hypothetical protein G4228_012599 [Cervus hanglu yarkandensis]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||
| cysta_beta | TIGR01137 | cystathionine beta-synthase; Members of this family closely resemble cysteine synthase but ... |
198-666 | 0e+00 | |||||||
cystathionine beta-synthase; Members of this family closely resemble cysteine synthase but contain an additional C-terminal CBS domain. The function of any bacterial member included in this family is proposed but not proven. [Amino acid biosynthesis, Serine family] : Pssm-ID: 273464 [Multi-domain] Cd Length: 455 Bit Score: 797.09 E-value: 0e+00
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| RRM_U2AF35 | cd12538 | RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ... |
43-146 | 4.01e-76 | |||||||
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain. : Pssm-ID: 409954 [Multi-domain] Cd Length: 104 Bit Score: 239.19 E-value: 4.01e-76
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| zf-CCCH | pfam00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar); |
149-175 | 9.10e-06 | |||||||
Zinc finger C-x8-C-x5-C-x3-H type (and similar); : Pssm-ID: 459885 [Multi-domain] Cd Length: 27 Bit Score: 42.57 E-value: 9.10e-06
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| zf-CCCH | pfam00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar); |
13-39 | 1.86e-05 | |||||||
Zinc finger C-x8-C-x5-C-x3-H type (and similar); : Pssm-ID: 459885 [Multi-domain] Cd Length: 27 Bit Score: 41.80 E-value: 1.86e-05
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| Name | Accession | Description | Interval | E-value | |||||||
| cysta_beta | TIGR01137 | cystathionine beta-synthase; Members of this family closely resemble cysteine synthase but ... |
198-666 | 0e+00 | |||||||
cystathionine beta-synthase; Members of this family closely resemble cysteine synthase but contain an additional C-terminal CBS domain. The function of any bacterial member included in this family is proposed but not proven. [Amino acid biosynthesis, Serine family] Pssm-ID: 273464 [Multi-domain] Cd Length: 455 Bit Score: 797.09 E-value: 0e+00
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| CBS_like | cd01561 | CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS ... |
207-505 | 3.61e-161 | |||||||
CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine. Deficiency of CBS leads to homocystinuria, an inherited disease of sulfur metabolism characterized by increased levels of the toxic metabolite homocysteine. Cysteine synthase on the other hand catalyzes the last step of cysteine biosynthesis. This subgroup also includes an O-Phosphoserine sulfhydrylase found in hyperthermophilic archaea which produces L-cysteine from sulfide and the more thermostable O-phospho-L-serine. Pssm-ID: 107204 [Multi-domain] Cd Length: 291 Bit Score: 465.45 E-value: 3.61e-161
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| CysK | COG0031 | Cysteine synthase [Amino acid transport and metabolism]; Cysteine synthase is part of the ... |
197-506 | 3.46e-155 | |||||||
Cysteine synthase [Amino acid transport and metabolism]; Cysteine synthase is part of the Pathway/BioSystem: Cysteine biosynthesis Pssm-ID: 439802 [Multi-domain] Cd Length: 301 Bit Score: 450.27 E-value: 3.46e-155
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| PRK10717 | PRK10717 | cysteine synthase A; Provisional |
196-518 | 6.53e-112 | |||||||
cysteine synthase A; Provisional Pssm-ID: 182672 [Multi-domain] Cd Length: 330 Bit Score: 340.69 E-value: 6.53e-112
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| PALP | pfam00291 | Pyridoxal-phosphate dependent enzyme; Members of this family are all pyridoxal-phosphate ... |
206-498 | 7.06e-78 | |||||||
Pyridoxal-phosphate dependent enzyme; Members of this family are all pyridoxal-phosphate dependent enzymes. This family includes: serine dehydratase EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16, tryptophan synthase beta chain EC:4.2.1.20, threonine synthase EC:4.2.99.2, cysteine synthase EC:4.2.99.8 P11096, cystathionine beta-synthase EC:4.2.1.22, 1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4. Pssm-ID: 459749 [Multi-domain] Cd Length: 295 Bit Score: 251.08 E-value: 7.06e-78
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| RRM_U2AF35 | cd12538 | RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ... |
43-146 | 4.01e-76 | |||||||
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain. Pssm-ID: 409954 [Multi-domain] Cd Length: 104 Bit Score: 239.19 E-value: 4.01e-76
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| RRM_1 | smart00361 | RNA recognition motif; |
78-143 | 5.91e-19 | |||||||
RNA recognition motif; Pssm-ID: 214637 [Multi-domain] Cd Length: 70 Bit Score: 81.30 E-value: 5.91e-19
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| CBS | smart00116 | Domain in cystathionine beta-synthase and other proteins; Domain present in all 3 forms of ... |
544-591 | 4.36e-10 | |||||||
Domain in cystathionine beta-synthase and other proteins; Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease. Pssm-ID: 214522 [Multi-domain] Cd Length: 49 Bit Score: 55.60 E-value: 4.36e-10
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| RRM_1 | pfam00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ... |
91-141 | 8.62e-06 | |||||||
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 43.76 E-value: 8.62e-06
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| zf-CCCH | pfam00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar); |
149-175 | 9.10e-06 | |||||||
Zinc finger C-x8-C-x5-C-x3-H type (and similar); Pssm-ID: 459885 [Multi-domain] Cd Length: 27 Bit Score: 42.57 E-value: 9.10e-06
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| zf-CCCH | pfam00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar); |
13-39 | 1.86e-05 | |||||||
Zinc finger C-x8-C-x5-C-x3-H type (and similar); Pssm-ID: 459885 [Multi-domain] Cd Length: 27 Bit Score: 41.80 E-value: 1.86e-05
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| ZnF_C3H1 | smart00356 | zinc finger; |
149-173 | 4.26e-05 | |||||||
zinc finger; Pssm-ID: 214632 [Multi-domain] Cd Length: 27 Bit Score: 40.69 E-value: 4.26e-05
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| SF-CC1 | TIGR01622 | splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ... |
70-154 | 3.86e-04 | |||||||
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Pssm-ID: 273721 [Multi-domain] Cd Length: 494 Bit Score: 43.37 E-value: 3.86e-04
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| Name | Accession | Description | Interval | E-value | |||||||
| cysta_beta | TIGR01137 | cystathionine beta-synthase; Members of this family closely resemble cysteine synthase but ... |
198-666 | 0e+00 | |||||||
cystathionine beta-synthase; Members of this family closely resemble cysteine synthase but contain an additional C-terminal CBS domain. The function of any bacterial member included in this family is proposed but not proven. [Amino acid biosynthesis, Serine family] Pssm-ID: 273464 [Multi-domain] Cd Length: 455 Bit Score: 797.09 E-value: 0e+00
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| CBS_like | cd01561 | CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS ... |
207-505 | 3.61e-161 | |||||||
CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine. Deficiency of CBS leads to homocystinuria, an inherited disease of sulfur metabolism characterized by increased levels of the toxic metabolite homocysteine. Cysteine synthase on the other hand catalyzes the last step of cysteine biosynthesis. This subgroup also includes an O-Phosphoserine sulfhydrylase found in hyperthermophilic archaea which produces L-cysteine from sulfide and the more thermostable O-phospho-L-serine. Pssm-ID: 107204 [Multi-domain] Cd Length: 291 Bit Score: 465.45 E-value: 3.61e-161
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| CysK | COG0031 | Cysteine synthase [Amino acid transport and metabolism]; Cysteine synthase is part of the ... |
197-506 | 3.46e-155 | |||||||
Cysteine synthase [Amino acid transport and metabolism]; Cysteine synthase is part of the Pathway/BioSystem: Cysteine biosynthesis Pssm-ID: 439802 [Multi-domain] Cd Length: 301 Bit Score: 450.27 E-value: 3.46e-155
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| PRK10717 | PRK10717 | cysteine synthase A; Provisional |
196-518 | 6.53e-112 | |||||||
cysteine synthase A; Provisional Pssm-ID: 182672 [Multi-domain] Cd Length: 330 Bit Score: 340.69 E-value: 6.53e-112
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| cysK | TIGR01139 | cysteine synthase A; This model distinguishes cysteine synthase A (CysK) from cysteine ... |
206-505 | 2.50e-109 | |||||||
cysteine synthase A; This model distinguishes cysteine synthase A (CysK) from cysteine synthase B (CysM). CysM differs in having a broader specificity that also allows the use of thiosulfate to produce cysteine thiosulfonate. [Amino acid biosynthesis, Serine family] Pssm-ID: 273465 Cd Length: 298 Bit Score: 332.79 E-value: 2.50e-109
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| cysKM | TIGR01136 | cysteine synthase; This model discriminates cysteine synthases (EC 2.5.1.47) (both CysK and ... |
202-505 | 2.86e-107 | |||||||
cysteine synthase; This model discriminates cysteine synthases (EC 2.5.1.47) (both CysK and CysM) from cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain lacking from this protein. Bacterial proteins lacking the CBS domain but otherwise showing resemblamnce to cystathionine beta-synthases and considerable phylogenetic distance from known cysteine synthases were excluded from the seed and score below the trusted cutoff. [Amino acid biosynthesis, Serine family] Pssm-ID: 273463 Cd Length: 299 Bit Score: 327.32 E-value: 2.86e-107
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| Trp-synth-beta_II | cd00640 | Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP) ... |
209-499 | 2.65e-80 | |||||||
Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine. Pssm-ID: 107202 [Multi-domain] Cd Length: 244 Bit Score: 255.52 E-value: 2.65e-80
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| cysM | PRK11761 | cysteine synthase CysM; |
200-505 | 1.46e-78 | |||||||
cysteine synthase CysM; Pssm-ID: 236972 Cd Length: 296 Bit Score: 252.87 E-value: 1.46e-78
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| PLP_SbnA_fam | TIGR03945 | 2,3-diaminopropionate biosynthesis protein SbnA; Members of this family include SbnA, a ... |
202-512 | 3.56e-78 | |||||||
2,3-diaminopropionate biosynthesis protein SbnA; Members of this family include SbnA, a protein of the staphyloferrin B biosynthesis operon of Staphylococcus aureus. SbnA and SbnB together appear to synthesize 2,3-diaminopropionate, a precursor of certain siderophores and other secondary metabolites. SbnA is a pyridoxal phosphate-dependent enzyme. [Cellular processes, Biosynthesis of natural products] Pssm-ID: 274872 [Multi-domain] Cd Length: 304 Bit Score: 252.12 E-value: 3.56e-78
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| PALP | pfam00291 | Pyridoxal-phosphate dependent enzyme; Members of this family are all pyridoxal-phosphate ... |
206-498 | 7.06e-78 | |||||||
Pyridoxal-phosphate dependent enzyme; Members of this family are all pyridoxal-phosphate dependent enzymes. This family includes: serine dehydratase EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16, tryptophan synthase beta chain EC:4.2.1.20, threonine synthase EC:4.2.99.2, cysteine synthase EC:4.2.99.8 P11096, cystathionine beta-synthase EC:4.2.1.22, 1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4. Pssm-ID: 459749 [Multi-domain] Cd Length: 295 Bit Score: 251.08 E-value: 7.06e-78
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| RRM_U2AF35 | cd12538 | RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ... |
43-146 | 4.01e-76 | |||||||
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain. Pssm-ID: 409954 [Multi-domain] Cd Length: 104 Bit Score: 239.19 E-value: 4.01e-76
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| PLN02565 | PLN02565 | cysteine synthase |
198-510 | 1.30e-75 | |||||||
cysteine synthase Pssm-ID: 166206 Cd Length: 322 Bit Score: 245.99 E-value: 1.30e-75
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| cysM | TIGR01138 | cysteine synthase B; CysM differs from CysK in that it can also use thiosulfate instead of ... |
202-505 | 2.29e-70 | |||||||
cysteine synthase B; CysM differs from CysK in that it can also use thiosulfate instead of sulfide, to produce cysteine thiosulfonate instead of cysteine. Alternate name: O-acetylserine (thiol)-lyase [Amino acid biosynthesis, Serine family] Pssm-ID: 130208 [Multi-domain] Cd Length: 290 Bit Score: 230.96 E-value: 2.29e-70
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| PLN00011 | PLN00011 | cysteine synthase |
201-510 | 4.83e-68 | |||||||
cysteine synthase Pssm-ID: 177651 Cd Length: 323 Bit Score: 226.04 E-value: 4.83e-68
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| PLN03013 | PLN03013 | cysteine synthase |
188-505 | 7.47e-65 | |||||||
cysteine synthase Pssm-ID: 178587 [Multi-domain] Cd Length: 429 Bit Score: 220.80 E-value: 7.47e-65
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| PLN02556 | PLN02556 | cysteine synthase/L-3-cyanoalanine synthase |
195-511 | 7.65e-65 | |||||||
cysteine synthase/L-3-cyanoalanine synthase Pssm-ID: 178171 [Multi-domain] Cd Length: 368 Bit Score: 219.06 E-value: 7.65e-65
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| PLN02356 | PLN02356 | phosphateglycerate kinase |
188-518 | 4.10e-58 | |||||||
phosphateglycerate kinase Pssm-ID: 215204 Cd Length: 423 Bit Score: 202.53 E-value: 4.10e-58
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| CBS_pair_CBS | cd04608 | Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the ... |
534-664 | 7.66e-56 | |||||||
Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream. Cystathionine beta-synthase (CBS ) contains, besides the C-terminal regulatory CBS-pair, an N-terminal heme-binding module, followed by a pyridoxal phosphate (PLP) domain, which houses the active site. It is the first enzyme in the transsulfuration pathway, catalyzing the conversion of serine and homocysteine to cystathionine and water. In general, CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). Pssm-ID: 341382 [Multi-domain] Cd Length: 120 Bit Score: 185.81 E-value: 7.66e-56
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| RRM_U2AF35_like | cd12287 | RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ... |
45-146 | 3.95e-45 | |||||||
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins; This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR) -rich segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants. Pssm-ID: 409729 [Multi-domain] Cd Length: 101 Bit Score: 156.27 E-value: 3.95e-45
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| RRM_U2AF35B | cd12539 | RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B); This ... |
44-146 | 4.35e-38 | |||||||
RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B); This subgroup corresponds to the RRM of U2AF35B, also termed zinc finger CCCH domain-containing protein 60 (C3H60), which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. Members in this family are mainly found in plant. They show high sequence homology to vertebrates U2AF35 that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. U2AF35B contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants. Pssm-ID: 409955 [Multi-domain] Cd Length: 102 Bit Score: 136.76 E-value: 4.35e-38
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| Thr-dehyd | cd01562 | Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. ... |
209-496 | 5.18e-26 | |||||||
Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly converted into NH4+. The direct deamination is catalyzed by threonine dehydratase, in which pyridoxal phosphate (PLP) is the prosthetic group. Threonine dehydratase is widely distributed in all three major phylogenetic divisions. Pssm-ID: 107205 [Multi-domain] Cd Length: 304 Bit Score: 108.73 E-value: 5.18e-26
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| IlvA | COG1171 | Threonine deaminase [Amino acid transport and metabolism]; Threonine deaminase is part of the ... |
209-496 | 7.93e-26 | |||||||
Threonine deaminase [Amino acid transport and metabolism]; Threonine deaminase is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis Pssm-ID: 440784 [Multi-domain] Cd Length: 327 Bit Score: 108.97 E-value: 7.93e-26
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| PRK06815 | PRK06815 | threonine/serine dehydratase; |
210-496 | 8.71e-24 | |||||||
threonine/serine dehydratase; Pssm-ID: 180709 [Multi-domain] Cd Length: 317 Bit Score: 102.46 E-value: 8.71e-24
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| RRM_U2AFBPL | cd12540 | RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 ... |
56-146 | 6.63e-20 | |||||||
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins; This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. Pssm-ID: 409956 [Multi-domain] Cd Length: 105 Bit Score: 85.39 E-value: 6.63e-20
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| RRM_1 | smart00361 | RNA recognition motif; |
78-143 | 5.91e-19 | |||||||
RNA recognition motif; Pssm-ID: 214637 [Multi-domain] Cd Length: 70 Bit Score: 81.30 E-value: 5.91e-19
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| Thr-synth_1 | cd01563 | Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last ... |
199-496 | 2.30e-18 | |||||||
Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants, OPH is an intermediate between the methionine and threonine/isoleucine pathways. Thus threonine synthase competes for OPH with cystathionine-gamma-synthase, the first enzyme in the methionine pathway. These enzymes are in general dimers. Members of this CD, Thr-synth_1, are widely distributed in bacteria, archaea and higher plants. Pssm-ID: 107206 [Multi-domain] Cd Length: 324 Bit Score: 86.88 E-value: 2.30e-18
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| PRK06381 | PRK06381 | threonine synthase; Validated |
204-496 | 1.76e-16 | |||||||
threonine synthase; Validated Pssm-ID: 235789 Cd Length: 319 Bit Score: 80.91 E-value: 1.76e-16
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| ThrC | COG0498 | Threonine synthase [Amino acid transport and metabolism]; Threonine synthase is part of the ... |
207-503 | 4.70e-14 | |||||||
Threonine synthase [Amino acid transport and metabolism]; Threonine synthase is part of the Pathway/BioSystem: Threonine biosynthesis Pssm-ID: 440264 [Multi-domain] Cd Length: 394 Bit Score: 74.47 E-value: 4.70e-14
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| PLN02970 | PLN02970 | serine racemase |
226-407 | 2.22e-13 | |||||||
serine racemase Pssm-ID: 215524 [Multi-domain] Cd Length: 328 Bit Score: 71.63 E-value: 2.22e-13
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| PRK07048 | PRK07048 | threo-3-hydroxy-L-aspartate ammonia-lyase; |
226-405 | 2.34e-13 | |||||||
threo-3-hydroxy-L-aspartate ammonia-lyase; Pssm-ID: 235918 [Multi-domain] Cd Length: 321 Bit Score: 71.59 E-value: 2.34e-13
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| PRK08246 | PRK08246 | serine/threonine dehydratase; |
209-407 | 3.52e-13 | |||||||
serine/threonine dehydratase; Pssm-ID: 181319 [Multi-domain] Cd Length: 310 Bit Score: 70.75 E-value: 3.52e-13
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| RRM3_RBM39_like | cd12285 | RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar ... |
79-146 | 3.85e-12 | |||||||
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. Pssm-ID: 409727 [Multi-domain] Cd Length: 85 Bit Score: 62.57 E-value: 3.85e-12
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| PRK12483 | PRK12483 | threonine dehydratase; Reviewed |
264-407 | 1.24e-10 | |||||||
threonine dehydratase; Reviewed Pssm-ID: 237111 [Multi-domain] Cd Length: 521 Bit Score: 64.43 E-value: 1.24e-10
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| PRK09224 | PRK09224 | threonine ammonia-lyase IlvA; |
270-407 | 1.77e-10 | |||||||
threonine ammonia-lyase IlvA; Pssm-ID: 236417 [Multi-domain] Cd Length: 504 Bit Score: 64.00 E-value: 1.77e-10
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| PRK06608 | PRK06608 | serine/threonine dehydratase; |
202-404 | 1.92e-10 | |||||||
serine/threonine dehydratase; Pssm-ID: 235842 [Multi-domain] Cd Length: 338 Bit Score: 62.87 E-value: 1.92e-10
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| CBS | smart00116 | Domain in cystathionine beta-synthase and other proteins; Domain present in all 3 forms of ... |
544-591 | 4.36e-10 | |||||||
Domain in cystathionine beta-synthase and other proteins; Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease. Pssm-ID: 214522 [Multi-domain] Cd Length: 49 Bit Score: 55.60 E-value: 4.36e-10
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| RRM_SF | cd00590 | RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ... |
83-143 | 8.10e-10 | |||||||
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 55.37 E-value: 8.10e-10
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| RRM3_U2AF65 | cd12232 | RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor ... |
71-143 | 2.46e-09 | |||||||
RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Pssm-ID: 409679 [Multi-domain] Cd Length: 89 Bit Score: 54.52 E-value: 2.46e-09
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| PRK08638 | PRK08638 | bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB; |
202-405 | 5.82e-09 | |||||||
bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB; Pssm-ID: 236317 [Multi-domain] Cd Length: 333 Bit Score: 58.21 E-value: 5.82e-09
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| CBS_pair_SF | cd02205 | Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains superfamily; The CBS ... |
544-637 | 8.57e-09 | |||||||
Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains superfamily; The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). Pssm-ID: 341358 [Multi-domain] Cd Length: 113 Bit Score: 53.79 E-value: 8.57e-09
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| PRK06110 | PRK06110 | threonine dehydratase; |
223-311 | 9.39e-09 | |||||||
threonine dehydratase; Pssm-ID: 235699 Cd Length: 322 Bit Score: 57.70 E-value: 9.39e-09
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| thrC | TIGR00260 | threonine synthase; Involved in threonine biosynthesis it catalyses the reaction ... |
197-403 | 1.18e-08 | |||||||
threonine synthase; Involved in threonine biosynthesis it catalyses the reaction O-PHOSPHO-L-HOMOSERINE + H(2)O = L-THREONINE + ORTHOPHOSPHATE using pyridoxal phosphate as a cofactor. the enzyme is distantly related to the serine/threonine dehydratases which are also pyridoxal-phosphate dependent enzymes. the pyridoxal-phosphate binding site is a Lys (K) residues present at residue 70 of the model. [Amino acid biosynthesis, Aspartate family] Pssm-ID: 272986 [Multi-domain] Cd Length: 327 Bit Score: 57.39 E-value: 1.18e-08
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| PRK06450 | PRK06450 | threonine synthase; Validated |
197-405 | 3.38e-08 | |||||||
threonine synthase; Validated Pssm-ID: 180565 [Multi-domain] Cd Length: 338 Bit Score: 55.90 E-value: 3.38e-08
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| RRM2_TatSF1_like | cd12282 | RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar ... |
71-150 | 5.51e-08 | |||||||
RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. Pssm-ID: 409724 [Multi-domain] Cd Length: 91 Bit Score: 50.70 E-value: 5.51e-08
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| PLN02550 | PLN02550 | threonine dehydratase |
208-404 | 1.17e-07 | |||||||
threonine dehydratase Pssm-ID: 178165 [Multi-domain] Cd Length: 591 Bit Score: 54.93 E-value: 1.17e-07
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| CBS | pfam00571 | CBS domain; CBS domains are small intracellular modules that pair together to form a stable ... |
536-591 | 1.70e-07 | |||||||
CBS domain; CBS domains are small intracellular modules that pair together to form a stable globular domain. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet. CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet. CBS domain pairs from AMPK bind AMP or ATP. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP. Pssm-ID: 425756 [Multi-domain] Cd Length: 57 Bit Score: 48.36 E-value: 1.70e-07
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| PRK07334 | PRK07334 | threonine dehydratase; Provisional |
208-428 | 2.36e-07 | |||||||
threonine dehydratase; Provisional Pssm-ID: 235994 [Multi-domain] Cd Length: 403 Bit Score: 53.74 E-value: 2.36e-07
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| COG3448 | COG3448 | CBS-domain-containing membrane protein [Signal transduction mechanisms]; |
544-672 | 2.51e-07 | |||||||
CBS-domain-containing membrane protein [Signal transduction mechanisms]; Pssm-ID: 442671 [Multi-domain] Cd Length: 136 Bit Score: 50.25 E-value: 2.51e-07
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| COG2524 | COG2524 | Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]; |
534-665 | 2.56e-07 | |||||||
Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]; Pssm-ID: 442013 [Multi-domain] Cd Length: 206 Bit Score: 51.81 E-value: 2.56e-07
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| CBS | COG0517 | CBS domain [Signal transduction mechanisms]; |
534-662 | 2.77e-07 | |||||||
CBS domain [Signal transduction mechanisms]; Pssm-ID: 440283 [Multi-domain] Cd Length: 128 Bit Score: 49.86 E-value: 2.77e-07
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| RRM | smart00360 | RNA recognition motif; |
83-141 | 5.92e-07 | |||||||
RNA recognition motif; Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 47.20 E-value: 5.92e-07
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| PRK08206 | PRK08206 | diaminopropionate ammonia-lyase; Provisional |
263-316 | 6.56e-07 | |||||||
diaminopropionate ammonia-lyase; Provisional Pssm-ID: 236186 Cd Length: 399 Bit Score: 52.19 E-value: 6.56e-07
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| RRM_UHM_SPF45 | cd12647 | RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar ... |
79-151 | 7.98e-07 | |||||||
RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subgroup corresponds to the RRM of SPF45, also termed RNA-binding motif protein 17 (RBM17), an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. Pssm-ID: 410051 [Multi-domain] Cd Length: 95 Bit Score: 47.66 E-value: 7.98e-07
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| PRK03910 | PRK03910 | D-cysteine desulfhydrase; Validated |
251-467 | 1.02e-06 | |||||||
D-cysteine desulfhydrase; Validated Pssm-ID: 179673 Cd Length: 331 Bit Score: 51.37 E-value: 1.02e-06
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| RRM_UHM_SPF45_PUF60 | cd12374 | RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar ... |
79-146 | 1.02e-06 | |||||||
RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RRMs and a C-terminal UHM domain. Pssm-ID: 409809 [Multi-domain] Cd Length: 85 Bit Score: 46.83 E-value: 1.02e-06
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| eutB | PRK07476 | threonine dehydratase; Provisional |
209-496 | 1.02e-06 | |||||||
threonine dehydratase; Provisional Pssm-ID: 236025 [Multi-domain] Cd Length: 322 Bit Score: 51.12 E-value: 1.02e-06
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| RRM3_UHM_PUF60 | cd12648 | RNA recognition motif 3 (RRM3) found in UHM domain of poly(U)-binding-splicing factor PUF60 ... |
76-150 | 1.45e-06 | |||||||
RNA recognition motif 3 (RRM3) found in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins; This subgroup corresponds to the RRM3 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1), an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. The research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. Pssm-ID: 410052 [Multi-domain] Cd Length: 98 Bit Score: 47.02 E-value: 1.45e-06
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| PRK08639 | PRK08639 | threonine dehydratase; Validated |
359-406 | 1.74e-06 | |||||||
threonine dehydratase; Validated Pssm-ID: 236318 [Multi-domain] Cd Length: 420 Bit Score: 50.96 E-value: 1.74e-06
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| PRK05638 | PRK05638 | threonine synthase; Validated |
154-499 | 2.12e-06 | |||||||
threonine synthase; Validated Pssm-ID: 235539 [Multi-domain] Cd Length: 442 Bit Score: 50.58 E-value: 2.12e-06
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| CBS | COG0517 | CBS domain [Signal transduction mechanisms]; |
531-591 | 2.13e-06 | |||||||
CBS domain [Signal transduction mechanisms]; Pssm-ID: 440283 [Multi-domain] Cd Length: 128 Bit Score: 47.17 E-value: 2.13e-06
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| PRK08329 | PRK08329 | threonine synthase; Validated |
154-406 | 6.17e-06 | |||||||
threonine synthase; Validated Pssm-ID: 236244 [Multi-domain] Cd Length: 347 Bit Score: 49.05 E-value: 6.17e-06
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| L-Ser-dehyd | cd06448 | Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the ... |
209-407 | 8.48e-06 | |||||||
Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- , D-serine, or L-threonine to pyruvate/ketobutyrate and ammonia. Pssm-ID: 107209 Cd Length: 316 Bit Score: 48.45 E-value: 8.48e-06
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| RRM_1 | pfam00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ... |
91-141 | 8.62e-06 | |||||||
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 43.76 E-value: 8.62e-06
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| zf-CCCH | pfam00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar); |
149-175 | 9.10e-06 | |||||||
Zinc finger C-x8-C-x5-C-x3-H type (and similar); Pssm-ID: 459885 [Multi-domain] Cd Length: 27 Bit Score: 42.57 E-value: 9.10e-06
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| COG2905 | COG2905 | Signal-transduction protein containing cAMP-binding, CBS, and nucleotidyltransferase domains ... |
536-668 | 1.04e-05 | |||||||
Signal-transduction protein containing cAMP-binding, CBS, and nucleotidyltransferase domains [Signal transduction mechanisms]; Pssm-ID: 442149 [Multi-domain] Cd Length: 124 Bit Score: 45.21 E-value: 1.04e-05
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| zf-CCCH | pfam00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar); |
13-39 | 1.86e-05 | |||||||
Zinc finger C-x8-C-x5-C-x3-H type (and similar); Pssm-ID: 459885 [Multi-domain] Cd Length: 27 Bit Score: 41.80 E-value: 1.86e-05
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| PRK08197 | PRK08197 | threonine synthase; Validated |
207-312 | 2.69e-05 | |||||||
threonine synthase; Validated Pssm-ID: 181283 [Multi-domain] Cd Length: 394 Bit Score: 46.92 E-value: 2.69e-05
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| COG2524 | COG2524 | Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]; |
453-590 | 4.11e-05 | |||||||
Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]; Pssm-ID: 442013 [Multi-domain] Cd Length: 206 Bit Score: 45.26 E-value: 4.11e-05
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| ZnF_C3H1 | smart00356 | zinc finger; |
149-173 | 4.26e-05 | |||||||
zinc finger; Pssm-ID: 214632 [Multi-domain] Cd Length: 27 Bit Score: 40.69 E-value: 4.26e-05
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| CBS_pair_SF | cd02205 | Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains superfamily; The CBS ... |
533-587 | 4.83e-05 | |||||||
Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains superfamily; The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). Pssm-ID: 341358 [Multi-domain] Cd Length: 113 Bit Score: 43.00 E-value: 4.83e-05
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| RRM_Aly_REF_like | cd12418 | RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ... |
77-144 | 6.81e-05 | |||||||
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. Pssm-ID: 409852 [Multi-domain] Cd Length: 75 Bit Score: 41.41 E-value: 6.81e-05
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| ETR | cd08290 | 2-enoyl thioester reductase (ETR); 2-enoyl thioester reductase (ETR) catalyzes the ... |
247-313 | 7.60e-05 | |||||||
2-enoyl thioester reductase (ETR); 2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the alcohol dehydrogenases in this family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains, at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. Candida tropicalis enoyl thioester reductase (Etr1p) catalyzes the NADPH-dependent reduction of trans-2-enoyl thioesters in mitochondrial fatty acid synthesis. Etr1p forms homodimers, with each subunit containing a nucleotide-binding Rossmann fold domain and a catalytic domain. Pssm-ID: 176250 [Multi-domain] Cd Length: 341 Bit Score: 45.29 E-value: 7.60e-05
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| RRM1_2_CoAA_like | cd12343 | RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ... |
91-143 | 8.16e-05 | |||||||
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. Pssm-ID: 409779 [Multi-domain] Cd Length: 66 Bit Score: 41.06 E-value: 8.16e-05
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| RRM3_I_PABPs | cd12380 | RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ... |
79-142 | 9.33e-05 | |||||||
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. Pssm-ID: 409814 [Multi-domain] Cd Length: 80 Bit Score: 41.39 E-value: 9.33e-05
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| YtoI | COG4109 | Predicted transcriptional regulator containing CBS domains [Transcription]; |
533-591 | 9.82e-05 | |||||||
Predicted transcriptional regulator containing CBS domains [Transcription]; Pssm-ID: 443285 [Multi-domain] Cd Length: 135 Bit Score: 42.59 E-value: 9.82e-05
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| PRK14869 | PRK14869 | putative manganese-dependent inorganic diphosphatase; |
533-591 | 1.40e-04 | |||||||
putative manganese-dependent inorganic diphosphatase; Pssm-ID: 237843 [Multi-domain] Cd Length: 546 Bit Score: 45.21 E-value: 1.40e-04
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| RRM_Set1B | cd12549 | RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B); This ... |
79-160 | 2.40e-04 | |||||||
RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B); This subgroup corresponds to the RRM of Setd1B, also termed SET domain-containing protein 1B (Set1B), or lysine N-methyltransferase 2G, a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1B is localized to euchromatic nuclear speckles and associates with a complex containing six human homologs of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). Set1B complex is a histone methyltransferase that produces trimethylated histone H3 at Lys4. Set1B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. Pssm-ID: 409965 [Multi-domain] Cd Length: 93 Bit Score: 40.71 E-value: 2.40e-04
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| RRM1_RBM28_like | cd12413 | RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ... |
79-144 | 2.66e-04 | |||||||
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. Pssm-ID: 409847 [Multi-domain] Cd Length: 79 Bit Score: 39.88 E-value: 2.66e-04
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| SF-CC1 | TIGR01622 | splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ... |
70-154 | 3.86e-04 | |||||||
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Pssm-ID: 273721 [Multi-domain] Cd Length: 494 Bit Score: 43.37 E-value: 3.86e-04
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| CBS_pair_Mg_transporter | cd04606 | Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the magnesium ... |
545-662 | 4.11e-04 | |||||||
Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the magnesium transporter, MgtE; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other divalent cations into the cell via two highly conserved aspartates. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). Pssm-ID: 341380 [Multi-domain] Cd Length: 121 Bit Score: 40.39 E-value: 4.11e-04
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| RBD_RRM1_NPL3 | cd12340 | RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ... |
83-144 | 4.53e-04 | |||||||
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. Pssm-ID: 409777 [Multi-domain] Cd Length: 69 Bit Score: 38.92 E-value: 4.53e-04
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| YtoI | COG4109 | Predicted transcriptional regulator containing CBS domains [Transcription]; |
544-637 | 7.43e-04 | |||||||
Predicted transcriptional regulator containing CBS domains [Transcription]; Pssm-ID: 443285 [Multi-domain] Cd Length: 135 Bit Score: 40.28 E-value: 7.43e-04
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| CBS_pair_IMPDH | cd04601 | Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' ... |
544-582 | 8.68e-04 | |||||||
Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key role in the regulation of cell proliferation and differentiation. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). Pssm-ID: 341376 [Multi-domain] Cd Length: 110 Bit Score: 39.32 E-value: 8.68e-04
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| MgtE | COG2239 | Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; |
545-691 | 9.43e-04 | |||||||
Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Pssm-ID: 441840 [Multi-domain] Cd Length: 443 Bit Score: 42.36 E-value: 9.43e-04
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| AF2118 | COG3620 | Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ... |
536-663 | 1.14e-03 | |||||||
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription]; Pssm-ID: 442838 [Multi-domain] Cd Length: 95 Bit Score: 38.85 E-value: 1.14e-03
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| CBS_pair_NTP_transferase_assoc | cd04607 | Two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the ... |
544-588 | 1.18e-03 | |||||||
Two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). Pssm-ID: 341381 [Multi-domain] Cd Length: 112 Bit Score: 38.97 E-value: 1.18e-03
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| U2AF_lg | TIGR01642 | U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ... |
76-140 | 1.19e-03 | |||||||
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Pssm-ID: 273727 [Multi-domain] Cd Length: 509 Bit Score: 42.19 E-value: 1.19e-03
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| CBS_pair_BON_assoc | cd04586 | Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the ... |
544-582 | 2.46e-03 | |||||||
Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain. BON is a putative phospholipid-binding domain found in a family of osmotic shock protection proteins. It is also found in some secretins and a group of potential haemolysins. Its likely function is attachment to phospholipid membranes. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). Pssm-ID: 341362 [Multi-domain] Cd Length: 137 Bit Score: 38.56 E-value: 2.46e-03
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| RRM1_gar2 | cd12447 | RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ... |
91-145 | 3.50e-03 | |||||||
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. Pssm-ID: 409881 [Multi-domain] Cd Length: 76 Bit Score: 36.64 E-value: 3.50e-03
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| CBS_pair_Mg_transporter | cd04606 | Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the magnesium ... |
544-582 | 4.81e-03 | |||||||
Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the magnesium transporter, MgtE; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other divalent cations into the cell via two highly conserved aspartates. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). Pssm-ID: 341380 [Multi-domain] Cd Length: 121 Bit Score: 37.31 E-value: 4.81e-03
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| RRM3_Prp24 | cd12298 | RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ... |
83-144 | 4.85e-03 | |||||||
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. Pssm-ID: 409739 [Multi-domain] Cd Length: 78 Bit Score: 36.47 E-value: 4.85e-03
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| CBS_pair_plant_CBSX | cd17789 | Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains from plant CBSX ... |
536-587 | 5.42e-03 | |||||||
Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains from plant CBSX proteins; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains of plant single cystathionine beta-synthase (CBS) pair proteins (CBSX). CBSX1 and CBSX2 have been identified as redox regulators of the thioredoxin (Trx) system. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). Pssm-ID: 341425 [Multi-domain] Cd Length: 141 Bit Score: 37.84 E-value: 5.42e-03
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| RRM_Set1 | cd12304 | RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases; This ... |
88-159 | 5.89e-03 | |||||||
RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases; This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. Pssm-ID: 409745 [Multi-domain] Cd Length: 93 Bit Score: 36.56 E-value: 5.89e-03
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| RRM3_RBM19_RRM2_MRD1 | cd12316 | RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ... |
83-141 | 7.28e-03 | |||||||
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. Pssm-ID: 409755 [Multi-domain] Cd Length: 74 Bit Score: 35.78 E-value: 7.28e-03
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