query: 189 TQEDYLYKGRITNH---ILSGEFYRNMDLSPLNPDTDRIMICGSPTMIVDMKDLLIAKKF 245 ++ + ++GR +L D L+ D D + CGSP M+ +D + K Sbjct: 164 SEPEEGWQGRTGLVHEAVLE-------DFPDLS-DFD-VYACGSPEMVYAARDDFVEKGL 214 Query: 246 RE 247 E Sbjct: 215 PE 216 >gnl|CDD|144531 pfam00970, FAD_binding_6, Oxidoreductase FAD-binding domain. Length = 99 Score = 52.6 bits (127), Expect = 1e-07 Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 7/86 (8%) Query: 16 SVISIKHYTDRLFRFCITRPK-SFRFRSGEFVMLGLMVNGRRISRAYSMASPCWDDKLEF 74 S+ H T R FRF + P G+ + L L ++G+ + RAYS AS D + Sbjct: 6 EKESLSHDT-RRFRFALPSPDQVLGLPPGQHIFLRLPIDGKLVVRAYSPASS--PDDVGE 62 Query: 75 FSI---KVEQGPLTTHLQNIQPGDTI 97 + G ++ +L +++ GDT+ Sbjct: 63 LELLVKVYPGGKMSQYLDSLKVGDTV 88 >gnl|CDD|99793 cd06196, FNR_like_1, Ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which varies in orientation with respect to the NAD(P) binding domain. The N-terminal region may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP+ to NADPH.. Length = 218 Score = 51.1 bits (123), Expect = 3e-07 Identities = 60/240 (25%), Positives = 95/240 (39%), Gaps = 49/240 (20%) Query: 16 SVISIKHYTDRLFRFCITRPKSFRFRSGEFVMLGLMVNG-RRISRAYSMASPCWDDKLEF 74 +++SI+ T + R +P+ + F G+ + + G R R ++ S DD LEF Sbjct: 4 TLLSIEPVTHDVKRLRFDKPEGYDFTPGQATEVAIDKPGWRDEKRPFTFTSLPEDDVLEF 63 Query: 75 FSIKV--EQGPLTTHLQNIQPGDTILLHK-------KSTGTLVLDALIPGNRLYLFSTGT 125 IK + +T L +QPGDT+L+ K G I G G Sbjct: 64 -VIKSYPDHDGVTEQLGRLQPGDTLLIEDPWGAIEYKGPGVF-----IAG--------GA 109 Query: 126 GIAPFVSVIRDPGTYEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLIGQKLKFY 185 GI PF++++RD K + + + D++ + DE L+ ++G LKF Sbjct: 110 GITPFIAILRDLAAKGKLE------GNTLIFANKTEKDIILK---DE-LEKMLG--LKFI 157 Query: 186 RTVTQEDY--LYKGRITNHILSGEFYRNMDLSPLNPDTDRIM-ICGSPTMIVDMKDLLIA 242 VT E GRI F L D ++ +CG P M + L Sbjct: 158 NVVTDEKDPGYAHGRID-----KAF-----LKQHVTDFNQHFYVCGPPPMEEAINGALKE 207 >gnl|CDD|99807 cd06211, phenol_2-monooxygenase_like, Phenol 2-monooxygenase (phenol hydroxylase) is a flavoprotein monooxygenase, able to use molecular oxygen as a substrate in the microbial degredation of phenol. This protein is encoded by a single gene and uses a tightly bound FAD cofactor in the NAD(P)H dependent conversion of phenol and O2 to catechol and H2O. This group is related to the NAD binding ferredoxin reductases.. Length = 238 Score = 47.3 bits (113), Expect = 4e-06 Identities = 31/142 (21%), Positives = 60/142 (42%), Gaps = 26/142 (18%) Query: 8 LPVNVYCESVISIKHYTD--RLFRFCITRPKSFRFRSGEFVMLGLMVNGRRISRAYSMAS 65 L V + +V+ I+ T + R + P+ F++G++V L G +RA+S+AS Sbjct: 2 LNVKDFEGTVVEIEDLTPTIKGVRLKLDEPEEIEFQAGQYV--NLQAPGYEGTRAFSIAS 59 Query: 66 -PCWDDKLEFFSIKVEQGPLTTHL-QNIQPGDTILL---------HKKSTGTLVLDALIP 114 P ++E V G TT++ + ++ GD + + ++ A Sbjct: 60 SPSDAGEIELHIRLVPGGIATTYVHKQLKEGDELEISGPYGDFFVRDSDQRPIIFIA--- 116 Query: 115 GNRLYLFSTGTGIAPFVSVIRD 136 G+G++ S+I D Sbjct: 117 --------GGSGLSSPRSMILD 130 >gnl|CDD|99781 cd06184, flavohem_like_fad_nad_binding, FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The hemoglobin domain adopts a globin fold with an embedded heme molecule. Flavohemoglobins also have a C-terminal reductase domain with bindiing sites for FAD and NAD(P)H. This domain catalyzes the conversion of NO + O2 + NAD(P)H to NO3- + NAD(P)+. Instead of the oxygen transport function of hemoglobins, flavohemoglobins seem to act in NO dioxygenation and NO signalling.. Length = 247 Score = 46.8 bits (112), Expect = 6e-06 Identities = 48/224 (21%), Positives = 84/224 (37%), Gaps = 49/224 (21%) Query: 40 FRSGEFVMLGLMV--NGRRISRAYSMASPCWDDKLEF-FSIK-VEQGPLTTHL-QNIQPG 94 F G+++ + + + G R R YS++ + + S+K G ++ +L N++ G Sbjct: 37 FLPGQYLSVRVKLPGLGYRQIRQYSLSD--APNGDYYRISVKREPGGLVSNYLHDNVKVG 94 Query: 95 DTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIRDPGTYEKFDEVIVTQTCRQ 154 D + + + G VLD L L S G GI P +S++ + R Sbjct: 95 DVLEVSAPA-GDFVLDEASDRP-LVLISAGVGITPMLSMLE---------ALAAEGPGRP 143 Query: 155 VVELQYGIDVMH------EISQDEILKDLIGQ--KLK---FYRTVTQED----YLYKGRI 199 V +H + + L++L + LK FY D Y + GRI Sbjct: 144 VT-------FIHAARNSAVHAFRDELEELAARLPNLKLHVFYSEPEAGDREEDYDHAGRI 196 Query: 200 TNHILSGEFYRNMDLSPLNPDTDRIMICGSPTMIVDMKDLLIAK 243 +L L D D +CG + +++ L A Sbjct: 197 DLALLRELL--------LPADAD-FYLCGPVPFMQAVREGLKAL 231 >gnl|CDD|99798 cd06201, SiR_like2, Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH. Cypor (including cyt -450 reductase, nitric oxide synthase, and methionine synthase reductase) are ferredoxin reductase (FNR)-like proteins with an additional N-terminal FMN domain and a connecting sub-domain inserted within the flavin binding portion of the FNR-like domain. The connecting domain orients the N-terminal FMN domain with the C-terminal FNR domain. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 289 Score = 46.6 bits (111), Expect = 7e-06 Identities = 31/99 (31%), Positives = 45/99 (45%), Gaps = 6/99 (6%) Query: 39 RFRSGEFVMLGLMVNGRRISRAYSMASPCWDDKLEFFSIKVEQGPLTTHLQNIQPGDTIL 98 F +G+ +LG++ G + R YS+AS D LE K G + +L ++PGDTI Sbjct: 83 SFEAGD--LLGILPPGSDVPRFYSLASSSSDGFLEICVRKHPGGLCSGYLHGLKPGDTIK 140 Query: 99 LHKKSTGTLVLDALIPGNR-LYLFSTGTGIAPFVSVIRD 136 + + G + L GTGIAP IR Sbjct: 141 AFIRPNPSFRPAK---GAAPVILIGAGTGIAPLAGFIRA 176 >gnl|CDD|99787 cd06190, T4MO_e_transfer_like, Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P. mendocina) to ferredoxin to an iron-containing oxygenase. TmoF is homologous to other mono- and dioxygenase systems within the ferredoxin reductase family.. Length = 232 Score = 45.7 bits (109), Expect = 1e-05 Identities = 32/116 (27%), Positives = 50/116 (43%), Gaps = 8/116 (6%) Query: 24 TDRLFRFCITRPKSFRFRSGEFVMLGLM-VNGRRISRAYSMASPCWDDKLEFFSIK-VEQ 81 T + F F G++ +L L V G R AYSMA+ F IK Sbjct: 8 THDVAEFRFALDGPADFLPGQYALLALPGVEGAR---AYSMANLANASGEWEFIIKRKPG 64 Query: 82 GPLTTHL-QNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIRD 136 G + L N++PGD + L G L + + + + G+G+AP +S++R Sbjct: 65 GAASNALFDNLEPGDELELDG-PYGLAYLRPDEDRDIVCI-AGGSGLAPMLSILRG 118 >gnl|CDD|99808 cd06212, monooxygenase_like, The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. These flavoprotein monooxygenases use molecular oxygen as a substrate and require reduced FAD. One atom of oxygen is incorportated into the aromatic compond, while the other is used to form a molecule of water. In contrast dioxygenases add both atoms of oxygen to the substrate.. Length = 232 Score = 44.6 bits (106), Expect = 3e-05 Identities = 32/113 (28%), Positives = 55/113 (48%), Gaps = 6/113 (5%) Query: 26 RLFRFCITRPKSFRFRSGEFVMLGLMVNGRRISRAYSMA-SPCWDDKLEFFSIKVEQGPL 84 R R + P+ +F +G++V + V G +R++SMA +P +LEF K G Sbjct: 16 RRLRLRLEEPEPIKFFAGQYVDIT--VPGTEETRSFSMANTPADPGRLEFIIKKYPGGLF 73 Query: 85 TTHL-QNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIRD 136 ++ L + GD + + GT L + L G+G+AP +S++RD Sbjct: 74 SSFLDDGLAVGDPVTV-TGPYGTCTLRESRDR-PIVLIGGGSGMAPLLSLLRD 124 >gnl|CDD|99791 cd06194, FNR_N-term_Iron_sulfur_binding, Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an N-terminal Iron-Sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 222 Score = 44.2 bits (105), Expect = 3e-05 Identities = 31/126 (24%), Positives = 52/126 (41%), Gaps = 14/126 (11%) Query: 17 VISIKHYTDRLFRFCITRPKSFRFRSGEFVML----GLMVNGRRISRAYSMAS-PCWDDK 71 V+S++ + + R + + + G++V L GL R+YS S P D++ Sbjct: 1 VVSLQRLSPDVLRVRLEPDRPLPYLPGQYVNLRRAGGLA-------RSYSPTSLPDGDNE 53 Query: 72 LEFFSIKVEQGPLTTHL-QNIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPF 130 LEF + G + L + +PG + L + G L L GTG+AP Sbjct: 54 LEFHIRRKPNGAFSGWLGEEARPGHALRL-QGPFGQAFYRPEYGEGPLLLVGAGTGLAPL 112 Query: 131 VSVIRD 136 + R Sbjct: 113 WGIARA 118 >gnl|CDD|143941 pfam00175, NAD_binding_1, Oxidoreductase NAD-binding domain. Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity. Length = 106 Score = 41.5 bits (98), Expect = 2e-04 Identities = 27/118 (22%), Positives = 49/118 (41%), Gaps = 21/118 (17%) Query: 120 LFSTGTGIAPFVSVIRDPGTYEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLIG 179 + + GTGIAP SV++ ++ + +V L YG ++ E L++L Sbjct: 1 MIAGGTGIAPLYSVLK---------ALLEDEDGTEVY-LVYGNRTEDDLLLREELEELAK 50 Query: 180 Q--KLKFYRTVTQED--YLYKGRITNHILSGEFYRNMDLSPLNPDTDRIMICGSPTMI 233 + LK +D Y KG +T+ +L + + + +CG P M+ Sbjct: 51 KYPNLKVVAVSRTDDGWYGRKGYVTDALLE-------EHLSEDLGDTDVYVCGPPPMM 101 >gnl|CDD|99789 cd06192, DHOD_e_trans_like, FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as NAD binding. NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP+ to NADPH.. Length = 243 Score = 38.8 bits (91), Expect = 0.001 Identities = 43/219 (19%), Positives = 78/219 (35%), Gaps = 33/219 (15%) Query: 17 VISIKHYTDRLFRFCITRPKSFR-FRSGEFVMLGLMVNGRRISRAYSMASPCWDDKLEFF 75 ++ + L I P + R FR G+FV L + S+A D + Sbjct: 1 IVKKEQLEPNLVLLTIKAPLAARLFRPGQFVFLRNFESPGLERIPLSLAG--VDPEEGTI 58 Query: 76 SIKVE-QGPLTTHLQNIQPGDTILLHKKS-TGTLVLDALIPGNRLYLFSTGTGIAPFVSV 133 S+ VE +GP T + ++PG+ + + G G + L + G G+AP + + Sbjct: 59 SLLVEIRGPKTKLIAELKPGEKLDVMGPLGNGFEGPK---KGGTVLLVAGGIGLAPLLPI 115 Query: 134 IRDPGTYEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLIGQKLKFYRTVTQEDY 193 + ++V V ++ E + + + EI T Sbjct: 116 AKK--LAANGNKVTVLAGAKKAKEE-FLDEYFELPADVEIW-------------TTD--- 156 Query: 194 LYKGRITNHILSGEFYRNMDLSPLNPDTDRIMICGSPTM 232 G + + + + L D DRI++ GS M Sbjct: 157 --DGELGLEGKVTDSDKPIPLE----DVDRIIVAGSDIM 189 >gnl|CDD|99800 cd06203, methionine_synthase_red, Human methionine synthase reductase (MSR) restores methionine sythase which is responsible for the regeneration of methionine from homocysteine, as well as the coversion of methyltetrahydrofolate to tetrahydrofolate. In MSR, electrons are transferred from NADPH to FAD to FMN to cob(II)alamin. MSR resembles proteins of the cytochrome p450 family including nitric oxide synthase, the alpha subunit of sulfite reductase, but contains an extended hinge region. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPORs resemble ferredoxin reductase (FNR) but have a connecting subdomain inserted within the flavin binding region, which helps orient the FMN binding doamin with the FNR module. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 398 Score = 37.3 bits (87), Expect = 0.005 Identities = 24/89 (26%), Positives = 35/89 (39%), Gaps = 12/89 (13%) Query: 55 RRISRAYSMASP--CWDDKLEF-FSI--KVEQGPLTTH------LQNIQPGDTILLHKKS 103 R R YS+AS KL F FS+ +G L T L G + + +S Sbjct: 171 RLQPRPYSIASSPLEGPGKLRFIFSVVEFPAKG-LCTSWLESLCLSASSHGVKVPFYLRS 229 Query: 104 TGTLVLDALIPGNRLYLFSTGTGIAPFVS 132 + L + + GTG+APF+ Sbjct: 230 SSRFRLPPDDLRRPIIMVGPGTGVAPFLG 258 >gnl|CDD|35262 KOG0039, KOG0039, KOG0039, Ferric reductase, NADH/NADPH oxidase and related proteins [Inorganic ion transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism]. Length = 646 Score = 36.9 bits (85), Expect = 0.006 Identities = 32/191 (16%), Positives = 64/191 (33%), Gaps = 18/191 (9%) Query: 16 SVISIKHYTDRLFRFCITRPKSFRFRSGEFVMLGLMVNGRRISRAYSMASPCWDDKLEFF 75 + + + +++P F+++ G+++ + + +++ S DD L Sbjct: 358 KIAKVVLLPSDVLELIMSKPPGFKYKPGQYIFVNCPSLSKLEWHPFTITSAPEDDFLSVH 417 Query: 76 SIKVEQGPLTTHLQNI-------QPGDTILLHKKST-----GTLVLDALIPGNRLYLFST 123 IK G T L+N D K G D L L Sbjct: 418 -IKA-LGDWTEKLRNAFSEVSQPPESDKSYPFPKILIDGPYGAPSQDVFKYEV-LVLVGG 474 Query: 124 GTGIAPFVSVIRD---PGTYEKFDEVIVTQTCRQVVELQYGIDVMHEISQDEILKDLIGQ 180 G G+ PF S+++D + + + ++ Y V E E K L+ + Sbjct: 475 GIGVTPFASILKDLLNKISLGRTKAPTSDYSDSLKLKKVYFYWVTREQRSFEWFKGLLTE 534 Query: 181 KLKFYRTVTQE 191 ++ + E Sbjct: 535 VEEYDSSGVIE 545 >gnl|CDD|36374 KOG1159, KOG1159, KOG1159, NADP-dependent flavoprotein reductase [Energy production and conversion]. Length = 574 Score = 35.3 bits (81), Expect = 0.016 Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 11/85 (12%) Query: 59 RAYSMASPCWDDKLEFFSIKVE---------QGPLTTHLQNIQPGDTILLHKKSTGTLVL 109 RA+S+AS LE VE +G + L +++PGD I + K GTL Sbjct: 369 RAFSIASSPGAHHLELLVAIVEYKTILKEPRRGLCSNWLASLKPGDEIPI-KVRPGTLYF 427 Query: 110 DALIPGNRLYLFSTGTGIAPFVSVI 134 + L + GTG+APF ++I Sbjct: 428 PSD-LNKPLIMVGPGTGVAPFRALI 451 >gnl|CDD|99804 cd06208, CYPOR_like_FNR, These ferredoxin reductases are related to the NADPH cytochrome p450 reductases (CYPOR), but lack the FAD-binding region connecting sub-domain. Ferredoxin-NADP+ reductase (FNR) is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins, such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap between the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2, which then transfers two electrons and a proton to NADP+ to form NADPH. CYPOR serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases, sulfite reducatase, and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPOR has a C-terminal FNR-like FAD and NAD binding module, an FMN-binding domain, and an additional connecting domain (inserted within the FAD binding region) that orients the FNR and FMN -binding domains. The C-terminal domain contains most of the NADP(H) binding residues, and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule, which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 286 Score = 35.0 bits (81), Expect = 0.021 Identities = 29/106 (27%), Positives = 48/106 (45%), Gaps = 31/106 (29%) Query: 53 NGR-RISRAYSMASP-------------C------WDDKLEFFSIKVEQGPLTTHLQNIQ 92 NG+ R YS+AS C D + + + ++G + +L +++ Sbjct: 58 NGKPHKLRLYSIASSRYGDDGDGKTLSLCVKRLVYTDPETD----ETKKGVCSNYLCDLK 113 Query: 93 PGDTILLHKKSTGTLVLDALIP---GNRLYLFSTGTGIAPFVSVIR 135 PGD + + TG + L+P L + +TGTGIAPF S +R Sbjct: 114 PGDDVQI----TGPVGKTMLLPEDPNATLIMIATGTGIAPFRSFLR 155 >gnl|CDD|99802 cd06206, bifunctional_CYPOR, These bifunctional proteins fuse N-terminal cytochrome p450 with a cytochrome p450 reductase (CYPOR). NADPH cytochrome p450 reductase serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 384 Score = 34.5 bits (80), Expect = 0.028 Identities = 29/104 (27%), Positives = 46/104 (44%), Gaps = 24/104 (23%) Query: 43 GEFV-MLGLMVNGRRISRAYSMAS-PCWDDK---LEF-------FSIKVE-QGPLTTHLQ 89 F+ ML M R R YS++S P D L S + +G +++L Sbjct: 150 ATFLAMLPPM----RP-RQYSISSSPLVDPGHATLTVSVLDAPALSGQGRYRGVASSYLS 204 Query: 90 NIQPGDTILLH-KKSTGT--LVLDALIPGNRLYLFSTGTGIAPF 130 +++PGD+I + + S D P L + + GTG+APF Sbjct: 205 SLRPGDSIHVSVRPSHSAFRPPSDPSTP---LIMIAAGTGLAPF 245 >gnl|CDD|33854 COG4097, COG4097, Predicted ferric reductase [Inorganic ion transport and metabolism]. Length = 438 Score = 33.8 bits (77), Expect = 0.051 Identities = 25/125 (20%), Positives = 50/125 (40%), Gaps = 7/125 (5%) Query: 13 YCESVISIKHYTDRLFRFCITRPKSFRFRSGEFVMLGLMVNGRRI-SRAYSMASPCWDDK 71 Y V + + I + +++G+F L + + R+ +++A + Sbjct: 216 YLGKVTAPQRGNVDTLEITIGLQGPWLYQAGQFAFLKIEIEEFRMRPHPFTIACSHEGSE 275 Query: 72 LEFFSIKVEQGPLTTHLQ-NIQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPF 130 L F SIK G T L+ N++ G + + G + + + G GI PF Sbjct: 276 LRF-SIK-ALGDFTKTLKDNLKVGTKLEV-DGPYGKFDFERGLNTQ--VWIAGGIGITPF 330 Query: 131 VSVIR 135 +S++ Sbjct: 331 ISMLF 335 >gnl|CDD|99783 cd06186, NOX_Duox_like_FAD_NADP, NADPH oxidase (NOX) catalyzes the generation of reactive oxygen species (ROS) such as superoxide and hydrogen peroxide. ROS were originally identified as bactericidal agents in phagocytes, but are now also implicated in cell signaling and metabolism. NOX has a 6-alpha helix heme-binding transmembrane domain fused to a flavoprotein with the nucleotide binding domain located in the cytoplasm. Duox enzymes link a peroxidase domain to the NOX domain via a single transmembrane and EF-hand Ca2+ binding sites. The flavoprotein module has a ferredoxin like FAD/NADPH binding domain. In classical phagocytic NOX2, electron transfer occurs from NADPH to FAD to the heme of cytb to oxygen leading to superoxide formation.. Length = 210 Score = 32.7 bits (75), Expect = 0.096 Identities = 29/131 (22%), Positives = 51/131 (38%), Gaps = 32/131 (24%) Query: 25 DRLFRFCITRPKSFRFRSGEFVMLGLMVNGRRISRA-----YSMAS--PCWDDKLEFFSI 77 + R I +PK F+++ G+ V L N + +++AS D L I Sbjct: 10 SDVIRLTIPKPKPFKWKPGQHVYL----NFPSLLSFWQSHPFTIASSPEDEQDTLSLI-I 64 Query: 78 KVEQGPLTTHLQNIQPGDTILLHKKSTGTLVLDALIPG------------NRLYLFSTGT 125 + ++G TT L K G + L L+ G + + L + G+ Sbjct: 65 RAKKGF-TTRLLR-------KALKSPGGGVSLKVLVEGPYGSSSEDLLSYDNVLLVAGGS 116 Query: 126 GIAPFVSVIRD 136 GI + ++RD Sbjct: 117 GITFVLPILRD 127 >gnl|CDD|99803 cd06207, CyPoR_like, NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 382 Score = 32.2 bits (74), Expect = 0.15 Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 6/68 (8%) Query: 69 DDKLEFFSIKVEQGPLTTHLQNIQPGDTI-LLHKKSTGTLVLDALIPGNRLYLFSTGTGI 127 K + G +++L ++ G + + KKS+ L D P + + GTG+ Sbjct: 188 SWKTPSGRSR--YGLCSSYLAGLKVGQRVTVFIKKSSFKLPKDPKKP---IIMVGPGTGL 242 Query: 128 APFVSVIR 135 APF + ++ Sbjct: 243 APFRAFLQ 250 >gnl|CDD|147411 pfam05203, Hom_end_hint, Hom_end-associated Hint. Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a a second domain containing the protein-splicing active site. This Domain corresponds to the latter protein-splicing domain. Length = 438 Score = 30.2 bits (68), Expect = 0.63 Identities = 23/117 (19%), Positives = 38/117 (32%), Gaps = 12/117 (10%) Query: 153 RQVVELQYGIDVMHEISQDEILKDLIGQKLKFYRTVTQEDYLY---KGRITNHILSGEFY 209 R+V+ L G D M+ I+Q + F + L R+ N + G Sbjct: 35 RRVIGLPRGRDTMYRITQKTKHRVY--DLESFVCNANHKLVLRTPQNVRLENRTIRGNTV 92 Query: 210 RNMDLSPLNPDTDR-IMICGS-----PTMIVDMKDLLIAKKFREGSNSRPG-TFVVE 259 R +L R I I P + + AK+F + + +E Sbjct: 93 RWRNLEETLTTDGRIIEIVKEHHKSFPHTEGEERAKEFAKEFASVIATGEYIEWEIE 149 >gnl|CDD|30718 COG0369, CysJ, Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism]. Length = 587 Score = 29.6 bits (66), Expect = 0.87 Identities = 47/209 (22%), Positives = 86/209 (41%), Gaps = 31/209 (14%) Query: 59 RAYSMASPCWD--DKLEFFSIKVE--------QGPLTTHLQNIQP-GDTILLHKKSTGTL 107 R YS+AS D++ V G + +L ++ GDTI + + Sbjct: 374 RLYSIASSPGVSPDEVHLTVGVVRYQAEGRERYGVCSGYLADLLEEGDTIPVFVQPNKNF 433 Query: 108 VL--DALIPGNRLYLFSTGTGIAPFVSVIRDPGTYEKFDEVIVTQTCRQVVELQYGIDVM 165 L D P + + GTGIAPF + +++ + + CR E D + Sbjct: 434 RLPEDPETP---IIMIGPGTGIAPFRAFVQERAANGAEGKNWLFFGCRHFTE-----DFL 485 Query: 166 HEISQDEILKDLIGQKLKFYRTVTQEDYLY-KGRITNHILSGEFYRNMDLSPLNPDTDRI 224 ++ +E LKD + +L + QE+ +Y + R+ + E + ++ + I Sbjct: 486 YQEEWEEYLKDGVLTRLDLAFSRDQEEKIYVQDRLREQ--ADELWEWLE------EGAHI 537 Query: 225 MICGSPT-MIVDMKDLLIAKKFREGSNSR 252 +CG M D+++ L+ +EG SR Sbjct: 538 YVCGDAKGMAKDVEEALLDILAKEGGLSR 566 >gnl|CDD|38588 KOG3378, KOG3378, KOG3378, Hemoglobin-like flavoprotein [Energy production and conversion]. Length = 385 Score = 28.9 bits (64), Expect = 1.5 Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 4/81 (4%) Query: 59 RAYSMASPCWDDKLEFFSIKVEQGPLTTHL--QNIQPGDTILLHKKSTGTLVLDALIPGN 116 + S ++ S++ G + ++ N++ GD + + + + + N Sbjct: 204 YSLSNRVDTCRNQFRI-SVRRVAGGVVSNFVHDNLKVGDIVGVSPPAGNFVYKRSEENVN 262 Query: 117 R-LYLFSTGTGIAPFVSVIRD 136 R L F+ G GI P + +I Sbjct: 263 RPLLCFAGGIGITPLIPIIET 283 >gnl|CDD|99795 cd06198, FNR_like_3, NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP+ to NADPH.. Length = 216 Score = 28.8 bits (65), Expect = 1.5 Identities = 23/106 (21%), Positives = 43/106 (40%), Gaps = 13/106 (12%) Query: 36 KSFRFRSGEFVMLGLMVNGRRISRAYSMASPCWDDKLE-FFSIKVEQGPLTTHL-QNIQP 93 + R+G+F L +G ++++S D F+IK G T L + ++P Sbjct: 19 PALGHRAGQFAFLRFDASGWEEPHPFTISSA-PDPDGRLRFTIK-ALGDYTRRLAERLKP 76 Query: 94 GDTILL---HKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIRD 136 G + + + G D R + G GI PF++++ Sbjct: 77 GTRVTVEGPY----GRFTFDD--RRARQIWIAGGIGITPFLALLEA 116 >gnl|CDD|33716 COG3934, COG3934, Endo-beta-mannanase [Carbohydrate transport and metabolism]. Length = 587 Score = 28.8 bits (64), Expect = 1.7 Identities = 12/67 (17%), Positives = 22/67 (32%), Gaps = 1/67 (1%) Query: 185 YRTVTQEDYLYKGRITNHILSGEFYRNMDLSPLNPDTDRIMICGSPTMIVDMKDLLIAKK 244 + + ++ GR YR+ D + D +MI PT V L+ Sbjct: 359 PLFIRVFNLIFDGRQF-TPGQPTTYRDRDYKTMLDDAKLLMIPSGPTAGVTTWAWLLKGV 417 Query: 245 FREGSNS 251 + + Sbjct: 418 VNQVPDV 424 >gnl|CDD|99779 cd06182, CYPOR_like, NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPOR has a C-terminal ferredoxin reducatase (FNR)- like FAD and NAD binding module, an FMN-binding domain, and an additional conecting domain (inserted within the FAD binding region) that orients the FNR and FMN binding domains. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria and participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2, which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 267 Score = 28.5 bits (64), Expect = 2.1 Identities = 25/123 (20%), Positives = 47/123 (38%), Gaps = 18/123 (14%) Query: 26 RLFRFCITRPKSFRFRSGEFVMLGLMVNGRRISRAYSMAS--PCWDDKLEFFSIKVE--- 80 R F ++ +++ G+ LG++ R YS+AS ++ V Sbjct: 18 RHLEFDLSGNSVLKYQPGD--HLGVIPPNPLQPRYYSIASSPDVDPGEVHLCVRVVSYEA 75 Query: 81 ------QGPLTTHLQNIQPGDTILLHKKSTGTLVL--DALIPGNRLYLFSTGTGIAPFVS 132 +G + L +Q G + + + + L D P + + GTGIAPF Sbjct: 76 PAGRIRKGVCSNFLAGLQLGAKVTVFIRPAPSFRLPKDPTTP---IIMVGPGTGIAPFRG 132 Query: 133 VIR 135 ++ Sbjct: 133 FLQ 135 >gnl|CDD|36373 KOG1158, KOG1158, KOG1158, NADP/FAD dependent oxidoreductase [Energy production and conversion]. Length = 645 Score = 28.4 bits (63), Expect = 2.1 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 6/58 (10%) Query: 82 GPLTTHLQNIQPGD---TILLHKKSTGTLVLDALIPGNRLYLFSTGTGIAPFVSVIRD 136 G + L N++PG+ + KS L D P + + GTGIAPF +++ Sbjct: 458 GVCSNWLSNLKPGEKVPNPVPVGKSMFRLPSDPSTP---IIMIGPGTGIAPFRGFLQE 512 >gnl|CDD|31540 COG1349, GlpR, Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]. Length = 253 Score = 28.3 bits (63), Expect = 2.2 Identities = 22/81 (27%), Positives = 31/81 (38%), Gaps = 7/81 (8%) Query: 91 IQPGDTILLHKKSTGTLVLDALIPGNRLYLFSTGTGIA------PFVSVIRDPGTYEKFD 144 I+ GDTI L +T + AL N L + + IA P + VI GT K Sbjct: 89 IEDGDTIFLDAGTTTLALARALPDDNNLTVITNSLNIAAALLEKPNIEVILLGGTVRKKS 148 Query: 145 EVIVTQTCRQVVELQYGIDVM 165 V + + Q+ D Sbjct: 149 GSFVGPLAEEFLR-QFNFDKA 168 >gnl|CDD|99799 cd06202, Nitric_oxide_synthase, The ferredoxin-reductase (FNR) like C-terminal domain of the nitric oxide synthase (NOS) fuses with a heme-containing N-terminal oxidase domain. The reductase portion is similar in structure to NADPH dependent cytochrome-450 reductase (CYPOR), having an inserted connecting sub-domain within the FAD binding portion of FNR. NOS differs from CYPOR in a requirement for the cofactor tetrahydrobiopterin and unlike most CYPOR is dimeric. Nitric oxide synthase produces nitric oxide in the conversion of L-arginine to L-citruline. NOS has been implicated in a variety of processes including cytotoxicity, anti-inflamation, neurotransmission, and vascular smooth muscle relaxation.. Length = 406 Score = 27.3 bits (61), Expect = 4.3 Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 10/59 (16%) Query: 81 QGPL-----TTHLQNIQPGDTILLHKKSTGTLVL--DALIPGNRLYLFSTGTGIAPFVS 132 QGP+ +T L + PGDT+ +S + L D +P + + GTGIAPF S Sbjct: 208 QGPVHHGVCSTWLNGLTPGDTVPCFVRSAPSFHLPEDPSVP---VIMVGPGTGIAPFRS 263 >gnl|CDD|99785 cd06188, NADH_quinone_reductase, Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase, and has NADH and FAD binding sites. (Na+-NQR) is distinct from H+-translocating NADH:quinone oxidoreductases and noncoupled NADH:quinone oxidoreductases. The NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain of this group typically contains an iron-sulfur cluster binding domain.. Length = 283 Score = 27.3 bits (61), Expect = 5.0 Identities = 11/51 (21%), Positives = 27/51 (52%), Gaps = 10/51 (19%) Query: 57 ISRAYSMASPCWDDKLEFFSIKVEQGPL----------TTHLQNIQPGDTI 97 +SRAYS+A+ ++ ++++ P ++++ N++PGD + Sbjct: 85 VSRAYSLANYPAEEGELKLNVRIATPPPGNSDIPPGIGSSYIFNLKPGDKV 135 >gnl|CDD|99915 cd05532, POLBc_alpha, DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.. Length = 400 Score = 27.2 bits (61), Expect = 5.4 Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 9/61 (14%) Query: 195 YKGRITNHIL--SGEFYRNMDLSPLNPDTDRIMICGSPTMIVDMKDLL-IAKKFREGSNS 251 KGR IL + + M+L + DTD IMI T D ++ + K ++ N Sbjct: 139 SKGR---EILQKTKDLVEKMNLEVIYGDTDSIMIN---TGTTDYEEAKKLGNKIKKEVNK 192 Query: 252 R 252 Sbjct: 193 S 193 >gnl|CDD|132891 cd07051, BMC_like_1_repeat1, Bacterial Micro-Compartment (BMC)-like domain 1 repeat 1. BMC-like domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of the carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view. Proteins in this CD contain two tandem BMC domains. This CD includes repeat 1 (the first BMC domain of BMC like 1 proteins). Length = 111 Score = 26.9 bits (60), Expect = 5.7 Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 2/41 (4%) Query: 154 QVVELQYGIDVMHEISQDEILKDLIGQKLKFYRTVTQEDYL 194 QVVE Q+G+ +H SQ E+L G + +T+ED L Sbjct: 63 QVVERQFGLLELHSRSQSEVLA--AGDAVLDALGLTEEDRL 101 >gnl|CDD|176249 cd08289, MDR_yhfp_like, Yhfp putative quinone oxidoreductases. yhfp putative quinone oxidoreductases (QOR). QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. Length = 326 Score = 26.5 bits (59), Expect = 8.2 Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 13/60 (21%) Query: 111 ALIPGNRL---YLFSTGTGIAPFVSVIRDPGTYEKFDEVIVTQTCRQVVELQYGIDVMHE 167 A IPG ++ Y F G +A V DP ++ DEVIVT Y + V H Sbjct: 46 ASIPGGKIVKRYPFIPGIDLAGTVVESNDPR-FKPGDEVIVT---------SYDLGVSHH 95 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 0.324 0.141 0.421 Gapped Lambda K H 0.267 0.0632 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,272,276 Number of extensions: 173018 Number of successful extensions: 577 Number of sequences better than 10.0: 1 Number of HSP's gapped: 531 Number of HSP's successfully gapped: 55 Length of query: 264 Length of database: 6,263,737 Length adjustment: 92 Effective length of query: 172 Effective length of database: 4,275,709 Effective search space: 735421948 Effective search space used: 735421948 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 56 (25.6 bits)