brahma, isoform E [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 |
739-1368 | 1.59e-165 | |||||||||
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: 529.76 E-value: 1.59e-165
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| Bromo_SNF2L2 | cd05516 | Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ... |
1425-1530 | 2.46e-55 | |||||||||
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. : Pssm-ID: 99947 Cd Length: 107 Bit Score: 187.63 E-value: 2.46e-55
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| HSA | smart00573 | domain in helicases and associated with SANT domains; |
501-573 | 1.73e-23 | |||||||||
domain in helicases and associated with SANT domains; : Pssm-ID: 214727 [Multi-domain] Cd Length: 73 Bit Score: 95.54 E-value: 1.73e-23
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| BRK | pfam07533 | BRK domain; The function of this domain is unknown. It is often found associated with ... |
650-691 | 1.23e-16 | |||||||||
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: 74.85 E-value: 1.23e-16
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| PTZ00121 super family | cl31754 | MAEBL; Provisional |
477-651 | 6.87e-06 | |||||||||
MAEBL; Provisional The actual alignment was detected with superfamily member PTZ00121: Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 51.30 E-value: 6.87e-06
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| QLQ | pfam08880 | QLQ; The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found ... |
173-202 | 4.39e-05 | |||||||||
QLQ; The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. This domain has thus been postulated to be involved in mediating protein interactions. : Pssm-ID: 462622 Cd Length: 35 Bit Score: 41.94 E-value: 4.39e-05
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| Pro-rich | pfam15240 | Proline-rich protein; This family includes several eukaryotic proline-rich proteins. |
247-401 | 7.17e-04 | |||||||||
Proline-rich protein; This family includes several eukaryotic proline-rich proteins. : Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 42.33 E-value: 7.17e-04
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| Name | Accession | Description | Interval | E-value | |||||||||
| PLN03142 | PLN03142 | Probable chromatin-remodeling complex ATPase chain; Provisional |
739-1368 | 1.59e-165 | |||||||||
Probable chromatin-remodeling complex ATPase chain; Provisional Pssm-ID: 215601 [Multi-domain] Cd Length: 1033 Bit Score: 529.76 E-value: 1.59e-165
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| DEXHc_SMARCA2_SMARCA4 | cd17996 | DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ... |
770-1000 | 2.63e-165 | |||||||||
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: 499.20 E-value: 2.63e-165
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
661-1248 | 5.67e-125 | |||||||||
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: 5.67e-125
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| SNF2-rel_dom | pfam00176 | SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
776-1071 | 1.66e-117 | |||||||||
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: 372.02 E-value: 1.66e-117
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| Bromo_SNF2L2 | cd05516 | Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ... |
1425-1530 | 2.46e-55 | |||||||||
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99947 Cd Length: 107 Bit Score: 187.63 E-value: 2.46e-55
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| BROMO | smart00297 | bromo domain; |
1423-1523 | 4.04e-30 | |||||||||
bromo domain; Pssm-ID: 197636 [Multi-domain] Cd Length: 107 Bit Score: 115.45 E-value: 4.04e-30
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
772-961 | 7.29e-29 | |||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 115.28 E-value: 7.29e-29
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| HSA | smart00573 | domain in helicases and associated with SANT domains; |
501-573 | 1.73e-23 | |||||||||
domain in helicases and associated with SANT domains; Pssm-ID: 214727 [Multi-domain] Cd Length: 73 Bit Score: 95.54 E-value: 1.73e-23
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| HSA | pfam07529 | HSA domain; This domain is predicted to bind DNA and is often found associated with helicases. ... |
502-568 | 1.17e-18 | |||||||||
HSA domain; This domain is predicted to bind DNA and is often found associated with helicases. This region does not form a compact domain in the known structures. Pssm-ID: 462194 [Multi-domain] Cd Length: 67 Bit Score: 81.46 E-value: 1.17e-18
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| COG5076 | COG5076 | Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ... |
1405-1524 | 1.33e-17 | |||||||||
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]; Pssm-ID: 227408 [Multi-domain] Cd Length: 371 Bit Score: 86.78 E-value: 1.33e-17
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| BRK | pfam07533 | BRK domain; The function of this domain is unknown. It is often found associated with ... |
650-691 | 1.23e-16 | |||||||||
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: 74.85 E-value: 1.23e-16
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| Bromodomain | pfam00439 | Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ... |
1432-1516 | 1.34e-16 | |||||||||
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 425683 [Multi-domain] Cd Length: 84 Bit Score: 76.20 E-value: 1.34e-16
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| BRK | smart00592 | domain in transcription and CHROMO domain helicases; |
649-693 | 2.78e-16 | |||||||||
domain in transcription and CHROMO domain helicases; Pssm-ID: 197800 Cd Length: 45 Bit Score: 73.92 E-value: 2.78e-16
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
477-651 | 6.87e-06 | |||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 51.30 E-value: 6.87e-06
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
405-643 | 7.94e-06 | |||||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 50.71 E-value: 7.94e-06
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| SMC_N | pfam02463 | RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ... |
407-645 | 3.48e-05 | |||||||||
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 48.81 E-value: 3.48e-05
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| QLQ | pfam08880 | QLQ; The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found ... |
173-202 | 4.39e-05 | |||||||||
QLQ; The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. This domain has thus been postulated to be involved in mediating protein interactions. Pssm-ID: 462622 Cd Length: 35 Bit Score: 41.94 E-value: 4.39e-05
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| QLQ | smart00951 | QLQ is named after the conserved Gln, Leu, Gln motif; QLQ is found at the N-terminus of SWI2 ... |
172-202 | 6.20e-05 | |||||||||
QLQ is named after the conserved Gln, Leu, Gln motif; QLQ is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions. Pssm-ID: 214931 Cd Length: 36 Bit Score: 41.36 E-value: 6.20e-05
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| PRK11637 | PRK11637 | AmiB activator; Provisional |
451-569 | 2.53e-04 | |||||||||
AmiB activator; Provisional Pssm-ID: 236942 [Multi-domain] Cd Length: 428 Bit Score: 45.45 E-value: 2.53e-04
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| Pro-rich | pfam15240 | Proline-rich protein; This family includes several eukaryotic proline-rich proteins. |
247-401 | 7.17e-04 | |||||||||
Proline-rich protein; This family includes several eukaryotic proline-rich proteins. Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 42.33 E-value: 7.17e-04
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
367-611 | 1.59e-03 | |||||||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 42.53 E-value: 1.59e-03
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| PHA03378 | PHA03378 | EBNA-3B; Provisional |
255-388 | 2.95e-03 | |||||||||
EBNA-3B; Provisional Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 42.36 E-value: 2.95e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| PLN03142 | PLN03142 | Probable chromatin-remodeling complex ATPase chain; Provisional |
739-1368 | 1.59e-165 | |||||||||
Probable chromatin-remodeling complex ATPase chain; Provisional Pssm-ID: 215601 [Multi-domain] Cd Length: 1033 Bit Score: 529.76 E-value: 1.59e-165
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| DEXHc_SMARCA2_SMARCA4 | cd17996 | DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ... |
770-1000 | 2.63e-165 | |||||||||
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: 499.20 E-value: 2.63e-165
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| DEXHc_SMARCA4 | cd18062 | DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ... |
750-1000 | 2.29e-142 | |||||||||
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: 438.32 E-value: 2.29e-142
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| DEXHc_SMARCA2 | cd18063 | DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent ... |
750-1000 | 2.58e-139 | |||||||||
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: 430.25 E-value: 2.58e-139
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
661-1248 | 5.67e-125 | |||||||||
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: 5.67e-125
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| SNF2-rel_dom | pfam00176 | SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
776-1071 | 1.66e-117 | |||||||||
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: 372.02 E-value: 1.66e-117
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| DEXHc_HELLS_SMARCA6 | cd18009 | DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ... |
770-1000 | 1.05e-93 | |||||||||
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: 302.77 E-value: 1.05e-93
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| DEXHc_SMARCA1_SMARCA5 | cd17997 | DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ... |
770-1000 | 1.31e-93 | |||||||||
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: 301.93 E-value: 1.31e-93
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| DEXQc_SRCAP | cd18003 | DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ... |
773-998 | 4.99e-85 | |||||||||
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: 277.31 E-value: 4.99e-85
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| DEXHc_CHD1_2 | cd17993 | DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ... |
772-998 | 1.80e-81 | |||||||||
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: 266.91 E-value: 1.80e-81
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| DEXHc_Snf | cd17919 | DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
773-952 | 5.00e-79 | |||||||||
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: 258.65 E-value: 5.00e-79
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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; ... |
773-998 | 2.63e-76 | |||||||||
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: 252.55 E-value: 2.63e-76
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| DEXHc_SMARCA5 | cd18064 | DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ... |
771-1010 | 5.63e-70 | |||||||||
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: 235.33 E-value: 5.63e-70
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| DEXHc_SMARCA1 | cd18065 | DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ... |
763-1000 | 7.83e-70 | |||||||||
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: 234.53 E-value: 7.83e-70
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| DEXQc_INO80 | cd18002 | DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ... |
773-998 | 4.34e-66 | |||||||||
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: 223.54 E-value: 4.34e-66
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| DEXHc_CHD2 | cd18054 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ... |
773-998 | 1.18e-64 | |||||||||
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: 219.49 E-value: 1.18e-64
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| DEXHc_CHD1L | cd18006 | DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ... |
773-998 | 5.08e-64 | |||||||||
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: 216.92 E-value: 5.08e-64
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| DEXQc_arch_SWI2_SNF2 | cd18012 | DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ... |
769-1000 | 1.15e-60 | |||||||||
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: 207.42 E-value: 1.15e-60
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| DEXHc_CHD3_4_5 | cd17994 | DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; ... |
773-998 | 1.89e-59 | |||||||||
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: 203.05 E-value: 1.89e-59
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| SF2_C_SNF | cd18793 | C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
1096-1223 | 6.60e-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: 190.38 E-value: 6.60e-56
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| Bromo_SNF2L2 | cd05516 | Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ... |
1425-1530 | 2.46e-55 | |||||||||
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99947 Cd Length: 107 Bit Score: 187.63 E-value: 2.46e-55
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| DEXHc_SMARCAD1 | cd17998 | DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ... |
773-952 | 4.18e-54 | |||||||||
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: 187.21 E-value: 4.18e-54
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| DEXHc_CHD1 | cd18053 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ... |
773-998 | 1.37e-51 | |||||||||
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: 182.17 E-value: 1.37e-51
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| DEXHc_ERCC6L | cd18001 | DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ... |
773-998 | 2.14e-50 | |||||||||
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: 178.33 E-value: 2.14e-50
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| DEXHc_CHD5 | cd18057 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ... |
773-998 | 2.46e-50 | |||||||||
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: 178.33 E-value: 2.46e-50
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| DEXHc_Mot1 | cd17999 | DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ... |
773-998 | 2.59e-50 | |||||||||
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: 178.31 E-value: 2.59e-50
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| DEXHc_ERCC6 | cd18000 | DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ... |
773-949 | 1.20e-49 | |||||||||
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: 174.82 E-value: 1.20e-49
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| DEXHc_CHD6 | cd18058 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ... |
773-998 | 2.79e-49 | |||||||||
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: 174.85 E-value: 2.79e-49
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| DEXHc_CHD3 | cd18055 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ... |
773-998 | 6.10e-49 | |||||||||
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: 174.43 E-value: 6.10e-49
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| DEXHc_CHD7 | cd18059 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ... |
773-998 | 5.77e-48 | |||||||||
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: 170.98 E-value: 5.77e-48
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| DEXHc_CHD8 | cd18060 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ... |
773-998 | 1.59e-47 | |||||||||
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: 169.85 E-value: 1.59e-47
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| DEXHc_CHD4 | cd18056 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ... |
773-998 | 4.69e-46 | |||||||||
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: 166.01 E-value: 4.69e-46
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| DEXHc_ERCC6L2 | cd18005 | DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ... |
773-998 | 3.78e-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: 163.70 E-value: 3.78e-45
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| DEXHc_CHD9 | cd18061 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ... |
773-998 | 1.32e-44 | |||||||||
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: 161.33 E-value: 1.32e-44
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| DEXHc_RAD54 | cd18004 | DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ... |
773-998 | 3.83e-39 | |||||||||
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: 146.28 E-value: 3.83e-39
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| DEXDc_SHPRH-like | cd18008 | DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ... |
773-998 | 8.51e-39 | |||||||||
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: 145.51 E-value: 8.51e-39
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| DEXHc_ATRX-like | cd18007 | DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ... |
773-965 | 2.03e-35 | |||||||||
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: 135.50 E-value: 2.03e-35
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| BROMO | smart00297 | bromo domain; |
1423-1523 | 4.04e-30 | |||||||||
bromo domain; Pssm-ID: 197636 [Multi-domain] Cd Length: 107 Bit Score: 115.45 E-value: 4.04e-30
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| DEXHc_RAD54B | cd18066 | DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ... |
773-998 | 4.61e-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: 117.25 E-value: 4.61e-29
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| DEXHc_HLTF1_SMARC3 | cd18071 | DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ... |
773-998 | 6.31e-29 | |||||||||
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: 116.80 E-value: 6.31e-29
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
772-961 | 7.29e-29 | |||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 115.28 E-value: 7.29e-29
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
1098-1212 | 8.61e-28 | |||||||||
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: 108.84 E-value: 8.61e-28
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| Bromo_SNF2 | cd05519 | Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ... |
1427-1524 | 1.04e-26 | |||||||||
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99950 Cd Length: 103 Bit Score: 105.50 E-value: 1.04e-26
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| Bromodomain | cd04369 | Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ... |
1427-1523 | 4.12e-26 | |||||||||
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine. Pssm-ID: 99922 [Multi-domain] Cd Length: 99 Bit Score: 103.99 E-value: 4.12e-26
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| Bromo_polybromo_V | cd05515 | Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ... |
1440-1529 | 9.55e-26 | |||||||||
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. Pssm-ID: 99946 Cd Length: 105 Bit Score: 103.15 E-value: 9.55e-26
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| DEXHc_RAD54A | cd18067 | DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ... |
773-998 | 1.46e-25 | |||||||||
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: 107.17 E-value: 1.46e-25
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| DEXHc_HARP_SMARCAL1 | cd18010 | DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ... |
773-952 | 5.08e-24 | |||||||||
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: 101.90 E-value: 5.08e-24
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| HSA | smart00573 | domain in helicases and associated with SANT domains; |
501-573 | 1.73e-23 | |||||||||
domain in helicases and associated with SANT domains; Pssm-ID: 214727 [Multi-domain] Cd Length: 73 Bit Score: 95.54 E-value: 1.73e-23
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| Bromo_polybromo_II | cd05517 | Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ... |
1426-1527 | 2.65e-23 | |||||||||
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. Pssm-ID: 99948 Cd Length: 103 Bit Score: 95.97 E-value: 2.65e-23
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| DEXHc_ARIP4 | cd18069 | DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called ... |
773-965 | 5.69e-23 | |||||||||
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: 99.12 E-value: 5.69e-23
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
1129-1212 | 8.97e-23 | |||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 93.82 E-value: 8.97e-23
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| Bromo_polybromo_III | cd05520 | Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ... |
1441-1522 | 1.53e-21 | |||||||||
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. Pssm-ID: 99951 Cd Length: 103 Bit Score: 90.86 E-value: 1.53e-21
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| DEXHc_TTF2 | cd18072 | DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ... |
773-998 | 2.01e-20 | |||||||||
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: 92.16 E-value: 2.01e-20
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| Bromo_polybromo_IV | cd05518 | Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ... |
1426-1522 | 7.14e-20 | |||||||||
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. Pssm-ID: 99949 [Multi-domain] Cd Length: 103 Bit Score: 86.35 E-value: 7.14e-20
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| DEXDc_RapA | cd18011 | DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
795-952 | 1.39e-19 | |||||||||
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: 88.89 E-value: 1.39e-19
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| SnAC | pfam14619 | Snf2-ATP coupling, chromatin remodelling complex; This domain appears to play a crucial role ... |
1308-1375 | 3.39e-19 | |||||||||
Snf2-ATP coupling, chromatin remodelling complex; This domain appears to play a crucial role in chromatin remodelling for yeast SWI/SNF. It binds histones. It is required for mobilising nucleosomes and lies within the catalytic subunit of the yeast SWI/SNF. It is found to be universally conserved. Pssm-ID: 464219 [Multi-domain] Cd Length: 69 Bit Score: 83.08 E-value: 3.39e-19
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| Bromo_polybromo_I | cd05524 | Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ... |
1431-1530 | 5.08e-19 | |||||||||
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. Pssm-ID: 99954 [Multi-domain] Cd Length: 113 Bit Score: 84.31 E-value: 5.08e-19
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| DEXHc_ATRX | cd18068 | DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ... |
794-986 | 5.52e-19 | |||||||||
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: 88.41 E-value: 5.52e-19
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| HSA | pfam07529 | HSA domain; This domain is predicted to bind DNA and is often found associated with helicases. ... |
502-568 | 1.17e-18 | |||||||||
HSA domain; This domain is predicted to bind DNA and is often found associated with helicases. This region does not form a compact domain in the known structures. Pssm-ID: 462194 [Multi-domain] Cd Length: 67 Bit Score: 81.46 E-value: 1.17e-18
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| COG5076 | COG5076 | Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ... |
1405-1524 | 1.33e-17 | |||||||||
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]; Pssm-ID: 227408 [Multi-domain] Cd Length: 371 Bit Score: 86.78 E-value: 1.33e-17
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| BRK | pfam07533 | BRK domain; The function of this domain is unknown. It is often found associated with ... |
650-691 | 1.23e-16 | |||||||||
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: 74.85 E-value: 1.23e-16
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| Bromodomain | pfam00439 | Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ... |
1432-1516 | 1.34e-16 | |||||||||
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 425683 [Multi-domain] Cd Length: 84 Bit Score: 76.20 E-value: 1.34e-16
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| BRK | smart00592 | domain in transcription and CHROMO domain helicases; |
649-693 | 2.78e-16 | |||||||||
domain in transcription and CHROMO domain helicases; Pssm-ID: 197800 Cd Length: 45 Bit Score: 73.92 E-value: 2.78e-16
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| Bromo_ASH1 | cd05525 | Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ... |
1433-1528 | 9.36e-15 | |||||||||
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99955 [Multi-domain] Cd Length: 106 Bit Score: 71.65 E-value: 9.36e-15
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| Bromo_gcn5_like | cd05509 | Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ... |
1429-1524 | 2.63e-14 | |||||||||
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99941 [Multi-domain] Cd Length: 101 Bit Score: 70.28 E-value: 2.63e-14
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| Bromo_Rsc1_2_II | cd05522 | Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ... |
1434-1523 | 2.63e-13 | |||||||||
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99953 [Multi-domain] Cd Length: 104 Bit Score: 67.65 E-value: 2.63e-13
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| Bromo_Acf1_like | cd05504 | Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ... |
1416-1524 | 4.62e-13 | |||||||||
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99936 Cd Length: 115 Bit Score: 67.04 E-value: 4.62e-13
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| DEXQc_bact_SNF2 | cd18013 | DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ... |
773-963 | 4.10e-12 | |||||||||
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: 67.37 E-value: 4.10e-12
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| DEXQc_SHPRH | cd18070 | DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ... |
773-962 | 1.66e-11 | |||||||||
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: 66.60 E-value: 1.66e-11
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| Bromo_Rsc1_2_I | cd05521 | Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ... |
1441-1521 | 3.50e-11 | |||||||||
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99952 Cd Length: 106 Bit Score: 61.57 E-value: 3.50e-11
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| Bromo_brd7_like | cd05513 | Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ... |
1461-1513 | 3.50e-10 | |||||||||
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99945 Cd Length: 98 Bit Score: 58.58 E-value: 3.50e-10
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| Bromo_Brdt_I_like | cd05497 | Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ... |
1460-1531 | 8.15e-10 | |||||||||
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99929 Cd Length: 107 Bit Score: 57.82 E-value: 8.15e-10
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| Bromo_Brdt_II_like | cd05498 | Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ... |
1460-1523 | 2.91e-09 | |||||||||
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99930 Cd Length: 102 Bit Score: 55.75 E-value: 2.91e-09
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| Bromo_cbp_like | cd05495 | Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ... |
1448-1524 | 2.00e-08 | |||||||||
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99927 Cd Length: 108 Bit Score: 53.60 E-value: 2.00e-08
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
725-932 | 2.18e-08 | |||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 58.88 E-value: 2.18e-08
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
772-932 | 3.40e-08 | |||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 54.60 E-value: 3.40e-08
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| Bromo_brd1_like | cd05512 | Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ... |
1461-1520 | 5.08e-08 | |||||||||
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99944 Cd Length: 98 Bit Score: 52.40 E-value: 5.08e-08
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| Bromo_AAA | cd05528 | Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ... |
1461-1506 | 6.20e-08 | |||||||||
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver Pssm-ID: 99957 Cd Length: 112 Bit Score: 52.36 E-value: 6.20e-08
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| Bromo_SPT7_like | cd05510 | Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ... |
1448-1510 | 9.60e-08 | |||||||||
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99942 [Multi-domain] Cd Length: 112 Bit Score: 52.06 E-value: 9.60e-08
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| Bromo_TFIID | cd05511 | Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ... |
1448-1510 | 3.58e-07 | |||||||||
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99943 [Multi-domain] Cd Length: 112 Bit Score: 50.34 E-value: 3.58e-07
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| Bromo_BDF1_2_II | cd05499 | Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ... |
1447-1523 | 3.76e-07 | |||||||||
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99931 Cd Length: 102 Bit Score: 49.98 E-value: 3.76e-07
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
773-932 | 5.45e-07 | |||||||||
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: 50.77 E-value: 5.45e-07
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| Bromo_BAZ2A_B_like | cd05503 | Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ... |
1450-1523 | 2.53e-06 | |||||||||
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99935 Cd Length: 97 Bit Score: 47.37 E-value: 2.53e-06
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| Bromo_BDF1_2_I | cd05500 | Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ... |
1426-1523 | 3.01e-06 | |||||||||
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99932 Cd Length: 103 Bit Score: 47.31 E-value: 3.01e-06
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| Bromo_tif1_like | cd05502 | Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ... |
1447-1523 | 3.05e-06 | |||||||||
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99934 [Multi-domain] Cd Length: 109 Bit Score: 47.67 E-value: 3.05e-06
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
477-651 | 6.87e-06 | |||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 51.30 E-value: 6.87e-06
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
405-643 | 7.94e-06 | |||||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 50.71 E-value: 7.94e-06
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| Bromo_WDR9_II | cd05496 | Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ... |
1448-1523 | 2.38e-05 | |||||||||
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99928 Cd Length: 119 Bit Score: 45.14 E-value: 2.38e-05
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| SMC_N | pfam02463 | RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ... |
407-645 | 3.48e-05 | |||||||||
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 48.81 E-value: 3.48e-05
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
409-591 | 3.89e-05 | |||||||||
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain. Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 47.61 E-value: 3.89e-05
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| QLQ | pfam08880 | QLQ; The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found ... |
173-202 | 4.39e-05 | |||||||||
QLQ; The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. This domain has thus been postulated to be involved in mediating protein interactions. Pssm-ID: 462622 Cd Length: 35 Bit Score: 41.94 E-value: 4.39e-05
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| QLQ | smart00951 | QLQ is named after the conserved Gln, Leu, Gln motif; QLQ is found at the N-terminus of SWI2 ... |
172-202 | 6.20e-05 | |||||||||
QLQ is named after the conserved Gln, Leu, Gln motif; QLQ is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions. Pssm-ID: 214931 Cd Length: 36 Bit Score: 41.36 E-value: 6.20e-05
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
1165-1215 | 6.81e-05 | |||||||||
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: 42.69 E-value: 6.81e-05
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| Bromo_brd8_like | cd05507 | Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ... |
1424-1506 | 8.29e-05 | |||||||||
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99939 Cd Length: 104 Bit Score: 43.12 E-value: 8.29e-05
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| Bromo_WSTF_like | cd05505 | Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ... |
1427-1512 | 9.85e-05 | |||||||||
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99937 Cd Length: 97 Bit Score: 42.91 E-value: 9.85e-05
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| Bromo_plant1 | cd05506 | Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ... |
1428-1523 | 1.19e-04 | |||||||||
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99938 Cd Length: 99 Bit Score: 42.70 E-value: 1.19e-04
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| DUF4670 | pfam15709 | Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ... |
485-636 | 1.31e-04 | |||||||||
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length. Pssm-ID: 464815 [Multi-domain] Cd Length: 522 Bit Score: 46.48 E-value: 1.31e-04
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| Bromo_polybromo_VI | cd05526 | Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which ... |
1427-1531 | 1.56e-04 | |||||||||
Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. Pssm-ID: 99956 Cd Length: 110 Bit Score: 42.74 E-value: 1.56e-04
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| PRK11637 | PRK11637 | AmiB activator; Provisional |
451-569 | 2.53e-04 | |||||||||
AmiB activator; Provisional Pssm-ID: 236942 [Multi-domain] Cd Length: 428 Bit Score: 45.45 E-value: 2.53e-04
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| Bromo_WDR9_I_like | cd05529 | Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ... |
1432-1512 | 2.94e-04 | |||||||||
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Pssm-ID: 99958 Cd Length: 128 Bit Score: 42.32 E-value: 2.94e-04
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
484-633 | 3.41e-04 | |||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 45.52 E-value: 3.41e-04
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| Pro-rich | pfam15240 | Proline-rich protein; This family includes several eukaryotic proline-rich proteins. |
247-401 | 7.17e-04 | |||||||||
Proline-rich protein; This family includes several eukaryotic proline-rich proteins. Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 42.33 E-value: 7.17e-04
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| Atrophin-1 | pfam03154 | Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ... |
251-398 | 7.39e-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: 44.37 E-value: 7.39e-04
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| MISS | pfam15822 | MAPK-interacting and spindle-stabilising protein-like; MISS is a family of eukaryotic ... |
249-390 | 1.01e-03 | |||||||||
MAPK-interacting and spindle-stabilising protein-like; MISS is a family of eukaryotic MAPK-interacting and spindle-stabilising protein-like proteins. MISS is rich in prolines and has four potential MAPK-phosphorylation sites, a MAPK-docking site, a PEST sequence (PEST motif) and a bipartite nuclear localization signal. The endogenous protein accumulates during mouse meiotic maturation and is found as discrete dots on the MII spindle. MISS is the first example of a physiological MAPK-substrate that is stabilized in MII that specifically regulates MII spindle integrity during the CSF arrest. Pssm-ID: 318115 [Multi-domain] Cd Length: 238 Bit Score: 42.67 E-value: 1.01e-03
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
478-764 | 1.04e-03 | |||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 43.98 E-value: 1.04e-03
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| DUF4670 | pfam15709 | Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ... |
406-577 | 1.49e-03 | |||||||||
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length. Pssm-ID: 464815 [Multi-domain] Cd Length: 522 Bit Score: 43.02 E-value: 1.49e-03
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
367-611 | 1.59e-03 | |||||||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 42.53 E-value: 1.59e-03
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
407-577 | 1.94e-03 | |||||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 43.00 E-value: 1.94e-03
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| DUF4659 | pfam15558 | Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins ... |
410-586 | 2.89e-03 | |||||||||
Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins in this family are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important. Pssm-ID: 464768 [Multi-domain] Cd Length: 374 Bit Score: 41.95 E-value: 2.89e-03
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| PHA03378 | PHA03378 | EBNA-3B; Provisional |
255-388 | 2.95e-03 | |||||||||
EBNA-3B; Provisional Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 42.36 E-value: 2.95e-03
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
478-634 | 3.12e-03 | |||||||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 42.06 E-value: 3.12e-03
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
486-629 | 3.52e-03 | |||||||||
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain. Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 41.44 E-value: 3.52e-03
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
793-931 | 3.68e-03 | |||||||||
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: 39.69 E-value: 3.68e-03
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| sbcc | TIGR00618 | exonuclease SbcC; All proteins in this family for which functions are known are part of an ... |
408-629 | 3.78e-03 | |||||||||
exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. 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: 129705 [Multi-domain] Cd Length: 1042 Bit Score: 42.26 E-value: 3.78e-03
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| DUF5401 | pfam17380 | Family of unknown function (DUF5401); This is a family of unknown function found in ... |
410-634 | 4.70e-03 | |||||||||
Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea. Pssm-ID: 375164 [Multi-domain] Cd Length: 722 Bit Score: 41.65 E-value: 4.70e-03
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| Drf_FH1 | pfam06346 | Formin Homology Region 1; This region is found in some of the Diaphanous related formins (Drfs) ... |
251-390 | 5.04e-03 | |||||||||
Formin Homology Region 1; This region is found in some of the Diaphanous related formins (Drfs). It consists of low complexity repeats of around 12 residues. Pssm-ID: 461881 [Multi-domain] Cd Length: 157 Bit Score: 39.47 E-value: 5.04e-03
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
409-607 | 8.73e-03 | |||||||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 40.91 E-value: 8.73e-03
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| EnvC | COG4942 | Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ... |
416-626 | 9.01e-03 | |||||||||
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 40.52 E-value: 9.01e-03
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| HDA2-3 | pfam11496 | Class II histone deacetylase complex subunits 2 and 3; This family of class II histone ... |
1097-1229 | 9.41e-03 | |||||||||
Class II histone deacetylase complex subunits 2 and 3; This family of class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi, The member from S. pombe is referred to as Ccq1 in Swiss:Q10432. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase complex. HDA1 interacts with itself and with the HDA2-HDA3 subcomplex to form a probable tetramer and these interactions are necessary for catalytic activity. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. HDA2 and HDA3 have a conserved coiled-coil domain towards their C-terminus. Pssm-ID: 402894 Cd Length: 281 Bit Score: 40.00 E-value: 9.41e-03
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