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Conserved domains on  [gi|227079015|gb|EEI16978|]
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rieske [2Fe-2S] domain protein [Corynebacterium lipophiloflavum DSM 44291]

Protein Classification

ubiquinol-cytochrome c reductase iron-sulfur subunit( domain architecture ID 18339963)

ubiquinol-cytochrome c reductase iron-sulfur subunit such as Mycobacterium tuberculosis cytochrome bc1 reductase complex subunit QcrA and Bacillus subtilis menaquinol-cytochrome c reductase iron-sulfur subunit

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
QcrA_N pfam19297
QcrA subunit N-terminal region; This entry describes the N-terminal region of the QcrA subunit ...
 2-225 5.51e-127

QcrA subunit N-terminal region; This entry describes the N-terminal region of the QcrA subunit which is part of respiratory complex III. This region includes anchoring transmembrane helical regions.


:

Pssm-ID: 466030  Cd Length: 221  Bit Score: 364.96  E-value: 5.51e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015    2 SNEVKKNYTDAELDRMNNAELAALGTELDDVTVAYRKERFPVEGDPREKAAAAGINVWLTISIVMGLAFLGVYLFWPWEP 81
Cdd:pfam19297   1 MSGVPKDPTDPELAAMSREELVRLGTRLDGVEIVHREPRFPVPGTKAEKRAERQVALWFLLAGLAALAFLVVYLFWPWEY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015   82 KFHGDEGLWMYTLYTPLLGLTSMLALGALGIAIIQYVKKFVPEEISVQRRHDGRSSELDRRTTTALLNDAWETSTLGRRK 161
Cdd:pfam19297  81 KLPGDEGYWLYTLYTPLLGLTLGLSILSLGIGAVLYVKKFIPEEISVQDRHDGPSSEVDRRTTVATLNDALETSTLGRRK 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 227079015  162 VMQGLLGGAGLLTGLIIIAPL-GGLIKNPWRPrhelNYYGDGTLWTHGWTKIEEGVKVYLGRDTG 225
Cdd:pfam19297 161 LIKGSLGFGLGAFGLVVAAPLlGGLIKNPWKP----AYGGDGTLWTTGWTPREPGEKVYLRRDTG 221
QcrA/PetC COG0723
Rieske Fe-S protein [Energy production and conversion];
310-392 7.17e-27

Rieske Fe-S protein [Energy production and conversion];


:

Pssm-ID: 440487 [Multi-domain]  Cd Length: 118  Bit Score: 103.54  E-value: 7.17e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015 310 RVVEREGQETF-------HYGDYYAYSKICTHIGCPTSlYEAQTNRILCPCHQSQFDAlhYGKPVFGPAARALPQLPVTV 382
Cdd:COG0723   32 KVVEWRGKPVFvvrtpvrGDGEIVAVSAICTHLGCPVT-WNADEGGFDCPCHGSRFDP--DGRVLKGPAPRPLPVPPLEV 108

                         90
                 ....*....|
gi 227079015 383 DEEGYLVASG 392
Cdd:COG0723  109 DDDKLLIGVG 118
 
Name Accession Description Interval E-value
QcrA_N pfam19297
QcrA subunit N-terminal region; This entry describes the N-terminal region of the QcrA subunit ...
 2-225 5.51e-127

QcrA subunit N-terminal region; This entry describes the N-terminal region of the QcrA subunit which is part of respiratory complex III. This region includes anchoring transmembrane helical regions.


Pssm-ID: 466030  Cd Length: 221  Bit Score: 364.96  E-value: 5.51e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015    2 SNEVKKNYTDAELDRMNNAELAALGTELDDVTVAYRKERFPVEGDPREKAAAAGINVWLTISIVMGLAFLGVYLFWPWEP 81
Cdd:pfam19297   1 MSGVPKDPTDPELAAMSREELVRLGTRLDGVEIVHREPRFPVPGTKAEKRAERQVALWFLLAGLAALAFLVVYLFWPWEY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015   82 KFHGDEGLWMYTLYTPLLGLTSMLALGALGIAIIQYVKKFVPEEISVQRRHDGRSSELDRRTTTALLNDAWETSTLGRRK 161
Cdd:pfam19297  81 KLPGDEGYWLYTLYTPLLGLTLGLSILSLGIGAVLYVKKFIPEEISVQDRHDGPSSEVDRRTTVATLNDALETSTLGRRK 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 227079015  162 VMQGLLGGAGLLTGLIIIAPL-GGLIKNPWRPrhelNYYGDGTLWTHGWTKIEEGVKVYLGRDTG 225
Cdd:pfam19297 161 LIKGSLGFGLGAFGLVVAAPLlGGLIKNPWKP----AYGGDGTLWTTGWTPREPGEKVYLRRDTG 221
QcrA/PetC COG0723
Rieske Fe-S protein [Energy production and conversion];
310-392 7.17e-27

Rieske Fe-S protein [Energy production and conversion];


Pssm-ID: 440487 [Multi-domain]  Cd Length: 118  Bit Score: 103.54  E-value: 7.17e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015 310 RVVEREGQETF-------HYGDYYAYSKICTHIGCPTSlYEAQTNRILCPCHQSQFDAlhYGKPVFGPAARALPQLPVTV 382
Cdd:COG0723   32 KVVEWRGKPVFvvrtpvrGDGEIVAVSAICTHLGCPVT-WNADEGGFDCPCHGSRFDP--DGRVLKGPAPRPLPVPPLEV 108

                         90
                 ....*....|
gi 227079015 383 DEEGYLVASG 392
Cdd:COG0723  109 DDDKLLIGVG 118
Rieske cd03467
Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron ...
 306-389 6.46e-24

Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis.


Pssm-ID: 239550 [Multi-domain]  Cd Length: 98  Bit Score: 94.86  E-value: 6.46e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015 306 EDANRVVEREGQETF----HYGDYYAYSKICTHIGCPTSLYEAQTNRILCPCHQSQFDaLHYGKPVFGPAARALPQLPVT 381
Cdd:cd03467   12 PGGGRVVVVGGGPVVvvrrEGGEVYALSNRCTHQGCPLSEGEGEDGCIVCPCHGSRFD-LRTGEVVSGPAPRPLPKYPVK 90


                 ....*...
gi 227079015 382 VDEEGYLV 389
Cdd:cd03467   91 VEGDGVVW 98
arsenite_ox_S TIGR02694
arsenite oxidase, small subunit; This model represents the small subunit of an arsenite ...
 323-392 1.25e-15

arsenite oxidase, small subunit; This model represents the small subunit of an arsenite oxidase complex. It is a Rieske protein and appears to rely on the Tat (twin-arginine translocation) system to cross the membrane. Although this enzyme could run in the direction of arsenate reduction to arsenite in principle, the relevant biological function is arsenite oxidation for energy metabolism, not arsenic resistance. Homologs to both large (TIGR02693) and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7. [Energy metabolism, Electron transport]


Pssm-ID: 131741  Cd Length: 129  Bit Score: 73.00  E-value: 1.25e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015  323 GDYYAYSKICTHIGCPTSlYEAQTNRILCPCHQSQFDALHYGKPVFGPAARALPQLPVTVDEEGYLVASG 392
Cdd:TIGR02694  49 GDIVAFSTLCTHMGCPVS-YSADNKTFNCPCHFSVFDPEKGGQQVWGQATQNLPQIVLRVADNGDIFAEG 117
Rieske pfam00355
Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines ...
 305-379 3.74e-09

Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilizes the protein.


Pssm-ID: 425632 [Multi-domain]  Cd Length: 89  Bit Score: 53.51  E-value: 3.74e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015  305 SEDANRVVEREGQETFHY----GDYYAYSKICTHIGCPTSL-YEAQTNRILCPCHQSQFDalHYGKPVFGPAARALPQLP 379
Cdd:pfam00355  12 PEGEPKVVEVGGEPLVVFrdedGELYALEDRCPHRGAPLSEgKVNGGGRLECPYHGWRFD--GTGKVVKVPAPRPLKSYP 89
PRK13474 PRK13474
cytochrome b6-f complex iron-sulfur subunit; Provisional
 326-390 4.63e-08

cytochrome b6-f complex iron-sulfur subunit; Provisional


Pssm-ID: 237392 [Multi-domain]  Cd Length: 178  Bit Score: 52.35  E-value: 4.63e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 227079015 326 YAYSKICTHIGCpTSLYEAQTNRILCPCHQSQFDAlhYGKPVFGPAARALPQLPVTVDEEGYLVA 390
Cdd:PRK13474 101 YGINAVCTHLGC-VVPWNSGENKFQCPCHGSQYDA--TGKVVRGPAPLSLALVHVTVEDDKVLFS 162
 
Name Accession Description Interval E-value
QcrA_N pfam19297
QcrA subunit N-terminal region; This entry describes the N-terminal region of the QcrA subunit ...
 2-225 5.51e-127

QcrA subunit N-terminal region; This entry describes the N-terminal region of the QcrA subunit which is part of respiratory complex III. This region includes anchoring transmembrane helical regions.


Pssm-ID: 466030  Cd Length: 221  Bit Score: 364.96  E-value: 5.51e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015    2 SNEVKKNYTDAELDRMNNAELAALGTELDDVTVAYRKERFPVEGDPREKAAAAGINVWLTISIVMGLAFLGVYLFWPWEP 81
Cdd:pfam19297   1 MSGVPKDPTDPELAAMSREELVRLGTRLDGVEIVHREPRFPVPGTKAEKRAERQVALWFLLAGLAALAFLVVYLFWPWEY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015   82 KFHGDEGLWMYTLYTPLLGLTSMLALGALGIAIIQYVKKFVPEEISVQRRHDGRSSELDRRTTTALLNDAWETSTLGRRK 161
Cdd:pfam19297  81 KLPGDEGYWLYTLYTPLLGLTLGLSILSLGIGAVLYVKKFIPEEISVQDRHDGPSSEVDRRTTVATLNDALETSTLGRRK 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 227079015  162 VMQGLLGGAGLLTGLIIIAPL-GGLIKNPWRPrhelNYYGDGTLWTHGWTKIEEGVKVYLGRDTG 225
Cdd:pfam19297 161 LIKGSLGFGLGAFGLVVAAPLlGGLIKNPWKP----AYGGDGTLWTTGWTPREPGEKVYLRRDTG 221
QcrA/PetC COG0723
Rieske Fe-S protein [Energy production and conversion];
310-392 7.17e-27

Rieske Fe-S protein [Energy production and conversion];


Pssm-ID: 440487 [Multi-domain]  Cd Length: 118  Bit Score: 103.54  E-value: 7.17e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015 310 RVVEREGQETF-------HYGDYYAYSKICTHIGCPTSlYEAQTNRILCPCHQSQFDAlhYGKPVFGPAARALPQLPVTV 382
Cdd:COG0723   32 KVVEWRGKPVFvvrtpvrGDGEIVAVSAICTHLGCPVT-WNADEGGFDCPCHGSRFDP--DGRVLKGPAPRPLPVPPLEV 108

                         90
                 ....*....|
gi 227079015 383 DEEGYLVASG 392
Cdd:COG0723  109 DDDKLLIGVG 118
Rieske cd03467
Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron ...
 306-389 6.46e-24

Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis.


Pssm-ID: 239550 [Multi-domain]  Cd Length: 98  Bit Score: 94.86  E-value: 6.46e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015 306 EDANRVVEREGQETF----HYGDYYAYSKICTHIGCPTSLYEAQTNRILCPCHQSQFDaLHYGKPVFGPAARALPQLPVT 381
Cdd:cd03467   12 PGGGRVVVVGGGPVVvvrrEGGEVYALSNRCTHQGCPLSEGEGEDGCIVCPCHGSRFD-LRTGEVVSGPAPRPLPKYPVK 90


                 ....*...
gi 227079015 382 VDEEGYLV 389
Cdd:cd03467   91 VEGDGVVW 98
Rieske_ArOX_small cd03476
Small subunit of Arsenite oxidase (ArOX) family, Rieske domain; ArOX is a molybdenum/iron ...
 323-386 1.78e-18

Small subunit of Arsenite oxidase (ArOX) family, Rieske domain; ArOX is a molybdenum/iron protein involved in the detoxification of arsenic, oxidizing it to arsenate. It consists of two subunits, a large subunit similar to members of the DMSO reductase family of molybdenum enzymes and a small subunit with a Rieske-type [2Fe-2S] cluster. The large subunit of ArOX contains the molybdenum site at which the oxidation of arsenite occurs. The small subunit contains a domain homologous to the Rieske domains of the cytochrome bc(1) and cytochrome b6f complexes as well as naphthalene 1,2-dioxygenase. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer.


Pssm-ID: 239558  Cd Length: 126  Bit Score: 80.89  E-value: 1.78e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 227079015 323 GDYYAYSKICTHIGCPTSlYEAQTNRILCPCHQSQFDALHYGKPVFGPAARALPQLPVTVDEEG 386
Cdd:cd03476   46 NDIVAFSALCTHMGCPLT-YDPSNKTFVCPCHFSQFDPARGGQMVSGQATQNLPQIVLEYDEAS 108
arsenite_ox_S TIGR02694
arsenite oxidase, small subunit; This model represents the small subunit of an arsenite ...
 323-392 1.25e-15

arsenite oxidase, small subunit; This model represents the small subunit of an arsenite oxidase complex. It is a Rieske protein and appears to rely on the Tat (twin-arginine translocation) system to cross the membrane. Although this enzyme could run in the direction of arsenate reduction to arsenite in principle, the relevant biological function is arsenite oxidation for energy metabolism, not arsenic resistance. Homologs to both large (TIGR02693) and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7. [Energy metabolism, Electron transport]


Pssm-ID: 131741  Cd Length: 129  Bit Score: 73.00  E-value: 1.25e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015  323 GDYYAYSKICTHIGCPTSlYEAQTNRILCPCHQSQFDALHYGKPVFGPAARALPQLPVTVDEEGYLVASG 392
Cdd:TIGR02694  49 GDIVAFSTLCTHMGCPVS-YSADNKTFNCPCHFSVFDPEKGGQQVWGQATQNLPQIVLRVADNGDIFAEG 117
NirD COG2146
Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion ...
 310-390 5.58e-11

Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 441749 [Multi-domain]  Cd Length: 103  Bit Score: 59.08  E-value: 5.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015 310 RVVEREGQET--FHYGD-YYAYSKICTHIGCPtsLYEAQTN--RILCPCHQSQFDaLHYGKPVFGPAARALPQLPVTVDE 384
Cdd:COG2146   18 VVVEVGGKQIavFRTDGeVYAYDNRCPHQGAP--LSEGIVDggVVTCPLHGARFD-LRTGECLGGPATEPLKTYPVRVED 94


                 ....*.
gi 227079015 385 EGYLVA 390
Cdd:COG2146   95 GDVYVD 100
Rieske pfam00355
Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines ...
 305-379 3.74e-09

Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilizes the protein.


Pssm-ID: 425632 [Multi-domain]  Cd Length: 89  Bit Score: 53.51  E-value: 3.74e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015  305 SEDANRVVEREGQETFHY----GDYYAYSKICTHIGCPTSL-YEAQTNRILCPCHQSQFDalHYGKPVFGPAARALPQLP 379
Cdd:pfam00355  12 PEGEPKVVEVGGEPLVVFrdedGELYALEDRCPHRGAPLSEgKVNGGGRLECPYHGWRFD--GTGKVVKVPAPRPLKSYP 89
Rieske_cytochrome_b6f cd03471
Iron-sulfur protein (ISP) component of the b6f complex family, Rieske domain; The Rieske ...
 315-391 4.94e-09

Iron-sulfur protein (ISP) component of the b6f complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The cytochrome b6f complex from Mastigocladus laminosus, a thermophilic cyanobacterium, contains four large subunits, including cytochrome f, cytochrome b6, the Rieske ISP, and subunit IV; as well as four small hydrophobic subunits, PetG, PetL, PetM, and PetN. Rieske ISP, one of the large subunits of the cytochrome bc-type complexes, is involved in respiratory and photosynthetic electron transfer. The core of the chloroplast b6f complex is similar to the analogous respiratory cytochrome bc(1) complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different.


Pssm-ID: 239553  Cd Length: 126  Bit Score: 54.29  E-value: 4.94e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 227079015 315 EGQETFhygDYYAYSKICTHIGCpTSLYEAQTNRILCPCHQSQFDAlhYGKPVFGPAARALPQLPVTVDeEGYLVAS 391
Cdd:cd03471   41 EEDKTI---ANYGINAVCTHLGC-VVPWNAAENKFKCPCHGSQYDA--TGKVVRGPAPLSLALVHATVD-DDKVVLS 110
PRK13474 PRK13474
cytochrome b6-f complex iron-sulfur subunit; Provisional
 326-390 4.63e-08

cytochrome b6-f complex iron-sulfur subunit; Provisional


Pssm-ID: 237392 [Multi-domain]  Cd Length: 178  Bit Score: 52.35  E-value: 4.63e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 227079015 326 YAYSKICTHIGCpTSLYEAQTNRILCPCHQSQFDAlhYGKPVFGPAARALPQLPVTVDEEGYLVA 390
Cdd:PRK13474 101 YGINAVCTHLGC-VVPWNSGENKFQCPCHGSQYDA--TGKVVRGPAPLSLALVHVTVEDDKVLFS 162
Rieske_SoxF_SoxL cd03475
SoxF and SoxL family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain ...
 322-402 1.20e-07

SoxF and SoxL family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. SoxF is a subunit of the terminal oxidase supercomplex SoxM in the plasma membrane of Sulfolobus acidocaldarius that combines features of a cytochrome bc(1) complex and a cytochrome. The Rieske domain of SoxF has a 12 residue insertion which is not found in eukaryotic and bacterial Rieske proteins and is thought to influence the redox properties of the iron-sulfur cluster. SoxL is a Rieske protein which may be part of an archaeal bc-complex homologue whose physiological function is still unknown. SoxL has two features not seen in other Rieske proteins; (i) a significantly greater distance between the two cluster-binding sites and (ii) an unexpected Pro -> Asp substitution at one of the cluster binding sites. SoxF and SoxL are found in archaea and in bacteria.


Pssm-ID: 239557  Cd Length: 171  Bit Score: 51.34  E-value: 1.20e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015 322 YGDYYAYSKICTHIGC-PTSLYEAQTNR--------------ILCPCHQSQFDALHYGKPVFGPAARALPQLPVTVDEE- 385
Cdd:cd03475   74 NKSIVAFSAICQHLGCqPPPIVSYPSYYppdkapglaskgavIHCCCHGSTYDPYKGGVVLTGPAPRPLPAVILEYDSSt 153

                         90
                 ....*....|....*..
gi 227079015 386 GYLVASGNfiepVGPAF 402
Cdd:cd03475  154 DDLYAVGT----LGPEF 166
Rieske_cytochrome_bc1 cd03470
Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske ...
 331-376 6.20e-06

Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes are central components of the respiratory and photosynthetic electron transport chains, respectively, which carry out similar core electron and proton transfer steps. The bc(1) and b6f complexes share a common core structure of three catalytic subunits: cyt b, the Rieske ISP, and either a cyt c1 in the bc(1) complex or cyt f in the b6f complex, which are arranged in an integral membrane-bound dimeric complex. While the core of the b6f complex is similar to that of the bc(1) complex, the domain arrangement outside the core and the complement of prosthetic groups are strikingly different.


Pssm-ID: 239552  Cd Length: 126  Bit Score: 45.24  E-value: 6.20e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 227079015 331 ICTHIGCPTSLYEAQTNRILCPCHQSQFDAlhYGKPVFGPAARALP 376
Cdd:cd03470   68 ICTHLGCVPTYRAGDYGGFFCPCHGSHYDA--SGRIRKGPAPLNLE 111
Rieske_RO_ferredoxin cd03528
Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the ...
 306-383 1.14e-05

Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the insertions that give other Rieske proteins unique structural features are missing. CARDO catalyzes dihydroxylation at the C1 and C9a positions of carbazole. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.


Pssm-ID: 239604 [Multi-domain]  Cd Length: 98  Bit Score: 43.63  E-value: 1.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015 306 EDANRVVEREGQE--TFHYGD-YYAYSKICTHIGCPTSLYEAQTNRILCPCHQSQFDaLHYGKPVFGPAARALPQLPVTV 382
Cdd:cd03528   12 EGEPKRVDVGGRPiaVYRVDGeFYATDDLCTHGDASLSEGYVEGGVIECPLHGGRFD-LRTGKALSLPATEPLKTYPVKV 90


                 .
gi 227079015 383 D 383
Cdd:cd03528   91 E 91
Rieske_YhfW_C cd03477
YhfW family, C-terminal Rieske domain; YhfW is a protein of unknown function with an ...
 305-377 7.19e-05

YhfW family, C-terminal Rieske domain; YhfW is a protein of unknown function with an N-terminal DadA-like (glycine/D-amino acid dehydrogenase) domain and a C-terminal Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. It is commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. YhfW is found in bacteria, some eukaryotes and archaea.


Pssm-ID: 239559 [Multi-domain]  Cd Length: 91  Bit Score: 41.14  E-value: 7.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227079015 305 SEDAN----RVVEREGQETFHY----GDYYAYSKICTHIGCptslyeaqtnrIL----------CPCHQSQFDAlhYGKP 366
Cdd:cd03477    5 IEDLApgegGVVNIGGKRLAVYrdedGVLHTVSATCTHLGC-----------IVhwndaekswdCPCHGSRFSY--DGEV 71

                         90
                 ....*....|.
gi 227079015 367 VFGPAARALPQ 377
Cdd:cd03477   72 IEGPAVSGLKP 82
PRK09965 PRK09965
3-phenylpropionate dioxygenase ferredoxin subunit; Provisional
 320-383 7.70e-04

3-phenylpropionate dioxygenase ferredoxin subunit; Provisional


Pssm-ID: 170182 [Multi-domain]  Cd Length: 106  Bit Score: 38.60  E-value: 7.70e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 227079015 320 FHY-GDYYAYSKICTHIGcpTSLYEA---QTNRILCPCHQSQFDaLHYGKPVFGPAARALPQLPVTVD 383
Cdd:PRK09965  29 FNVgGEFYAIDDRCSHGN--ASLSEGyleDDATVECPLHAASFC-LRTGKALCLPATDPLRTYPVHVE 93
 
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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