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Conserved domains on  [gi|490240521|ref|WP_004138782|]
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MULTISPECIES: Fe-S cluster assembly protein NifU [Klebsiella]

Protein Classification

similar to nitrogen fixation protein NifU( domain architecture ID 11493443)

protein similar to nitrogen fixation protein NifU

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NifU_proper TIGR02000
Fe-S cluster assembly protein NifU; Three different but partially homologous Fe-S cluster ...
 1-274 0e+00

Fe-S cluster assembly protein NifU; Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation]


:

Pssm-ID: 273921 [Multi-domain]  Cd Length: 290  Bit Score: 505.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521    1 MWNYSEKVKDHFFNPRNARVVDNANAVGDVGSLSCGDALRLMLRVDPQSEIIEEAGFQTFGCGSAIASSSALTELIIGHT 80
Cdd:TIGR02000   1 MWDYTDKVKEHFYNPKNAGVVEDANAVGEVGSISCGDALRLMLKVDPESDKIVDAGFQTFGCGSAIASSSALTEMIKGLT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521   81 LAEAGQITNQQIADYLDGLPPEKMHCSVMGQEALRAAIANFRGESLEEEHDEGKLICKCFGVDEGHIRRAVQNNGLTTLA 160
Cdd:TIGR02000  81 LDEALKVSNQDIADYLGGLPPEKMHCSVMGQEALEAAIANYRGEPLEDDHDEGALVCKCFGVDENMVRRAVIENDLTTLE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521  161 EVINYTKAGGGCTSCHEKIELALAEILAQQPQTTPAVASGKDP----------------HWQSVVDTIAELRPHIQADGG 224
Cdd:TIGR02000 161 EVTNYTKAGGGCGSCHEKIEDVLKEVLANKGATNPANAGGSKPtnkpnsgqkrpltnvqRIQLIQKVLEEVRPVLQADGG 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 490240521  225 DMALLSVTNHQVTVSLSGSCSGCMMTDMTLAWLQQKLMERTGCYMEVVAA 274
Cdd:TIGR02000 241 DVELYDVDGKIVYVVLTGACSGCSMSTMTLKGIQQRLRERLGEFVVVEAV 290
 
Name Accession Description Interval E-value
NifU_proper TIGR02000
Fe-S cluster assembly protein NifU; Three different but partially homologous Fe-S cluster ...
 1-274 0e+00

Fe-S cluster assembly protein NifU; Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation]


Pssm-ID: 273921 [Multi-domain]  Cd Length: 290  Bit Score: 505.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521    1 MWNYSEKVKDHFFNPRNARVVDNANAVGDVGSLSCGDALRLMLRVDPQSEIIEEAGFQTFGCGSAIASSSALTELIIGHT 80
Cdd:TIGR02000   1 MWDYTDKVKEHFYNPKNAGVVEDANAVGEVGSISCGDALRLMLKVDPESDKIVDAGFQTFGCGSAIASSSALTEMIKGLT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521   81 LAEAGQITNQQIADYLDGLPPEKMHCSVMGQEALRAAIANFRGESLEEEHDEGKLICKCFGVDEGHIRRAVQNNGLTTLA 160
Cdd:TIGR02000  81 LDEALKVSNQDIADYLGGLPPEKMHCSVMGQEALEAAIANYRGEPLEDDHDEGALVCKCFGVDENMVRRAVIENDLTTLE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521  161 EVINYTKAGGGCTSCHEKIELALAEILAQQPQTTPAVASGKDP----------------HWQSVVDTIAELRPHIQADGG 224
Cdd:TIGR02000 161 EVTNYTKAGGGCGSCHEKIEDVLKEVLANKGATNPANAGGSKPtnkpnsgqkrpltnvqRIQLIQKVLEEVRPVLQADGG 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 490240521  225 DMALLSVTNHQVTVSLSGSCSGCMMTDMTLAWLQQKLMERTGCYMEVVAA 274
Cdd:TIGR02000 241 DVELYDVDGKIVYVVLTGACSGCSMSTMTLKGIQQRLRERLGEFVVVEAV 290
NifU_N pfam01592
NifU-like N terminal domain; This domain is found in NifU in combination with pfam01106. This ...
 4-123 1.88e-57

NifU-like N terminal domain; This domain is found in NifU in combination with pfam01106. This domain is found on isolated in several bacterial species. The nif genes are responsible for nitrogen fixation. However this domain is found in bacteria that do not fix nitrogen, so it may have a broader significance in the cell than nitrogen fixation. These proteins appear to be scaffold proteins for iron-sulfur clusters.


Pssm-ID: 426336  Cd Length: 127  Bit Score: 179.91  E-value: 1.88e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521    4 YSEKVKDHFFNPRNARVVDNANA-VGDVGSLSCGDALRLMLRVDPQSEIIEEAGFQTFGCGSAIASSSALTELIIGHTLA 82
Cdd:pfam01592   2 YTDKVLDHYKNPRNVGVLEDADAgVGDVGNPACGDAMRLQIKVDESTDRIEDAKFKTFGCGSAIASSSMLTELVKGKTIE 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 490240521   83 EAGQITNQQIADYLDGLPPEKMHCSVMGQEALRAAIANFRG 123
Cdd:pfam01592  82 EALKITNTDIAEELGGLPPVKMHCSVLADDALKAAIADYPG 122
IscU COG0822
Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, ...
 2-124 3.61e-47

Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440584  Cd Length: 128  Bit Score: 153.45  E-value: 3.61e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521   2 WNYSEKVKDHFFNPRNARVVDNANAVGDVGSLSCGDALRLMLRVDPqsEIIEEAGFQTFGCGSAIASSSALTELIIGHTL 81
Cdd:COG0822    4 DLYSEKILDHAKNPRNVGELEDADGSGEGGNPLCGDTVTLYLKVDD--GRIEDAKFEGFGCAISQASASMLTELVKGKTL 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 490240521  82 AEAGQITNQ--QIADyLDGLP--PEKMHCSVMGQEALRAAIANFRGE 124
Cdd:COG0822   82 EEALALTDEfgDLAA-LGGLPkfPARVKCALLAWDALKAALADYRAK 127
IscU_like cd06664
Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU ...
 4-117 1.38e-40

Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.


Pssm-ID: 143480  Cd Length: 123  Bit Score: 136.61  E-value: 1.38e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521   4 YSEKVKDHFFNPRNARVVDNANAVGDVGSLSCGDALRLMLRVDPqsEIIEEAGFQTFGCGSAIASSSALTELIIGHTLAE 83
Cdd:cd06664    2 YSEIILDHYRNPRNVGRLEDADGTGEVGNPLCGDEITLYLKVED--GRITDAKFQGFGCAISIASASLLTELIKGKTLDE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 490240521  84 AGQITNQQIADYLD----------GLPPEKMHCSVMGQEALRAA 117
Cdd:cd06664   80 ALKLLNKDIAMLDGkeelaalagvGLPPARIHCALLAWKALKAA 123
PRK14989 PRK14989
nitrite reductase subunit NirD; Provisional
 136-190 3.75e-05

nitrite reductase subunit NirD; Provisional


Pssm-ID: 184951 [Multi-domain]  Cd Length: 847  Bit Score: 44.72  E-value: 3.75e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490240521 136 ICKCFGVDEGHIRRAVqNNGLTTLAEVINYTKAGGGCTSCHEKIELALAEILAQQ 190
Cdd:PRK14989 424 ICSCFDVTKGDLIAAI-NKGCHTVAALKAETKAGTGCGGCIPLVTQVLNAELAKQ 477
 
Name Accession Description Interval E-value
NifU_proper TIGR02000
Fe-S cluster assembly protein NifU; Three different but partially homologous Fe-S cluster ...
 1-274 0e+00

Fe-S cluster assembly protein NifU; Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation]


Pssm-ID: 273921 [Multi-domain]  Cd Length: 290  Bit Score: 505.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521    1 MWNYSEKVKDHFFNPRNARVVDNANAVGDVGSLSCGDALRLMLRVDPQSEIIEEAGFQTFGCGSAIASSSALTELIIGHT 80
Cdd:TIGR02000   1 MWDYTDKVKEHFYNPKNAGVVEDANAVGEVGSISCGDALRLMLKVDPESDKIVDAGFQTFGCGSAIASSSALTEMIKGLT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521   81 LAEAGQITNQQIADYLDGLPPEKMHCSVMGQEALRAAIANFRGESLEEEHDEGKLICKCFGVDEGHIRRAVQNNGLTTLA 160
Cdd:TIGR02000  81 LDEALKVSNQDIADYLGGLPPEKMHCSVMGQEALEAAIANYRGEPLEDDHDEGALVCKCFGVDENMVRRAVIENDLTTLE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521  161 EVINYTKAGGGCTSCHEKIELALAEILAQQPQTTPAVASGKDP----------------HWQSVVDTIAELRPHIQADGG 224
Cdd:TIGR02000 161 EVTNYTKAGGGCGSCHEKIEDVLKEVLANKGATNPANAGGSKPtnkpnsgqkrpltnvqRIQLIQKVLEEVRPVLQADGG 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 490240521  225 DMALLSVTNHQVTVSLSGSCSGCMMTDMTLAWLQQKLMERTGCYMEVVAA 274
Cdd:TIGR02000 241 DVELYDVDGKIVYVVLTGACSGCSMSTMTLKGIQQRLRERLGEFVVVEAV 290
NifU_N pfam01592
NifU-like N terminal domain; This domain is found in NifU in combination with pfam01106. This ...
 4-123 1.88e-57

NifU-like N terminal domain; This domain is found in NifU in combination with pfam01106. This domain is found on isolated in several bacterial species. The nif genes are responsible for nitrogen fixation. However this domain is found in bacteria that do not fix nitrogen, so it may have a broader significance in the cell than nitrogen fixation. These proteins appear to be scaffold proteins for iron-sulfur clusters.


Pssm-ID: 426336  Cd Length: 127  Bit Score: 179.91  E-value: 1.88e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521    4 YSEKVKDHFFNPRNARVVDNANA-VGDVGSLSCGDALRLMLRVDPQSEIIEEAGFQTFGCGSAIASSSALTELIIGHTLA 82
Cdd:pfam01592   2 YTDKVLDHYKNPRNVGVLEDADAgVGDVGNPACGDAMRLQIKVDESTDRIEDAKFKTFGCGSAIASSSMLTELVKGKTIE 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 490240521   83 EAGQITNQQIADYLDGLPPEKMHCSVMGQEALRAAIANFRG 123
Cdd:pfam01592  82 EALKITNTDIAEELGGLPPVKMHCSVLADDALKAAIADYPG 122
NifU_clost TIGR03419
FeS cluster assembly scaffold protein NifU, Clostridium type; NifU and NifS form a pair of ...
 4-122 2.26e-51

FeS cluster assembly scaffold protein NifU, Clostridium type; NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 132460  Cd Length: 121  Bit Score: 164.14  E-value: 2.26e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521    4 YSEKVKDHFFNPRNARVVDNANAVGDVGSLSCGDALRLMLRVDpqSEIIEEAGFQTFGCGSAIASSSALTELIIGHTLAE 83
Cdd:TIGR03419   1 YSEKVMDHFMNPRNVGEIENADGVGEVGNPKCGDIMKIFLKVE--DDIIKDVKFKTFGCGAAIASSSMATEMIKGKTLEE 78

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 490240521   84 AGQITNQQIADYLDGLPPEKMHCSVMGQEALRAAIANFR 122
Cdd:TIGR03419  79 AWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYR 117
IscU COG0822
Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, ...
 2-124 3.61e-47

Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440584  Cd Length: 128  Bit Score: 153.45  E-value: 3.61e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521   2 WNYSEKVKDHFFNPRNARVVDNANAVGDVGSLSCGDALRLMLRVDPqsEIIEEAGFQTFGCGSAIASSSALTELIIGHTL 81
Cdd:COG0822    4 DLYSEKILDHAKNPRNVGELEDADGSGEGGNPLCGDTVTLYLKVDD--GRIEDAKFEGFGCAISQASASMLTELVKGKTL 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 490240521  82 AEAGQITNQ--QIADyLDGLP--PEKMHCSVMGQEALRAAIANFRGE 124
Cdd:COG0822   82 EEALALTDEfgDLAA-LGGLPkfPARVKCALLAWDALKAALADYRAK 127
IscU_like cd06664
Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU ...
 4-117 1.38e-40

Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.


Pssm-ID: 143480  Cd Length: 123  Bit Score: 136.61  E-value: 1.38e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521   4 YSEKVKDHFFNPRNARVVDNANAVGDVGSLSCGDALRLMLRVDPqsEIIEEAGFQTFGCGSAIASSSALTELIIGHTLAE 83
Cdd:cd06664    2 YSEIILDHYRNPRNVGRLEDADGTGEVGNPLCGDEITLYLKVED--GRITDAKFQGFGCAISIASASLLTELIKGKTLDE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 490240521  84 AGQITNQQIADYLD----------GLPPEKMHCSVMGQEALRAA 117
Cdd:cd06664   80 ALKLLNKDIAMLDGkeelaalagvGLPPARIHCALLAWKALKAA 123
NifU_Fer2_BFD-like cd19947
bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of nitrogen fixation ...
 132-186 1.79e-26

bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of nitrogen fixation protein NifU and similar proteins; This family includes the BFD-like [2Fe-2S]-binding domain of Azotobacter vinelandii and Klebsiella pneumoniae nitrogen fixation protein NifU. NifU binds one Fe cation per subunit and one [2Fe-2S] cluster per subunit, and is involved in the formation or repair of [Fe-S] clusters present in iron-sulfur proteins. The BFD-like [2Fe-2S]-binding domain is found in a variety of other proteins including bacterioferritin-associated ferredoxin (BFD), the large subunit of NADH-dependent nitrite reductase, and Cu+ chaperone CopZ. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport.


Pssm-ID: 381080 [Multi-domain]  Cd Length: 55  Bit Score: 98.12  E-value: 1.79e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490240521 132 EGKLICKCFGVDEGHIRRAVQNNGLTTLAEVINYTKAGGGCTSCHEKIELALAEI 186
Cdd:cd19947    1 EGAIVCKCFGVTEVMIERAIRENNLTTVEDVTNYTKAGGGCGSCHEKIEDILDRV 55
NifU COG0694
Fe-S cluster biogenesis protein NfuA, 4Fe-4S-binding domain [Posttranslational modification, ...
 109-273 4.69e-18

Fe-S cluster biogenesis protein NfuA, 4Fe-4S-binding domain [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440458 [Multi-domain]  Cd Length: 176  Bit Score: 79.31  E-value: 4.69e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521 109 MGQEALRAAIANFRGESLEEEHDEGKLICKCFGVDEGHIRRAVQNNGLTTLAEVINYTKAGGGCTSCHEKIELALAEILA 188
Cdd:COG0694    1 AQAAALKLLPEEPGGELIRGEVAAPGAPAAAALLLAEAPEVEEDDDVVVVAAVFVAVTDELSGPLLELAIIDAILAAAGG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521 189 QQPQTTPAVASGKDPHWQSVVDT----------IAELRPHIQADGGDMALLSVTNHQVTVSLSGSCSGCMMTDMTL-AWL 257
Cdd:COG0694   81 QLTLAAPDAAVAEVLSFHALTDAeleerieevlDEEIRPALASDGGDIELVDVEDGVVYVRLGGACSGCPSSTMTLkNGI 160

                        170
                 ....*....|....*.
gi 490240521 258 QQKLMERTGCYMEVVA 273
Cdd:COG0694  161 ERALKERVPEVKEVEA 176
NifU pfam01106
NifU-like domain; This is an alignment of the carboxy-terminal domain. This is the only common ...
 206-272 1.19e-17

NifU-like domain; This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown.


Pssm-ID: 460066 [Multi-domain]  Cd Length: 67  Bit Score: 75.17  E-value: 1.19e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490240521  206 QSVVDTiaELRPHIQADGGDMALLSVTNHQVTVSLSGSCSGCMMTDMTL-AWLQQKLMERTGCYMEVV 272
Cdd:pfam01106   2 EEVLEE--EIRPALQADGGDIELVDVDDGVVYVRLQGACSGCPSSTMTLkNGIEQALKEKVPEVKRVE 67
Fer2_BFD pfam04324
BFD-like [2Fe-2S] binding domain; The two Fe ions are each coordinated by two conserved ...
 135-189 1.61e-15

BFD-like [2Fe-2S] binding domain; The two Fe ions are each coordinated by two conserved cysteine residues. This domain occurs alone in small proteins such as Bacterioferritin-associated ferredoxin (BFD). The function of BFD is not known, but it may may be a general redox and/or regulatory component involved in the iron storage or mobilization functions of bacterioferritin in bacteria. This domain is also found in nitrate reductase proteins in association with Nitrite and sulphite reductase 4Fe-4S domain (pfam01077), Nitrite/Sulfite reductase ferredoxin-like half domain (pfam03460) and Pyridine nucleotide-disulphide oxidoreductase (pfam00070). It is also found in NifU nitrogen fixation proteins, in association with NifU-like N terminal domain (pfam01592) and NifU-like domain (pfam01106).


Pssm-ID: 461261 [Multi-domain]  Cd Length: 50  Bit Score: 68.71  E-value: 1.61e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 490240521  135 LICKCFGVDEGHIRRAVQNNgLTTLAEVINYTKAGGGCTSCHEKIElalaEILAQ 189
Cdd:pfam04324   1 IVCRCFGVTDGEIRDAIREG-LTTVEEVKRRTKAGTGCGSCRPAIE----EILAE 50
SUF_scaf_2 TIGR01994
SUF system FeS assembly protein, NifU family; Three iron-sulfur cluster assembly systems are ...
 4-119 7.37e-15

SUF system FeS assembly protein, NifU family; Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 273918  Cd Length: 137  Bit Score: 69.66  E-value: 7.37e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521    4 YSEKVKDHFFNPRNARVVDNANAVGDVGSLSCGDALRLMLRVDpqSEIIEEAGFQTFGCGSAIASSSALTELIIGHTLAE 83
Cdd:TIGR01994   5 YRQVILDHYKNPRHRGKLEDATVQERGHNPTCGDEITLTVKLE--GDRIEDIAFEGEGCSISQASASMMTELIKGKTVEE 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 490240521   84 A------------GQITNQQIADYLDGLP-------PEKMHCSVMGQEALRAAIA 119
Cdd:TIGR01994  83 AlslveafsemiqGQETDEDEEKLGDAEAlagvakfPARIKCATLAWKALERALA 137
Fer2_BFD-like cd19942
[2Fe-2S]-binding domain of bacterioferritin-associated ferredoxin (BFD) and related proteins; ...
 134-180 9.23e-11

[2Fe-2S]-binding domain of bacterioferritin-associated ferredoxin (BFD) and related proteins; The BFD-like [2Fe-2S]-binding domain comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. The Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport. BFD-like [2Fe-2S]-binding domains are found in proteins such as bacterioferritin-associated ferredoxin (BFD), the large subunit of NADH-dependent nitrite reductase, Cu+ chaperone CopZ, anaerobic glycerol 3-phosphate dehydrogenase subunit A, hydrogen cyanide synthase subunit B, nitrogen fixation protein NifU, prokaryotic assimilatory nitrate reductase catalytic subunit NasA, and archaeal proline dehydrogenase PDH1. This superfamily also includes uncharacterized proteins having an N-terminal BFD-like [2Fe-2S]-binding domain and a C-terminal domain belonging to the Ni,Fe-hydrogenase I small subunit family.


Pssm-ID: 381075 [Multi-domain]  Cd Length: 49  Bit Score: 55.91  E-value: 9.23e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 490240521 134 KLICKCFGVDEGHIRRAVQNNGLTTLAEVINYTKAGGGCTSCHEKIE 180
Cdd:cd19942    1 ALVCECFAVTEKELREAIRKGGLKTVEELLTGTGAGGGCGVCHPHVA 47
NasA-like_Fer2_BFD-like cd19948
bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain at the C-terminus of ...
 133-185 3.94e-10

bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain at the C-terminus of prokaryotic assimilatory nitrate reductase catalytic subunit NasA and similar proteins; The BFD-like [2Fe-2S]-binding domain described in this family is found at the C-terminus of prokaryotic assimilatory nitrate reductase catalytic subunit (NasA) such as Rhodobacter capsulatus E1F1 NasA. Nitrate reductase catalyzes the reduction of nitrate to nitrite, the first step of nitrate assimilation. R. capsulatus E1F1 nitrate reductase is composed of this NasA subunit and a small diaphorase subunit with FAD. Note that this [2Fe-2S]-binding domain is not always present; for example, it is absent from the characterized haloaechean Haloferax mediterranei NasA; both, however, have an [4Fe-4S] binding domain at their N-terminus. The BFD-like [2Fe-2S]-binding domain is found in a variety of other proteins including bacterioferritin-associated ferredoxin (BFD), the large subunit of NADH-dependent nitrite reductase, and Cu+ chaperone CopZ. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport.


Pssm-ID: 381081 [Multi-domain]  Cd Length: 53  Bit Score: 54.45  E-value: 3.94e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 490240521 133 GKLICKCFGVDEGHIRRAVQNNGLTTLAEVINYTKAGGGCTSCHEKIELALAE 185
Cdd:cd19948    1 GRTVCACFSVGENTIRRAIADNGLTSVAQVGTCLKAGTNCGSCVPEIQKLLSE 53
NirB_Fer2_BFD-like_1 cd19943
first bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of the large ...
 136-175 1.74e-09

first bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of the large subunit of the NADH-dependent nitrite reductase; The NADH-dependent nitrite reductase (NirBD) complex comprises a large and a small subunit, and is also known as nitrite reductase (reduced nicotinamide adenine dinucleotide), NADH-nitrite oxidoreductase, and assimilatory nitrite reductase. NirBD uses NADH as electron donor, and FAD, iron-sulfur cluster, and siroheme cofactors, all embedded in the large subunit NirB to catalyze the 6-electron reduction of nitrite to ammonium. NirBD plays a role in regulating nitric oxide homeostasis in Streptomyces coelicolor. In addition to NirB, the BFD-like [2Fe-2S]-binding domain is found in a variety of proteins including bacterioferritin-associated ferredoxin (BFD) and Cu+ chaperone CopZ. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport.


Pssm-ID: 381076 [Multi-domain]  Cd Length: 53  Bit Score: 52.62  E-value: 1.74e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 490240521 136 ICKCFGVDEGHIRRAVQNNGLTTLAEVINYTKAGGGCTSC 175
Cdd:cd19943    6 VCGCNGVSKGAIVQAIQEKGLTTLDEVKACTKASTSCGGC 45
Bfd COG2906
Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism];
136-188 5.82e-09

Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism];


Pssm-ID: 442150 [Multi-domain]  Cd Length: 54  Bit Score: 50.97  E-value: 5.82e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 490240521 136 ICKCFGVDEGHIRRAVQNnGLTTLAEVINYTKAGGGCTSCHEKIELALAEILA 188
Cdd:COG2906    3 VCLCNGVTDRQIRAAIAE-GATSLEELRAALGAGTQCGSCVPEARELLAEALA 54
nitri_red_nirB TIGR02374
nitrite reductase [NAD(P)H], large subunit; [Central intermediary metabolism, Nitrogen ...
 136-216 5.92e-08

nitrite reductase [NAD(P)H], large subunit; [Central intermediary metabolism, Nitrogen metabolism]


Pssm-ID: 162827 [Multi-domain]  Cd Length: 785  Bit Score: 53.29  E-value: 5.92e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490240521  136 ICKCFGVDEGHIRRAVQNNGLTTLAEVINYTKAGGGCTSCHEKIELAL-AEILAQQPQTTPAVASGKDphwQSVVDTIAE 214
Cdd:TIGR02374 412 ICSCNTVTKGAIIDAIHTGSCTTVEELKACTKAGTSCGGCKPLVEQLLrAELNSQYTASTPALCECTD---FSRDELFEE 488


                  ..
gi 490240521  215 LR 216
Cdd:TIGR02374 489 IQ 490
CopZ-like_Fer2_BFD-like cd10141
bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of Archaeoglobus ...
 134-178 5.15e-07

bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of Archaeoglobus fulgidus CopZ, and similar proteins; Archaeoglobus fulgidus CopZ is a fusion of a redox-active domain (containing a mononuclear metal center and an [2Fe-2S] cluster) with a CXXC-containing copper-binding domain. It is a soluble Cu+ chaperone which delivers cytoplasmic Cu+ to the transmembrane metal-binding sites in the Cu+-ATPase CopA; CopA couples the hydrolysis of ATP to the efflux of cytoplasmic Cu+. In addition to CopZ, the BFD-like [2Fe-2S]-binding domain is found in a variety of other proteins including bacterioferritin-associated ferredoxin (BFD), and the large subunit of NADH-dependent nitrite reductase. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport.


Pssm-ID: 381074 [Multi-domain]  Cd Length: 58  Bit Score: 45.68  E-value: 5.15e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 490240521 134 KLICKCFGVDEGHIRRAVQNNGLTTLAEVINYTKAGGGctSCHEK 178
Cdd:cd10141    2 KPVCYCFGVTEEDIIEAVAETGATTVEEIRATGKAGRC--ACEVN 44
PRK14989 PRK14989
nitrite reductase subunit NirD; Provisional
 136-190 3.75e-05

nitrite reductase subunit NirD; Provisional


Pssm-ID: 184951 [Multi-domain]  Cd Length: 847  Bit Score: 44.72  E-value: 3.75e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490240521 136 ICKCFGVDEGHIRRAVqNNGLTTLAEVINYTKAGGGCTSCHEKIELALAEILAQQ 190
Cdd:PRK14989 424 ICSCFDVTKGDLIAAI-NKGCHTVAALKAETKAGTGCGGCIPLVTQVLNAELAKQ 477
NirB_Fer2_BFD-like_2 cd19944
second bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of the large ...
 136-175 3.46e-04

second bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of the large subunit of the NADH-dependent nitrite reductase; The NADH-dependent nitrite reductase (NirBD) complex comprises a large (NirB) and a small (NirD) subunit, and is also known as nitrite reductase (reduced nicotinamide adenine dinucleotide), NADH-nitrite oxidoreductase, and assimilatory nitrite reductase. NirBD uses NADH as electron donor, and FAD, iron-sulfur cluster, and siroheme cofactors, all embedded in the large subunit NirB to catalyze the 6-electron reduction of nitrite to ammonium. Some of the second [2Fe-2S]-binding domains, have one of the Cys residues replaced by a His residue, they may interact with non-Rieske NirD subunits. NirBD plays a role in regulating nitric oxide homeostasis in Streptomyces coelicolor. In addition to NirB, the BFD-like [2Fe-2S]-binding domain is found in a variety of proteins including bacterioferritin-associated ferredoxin (BFD) and Cu+ chaperone CopZ. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport.


Pssm-ID: 381077 [Multi-domain]  Cd Length: 52  Bit Score: 37.55  E-value: 3.46e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 490240521 136 ICKCFGVDEGHIRRAVQNNGLTTLAEVINY--TKAGGGCTSC 175
Cdd:cd19944    3 LCSCTDLSHDEVREAIQEHGLTSFEEVMAAlgWKTPDGCEKC 44
 
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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