Hom_end-associated Hint; Homing endonucleases are encoded by mobile DNA elements that are ...
29-481
0e+00
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: 651.03 E-value: 0e+00
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
1-38
1.08e-14
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.
The actual alignment was detected with superfamily member cd01134:
Pssm-ID: 476819 [Multi-domain] Cd Length: 288 Bit Score: 74.53 E-value: 1.08e-14
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
475-516
1.95e-12
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.
The actual alignment was detected with superfamily member cd01134:
Pssm-ID: 476819 [Multi-domain] Cd Length: 288 Bit Score: 67.60 E-value: 1.95e-12
Hom_end-associated Hint; Homing endonucleases are encoded by mobile DNA elements that are ...
29-481
0e+00
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: 651.03 E-value: 0e+00
V/A-type ATP synthase catalytic subunit A; V/A-type ATP synthase catalytic subunit A. These ...
1-38
1.08e-14
V/A-type ATP synthase catalytic subunit A; V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. Vacuolar (V-type) ATPases play major roles in endomembrane and plasma membrane proton transport in eukaryotes. They are found in multiple intracellular membranes including vacuoles, endosomes, lysosomes, Golgi-derived vesicles, secretory vesicles, as well as the plasma membrane. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.
Pssm-ID: 410878 [Multi-domain] Cd Length: 288 Bit Score: 74.53 E-value: 1.08e-14
V/A-type ATP synthase catalytic subunit A; V/A-type ATP synthase catalytic subunit A. These ...
475-516
1.95e-12
V/A-type ATP synthase catalytic subunit A; V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. Vacuolar (V-type) ATPases play major roles in endomembrane and plasma membrane proton transport in eukaryotes. They are found in multiple intracellular membranes including vacuoles, endosomes, lysosomes, Golgi-derived vesicles, secretory vesicles, as well as the plasma membrane. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.
Pssm-ID: 410878 [Multi-domain] Cd Length: 288 Bit Score: 67.60 E-value: 1.95e-12
Archaeal/vacuolar-type H+-ATPase catalytic subunit A/Vma1 [Energy production and conversion]; ...
478-516
1.42e-09
Archaeal/vacuolar-type H+-ATPase catalytic subunit A/Vma1 [Energy production and conversion]; Archaeal/vacuolar-type H+-ATPase catalytic subunit A/Vma1 is part of the Pathway/BioSystem: A/V-type ATP synthase
Pssm-ID: 440769 [Multi-domain] Cd Length: 583 Bit Score: 60.49 E-value: 1.42e-09
Hint (Hedgehog/Intein) domain N-terminal region; Hedgehog/Intein domain, N-terminal region. ...
28-133
1.95e-08
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: 51.89 E-value: 1.95e-08
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
29-118
1.06e-05
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: 44.95 E-value: 1.06e-05
ATP synthase alpha/beta family, nucleotide-binding domain; This entry includes the ATP ...
1-29
3.96e-04
ATP synthase alpha/beta family, nucleotide-binding domain; This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho.
Pssm-ID: 425417 [Multi-domain] Cd Length: 212 Bit Score: 41.96 E-value: 3.96e-04
Hom_end-associated Hint; Homing endonucleases are encoded by mobile DNA elements that are ...
29-481
0e+00
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: 651.03 E-value: 0e+00
V/A-type ATP synthase catalytic subunit A; V/A-type ATP synthase catalytic subunit A. These ...
1-38
1.08e-14
V/A-type ATP synthase catalytic subunit A; V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. Vacuolar (V-type) ATPases play major roles in endomembrane and plasma membrane proton transport in eukaryotes. They are found in multiple intracellular membranes including vacuoles, endosomes, lysosomes, Golgi-derived vesicles, secretory vesicles, as well as the plasma membrane. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.
Pssm-ID: 410878 [Multi-domain] Cd Length: 288 Bit Score: 74.53 E-value: 1.08e-14
V/A-type ATP synthase catalytic subunit A; V/A-type ATP synthase catalytic subunit A. These ...
475-516
1.95e-12
V/A-type ATP synthase catalytic subunit A; V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. Vacuolar (V-type) ATPases play major roles in endomembrane and plasma membrane proton transport in eukaryotes. They are found in multiple intracellular membranes including vacuoles, endosomes, lysosomes, Golgi-derived vesicles, secretory vesicles, as well as the plasma membrane. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.
Pssm-ID: 410878 [Multi-domain] Cd Length: 288 Bit Score: 67.60 E-value: 1.95e-12
Archaeal/vacuolar-type H+-ATPase catalytic subunit A/Vma1 [Energy production and conversion]; ...
478-516
1.42e-09
Archaeal/vacuolar-type H+-ATPase catalytic subunit A/Vma1 [Energy production and conversion]; Archaeal/vacuolar-type H+-ATPase catalytic subunit A/Vma1 is part of the Pathway/BioSystem: A/V-type ATP synthase
Pssm-ID: 440769 [Multi-domain] Cd Length: 583 Bit Score: 60.49 E-value: 1.42e-09
Hint (Hedgehog/Intein) domain N-terminal region; Hedgehog/Intein domain, N-terminal region. ...
28-133
1.95e-08
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: 51.89 E-value: 1.95e-08
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
29-118
1.06e-05
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: 44.95 E-value: 1.06e-05
Intein splicing domain; Inteins are segments of protein which excise themselves from a ...
256-482
3.68e-04
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: 42.83 E-value: 3.68e-04
ATP synthase alpha/beta family, nucleotide-binding domain; This entry includes the ATP ...
1-29
3.96e-04
ATP synthase alpha/beta family, nucleotide-binding domain; This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho.
Pssm-ID: 425417 [Multi-domain] Cd Length: 212 Bit Score: 41.96 E-value: 3.96e-04
Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. ...
444-486
2.33e-03
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: 36.00 E-value: 2.33e-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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