RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780364|ref|YP_003064777.1| ferredoxin-NADP+ reductase
protein [Candidatus Liberibacter asiaticus str. psy62]
         (224 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 =  216 bits (553), Expect = 3e-57
 Identities = 84/212 (39%), Positives = 118/212 (55%), Gaps = 14/212 (6%)

Query: 17  VISVKHYTDRLFRFCITRPKSFRFRSGEFVMLGLIVN-GRPIFRAYSIASPCRDDKLEFC 75
           V+  + +TD LF F +TR   FRF++G+F  LGL  + G+ + RAYSIAS   ++ LEF 
Sbjct: 2   VLKRRDWTDDLFSFRVTRDIPFRFQAGQFTKLGLPNDDGKLVRRAYSIASAPYEENLEFY 61

Query: 76  SIKVDKGFFTTYLQNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIR 135
            I V  G  T  L  ++PGDTI + KK TG L LD + PG RL+L + GTGIAPF SM+R
Sbjct: 62  IILVPDGPLTPRLFKLKPGDTIYVGKKPTGFLTLDEVPPGKRLWLLATGTGIAPFLSMLR 121

Query: 136 DPETYKKFDEVIITHTCGRVAELQYGIDVMHEISQDEI--LKDLIGQKLKFYRTVTQEDY 193
           D E +++FD++++ H      EL Y         QDEI  L      K ++   V++E  
Sbjct: 122 DLEIWERFDKIVLVHGVRYAEELAY---------QDEIEALAKQYNGKFRYVPIVSREKE 172

Query: 194 --LYKGRITNHILSGEFYRNMGLSPLNPDTRI 223
                GRI + I SGE   + GL      + +
Sbjct: 173 NGALTGRIPDLIESGELEEHAGLPLDPETSHV 204


>gnl|CDD|31221 COG1018, Hmp, Flavodoxin reductases (ferredoxin-NADPH reductases)
           family 1 [Energy production and conversion].
          Length = 266

 Score =  121 bits (305), Expect = 1e-28
 Identities = 62/219 (28%), Positives = 104/219 (47%), Gaps = 15/219 (6%)

Query: 17  VISVKHYTDRLFRFCITRPKSFR--FRSGEFVMLGLIVNGRPIFRAYSIASPCRDDKLEF 74
           V SV+  TD +F F +  P   R  F  G+++ +GL   G P+ RAYS++S   +D L  
Sbjct: 10  VTSVEPETDDVFSFTLEPPDGLRLDFEPGQYITVGLPNGGEPLLRAYSLSSAPDEDSLYR 69

Query: 75  CSIKV-DKGFFTTYLQ-NIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFAS 132
            S+K  D G  + +L  +++ GDT+ +     GD +LD  +P  +L L + G GI PF S
Sbjct: 70  ISVKREDGGGGSNWLHDHLKVGDTLEV-SAPAGDFVLD-DLPERKLLLLAGGIGITPFLS 127

Query: 133 MIRDPETYKKFDEVIITHTCGRVAELQYG--IDVMHEISQDEILKDLIGQ-KLKFYRTVT 189
           M+R         +V++ H     A+L +   +++  E+    +L     + KL+    V+
Sbjct: 128 MLRTLLDRGP-ADVVLVHAARTPADLAFRDELELAAELPNALLLGLYTERGKLQGRIDVS 186

Query: 190 QEDYLY--KGRITNHILSGEFYRNMGLSPLN---PDTRI 223
           +        GR       G F + + L+      PD R+
Sbjct: 187 RLLSAAPDGGREVYLCGPGPFMQAVRLALEALGVPDDRV 225


>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 = 85.2 bits (211), Expect = 1e-17
 Identities = 53/194 (27%), Positives = 86/194 (44%), Gaps = 15/194 (7%)

Query: 18  ISVKHYTDRLFRFCITRPKSFRFRSGEFVMLGLIVNGRPIFRAYSIAS-PCRDDKLEFCS 76
           ++ +  TD +  F +  P  F F+ G++V L L  +GR + RAYSIAS P  + +LE   
Sbjct: 1   VATEDVTDDVRLFRLQLPNGFSFKPGQYVDLHLPGDGRGLRRAYSIASSPDEEGELELTV 60

Query: 77  IKVDKGFFTTYLQNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIRD 136
             V  G F+ +L +++PGD + +     GD  L        + L + G GI PF SM+R 
Sbjct: 61  KIVPGGPFSAWLHDLKPGDEVEVSGP-GGDFFLPLE-ESGPVVLIAGGIGITPFRSMLRH 118

Query: 137 PETYKKFDEVIITHTCGRVAELQYGIDVMHEISQDEILKDLI--GQKLKFYRTVTQEDYL 194
               K   E+ + +     A+L +          DE L++L   G   +    +++E   
Sbjct: 119 LAADKPGGEITLLYGARTPADLLF---------LDE-LEELAKEGPNFRLVLALSRESEA 168

Query: 195 YKGRITNHILSGEF 208
             G         E 
Sbjct: 169 KLGPGGRIDREAEI 182


>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 = 72.2 bits (178), Expect = 1e-13
 Identities = 42/193 (21%), Positives = 81/193 (41%), Gaps = 18/193 (9%)

Query: 17  VISVKHYTDRLFRFCITRPKSFRFRSGEFVMLGLIVNGRPI-FRAYSIASPCRDD-KLEF 74
           V+SV+  T  +    +   +   F +G++V + +   GRP  +RAYS A+P  +D ++EF
Sbjct: 1   VVSVERLTHDIAVVRLQLDQPLPFWAGQYVNVTVP--GRPRTWRAYSPANPPNEDGEIEF 58

Query: 75  CSIKVDKGFFTTYL-QNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASM 133
               V  G  +  L   ++ GD + L     G   L        L +   GTG+AP  ++
Sbjct: 59  HVRAVPGGRVSNALHDELKVGDRVRL-SGPYGTFYLRRDHDRPVLCIAG-GTGLAPLRAI 116

Query: 134 IRDPETYKKFDEVIITHTCGRVAELQYGIDVMHEISQDEILKDLIGQKLKFYRTVTQED- 192
           + D     +   V +        +L Y ++ +  ++            L+    V+ E+ 
Sbjct: 117 VEDALRRGEPRPVHLFFGARTERDL-YDLEGLLALAARH-------PWLRVVPVVSHEEG 168

Query: 193 --YLYKGRITNHI 203
                +G +T+ +
Sbjct: 169 AWTGRRGLVTDVV 181


>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 = 67.6 bits (166), Expect = 2e-12
 Identities = 37/111 (33%), Positives = 60/111 (54%), Gaps = 6/111 (5%)

Query: 28  FRFCITRPKSFRFRSGEFVMLGLIVNGRPIFRAYSIAS-PCRDDKLEFCSIK-VDKGFFT 85
           FRF       F ++ G+F+ L L ++G  ++RAY+++S P R D L   ++K V  G  +
Sbjct: 16  FRFAAPDGSLFAYKPGQFLTLELEIDGETVYRAYTLSSSPSRPDSLSI-TVKRVPGGLVS 74

Query: 86  TYL-QNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIR 135
            +L  N++ GD +     + G+  L    P ++L L S G+GI P  SM R
Sbjct: 75  NWLHDNLKVGDELWASGPA-GEFTL-IDHPADKLLLLSAGSGITPMMSMAR 123


>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 = 66.8 bits (164), Expect = 5e-12
 Identities = 32/100 (32%), Positives = 54/100 (54%), Gaps = 4/100 (4%)

Query: 38  FRFRSGEFVMLGLIVNGRPIFRAYSIASPCRDDKLEFCSIK-VDKGFFTTYL-QNIQPGD 95
           FR+R G+F+ L + ++G  + R+YSI S   DD+L   ++K V  G F+ +    ++ GD
Sbjct: 31  FRYRPGQFLTLRVPIDGEEVRRSYSICSSPGDDELRI-TVKRVPGGRFSNWANDELKAGD 89

Query: 96  TILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIR 135
           T+ +     G   L  L       LF+ G+GI P  S+++
Sbjct: 90  TLEVM-PPAGRFTLPPLPGARHYVLFAAGSGITPVLSILK 128


>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 = 64.9 bits (158), Expect = 2e-11
 Identities = 35/111 (31%), Positives = 53/111 (47%), Gaps = 3/111 (2%)

Query: 26  RLFRFCITRPKSFRFRSGEFVMLGLIVNGRPIFRAYSIASPCRDDKLEFCSIKVDKGFFT 85
               F +  P  + FR G+ V L L  +G  + R YS+ S    D++     +V  G  +
Sbjct: 14  VTIVFAVPGPLQYGFRPGQHVTLKLDFDGEELRRCYSLCSSPAPDEISITVKRVPGGRVS 73

Query: 86  TYL-QNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIR 135
            YL ++IQPG T+ +     G  +     PG R  L + G+GI P  +MIR
Sbjct: 74  NYLREHIQPGMTVEV-MGPQGHFVYQPQPPG-RYLLVAAGSGITPLMAMIR 122


>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 = 61.6 bits (150), Expect = 2e-10
 Identities = 34/106 (32%), Positives = 47/106 (44%), Gaps = 6/106 (5%)

Query: 39  RFRSGEFVMLGLIVNGRPIFRAYSIASPCRDDKLEFCSIKVDKGFFTTYLQNIQPGDTIL 98
            F +G+  +LG++  G  + R YS+AS   D  LE C  K   G  + YL  ++PGDTI 
Sbjct: 83  SFEAGD--LLGILPPGSDVPRFYSLASSSSDGFLEICVRKHPGGLCSGYLHGLKPGDTIK 140

Query: 99  LHKKSTGDLILDSLIPGNR-LYLFSMGTGIAPFASMIRDPETYKKF 143
              +            G   + L   GTGIAP A  IR     +  
Sbjct: 141 AFIRPNPSFRPAK---GAAPVILIGAGTGIAPLAGFIRANAARRPM 183


>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 = 6e-10
 Identities = 35/108 (32%), Positives = 59/108 (54%), Gaps = 7/108 (6%)

Query: 34  RP--KSFRFRSGEFVMLGLIVNGRPIFRAYSIAS-PCRDDKLEFCSIK-VDKGFFTTYL- 88
           RP       R+G+ V LG+ ++G   +R+YS++S P ++D     ++K    G  + +L 
Sbjct: 38  RPNRGWPGHRAGQHVRLGVEIDGVRHWRSYSLSSSPTQEDGTITLTVKAQPDGLVSNWLV 97

Query: 89  QNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIRD 136
            ++ PGD + L  +  GD +L   +P  RL L + G+GI P  SM+R 
Sbjct: 98  NHLAPGDVVEL-SQPQGDFVLPDPLPP-RLLLIAAGSGITPVMSMLRT 143


>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 = 56.1 bits (136), Expect = 6e-09
 Identities = 34/113 (30%), Positives = 56/113 (49%), Gaps = 5/113 (4%)

Query: 26  RLFRFCITRPKSFRFRSGEFVMLGL-IVNGRPIFRAYSIAS-PCRDDKLEFCSIKVDKGF 83
           + FR  +       F +G+ V L L  ++G    R+YSIAS P +  ++E    +V  G 
Sbjct: 17  KTFRLAVPDGVPPPFLAGQHVDLRLTAIDGYTAQRSYSIASSPTQRGRVELTVKRVPGGE 76

Query: 84  FTTYL-QNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIR 135
            + YL   ++ GD + + +   G    + L  G+ + L + G+GI P  SMIR
Sbjct: 77  VSPYLHDEVKVGDLLEV-RGPIGTFTWNPL-HGDPVVLLAGGSGIVPLMSMIR 127


>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 = 54.6 bits (132), Expect = 2e-08
 Identities = 32/125 (25%), Positives = 52/125 (41%), Gaps = 24/125 (19%)

Query: 23  YTDRLFRFCITRPKSFRFRSGEFVMLGLIVNGRPIFRAYSIAS-PCRDDKLEFCSIKVDK 81
            T +  R  +  P+   F++G++V   L   G    RA+SIAS P    ++E     V  
Sbjct: 19  PTIKGVRLKLDEPEEIEFQAGQYV--NLQAPGYEGTRAFSIASSPSDAGEIELHIRLVPG 76

Query: 82  GFFTTYL-QNIQPGDTILL---------HKKSTGDLILDSLIPGNRLYLFSMGTGIAPFA 131
           G  TTY+ + ++ GD + +                +I    I G        G+G++   
Sbjct: 77  GIATTYVHKQLKEGDELEISGPYGDFFVRDSDQRPII---FIAG--------GSGLSSPR 125

Query: 132 SMIRD 136
           SMI D
Sbjct: 126 SMILD 130


>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 = 53.9 bits (130), Expect = 4e-08
 Identities = 32/105 (30%), Positives = 50/105 (47%), Gaps = 6/105 (5%)

Query: 33  TRPKSFRFRSGEFVMLGLIVNGRPIFRAYSIAS-PCRDDKLEFCSIKVDKGFFTTYLQN- 90
               +  F  G+FV +   + G    R+YS+A+ P  D +LEF    +  G F+TYL+  
Sbjct: 28  GAGIAAEFVPGQFVEIE--IPGTDTRRSYSLANTPNWDGRLEFLIRLLPGGAFSTYLETR 85

Query: 91  IQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIR 135
            + G  + L +   G   L       R +  + GTG+AP  SM+R
Sbjct: 86  AKVGQRLNL-RGPLGAFGLRENGLRPR-WFVAGGTGLAPLLSMLR 128


>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 = 53.7 bits (130), Expect = 4e-08
 Identities = 31/123 (25%), Positives = 52/123 (42%), Gaps = 6/123 (4%)

Query: 16  SVISVKHYTDRLFRFCITRPKS-FRFRSGEFVMLGLIVNGRPIFRAYS-IASPCRDDKLE 73
           S   + H   R+FRF +  P        G+ V L    +G  + R Y+ I+        +
Sbjct: 5   SKEDISH-DTRIFRFELPSPDQVLGLPVGQHVELKAPDDGEQVVRPYTPISPDDDKGYFD 63

Query: 74  FCSIKV-DKGFFTTYLQNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFAS 132
              IK+   G  + YL +++PGDT+ + +   G            + + + GTGI P   
Sbjct: 64  LL-IKIYPGGKMSQYLHSLKPGDTVEI-RGPFGKFEYKPNGKVKHIGMIAGGTGITPMLQ 121

Query: 133 MIR 135
           +IR
Sbjct: 122 LIR 124


>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 = 52.6 bits (127), Expect = 9e-08
 Identities = 35/130 (26%), Positives = 57/130 (43%), Gaps = 25/130 (19%)

Query: 16  SVISVKHYTDRLFRFCITRPKSFRFRSGEFVMLGLIVNGRPIFRAYSIAS-PCRDDKLEF 74
            V S++   D ++R  +  P    F +G+++ L L+ +G    R +SIAS P  D ++E 
Sbjct: 2   KVESIEPLNDDVYRVRLKPPAPLDFLAGQYLDL-LLDDGDK--RPFSIASAPHEDGEIEL 58

Query: 75  CSIKVDKGFFTTY-LQNIQPGDTI---------LLHKKSTGDLILDSLIPGNRLYLFSMG 124
               V  G F+ Y  + ++    +          L + S   LI   LI G        G
Sbjct: 59  HIRAVPGGSFSDYVFEELKENGLVRIEGPLGDFFLREDSDRPLI---LIAG--------G 107

Query: 125 TGIAPFASMI 134
           TG AP  S++
Sbjct: 108 TGFAPIKSIL 117


>gnl|CDD|144531 pfam00970, FAD_binding_6, Oxidoreductase FAD-binding domain. 
          Length = 99

 Score = 51.8 bits (125), Expect = 1e-07
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 26 RLFRFCITRPK-SFRFRSGEFVMLGLIVNGRPIFRAYSIASPCRDDK-LEFCSIKVDKGF 83
          R FRF +  P        G+ + L L ++G+ + RAYS AS   D   LE        G 
Sbjct: 15 RRFRFALPSPDQVLGLPPGQHIFLRLPIDGKLVVRAYSPASSPDDVGELELLVKVYPGGK 74

Query: 84 FTTYLQNIQPGDTI 97
           + YL +++ GDT+
Sbjct: 75 MSQYLDSLKVGDTV 88


>gnl|CDD|30889 COG0543, UbiB, 2-polyprenylphenol hydroxylase and related
           flavodoxin oxidoreductases [Coenzyme metabolism / Energy
           production and conversion].
          Length = 252

 Score = 50.0 bits (119), Expect = 5e-07
 Identities = 37/146 (25%), Positives = 67/146 (45%), Gaps = 8/146 (5%)

Query: 5   SSELAADVYCESVISVKHYTDRLFRFCIT-RPKSFRFRSGEFVMLGLIVNGRPIFRAYSI 63
            + LA  +  + V+  +  +   F   +     +  F+ G+FVML +    R   R YS+
Sbjct: 1   ENPLALLMSYK-VVEKEEISPDTFLLRLRLPFVALTFKPGQFVMLRVPGGVR---RPYSL 56

Query: 64  AS-PCRDDKLEFCSIKVDKGFFTTYLQNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFS 122
           AS P    +LE      + G  T Y+  ++ GD I + +   G+  L   I G  + L +
Sbjct: 57  ASAPDDKGELELHIRVYEVGKVTKYIFGLKEGDKIRV-RGPLGNGFLREKI-GKPVLLIA 114

Query: 123 MGTGIAPFASMIRDPETYKKFDEVII 148
            GTGIAP  ++ ++ +     ++V +
Sbjct: 115 GGTGIAPLYAIAKELKEKGDANKVTL 140


>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 = 49.9 bits (120), Expect = 6e-07
 Identities = 36/100 (36%), Positives = 50/100 (50%), Gaps = 8/100 (8%)

Query: 38  FRFRSGEFVMLGLIVNGRPIFRAYSIASPCRDDKLEFCSIKVDKGFFTTYLQN-IQPGDT 96
             F  G++V L   V G    R+YS +S   D +LEF    +  G  ++YL++  QPGD 
Sbjct: 29  LAFLPGQYVNLQ--VPGTDETRSYSFSSAPGDPRLEFLIRLLPGGAMSSYLRDRAQPGDR 86

Query: 97  ILLHKKSTGDLILDSLIPGNRLYLF-SMGTGIAPFASMIR 135
           + L    TG L    L    R  L  + GTG+APF SM+ 
Sbjct: 87  LTL----TGPLGSFYLREVKRPLLMLAGGTGLAPFLSMLD 122


>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 = 49.1 bits (118), Expect = 9e-07
 Identities = 43/141 (30%), Positives = 58/141 (41%), Gaps = 36/141 (25%)

Query: 20  VKHYTDRLFRFCITRPKSFRFRSGEFVMLGLIVNGR-PIFRAYSIAS-PCRDDKLEFCSI 77
           +K +T    R      + F F+ G+FVML L   G  PI    SI+S P R   LE    
Sbjct: 11  IKTFT---LRLEDDDEELFTFKPGQFVMLSLPGVGEAPI----SISSDPTRRGPLELTIR 63

Query: 78  KVDKGFFTTYLQNIQPGDTILL----------HKKSTGDLILDSLIPGNRLYLFSMGTGI 127
           +V  G  T  L  ++PGDT+ L           +    DL+   L+ G        G G+
Sbjct: 64  RV--GRVTEALHELKPGDTVGLRGPFGNGFPVEEMKGKDLL---LVAG--------GLGL 110

Query: 128 APFASMIRD----PETYKKFD 144
           AP  S+I       E Y K  
Sbjct: 111 APLRSLINYILDNREDYGKVT 131


>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 = 47.3 bits (113), Expect = 3e-06
 Identities = 36/147 (24%), Positives = 60/147 (40%), Gaps = 34/147 (23%)

Query: 26  RLFRFCITRPKSFRFRSGEFVMLGLIVNGRPIFRAYSIA-SPCRDDKLEFCSIKVDKGFF 84
           R  R  +  P+  +F +G++V   + V G    R++S+A +P    +LEF   K   G F
Sbjct: 16  RRLRLRLEEPEPIKFFAGQYV--DITVPGTEETRSFSMANTPADPGRLEFIIKKYPGGLF 73

Query: 85  TTYL-QNIQPGD---------TILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMI 134
           +++L   +  GD         T  L +     ++   LI G        G+G+AP  S++
Sbjct: 74  SSFLDDGLAVGDPVTVTGPYGTCTLRESRDRPIV---LIGG--------GSGMAPLLSLL 122

Query: 135 RDPETYKKFDEVIITHTCGRVAELQYG 161
           RD          +      R     YG
Sbjct: 123 RD----------MAASGSDRPVRFFYG 139


>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 = 46.9 bits (112), Expect = 4e-06
 Identities = 32/147 (21%), Positives = 55/147 (37%), Gaps = 26/147 (17%)

Query: 2   CDVSSELAADVYCESVISVKHYTDRLFRFCITRPKSFRFRSGEFVMLGLIVNGRPIFRAY 61
             V+ +L       S   ++        F ++     +++ G+   LG+I       R Y
Sbjct: 2   ITVNRKLTPPDSPRSTRHLE--------FDLSGNSVLKYQPGD--HLGVIPPNPLQPRYY 51

Query: 62  SIASPCRDD--KLEFCSIKVD---------KGFFTTYLQNIQPGDTILLHKKSTGDLIL- 109
           SIAS    D  ++  C   V          KG  + +L  +Q G  + +  +      L 
Sbjct: 52  SIASSPDVDPGEVHLCVRVVSYEAPAGRIRKGVCSNFLAGLQLGAKVTVFIRPAPSFRLP 111

Query: 110 -DSLIPGNRLYLFSMGTGIAPFASMIR 135
            D   P   + +   GTGIAPF   ++
Sbjct: 112 KDPTTP---IIMVGPGTGIAPFRGFLQ 135


>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 = 45.0 bits (107), Expect = 2e-05
 Identities = 32/100 (32%), Positives = 45/100 (45%), Gaps = 19/100 (19%)

Query: 53  NGRP-IFRAYSIASPCRD------DKLEFC----------SIKVDKGFFTTYLQNIQPGD 95
           NG+P   R YSIAS  R         L  C          + +  KG  + YL +++PGD
Sbjct: 58  NGKPHKLRLYSIASS-RYGDDGDGKTLSLCVKRLVYTDPETDETKKGVCSNYLCDLKPGD 116

Query: 96  TILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIR 135
            + +     G  +L    P   L + + GTGIAPF S +R
Sbjct: 117 DVQI-TGPVGKTMLLPEDPNATLIMIATGTGIAPFRSFLR 155


>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 = 43.8 bits (104), Expect = 4e-05
 Identities = 29/115 (25%), Positives = 48/115 (41%), Gaps = 6/115 (5%)

Query: 24  TDRLFRFCITRPKSFRFRSGEFVMLGLIVNGRPIFRAYSIAS-PCRDDKLEFCSIKVDKG 82
           +  + R  +   +   +  G++V   L   G    R+YS  S P  D++LEF   +   G
Sbjct: 8   SPDVLRVRLEPDRPLPYLPGQYV--NLRRAGGLA-RSYSPTSLPDGDNELEFHIRRKPNG 64

Query: 83  FFTTYL-QNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIRD 136
            F+ +L +  +PG  + L +   G            L L   GTG+AP   + R 
Sbjct: 65  AFSGWLGEEARPGHALRL-QGPFGQAFYRPEYGEGPLLLVGAGTGLAPLWGIARA 118


>gnl|CDD|35754 KOG0534, KOG0534, KOG0534, NADH-cytochrome b-5 reductase [Coenzyme
           transport and metabolism, Energy production and
           conversion].
          Length = 286

 Score = 43.0 bits (101), Expect = 7e-05
 Identities = 28/119 (23%), Positives = 50/119 (42%), Gaps = 5/119 (4%)

Query: 19  SVKHYTDRLFRFCITRPKS-FRFRSGEFVMLGLIVNGRPIFRAYS-IASPCRDDKLEFCS 76
            + H T  LFRF +           G+ V+L   + G+ + R Y+ ++        +   
Sbjct: 61  ELSHDT-SLFRFVLPSADHVLGLPIGQHVVLKAPIGGKLVVRPYTPVSLDDDKGYFDLVV 119

Query: 77  IKVDKGFFTTYLQNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIR 135
               KG  + +L +++ GDT+   +   G+   D       L + + GTGI P   +IR
Sbjct: 120 KVYPKGKMSQHLDSLKIGDTVEF-RGPIGEFKYDPQ-KAKHLGMIAGGTGITPMLQLIR 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 = 42.2 bits (100), Expect = 1e-04
 Identities = 33/125 (26%), Positives = 54/125 (43%), Gaps = 12/125 (9%)

Query: 17  VISVKHYTDRLFRFCITRPKSFRFRSGEFVMLGLI-VNGRPIFRAYSIASPCRDD-KLEF 74
           ++ V+  T  +  F         F  G++ +L L  V G    RAYS+A+      + EF
Sbjct: 1   LVDVRELTHDVAEFRFALDGPADFLPGQYALLALPGVEGA---RAYSMANLANASGEWEF 57

Query: 75  CSIKVDKGFFTTYL-QNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSM--GTGIAPFA 131
              +   G  +  L  N++PGD + L     G   L  L P     +  +  G+G+AP  
Sbjct: 58  IIKRKPGGAASNALFDNLEPGDELEL----DGPYGLAYLRPDEDRDIVCIAGGSGLAPML 113

Query: 132 SMIRD 136
           S++R 
Sbjct: 114 SILRG 118


>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 = 41.8 bits (99), Expect = 2e-04
 Identities = 28/100 (28%), Positives = 45/100 (45%), Gaps = 7/100 (7%)

Query: 40  FRSGEFVMLGLIV--NGRPIFRAYSIASPCRDDKLEFCSIK-VDKGFFTTYL-QNIQPGD 95
           F  G+++ + + +   G    R YS++     D     S+K    G  + YL  N++ GD
Sbjct: 37  FLPGQYLSVRVKLPGLGYRQIRQYSLSDAPNGDYYRI-SVKREPGGLVSNYLHDNVKVGD 95

Query: 96  TILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIR 135
            + +   + GD +LD       L L S G GI P  SM+ 
Sbjct: 96  VLEVSAPA-GDFVLDEASDRP-LVLISAGVGITPMLSMLE 133


>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 = 41.9 bits (99), Expect = 2e-04
 Identities = 23/98 (23%), Positives = 39/98 (39%), Gaps = 19/98 (19%)

Query: 59  RAYSIAS-----PCR--------DDKLEFCSIKVDKGFFTTYLQNIQPGDTI-LLHKKST 104
           R YSI+S     P            K      +   G  ++YL  ++ G  + +  KKS+
Sbjct: 165 RYYSISSSPLKNPNEVHLLVSLVSWKTPSGRSR--YGLCSSYLAGLKVGQRVTVFIKKSS 222

Query: 105 GDLILDSLIPGNRLYLFSMGTGIAPFASMIRDPETYKK 142
             L  D   P   + +   GTG+APF + +++      
Sbjct: 223 FKLPKDPKKP---IIMVGPGTGLAPFRAFLQERAALLA 257


>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 = 39.9 bits (94), Expect = 5e-04
 Identities = 53/196 (27%), Positives = 77/196 (39%), Gaps = 35/196 (17%)

Query: 28  FRFCITRPKSFRFRSGEFVMLGLIVNG-RPIFRAYSIASPCRDDKLEFCSIKV--DKGFF 84
            R    +P+ + F  G+   + +   G R   R ++  S   DD LEF  IK   D    
Sbjct: 16  KRLRFDKPEGYDFTPGQATEVAIDKPGWRDEKRPFTFTSLPEDDVLEF-VIKSYPDHDGV 74

Query: 85  TTYLQNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIRDPETYKKFD 144
           T  L  +QPGDT+L+  +     I     PG      + G GI PF +++RD     K +
Sbjct: 75  TEQLGRLQPGDTLLI--EDPWGAIEYKG-PG---VFIAGGAGITPFIAILRDLAAKGKLE 128

Query: 145 EVIITHTCGRVAELQYGIDVMHEISQDEILKDLIGQKL--KFYRTVTQEDY--LYKGRIT 200
                +T      L +      +  +D ILKD + + L  KF   VT E       GRI 
Sbjct: 129 ----GNT------LIFAN----KTEKDIILKDELEKMLGLKFINVVTDEKDPGYAHGRID 174

Query: 201 -------NHILSGEFY 209
                      +  FY
Sbjct: 175 KAFLKQHVTDFNQHFY 190


>gnl|CDD|33854 COG4097, COG4097, Predicted ferric reductase [Inorganic ion
           transport and metabolism].
          Length = 438

 Score = 39.2 bits (91), Expect = 0.001
 Identities = 27/124 (21%), Positives = 46/124 (37%), Gaps = 5/124 (4%)

Query: 13  YCESVISVKHYTDRLFRFCITRPKSFRFRSGEFVMLGL-IVNGRPIFRAYSIASPCRDDK 71
           Y   V + +          I     + +++G+F  L + I   R     ++IA      +
Sbjct: 216 YLGKVTAPQRGNVDTLEITIGLQGPWLYQAGQFAFLKIEIEEFRMRPHPFTIACSHEGSE 275

Query: 72  LEFCSIKVDKGFFTTYLQNIQPGDTILLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFA 131
           L F SIK    F  T   N++ G  + +     G    +  +        + G GI PF 
Sbjct: 276 LRF-SIKALGDFTKTLKDNLKVGTKLEV-DGPYGKFDFERGLNTQ--VWIAGGIGITPFI 331

Query: 132 SMIR 135
           SM+ 
Sbjct: 332 SMLF 335


>gnl|CDD|36374 KOG1159, KOG1159, KOG1159, NADP-dependent flavoprotein reductase
           [Energy production and conversion].
          Length = 574

 Score = 37.2 bits (86), Expect = 0.003
 Identities = 28/98 (28%), Positives = 45/98 (45%), Gaps = 11/98 (11%)

Query: 59  RAYSIASPCRDDKLEFCSIKVD---------KGFFTTYLQNIQPGDTILLHKKSTGDLIL 109
           RA+SIAS      LE     V+         +G  + +L +++PGD I + K   G L  
Sbjct: 369 RAFSIASSPGAHHLELLVAIVEYKTILKEPRRGLCSNWLASLKPGDEIPI-KVRPGTLYF 427

Query: 110 DSLIPGNRLYLFSMGTGIAPFASMIRDPETYKKFDEVI 147
            S      L +   GTG+APF ++I++       + V+
Sbjct: 428 PSD-LNKPLIMVGPGTGVAPFRALIQERIYQGDKENVL 464


>gnl|CDD|99809 cd06213, oxygenase_e_transfer_subunit, The oxygenase reductase
           FAD/NADH binding domain acts as part of the
           multi-component bacterial oxygenases which oxidize
           hydrocarbons. 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 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 = 227

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 30/124 (24%), Positives = 61/124 (49%), Gaps = 9/124 (7%)

Query: 16  SVISVKHYTDRLFRFCITRPKSFRFRSGEFVMLGLIVNGRPIFRAYSIA-SPCRDDKLEF 74
           ++++ +  T  + R  +   +   +++G++  L L   G P  R+YS A +P  D +L F
Sbjct: 4   TIVAQERLTHDIVRLTVQLDRPIAYKAGQYAELTL--PGLPAARSYSFANAPQGDGQLSF 61

Query: 75  CSIKVDKGFFTTYLQN-IQPGDTILLHKKSTGDLILDSLIPGNR-LYLFSMGTGIAPFAS 132
              KV  G F+ +L    + G+ + + +   GD  L    PG+  +   + G+G+AP  +
Sbjct: 62  HIRKVPGGAFSGWLFGADRTGERLTV-RGPFGDFWLR---PGDAPILCIAGGSGLAPILA 117

Query: 133 MIRD 136
           ++  
Sbjct: 118 ILEQ 121


>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 = 36.5 bits (84), Expect = 0.006
 Identities = 36/197 (18%), Positives = 68/197 (34%), Gaps = 30/197 (15%)

Query: 16  SVISVKHYTDRLFRFCITRPKSFRFRSGEFVMLGLIVNGRPIFRAYSIASPCRDDKLEFC 75
            +  V      +    +++P  F+++ G+++ +      +  +  ++I S   DD L   
Sbjct: 358 KIAKVVLLPSDVLELIMSKPPGFKYKPGQYIFVNCPSLSKLEWHPFTITSAPEDDFLS-V 416

Query: 76  SIKVDKGFFTTYLQNI-------QPGDTILLHKKSTGDLILDSLIPGNR-------LYLF 121
            IK     +T  L+N           D      K    LI       ++       L L 
Sbjct: 417 HIKALGD-WTEKLRNAFSEVSQPPESDKSYPFPKI---LIDGPYGAPSQDVFKYEVLVLV 472

Query: 122 SMGTGIAPFASMIRD-------PETYKKFDEVIITHTCGRVAELQYGIDVMHEISQDEIL 174
             G G+ PFAS+++D         T     +   +    +V    Y   V  E    E  
Sbjct: 473 GGGIGVTPFASILKDLLNKISLGRTKAPTSDYSDSLKLKKV----YFYWVTREQRSFEWF 528

Query: 175 KDLIGQKLKFYRTVTQE 191
           K L+ +  ++  +   E
Sbjct: 529 KGLLTEVEEYDSSGVIE 545


>gnl|CDD|30718 COG0369, CysJ, Sulfite reductase, alpha subunit (flavoprotein)
           [Inorganic ion transport and metabolism].
          Length = 587

 Score = 36.1 bits (83), Expect = 0.008
 Identities = 35/162 (21%), Positives = 58/162 (35%), Gaps = 21/162 (12%)

Query: 5   SSELAADVYCESVISVKHYTDRLFRFCITRPKSFRFRSGEFVMLGLIVNGRPIF-RAYSI 63
             EL   +    +  ++ Y  R     + R     F   +     LI    P+  R YSI
Sbjct: 323 QEELRRLLEQLDIADLQDYAKRRTLIDVLR----DFPPAKLPAEELIDLLPPLKPRLYSI 378

Query: 64  ASPCRD--DKLEFCSIKVDK--------GFFTTYLQNIQP-GDTILLHKKSTGDLIL--D 110
           AS      D++      V          G  + YL ++   GDTI +  +   +  L  D
Sbjct: 379 ASSPGVSPDEVHLTVGVVRYQAEGRERYGVCSGYLADLLEEGDTIPVFVQPNKNFRLPED 438

Query: 111 SLIPGNRLYLFSMGTGIAPFASMIRDPETYKKFDEVIITHTC 152
              P   + +   GTGIAPF + +++        +  +   C
Sbjct: 439 PETP---IIMIGPGTGIAPFRAFVQERAANGAEGKNWLFFGC 477


>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 = 36.1 bits (84), Expect = 0.008
 Identities = 30/106 (28%), Positives = 47/106 (44%), Gaps = 28/106 (26%)

Query: 43  GEFV-MLGLIVNGRPIFRAYSIAS-PCRDDKLEFCSIKVD-------------KGFFTTY 87
             F+ ML  +   RP  R YSI+S P  D      ++ V              +G  ++Y
Sbjct: 150 ATFLAMLPPM---RP--RQYSISSSPLVDPGH--ATLTVSVLDAPALSGQGRYRGVASSY 202

Query: 88  LQNIQPGDTILLH-KKSTGDLIL--DSLIPGNRLYLFSMGTGIAPF 130
           L +++PGD+I +  + S        D   P   L + + GTG+APF
Sbjct: 203 LSSLRPGDSIHVSVRPSHSAFRPPSDPSTP---LIMIAAGTGLAPF 245


>gnl|CDD|36373 KOG1158, KOG1158, KOG1158, NADP/FAD dependent oxidoreductase
           [Energy production and conversion].
          Length = 645

 Score = 35.3 bits (81), Expect = 0.014
 Identities = 24/99 (24%), Positives = 42/99 (42%), Gaps = 18/99 (18%)

Query: 59  RAYSIASPCR--DDKLEFCSIKVD----------KGFFTTYLQNIQPGD---TILLHKKS 103
           R YSI+S  +   +++      V+           G  + +L N++PG+     +   KS
Sbjct: 423 RYYSISSSPKVHPNEVHLTVTVVEYGTPDGGPKRYGVCSNWLSNLKPGEKVPNPVPVGKS 482

Query: 104 TGDLILDSLIPGNRLYLFSMGTGIAPFASMIRDPETYKK 142
              L  D   P   + +   GTGIAPF   +++    K+
Sbjct: 483 MFRLPSDPSTP---IIMIGPGTGIAPFRGFLQERLFLKQ 518


>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 = 34.6 bits (80), Expect = 0.021
 Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 10/82 (12%)

Query: 59  RAYSIASPCRDD--KLEFC-SI--KVDKGFFTTYL-----QNIQPGDTILLHKKSTGDLI 108
           R YSIAS   +   KL F  S+     KG  T++L          G  +  + +S+    
Sbjct: 175 RPYSIASSPLEGPGKLRFIFSVVEFPAKGLCTSWLESLCLSASSHGVKVPFYLRSSSRFR 234

Query: 109 LDSLIPGNRLYLFSMGTGIAPF 130
           L        + +   GTG+APF
Sbjct: 235 LPPDDLRRPIIMVGPGTGVAPF 256


>gnl|CDD|38588 KOG3378, KOG3378, KOG3378, Hemoglobin-like flavoprotein [Energy
           production and conversion].
          Length = 385

 Score = 30.8 bits (69), Expect = 0.27
 Identities = 16/80 (20%), Positives = 31/80 (38%), Gaps = 2/80 (2%)

Query: 59  RAYSIASPCRDDKLEFCSIKVDKGFFTTYL-QNIQPGDTILLHKKSTGDLILDSLIPGNR 117
            + S       ++      +V  G  + ++  N++ GD + +   +   +   S    NR
Sbjct: 204 YSLSNRVDTCRNQFRISVRRVAGGVVSNFVHDNLKVGDIVGVSPPAGNFVYKRSEENVNR 263

Query: 118 -LYLFSMGTGIAPFASMIRD 136
            L  F+ G GI P   +I  
Sbjct: 264 PLLCFAGGIGITPLIPIIET 283


>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 = 29.2 bits (66), Expect = 0.90
 Identities = 29/127 (22%), Positives = 52/127 (40%), Gaps = 24/127 (18%)

Query: 25  DRLFRFCITRPKSFRFRSGEFVMLGLIVNGRPIFRA-----YSIASPCRD--DKLEFCSI 77
             + R  I +PK F+++ G+ V L    N   +        ++IAS   D  D L    I
Sbjct: 10  SDVIRLTIPKPKPFKWKPGQHVYL----NFPSLLSFWQSHPFTIASSPEDEQDTLSLI-I 64

Query: 78  KVDKGFFTTYLQNIQPGDTILLHKKSTGDLILD--------SLIPGNRLYLFSMGTGIAP 129
           +  KGF T  L+         +  K    ++++         L+  + + L + G+GI  
Sbjct: 65  RAKKGFTTRLLRKALKSPGGGVSLK----VLVEGPYGSSSEDLLSYDNVLLVAGGSGITF 120

Query: 130 FASMIRD 136
              ++RD
Sbjct: 121 VLPILRD 127


>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 = 29.1 bits (66), Expect = 1.0
 Identities = 25/113 (22%), Positives = 43/113 (38%), Gaps = 27/113 (23%)

Query: 36  KSFRFRSGEFVMLGLIVNGRPIFRA--YSIAS-PCRDDKLEFCSIKVDKGFFTTYL-QNI 91
            +   R+G+F    L  +         ++I+S P  D +L F +IK   G +T  L + +
Sbjct: 19  PALGHRAGQFA--FLRFDASGWEEPHPFTISSAPDPDGRLRF-TIK-ALGDYTRRLAERL 74

Query: 92  QPGDTILL--------HKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIRD 136
           +PG  + +                I    I G        G GI PF +++  
Sbjct: 75  KPGTRVTVEGPYGRFTFDDRRARQIW---IAG--------GIGITPFLALLEA 116


>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 = 28.8 bits (65), Expect = 1.4
 Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 11/65 (16%)

Query: 44  EFVMLGLI-VNGRPIFRAYSIAS-PCRDDKLEFC---------SIKVDKGFFTTYLQNIQ 92
           +F +  L+  +  P+ RAYS+A+ P  + +L+           +  +  G  ++Y+ N++
Sbjct: 71  KFGLWQLVFKHDEPVSRAYSLANYPAEEGELKLNVRIATPPPGNSDIPPGIGSSYIFNLK 130

Query: 93  PGDTI 97
           PGD +
Sbjct: 131 PGDKV 135


>gnl|CDD|31411 COG1218, CysQ, 3'-Phosphoadenosine 5'-phosphosulfate (PAPS)
           3'-phosphatase [Inorganic ion transport and metabolism].
          Length = 276

 Score = 28.4 bits (63), Expect = 1.5
 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 7/47 (14%)

Query: 29  RFCITRP----KSFRFRSGEF-VMLGLIVNGRPIFRAYSIASPCRDD 70
           RF +  P    K F  R+G+F V + LI NG P+     + +P    
Sbjct: 85  RFWLVDPLDGTKEFIKRNGDFAVNIALIENGVPVLGV--VYAPETGK 129


>gnl|CDD|99816 cd06220, DHOD_e_trans_like2, FAD/NAD binding domain in the 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 3 cofactors: FMN,
           FAD, and an [2Fe-2S] cluster..
          Length = 233

 Score = 28.4 bits (64), Expect = 1.7
 Identities = 34/131 (25%), Positives = 55/131 (41%), Gaps = 34/131 (25%)

Query: 26  RLFRFCITRPKSFRFRSGEFVMLGLI-VNGRPIFRAYSIASPCRDDKLEFCSIKVDK-GF 83
           + F F       F F+ G+FVM+ +  V+  P+    S++     +     SI V K G 
Sbjct: 14  KTFVF----DWDFDFKPGQFVMVWVPGVDEIPM----SLSYIDGPN-----SITVKKVGE 60

Query: 84  FTTYLQNIQPGDTILL------HKKSTGDLILDSLIPGNRLYLFSMGTGIAPFASMIRDP 137
            T+ L +++ GD + +        +  G  +L  LI G        G GIAP A +    
Sbjct: 61  ATSALHDLKEGDKLGIRGPYGNGFELVGGKVL--LIGG--------GIGIAPLAPLAER- 109

Query: 138 ETYKKFDEVII 148
              KK  +V +
Sbjct: 110 --LKKAADVTV 118


>gnl|CDD|33061 COG3250, LacZ, Beta-galactosidase/beta-glucuronidase [Carbohydrate
           transport and metabolism].
          Length = 808

 Score = 28.0 bits (62), Expect = 2.1
 Identities = 8/26 (30%), Positives = 13/26 (50%)

Query: 33  TRPKSFRFRSGEFVMLGLIVNGRPIF 58
                  FR+ E     L++NG+P+F
Sbjct: 276 AEALRIGFRTVEIKDGLLLINGKPVF 301


>gnl|CDD|39879 KOG4681, KOG4681, KOG4681, Uncharacterized conserved protein
          [Function unknown].
          Length = 280

 Score = 27.7 bits (61), Expect = 3.1
 Identities = 6/30 (20%), Positives = 15/30 (50%)

Query: 41 RSGEFVMLGLIVNGRPIFRAYSIASPCRDD 70
              F ++GL++ G  ++R ++ + P    
Sbjct: 65 FGLSFGLMGLVLGGAYLYRYFAPSPPNARR 94


>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 = 26.9 bits (60), Expect = 4.1
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 5/53 (9%)

Query: 82  GFFTTYLQNIQPGDTI--LLHKKSTGDLILDSLIPGNRLYLFSMGTGIAPFAS 132
           G  +T+L  + PGDT+   +    +  L  D  +P   + +   GTGIAPF S
Sbjct: 214 GVCSTWLNGLTPGDTVPCFVRSAPSFHLPEDPSVP---VIMVGPGTGIAPFRS 263


>gnl|CDD|30136 cd01638, CysQ, CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS)
           3'-phosphatase, is a bacterial member of the inositol
           monophosphatase family. It has been proposed that CysQ
           helps control intracellular levels of PAPS, which is an
           intermediate in cysteine biosynthesis (a principal route
           of sulfur assimilation)..
          Length = 242

 Score = 26.8 bits (59), Expect = 4.9
 Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 3/35 (8%)

Query: 36  KSFRFRSGEF-VMLGLIVNGRPIFRAYSIASPCRD 69
           + F   +GEF V + L+ +GRP+     + +P   
Sbjct: 86  REFIKGNGEFAVNIALVEDGRPVLGV--VYAPALG 118


>gnl|CDD|36371 KOG1156, KOG1156, KOG1156, N-terminal acetyltransferase [Chromatin
           structure and dynamics].
          Length = 700

 Score = 26.4 bits (58), Expect = 6.5
 Identities = 14/55 (25%), Positives = 20/55 (36%), Gaps = 14/55 (25%)

Query: 170 QDEILKDLIGQKL-----------KFYRTVTQEDYLYKGRITNHILSGEFYRNMG 213
             +I +D  G+KL           KF   +       K +   +ILS E Y   G
Sbjct: 622 PVDIDEDPFGEKLLKTEDPLEEARKFLPNLQH---KGKEKGETYILSFELYYRKG 673


>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 = 26.1 bits (58), Expect = 8.9
 Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 14/85 (16%)

Query: 124 GTGIAPFASMIRDPETYKKFDEVIITHTCGRVAELQYGIDVMHEISQDEILKDLIGQ--K 181
           GTGIAP  S+++           ++    G    L YG     ++   E L++L  +   
Sbjct: 5   GTGIAPLYSVLK----------ALLEDEDGTEVYLVYGNRTEDDLLLREELEELAKKYPN 54

Query: 182 LKFYRTVTQED--YLYKGRITNHIL 204
           LK       +D  Y  KG +T+ +L
Sbjct: 55  LKVVAVSRTDDGWYGRKGYVTDALL 79


>gnl|CDD|30722 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
          Length = 414

 Score = 26.0 bits (57), Expect = 9.9
 Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 8/59 (13%)

Query: 134 IRDPETYKKFDEVIITHTCGRV------AELQYGIDVMHEISQDEILKDLIGQKLKFYR 186
           +         +E +I  TC RV            I  + E+    I  + +G+ L   R
Sbjct: 32  LDQLLHQPSIEEAVILSTCNRVEIYAVVHTGSELIRFLAELHGLSI--EDLGKYLYVLR 88


  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
   0.325    0.143    0.428 

Gapped
Lambda     K      H
   0.267   0.0759    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,798,192
Number of extensions: 147336
Number of successful extensions: 514
Number of sequences better than 10.0: 1
Number of HSP's gapped: 469
Number of HSP's successfully gapped: 57
Length of query: 224
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 134
Effective length of database: 4,318,927
Effective search space: 578736218
Effective search space used: 578736218
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 (21.6 bits)
S2: 55 (24.9 bits)