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Conserved domains on  [gi|488156928|ref|WP_002228136|]
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MULTISPECIES: bacterioferritin-associated ferredoxin [Yersinia pseudotuberculosis complex]

Protein Classification

bacterioferritin-associated ferredoxin( domain architecture ID 10013545)

bacterioferritin-associated ferredoxin is a (2Fe-2S)-binding protein that may participate either in the release/delivery of iron from/to bacterioferritin (or other iron complexes), or in the iron-dependent regulation of bacterioferritin expression

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10509 PRK10509
bacterioferritin-associated ferredoxin; Provisional
 1-64 1.57e-34

bacterioferritin-associated ferredoxin; Provisional


:

Pssm-ID: 182506 [Multi-domain]  Cd Length: 64  Bit Score: 111.37  E-value: 1.57e-34
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488156928  1 MYVCLCNAVSDKVIRKAVRQHQPHTVKQLRQLVPIGSDCGKCIRQAREILIEELANIPEMNDVA 64
Cdd:PRK10509  1 MYVCLCNGVSDKKIRQAVRQFHPQSFQQLRKFVPVGNQCGKCIRAAREVMQDELMQMPEFKEIA 64
 
Name Accession Description Interval E-value
PRK10509 PRK10509
bacterioferritin-associated ferredoxin; Provisional
 1-64 1.57e-34

bacterioferritin-associated ferredoxin; Provisional


Pssm-ID: 182506 [Multi-domain]  Cd Length: 64  Bit Score: 111.37  E-value: 1.57e-34
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488156928  1 MYVCLCNAVSDKVIRKAVRQHQPHTVKQLRQLVPIGSDCGKCIRQAREILIEELANIPEMNDVA 64
Cdd:PRK10509  1 MYVCLCNGVSDKKIRQAVRQFHPQSFQQLRKFVPVGNQCGKCIRAAREVMQDELMQMPEFKEIA 64
Fer2_BFD cd19945
bacterioferritin-associated ferredoxin (BFD) [2Fe-2S]-binding domain; This family includes ...
 1-55 2.70e-19

bacterioferritin-associated ferredoxin (BFD) [2Fe-2S]-binding domain; This family includes Escherichia coli and Pseudomonas aeruginosa bacterioferritin-associated ferredoxin BFD which binds an [2Fe-2S] cluster and appears to interact with bacterioferritin (E. coli BFR/YheA and P. aeruginosa BfrB), a dynamic regulator of intracellular iron levels. It has been suggested that BFD and bacterioferritin form an electron transfer complex which may participate in the iron storage or iron immobilization functions of bacterioferritin. For Pseudomonas aeruginosa, it has been shown that mobilization of Fe3+ stored in BfrB requires interaction with BFD, which transfers electrons to reduce Fe3+ in the internal cavity of BfrB for subsequent release of Fe2+. The stability of BFD may be aided by an anion-binding site found within this domain. In addition to BFD, the BFD-like [2Fe-2S]-binding domain is found in a variety of proteins such as the large subunit of NADH-dependent nitrite reductase and the 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: 381078 [Multi-domain]  Cd Length: 54  Bit Score: 72.62  E-value: 2.70e-19
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 488156928  1 MYVCLCNAVSDKVIRKAVRQHqPHTVKQLRQLVPIGSDCGKCIRQAREILIEELA 55
Cdd:cd19945   1 MYVCLCNGITDKQIRQAVAQG-ATSLRELREQLGVGSQCGKCARMARQVLEEELA 54
Bfd COG2906
Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism];
1-55 1.17e-15

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


Pssm-ID: 442150 [Multi-domain]  Cd Length: 54  Bit Score: 63.30  E-value: 1.17e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 488156928  1 MYVCLCNAVSDKVIRKAVRQHqPHTVKQLRQLVPIGSDCGKCIRQAREILIEELA 55
Cdd:COG2906   1 MYVCLCNGVTDRQIRAAIAEG-ATSLEELRAALGAGTQCGSCVPEARELLAEALA 54
Fer2_BFD pfam04324
BFD-like [2Fe-2S] binding domain; The two Fe ions are each coordinated by two conserved ...
 2-52 6.29e-13

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: 56.39  E-value: 6.29e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 488156928   2 YVCLCNAVSDKVIRKAVRqHQPHTVKQLRQLVPIGSDCGKCIRQAREILIE 52
Cdd:pfam04324  1 IVCRCFGVTDGEIRDAIR-EGLTTVEEVKRRTKAGTGCGSCRPAIEEILAE 50
nitri_red_nirB TIGR02374
nitrite reductase [NAD(P)H], large subunit; [Central intermediary metabolism, Nitrogen ...
 3-55 6.81e-04

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


Pssm-ID: 162827 [Multi-domain]  Cd Length: 785  Bit Score: 35.57  E-value: 6.81e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 488156928    3 VCLCNAVSDKVIRKAVRQHQPHTVKQLRQLVPIGSDCGKCIRQAREILIEELA 55
Cdd:TIGR02374 412 ICSCNTVTKGAIIDAIHTGSCTTVEELKACTKAGTSCGGCKPLVEQLLRAELN 464
 
Name Accession Description Interval E-value
PRK10509 PRK10509
bacterioferritin-associated ferredoxin; Provisional
 1-64 1.57e-34

bacterioferritin-associated ferredoxin; Provisional


Pssm-ID: 182506 [Multi-domain]  Cd Length: 64  Bit Score: 111.37  E-value: 1.57e-34
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488156928  1 MYVCLCNAVSDKVIRKAVRQHQPHTVKQLRQLVPIGSDCGKCIRQAREILIEELANIPEMNDVA 64
Cdd:PRK10509  1 MYVCLCNGVSDKKIRQAVRQFHPQSFQQLRKFVPVGNQCGKCIRAAREVMQDELMQMPEFKEIA 64
Fer2_BFD cd19945
bacterioferritin-associated ferredoxin (BFD) [2Fe-2S]-binding domain; This family includes ...
 1-55 2.70e-19

bacterioferritin-associated ferredoxin (BFD) [2Fe-2S]-binding domain; This family includes Escherichia coli and Pseudomonas aeruginosa bacterioferritin-associated ferredoxin BFD which binds an [2Fe-2S] cluster and appears to interact with bacterioferritin (E. coli BFR/YheA and P. aeruginosa BfrB), a dynamic regulator of intracellular iron levels. It has been suggested that BFD and bacterioferritin form an electron transfer complex which may participate in the iron storage or iron immobilization functions of bacterioferritin. For Pseudomonas aeruginosa, it has been shown that mobilization of Fe3+ stored in BfrB requires interaction with BFD, which transfers electrons to reduce Fe3+ in the internal cavity of BfrB for subsequent release of Fe2+. The stability of BFD may be aided by an anion-binding site found within this domain. In addition to BFD, the BFD-like [2Fe-2S]-binding domain is found in a variety of proteins such as the large subunit of NADH-dependent nitrite reductase and the 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: 381078 [Multi-domain]  Cd Length: 54  Bit Score: 72.62  E-value: 2.70e-19
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 488156928  1 MYVCLCNAVSDKVIRKAVRQHqPHTVKQLRQLVPIGSDCGKCIRQAREILIEELA 55
Cdd:cd19945   1 MYVCLCNGITDKQIRQAVAQG-ATSLRELREQLGVGSQCGKCARMARQVLEEELA 54
Bfd COG2906
Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism];
1-55 1.17e-15

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


Pssm-ID: 442150 [Multi-domain]  Cd Length: 54  Bit Score: 63.30  E-value: 1.17e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 488156928  1 MYVCLCNAVSDKVIRKAVRQHqPHTVKQLRQLVPIGSDCGKCIRQAREILIEELA 55
Cdd:COG2906   1 MYVCLCNGVTDRQIRAAIAEG-ATSLEELRAALGAGTQCGSCVPEARELLAEALA 54
Fer2_BFD pfam04324
BFD-like [2Fe-2S] binding domain; The two Fe ions are each coordinated by two conserved ...
 2-52 6.29e-13

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: 56.39  E-value: 6.29e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 488156928   2 YVCLCNAVSDKVIRKAVRqHQPHTVKQLRQLVPIGSDCGKCIRQAREILIE 52
Cdd:pfam04324  1 IVCRCFGVTDGEIRDAIR-EGLTTVEEVKRRTKAGTGCGSCRPAIEEILAE 50
NirB_Fer2_BFD-like_1 cd19943
first bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of the large ...
 3-50 1.07e-06

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: 40.68  E-value: 1.07e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 488156928  3 VCLCNAVSDKVIRKAVRQHQPHTVKQLRQLVPIGSDCGKCIRQAREIL 50
Cdd:cd19943   6 VCGCNGVSKGAIVQAIQEKGLTTLDEVKACTKASTSCGGCTPLVEQLL 53
NifU_Fer2_BFD-like cd19947
bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of nitrogen fixation ...
 3-52 6.82e-06

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: 38.80  E-value: 6.82e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 488156928  3 VCLCNAVSDKVIRKAVRQHQPHTVKQLRQLVPIGSDCGKCIRQAREILIE 52
Cdd:cd19947   5 VCKCFGVTEVMIERAIRENNLTTVEDVTNYTKAGGGCGSCHEKIEDILDR 54
NasA-like_Fer2_BFD-like cd19948
bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain at the C-terminus of ...
 3-52 5.84e-05

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: 36.35  E-value: 5.84e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 488156928  3 VCLCNAVSDKVIRKAVRQHQPHTVKQLRQLVPIGSDCGKCIRQAREILIE 52
Cdd:cd19948   4 VCACFSVGENTIRRAIADNGLTSVAQVGTCLKAGTNCGSCVPEIQKLLSE 53
nitri_red_nirB TIGR02374
nitrite reductase [NAD(P)H], large subunit; [Central intermediary metabolism, Nitrogen ...
 3-55 6.81e-04

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


Pssm-ID: 162827 [Multi-domain]  Cd Length: 785  Bit Score: 35.57  E-value: 6.81e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 488156928    3 VCLCNAVSDKVIRKAVRQHQPHTVKQLRQLVPIGSDCGKCIRQAREILIEELA 55
Cdd:TIGR02374 412 ICSCNTVTKGAIIDAIHTGSCTTVEELKACTKAGTSCGGCKPLVEQLLRAELN 464
Fer2_BFD-like cd19942
[2Fe-2S]-binding domain of bacterioferritin-associated ferredoxin (BFD) and related proteins; ...
 1-43 1.59e-03

[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: 32.41  E-value: 1.59e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 488156928  1 MYVCLCNAVSDKVIRKAVRQHQPHTVKQLRQLVPIGSDCGKCI 43
Cdd:cd19942   1 ALVCECFAVTEKELREAIRKGGLKTVEELLTGTGAGGGCGVCH 43
 
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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