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Conserved domains on  [gi|488294523|ref|WP_002365731|]
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MULTISPECIES: dihydroorotate dehydrogenase electron transfer subunit [Enterococcus]

Protein Classification

dihydroorotate dehydrogenase electron transfer subunit( domain architecture ID 10153129)

dihydroorotate dehydrogenase (DHODH), PyrK subunit, catalyzes, together with PyrD, the oxidation of (S)-dihydroorotate to orotate, an essential step in the pyrimidine de novo biosynthesis.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DHOD_e_trans cd06218
FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. ...
 10-257 3.28e-116

FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. 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.


:

Pssm-ID: 99814 [Multi-domain]  Cd Length: 246  Bit Score: 332.97  E-value: 3.28e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  10 IVAQKQLAPRIYQLDLQGELVKEMTRPGQFVHIKVPRA-DLLLRRPISINQIDHSNETCRLIYRVEGAGTEVFATMKAGE 88
Cdd:cd06218    1 VLSNREIADDIYRLVLEAPEIAAAAKPGQFVMLRVPDGsDPLLRRPISIHDVDPEEGTITLLYKVVGKGTRLLSELKAGD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  89 QLDILGPLGNGFDITTvaAGQTAFIVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMALG-ETHFATDD 167
Cdd:cd06218   81 ELDVLGPLGNGFDLPD--DDGKVLLVGGGIGIAPLLFLAKQLAERGIKVTVLLGFRSADDLFLVEEFEALGaEVYVATDD 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 168 GSFGAHGNVGRLLSEALAKGRiPDAVYACGANGMLKAIDSLFPTH-PHVYLSLEERMACGIGACYACVCHKKGDTTGAKs 246
Cdd:cd06218  159 GSAGTKGFVTDLLKELLAEAR-PDVVYACGPEPMLKAVAELAAERgVPCQVSLEERMACGIGACLGCVVKTKDDEGGYK- 236

                        250
                 ....*....|.
gi 488294523 247 vKVCDEGPIFK 257
Cdd:cd06218  237 -RVCKDGPVFD 246
 
Name Accession Description Interval E-value
DHOD_e_trans cd06218
FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. ...
 10-257 3.28e-116

FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. 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.


Pssm-ID: 99814 [Multi-domain]  Cd Length: 246  Bit Score: 332.97  E-value: 3.28e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  10 IVAQKQLAPRIYQLDLQGELVKEMTRPGQFVHIKVPRA-DLLLRRPISINQIDHSNETCRLIYRVEGAGTEVFATMKAGE 88
Cdd:cd06218    1 VLSNREIADDIYRLVLEAPEIAAAAKPGQFVMLRVPDGsDPLLRRPISIHDVDPEEGTITLLYKVVGKGTRLLSELKAGD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  89 QLDILGPLGNGFDITTvaAGQTAFIVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMALG-ETHFATDD 167
Cdd:cd06218   81 ELDVLGPLGNGFDLPD--DDGKVLLVGGGIGIAPLLFLAKQLAERGIKVTVLLGFRSADDLFLVEEFEALGaEVYVATDD 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 168 GSFGAHGNVGRLLSEALAKGRiPDAVYACGANGMLKAIDSLFPTH-PHVYLSLEERMACGIGACYACVCHKKGDTTGAKs 246
Cdd:cd06218  159 GSAGTKGFVTDLLKELLAEAR-PDVVYACGPEPMLKAVAELAAERgVPCQVSLEERMACGIGACLGCVVKTKDDEGGYK- 236

                        250
                 ....*....|.
gi 488294523 247 vKVCDEGPIFK 257
Cdd:cd06218  237 -RVCKDGPVFD 246
PRK00054 PRK00054
dihydroorotate dehydrogenase electron transfer subunit; Reviewed
 4-263 7.97e-106

dihydroorotate dehydrogenase electron transfer subunit; Reviewed


Pssm-ID: 234601 [Multi-domain]  Cd Length: 250  Bit Score: 306.80  E-value: 7.97e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   4 KQEMMTIVAQKQLAPRIYQLDLQGElVKEMTRPGQFVHIKVPRADLLLRRPISINQIDhsNETCRLIYRVEGAGTEVFAT 83
Cdd:PRK00054   3 KPENMKIVENKEIAPNIYTLVLDGE-KVFDMKPGQFVMVWVPGVEPLLERPISISDID--KNEITILYRKVGEGTKKLSK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  84 MKAGEQLDILGPLGNGFDITTVaaGQTAFIVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMALGETHF 163
Cdd:PRK00054  80 LKEGDELDIRGPLGNGFDLEEI--GGKVLLVGGGIGVAPLYELAKELKKKGVEVTTVLGARTKDEVIFEEEFAKVGDVYV 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 164 ATDDGSFGAHGNVGRLLSEALAKgriPDAVYACGANGMLKAIDSLFPTHP-HVYLSLEERMACGIGACYACVCHKKGDtt 242
Cdd:PRK00054 158 TTDDGSYGFKGFVTDVLDELDSE---YDAIYSCGPEIMMKKVVEILKEKKvPAYVSLERRMKCGIGACGACVCDTETG-- 232

                        250       260
                 ....*....|....*....|.
gi 488294523 243 gakSVKVCDEGPIFKASEVIL 263
Cdd:PRK00054 233 ---GKRVCKDGPVFSGGELVL 250
Mcr1 COG0543
NAD(P)H-flavin reductase [Coenzyme transport and metabolism, Energy production and conversion]; ...
 9-263 1.55e-80

NAD(P)H-flavin reductase [Coenzyme transport and metabolism, Energy production and conversion];


Pssm-ID: 440309 [Multi-domain]  Cd Length: 247  Bit Score: 242.46  E-value: 1.55e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   9 TIVAQKQLAPRIYQLDLQGELVKEMTRPGQFVHIKVPraDLLLRRPISINQIDHSNETCRLIYRVEGAGTEVFATMKAGE 88
Cdd:COG0543    1 KVVSVERLAPDVYLLRLEAPLIALKFKPGQFVMLRVP--GDGLRRPFSIASAPREDGTIELHIRVVGKGTRALAELKPGD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  89 QLDILGPLGNGFDITtvAAGQTAFIVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMALGETHF--ATD 166
Cdd:COG0543   79 ELDVRGPLGNGFPLE--DSGRPVLLVAGGTGLAPLRSLAEALLARGRRVTLYLGARTPEDLYLLDELEALADFRVvvTTD 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 167 DGSFGAHGNVGRLLSEALAKGRiPDAVYACGANGMLKAIDSLFPTH----PHVYLSLEERMACGIGACYACVCHKKGdtt 242
Cdd:COG0543  157 DGWYGRKGFVTDALKELLAEDS-GDDVYACGPPPMMKAVAELLLERgvppERIYVSLERRMACGIGMCGGCVVPVGG--- 232

                        250       260
                 ....*....|....*....|.
gi 488294523 243 gaksvkVCDEGPIFKASEVIL 263
Cdd:COG0543  233 ------GCKDGPVFDAAEVDW 247
DHODB_Fe-S_bind pfam10418
Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B; Lactococcus lactis is ...
 220-261 4.10e-15

Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B; Lactococcus lactis is one of the few organizms with two dihydroorotate dehydrogenases, DHODs, A and B. The B enzyme is a prototype for DHODs in Gram-positive bacteria that use NAD+ as the second substrate. DHODB is a hetero-tetramer composed of a central homodimer of PyrDB subunits resembling the DHODA structure and two PyrK subunits along with three different cofactors: FMN, FAD, and a [2Fe-2S] cluster. The [2Fe-2S] iron-sulfur cluster binds to this C-terminal domain of the PyrK subunit, which is at the interface between the flavin and NAD binding domains and contains three beta-strands. The four cysteine residues at the N-terminal part of this domain are the ones that bind, in pairs, to the iron-sulfur cluster. The conformation of the whole molecule means that the iron-sulfur cluster is localized in a well-ordered part of this domain close to the FAD binding site. The FAD and and NAD binding domains are FAD_binding_6, pfam00970 and NAD_binding_1, pfam00175.


Pssm-ID: 463084 [Multi-domain]  Cd Length: 40  Bit Score: 67.24  E-value: 4.10e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 488294523  220 EERMACGIGACYACVCHKKGDTTGAKsvKVCDEGPIFKASEV 261
Cdd:pfam10418   1 EERMACGVGACGGCVVKTKGGDGEYK--RVCVDGPVFDADEV 40
 
Name Accession Description Interval E-value
DHOD_e_trans cd06218
FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. ...
 10-257 3.28e-116

FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. 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.


Pssm-ID: 99814 [Multi-domain]  Cd Length: 246  Bit Score: 332.97  E-value: 3.28e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  10 IVAQKQLAPRIYQLDLQGELVKEMTRPGQFVHIKVPRA-DLLLRRPISINQIDHSNETCRLIYRVEGAGTEVFATMKAGE 88
Cdd:cd06218    1 VLSNREIADDIYRLVLEAPEIAAAAKPGQFVMLRVPDGsDPLLRRPISIHDVDPEEGTITLLYKVVGKGTRLLSELKAGD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  89 QLDILGPLGNGFDITTvaAGQTAFIVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMALG-ETHFATDD 167
Cdd:cd06218   81 ELDVLGPLGNGFDLPD--DDGKVLLVGGGIGIAPLLFLAKQLAERGIKVTVLLGFRSADDLFLVEEFEALGaEVYVATDD 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 168 GSFGAHGNVGRLLSEALAKGRiPDAVYACGANGMLKAIDSLFPTH-PHVYLSLEERMACGIGACYACVCHKKGDTTGAKs 246
Cdd:cd06218  159 GSAGTKGFVTDLLKELLAEAR-PDVVYACGPEPMLKAVAELAAERgVPCQVSLEERMACGIGACLGCVVKTKDDEGGYK- 236

                        250
                 ....*....|.
gi 488294523 247 vKVCDEGPIFK 257
Cdd:cd06218  237 -RVCKDGPVFD 246
PRK00054 PRK00054
dihydroorotate dehydrogenase electron transfer subunit; Reviewed
 4-263 7.97e-106

dihydroorotate dehydrogenase electron transfer subunit; Reviewed


Pssm-ID: 234601 [Multi-domain]  Cd Length: 250  Bit Score: 306.80  E-value: 7.97e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   4 KQEMMTIVAQKQLAPRIYQLDLQGElVKEMTRPGQFVHIKVPRADLLLRRPISINQIDhsNETCRLIYRVEGAGTEVFAT 83
Cdd:PRK00054   3 KPENMKIVENKEIAPNIYTLVLDGE-KVFDMKPGQFVMVWVPGVEPLLERPISISDID--KNEITILYRKVGEGTKKLSK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  84 MKAGEQLDILGPLGNGFDITTVaaGQTAFIVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMALGETHF 163
Cdd:PRK00054  80 LKEGDELDIRGPLGNGFDLEEI--GGKVLLVGGGIGVAPLYELAKELKKKGVEVTTVLGARTKDEVIFEEEFAKVGDVYV 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 164 ATDDGSFGAHGNVGRLLSEALAKgriPDAVYACGANGMLKAIDSLFPTHP-HVYLSLEERMACGIGACYACVCHKKGDtt 242
Cdd:PRK00054 158 TTDDGSYGFKGFVTDVLDELDSE---YDAIYSCGPEIMMKKVVEILKEKKvPAYVSLERRMKCGIGACGACVCDTETG-- 232

                        250       260
                 ....*....|....*....|.
gi 488294523 243 gakSVKVCDEGPIFKASEVIL 263
Cdd:PRK00054 233 ---GKRVCKDGPVFSGGELVL 250
Mcr1 COG0543
NAD(P)H-flavin reductase [Coenzyme transport and metabolism, Energy production and conversion]; ...
 9-263 1.55e-80

NAD(P)H-flavin reductase [Coenzyme transport and metabolism, Energy production and conversion];


Pssm-ID: 440309 [Multi-domain]  Cd Length: 247  Bit Score: 242.46  E-value: 1.55e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   9 TIVAQKQLAPRIYQLDLQGELVKEMTRPGQFVHIKVPraDLLLRRPISINQIDHSNETCRLIYRVEGAGTEVFATMKAGE 88
Cdd:COG0543    1 KVVSVERLAPDVYLLRLEAPLIALKFKPGQFVMLRVP--GDGLRRPFSIASAPREDGTIELHIRVVGKGTRALAELKPGD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  89 QLDILGPLGNGFDITtvAAGQTAFIVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMALGETHF--ATD 166
Cdd:COG0543   79 ELDVRGPLGNGFPLE--DSGRPVLLVAGGTGLAPLRSLAEALLARGRRVTLYLGARTPEDLYLLDELEALADFRVvvTTD 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 167 DGSFGAHGNVGRLLSEALAKGRiPDAVYACGANGMLKAIDSLFPTH----PHVYLSLEERMACGIGACYACVCHKKGdtt 242
Cdd:COG0543  157 DGWYGRKGFVTDALKELLAEDS-GDDVYACGPPPMMKAVAELLLERgvppERIYVSLERRMACGIGMCGGCVVPVGG--- 232

                        250       260
                 ....*....|....*....|.
gi 488294523 243 gaksvkVCDEGPIFKASEVIL 263
Cdd:COG0543  233 ------GCKDGPVFDAAEVDW 247
DHOD_e_trans_like cd06192
FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like ...
 10-257 2.15e-55

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.


Pssm-ID: 99789 [Multi-domain]  Cd Length: 243  Bit Score: 178.29  E-value: 2.15e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  10 IVAQKQLAPRIYQLDLQGELVKEMTRPGQFVHIKVPRADLLLRRPISINQIDHSNETCRLIYRVEGAGTEVFATMKAGEQ 89
Cdd:cd06192    1 IVKKEQLEPNLVLLTIKAPLAARLFRPGQFVFLRNFESPGLERIPLSLAGVDPEEGTISLLVEIRGPKTKLIAELKPGEK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  90 LDILGPLGNGFDITTvaAGQTAFIVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMALGETHF-ATDDG 168
Cdd:cd06192   81 LDVMGPLGNGFEGPK--KGGTVLLVAGGIGLAPLLPIAKKLAANGNKVTVLAGAKKAKEEFLDEYFELPADVEIwTTDDG 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 169 SFGAHGNVGrlLSEALAKGRIPDAVYACGANGMLK----AIDSLFPTHPhVYLSLEERMACGIGACYACVCHKKGdttga 244
Cdd:cd06192  159 ELGLEGKVT--DSDKPIPLEDVDRIIVAGSDIMMKavveALDEWLQLIK-ASVSNNSPMCCGIGICGACTIETKH----- 230

                        250
                 ....*....|...
gi 488294523 245 KSVKVCDEGPIFK 257
Cdd:cd06192  231 GVKRLCKDGPVFR 243
DHOD_e_trans_like1 cd06219
FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like ...
 9-261 8.41e-44

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 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, and then transfers a hydride ion to convert NADP+ to NADPH.


Pssm-ID: 99815 [Multi-domain]  Cd Length: 248  Bit Score: 148.49  E-value: 8.41e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   9 TIVAQKQLAPRIYQLDLQGELVKEMTRPGQFVHIKV-PRADlllRRPISINQIDHSNETCRLIYRVEGAGTEVFATMKAG 87
Cdd:cd06219    2 KILEKEELAPNVKLFEIEAPLIAKKAKPGQFVIVRAdEKGE---RIPLTIADWDPEKGTITIVVQVVGKSTRELATLEEG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  88 EQL-DILGPLGNGFDITTVaagQTAFIVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMALG-ETHFAT 165
Cdd:cd06219   79 DKIhDVVGPLGKPSEIENY---GTVVFVGGGVGIAPIYPIAKALKEAGNRVITIIGARTKDLVILEDEFRAVSdELIITT 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 166 DDGSFGAHGNVGRLLSEALAKGRIPDAVYACGANGMLKAIDSLfpTHPH---VYLSLEERMACGIGACYACVChkkgdTT 242
Cdd:cd06219  156 DDGSYGEKGFVTDPLKELIESGEKVDLVIAIGPPIMMKAVSEL--TRPYgipTVVSLNPIMVDGTGMCGACRV-----TV 228

                        250
                 ....*....|....*....
gi 488294523 243 GAKSVKVCDEGPIFKASEV 261
Cdd:cd06219  229 GGETKFACVDGPEFDAHKV 247
PRK06222 PRK06222
sulfide/dihydroorotate dehydrogenase-like FAD/NAD-binding protein;
7-261 1.26e-42

sulfide/dihydroorotate dehydrogenase-like FAD/NAD-binding protein;


Pssm-ID: 235747 [Multi-domain]  Cd Length: 281  Bit Score: 146.49  E-value: 1.26e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   7 MMTIVAQKQLAPRIYQLDLQGELVKEMTRPGQFVHIKV-PRADlllRRPISINQIDHSNETCRLIYRVEGAGTEVFATMK 85
Cdd:PRK06222   1 MYKILEKEELAPNVFLMEIEAPRVAKKAKPGQFVIVRIdEKGE---RIPLTIADYDREKGTITIVFQAVGKSTRKLAELK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  86 AGEQ-LDILGPLGNGFDIT---TVAAgqtafiVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMAL-GE 160
Cdd:PRK06222  78 EGDSiLDVVGPLGKPSEIEkfgTVVC------VGGGVGIAPVYPIAKALKEAGNKVITIIGARNKDLLILEDEMKAVsDE 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 161 THFATDDGSFGAHGNVGRLLSEALAKGRIPDAVYACGANGMLKAIDSLfpTHPH---VYLSLEERMACGIGACYACVChk 237
Cdd:PRK06222 152 LYVTTDDGSYGRKGFVTDVLKELLESGKKVDRVVAIGPVIMMKFVAEL--TKPYgikTIVSLNPIMVDGTGMCGACRV-- 227

                        250       260
                 ....*....|....*....|....
gi 488294523 238 kgdTTGAKSVKVCDEGPIFKASEV 261
Cdd:PRK06222 228 ---TVGGETKFACVDGPEFDGHLV 248
DHOD_e_trans_like2 cd06220
FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like ...
 35-260 3.23e-39

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.


Pssm-ID: 99816 [Multi-domain]  Cd Length: 233  Bit Score: 136.22  E-value: 3.23e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  35 RPGQFVHIKVPRADLLlrrPISINQIDHSNETcrLIYRVeGAGTEVFATMKAGEQLDILGPLGNGFDITtvaaGQTAFIV 114
Cdd:cd06220   25 KPGQFVMVWVPGVDEI---PMSLSYIDGPNSI--TVKKV-GEATSALHDLKEGDKLGIRGPYGNGFELV----GGKVLLI 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 115 GGGIGIPPLYELSKQLnEKGVKVIHFLGYASKEVAYYQQEFMALGETHFATDDGSFGAHGNVGRLLSEALAKGriPDAVY 194
Cdd:cd06220   95 GGGIGIAPLAPLAERL-KKAADVTVLLGARTKEELLFLDRLRKSDELIVTTDDGSYGFKGFVTDLLKELDLEE--YDAIY 171

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488294523 195 ACGANGMLKAI-DSLFPTHPHVYLSLEERMACGIGACYACVCHKKGDttgaksvKVCDEGPIFKASE 260
Cdd:cd06220  172 VCGPEIMMYKVlEILDERGVRAQFSLERYMKCGIGICGSCCIDPTGL-------RVCRDGPVFDGEQ 231
PRK12778 PRK12778
bifunctional dihydroorotate dehydrogenase B NAD binding subunit/NADPH-dependent glutamate ...
 7-261 8.05e-34

bifunctional dihydroorotate dehydrogenase B NAD binding subunit/NADPH-dependent glutamate synthase;


Pssm-ID: 237200 [Multi-domain]  Cd Length: 752  Bit Score: 129.09  E-value: 8.05e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   7 MMTIVAQKQLAPRIYQLDLQGELVKEMTRPGQFVHIKVprADLLLRRPISINQIDHSNETCRLIYRVEGAGTEVFATMKA 86
Cdd:PRK12778   1 MNKIVEKEIFSEKVFLLEIEAPLIAKSRKPGQFVIVRV--GEKGERIPLTIADADPEKGTITLVIQEVGLSTTKLCELNE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  87 GEQL-DILGPLGNGFDITTVAagqTAFIVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMAL-GETHFA 164
Cdd:PRK12778  79 GDYItDVVGPLGNPSEIENYG---TVVCAGGGVGVAPMLPIVKALKAAGNRVITILGGRSKELIILEDEMRESsDEVIIM 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 165 TDDGSFGAHGNVGRLLSEALAKGRIPDAVYACGANGMLKAIDSL-----FPTHphvyLSLEERMACGIGACYACVChkkg 239
Cdd:PRK12778 156 TDDGSYGRKGLVTDGLEEVIKRETKVDKVFAIGPAIMMKFVCLLtkkygIPTI----VSLNTIMVDGTGMCGACRV---- 227

                        250       260
                 ....*....|....*....|..
gi 488294523 240 dTTGAKSVKVCDEGPIFKASEV 261
Cdd:PRK12778 228 -TVGGKTKFACVDGPEFDGHLV 248
sulfite_reductase_like cd06221
Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural ...
 10-256 9.96e-27

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+.


Pssm-ID: 99817 [Multi-domain]  Cd Length: 253  Bit Score: 104.23  E-value: 9.96e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  10 IVAQKQLAPRIYQLDLQGELVKEMT---RPGQFVHIKVPRADlllRRPISINQIDHSNETCRLIYRVEGAGTEVFATMKA 86
Cdd:cd06221    1 IVEVVDETEDIKTFTLRLEDDDEELftfKPGQFVMLSLPGVG---EAPISISSDPTRRGPLELTIRRVGRVTEALHELKP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  87 GEQLDILGPLGNGFDITTvAAGQTAFIVGGGIGIPPLYELSKQLN---EKGVKVIHFLGYASKEVAYYQQEFMAL----- 158
Cdd:cd06221   78 GDTVGLRGPFGNGFPVEE-MKGKDLLLVAGGLGLAPLRSLINYILdnrEDYGKVTLLYGARTPEDLLFKEELKEWakrsd 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 159 GETHFATDDGSFGAHGNVGR---LLSEALAKgriPDAVYA--CGANGMLKAIDSLFPTH----PHVYLSLEERMACGIGA 229
Cdd:cd06221  157 VEVILTVDRAEEGWTGNVGLvtdLLPELTLD---PDNTVAivCGPPIMMRFVAKELLKLgvpeEQIWVSLERRMKCGVGK 233

                        250       260
                 ....*....|....*....|....*..
gi 488294523 230 CYACVChkkgdttGAKSvkVCDEGPIF 256
Cdd:cd06221  234 CGHCQI-------GPKY--VCKDGPVF 251
FNR_like cd00322
Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a ...
 11-209 4.16e-24

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).


Pssm-ID: 99778 [Multi-domain]  Cd Length: 223  Bit Score: 96.36  E-value: 4.16e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  11 VAQKQLAPRIYQLDLQGELVKEMtRPGQFVHIKVPRADLLLRRPISINQIDHSNETCRLIYRVE--GAGTEVFATMKAGE 88
Cdd:cd00322    1 VATEDVTDDVRLFRLQLPNGFSF-KPGQYVDLHLPGDGRGLRRAYSIASSPDEEGELELTVKIVpgGPFSAWLHDLKPGD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  89 QLDILGPLGNGFDIttVAAGQTAFIVGGGIGIPPLYELSKQLNEK--GVKVIHFLGYASKEVAYYQQEFMALGET----- 161
Cdd:cd00322   80 EVEVSGPGGDFFLP--LEESGPVVLIAGGIGITPFRSMLRHLAADkpGGEITLLYGARTPADLLFLDELEELAKEgpnfr 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488294523 162 -HFATDDGSFGAHGNVGRLLSEALAKGRIPD----AVYACGANGMLKAIDSLF 209
Cdd:cd00322  158 lVLALSRESEAKLGPGGRIDREAEILALLPDdsgaLVYICGPPAMAKAVREAL 210
PRK12775 PRK12775
putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin ...
 7-261 2.50e-20

putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional


Pssm-ID: 183738 [Multi-domain]  Cd Length: 1006  Bit Score: 90.00  E-value: 2.50e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523    7 MMTIVAQKQLAPRIYQLDLQGELVKEMTRPGQFVHIKVprADLLLRRPISINQIDHSNETCRLIYRVEGAGT-EVFATMK 85
Cdd:PRK12775    1 MYSIVRREAFSDTTFLWEVEAPDVAASAEPGHFVMLRL--YEGAERIPLTVADFDRKKGTITMVVQALGKTTrEMMTKFK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   86 AGEQL-DILGPLGNGFDITTvaAGQTAFiVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMALG-ETHF 163
Cdd:PRK12775   79 AGDTFeDFVGPLGLPQHIDK--AGHVVL-VGGGLGVAPVYPQLRAFKEAGARTTGIIGFRNKDLVFWEDKFGKYCdDLIV 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  164 ATDDGSFGAHGNVGRLLSEALAKGRiPDAVYACGANGMLKA-IDSLFPTHPHVYLSLEERMACGIGACYACVChkkgdTT 242
Cdd:PRK12775  156 CTDDGSYGKPGFVTAALKEVCEKDK-PDLVVAIGPLPMMNAcVETTRPFGVKTMVSLNAIMVDGTGMCGSCRV-----TV 229

                         250
                  ....*....|....*....
gi 488294523  243 GAKSVKVCDEGPIFKASEV 261
Cdd:PRK12775  230 GGEVKFACVDGPDFDGHKV 248
PRK12779 PRK12779
putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; ...
 9-234 3.46e-18

putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Provisional


Pssm-ID: 183740 [Multi-domain]  Cd Length: 944  Bit Score: 83.73  E-value: 3.46e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   9 TIVAQKQLAPRIYQLDLQGELVKEMTRPGQFVHIkVP--RADLLlrrPISINQIDHSNETCRLIYRVEGAGTEVFATMKA 86
Cdd:PRK12779 652 TIVGKVQLAGGIVEFTVRAPMVARSAQAGQFVRV-LPweKGELI---PLTLADWDAEKGTIDLVVQGMGTSSLEINRMAI 727

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  87 GEQLD-ILGPLGNGFDITTVAAGQTAFIVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYY----------QQEF 155
Cdd:PRK12779 728 GDAFSgIAGPLGRASELHRYEGNQTVVFCAGGVGLPPVYPIMRAHLRLGNHVTLISGFRAKEFLFWtgddervgklKAEF 807

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 156 MALGETHFATDDGSFGAHGNVGRLLSEAL-----AKGRIPDAVYACGANGMLKAIDSLfpTHPH---VYLSLEERMACGI 227
Cdd:PRK12779 808 GDQLDVIYTTNDGSFGVKGFVTGPLEEMLkanqqGKGRTIAEVIAIGPPLMMRAVSDL--TKPYgvkTVASLNSIMVDAT 885


                 ....*..
gi 488294523 228 GACYACV 234
Cdd:PRK12779 886 GMCGACM 892
PRK08345 PRK08345
cytochrome-c3 hydrogenase subunit gamma; Provisional
 28-256 3.72e-16

cytochrome-c3 hydrogenase subunit gamma; Provisional


Pssm-ID: 236247 [Multi-domain]  Cd Length: 289  Bit Score: 76.38  E-value: 3.72e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  28 ELVKEMT-RPGQFVHIKVPRADlllRRPISINQIDHSNETCRLIYRVEGAGTEVFATMKAGEQLDILGPLGNGFDITTVA 106
Cdd:PRK08345  31 ELAESFTfKPGQFVQVTIPGVG---EVPISICSSPTRKGFFELCIRRAGRVTTVIHRLKEGDIVGVRGPYGNGFPVDEME 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 107 aGQTAFIVGGGIGIPPLYELSKQLNEKGVKV--IHFL-GYASKEVAYYQQEFMAL---GE-----THFATDDGSFGAHGn 175
Cdd:PRK08345 108 -GMDLLLIAGGLGMAPLRSVLLYAMDNRWKYgnITLIyGAKYYEDLLFYDELIKDlaeAEnvkiiQSVTRDPEWPGCHG- 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 176 VGRLLSEALAKGRI----------PDAVYA--CGANGMLKA-----IDSLFPTHpHVYLSLEERMACGIGACYACVchkk 238
Cdd:PRK08345 186 LPQGFIERVCKGVVtdlfreantdPKNTYAaiCGPPVMYKFvfkelINRGYRPE-RIYVTLERRMRCGIGKCGHCI---- 260

                        250
                 ....*....|....*....
gi 488294523 239 gdTTGAKSVK-VCDEGPIF 256
Cdd:PRK08345 261 --VGTSTSIKyVCKDGPVF 277
DHODB_Fe-S_bind pfam10418
Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B; Lactococcus lactis is ...
 220-261 4.10e-15

Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B; Lactococcus lactis is one of the few organizms with two dihydroorotate dehydrogenases, DHODs, A and B. The B enzyme is a prototype for DHODs in Gram-positive bacteria that use NAD+ as the second substrate. DHODB is a hetero-tetramer composed of a central homodimer of PyrDB subunits resembling the DHODA structure and two PyrK subunits along with three different cofactors: FMN, FAD, and a [2Fe-2S] cluster. The [2Fe-2S] iron-sulfur cluster binds to this C-terminal domain of the PyrK subunit, which is at the interface between the flavin and NAD binding domains and contains three beta-strands. The four cysteine residues at the N-terminal part of this domain are the ones that bind, in pairs, to the iron-sulfur cluster. The conformation of the whole molecule means that the iron-sulfur cluster is localized in a well-ordered part of this domain close to the FAD binding site. The FAD and and NAD binding domains are FAD_binding_6, pfam00970 and NAD_binding_1, pfam00175.


Pssm-ID: 463084 [Multi-domain]  Cd Length: 40  Bit Score: 67.24  E-value: 4.10e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 488294523  220 EERMACGIGACYACVCHKKGDTTGAKsvKVCDEGPIFKASEV 261
Cdd:pfam10418   1 EERMACGVGACGGCVVKTKGGDGEYK--RVCVDGPVFDADEV 40
Fpr COG1018
Flavodoxin/ferredoxin--NADP reductase [Energy production and conversion];
35-205 2.33e-12

Flavodoxin/ferredoxin--NADP reductase [Energy production and conversion];


Pssm-ID: 440641 [Multi-domain]  Cd Length: 231  Bit Score: 64.81  E-value: 2.33e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  35 RPGQFVHIKVPRADLLLRRPISI-NqiDHSNETCRL-IYRVE-GAGTE-VFATMKAGEQLDILGPLGNgFDITTVAAGQT 110
Cdd:COG1018   35 RPGQFVTLRLPIDGKPLRRAYSLsS--APGDGRLEItVKRVPgGGGSNwLHDHLKVGDTLEVSGPRGD-FVLDPEPARPL 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 111 AFIvGGGIGIPPLYELSKQL--NEKGVKVIHFLGYASKEVAYYQQEFMALGET------HFATDDGSFGAHGNVGRLLSE 182
Cdd:COG1018  112 LLI-AGGIGITPFLSMLRTLlaRGPFRPVTLVYGARSPADLAFRDELEALAARhprlrlHPVLSREPAGLQGRLDAELLA 190

                        170       180
                 ....*....|....*....|...
gi 488294523 183 ALAKGRIPDAVYACGANGMLKAI 205
Cdd:COG1018  191 ALLPDPADAHVYLCGPPPMMEAV 213
PRK05802 PRK05802
sulfide/dihydroorotate dehydrogenase-like FAD/NAD-binding protein;
20-240 3.43e-12

sulfide/dihydroorotate dehydrogenase-like FAD/NAD-binding protein;


Pssm-ID: 235613 [Multi-domain]  Cd Length: 320  Bit Score: 65.00  E-value: 3.43e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  20 IYQLDLQGELVKEMTRPGQFVHIKVPRADLLLRRPISINQIDHSNETCRLIYRVEGAGTEVFATMKAGEQLDILGPLGNG 99
Cdd:PRK05802  81 ILTLKVPHKLARDLVYPGSFVFLRNKNSSSFFDVPISIMEADTEENIIKVAIEIRGVKTKKIAKLNKGDEILLRGPYWNG 160

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 100 -FDITTV--AAGQTAFIVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVAYYQQEFMALG-ETHFAT--DDGSFGAH 173
Cdd:PRK05802 161 iLGLKNIksTKNGKSLVIARGIGQAPGVPVIKKLYSNGNKIIVIIDKGPFKNNFIKEYLELYNiEIIELNllDDGELSEE 240

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 174 GNvgRLLSEALAKGRIpDAVYACGANGM-LKAIDSLFPTHPHVYLSL--EERMACGIGACYACVCHKKGD 240
Cdd:PRK05802 241 GK--DILKEIIKKEDI-NLIHCGGSDILhYKIIEYLDKLNEKIKLSCsnNAKMCCGEGICGACTVRYGGH 307
FNR_iron_sulfur_binding_3 cd06217
Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding ...
 35-205 7.19e-11

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.


Pssm-ID: 99813 [Multi-domain]  Cd Length: 235  Bit Score: 60.36  E-value: 7.19e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  35 RPGQFVHIKVPRAD-LLLRRPISINQIDHSNETCRL-IYRVEGAgtEV---FATM-KAGEQLDILGPLGnGFDITTVAAG 108
Cdd:cd06217   32 LAGQHVDLRLTAIDgYTAQRSYSIASSPTQRGRVELtVKRVPGG--EVspyLHDEvKVGDLLEVRGPIG-TFTWNPLHGD 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 109 QTAFIvGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVA--YYQQEFMALGE-------THFATDDGSFGAHGNVGRL 179
Cdd:cd06217  109 PVVLL-AGGSGIVPLMSMIRYRRDLGWPVPFRLLYSARTAEdvIFRDELEQLARrhpnlhvTEALTRAAPADWLGPAGRI 187

                        170       180
                 ....*....|....*....|....*....
gi 488294523 180 LSEALAKGRIPDA---VYACGANGMLKAI 205
Cdd:cd06217  188 TADLIAELVPPLAgrrVYVCGPPAFVEAA 216
FNR_iron_sulfur_binding_1 cd06215
Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding ...
 35-209 2.71e-10

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.


Pssm-ID: 99811 [Multi-domain]  Cd Length: 231  Bit Score: 58.76  E-value: 2.71e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  35 RPGQFVHIKVPRADLLLRRPISINQIDHSNETCRL-IYRVE-GAGTEVFA-TMKAGEQLDILGPLGnGFDITTVAAGQTA 111
Cdd:cd06215   29 KPGQFLTLELEIDGETVYRAYTLSSSPSRPDSLSItVKRVPgGLVSNWLHdNLKVGDELWASGPAG-EFTLIDHPADKLL 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 112 FIvGGGIGIPPLYELSKQLNEKGVKV-IHFLGYA-SKEVAYYQQEFMALGETH-------FATDDGSFGAHGNVGRlLSE 182
Cdd:cd06215  108 LL-SAGSGITPMMSMARWLLDTRPDAdIVFIHSArSPADIIFADELEELARRHpnfrlhlILEQPAPGAWGGYRGR-LNA 185

                        170       180       190
                 ....*....|....*....|....*....|.
gi 488294523 183 ALAKGRIPDA----VYACGANGMLKAIDSLF 209
Cdd:cd06215  186 ELLALLVPDLkertVFVCGPAGFMKAVKSLL 216
FNR_like_3 cd06198
NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer ...
 35-205 7.03e-10

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.


Pssm-ID: 99795 [Multi-domain]  Cd Length: 216  Bit Score: 57.27  E-value: 7.03e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  35 RPGQFVHIKVPRADLLLRRPISINQIDHSNETCRLIYRVEGAGT-EVFATMKAGEQLDILGPLGnGFDITTVAAGQtaFI 113
Cdd:cd06198   24 RAGQFAFLRFDASGWEEPHPFTISSAPDPDGRLRFTIKALGDYTrRLAERLKPGTRVTVEGPYG-RFTFDDRRARQ--IW 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 114 VGGGIGIPP----LYELSKQLNEKGVKVIHflGYASKEVAYYQQEFMALGETHFAT----DDGSfgahgnVGRLLSEALA 185
Cdd:cd06198  101 IAGGIGITPflalLEALAARGDARPVTLFY--CVRDPEDAVFLDELRALAAAAGVVlhviDSPS------DGRLTLEQLV 172

                        170       180
                 ....*....|....*....|....
gi 488294523 186 KGRIPDA----VYACGANGMLKAI 205
Cdd:cd06198  173 RALVPDLadadVWFCGPPGMADAL 196
monooxygenase_like cd06212
The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial ...
 9-211 1.14e-09

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.


Pssm-ID: 99808 [Multi-domain]  Cd Length: 232  Bit Score: 56.96  E-value: 1.14e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   9 TIVAQKQLAPRIYQLDLQGELVKEMT-RPGQFVHIKVPRADLllRRPISINQIDHSNETCRLIYRV--EGAGTEVFAT-M 84
Cdd:cd06212    4 TVVAVEALTHDIRRLRLRLEEPEPIKfFAGQYVDITVPGTEE--TRSFSMANTPADPGRLEFIIKKypGGLFSSFLDDgL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  85 KAGEQLDILGPLGnGFDITTVAAGQTAFIvGGGIGIPPLYELSKQLNEKGVK--VIHFLGYASKEVAYYQQEFMALGE-- 160
Cdd:cd06212   82 AVGDPVTVTGPYG-TCTLRESRDRPIVLI-GGGSGMAPLLSLLRDMAASGSDrpVRFFYGARTARDLFYLEEIAALGEki 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 161 ---------THFATDDGSFGAHGNVGRLLSEALAKGRIPDaVYACGANGMlkaIDSLFPT 211
Cdd:cd06212  160 pdftfipalSESPDDEGWSGETGLVTEVVQRNEATLAGCD-VYLCGPPPM---IDAALPV 215
COG4097 COG4097
Predicted ferric reductase [Inorganic ion transport and metabolism];
9-205 1.21e-09

Predicted ferric reductase [Inorganic ion transport and metabolism];


Pssm-ID: 443273 [Multi-domain]  Cd Length: 442  Bit Score: 57.98  E-value: 1.21e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   9 TIVAQKQLAPRIYQLDLQGELVKEMT-RPGQFVHIKVPRADLLLRR-PISINQIDHSNETCRLIYRVEGAGTEVFATMKA 86
Cdd:COG4097  218 RVESVEPEAGDVVELTLRPEGGRWLGhRAGQFAFLRFDGSPFWEEAhPFSISSAPGGDGRLRFTIKALGDFTRRLGRLKP 297

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  87 GEQLDILGPLGNgFDITTVAAGQTAFIVGGGIGIPPLYELSKQLNEKG---VKVIHFLGYASKEVAYYQQEFMALGE--- 160
Cdd:COG4097  298 GTRVYVEGPYGR-FTFDRRDTAPRQVWIAGGIGITPFLALLRALAARPgdqRPVDLFYCVRDEEDAPFLEELRALAArla 376

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488294523 161 ----THFATDDGsfgahgnvGRLLSEALAKgRIPDA----VYACGANGMLKAI 205
Cdd:COG4097  377 glrlHLVVSDED--------GRLTAERLRR-LVPDLaeadVFFCGPPGMMDAL 420
MMO_FAD_NAD_binding cd06210
Methane monooxygenase (MMO) reductase of methanotrophs catalyzes the NADH-dependent ...
 10-204 2.56e-09

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.


Pssm-ID: 99806  Cd Length: 236  Bit Score: 56.20  E-value: 2.56e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  10 IVAQKQLAPRIYQLDLQGELVKEMTR-----PGQFVHIKVPRADLllRRPISINQIdhSNETCRL---IYRVEGAGTEVF 81
Cdd:cd06210    6 IVAVDRVSSNVVRLRLQPDDAEGAGIaaefvPGQFVEIEIPGTDT--RRSYSLANT--PNWDGRLeflIRLLPGGAFSTY 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  82 ATMKA--GEQLDILGPLG------NGFdittvaagQTAFIVGGGIGIPPLYELSKQLNEKGV---KVIHFlGYASKEVAY 150
Cdd:cd06210   82 LETRAkvGQRLNLRGPLGafglreNGL--------RPRWFVAGGTGLAPLLSMLRRMAEWGEpqeARLFF-GVNTEAELF 152

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488294523 151 YQQEFMALGET------HFAT---DDGSFGAHGNVGRLLSEALAKGRIPDAVYACGANGMLKA 204
Cdd:cd06210  153 YLDELKRLADSlpnltvRICVwrpGGEWEGYRGTVVDALREDLASSDAKPDIYLCGPPGMVDA 215
O2ase_reductase_like cd06187
The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial ...
 10-205 5.12e-09

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.


Pssm-ID: 99784 [Multi-domain]  Cd Length: 224  Bit Score: 54.91  E-value: 5.12e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  10 IVAQKQLAPRIYQLDLQgeLVKEMT-RPGQFVHIKVPRADlLLRRPISI-NQIDHSNETCRLIYRV-EGAGTE-VFATMK 85
Cdd:cd06187    1 VVSVERLTHDIAVVRLQ--LDQPLPfWAGQYVNVTVPGRP-RTWRAYSPaNPPNEDGEIEFHVRAVpGGRVSNaLHDELK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  86 AGEQLDILGPLGnGFDITTVAAGQTAFIvGGGIGIPPLYELSKQLNEKGVK--VIHFLGYASKEVAYYQQEFMALGETH- 162
Cdd:cd06187   78 VGDRVRLSGPYG-TFYLRRDHDRPVLCI-AGGTGLAPLRAIVEDALRRGEPrpVHLFFGARTERDLYDLEGLLALAARHp 155

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 488294523 163 -F-------ATDDGSFGAHGNVGRLLSEALAKGRIPDaVYACGANGMLKAI 205
Cdd:cd06187  156 wLrvvpvvsHEEGAWTGRRGLVTDVVGRDGPDWADHD-IYICGPPAMVDAT 205
phenol_2-monooxygenase_like cd06211
Phenol 2-monooxygenase (phenol hydroxylase) is a flavoprotein monooxygenase, able to use ...
 9-211 2.41e-08

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.


Pssm-ID: 99807  Cd Length: 238  Bit Score: 53.10  E-value: 2.41e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   9 TIVAQKQLAPRIYQLDLqgELVKEMT---RPGQFVHIKVPraDLLLRRPISI-NQIDHSNETCRLIYRVEG--AGTEVFA 82
Cdd:cd06211   10 TVVEIEDLTPTIKGVRL--KLDEPEEiefQAGQYVNLQAP--GYEGTRAFSIaSSPSDAGEIELHIRLVPGgiATTYVHK 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  83 TMKAGEQLDILGPLGNGFdiTTVAAGQTAFIVGGGIGIPPLYELSKQLNEKGV--KVIHFLGYASKEVAYYQQEFMALGE 160
Cdd:cd06211   86 QLKEGDELEISGPYGDFF--VRDSDQRPIIFIAGGSGLSSPRSMILDLLERGDtrKITLFFGARTRAELYYLDEFEALEK 163

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488294523 161 THfatDDGSFGAhgnvgrLLSEALA-------KGRIPDAV-------------YACGANGMlkaIDSLFPT 211
Cdd:cd06211  164 DH---PNFKYVP------ALSREPPesnwkgfTGFVHDAAkkhfkndfrghkaYLCGPPPM---IDACIKT 222
PA_degradation_oxidoreductase_like cd06214
NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation ...
 35-205 1.25e-07

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.


Pssm-ID: 99810 [Multi-domain]  Cd Length: 241  Bit Score: 51.00  E-value: 1.25e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  35 RPGQFVHIKVPRADLLLRRPISINQIDHSNETCRLIYRVEGAGTEVFA--TMKAGEQLDILGPLGNgFDITTVAAGQTAF 112
Cdd:cd06214   34 RPGQFLTLRVPIDGEEVRRSYSICSSPGDDELRITVKRVPGGRFSNWAndELKAGDTLEVMPPAGR-FTLPPLPGARHYV 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 113 IVGGGIGIPPLYELSKQLNEKGVKVIHFLGYASKEVA--YYQQEFMALGETH---------FATDDGsfGAHGNVGRL-- 179
Cdd:cd06214  113 LFAAGSGITPVLSILKTALAREPASRVTLVYGNRTEAsvIFREELADLKARYpdrltvihvLSREQG--DPDLLRGRLda 190

                        170       180       190
                 ....*....|....*....|....*....|.
gi 488294523 180 -----LSEALAKGRIPDAVYACGANGMLKAI 205
Cdd:cd06214  191 aklnaLLKNLLDATEFDEAFLCGPEPMMDAV 221
FNR_iron_sulfur_binding_2 cd06216
Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding ...
 10-214 1.82e-07

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.


Pssm-ID: 99812 [Multi-domain]  Cd Length: 243  Bit Score: 50.69  E-value: 1.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  10 IVAQKQLAPRIYQLDLQ-GELVKEMtRPGQFVHIKVPRADLLLRRPISINQIDH-SNETCRL-IYRV-EGAGTEVFAT-M 84
Cdd:cd06216   22 VVAVRPETADMVTLTLRpNRGWPGH-RAGQHVRLGVEIDGVRHWRSYSLSSSPTqEDGTITLtVKAQpDGLVSNWLVNhL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  85 KAGEQLDILGPLGNgFDITTVAAGQTAFIVGGGiGIPPLYELSKQLNEKG----VKVIHFlGYASKEVAYyQQEFMALGE 160
Cdd:cd06216  101 APGDVVELSQPQGD-FVLPDPLPPRLLLIAAGS-GITPVMSMLRTLLARGptadVVLLYY-ARTREDVIF-ADELRALAA 176

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488294523 161 TH-------FATDDGsfgahgNVGRLLSEALAkGRIPD----AVYACGANGMLKAIDSLFPTHPH 214
Cdd:cd06216  177 QHpnlrlhlLYTREE------LDGRLSAAHLD-AVVPDladrQVYACGPPGFLDAAEELLEAAGL 234
PDR_like cd06185
Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron ...
 15-205 1.61e-05

Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur [2Fe-2S] cluster domain. Although structurally homologous to FNR, PDR binds FMN rather than FAD in it's FNR-like domain. Electron transfer between pyrimidines and iron-sulfur clusters (Rieske center [2Fe-2S]) or heme groups is mediated by flavins in respiration, photosynthesis, and oxygenase systems. Type I dioxygenase systems, including the hydroxylate phthalate system, have 2 components, a monomeric reductase consisting of a flavin and a 2Fe-2S center and a multimeric oxygenase. In contrast to other Rieske dioxygenases the ferredoxin like domain is C-, not N-terminal.


Pssm-ID: 99782 [Multi-domain]  Cd Length: 211  Bit Score: 44.78  E-value: 1.61e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  15 QLAPRIYQLDL---QGELVKEMTrPGQFVHIKVPRAdllLRRPISInqIDHSNETCRliYRV------EGAG--TEVFAT 83
Cdd:cd06185    5 DEAPDIRSFELeapDGAPLPAFE-PGAHIDVHLPNG---LVRQYSL--CGDPADRDR--YRIavlrepASRGgsRYMHEL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  84 MKAGEQLDILGPlGNGFDITTvAAGQTAFIvGGGIGIPPLYELSKQLNEKGVKV-IHFLGyASKEVAYYQQEFMAL--GE 160
Cdd:cd06185   77 LRVGDELEVSAP-RNLFPLDE-AARRHLLI-AGGIGITPILSMARALAARGADFeLHYAG-RSREDAAFLDELAALpgDR 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 488294523 161 THFATDDGSfgahgnvGRL-LSEALAKGRIPDAVYACGANGMLKAI 205
Cdd:cd06185  153 VHLHFDDEG-------GRLdLAALLAAPPAGTHVYVCGPEGMMDAV 191
FNR_iron_sulfur_binding cd06191
Iron-sulfur binding Ferredoxin Reductase (FNR) proteins combine the FAD and NAD(P) binding ...
 35-208 4.49e-05

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).


Pssm-ID: 99788 [Multi-domain]  Cd Length: 231  Bit Score: 43.67  E-value: 4.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  35 RPGQFVHIKVPRADLLLRRPISINQIDHSNETCRLIYRVEGAGTEVFAT--MKAGEQLDILGPLGNgFDITTVAAGQTAF 112
Cdd:cd06191   29 RPGQHVTLKLDFDGEELRRCYSLCSSPAPDEISITVKRVPGGRVSNYLRehIQPGMTVEVMGPQGH-FVYQPQPPGRYLL 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 113 IVGGGiGIPPLYELSK--QLNEKGVKVIHFLGYASKEVAYYQQEFMALGETH--------FATDDG-SFGAHGNVGRLLS 181
Cdd:cd06191  108 VAAGS-GITPLMAMIRatLQTAPESDFTLIHSARTPADMIFAQELRELADKPqrlrllciFTRETLdSDLLHGRIDGEQS 186

                        170       180
                 ....*....|....*....|....*....
gi 488294523 182 --EALAKGRIPDAVYACGANGMLKAIDSL 208
Cdd:cd06191  187 lgAALIPDRLEREAFICGPAGMMDAVETA 215
cyt_b5_reduct_like cd06183
Cytochrome b5 reductase catalyzes the reduction of 2 molecules of cytochrome b5 using NADH as ...
 9-203 1.76e-04

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.


Pssm-ID: 99780 [Multi-domain]  Cd Length: 234  Bit Score: 41.78  E-value: 1.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   9 TIVAQKQLAP--RIYQLDLQGELvKEMTRP-GQFVHIKVPRADLLLRRPIS-INQIDHSNETCRLI--YRvEGAGTEVFA 82
Cdd:cd06183    2 KLVSKEDISHdtRIFRFELPSPD-QVLGLPvGQHVELKAPDDGEQVVRPYTpISPDDDKGYFDLLIkiYP-GGKMSQYLH 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  83 TMKAGEQLDILGPLGNgFDITTVAAGQTAFIVGGGIGIPPLYELSKQL--NEKGVKVIHFLgYASK---EVAYYQQ-EFM 156
Cdd:cd06183   80 SLKPGDTVEIRGPFGK-FEYKPNGKVKHIGMIAGGTGITPMLQLIRAIlkDPEDKTKISLL-YANRteeDILLREElDEL 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488294523 157 ALG-----ETHFATDDGSFGAHGNVGR----LLSEALAKGRIPDA-VYACGANGMLK 203
Cdd:cd06183  158 AKKhpdrfKVHYVLSRPPEGWKGGVGFitkeMIKEHLPPPPSEDTlVLVCGPPPMIE 214
FAD_binding_6 pfam00970
Oxidoreductase FAD-binding domain;
19-98 2.12e-04

Oxidoreductase FAD-binding domain;


Pssm-ID: 425968 [Multi-domain]  Cd Length: 99  Bit Score: 39.49  E-value: 2.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   19 RIYQLDLQGELVKEMTRPGQFVHIKVPRADLLLRRPISINQIDHSNETCRLIYRV--EGAGTEVFATMKAGEQLDILGPL 96
Cdd:pfam00970  15 RIFRFALPHPDQVLGLPVGQHLFLRLPIDGELVIRSYTPISSDDDKGYLELLVKVypGGKMSQYLDELKIGDTIDFKGPL 94


                  ..
gi 488294523   97 GN 98
Cdd:pfam00970  95 GR 96
NAD_binding_1 pfam00175
Oxidoreductase NAD-binding domain; Xanthine dehydrogenases, that also bind FAD/NAD, have ...
 114-205 6.65e-04

Oxidoreductase NAD-binding domain; Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity.


Pssm-ID: 425503 [Multi-domain]  Cd Length: 109  Bit Score: 38.39  E-value: 6.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  114 VGGGIGIPPLYELSKQL---NEKGVKVIHFLGYASKEVAYYQQEFMALGETH------FAT----DDGSFGAHGNVGRLL 180
Cdd:pfam00175   2 IAGGTGIAPVRSMLRAIledPKDPTQVVLVFGNRNEDDILYREELDELAEKHpgrltvVYVvsrpEAGWTGGKGRVQDAL 81

                          90       100
                  ....*....|....*....|....*.
gi 488294523  181 SEALAKGRIPDA-VYACGANGMLKAI 205
Cdd:pfam00175  82 LEDHLSLPDEEThVYVCGPPGMIKAV 107
FNR_like_1 cd06196
Ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain ...
 70-205 9.52e-04

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.


Pssm-ID: 99793 [Multi-domain]  Cd Length: 218  Bit Score: 39.53  E-value: 9.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  70 IYRVEGAGTEVFATMKAGEQLDILGPLGNGFDIttvaaGQTAFIVGGGiGIPPLYELSKQLNEKGVKVIHFLGYASKEVA 149
Cdd:cd06196   67 SYPDHDGVTEQLGRLQPGDTLLIEDPWGAIEYK-----GPGVFIAGGA-GITPFIAILRDLAAKGKLEGNTLIFANKTEK 140

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488294523 150 --YYQQEFMA-LGE--THFATDDGSFG-AHGnvgrLLSEALAKGRIPDA---VYACGANGMLKAI 205
Cdd:cd06196  141 diILKDELEKmLGLkfINVVTDEKDPGyAHG----RIDKAFLKQHVTDFnqhFYVCGPPPMEEAI 201
oxygenase_e_transfer_subunit cd06213
The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial ...
 9-208 1.41e-03

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.


Pssm-ID: 99809  Cd Length: 227  Bit Score: 38.83  E-value: 1.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523   9 TIVAQKQLAPRIYQLDLQgeLVKEMT-RPGQFVHIKVPRADLLlrRPISI-NQIDHSNETCRLIYRVE-GAGTE-VFATM 84
Cdd:cd06213    4 TIVAQERLTHDIVRLTVQ--LDRPIAyKAGQYAELTLPGLPAA--RSYSFaNAPQGDGQLSFHIRKVPgGAFSGwLFGAD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  85 KAGEQLDILGPLGngfDITTVAAGQTAFIVGGGIGIPPLYELSKQLNEKGVK--VIHFLG-------YASKEVAYYQQEF 155
Cdd:cd06213   80 RTGERLTVRGPFG---DFWLRPGDAPILCIAGGSGLAPILAILEQARAAGTKrdVTLLFGartqrdlYALDEIAAIAARW 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488294523 156 MalGETHF--------ATDDGSfGAHGnvgrLLSEALAKGRIPDA-VYACGANGMLK-AIDSL 208
Cdd:cd06213  157 R--GRFRFipvlseepADSSWK-GARG----LVTEHIAEVLLAATeAYLCGPPAMIDaAIAVL 212
NADH_quinone_reductase cd06188
Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) ...
 85-162 1.81e-03

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.


Pssm-ID: 99785 [Multi-domain]  Cd Length: 283  Bit Score: 38.82  E-value: 1.81e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  85 KAGEQLDILGPLGNGFDITTvaaGQTAFIVGGGIGIPPL----YELSKQLNEKGvKVIHFLGYASKEVAYYQQEFMALGE 160
Cdd:cd06188  130 KPGDKVTASGPFGEFFIKDT---DREMVFIGGGAGMAPLrshiFHLLKTLKSKR-KISFWYGARSLKELFYQEEFEALEK 205


                 ..
gi 488294523 161 TH 162
Cdd:cd06188  206 EF 207
flavohem_like_fad_nad_binding cd06184
FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain ...
 35-205 1.81e-03

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.


Pssm-ID: 99781  Cd Length: 247  Bit Score: 38.69  E-value: 1.81e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  35 RPGQFVHIKVPRADLLLR--RPISINQIDHSNEtcrliYRV----EGAGtEV----FATMKAGEQLDILGPLGNgFDITT 104
Cdd:cd06184   38 LPGQYLSVRVKLPGLGYRqiRQYSLSDAPNGDY-----YRIsvkrEPGG-LVsnylHDNVKVGDVLEVSAPAGD-FVLDE 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 105 VAAGQTAFIvGGGIGIPP----LYELSKQLNEKGVKVIHflGYASKEVAYYQQEFMALGETH-------F---ATDDGSF 170
Cdd:cd06184  111 ASDRPLVLI-SAGVGITPmlsmLEALAAEGPGRPVTFIH--AARNSAVHAFRDELEELAARLpnlklhvFysePEAGDRE 187

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 488294523 171 GAHGNVGRLLSEALAKGRIP-DA-VYACGANGMLKAI 205
Cdd:cd06184  188 EDYDHAGRIDLALLRELLLPaDAdFYLCGPVPFMQAV 224
FNR_N-term_Iron_sulfur_binding cd06194
Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding ...
 35-204 7.63e-03

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.


Pssm-ID: 99791 [Multi-domain]  Cd Length: 222  Bit Score: 36.86  E-value: 7.63e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523  35 RPGQfvHIKVPRADLLLRrPISINQI-DHSNETCRLIYRV-EGA-GTEVFATMKAGEQLDILGPLGNGFditTVAAGQTA 111
Cdd:cd06194   25 LPGQ--YVNLRRAGGLAR-SYSPTSLpDGDNELEFHIRRKpNGAfSGWLGEEARPGHALRLQGPFGQAF---YRPEYGEG 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294523 112 --FIVGGGIGIPPLYELSKQLNEKG----VKVIHflgyASKEVA--YYQQEFMALGETHFATD-----DGSFGAHG--NV 176
Cdd:cd06194   99 plLLVGAGTGLAPLWGIARAALRQGhqgeIRLVH----GARDPDdlYLHPALLWLAREHPNFRyipcvSEGSQGDPrvRA 174

                        170       180
                 ....*....|....*....|....*...
gi 488294523 177 GRLLSEALAKGRiPDAVYACGANGMLKA 204
Cdd:cd06194  175 GRIAAHLPPLTR-DDVVYLCGAPSMVNA 201
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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