kismet, isoform D [Drosophila melanogaster]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||
| PLN03142 super family | cl33647 | Probable chromatin-remodeling complex ATPase chain; Provisional |
2029-2606 | 5.60e-156 | |||||||||
Probable chromatin-remodeling complex ATPase chain; Provisional The actual alignment was detected with superfamily member PLN03142: Pssm-ID: 215601 [Multi-domain] Cd Length: 1033 Bit Score: 515.12 E-value: 5.60e-156
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| CD2_tandem_CHD5-9_like | cd18663 | repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ... |
1937-1995 | 6.43e-33 | |||||||||
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. : Pssm-ID: 349310 [Multi-domain] Cd Length: 59 Bit Score: 123.17 E-value: 6.43e-33
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| CD1_tandem_CHD5-9_like | cd18668 | repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ... |
1851-1918 | 2.09e-27 | |||||||||
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. : Pssm-ID: 349315 [Multi-domain] Cd Length: 68 Bit Score: 107.81 E-value: 2.09e-27
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| BRK | pfam07533 | BRK domain; The function of this domain is unknown. It is often found associated with ... |
4394-4437 | 3.09e-18 | |||||||||
BRK domain; The function of this domain is unknown. It is often found associated with helicases and transcription factors. : Pssm-ID: 462196 Cd Length: 44 Bit Score: 81.02 E-value: 3.09e-18
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| PTZ00121 super family | cl31754 | MAEBL; Provisional |
1419-1923 | 6.61e-14 | |||||||||
MAEBL; Provisional The actual alignment was detected with superfamily member PTZ00121: Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 79.41 E-value: 6.61e-14
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| PTZ00341 super family | cl31759 | Ring-infected erythrocyte surface antigen; Provisional |
3488-3713 | 1.33e-06 | |||||||||
Ring-infected erythrocyte surface antigen; Provisional The actual alignment was detected with superfamily member PTZ00341: Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 55.18 E-value: 1.33e-06
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| Atrophin-1 super family | cl38111 | Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ... |
221-533 | 5.44e-04 | |||||||||
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. The actual alignment was detected with superfamily member pfam03154: Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 46.68 E-value: 5.44e-04
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| Med15 super family | cl26621 | ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ... |
1056-1265 | 1.39e-03 | |||||||||
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. The actual alignment was detected with superfamily member pfam09606: Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 45.00 E-value: 1.39e-03
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| PRK12678 super family | cl36163 | transcription termination factor Rho; Provisional |
1319-1500 | 8.36e-03 | |||||||||
transcription termination factor Rho; Provisional The actual alignment was detected with superfamily member PRK12678: Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 42.58 E-value: 8.36e-03
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| Name | Accession | Description | Interval | E-value | ||||||||||
| PLN03142 | PLN03142 | Probable chromatin-remodeling complex ATPase chain; Provisional |
2029-2606 | 5.60e-156 | ||||||||||
Probable chromatin-remodeling complex ATPase chain; Provisional Pssm-ID: 215601 [Multi-domain] Cd Length: 1033 Bit Score: 515.12 E-value: 5.60e-156
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| DEXHc_CHD6_7_8_9 | cd17995 | DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ... |
2029-2250 | 1.51e-141 | ||||||||||
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; Chromodomain-helicase-DNA-binding protein 6-9 (CHD6, CHD7, CHD8, and CHD9) are members of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350753 [Multi-domain] Cd Length: 223 Bit Score: 440.92 E-value: 1.51e-141
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
2028-2500 | 2.86e-123 | ||||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 407.69 E-value: 2.86e-123
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| SNF2-rel_dom | pfam00176 | SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
2032-2319 | 7.50e-91 | ||||||||||
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 298.44 E-value: 7.50e-91
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| CD2_tandem_CHD5-9_like | cd18663 | repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ... |
1937-1995 | 6.43e-33 | ||||||||||
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349310 [Multi-domain] Cd Length: 59 Bit Score: 123.17 E-value: 6.43e-33
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
2023-2215 | 1.38e-27 | ||||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 113.36 E-value: 1.38e-27
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| CD1_tandem_CHD5-9_like | cd18668 | repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ... |
1851-1918 | 2.09e-27 | ||||||||||
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349315 [Multi-domain] Cd Length: 68 Bit Score: 107.81 E-value: 2.09e-27
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| DISARM_DrmD_b | NF038318 | DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component ... |
1988-2498 | 6.53e-26 | ||||||||||
DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component of class 1 DISARM (Defence Island System Associated with Restriction Modification), which contains a DNA adenine N6 methyltransferase. This HMM describes a distinct form that is somewhat shorter than the majority of DrmD proteins. Pssm-ID: 468472 [Multi-domain] Cd Length: 868 Bit Score: 118.25 E-value: 6.53e-26
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| BRK | pfam07533 | BRK domain; The function of this domain is unknown. It is often found associated with ... |
4394-4437 | 3.09e-18 | ||||||||||
BRK domain; The function of this domain is unknown. It is often found associated with helicases and transcription factors. Pssm-ID: 462196 Cd Length: 44 Bit Score: 81.02 E-value: 3.09e-18
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| BRK | smart00592 | domain in transcription and CHROMO domain helicases; |
4395-4439 | 3.22e-17 | ||||||||||
domain in transcription and CHROMO domain helicases; Pssm-ID: 197800 Cd Length: 45 Bit Score: 78.16 E-value: 3.22e-17
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
1419-1923 | 6.61e-14 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 79.41 E-value: 6.61e-14
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| Chromo | pfam00385 | Chromo (CHRromatin organization MOdifier) domain; |
1941-1993 | 1.61e-12 | ||||||||||
Chromo (CHRromatin organization MOdifier) domain; Pssm-ID: 459793 [Multi-domain] Cd Length: 52 Bit Score: 64.91 E-value: 1.61e-12
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| MDN1 | COG5271 | Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal ... |
1242-1881 | 1.20e-11 | ||||||||||
Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]; Pssm-ID: 444083 [Multi-domain] Cd Length: 1028 Bit Score: 71.97 E-value: 1.20e-11
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| CHROMO | smart00298 | Chromatin organization modifier domain; |
1941-1993 | 5.04e-09 | ||||||||||
Chromatin organization modifier domain; Pssm-ID: 214605 [Multi-domain] Cd Length: 55 Bit Score: 55.30 E-value: 5.04e-09
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| MSCRAMM_ClfA | NF033609 | MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ... |
1335-1792 | 3.24e-07 | ||||||||||
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif. Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 57.23 E-value: 3.24e-07
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| PTZ00341 | PTZ00341 | Ring-infected erythrocyte surface antigen; Provisional |
3488-3713 | 1.33e-06 | ||||||||||
Ring-infected erythrocyte surface antigen; Provisional Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 55.18 E-value: 1.33e-06
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| MSCRAMM_ClfA | NF033609 | MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ... |
1532-1867 | 1.40e-06 | ||||||||||
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif. Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 55.30 E-value: 1.40e-06
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| 2A1904 | TIGR00927 | K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ... |
1572-1859 | 5.01e-06 | ||||||||||
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds] Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 53.46 E-value: 5.01e-06
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| DMP1 | pfam07263 | Dentin matrix protein 1 (DMP1); This family consists of several mammalian dentin matrix ... |
1359-1747 | 7.78e-06 | ||||||||||
Dentin matrix protein 1 (DMP1); This family consists of several mammalian dentin matrix protein 1 (DMP1) sequences. The dentin matrix acidic phosphoprotein 1 (DMP1) gene has been mapped to human chromosome 4q21. DMP1 is a bone and teeth specific protein initially identified from mineralized dentin. DMP1 is primarily localized in the nuclear compartment of undifferentiated osteoblasts. In the nucleus, DMP1 acts as a transcriptional component for activation of osteoblast-specific genes like osteocalcin. During the early phase of osteoblast maturation, Ca(2+) surges into the nucleus from the cytoplasm, triggering the phosphorylation of DMP1 by a nuclear isoform of casein kinase II. This phosphorylated DMP1 is then exported out into the extracellular matrix, where it regulates nucleation of hydroxyapatite. DMP1 is a unique molecule that initiates osteoblast differentiation by transcription in the nucleus and orchestrates mineralized matrix formation extracellularly, at later stages of osteoblast maturation. The DMP1 gene has been found to be ectopically expressed in lung cancer although the reason for this is unknown. Pssm-ID: 462128 [Multi-domain] Cd Length: 519 Bit Score: 52.24 E-value: 7.78e-06
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| CHROMO | smart00298 | Chromatin organization modifier domain; |
1879-1921 | 3.66e-05 | ||||||||||
Chromatin organization modifier domain; Pssm-ID: 214605 [Multi-domain] Cd Length: 55 Bit Score: 44.13 E-value: 3.66e-05
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| Chromo | pfam00385 | Chromo (CHRromatin organization MOdifier) domain; |
1879-1919 | 8.39e-05 | ||||||||||
Chromo (CHRromatin organization MOdifier) domain; Pssm-ID: 459793 [Multi-domain] Cd Length: 52 Bit Score: 42.95 E-value: 8.39e-05
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| Atrophin-1 | pfam03154 | Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ... |
221-533 | 5.44e-04 | ||||||||||
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 46.68 E-value: 5.44e-04
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| MSCRAMM_ClfA | NF033609 | MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ... |
1334-1673 | 5.47e-04 | ||||||||||
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif. Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 46.44 E-value: 5.47e-04
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| Med15 | pfam09606 | ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ... |
1056-1265 | 1.39e-03 | ||||||||||
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 45.00 E-value: 1.39e-03
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| PRK12678 | PRK12678 | transcription termination factor Rho; Provisional |
1319-1500 | 8.36e-03 | ||||||||||
transcription termination factor Rho; Provisional Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 42.58 E-value: 8.36e-03
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| Name | Accession | Description | Interval | E-value | ||||||||||
| PLN03142 | PLN03142 | Probable chromatin-remodeling complex ATPase chain; Provisional |
2029-2606 | 5.60e-156 | ||||||||||
Probable chromatin-remodeling complex ATPase chain; Provisional Pssm-ID: 215601 [Multi-domain] Cd Length: 1033 Bit Score: 515.12 E-value: 5.60e-156
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| DEXHc_CHD6_7_8_9 | cd17995 | DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ... |
2029-2250 | 1.51e-141 | ||||||||||
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; Chromodomain-helicase-DNA-binding protein 6-9 (CHD6, CHD7, CHD8, and CHD9) are members of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350753 [Multi-domain] Cd Length: 223 Bit Score: 440.92 E-value: 1.51e-141
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
2028-2500 | 2.86e-123 | ||||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 407.69 E-value: 2.86e-123
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| DEXHc_CHD6 | cd18058 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ... |
2029-2250 | 6.84e-112 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; Chromodomain-helicase-DNA-binding protein 6 (CHD6) is a DNA-dependent ATPase that plays a role in chromatin remodeling. It regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin. It activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2.2 and acts as a transcriptional repressor of different viruses including influenza virus or papillomavirus. During influenza virus infection, the viral polymerase complex localizes CHD6 to inactive chromatin where it gets degraded in a proteasome independent-manner. CHD6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350816 [Multi-domain] Cd Length: 222 Bit Score: 355.89 E-value: 6.84e-112
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| DEXHc_CHD8 | cd18060 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ... |
2029-2250 | 5.07e-110 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; Chromodomain-helicase-DNA-binding protein 8 (CHD8) is a DNA helicase that acts as a chromatin remodeling factor and regulates transcription. It also acts as a transcription repressor by remodeling chromatin structure and recruiting histone H1 to target genes. It suppresses p53/TP53-mediated apoptosis by recruiting histone H1 and preventing p53/TP53 transactivation activity and of STAT3 activity by suppressing the LIF-induced STAT3 transcriptional activity. It also acts as a negative regulator of Wnt signaling pathway and CTNNB1-targeted gene expression. CHD8 is also involved in both enhancer blocking and epigenetic remodeling at chromatin boundary via its interaction with CTCF. It also acts as a transcription activator via its interaction with ZNF143 by participating in efficient U6 RNA polymerase III transcription. CHD8 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350818 [Multi-domain] Cd Length: 222 Bit Score: 350.51 E-value: 5.07e-110
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| DEXHc_CHD7 | cd18059 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ... |
2029-2250 | 1.30e-107 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; Chromodomain-helicase-DNA-binding protein 7 (CHD7) is a probable transcription regulator. It may be involved in the 45S precursor rRNA production. CHD7 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350817 [Multi-domain] Cd Length: 222 Bit Score: 343.55 E-value: 1.30e-107
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| DEXHc_CHD9 | cd18061 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ... |
2029-2250 | 9.72e-106 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; Chromodomain-helicase-DNA-binding protein 9 (CHD9) acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. It is proposed to be a ATP-dependent chromatin remodeling protein. CHD9 has DNA-dependent ATPase activity and binds to A/T-rich DNA. It also associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis. CHD9 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350819 [Multi-domain] Cd Length: 222 Bit Score: 338.52 E-value: 9.72e-106
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| SNF2-rel_dom | pfam00176 | SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
2032-2319 | 7.50e-91 | ||||||||||
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 298.44 E-value: 7.50e-91
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| DEXHc_CHD1_2 | cd17993 | DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ... |
2029-2250 | 7.81e-84 | ||||||||||
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and similar proteins; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as the substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but is also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. Both are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350751 [Multi-domain] Cd Length: 218 Bit Score: 275.39 E-value: 7.81e-84
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| DEXHc_Snf | cd17919 | DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
2029-2214 | 2.43e-77 | ||||||||||
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350677 [Multi-domain] Cd Length: 182 Bit Score: 255.18 E-value: 2.43e-77
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| DEXHc_HELLS_SMARCA6 | cd18009 | DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ... |
2026-2252 | 2.05e-74 | ||||||||||
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or SMARCA6) is a major epigenetic regulator crucial for normal heterochromatin structure and function. HELLS is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350767 [Multi-domain] Cd Length: 236 Bit Score: 249.23 E-value: 2.05e-74
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| DEXHc_CHD3_4_5 | cd17994 | DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; ... |
2029-2250 | 8.39e-74 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD3, CHD4, and CHD5 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350752 [Multi-domain] Cd Length: 196 Bit Score: 245.81 E-value: 8.39e-74
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| DEXHc_SMARCA1_SMARCA5 | cd17997 | DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ... |
2026-2252 | 1.34e-70 | ||||||||||
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 and 5 (SMARCA1 and SMARCA5) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350755 [Multi-domain] Cd Length: 222 Bit Score: 237.60 E-value: 1.34e-70
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| DEXHc_CHD2 | cd18054 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ... |
2017-2250 | 2.58e-70 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. CHD2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350812 [Multi-domain] Cd Length: 237 Bit Score: 237.60 E-value: 2.58e-70
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| DEXHc_CHD3 | cd18055 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ... |
2029-2250 | 6.78e-69 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. CHD3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350813 [Multi-domain] Cd Length: 232 Bit Score: 232.98 E-value: 6.78e-69
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| DEXHc_CHD5 | cd18057 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ... |
2029-2250 | 2.70e-67 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350815 [Multi-domain] Cd Length: 232 Bit Score: 228.41 E-value: 2.70e-67
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| DEXHc_CHD4 | cd18056 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ... |
2029-2250 | 4.01e-67 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. CHD4 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350814 [Multi-domain] Cd Length: 232 Bit Score: 228.03 E-value: 4.01e-67
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| DEXHc_SMARCA2_SMARCA4 | cd17996 | DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ... |
2026-2252 | 1.72e-65 | ||||||||||
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, members 2 and 4 (SMARCA2 and SMARCA4) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350754 [Multi-domain] Cd Length: 233 Bit Score: 223.40 E-value: 1.72e-65
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| DEXQc_arch_SWI2_SNF2 | cd18012 | DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ... |
2027-2252 | 4.49e-61 | ||||||||||
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350770 [Multi-domain] Cd Length: 218 Bit Score: 210.11 E-value: 4.49e-61
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| DEXHc_CHD1 | cd18053 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ... |
2017-2250 | 1.82e-60 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350811 [Multi-domain] Cd Length: 237 Bit Score: 209.14 E-value: 1.82e-60
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| SF2_C_SNF | cd18793 | C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
2350-2475 | 2.70e-56 | ||||||||||
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350180 [Multi-domain] Cd Length: 135 Bit Score: 193.08 E-value: 2.70e-56
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| DEXHc_CHD1L | cd18006 | DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ... |
2029-2250 | 3.11e-55 | ||||||||||
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, also known as ALC1) is involved in DNA repair by regulating chromatin relaxation following DNA damage. CHD1L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350764 [Multi-domain] Cd Length: 216 Bit Score: 193.42 E-value: 3.11e-55
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| DEXHc_SMARCA5 | cd18064 | DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ... |
2016-2263 | 5.33e-55 | ||||||||||
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 (SMARCA5, also called SNF2H) is the catalytic subunit of the four known chromatin-remodeling complexes: CHRAC, RSF, ACF/WCRF, and WICH. SMARCA5 plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding SMARCA5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350822 [Multi-domain] Cd Length: 244 Bit Score: 193.73 E-value: 5.33e-55
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| DEXHc_SMARCAD1 | cd17998 | DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ... |
2029-2217 | 1.30e-53 | ||||||||||
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1, also known as ATP-dependent helicase 1 or Hel1) possesses intrinsic ATP-dependent nucleosome-remodeling activity and is required for both DNA repair and heterochromatin organization. SMARCAD1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350756 [Multi-domain] Cd Length: 187 Bit Score: 187.59 E-value: 1.30e-53
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| DEXQc_SRCAP | cd18003 | DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ... |
2029-2250 | 1.29e-52 | ||||||||||
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or DOMO1) is the core catalytic component of the multiprotein chromatin-remodeling SRCAP complex, that is necessary for the incorporation of the histone variant H2A.Z into nucleosomes. SRCAP is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350761 [Multi-domain] Cd Length: 223 Bit Score: 186.02 E-value: 1.29e-52
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| DEXHc_SMARCA1 | cd18065 | DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ... |
2016-2252 | 3.22e-51 | ||||||||||
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1, also called SNF2L) is a component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes which promote the perturbation of chromatin structure in an ATP-dependent manner. SMARCA1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350823 [Multi-domain] Cd Length: 233 Bit Score: 182.52 E-value: 3.22e-51
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| DEXQc_INO80 | cd18002 | DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ... |
2029-2250 | 3.79e-51 | ||||||||||
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 chromatin remodeling complex. INO80 removes histone H3-containing nucleosomes from associated chromatin, promotes CENP-ACnp1 chromatin assembly at the centromere in a redundant manner with another chromatin-remodeling factor Chd1Hrp1. INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. INO80 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350760 [Multi-domain] Cd Length: 229 Bit Score: 181.93 E-value: 3.79e-51
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| DEXHc_SMARCA4 | cd18062 | DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ... |
2015-2252 | 9.22e-47 | ||||||||||
DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4, also known as transcription activator BRG1) is a component of the CREST-BRG1 complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. SMARCA4 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350820 [Multi-domain] Cd Length: 251 Bit Score: 170.23 E-value: 9.22e-47
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| DEXHc_ERCC6L2 | cd18005 | DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ... |
2029-2250 | 1.33e-45 | ||||||||||
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350763 [Multi-domain] Cd Length: 245 Bit Score: 166.79 E-value: 1.33e-45
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| DEXHc_SMARCA2 | cd18063 | DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent ... |
2015-2252 | 2.94e-45 | ||||||||||
DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2, also known as brahma homolog) is a component of the BAF complex. SMARCA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350821 [Multi-domain] Cd Length: 251 Bit Score: 166.01 E-value: 2.94e-45
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| DEXHc_ERCC6L | cd18001 | DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ... |
2029-2250 | 6.89e-45 | ||||||||||
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint helicase (ERCC6L, also known as RAD26L) is an essential component of the mitotic spindle assembly checkpoint, by acting as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase. ERCC6L is proposed to stimulate cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2. ERCC6L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350759 [Multi-domain] Cd Length: 232 Bit Score: 164.08 E-value: 6.89e-45
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| DEXHc_Mot1 | cd17999 | DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ... |
2029-2250 | 2.04e-43 | ||||||||||
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in eukaryotes) regulates transcription in association with TATA binding protein (TBP). Mot1, Ino80C, and NC2 function coordinately to regulate pervasive transcription in yeast and mammals. Mot1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350757 [Multi-domain] Cd Length: 232 Bit Score: 159.82 E-value: 2.04e-43
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| DEXDc_SHPRH-like | cd18008 | DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ... |
2029-2250 | 2.05e-43 | ||||||||||
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350766 [Multi-domain] Cd Length: 241 Bit Score: 160.15 E-value: 2.05e-43
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| DEXHc_RAD54 | cd18004 | DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ... |
2029-2250 | 3.86e-40 | ||||||||||
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350762 [Multi-domain] Cd Length: 240 Bit Score: 150.90 E-value: 3.86e-40
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| DEXHc_ATRX-like | cd18007 | DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ... |
2029-2227 | 6.99e-37 | ||||||||||
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350765 [Multi-domain] Cd Length: 239 Bit Score: 141.27 E-value: 6.99e-37
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| DEXHc_ERCC6 | cd18000 | DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ... |
2029-2214 | 6.84e-36 | ||||||||||
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350758 [Multi-domain] Cd Length: 193 Bit Score: 136.68 E-value: 6.84e-36
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| CD2_tandem_CHD5-9_like | cd18663 | repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ... |
1937-1995 | 6.43e-33 | ||||||||||
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349310 [Multi-domain] Cd Length: 59 Bit Score: 123.17 E-value: 6.43e-33
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| DEXHc_RAD54A | cd18067 | DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ... |
2029-2244 | 2.56e-30 | ||||||||||
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as RAD54L or RAD54, plays a role in homologous recombination related repair of DNA double-strand breaks. RAD54A is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350825 [Multi-domain] Cd Length: 243 Bit Score: 122.58 E-value: 2.56e-30
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| DEXHc_RAD54B | cd18066 | DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ... |
2029-2223 | 1.66e-29 | ||||||||||
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as RDH54, binds to double-stranded DNA, displays ATPase activity in the presence of DNA, and may have a role in meiotic and mitotic recombination. RAD54B is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350824 [Multi-domain] Cd Length: 235 Bit Score: 119.95 E-value: 1.66e-29
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| DEXHc_HARP_SMARCAL1 | cd18010 | DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ... |
2029-2250 | 3.98e-29 | ||||||||||
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1, also known as HARP) is recruited to stalled replication forks to promote repair and helps restart replication. It plays a role in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress. Mutations cause Schimke Immunoosseous Dysplasia. SMARCAL1 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350768 [Multi-domain] Cd Length: 213 Bit Score: 118.08 E-value: 3.98e-29
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
2023-2215 | 1.38e-27 | ||||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 113.36 E-value: 1.38e-27
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| DEXHc_HLTF1_SMARC3 | cd18071 | DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ... |
2029-2250 | 1.97e-27 | ||||||||||
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350829 [Multi-domain] Cd Length: 239 Bit Score: 114.10 E-value: 1.97e-27
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| CD1_tandem_CHD5-9_like | cd18668 | repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ... |
1851-1918 | 2.09e-27 | ||||||||||
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349315 [Multi-domain] Cd Length: 68 Bit Score: 107.81 E-value: 2.09e-27
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
2350-2464 | 1.55e-26 | ||||||||||
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 106.91 E-value: 1.55e-26
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| DISARM_DrmD_b | NF038318 | DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component ... |
1988-2498 | 6.53e-26 | ||||||||||
DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component of class 1 DISARM (Defence Island System Associated with Restriction Modification), which contains a DNA adenine N6 methyltransferase. This HMM describes a distinct form that is somewhat shorter than the majority of DrmD proteins. Pssm-ID: 468472 [Multi-domain] Cd Length: 868 Bit Score: 118.25 E-value: 6.53e-26
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| DEXHc_ATRX | cd18068 | DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ... |
2029-2227 | 6.68e-25 | ||||||||||
DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) is involved in transcriptional regulation and chromatin remodeling. Mutations in humans cause mental retardation, X-linked, syndromic, with hypotonic facies 1 (MRXSHF1) and alpha-thalassemia myelodysplasia syndrome (ATMDS). ATRX is part of the a DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350826 [Multi-domain] Cd Length: 246 Bit Score: 106.90 E-value: 6.68e-25
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| DEXDc_RapA | cd18011 | DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
2029-2250 | 1.13e-21 | ||||||||||
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 96.59 E-value: 1.13e-21
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
2380-2464 | 2.23e-21 | ||||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 91.12 E-value: 2.23e-21
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| DEXHc_ARIP4 | cd18069 | DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called ... |
2029-2227 | 2.29e-21 | ||||||||||
DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called RAD54 like 2 or RAD54L2 ) modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. ARIP4 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350827 [Multi-domain] Cd Length: 227 Bit Score: 96.04 E-value: 2.29e-21
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| DEXHc_TTF2 | cd18072 | DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ... |
2029-2250 | 1.20e-18 | ||||||||||
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called Forkhead-box E1/FOXE1 ) is a transcription termination factor that couples ATP hydrolysis with the removal of RNA polymerase II from the DNA template. Single nucleotide polymorphism (SNP) within the 5'-UTR of TTF2 is associated with thyroid cancer risk.TTF2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350830 [Multi-domain] Cd Length: 241 Bit Score: 88.69 E-value: 1.20e-18
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| BRK | pfam07533 | BRK domain; The function of this domain is unknown. It is often found associated with ... |
4394-4437 | 3.09e-18 | ||||||||||
BRK domain; The function of this domain is unknown. It is often found associated with helicases and transcription factors. Pssm-ID: 462196 Cd Length: 44 Bit Score: 81.02 E-value: 3.09e-18
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| CD2_tandem | cd18659 | repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ... |
1938-1993 | 2.06e-17 | ||||||||||
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349306 [Multi-domain] Cd Length: 54 Bit Score: 78.77 E-value: 2.06e-17
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| BRK | smart00592 | domain in transcription and CHROMO domain helicases; |
4395-4439 | 3.22e-17 | ||||||||||
domain in transcription and CHROMO domain helicases; Pssm-ID: 197800 Cd Length: 45 Bit Score: 78.16 E-value: 3.22e-17
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| DEXQc_SHPRH | cd18070 | DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ... |
2029-2218 | 6.90e-15 | ||||||||||
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350828 [Multi-domain] Cd Length: 257 Bit Score: 78.15 E-value: 6.90e-15
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
1419-1923 | 6.61e-14 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 79.41 E-value: 6.61e-14
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
1330-1923 | 2.51e-13 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 77.49 E-value: 2.51e-13
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| Chromo | pfam00385 | Chromo (CHRromatin organization MOdifier) domain; |
1941-1993 | 1.61e-12 | ||||||||||
Chromo (CHRromatin organization MOdifier) domain; Pssm-ID: 459793 [Multi-domain] Cd Length: 52 Bit Score: 64.91 E-value: 1.61e-12
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
1415-1999 | 5.78e-12 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 73.25 E-value: 5.78e-12
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| MDN1 | COG5271 | Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal ... |
1242-1881 | 1.20e-11 | ||||||||||
Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]; Pssm-ID: 444083 [Multi-domain] Cd Length: 1028 Bit Score: 71.97 E-value: 1.20e-11
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| DEXQc_bact_SNF2 | cd18013 | DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ... |
2029-2227 | 8.36e-11 | ||||||||||
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprise a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. The bacterial SNF2 present in this family are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350771 [Multi-domain] Cd Length: 218 Bit Score: 65.06 E-value: 8.36e-11
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
1326-1867 | 3.08e-10 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 67.47 E-value: 3.08e-10
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
2048-2196 | 7.98e-10 | ||||||||||
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region. Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 60.49 E-value: 7.98e-10
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| CD1_tandem | cd18660 | repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier ... |
1861-1917 | 8.94e-10 | ||||||||||
repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349307 [Multi-domain] Cd Length: 70 Bit Score: 57.76 E-value: 8.94e-10
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| CHROMO | smart00298 | Chromatin organization modifier domain; |
1941-1993 | 5.04e-09 | ||||||||||
Chromatin organization modifier domain; Pssm-ID: 214605 [Multi-domain] Cd Length: 55 Bit Score: 55.30 E-value: 5.04e-09
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| CD2_tandem_CHD3-4_like | cd18662 | repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ... |
1942-1991 | 1.15e-08 | ||||||||||
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349309 [Multi-domain] Cd Length: 55 Bit Score: 54.19 E-value: 1.15e-08
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
1326-1904 | 1.74e-08 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 61.70 E-value: 1.74e-08
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| CD_CSD | cd00024 | CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ... |
1941-1993 | 1.84e-08 | ||||||||||
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain. Pssm-ID: 349274 [Multi-domain] Cd Length: 50 Bit Score: 53.25 E-value: 1.84e-08
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1968-2590 | 1.28e-07 | ||||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 58.11 E-value: 1.28e-07
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| MSCRAMM_ClfA | NF033609 | MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ... |
1335-1792 | 3.24e-07 | ||||||||||
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif. Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 57.23 E-value: 3.24e-07
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| PRK05901 | PRK05901 | RNA polymerase sigma factor; Provisional |
1663-1869 | 8.49e-07 | ||||||||||
RNA polymerase sigma factor; Provisional Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 55.39 E-value: 8.49e-07
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| PTZ00341 | PTZ00341 | Ring-infected erythrocyte surface antigen; Provisional |
1591-1882 | 8.96e-07 | ||||||||||
Ring-infected erythrocyte surface antigen; Provisional Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 55.95 E-value: 8.96e-07
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| PTZ00341 | PTZ00341 | Ring-infected erythrocyte surface antigen; Provisional |
1682-1963 | 1.23e-06 | ||||||||||
Ring-infected erythrocyte surface antigen; Provisional Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 55.56 E-value: 1.23e-06
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| PTZ00341 | PTZ00341 | Ring-infected erythrocyte surface antigen; Provisional |
3488-3713 | 1.33e-06 | ||||||||||
Ring-infected erythrocyte surface antigen; Provisional Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 55.18 E-value: 1.33e-06
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| MSCRAMM_ClfA | NF033609 | MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ... |
1532-1867 | 1.40e-06 | ||||||||||
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif. Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 55.30 E-value: 1.40e-06
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| PRK12678 | PRK12678 | transcription termination factor Rho; Provisional |
1338-1541 | 2.32e-06 | ||||||||||
transcription termination factor Rho; Provisional Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 54.14 E-value: 2.32e-06
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| MDN1 | COG5271 | Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal ... |
1363-1874 | 4.92e-06 | ||||||||||
Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]; Pssm-ID: 444083 [Multi-domain] Cd Length: 1028 Bit Score: 53.48 E-value: 4.92e-06
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| 2A1904 | TIGR00927 | K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ... |
1572-1859 | 5.01e-06 | ||||||||||
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds] Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 53.46 E-value: 5.01e-06
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| DMP1 | pfam07263 | Dentin matrix protein 1 (DMP1); This family consists of several mammalian dentin matrix ... |
1359-1747 | 7.78e-06 | ||||||||||
Dentin matrix protein 1 (DMP1); This family consists of several mammalian dentin matrix protein 1 (DMP1) sequences. The dentin matrix acidic phosphoprotein 1 (DMP1) gene has been mapped to human chromosome 4q21. DMP1 is a bone and teeth specific protein initially identified from mineralized dentin. DMP1 is primarily localized in the nuclear compartment of undifferentiated osteoblasts. In the nucleus, DMP1 acts as a transcriptional component for activation of osteoblast-specific genes like osteocalcin. During the early phase of osteoblast maturation, Ca(2+) surges into the nucleus from the cytoplasm, triggering the phosphorylation of DMP1 by a nuclear isoform of casein kinase II. This phosphorylated DMP1 is then exported out into the extracellular matrix, where it regulates nucleation of hydroxyapatite. DMP1 is a unique molecule that initiates osteoblast differentiation by transcription in the nucleus and orchestrates mineralized matrix formation extracellularly, at later stages of osteoblast maturation. The DMP1 gene has been found to be ectopically expressed in lung cancer although the reason for this is unknown. Pssm-ID: 462128 [Multi-domain] Cd Length: 519 Bit Score: 52.24 E-value: 7.78e-06
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| CD1_tandem_CHD3-4_like | cd18667 | repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ... |
1853-1902 | 7.88e-06 | ||||||||||
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349314 [Multi-domain] Cd Length: 79 Bit Score: 46.95 E-value: 7.88e-06
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| PRK05901 | PRK05901 | RNA polymerase sigma factor; Provisional |
1591-1786 | 8.13e-06 | ||||||||||
RNA polymerase sigma factor; Provisional Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 52.30 E-value: 8.13e-06
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
2028-2171 | 9.73e-06 | ||||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 48.82 E-value: 9.73e-06
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
3496-3790 | 1.47e-05 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 52.07 E-value: 1.47e-05
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| 2A1904 | TIGR00927 | K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ... |
1668-1865 | 1.51e-05 | ||||||||||
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds] Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 51.92 E-value: 1.51e-05
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| CD2_tandem_ScCHD1_like | cd18664 | repeat 2 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein ... |
1938-1983 | 1.62e-05 | ||||||||||
repeat 2 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein 1, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349311 Cd Length: 59 Bit Score: 45.34 E-value: 1.62e-05
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| PTZ00108 | PTZ00108 | DNA topoisomerase 2-like protein; Provisional |
1655-1874 | 2.57e-05 | ||||||||||
DNA topoisomerase 2-like protein; Provisional Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 51.20 E-value: 2.57e-05
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
3516-3724 | 2.73e-05 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 50.91 E-value: 2.73e-05
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| chromodomain | cd18966 | CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ... |
1941-1986 | 2.87e-05 | ||||||||||
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. Pssm-ID: 349322 Cd Length: 49 Bit Score: 44.20 E-value: 2.87e-05
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| TFIIF_alpha | pfam05793 | Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); Transcription initiation ... |
1664-1856 | 2.99e-05 | ||||||||||
Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II. Pssm-ID: 310411 [Multi-domain] Cd Length: 528 Bit Score: 50.33 E-value: 2.99e-05
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| CHROMO | smart00298 | Chromatin organization modifier domain; |
1879-1921 | 3.66e-05 | ||||||||||
Chromatin organization modifier domain; Pssm-ID: 214605 [Multi-domain] Cd Length: 55 Bit Score: 44.13 E-value: 3.66e-05
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| PTZ00341 | PTZ00341 | Ring-infected erythrocyte surface antigen; Provisional |
1662-1873 | 3.83e-05 | ||||||||||
Ring-infected erythrocyte surface antigen; Provisional Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 50.56 E-value: 3.83e-05
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| PTZ00341 | PTZ00341 | Ring-infected erythrocyte surface antigen; Provisional |
1553-1839 | 5.14e-05 | ||||||||||
Ring-infected erythrocyte surface antigen; Provisional Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 50.17 E-value: 5.14e-05
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| Chromo | pfam00385 | Chromo (CHRromatin organization MOdifier) domain; |
1879-1919 | 8.39e-05 | ||||||||||
Chromo (CHRromatin organization MOdifier) domain; Pssm-ID: 459793 [Multi-domain] Cd Length: 52 Bit Score: 42.95 E-value: 8.39e-05
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
1657-1865 | 9.05e-05 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 49.37 E-value: 9.05e-05
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| Mpp10 | COG5384 | U3 small nucleolar ribonucleoprotein component [Translation, ribosomal structure and ... |
1660-1891 | 9.82e-05 | ||||||||||
U3 small nucleolar ribonucleoprotein component [Translation, ribosomal structure and biogenesis]; Pssm-ID: 227674 [Multi-domain] Cd Length: 569 Bit Score: 48.92 E-value: 9.82e-05
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
3496-3706 | 1.30e-04 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 48.98 E-value: 1.30e-04
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
3516-3717 | 1.34e-04 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 48.98 E-value: 1.34e-04
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| rad2 | TIGR00600 | DNA excision repair protein (rad2); All proteins in this family for which functions are known ... |
1394-1864 | 1.63e-04 | ||||||||||
DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273166 [Multi-domain] Cd Length: 1034 Bit Score: 48.36 E-value: 1.63e-04
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| COG5177 | COG5177 | Uncharacterized conserved protein [Function unknown]; |
1667-1900 | 1.64e-04 | ||||||||||
Uncharacterized conserved protein [Function unknown]; Pssm-ID: 227504 [Multi-domain] Cd Length: 769 Bit Score: 48.15 E-value: 1.64e-04
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| BMS1 | COG5192 | GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and ... |
1542-1871 | 2.25e-04 | ||||||||||
GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]; Pssm-ID: 227519 [Multi-domain] Cd Length: 1077 Bit Score: 47.81 E-value: 2.25e-04
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| 2A1904 | TIGR00927 | K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ... |
1663-1873 | 2.37e-04 | ||||||||||
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds] Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 47.68 E-value: 2.37e-04
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| Caldesmon | pfam02029 | Caldesmon; |
1666-1871 | 2.38e-04 | ||||||||||
Caldesmon; Pssm-ID: 460421 [Multi-domain] Cd Length: 495 Bit Score: 47.55 E-value: 2.38e-04
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| PHA03169 | PHA03169 | hypothetical protein; Provisional |
3515-3708 | 2.64e-04 | ||||||||||
hypothetical protein; Provisional Pssm-ID: 223003 [Multi-domain] Cd Length: 413 Bit Score: 47.27 E-value: 2.64e-04
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| CD_MarY1_POL_like | cd18975 | chromodomain of Tricholoma matsutake polyprotein, and similar proteins; This subgroup includes ... |
1941-1988 | 2.74e-04 | ||||||||||
chromodomain of Tricholoma matsutake polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in the polyprotein from the MarY1 Ty3/Gypsy long terminal repeat (LTR) retroelement from the from the Ectomycorrhizal Basidiomycete Tricholoma matsutake. The pol gene in TY3/gypsy elements generally encodes domains in the following order: prt-reverse transcriptase-RNase H-integrase, in marY1 POL the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349331 Cd Length: 49 Bit Score: 41.76 E-value: 2.74e-04
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| CD2_tandem_CHD1-2_like | cd18661 | repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ... |
1942-1978 | 2.82e-04 | ||||||||||
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 and CHD2. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349308 Cd Length: 58 Bit Score: 41.90 E-value: 2.82e-04
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| PRK03918 | PRK03918 | DNA double-strand break repair ATPase Rad50; |
1633-1882 | 3.00e-04 | ||||||||||
DNA double-strand break repair ATPase Rad50; Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 47.37 E-value: 3.00e-04
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
2029-2197 | 3.26e-04 | ||||||||||
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 44.22 E-value: 3.26e-04
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| COG5137 | COG5137 | Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics] ... |
1663-1777 | 3.60e-04 | ||||||||||
Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]; Pssm-ID: 227466 [Multi-domain] Cd Length: 279 Bit Score: 46.14 E-value: 3.60e-04
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| CD_POL_like | cd18974 | chromodomain of Penicillium solitum protein PENSOL_c198G03123; This subgroup includes the ... |
1941-1993 | 3.79e-04 | ||||||||||
chromodomain of Penicillium solitum protein PENSOL_c198G03123; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Penicillium solitum protein PENSOL_c198G03123 a putative polyprotein from a Ty3/Gypsy long terminal repeat (LTR) retroelement. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349330 Cd Length: 50 Bit Score: 41.31 E-value: 3.79e-04
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| CD1_tandem | cd18660 | repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier ... |
1938-1993 | 4.84e-04 | ||||||||||
repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349307 [Multi-domain] Cd Length: 70 Bit Score: 41.58 E-value: 4.84e-04
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| Atrophin-1 | pfam03154 | Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ... |
221-533 | 5.44e-04 | ||||||||||
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 46.68 E-value: 5.44e-04
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| MSCRAMM_ClfA | NF033609 | MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ... |
1334-1673 | 5.47e-04 | ||||||||||
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif. Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 46.44 E-value: 5.47e-04
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| PTZ00341 | PTZ00341 | Ring-infected erythrocyte surface antigen; Provisional |
3487-3706 | 5.52e-04 | ||||||||||
Ring-infected erythrocyte surface antigen; Provisional Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 46.70 E-value: 5.52e-04
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| PRK05901 | PRK05901 | RNA polymerase sigma factor; Provisional |
1694-1878 | 5.68e-04 | ||||||||||
RNA polymerase sigma factor; Provisional Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 46.14 E-value: 5.68e-04
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
2030-2197 | 6.35e-04 | ||||||||||
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 43.77 E-value: 6.35e-04
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| PRK05901 | PRK05901 | RNA polymerase sigma factor; Provisional |
1600-1793 | 6.35e-04 | ||||||||||
RNA polymerase sigma factor; Provisional Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 46.14 E-value: 6.35e-04
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| COG5593 | COG5593 | Nucleic-acid-binding protein possibly involved in ribosomal biogenesis [Translation, ribosomal ... |
1664-1807 | 7.53e-04 | ||||||||||
Nucleic-acid-binding protein possibly involved in ribosomal biogenesis [Translation, ribosomal structure and biogenesis]; Pssm-ID: 227880 [Multi-domain] Cd Length: 821 Bit Score: 46.19 E-value: 7.53e-04
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| CD_CMT3_like | cd18635 | chromodomain of chromomethylase 3, and similar proteins; CHRomatin Organization Modifier ... |
1941-1993 | 7.57e-04 | ||||||||||
chromodomain of chromomethylase 3, and similar proteins; CHRomatin Organization Modifier (chromo) domain of DNA (cytosine-5)-methyltransferase chromomethylase 3 (CMT3, EC:2.1.1.37), and similar proteins. CMT3 is primarily a CHG (where H is either A, T or C) methyltransferase and is predominantly expressed in actively replicating cells. The protein is involved in preferentially methylating transposon-related sequences, reducing their mobility. Studies suggest that in order to target DNA methylation, CMT3 associates with H3K9me2-containing nucleosomes through binding of its BAH- and chromo-domains to H3K9me2. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Pssm-ID: 349285 Cd Length: 57 Bit Score: 40.76 E-value: 7.57e-04
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| PRK05901 | PRK05901 | RNA polymerase sigma factor; Provisional |
1657-1858 | 7.72e-04 | ||||||||||
RNA polymerase sigma factor; Provisional Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 45.76 E-value: 7.72e-04
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| MAK16 | COG5129 | Nuclear protein with HMG-like acidic region [General function prediction only]; |
1671-1780 | 8.70e-04 | ||||||||||
Nuclear protein with HMG-like acidic region [General function prediction only]; Pssm-ID: 227458 [Multi-domain] Cd Length: 303 Bit Score: 45.04 E-value: 8.70e-04
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
2417-2467 | 1.16e-03 | ||||||||||
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 40.77 E-value: 1.16e-03
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| Med15 | pfam09606 | ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ... |
1056-1265 | 1.39e-03 | ||||||||||
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 45.00 E-value: 1.39e-03
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| MAK16 | COG5129 | Nuclear protein with HMG-like acidic region [General function prediction only]; |
1651-1809 | 1.71e-03 | ||||||||||
Nuclear protein with HMG-like acidic region [General function prediction only]; Pssm-ID: 227458 [Multi-domain] Cd Length: 303 Bit Score: 44.27 E-value: 1.71e-03
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| COG5137 | COG5137 | Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics] ... |
1663-1765 | 1.84e-03 | ||||||||||
Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]; Pssm-ID: 227466 [Multi-domain] Cd Length: 279 Bit Score: 43.83 E-value: 1.84e-03
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
1683-1866 | 2.79e-03 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 44.36 E-value: 2.79e-03
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| chromodomain | cd18968 | CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ... |
1941-1987 | 2.90e-03 | ||||||||||
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. Pssm-ID: 349324 Cd Length: 57 Bit Score: 38.87 E-value: 2.90e-03
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| CD3_cpSRP43_like | cd18628 | chromodomain 3 of chloroplast signal recognition particle 43 kDa protein, and similar proteins; ... |
1945-1991 | 3.22e-03 | ||||||||||
chromodomain 3 of chloroplast signal recognition particle 43 kDa protein, and similar proteins; This subgroup includes the chromodomain 3 of chloroplast SRP43 (cpSRP43), and similar proteins. CpSRP43 is a component of the chloroplast signal recognition particle (SRP) pathway. It forms a stable complex with cpSRP54 (cpSRP complex) which is required for the efficient posttranslational transport of members of the nuclearly encoded light harvesting chlorophyll-a/b-binding proteins (LHCPs) to the thylakoid membrane. Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromodomain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followed by a related chromo shadow domain. Pssm-ID: 349278 Cd Length: 51 Bit Score: 38.52 E-value: 3.22e-03
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| COG5137 | COG5137 | Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics] ... |
1658-1781 | 3.64e-03 | ||||||||||
Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]; Pssm-ID: 227466 [Multi-domain] Cd Length: 279 Bit Score: 43.06 E-value: 3.64e-03
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| Granin | pfam01271 | Granin (chromogranin or secretogranin); |
1595-1866 | 4.00e-03 | ||||||||||
Granin (chromogranin or secretogranin); Pssm-ID: 279595 [Multi-domain] Cd Length: 584 Bit Score: 43.48 E-value: 4.00e-03
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| PRK08581 | PRK08581 | amidase domain-containing protein; |
1558-1837 | 4.65e-03 | ||||||||||
amidase domain-containing protein; Pssm-ID: 236304 [Multi-domain] Cd Length: 619 Bit Score: 43.24 E-value: 4.65e-03
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| PRK05901 | PRK05901 | RNA polymerase sigma factor; Provisional |
1663-1826 | 4.67e-03 | ||||||||||
RNA polymerase sigma factor; Provisional Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 43.44 E-value: 4.67e-03
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| PTZ00108 | PTZ00108 | DNA topoisomerase 2-like protein; Provisional |
1517-1749 | 4.71e-03 | ||||||||||
DNA topoisomerase 2-like protein; Provisional Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 43.50 E-value: 4.71e-03
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| chromodomain | cd18969 | CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; for most members ... |
1941-1991 | 5.89e-03 | ||||||||||
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; for most members of this subgroup, the chromodomain is followed by a chromo shadow domain; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. For the majority of members of this subgroup, the chromodomain is followed by a chromo shadow domain (CSD). Pssm-ID: 349325 Cd Length: 56 Bit Score: 37.89 E-value: 5.89e-03
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| PRK12678 | PRK12678 | transcription termination factor Rho; Provisional |
1319-1500 | 8.36e-03 | ||||||||||
transcription termination factor Rho; Provisional Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 42.58 E-value: 8.36e-03
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