Fe-S cluster assembly protein SufB is part of the SufBCD complex, which is an ATP-binding cassette (ABC) protein that functions in the biosynthesis of nascent Fe-S clusters; contains Hedgehog/Intein endonuclease domain
FeS assembly protein SufB; This protein, SufB, forms a cytosolic complex SufBCD. This complex ...
600-837
2.27e-134
FeS assembly protein SufB; This protein, SufB, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
The actual alignment was detected with superfamily member TIGR01980:
Pssm-ID: 131035 [Multi-domain] Cd Length: 448 Bit Score: 407.91 E-value: 2.27e-134
FeS assembly protein SufB; This protein, SufB, forms a cytosolic complex SufBCD. This complex ...
30-253
2.14e-126
FeS assembly protein SufB; This protein, SufB, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
The actual alignment was detected with superfamily member TIGR01980:
Pssm-ID: 131035 [Multi-domain] Cd Length: 448 Bit Score: 387.11 E-value: 2.14e-126
FeS assembly protein SufB; This protein, SufB, forms a cytosolic complex SufBCD. This complex ...
600-837
2.27e-134
FeS assembly protein SufB; This protein, SufB, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 131035 [Multi-domain] Cd Length: 448 Bit Score: 407.91 E-value: 2.27e-134
FeS assembly protein SufB; This protein, SufB, forms a cytosolic complex SufBCD. This complex ...
30-253
2.14e-126
FeS assembly protein SufB; This protein, SufB, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 131035 [Multi-domain] Cd Length: 448 Bit Score: 387.11 E-value: 2.14e-126
SUF system FeS cluster assembly, SufBD; Iron-sulphur (FeS) clusters are important cofactors ...
620-817
7.94e-91
SUF system FeS cluster assembly, SufBD; Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S]. FeS cluster assembly is a complex process involving the mobilization of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. SufA is homologous to IscA, acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. This entry represents SufB and SufD proteins, which are homologous, and form part of the SufBCD complex in the SUF system. SufB accepts sulfur transferred from SufE, whereas SufD may play a role in iron acquisition.
Pssm-ID: 460219 [Multi-domain] Cd Length: 218 Bit Score: 285.50 E-value: 7.94e-91
Hint (Hedgehog/Intein) domain N-terminal region; Hedgehog/Intein domain, N-terminal region. ...
252-371
2.80e-13
Hint (Hedgehog/Intein) domain N-terminal region; Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Pssm-ID: 197642 [Multi-domain] Cd Length: 100 Bit Score: 66.52 E-value: 2.80e-13
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
253-375
6.03e-12
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.
Pssm-ID: 238035 [Multi-domain] Cd Length: 136 Bit Score: 63.83 E-value: 6.03e-12
SufBD protein N-terminal region; This entry represents the N-terminal part of the SufB and ...
161-221
1.06e-08
SufBD protein N-terminal region; This entry represents the N-terminal part of the SufB and SufD proteins. It has a right handed beta helix structure. This family is associated with the C-terminal region pfam01458
Pssm-ID: 437127 Cd Length: 172 Bit Score: 55.21 E-value: 1.06e-08
Intein splicing domain; Inteins are segments of protein which excise themselves from a ...
299-611
1.87e-08
Intein splicing domain; Inteins are segments of protein which excise themselves from a precursor protein and mediate the rejoining of the remainder of the precursor (the extein). Most inteins consist of a splicing domain which is split into two segments by a homing endonuclease domain. This domain represents the splicing domain.
Pssm-ID: 434290 [Multi-domain] Cd Length: 378 Bit Score: 57.47 E-value: 1.87e-08
FeS assembly protein SufB; This protein, SufB, forms a cytosolic complex SufBCD. This complex ...
600-837
2.27e-134
FeS assembly protein SufB; This protein, SufB, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 131035 [Multi-domain] Cd Length: 448 Bit Score: 407.91 E-value: 2.27e-134
FeS assembly protein SufB; This protein, SufB, forms a cytosolic complex SufBCD. This complex ...
30-253
2.14e-126
FeS assembly protein SufB; This protein, SufB, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 131035 [Multi-domain] Cd Length: 448 Bit Score: 387.11 E-value: 2.14e-126
SUF system FeS cluster assembly, SufBD; Iron-sulphur (FeS) clusters are important cofactors ...
620-817
7.94e-91
SUF system FeS cluster assembly, SufBD; Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S]. FeS cluster assembly is a complex process involving the mobilization of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. SufA is homologous to IscA, acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. This entry represents SufB and SufD proteins, which are homologous, and form part of the SufBCD complex in the SUF system. SufB accepts sulfur transferred from SufE, whereas SufD may play a role in iron acquisition.
Pssm-ID: 460219 [Multi-domain] Cd Length: 218 Bit Score: 285.50 E-value: 7.94e-91
FeS assembly protein SufD; This protein, SufD, forms a cytosolic complex SufBCD. This complex ...
619-828
4.04e-54
FeS assembly protein SufD; This protein, SufD, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. SufB and SufD are homologous. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 273908 Cd Length: 275 Bit Score: 188.98 E-value: 4.04e-54
Hint (Hedgehog/Intein) domain N-terminal region; Hedgehog/Intein domain, N-terminal region. ...
252-371
2.80e-13
Hint (Hedgehog/Intein) domain N-terminal region; Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Pssm-ID: 197642 [Multi-domain] Cd Length: 100 Bit Score: 66.52 E-value: 2.80e-13
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
253-375
6.03e-12
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.
Pssm-ID: 238035 [Multi-domain] Cd Length: 136 Bit Score: 63.83 E-value: 6.03e-12
SufBD protein N-terminal region; This entry represents the N-terminal part of the SufB and ...
161-221
1.06e-08
SufBD protein N-terminal region; This entry represents the N-terminal part of the SufB and SufD proteins. It has a right handed beta helix structure. This family is associated with the C-terminal region pfam01458
Pssm-ID: 437127 Cd Length: 172 Bit Score: 55.21 E-value: 1.06e-08
Intein splicing domain; Inteins are segments of protein which excise themselves from a ...
299-611
1.87e-08
Intein splicing domain; Inteins are segments of protein which excise themselves from a precursor protein and mediate the rejoining of the remainder of the precursor (the extein). Most inteins consist of a splicing domain which is split into two segments by a homing endonuclease domain. This domain represents the splicing domain.
Pssm-ID: 434290 [Multi-domain] Cd Length: 378 Bit Score: 57.47 E-value: 1.87e-08
Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. ...
571-617
2.75e-06
Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Pssm-ID: 197641 Cd Length: 46 Bit Score: 44.86 E-value: 2.75e-06
Hom_end-associated Hint; Homing endonucleases are encoded by mobile DNA elements that are ...
263-298
8.03e-05
Hom_end-associated Hint; Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a second domain containing the protein-splicing active site. This Domain corresponds to the latter protein-splicing domain.
Pssm-ID: 368334 [Multi-domain] Cd Length: 444 Bit Score: 45.89 E-value: 8.03e-05
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
559-611
5.04e-04
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.
Pssm-ID: 238035 [Multi-domain] Cd Length: 136 Bit Score: 41.10 E-value: 5.04e-04
intein C-terminal splicing region; This model represents the well-conserved C-terminal region ...
590-610
6.08e-03
intein C-terminal splicing region; This model represents the well-conserved C-terminal region of a large number of inteins. It is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. Inteins are regions encoded within proteins from which they remove themselves after translation in a self-splicing reaction, leaving the remainder of the coding region to form a complete, functional protein as if the intein were never there. Proteins with inteins include RecA, GyrA, ribonucleotide reductase, and others. Most inteins have a central region with putative endonuclease activity.
Pssm-ID: 213622 [Multi-domain] Cd Length: 21 Bit Score: 34.70 E-value: 6.08e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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