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Conserved domains on  [gi|951408741|ref|WP_057782781|]
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MULTISPECIES: SUF system NifU family Fe-S cluster assembly protein [Pediococcus]

Protein Classification

iron-sulfur cluster assembly scaffold protein( domain architecture ID 880)

iron-sulfur cluster assembly scaffold protein, similar to Thermotoga maritima IscU, on which IscS assembles Fe-S clusters

CATH:  3.90.1010.10
Gene Ontology:  GO:0016226|GO:0051536
PubMed:  15952888|15379587
SCOP:  4001402

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IscU_like super family cl00528
Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU ...
 6-143 1.73e-53

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.


The actual alignment was detected with superfamily member TIGR01994:

Pssm-ID: 444957  Cd Length: 137  Bit Score: 165.19  E-value: 1.73e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 951408741    6 LNQLYMAVVMDHASHPHHKLALPDATTSVELHNVSCGDDIRAFILMKDDKVQQVSFTGNGCTISQASASMMTDALAGLTK 85
Cdd:TIGR01994   1 LDSLYRQVILDHYKNPRHRGKLEDATVQERGHNPTCGDEITLTVKLEGDRIEDIAFEGEGCSISQASASMMTELIKGKTV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 951408741   86 TEAVAGCEAFFQLVMGKQIStKAKAWLGDAEILGSVAEFPARIKCATLAWHAAQEALE 143
Cdd:TIGR01994  81 EEALSLVEAFSEMIQGQETD-EDEEKLGDAEALAGVAKFPARIKCATLAWKALERALA 137
 
Name Accession Description Interval E-value
SUF_scaf_2 TIGR01994
SUF system FeS assembly protein, NifU family; Three iron-sulfur cluster assembly systems are ...
 6-143 1.73e-53

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: 165.19  E-value: 1.73e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 951408741    6 LNQLYMAVVMDHASHPHHKLALPDATTSVELHNVSCGDDIRAFILMKDDKVQQVSFTGNGCTISQASASMMTDALAGLTK 85
Cdd:TIGR01994   1 LDSLYRQVILDHYKNPRHRGKLEDATVQERGHNPTCGDEITLTVKLEGDRIEDIAFEGEGCSISQASASMMTELIKGKTV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 951408741   86 TEAVAGCEAFFQLVMGKQIStKAKAWLGDAEILGSVAEFPARIKCATLAWHAAQEALE 143
Cdd:TIGR01994  81 EEALSLVEAFSEMIQGQETD-EDEEKLGDAEALAGVAKFPARIKCATLAWKALERALA 137
IscU COG0822
Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, ...
 5-143 4.31e-46

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


Pssm-ID: 440584  Cd Length: 128  Bit Score: 146.14  E-value: 4.31e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 951408741   5 KLNQLYMAVVMDHASHPHHKLALPDATTSVELHNVSCGDDIRAFILMKDDKVQQVSFTGNGCTISQASASMMTDALAGLT 84
Cdd:COG0822    1 DLDDLYSEKILDHAKNPRNVGELEDADGSGEGGNPLCGDTVTLYLKVDDGRIEDAKFEGFGCAISQASASMLTELVKGKT 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 951408741  85 KTEAVAGCEAFfqlvmgkqistkakawlGDAEILGSVAEFPARIKCATLAWHAAQEALE 143
Cdd:COG0822   81 LEEALALTDEF-----------------GDLAALGGLPKFPARVKCALLAWDALKAALA 122
IscU_like cd06664
Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU ...
 9-141 1.36e-38

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: 126.98  E-value: 1.36e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 951408741   9 LYMAVVMDHASHPHHKLALPDATTSVELHNVSCGDDIRAFILMKDDKVQQVSFTGNGCTISQASASMMTDALAGLTKTEA 88
Cdd:cd06664    1 LYSEIILDHYRNPRNVGRLEDADGTGEVGNPLCGDEITLYLKVEDGRITDAKFQGFGCAISIASASLLTELIKGKTLDEA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 951408741  89 VAGCEAFFQLVMGKqistkakawlGDAEILGSVAEFPARIKCATLAWHAAQEA 141
Cdd:cd06664   81 LKLLNKDIAMLDGK----------EELAALAGVGLPPARIHCALLAWKALKAA 123
NifU_N pfam01592
NifU-like N terminal domain; This domain is found in NifU in combination with pfam01106. This ...
 9-131 1.26e-16

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: 70.90  E-value: 1.26e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 951408741    9 LYMAVVMDHASHPHHKLALPDATTSVELH-NVSCGDDIRAFILMKD--DKVQQVSFTGNGCTISQASASMMTDALAGLTK 85
Cdd:pfam01592   1 LYTDKVLDHYKNPRNVGVLEDADAGVGDVgNPACGDAMRLQIKVDEstDRIEDAKFKTFGCGSAIASSSMLTELVKGKTI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 951408741   86 TEAVA-GCEAFFQLVMGKQISTKAKAWLGDAEILGSVAEFPARIKCA 131
Cdd:pfam01592  81 EEALKiTNTDIAEELGGLPPVKMHCSVLADDALKAAIADYPGKNKCA 127
 
Name Accession Description Interval E-value
SUF_scaf_2 TIGR01994
SUF system FeS assembly protein, NifU family; Three iron-sulfur cluster assembly systems are ...
 6-143 1.73e-53

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: 165.19  E-value: 1.73e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 951408741    6 LNQLYMAVVMDHASHPHHKLALPDATTSVELHNVSCGDDIRAFILMKDDKVQQVSFTGNGCTISQASASMMTDALAGLTK 85
Cdd:TIGR01994   1 LDSLYRQVILDHYKNPRHRGKLEDATVQERGHNPTCGDEITLTVKLEGDRIEDIAFEGEGCSISQASASMMTELIKGKTV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 951408741   86 TEAVAGCEAFFQLVMGKQIStKAKAWLGDAEILGSVAEFPARIKCATLAWHAAQEALE 143
Cdd:TIGR01994  81 EEALSLVEAFSEMIQGQETD-EDEEKLGDAEALAGVAKFPARIKCATLAWKALERALA 137
IscU COG0822
Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, ...
 5-143 4.31e-46

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


Pssm-ID: 440584  Cd Length: 128  Bit Score: 146.14  E-value: 4.31e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 951408741   5 KLNQLYMAVVMDHASHPHHKLALPDATTSVELHNVSCGDDIRAFILMKDDKVQQVSFTGNGCTISQASASMMTDALAGLT 84
Cdd:COG0822    1 DLDDLYSEKILDHAKNPRNVGELEDADGSGEGGNPLCGDTVTLYLKVDDGRIEDAKFEGFGCAISQASASMLTELVKGKT 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 951408741  85 KTEAVAGCEAFfqlvmgkqistkakawlGDAEILGSVAEFPARIKCATLAWHAAQEALE 143
Cdd:COG0822   81 LEEALALTDEF-----------------GDLAALGGLPKFPARVKCALLAWDALKAALA 122
IscU_like cd06664
Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU ...
 9-141 1.36e-38

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: 126.98  E-value: 1.36e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 951408741   9 LYMAVVMDHASHPHHKLALPDATTSVELHNVSCGDDIRAFILMKDDKVQQVSFTGNGCTISQASASMMTDALAGLTKTEA 88
Cdd:cd06664    1 LYSEIILDHYRNPRNVGRLEDADGTGEVGNPLCGDEITLYLKVEDGRITDAKFQGFGCAISIASASLLTELIKGKTLDEA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 951408741  89 VAGCEAFFQLVMGKqistkakawlGDAEILGSVAEFPARIKCATLAWHAAQEA 141
Cdd:cd06664   81 LKLLNKDIAMLDGK----------EELAALAGVGLPPARIHCALLAWKALKAA 123
NifU_N pfam01592
NifU-like N terminal domain; This domain is found in NifU in combination with pfam01106. This ...
 9-131 1.26e-16

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: 70.90  E-value: 1.26e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 951408741    9 LYMAVVMDHASHPHHKLALPDATTSVELH-NVSCGDDIRAFILMKD--DKVQQVSFTGNGCTISQASASMMTDALAGLTK 85
Cdd:pfam01592   1 LYTDKVLDHYKNPRNVGVLEDADAGVGDVgNPACGDAMRLQIKVDEstDRIEDAKFKTFGCGSAIASSSMLTELVKGKTI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 951408741   86 TEAVA-GCEAFFQLVMGKQISTKAKAWLGDAEILGSVAEFPARIKCA 131
Cdd:pfam01592  81 EEALKiTNTDIAEELGGLPPVKMHCSVLADDALKAAIADYPGKNKCA 127
NifU_clost TIGR03419
FeS cluster assembly scaffold protein NifU, Clostridium type; NifU and NifS form a pair of ...
 10-143 1.01e-13

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: 63.22  E-value: 1.01e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 951408741   10 YMAVVMDHASHPHHKLALPDATTSVELHNVSCGDDIRAFILMKDDKVQQVSFTGNGCTISQASASMMTDALAGLTKTEAV 89
Cdd:TIGR03419   1 YSEKVMDHFMNPRNVGEIENADGVGEVGNPKCGDIMKIFLKVEDDIIKDVKFKTFGCGAAIASSSMATEMIKGKTLEEAW 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 951408741   90 agceaffqlvmgkQISTKAKawlgdAEILGSVAefPARIKCATLAWHAAQEALE 143
Cdd:TIGR03419  81 -------------ELTNKAV-----AEALDGLP--PVKMHCSVLAEEAIHKAIN 114
 
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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