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Conserved domains on  [gi|1048813845|dbj|BAV32586|]
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nitrite reductase [Sulfuricaulis limicola]

Protein Classification

nitrite reductase( domain architecture ID 12141884)

nitrite reductase (cytochrome cd1) is a bifunctional enzyme that catalyzes the one-electron reduction of nitrite to nitric oxide and the four-electron reduction of oxygen to water

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
8prop_hemeD1_NirS cd20779
eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NirS; ...
 136-582 0e+00

eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NirS; Cytochrome cd1 nitrite reductase NiR is a key denitrification enzyme that catalyzes the conversion of nitrite to nitric oxide in the nitrogen cycle. The crystal structure of the oxidized enzyme shows that the d1 heme iron of the active site is ligated by His/Tyr side chains, and the c heme iron is ligated by a His/His ligand pair. Nitrite reductase from Pseudomonas aeruginosa is a dimer of two identical subunits of 60 kDa, each containing one c and one d1 heme group. The c heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The d1 heme is the site where nitrite, and oxygen reduction occur. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis.


:

Pssm-ID: 467723 [Multi-domain]  Cd Length: 438  Bit Score: 825.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 136 NWGTSGDLTAEDVDLMARFLQHEPPTPPEFGMKEMKDTWKVLVAPDKRPKKKLNNINLANLFSVTLRDSGEVALIDGDTK 215
Cdd:cd20779     1 AWGKSGILTEEEIDLMARYLQLPPPAPPEFGMADMKASWKVIVPVAKRPTKPEHKRNWENFFGVILRDAGQVAIIDGDTK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 216 KIVNIVKTGYAVHISRTSASGRYLYVIGRDAKINLIDLWMEKPDNVAEIKIGLEARSVDTSKYKGYEDKYAIAGAYWPPQ 295
Cdd:cd20779    81 EIVSIVDTGFAVHILRSSASGRYFYTIGRDGKVTMIDLWMKKPTVVAEVKGCLDARSVDSSKYKGFEDKYAIVGCYWPPQ 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 296 FTIMKGDTLEPIKIVATRGFTVDTQEYHPEPRVASIVASHFKPEFVVNVKETGKILMVNYKDLDNLEVTEIGAARFLHDG 375
Cdd:cd20779   161 YVILDGLTLEPLKVVSTRGYTYDTGEYHPEPRVASIVASHFDPEWVVNVKETGQVWLVDYSDLKNLKVTMIEAERFLHDG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 376 GWDSTKRYFLVAANQSNKIAVVDAKEGELEKLVDVGKIPHPGRGANFIDPKFGPVWATGHLGDDTIALIGTDKEKHKANA 455
Cdd:cd20779   241 GWDHTKRYFLVAANARNKVVVVDTKTKKLVALVETGIKPHPGRGANWVDPKYGPVWATGHLGEGKIALIGTDPKGHPQYA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 456 WKVVRTLKGQGGGSLFIKTHPKSKNLWVDTALNPNAEISQSVAVFDIANLDKPYQVVKIAEmaglgegPKRVVQPEYNNK 535
Cdd:cd20779   321 WKVVRKIKLPGGGSLFIKTHPKSPWLWVDRTLNPDPKLARSVCVFDKKLLDKKYKCWPVAD-------HGRAVHFEYNKA 393

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*..
gi 1048813845 536 GDEVWFSVWNGKtqESAIVVVDDKTRKLKTVIKDKRLITPTGKFNVY 582
Cdd:cd20779   394 GDEVWVSVWDKK--PGAIVVYDDKTLKEKARITGDWLVTPTGKFNVY 438
CccA COG2010
Cytochrome c, mono- and diheme variants [Energy production and conversion];
68-161 8.86e-17

Cytochrome c, mono- and diheme variants [Energy production and conversion];


:

Pssm-ID: 441613 [Multi-domain]  Cd Length: 169  Bit Score: 78.07  E-value: 8.86e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845  68 TVVSPKAPALTTAEFTRAKQIYFERCAGCHGVLRKGATGK--PLTPDITLKKGTDYLKVFINYGSPAG-MPNWGtsGDLT 144
Cdd:COG2010    75 AAAAADAPAADAEALARGKALYEQNCAACHGADGKGGLGAapNLTDDALYGGDPEALVETILNGRPGGaMPAFG--GQLS 152

                          90
                  ....*....|....*..
gi 1048813845 145 AEDVDLMARFLQHEPPT 161
Cdd:COG2010   153 DEEIAALAAYLRSLSGN 169
 
Name Accession Description Interval E-value
8prop_hemeD1_NirS cd20779
eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NirS; ...
 136-582 0e+00

eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NirS; Cytochrome cd1 nitrite reductase NiR is a key denitrification enzyme that catalyzes the conversion of nitrite to nitric oxide in the nitrogen cycle. The crystal structure of the oxidized enzyme shows that the d1 heme iron of the active site is ligated by His/Tyr side chains, and the c heme iron is ligated by a His/His ligand pair. Nitrite reductase from Pseudomonas aeruginosa is a dimer of two identical subunits of 60 kDa, each containing one c and one d1 heme group. The c heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The d1 heme is the site where nitrite, and oxygen reduction occur. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis.


Pssm-ID: 467723 [Multi-domain]  Cd Length: 438  Bit Score: 825.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 136 NWGTSGDLTAEDVDLMARFLQHEPPTPPEFGMKEMKDTWKVLVAPDKRPKKKLNNINLANLFSVTLRDSGEVALIDGDTK 215
Cdd:cd20779     1 AWGKSGILTEEEIDLMARYLQLPPPAPPEFGMADMKASWKVIVPVAKRPTKPEHKRNWENFFGVILRDAGQVAIIDGDTK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 216 KIVNIVKTGYAVHISRTSASGRYLYVIGRDAKINLIDLWMEKPDNVAEIKIGLEARSVDTSKYKGYEDKYAIAGAYWPPQ 295
Cdd:cd20779    81 EIVSIVDTGFAVHILRSSASGRYFYTIGRDGKVTMIDLWMKKPTVVAEVKGCLDARSVDSSKYKGFEDKYAIVGCYWPPQ 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 296 FTIMKGDTLEPIKIVATRGFTVDTQEYHPEPRVASIVASHFKPEFVVNVKETGKILMVNYKDLDNLEVTEIGAARFLHDG 375
Cdd:cd20779   161 YVILDGLTLEPLKVVSTRGYTYDTGEYHPEPRVASIVASHFDPEWVVNVKETGQVWLVDYSDLKNLKVTMIEAERFLHDG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 376 GWDSTKRYFLVAANQSNKIAVVDAKEGELEKLVDVGKIPHPGRGANFIDPKFGPVWATGHLGDDTIALIGTDKEKHKANA 455
Cdd:cd20779   241 GWDHTKRYFLVAANARNKVVVVDTKTKKLVALVETGIKPHPGRGANWVDPKYGPVWATGHLGEGKIALIGTDPKGHPQYA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 456 WKVVRTLKGQGGGSLFIKTHPKSKNLWVDTALNPNAEISQSVAVFDIANLDKPYQVVKIAEmaglgegPKRVVQPEYNNK 535
Cdd:cd20779   321 WKVVRKIKLPGGGSLFIKTHPKSPWLWVDRTLNPDPKLARSVCVFDKKLLDKKYKCWPVAD-------HGRAVHFEYNKA 393

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*..
gi 1048813845 536 GDEVWFSVWNGKtqESAIVVVDDKTRKLKTVIKDKRLITPTGKFNVY 582
Cdd:cd20779   394 GDEVWVSVWDKK--PGAIVVYDDKTLKEKARITGDWLVTPTGKFNVY 438
Cytochrom_D1 pfam02239
Cytochrome D1 heme domain; Cytochrome cd1 (nitrite reductase) catalyzes the conversion of ...
 191-584 0e+00

Cytochrome D1 heme domain; Cytochrome cd1 (nitrite reductase) catalyzes the conversion of nitrite to nitric oxide in the nitrogen cycle. This family represents the d1 heme binding domain of cytochrome cd1, in which His/Tyr side chains ligate the d1 heme iron of the active site in the oxidized state.


Pssm-ID: 366994 [Multi-domain]  Cd Length: 368  Bit Score: 522.03  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 191 INLANLFSVTLRDSGEVALIDGDTKKIVNIVKTGYAVHISRTSAS-GRYLYVIGRDAKINLIDLWMEKpdNVAEIKIGLE 269
Cdd:pfam02239   1 RDLGNLFVVTERDAGSVALLDGDRKEILARVDTGYALHISRMFSSdGRYVYVIGRDGGLTKIDLWNQE--IVAEVRQGGN 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 270 ARSVDTSkykgYEDKYAIAGAYWPPQFTIMKGDTLEPIKIVATRGFTVDTqeyhPEPRVASIVASHFKPEFVVNVKETGK 349
Cdd:pfam02239  79 ARSVATS----YDGRYVIVGNYWPGQYVIMDGRTLELVKVIPARGMTGDS----PESRVAAIVASPGRPEFVVNLKDTGE 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 350 ILMVNYKDLDNLEVTEIGAARFLHDGGWDSTKRYFLVAANQSNKIAVVDAKEGELEKLVDVGKIPHPGRGANFIDPKFGP 429
Cdd:pfam02239 151 IWLVDYSDGKNLKTTFIEAAKFLHDGGFDPDGRYFMAAANASDKIAVWDTKRGKLVALLDYGKTPHPGPGANMPHLEGGP 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 430 VWATGHLGDDTIALIGTDKE-KHKANAWKVVRTLKGQGGGsLFIKTHPKSKNLWVDTALNPNaeiSQSVAVFDIANLdkp 508
Cdd:pfam02239 231 VWTTSHLGDFVTPLIGTDPVlVHDLQAWKQVKEIDVAGGG-LFVKTHPDSRYLWVDTFLNPD---NDSVAVIDSETL--- 303

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1048813845 509 YQVVKIAEMAGLGegpkrVVQPEYNNKGDEVWFSVWNGKTqesAIVVVDDKTRKLKTVIKdkrLITPTGKFNVYNT 584
Cdd:pfam02239 304 EKVLTLAPWPGLV-----VVHMEFNKRGDEVWLSVWDGKG---ALVVYDDKTLKLKKVIP---LNTPSGKFNVYNT 368
CccA COG2010
Cytochrome c, mono- and diheme variants [Energy production and conversion];
68-161 8.86e-17

Cytochrome c, mono- and diheme variants [Energy production and conversion];


Pssm-ID: 441613 [Multi-domain]  Cd Length: 169  Bit Score: 78.07  E-value: 8.86e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845  68 TVVSPKAPALTTAEFTRAKQIYFERCAGCHGVLRKGATGK--PLTPDITLKKGTDYLKVFINYGSPAG-MPNWGtsGDLT 144
Cdd:COG2010    75 AAAAADAPAADAEALARGKALYEQNCAACHGADGKGGLGAapNLTDDALYGGDPEALVETILNGRPGGaMPAFG--GQLS 152

                          90
                  ....*....|....*..
gi 1048813845 145 AEDVDLMARFLQHEPPT 161
Cdd:COG2010   153 DEEIAALAAYLRSLSGN 169
Cytochrome_CBB3 pfam13442
Cytochrome C oxidase, cbb3-type, subunit III;
80-155 2.20e-10

Cytochrome C oxidase, cbb3-type, subunit III;


Pssm-ID: 463879 [Multi-domain]  Cd Length: 67  Bit Score: 56.65  E-value: 2.20e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1048813845  80 AEFTRAKQIYFERCAGCHGvlrKGATGKPLTPDitlKKGTDYLKVFINYGsPAGMPNWGtsGDLTAEDVDLMARFL 155
Cdd:pfam13442   1 AAAAAGEALYAANCASCHG---TGGAGPSLAGR---ALPPEALVDIIRNG-KGAMPAFG--GDLSDEELEALAAYL 67
YncE COG3391
DNA-binding beta-propeller fold protein YncE [General function prediction only];
357-505 2.40e-07

DNA-binding beta-propeller fold protein YncE [General function prediction only];


Pssm-ID: 442618 [Multi-domain]  Cd Length: 237  Bit Score: 52.00  E-value: 2.40e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 357 DLDNLEVT-EIGAARFLHDGGWDSTKRYFLVAANQSNKIAVVDAKEGELEKLVDVGKIPHpgrgANFIDPKFGPVWATGH 435
Cdd:COG3391    96 DLATGKVVaTIPVGGGPRGLAVDPDGGRLYVADSGNGRVSVIDTATGKVVATIPVGAGPH----GIAVDPDGKRLYVANS 171

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1048813845 436 lGDDTIALIGTdkeKHKANAWKVVRTLKGqGGGSLFIKTHPKSKNLWVDTALNPNAE-ISQSVAVFDIANL 505
Cdd:COG3391   172 -GSNTVSVIVS---VIDTATGKVVATIPV-GGGPVGVAVSPDGRRLYVANRGSNTSNgGSNTVSVIDLATL 237
 
Name Accession Description Interval E-value
8prop_hemeD1_NirS cd20779
eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NirS; ...
 136-582 0e+00

eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NirS; Cytochrome cd1 nitrite reductase NiR is a key denitrification enzyme that catalyzes the conversion of nitrite to nitric oxide in the nitrogen cycle. The crystal structure of the oxidized enzyme shows that the d1 heme iron of the active site is ligated by His/Tyr side chains, and the c heme iron is ligated by a His/His ligand pair. Nitrite reductase from Pseudomonas aeruginosa is a dimer of two identical subunits of 60 kDa, each containing one c and one d1 heme group. The c heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The d1 heme is the site where nitrite, and oxygen reduction occur. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis.


Pssm-ID: 467723 [Multi-domain]  Cd Length: 438  Bit Score: 825.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 136 NWGTSGDLTAEDVDLMARFLQHEPPTPPEFGMKEMKDTWKVLVAPDKRPKKKLNNINLANLFSVTLRDSGEVALIDGDTK 215
Cdd:cd20779     1 AWGKSGILTEEEIDLMARYLQLPPPAPPEFGMADMKASWKVIVPVAKRPTKPEHKRNWENFFGVILRDAGQVAIIDGDTK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 216 KIVNIVKTGYAVHISRTSASGRYLYVIGRDAKINLIDLWMEKPDNVAEIKIGLEARSVDTSKYKGYEDKYAIAGAYWPPQ 295
Cdd:cd20779    81 EIVSIVDTGFAVHILRSSASGRYFYTIGRDGKVTMIDLWMKKPTVVAEVKGCLDARSVDSSKYKGFEDKYAIVGCYWPPQ 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 296 FTIMKGDTLEPIKIVATRGFTVDTQEYHPEPRVASIVASHFKPEFVVNVKETGKILMVNYKDLDNLEVTEIGAARFLHDG 375
Cdd:cd20779   161 YVILDGLTLEPLKVVSTRGYTYDTGEYHPEPRVASIVASHFDPEWVVNVKETGQVWLVDYSDLKNLKVTMIEAERFLHDG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 376 GWDSTKRYFLVAANQSNKIAVVDAKEGELEKLVDVGKIPHPGRGANFIDPKFGPVWATGHLGDDTIALIGTDKEKHKANA 455
Cdd:cd20779   241 GWDHTKRYFLVAANARNKVVVVDTKTKKLVALVETGIKPHPGRGANWVDPKYGPVWATGHLGEGKIALIGTDPKGHPQYA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 456 WKVVRTLKGQGGGSLFIKTHPKSKNLWVDTALNPNAEISQSVAVFDIANLDKPYQVVKIAEmaglgegPKRVVQPEYNNK 535
Cdd:cd20779   321 WKVVRKIKLPGGGSLFIKTHPKSPWLWVDRTLNPDPKLARSVCVFDKKLLDKKYKCWPVAD-------HGRAVHFEYNKA 393

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*..
gi 1048813845 536 GDEVWFSVWNGKtqESAIVVVDDKTRKLKTVIKDKRLITPTGKFNVY 582
Cdd:cd20779   394 GDEVWVSVWDKK--PGAIVVYDDKTLKEKARITGDWLVTPTGKFNVY 438
Cytochrom_D1 pfam02239
Cytochrome D1 heme domain; Cytochrome cd1 (nitrite reductase) catalyzes the conversion of ...
 191-584 0e+00

Cytochrome D1 heme domain; Cytochrome cd1 (nitrite reductase) catalyzes the conversion of nitrite to nitric oxide in the nitrogen cycle. This family represents the d1 heme binding domain of cytochrome cd1, in which His/Tyr side chains ligate the d1 heme iron of the active site in the oxidized state.


Pssm-ID: 366994 [Multi-domain]  Cd Length: 368  Bit Score: 522.03  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 191 INLANLFSVTLRDSGEVALIDGDTKKIVNIVKTGYAVHISRTSAS-GRYLYVIGRDAKINLIDLWMEKpdNVAEIKIGLE 269
Cdd:pfam02239   1 RDLGNLFVVTERDAGSVALLDGDRKEILARVDTGYALHISRMFSSdGRYVYVIGRDGGLTKIDLWNQE--IVAEVRQGGN 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 270 ARSVDTSkykgYEDKYAIAGAYWPPQFTIMKGDTLEPIKIVATRGFTVDTqeyhPEPRVASIVASHFKPEFVVNVKETGK 349
Cdd:pfam02239  79 ARSVATS----YDGRYVIVGNYWPGQYVIMDGRTLELVKVIPARGMTGDS----PESRVAAIVASPGRPEFVVNLKDTGE 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 350 ILMVNYKDLDNLEVTEIGAARFLHDGGWDSTKRYFLVAANQSNKIAVVDAKEGELEKLVDVGKIPHPGRGANFIDPKFGP 429
Cdd:pfam02239 151 IWLVDYSDGKNLKTTFIEAAKFLHDGGFDPDGRYFMAAANASDKIAVWDTKRGKLVALLDYGKTPHPGPGANMPHLEGGP 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 430 VWATGHLGDDTIALIGTDKE-KHKANAWKVVRTLKGQGGGsLFIKTHPKSKNLWVDTALNPNaeiSQSVAVFDIANLdkp 508
Cdd:pfam02239 231 VWTTSHLGDFVTPLIGTDPVlVHDLQAWKQVKEIDVAGGG-LFVKTHPDSRYLWVDTFLNPD---NDSVAVIDSETL--- 303

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1048813845 509 YQVVKIAEMAGLGegpkrVVQPEYNNKGDEVWFSVWNGKTqesAIVVVDDKTRKLKTVIKdkrLITPTGKFNVYNT 584
Cdd:pfam02239 304 EKVLTLAPWPGLV-----VVHMEFNKRGDEVWLSVWDGKG---ALVVYDDKTLKLKKVIP---LNTPSGKFNVYNT 368
8prop_hemeD1_NiR_alpha_gamma cd20781
eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NiR ...
 156-588 6.80e-159

eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NiR alpha and gamma proteobacteria subdivisions; Cytochrome cd1 (nitrite reductase) catalyzes in vitro the reduction of molecular oxygen to water and the reduction of nitrite to nitric oxide. Purification and characterization of NiR from several bacterial sources have shown that there are two distinct classes of dissimilatory NiRs that yield NO as the main reaction product, containing either copper or heme as cofactor, the heme-containing enzyme occurring more frequently. It forms a homodimer each containing one C and one D1 heme group. The C heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The D1 heme is the site where nitrite, and oxygen reduction occur. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis. Heme binding nitrite reductase from alphaproteobacteria and gammaproteobacteria are present here.


Pssm-ID: 467725 [Multi-domain]  Cd Length: 433  Bit Score: 461.48  E-value: 6.80e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 156 QHEPPTPPEFGMKEMKDTWKVLVAPDKRPKKKLNNINLANLFSVTLRDSGEVALIDGDTKKIVNIVKTGYAVHISRTSAS 235
Cdd:cd20781     1 QMEPPVPPEMSLALMKERHKVYVEPKDYPTKPLHGRNWENFFVVIERDAGKVAIIDGDKKEVVAHIDTGYAVHVLKASEH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 236 ---------GRYLYVIGRDAKINLIDLWMeKPDN--VAEIKIGLEARSVDTSkykgYEDKYAIAGAYWPPQFTIMKGDTL 304
Cdd:cd20781    81 hkvekaknpGRFWYTMGRDGKLTKIDLWQ-TPDKmlVAEVQIAYDARDVAVS----GDGKYVIGGGYWPPHFVIVDAETM 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 305 EPIKIVATRGFTVDTqEYHPEPRVASIVASHFKPEFVVNVKETGKILMVNYKDLDNLEVTEIGAARFLHDGGWDSTKRYF 384
Cdd:cd20781   156 EPLKVVSTRGVNVDG-EYVNESRVAAIYTTPNAPTFLVAVKELGQMWQVDYSDLDNLRIDQIDTAKFLHDGFFDPTGRYF 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 385 LVAANQSNKIAVVDAKEGELEKLVDVGKIPHPGRGANFIDPKFGPVWATGHLGDDTIALIGTDKEKHKANAWKVVRTLKG 464
Cdd:cd20781   235 QIAANASNKMVVVDTKTRKLEAMIDTGKLPHPGPGANWIDPKCGPVGGTTHLGEGKVTVWGNDPKGHPDQAWKICYEVET 314

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 465 QGGGsLFIKTHPKSKNLWVDTALNPNAEISQSVAVFDianlDKPYQVVKIAEmagLGEGPKRV-VQPEYNNKGDEVWFSV 543
Cdd:cd20781   315 DGPG-LFIRTHPNSDYVWADQTKHPEPEVQQSVQVID----KKTREIVKTIR---VTEEEGYVaVHMEFNQDGTEVWVSV 386

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*...
gi 1048813845 544 WN---GKTQESAIVVVDDKTRKLKTVIKDkrLITPTGKFNVYNTQHDV 588
Cdd:cd20781   387 WNrkdSKEPNGEIVVYDAKTLEEKARIKG--LYTPTGKFNVYNRVNHV 432
8prop_heme_binding_protein cd20718
eight-bladed beta-propeller heme-binding domain in cytochrome cd1 and similar proteins; ...
 168-582 2.43e-116

eight-bladed beta-propeller heme-binding domain in cytochrome cd1 and similar proteins; Members here contain an 8-bladed beta-propeller heme-binding domain in cytochrome cd1 (nitrite reductase) and similar proteins including NirN and NirF. During denitrification, nitrate (Nar), nitrite (Nir), nitric oxide (Nor), and nitrous oxide (Nos) reductases catalyze the reaction cascade of NO(3-)-> NO(2-)-> NO -> N2O -> N2. The integral membrane proteins NorC, NorB, and NosR form the core assembly platform that binds the nitrate reductase NarGHI and the periplasmic nitrite reductase NirS via its maturation factor NirF. NirN and NirF form a stable complex with the nitrite reductase NirS during enzyme maturation. NirF is involved in heme d1 insertion.


Pssm-ID: 467720 [Multi-domain]  Cd Length: 380  Bit Score: 350.48  E-value: 2.43e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 168 KEMKDTWKVLVAPDKRPKKKLNNINLANLFSVTLRDSGEVALIDGDTKKIVNIVKTGYA-VHISRTSASGRYLYVIGRDA 246
Cdd:cd20718     1 EDIKKSLEVLVPERELPPVAYGIWDLENLMVVVERDAGSVLVIDGSTHEVLGRIDDGGAqVHVVVFSPDGRFAYVISRDG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 247 KINLIDLWMEKPdnVAEIKIGLEARSVDTSKykgyEDKYAIAGAYWPPQFTIMKGDTLEPIKIVATRGFTVDTqeyHPEP 326
Cdd:cd20718    81 WLTKIDLYTLRP--VASIRIGVNSRGIALSD----DGKYVIAGNYEPGHVVILDADTLEPLKVIPTTGVNDDG---IIES 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 327 RVASIVASHFKPEFVVNVKETGKILMVNYKDLDNLEVTEIG-AARFLHDGGWDSTKRYFLVAANQSNKIAVVDAKEGELE 405
Cdd:cd20718   152 RVGAILETPPGPYFLVALKDAGSVWVIDYSDPDGNKVTDIGnIGRPLHDAFLDPDGRYFIVASQGSNTMWVLDLKTGKVV 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 406 KLVDVGKIPHPGRGANFIDpkfGPVWATGHLGDDTIALIGTDkekhkanAWKVVRTLKGQGGGsLFIKTHPKSKNLWVDT 485
Cdd:cd20718   232 ARIPTGKTPHPGPGATWGR---KGVTATPHLGEGIVTVWDLD-------TWKPVKYIPTPGPG-RFVRTHPSSPYVWADT 300

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 486 ALNPnaEISQSVAVFDIANldkPYQVVKIAEMAGlgegpKRVVQPEYNNKGDEVWFSVWNGktqeSAIVVVDDKTRKLKT 565
Cdd:cd20718   301 VFGP--ENADEIYVIDKET---LKVVKTLIPKPG-----KRALHPEFTRDGKYVYVSVWDG----GEVVVYDAETLELVK 366

                         410
                  ....*....|....*..
gi 1048813845 566 VIKDKrliTPTGKFNVY 582
Cdd:cd20718   367 RIPAE---TPTGIFNVG 380
8prop_hemeD1_cyt_cd1-like cd20783
eight-bladed heme d1-binding beta-propeller domain and similar proteins; Cytochrome cd1 (cyt ...
 168-582 5.62e-61

eight-bladed heme d1-binding beta-propeller domain and similar proteins; Cytochrome cd1 (cyt cd1) nitrite reductase catalyzes in vitro the reduction of molecular oxygen to water and the reduction of nitrite to nitric oxide). It is a dimer of two identical subunits of 60 kDa, each containing one c and one d1 heme group. The c heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The d1 heme is the site where nitrite, and oxygen reduction occur. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis.


Pssm-ID: 467727 [Multi-domain]  Cd Length: 388  Bit Score: 206.85  E-value: 5.62e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 168 KEMKDTWKVLVAPDKRPKKKLNNINLANLFSVTLRDSGEVALIDGDTKKIVNIVKTGYAVH-ISRTSASGRYLYVIGRDA 246
Cdd:cd20783     1 EDIAASREVLVPESELPAEPTHDGNVDNLLLVTEREARSIAVIDGDTHTLLGHIEAGYRAHgYTFSPTDGRWAYNLGRDG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 247 KINLIDLWMEKPdnVAEIKIGLEARSVDTSKykgyEDKYAIAGAYWPPQFTIMKGDTLEPIKIVATRGftVDTQEYHPEP 326
Cdd:cd20783    81 WLYKIDLYSLQP--VAKVRVGLDARGIAISD----DGKYLIAGNYIPATAVILDAKTLEPLKVIDTSG--VDPDGKMVDS 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 327 RVASIVA---SHFKPEFVVNVKETGKILMVNYKDLDNLEVTEIGAARFLHDGGWDSTKRYFLVAANQSNKIAVVDAKEGE 403
Cdd:cd20783   153 RVASVNDvapDLVGPYFLLALKEAGQVWRIDYSKPDFPITKVENVGHILHDGFLSPDNKTFYLASQTDNWMAAIDVATMK 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 404 LEKLVDVGKIPHPGRGAnfidpkfgpVW--------ATGHLGDDTIALIGTDKEkhkanawKVVRTLKGQGGGsLFIKTH 475
Cdd:cd20783   233 IVAKIPTGDKPHPGSGA---------VWeadgkeyaATVHAGEGKVTIWDLDTN-------EIVGEVPTSGPG-LFIRTT 295

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 476 PKSKNLWVDTALNPNAEisqSVAVFDIAnldKPYQVVKIAEmaglgEGpKRVVQPEYNNKGDEVWFSVWngktQESAIVV 555
Cdd:cd20783   296 ENMPYVWADSMFAPEPN---EITVHEKA---PPFKVVKRIT-----DG-TRTLHPEPTADGKYVYVSDW----DGNVVRV 359

                         410       420
                  ....*....|....*....|....*..
gi 1048813845 556 VDDKTRKLKTVIKDkrLITPTGKFNVY 582
Cdd:cd20783   360 YDAETLELVKEITG--ITTPTGIFNTS 384
8prop_hemeD1_cyt_cd1-like cd20782
cytochrome cd1 nitrate reductase eight-bladed heme d1-binding beta-propeller domain and ...
 162-579 1.66e-55

cytochrome cd1 nitrate reductase eight-bladed heme d1-binding beta-propeller domain and similar proteins; Cytochrome cd1 (cyt cd1) nitrite reductase catalyzes in vitro the reduction of molecular oxygen to water and the reduction of nitrite to nitric oxide). It is a dimer of two identical subunits of 60 kDa, each containing one c and one d1 heme group. The c heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The d1 heme is the site where nitrite, and oxygen reduction occur. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis.


Pssm-ID: 467726 [Multi-domain]  Cd Length: 415  Bit Score: 193.08  E-value: 1.66e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 162 PPEF---GMKEMKDTWKVLVAPDKRPKKKLNNINLANLFSVTLRDSGEVALIDG-DTKKIVNIVKTGYAVH-------IS 230
Cdd:cd20782    11 PPSFdyrDLEDIADSHEIHKEEEELPQEPQHDDDLRDLLVVAERRNASVSLVDTvNHERLGRIEDVGRAIHviefhrdLP 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 231 RTSASGRYLYVIGRDAKINLIDLWmeKPDNVAEIKIGLEARSVDTSKykgyEDKYAIAGAYWPPQFTIMKGDTLEPIKIV 310
Cdd:cd20782    91 ENEREGAYAYTQSRQGWVSKLDLF--GGERVARVRAGTDARDIAVSR----DSNYLIAGYYNPNHLVVVDAETMEPLKRI 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 311 ATRGFTVDTQEYhpEPRVASIVASHFKPEFVVNVKETGKILMVNYKDLDNLEVTEIGAARFLHDGGWDSTKRYFLVAANQ 390
Cdd:cd20782   165 PTHGVDPDGQSV--ESRVCTLYDVPGEGCFLAALKEAGQVWLIDYTQDDFPVVDEIDCGRTLHDGFFTPDGRYFMLASQT 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 391 SNKIAVVDAKEGELEKLVDVGKIPHPGRGAnfIDPKFGPVWaTGHLGDDTIALIGTDKekhkanaWKVVRTLKGQGGGsL 470
Cdd:cd20782   243 DNCMSVLDVEEREVVDRIPTAGVPHPGPGA--LDPDRGLAF-TTHVGTDAVTAWDTET-------WEPEADIEVPGGG-L 311

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 471 FIKTHPKSKNLWVDTALNPNAEISQSVAVFDIANLDKPyQVVKIAEMaglgeGPKRVVQPEYNNKGDEVWFSVWNGKTqe 550
Cdd:cd20782   312 FLRSHPDSDYVWGDVILDDTDRLDQLIYAIDPDTLEVA-TVIDTSEW-----GEGRAIHPEFSRDGEKVYVSHWDAGE-- 383

                         410       420
                  ....*....|....*....|....*....
gi 1048813845 551 saIVVVDDKTRKLKTVIKDkrLITPTGKF 579
Cdd:cd20782   384 --ILVFDSHTGELIEEIDG--LETPTGKF 408
8prop_hemeD1_NiR_delta_epsilon cd20780
eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NiR ...
 167-586 1.33e-36

eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NiR delta/epsilon subdivisions; Cytochrome cd1 (nitrite reductase) catalyzes in vitro the reduction of molecular oxygen to water and the reduction of nitrite to nitric oxide. Purification and characterization of NiR from several bacterial sources have shown that there are two distinct classes of dissimilatory NiRs that yield NO as the main reaction product, containing either copper or heme as cofactor- the heme-containing enzyme occurring more frequently. It forms a homodimer with each subunit containing one C and one D1 heme group. The C heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The D1 heme is the site where nitrite, and oxygen reduction occur. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis. The heme-binding nitrite reductase in delta and epsilon subdivisions are present here.


Pssm-ID: 467724 [Multi-domain]  Cd Length: 436  Bit Score: 141.90  E-value: 1.33e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 167 MKEMKDTWKVLVAPDKRPKKKLNNINLANLFSVTL---RDSGEVALIDGDTKKIVNIVKTGYAVHISRTSASG-RYLYVI 242
Cdd:cd20780    19 LDEVKKTWKKLADREELAKKYPHAVDVKSVTDITFateRDASLVDFIDGTTGKVLSRHKAGFAVHVTVTNKRNpRYAYSI 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 243 GRDAKINLIDLWMEKPDNVAEIKIGLEARSVDTSKykgyEDKYAIAGAYWPPQFTIMKGDTLEPIKIVATRGfTVDTQEY 322
Cdd:cd20780    99 SRSGRLTMFDLAAPGQPALASVQVGQESRGLAVSP----DGKYVMAGNYNPGGAVLCDAMTLEPLKVYDTSS-VIDPDGQ 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 323 HPEPRVASIVASHFKPEFVVNVKETGKILMVNYKDLDNLEVTEI-GAARFLHDGGWDSTK---RYFLVAANQSNKIAVVD 398
Cdd:cd20780   174 IGPSRVASIADTPYGPYFAFALKDAGHVYIVDYSKPDFPIVGDIpNIGKILHDAFLNEGEgfgRYLMIASQGSDVMGIVD 253

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 399 AKEGELEKLVDVGK--IPHPGRGAN-FIDPKFGPVWATG--HLGDDTIaligTDKEkhkanaWKVVRTLKGQGGGsLFIK 473
Cdd:cd20780   254 FKTKNLAAKVYTGPksKPHPGQGSSwYNKGLGKQLHATVsmNVGDVVI----WDSN------WDVVKHVPTAGGG-LFVG 322

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 474 THPKSKNLWVDTALNPNAEISQsVAVFDIANLDKPyQVVKIAEMAGLGEGPK---------RVVQPEYNNKGDEVWFSVW 544
Cdd:cd20780   323 TSEHTPYLWADCVLGGPDNYNK-VHLINKQTLETD-RIIKVGKTKGTLIDAKtkkvlqtwdRLLHAEPANHGKWTMISEW 400

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|..
gi 1048813845 545 NgktqESAIVVVDDKTRKLKTVIKDkrLITPTGKFNVYNTQH 586
Cdd:cd20780   401 T----TGRIGIYESKTGKFVKYIEN--LTTPTFTYSVEHRQH 436
8prop_hemeD1_cyt_cd1-like cd20785
eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase and ...
 159-579 1.99e-31

eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase and similar proteins; Cytochrome cd1 (cyt cd1) nitrite reductase catalyzes in vitro the reduction of molecular oxygen to water and the reduction of nitrite to nitric oxide). It is a dimer of two identical subunits of 60 kDa, each containing one c and one d1 heme group. The c heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The d1 heme is the site where nitrite, and oxygen reduction occur. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis.


Pssm-ID: 467729 [Multi-domain]  Cd Length: 412  Bit Score: 126.26  E-value: 1.99e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 159 PPTPPEFGMKEMKDTWKVLVAPD-KRPKKKLNNI-NLANLFSVTLR------DSGEVALIDGDTKKIVNIVKTGYAVHIS 230
Cdd:cd20785     2 PKRNPSWGLEDIRKSLEVLVADEsTLPSKPTYAIdDIDDLMAVMARgrygrgKGSKVVFFDGKTNRKVGEIPTGFAPHIM 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 231 RTSASG-RYLYVIGRDAKINLIDLWMEKPdnVAEIKIGLEARSVDTSkykgYEDKYAIAGAYWPPQFTIMKGDTLEPIKI 309
Cdd:cd20785    82 DFHPVNpRWAYVKTDTGEVYKIDLYSMQA--VRSVKAGLNGPSLAVS----RDGKYLAAGSFVPHTAVILDADTLEPLKY 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 310 VATRGftVDTQEYHPEPRVASIVASHFKPEFVVNVKETGKILMVNYkDLDNLEVTEI-GAARFLHDGGWDSTKRYFLVAA 388
Cdd:cd20785   156 FELEG--VDPDGKMVESDSGMITGTPYANYFAIALEQAGQVWIVDL-DKPGMPVTKIkNVGRHLHDAFLSPDGRYLMVAS 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 389 NQSNKIAVVDAKEGELEKLVDVGKIPHPGRGANF-IDPKFgpvwatghLGDDTIalIGTDKEKHKANAW-----KVVRTL 462
Cdd:cd20785   233 YDDNKNAVIDLKEKKVVKKIPAGCQPHLGSGAVVkVGGRL--------LGFGTN--IGSCDDKTVVTVWdmdtfEVVKQI 302

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 463 KgQGGGSLFIKTHPKSKNLWVDTalnpnaeISQSVAVFDIANLDK-PYQVVKIAEMAGlgegpkRVVQPEYNNKGDEVWF 541
Cdd:cd20785   303 P-VSGPTESPAAHPNAPYVAVDI-------VGKDPRARKIQLIDKnTLEVVKTLDVGG------HSHFPEYTADGDYLYV 368

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|
gi 1048813845 542 S--VWNGKtqesaIVVVDDKTrkLKTViKDKRLITPTGKF 579
Cdd:cd20785   369 SagYNGDR-----LVIYDSKT--LKKV-KEIPMESPAGIF 400
8prop_heme-binding_NirN cd20777
eight-bladed heme d1-binding beta-propeller domain in dihydro-heme d1 dehydrogenase NirN; The ...
 195-583 1.14e-30

eight-bladed heme d1-binding beta-propeller domain in dihydro-heme d1 dehydrogenase NirN; The monomeric dihydro-heme d1 dehydrogenase NirN is part of the denitrification process that enables biofilm formation of the opportunistic human pathogen Pseudomonas aeruginosa, making it more resilient to antibiotics and highly adaptable to different habitats. NirN, similar to the homodimeric cytochrome cd1 (nitrite reductase; NirS), consists of an eight-bladed heme d1-binding beta-propeller and a cytochrome c domain, but their relative orientation differs with respect to NirS. His147, His323 and Tyr461, but not His417 are essential for activity. All 8 blades of the propeller are included in this alignment.


Pssm-ID: 467721 [Multi-domain]  Cd Length: 405  Bit Score: 124.01  E-value: 1.14e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 195 NLFSVTLRDSGEVALIDGDTKKIVNIVKTGYAVHIS-RTSASGRYLYVIGRDAKINLIDLWMEKPdnVAEIKIGLEARSV 273
Cdd:cd20777    33 NLFVVVESGDHHVTVLDGDRFEPLARFPTRFALHGGpKFSPDGRFVYFASRDGWVTKYDLWNLKV--VAEVRAGLNTRNL 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 274 DTSKykgyEDKYAIAGAYWPPQFTIMKGDTLEPIKIVATRgftvDTQEYHPepRVASIVASHFKPEFVVNVKETGKILMV 353
Cdd:cd20777   111 AVSS----DGRYVAVANYLPHTLVLLDARDLSLLKVIPAA----DAQGRSS--RVSAVYDAPPRRSFVVALKDVPELWEL 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 354 NY-KDLDN--------------------LEVTEIGAARFLHDGGWDSTKRYFLVAANQSNKIAVVDAKEGELEKLVDVGK 412
Cdd:cd20777   181 SYdEGADPvpiglvhdflyeegaaspgfFAPRRIALPAPLDDFFFDPDYRNLLGASRQGGGGQVIDLDVGRVIASLPLSG 260

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 413 IPHPGRGANFIDPKfGPVWATGHLGDDTIALIGTDkekhkanAWKVVRTLKGQGGGsLFIKTHPKSKNLWVDTALNPNAe 492
Cdd:cd20777   261 MPHLGSGIYWKRDG-RRVMATPNLSRGVISVIDLQ-------TWAIVKEIPTPGPG-FFMRSHENSPYAWADVFMGPKR- 330

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 493 isQSVAVFDIANLdkpyQVVK-IAEMAGlgegpKRVVQPEYNNKGDEVWFSVWNgktQESAIVVVDDKTrkLKTVikdKR 571
Cdd:cd20777   331 --DKLHLIDKQTL----EIVKtLRPEPG-----KTAAHVEFTRDGRYALASVWE---DDGALIVYDAHT--LKEV---KR 391

                         410
                  ....*....|....
gi 1048813845 572 LIT--PTGKFNVYN 583
Cdd:cd20777   392 LPMnkPSGKYNVWN 405
8prop_hemeD1_cyt_cd1-like cd20784
cytochrome cd1 nitrate reductase eight-bladed heme d1-binding beta-propeller domain and ...
 163-583 1.20e-23

cytochrome cd1 nitrate reductase eight-bladed heme d1-binding beta-propeller domain and similar proteins; Cytochrome cd1 (cyt cd1) nitrite reductase catalyzes in vitro the reduction of molecular oxygen to water and the reduction of nitrite to nitric oxide). It is a dimer of two identical subunits of 60 kDa, each containing one c and one d1 heme group. The c heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The d1 heme is the site where nitrite, and oxygen reduction occur. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis.


Pssm-ID: 467728 [Multi-domain]  Cd Length: 367  Bit Score: 102.70  E-value: 1.20e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 163 PEFGMKEMKDTWKVLvapdKRPKKKLNNINLANLFSVTLRDSGEVALIDGDtkKIVNIVKTGyAVHIS-RTSASGRYLYV 241
Cdd:cd20784     2 IRWSKEDIKKSITIF----NDKPKPLEIKDIENITLVVERGGGKVWVMEGF--RVLDKFDFG-NVHGGiKFSPSGKKIYV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 242 IGRDAKINLIDLWMEKPdnVAEIKIGLEARSVDTSKykgyEDKYAIAGAYWPPQFTIMKGDTLEPIKIVATRGftvdtqe 321
Cdd:cd20784    75 PSRDGWIGKYDLKEGRE--TGKVRACINLRNIALSR----DGKYLAAACLLPENLVILDTKTLKPVKVIKLDG------- 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 322 yhpepRVASIVASHFKPEFVVNVKETGKILMVNYKDLdnlEVTEIGAARFLHDGGWDSTKRYFLVAANQSNKIAVVDAKE 401
Cdd:cd20784   142 -----KISAVYELYSKDKAIFTFRDKPKLGFLDTKTL---KIEYIKIKEPFEDFFIDPFEEYIIGTSRKGKKLYVYSLKD 213

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 402 GELEKLVDVGKIPHPGRGANFIDP-KFgpVWATGHLGDDTIALIgtdkekhKANAWKVVRTLKGQGGGsLFIKTHPKSKN 480
Cdd:cd20784   214 LKKVFEHKMEGMPHLFSATFWYKKgKF--YFATPHIKKPYVSIW-------KMYDWKFVKEIDLGGDG-FFVRTHPKTPY 283

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 481 LWVDTAlnpnaeiSQSVAVFDianlDKPYQVVKIAEMAGlgegpKRVVQPEYNNKGDEVWFSVWNgktQESAIVVVDDKT 560
Cdd:cd20784   284 LWVDNG-------TDKLVLID----KKDLSVKKITPPKG-----KKAIHTEFSGDGKYAYVSIYE---KDGALVVYDTFT 344

                         410       420
                  ....*....|....*....|...
gi 1048813845 561 RKLKTVIKDKRlitPTGKFNVYN 583
Cdd:cd20784   345 LKELKRYPANI---PVGKYNFVN 364
8prop_hemeD1_NirF cd20778
eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NirF; ...
 193-579 8.81e-18

eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NirF; Denitrification is a process that enables biofilm formation of the opportunistic human pathogen Pseudomonas aeruginosa, making it more resilient to antibiotics and highly adaptable to different habitats. During denitrification, nitrate (Nar), nitrite (Nir), nitric oxide (Nor), and nitrous oxide (Nos) reductases catalyze the reaction cascade of NO3- -> NO2- -> NO -> N2O -> N2. The integral membrane proteins NorC, NorB, and NosR form the core assembly platform that binds the nitrate reductase NarGHI and the periplasmic cytochrome cd1 (nitrite reductase) NirS via its maturation factor NirF. The nirFDLGHJE genes encode proteins required for heme d1 biosynthesis. NirS, NirF, and NirN, the monomeric dihydro-heme d1 dehydrogenase form a stable complex during nitrite reductase maturation. The nitrite reductase NirS is bound to the denitrification supercomplex via NorB, while the electron donor system NirM and the enzyme maturation machinery NirN-NirF-NirQ, interacting with NirS, are bound via NorC.


Pssm-ID: 467722 [Multi-domain]  Cd Length: 381  Bit Score: 85.41  E-value: 8.81e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 193 LANLFSVTLRDSGEVALIDGDTKKIVNIVkTGYAVHISRT---SASGRYLYVIGRDAKINLIDLWMEKPdnVAEIK---- 265
Cdd:cd20778    17 TGALGVVVEREAGSVFVVDRSKHESLGRI-EGLGNLSHATmvfSRDGRYAYVIGRDGGLSKVDLLTLKV--VARVKqsgn 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 266 -IGLeARSVDtskykgyeDKYAIAGAYWPPQFTIMKGDTLEPIK-IVATRGftvdtqEYHPEPRVASIVAshfKPE--FV 341
Cdd:cd20778    94 sIGG-AISQD--------GRYVAVANYDPGGVKILDADTLKVLAdIPAGSK------GGGQRSRVVGLVD---APGnrFI 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 342 VNVKETGKILMVNYKDLDNLEVTE-IGAARFLHDGGWDSTKRYFLVAANQSNKIAVVDAKEGELEKLVdvgKIPHPGRGa 420
Cdd:cd20778   156 FSLMDADEIWVLDASDPDFPVVKKfKDIGRMPYDALITPDGRYYIAGLFNSDGVGLLDLWKPERGVRR---ILLDYGKG- 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 421 nfiDPKFgPVWATGHLG-----DDTIALIGTDKEK---HKANAWKVVRT--LKGQgggSLFIKTHPKSKNLWVDTALNPN 490
Cdd:cd20778   232 ---EEKL-PVYKMPHLEgwavaGDKAFVPAVGEHRvlvYDTNDWKFIKSipLAGQ---PVFAVARPDGRYVWVNFSGPDN 304

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 491 AeisqSVAVFDIANLdkpyQVVKIAEMaglgegPKRVVQPEYNNKGDEVWFSVwngkTQESAIVVVDDKTRKLktvIKDK 570
Cdd:cd20778   305 D----TVQVIDTKTL----KVVKTLEP------GKRVLHMEFTPRGEAVYISV----NDDNKVVVYDTRTFRE---IKEV 363


                  ....*....
gi 1048813845 571 RLITPTGKF 579
Cdd:cd20778   364 PAKKPSGIF 372
CccA COG2010
Cytochrome c, mono- and diheme variants [Energy production and conversion];
68-161 8.86e-17

Cytochrome c, mono- and diheme variants [Energy production and conversion];


Pssm-ID: 441613 [Multi-domain]  Cd Length: 169  Bit Score: 78.07  E-value: 8.86e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845  68 TVVSPKAPALTTAEFTRAKQIYFERCAGCHGVLRKGATGK--PLTPDITLKKGTDYLKVFINYGSPAG-MPNWGtsGDLT 144
Cdd:COG2010    75 AAAAADAPAADAEALARGKALYEQNCAACHGADGKGGLGAapNLTDDALYGGDPEALVETILNGRPGGaMPAFG--GQLS 152

                          90
                  ....*....|....*..
gi 1048813845 145 AEDVDLMARFLQHEPPT 161
Cdd:COG2010   153 DEEIAALAAYLRSLSGN 169
Cytochrome_CBB3 pfam13442
Cytochrome C oxidase, cbb3-type, subunit III;
80-155 2.20e-10

Cytochrome C oxidase, cbb3-type, subunit III;


Pssm-ID: 463879 [Multi-domain]  Cd Length: 67  Bit Score: 56.65  E-value: 2.20e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1048813845  80 AEFTRAKQIYFERCAGCHGvlrKGATGKPLTPDitlKKGTDYLKVFINYGsPAGMPNWGtsGDLTAEDVDLMARFL 155
Cdd:pfam13442   1 AAAAAGEALYAANCASCHG---TGGAGPSLAGR---ALPPEALVDIIRNG-KGAMPAFG--GDLSDEELEALAAYL 67
TsdA COG3258
Thiosulfate dehydrogenase TsdA, contains C-terminal cytochrome c domain [Inorganic ion ...
 52-162 2.69e-09

Thiosulfate dehydrogenase TsdA, contains C-terminal cytochrome c domain [Inorganic ion transport and metabolism];


Pssm-ID: 442489 [Multi-domain]  Cd Length: 216  Bit Score: 57.56  E-value: 2.69e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845  52 MRYKGAPVPIKPEEAETVVSPKAPALTTAEFTRAKQIYFERCAGCHGVL---RKGATGKPLTPDI------TLKKGTDYL 122
Cdd:COG3258    87 LRWLSRGLPVGVKLDGRGLPKLPKPAASADVERGKALYAERCASCHGADgegQGRADGQYGFPPLwggdsyNDGAGMARL 166

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1048813845 123 KVFINYGSPAGMPnWGTSGDLTAEDV-DLMARFLQHEPPTP 162
Cdd:COG3258   167 GTLADFIKGRNMP-LGKPGSLSDDEAwDVAAYVRSLPRPVP 206
YncE COG3391
DNA-binding beta-propeller fold protein YncE [General function prediction only];
357-505 2.40e-07

DNA-binding beta-propeller fold protein YncE [General function prediction only];


Pssm-ID: 442618 [Multi-domain]  Cd Length: 237  Bit Score: 52.00  E-value: 2.40e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 357 DLDNLEVT-EIGAARFLHDGGWDSTKRYFLVAANQSNKIAVVDAKEGELEKLVDVGKIPHpgrgANFIDPKFGPVWATGH 435
Cdd:COG3391    96 DLATGKVVaTIPVGGGPRGLAVDPDGGRLYVADSGNGRVSVIDTATGKVVATIPVGAGPH----GIAVDPDGKRLYVANS 171

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1048813845 436 lGDDTIALIGTdkeKHKANAWKVVRTLKGqGGGSLFIKTHPKSKNLWVDTALNPNAE-ISQSVAVFDIANL 505
Cdd:COG3391   172 -GSNTVSVIVS---VIDTATGKVVATIPV-GGGPVGVAVSPDGRRLYVANRGSNTSNgGSNTVSVIDLATL 237
CytC5 COG3245
Cytochrome c5 [Energy production and conversion];
61-148 1.07e-04

Cytochrome c5 [Energy production and conversion];


Pssm-ID: 442476 [Multi-domain]  Cd Length: 108  Bit Score: 41.59  E-value: 1.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845  61 IKPEEAETVVSPKAPAlttaEFTRAKQIYFERCAGCHGVlrkGATGKPLTPDIT-----LKKGTDYL-KVFIN-YGspaG 133
Cdd:COG3245    15 IAPVGAVALAAAAAAA----AARSGEAVYNATCAACHAT---GVAGAPKLGDKAawaprIAKGMDTLlKHAINgFN---A 84

                          90
                  ....*....|....*
gi 1048813845 134 MPNWGTSGDLTAEDV 148
Cdd:COG3245    85 MPPKGGCADLSDDEV 99
Cytochrom_C pfam00034
Cytochrome c; The Pfam entry does not include all Prosite members. The cytochrome 556 and ...
 84-157 2.25e-04

Cytochrome c; The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, pfam06181, has now been merged into this family.


Pssm-ID: 459641 [Multi-domain]  Cd Length: 89  Bit Score: 40.21  E-value: 2.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845  84 RAKQIYFERCAGCHGVLRKGA--------------TGKPLTPDITLKKGT-DYLKVFINYGSPAGMPNWgtsGDLTAEDV 148
Cdd:pfam00034   2 RGKKLFAANCAACHGVNGEGAgaggpdlaglaaryPGDALGAIRENKHAIgGGGVDRAGGPPGTGMPAF---DGLTDEEI 78


                  ....*....
gi 1048813845 149 DLMARFLQH 157
Cdd:pfam00034  79 ADLVAYLLS 87
YncE COG3391
DNA-binding beta-propeller fold protein YncE [General function prediction only];
367-561 7.50e-04

DNA-binding beta-propeller fold protein YncE [General function prediction only];


Pssm-ID: 442618 [Multi-domain]  Cd Length: 237  Bit Score: 41.60  E-value: 7.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 367 GAARFLHDGGWDSTKRYFLVAANQSNKIAVVDAKEGELEKLVDVGKIPHPGRganfIDPKFGPVWATGHlGDDTIALIGT 446
Cdd:COG3391    65 AAVADADGADAGADGRRLYVANSGSGRVSVIDLATGKVVATIPVGGGPRGLA----VDPDGGRLYVADS-GNGRVSVIDT 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1048813845 447 DKekhkanaWKVVRTLKGqGGGSLFIKTHPKSKNLWVdtALNPNAEISQSVAVFDIANLdkpyqvvKIAEMAGLGEGPKR 526
Cdd:COG3391   140 AT-------GKVVATIPV-GAGPHGIAVDPDGKRLYV--ANSGSNTVSVIVSVIDTATG-------KVVATIPVGGGPVG 202

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1048813845 527 VVqpeYNNKGDEVWFS-VWNGKT--QESAIVVVDDKTR 561
Cdd:COG3391   203 VA---VSPDGRRLYVAnRGSNTSngGSNTVSVIDLATL 237
 
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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