Transcription activator BRG1 [Bagarius yarrelli]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||
| DEXHc_SMARCA4 | cd18062 | DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ... |
720-970 | 5.60e-171 | ||||||||
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: 525.76 E-value: 5.60e-171
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| PLN03142 super family | cl33647 | Probable chromatin-remodeling complex ATPase chain; Provisional |
739-1216 | 2.35e-158 | ||||||||
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: 520.90 E-value: 2.35e-158
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| AP_MHD_Cterm super family | cl10970 | C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); ... |
2527-2741 | 5.80e-142 | ||||||||
C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an endocytic adaptor syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related proteins. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. Stonins have been characterized as clathrin-dependent AP-2 mu chain related factors and may act as cargo-specific sorting adaptors in endocytosis. Coat protein complex I (COPI)-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. MuD is distantly related to the C-terminal domain of mu2 subunit of AP-2. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress responses. It shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, FCHo1/2, which represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein SGIP1 does have a C-terminal MHD and has been classified into this family as well. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15. The actual alignment was detected with superfamily member cd09259: Pssm-ID: 472082 Cd Length: 268 Bit Score: 443.31 E-value: 5.80e-142
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| Bromo_SNF2L2 | cd05516 | Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ... |
1410-1516 | 8.13e-62 | ||||||||
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: 206.89 E-value: 8.13e-62
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| longin-like super family | cl38905 | Longin-like domains; Longin-like domains are small protein domains present in a variety of ... |
2429-2515 | 2.80e-47 | ||||||||
Longin-like domains; Longin-like domains are small protein domains present in a variety of proteins and members of protein complexes involved in or required for different steps during the transport of proteins from the ribosome to the ER to the plasma membrane, via the Golgi apparatus. Examples are mu and sigma subunits of the heterotetrameric adaptor protein (AP) complex, zeta and delta subunits of the heterotetrameric F-COPI complex, a subgroup of R-SNARE proteins, a subfamily of the transport protein particle (TRAPP), and the signal recognition particle receptor subunit alpha (SR-alpha). The actual alignment was detected with superfamily member cd14835: Pssm-ID: 365781 Cd Length: 139 Bit Score: 166.57 E-value: 2.80e-47
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| ANKYR | COG0666 | Ankyrin repeat [Signal transduction mechanisms]; |
2763-2919 | 7.92e-32 | ||||||||
Ankyrin repeat [Signal transduction mechanisms]; : Pssm-ID: 440430 [Multi-domain] Cd Length: 289 Bit Score: 127.76 E-value: 7.92e-32
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| SnAC | pfam14619 | Snf2-ATP coupling, chromatin remodelling complex; This domain appears to play a crucial role ... |
1273-1340 | 4.10e-28 | ||||||||
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: 109.27 E-value: 4.10e-28
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| HSA | smart00573 | domain in helicases and associated with SANT domains; |
453-525 | 3.92e-26 | ||||||||
domain in helicases and associated with SANT domains; : Pssm-ID: 214727 [Multi-domain] Cd Length: 73 Bit Score: 103.63 E-value: 3.92e-26
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| BRK | pfam07533 | BRK domain; The function of this domain is unknown. It is often found associated with ... |
605-648 | 1.89e-15 | ||||||||
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: 72.16 E-value: 1.89e-15
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| QLQ | pfam08880 | QLQ; The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found ... |
175-209 | 5.80e-15 | ||||||||
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: 70.44 E-value: 5.80e-15
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1679-1713 | 4.63e-14 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure : Pssm-ID: 238060 Cd Length: 35 Bit Score: 68.00 E-value: 4.63e-14
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1596-1628 | 1.50e-13 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. : Pssm-ID: 197566 Cd Length: 33 Bit Score: 66.50 E-value: 1.50e-13
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1763-1797 | 2.02e-13 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure : Pssm-ID: 238060 Cd Length: 35 Bit Score: 66.46 E-value: 2.02e-13
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1717-1749 | 4.83e-13 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. : Pssm-ID: 197566 Cd Length: 33 Bit Score: 65.35 E-value: 4.83e-13
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| Ldl_recept_b | pfam00058 | Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif ... |
2096-2136 | 8.04e-12 | ||||||||
Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure. : Pssm-ID: 459654 Cd Length: 42 Bit Score: 61.79 E-value: 8.04e-12
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1801-1836 | 1.47e-11 | ||||||||
Low-density lipoprotein receptor domain class A; : Pssm-ID: 395011 Cd Length: 37 Bit Score: 61.11 E-value: 1.47e-11
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| LY | smart00135 | Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) ... |
2034-2075 | 1.96e-11 | ||||||||
Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin. : Pssm-ID: 214531 [Multi-domain] Cd Length: 43 Bit Score: 60.69 E-value: 1.96e-11
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| EGF_CA | smart00179 | Calcium-binding EGF-like domain; |
1920-1950 | 5.65e-10 | ||||||||
Calcium-binding EGF-like domain; : Pssm-ID: 214542 [Multi-domain] Cd Length: 39 Bit Score: 56.49 E-value: 5.65e-10
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| Med15 super family | cl26621 | ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ... |
19-351 | 6.25e-10 | ||||||||
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. The actual alignment was detected with superfamily member pfam09606: Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 65.03 E-value: 6.25e-10
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| FXa_inhibition | pfam14670 | Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is ... |
1884-1918 | 9.57e-10 | ||||||||
Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442. : Pssm-ID: 464251 [Multi-domain] Cd Length: 36 Bit Score: 55.71 E-value: 9.57e-10
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1638-1674 | 3.14e-09 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure : Pssm-ID: 238060 Cd Length: 35 Bit Score: 54.52 E-value: 3.14e-09
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1840-1874 | 1.21e-08 | ||||||||
Low-density lipoprotein receptor domain class A; : Pssm-ID: 395011 Cd Length: 37 Bit Score: 52.64 E-value: 1.21e-08
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| Smc super family | cl34174 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
357-570 | 2.95e-07 | ||||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; The actual alignment was detected with superfamily member COG1196: Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 56.48 E-value: 2.95e-07
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| FXa_inhibition | pfam14670 | Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is ... |
2241-2278 | 3.82e-06 | ||||||||
Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442. : Pssm-ID: 464251 [Multi-domain] Cd Length: 36 Bit Score: 45.70 E-value: 3.82e-06
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| LY | smart00135 | Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) ... |
2122-2160 | 6.17e-06 | ||||||||
Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin. : Pssm-ID: 214531 [Multi-domain] Cd Length: 43 Bit Score: 45.29 E-value: 6.17e-06
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| Ldl_recept_b super family | cl44468 | Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif ... |
2140-2182 | 6.20e-06 | ||||||||
Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure. The actual alignment was detected with superfamily member pfam00058: Pssm-ID: 459654 Cd Length: 42 Bit Score: 45.23 E-value: 6.20e-06
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| Ldl_recept_b super family | cl44468 | Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif ... |
2183-2223 | 3.42e-05 | ||||||||
Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure. The actual alignment was detected with superfamily member pfam00058: Pssm-ID: 459654 Cd Length: 42 Bit Score: 43.30 E-value: 3.42e-05
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| NHL super family | cl18310 | NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in ... |
2002-2102 | 7.89e-05 | ||||||||
NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. The repeats have a catalytic activity in Peptidyl-glycine alpha-amidating monooxygenase; proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Tripartite motif-containing protein 32 interacts with the activation domain of Tat. This interaction is mediated by the NHL repeats. The actual alignment was detected with superfamily member cd14962: Pssm-ID: 302697 [Multi-domain] Cd Length: 271 Bit Score: 47.20 E-value: 7.89e-05
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| Name | Accession | Description | Interval | E-value | ||||||||
| DEXHc_SMARCA4 | cd18062 | DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ... |
720-970 | 5.60e-171 | ||||||||
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: 525.76 E-value: 5.60e-171
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| PLN03142 | PLN03142 | Probable chromatin-remodeling complex ATPase chain; Provisional |
739-1216 | 2.35e-158 | ||||||||
Probable chromatin-remodeling complex ATPase chain; Provisional Pssm-ID: 215601 [Multi-domain] Cd Length: 1033 Bit Score: 520.90 E-value: 2.35e-158
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| AP-1_Mu1B_Cterm | cd09259 | C-terminal domain of medium Mu1B subunit in epithelial cell-specific clathrin-associated ... |
2527-2741 | 5.80e-142 | ||||||||
C-terminal domain of medium Mu1B subunit in epithelial cell-specific clathrin-associated adaptor protein (AP) complex AP-1; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1B subunit encoded by ap1m2 gene exclusively expressed in polarized epithelial cells. Epithelial cell-specific AP-1 is used to sort proteins to the basolateral plasma membrane, which involves the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). The phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1B subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic reside-binding. Besides, AP-1 mu1B subunit mediates the basolateral recycling of low-density lipoprotein receptor (LDLR) and transferrin receptor (TfR) from the sorting endosomes, where the basolateral sorting signal does not belong to the tyrosine-based signals. Thus, the binding site in mu1B subunit of AP-1 for the signals of LDLR and TfR might be distinct from that for YXXPhi signals. Pssm-ID: 271167 Cd Length: 268 Bit Score: 443.31 E-value: 5.80e-142
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
739-1200 | 2.54e-121 | ||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 401.14 E-value: 2.54e-121
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| SNF2-rel_dom | pfam00176 | SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
746-1041 | 4.89e-115 | ||||||||
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: 367.01 E-value: 4.89e-115
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| Adap_comp_sub | pfam00928 | Adaptor complexes medium subunit family; This family also contains members which are coatomer ... |
2530-2741 | 8.84e-79 | ||||||||
Adaptor complexes medium subunit family; This family also contains members which are coatomer subunits. Pssm-ID: 395742 Cd Length: 259 Bit Score: 261.85 E-value: 8.84e-79
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| Bromo_SNF2L2 | cd05516 | Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ... |
1410-1516 | 8.13e-62 | ||||||||
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: 206.89 E-value: 8.13e-62
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| SF2_C_SNF | cd18793 | C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
1068-1189 | 2.08e-52 | ||||||||
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: 181.14 E-value: 2.08e-52
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| AP1_Mu_N | cd14835 | AP-1 complex subunit mu N-terminal domain; AP-1 complex mu subunit is part of the ... |
2429-2515 | 2.80e-47 | ||||||||
AP-1 complex subunit mu N-terminal domain; AP-1 complex mu subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large gamma-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In the case of AP-1 the coat protein is clathrin. AP-1 binds the phospholipid PI(4)P which plays a role in its localisation to the trans-Golgi network (TGN)/endosome. The mu subunit is comprised of an N-terminal longin domain followed by a C-terminal domain which is involved in the binding of the Y-X-X-Phi sorting signal. Pssm-ID: 341439 Cd Length: 139 Bit Score: 166.57 E-value: 2.80e-47
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| ANKYR | COG0666 | Ankyrin repeat [Signal transduction mechanisms]; |
2763-2919 | 7.92e-32 | ||||||||
Ankyrin repeat [Signal transduction mechanisms]; Pssm-ID: 440430 [Multi-domain] Cd Length: 289 Bit Score: 127.76 E-value: 7.92e-32
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| BROMO | smart00297 | bromo domain; |
1408-1516 | 1.20e-31 | ||||||||
bromo domain; Pssm-ID: 197636 [Multi-domain] Cd Length: 107 Bit Score: 120.46 E-value: 1.20e-31
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
742-931 | 3.85e-31 | ||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 122.60 E-value: 3.85e-31
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| SnAC | pfam14619 | Snf2-ATP coupling, chromatin remodelling complex; This domain appears to play a crucial role ... |
1273-1340 | 4.10e-28 | ||||||||
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: 109.27 E-value: 4.10e-28
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| HSA | smart00573 | domain in helicases and associated with SANT domains; |
453-525 | 3.92e-26 | ||||||||
domain in helicases and associated with SANT domains; Pssm-ID: 214727 [Multi-domain] Cd Length: 73 Bit Score: 103.63 E-value: 3.92e-26
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
1069-1178 | 2.18e-24 | ||||||||
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: 99.98 E-value: 2.18e-24
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| HSA | pfam07529 | HSA domain; This domain is predicted to bind DNA and is often found associated with helicases. ... |
454-520 | 5.52e-23 | ||||||||
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: 94.56 E-value: 5.52e-23
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
1100-1178 | 1.32e-18 | ||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 82.64 E-value: 1.32e-18
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| COG5076 | COG5076 | Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ... |
1366-1518 | 2.32e-18 | ||||||||
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]; Pssm-ID: 227408 [Multi-domain] Cd Length: 371 Bit Score: 89.86 E-value: 2.32e-18
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| Bromodomain | pfam00439 | Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ... |
1414-1502 | 2.76e-18 | ||||||||
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: 81.59 E-value: 2.76e-18
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| BRK | pfam07533 | BRK domain; The function of this domain is unknown. It is often found associated with ... |
605-648 | 1.89e-15 | ||||||||
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: 72.16 E-value: 1.89e-15
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| QLQ | pfam08880 | QLQ; The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found ... |
175-209 | 5.80e-15 | ||||||||
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: 70.44 E-value: 5.80e-15
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| BRK | smart00592 | domain in transcription and CHROMO domain helicases; |
606-650 | 2.48e-14 | ||||||||
domain in transcription and CHROMO domain helicases; Pssm-ID: 197800 Cd Length: 45 Bit Score: 69.30 E-value: 2.48e-14
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1679-1713 | 4.63e-14 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 68.00 E-value: 4.63e-14
|
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1596-1628 | 1.50e-13 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 66.50 E-value: 1.50e-13
|
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1763-1797 | 2.02e-13 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 66.46 E-value: 2.02e-13
|
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1677-1713 | 3.49e-13 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 65.73 E-value: 3.49e-13
|
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| Ank_2 | pfam12796 | Ankyrin repeats (3 copies); |
2808-2882 | 4.04e-13 | ||||||||
Ankyrin repeats (3 copies); Pssm-ID: 463710 [Multi-domain] Cd Length: 91 Bit Score: 67.45 E-value: 4.04e-13
|
||||||||||||
| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1717-1749 | 4.83e-13 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 65.35 E-value: 4.83e-13
|
||||||||||||
| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1679-1710 | 7.21e-13 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 64.58 E-value: 7.21e-13
|
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1717-1754 | 7.92e-13 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 64.58 E-value: 7.92e-13
|
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1718-1754 | 2.39e-12 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 63.38 E-value: 2.39e-12
|
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1763-1794 | 3.21e-12 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 62.65 E-value: 3.21e-12
|
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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 ... |
175-208 | 3.50e-12 | ||||||||
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: 62.94 E-value: 3.50e-12
|
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1597-1629 | 3.85e-12 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 62.61 E-value: 3.85e-12
|
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| Ldl_recept_b | pfam00058 | Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif ... |
2096-2136 | 8.04e-12 | ||||||||
Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure. Pssm-ID: 459654 Cd Length: 42 Bit Score: 61.79 E-value: 8.04e-12
|
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1801-1836 | 1.47e-11 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 61.11 E-value: 1.47e-11
|
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| LY | smart00135 | Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) ... |
2034-2075 | 1.96e-11 | ||||||||
Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin. Pssm-ID: 214531 [Multi-domain] Cd Length: 43 Bit Score: 60.69 E-value: 1.96e-11
|
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1802-1836 | 2.94e-11 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 60.30 E-value: 2.94e-11
|
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1762-1797 | 8.04e-11 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 58.80 E-value: 8.04e-11
|
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| EGF_CA | smart00179 | Calcium-binding EGF-like domain; |
1920-1950 | 5.65e-10 | ||||||||
Calcium-binding EGF-like domain; Pssm-ID: 214542 [Multi-domain] Cd Length: 39 Bit Score: 56.49 E-value: 5.65e-10
|
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| Med15 | pfam09606 | ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ... |
19-351 | 6.25e-10 | ||||||||
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 65.03 E-value: 6.25e-10
|
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1801-1833 | 7.26e-10 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 56.10 E-value: 7.26e-10
|
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| FXa_inhibition | pfam14670 | Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is ... |
1884-1918 | 9.57e-10 | ||||||||
Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442. Pssm-ID: 464251 [Multi-domain] Cd Length: 36 Bit Score: 55.71 E-value: 9.57e-10
|
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| PTZ00322 | PTZ00322 | 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional |
2803-2921 | 1.17e-09 | ||||||||
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional Pssm-ID: 140343 [Multi-domain] Cd Length: 664 Bit Score: 64.15 E-value: 1.17e-09
|
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1638-1674 | 3.14e-09 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 54.52 E-value: 3.14e-09
|
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1596-1629 | 3.21e-09 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 54.56 E-value: 3.21e-09
|
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| EGF_CA | cd00054 | Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular ... |
1920-1950 | 4.21e-09 | ||||||||
Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements. Pssm-ID: 238011 Cd Length: 38 Bit Score: 54.18 E-value: 4.21e-09
|
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1840-1874 | 1.21e-08 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 52.64 E-value: 1.21e-08
|
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| LY | smart00135 | Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) ... |
2077-2119 | 1.38e-08 | ||||||||
Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin. Pssm-ID: 214531 [Multi-domain] Cd Length: 43 Bit Score: 52.60 E-value: 1.38e-08
|
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1844-1874 | 1.67e-08 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 52.21 E-value: 1.67e-08
|
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1636-1674 | 2.65e-08 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 51.87 E-value: 2.65e-08
|
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1846-1874 | 2.73e-08 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 51.87 E-value: 2.73e-08
|
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
102-351 | 2.82e-08 | ||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 59.95 E-value: 2.82e-08
|
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| Ldl_recept_b | pfam00058 | Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif ... |
2053-2093 | 1.49e-07 | ||||||||
Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure. Pssm-ID: 459654 Cd Length: 42 Bit Score: 49.85 E-value: 1.49e-07
|
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
357-570 | 2.95e-07 | ||||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 56.48 E-value: 2.95e-07
|
||||||||||||
| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1637-1671 | 5.58e-07 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 48.01 E-value: 5.58e-07
|
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| EGF_CA | pfam07645 | Calcium-binding EGF domain; |
1920-1948 | 1.82e-06 | ||||||||
Calcium-binding EGF domain; Pssm-ID: 429571 Cd Length: 32 Bit Score: 46.46 E-value: 1.82e-06
|
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| FXa_inhibition | pfam14670 | Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is ... |
2241-2278 | 3.82e-06 | ||||||||
Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442. Pssm-ID: 464251 [Multi-domain] Cd Length: 36 Bit Score: 45.70 E-value: 3.82e-06
|
||||||||||||
| LY | smart00135 | Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) ... |
2122-2160 | 6.17e-06 | ||||||||
Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin. Pssm-ID: 214531 [Multi-domain] Cd Length: 43 Bit Score: 45.29 E-value: 6.17e-06
|
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| Ldl_recept_b | pfam00058 | Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif ... |
2140-2182 | 6.20e-06 | ||||||||
Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure. Pssm-ID: 459654 Cd Length: 42 Bit Score: 45.23 E-value: 6.20e-06
|
||||||||||||
| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
358-543 | 8.40e-06 | ||||||||
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: 50.69 E-value: 8.40e-06
|
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| EGF_CA | smart00179 | Calcium-binding EGF-like domain; |
1880-1919 | 1.00e-05 | ||||||||
Calcium-binding EGF-like domain; Pssm-ID: 214542 [Multi-domain] Cd Length: 39 Bit Score: 44.55 E-value: 1.00e-05
|
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| Ldl_recept_b | pfam00058 | Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif ... |
2183-2223 | 3.42e-05 | ||||||||
Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure. Pssm-ID: 459654 Cd Length: 42 Bit Score: 43.30 E-value: 3.42e-05
|
||||||||||||
| EGF_CA | cd00054 | Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular ... |
1880-1919 | 4.10e-05 | ||||||||
Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements. Pssm-ID: 238011 Cd Length: 38 Bit Score: 43.01 E-value: 4.10e-05
|
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| NHL_like_6 | cd14962 | Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ... |
2002-2102 | 7.89e-05 | ||||||||
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. Pssm-ID: 271332 [Multi-domain] Cd Length: 271 Bit Score: 47.20 E-value: 7.89e-05
|
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
363-569 | 8.14e-05 | ||||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 48.53 E-value: 8.14e-05
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| YncE | COG3391 | DNA-binding beta-propeller fold protein YncE [General function prediction only]; |
1996-2147 | 1.61e-04 | ||||||||
DNA-binding beta-propeller fold protein YncE [General function prediction only]; Pssm-ID: 442618 [Multi-domain] Cd Length: 237 Bit Score: 45.84 E-value: 1.61e-04
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| PABP-1234 | TIGR01628 | polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ... |
178-424 | 4.44e-04 | ||||||||
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range. Pssm-ID: 130689 [Multi-domain] Cd Length: 562 Bit Score: 45.95 E-value: 4.44e-04
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| TRPV5-6 | cd22192 | Transient Receptor Potential channel, Vanilloid subfamily (TRPV), types 5 and 6; TRPV5 and ... |
2771-2901 | 5.25e-04 | ||||||||
Transient Receptor Potential channel, Vanilloid subfamily (TRPV), types 5 and 6; TRPV5 and TRPV6 (TRPV5/6) are two homologous members within the vanilloid subfamily of the transient receptor potential (TRP) family. TRPV5 and TRPV6 show only 30-40% homology with other members of the TRP family and have unique properties that differentiates them from other TRP channels. They mediate calcium uptake in epithelia and their expression is dramatically increased in numerous types of cancer. The structure of TRPV5/6 shows the typical topology features of all TRP family members, such as six transmembrane regions, a short hydrophobic stretch between transmembrane segments 5 and 6, which is predicted to form the Ca2+ pore, and large intracellular N- and C-terminal domains. The N-terminal domain of TRPV5/6 contains three ankyrin repeats. This structural element is present in several proteins and plays a role in protein-protein interactions. The N- and C-terminal tails of TRPV5/6 each contain an internal PDZ motif which can function as part of a molecular scaffold via interaction with PDZ-domain containing proteins. A major difference between the properties of TRPV5 and TRPV6 is in their tissue distribution: TRPV5 is predominantly expressed in the distal convoluted tubules (DCT) and connecting tubules (CNT) of the kidney, with limited expression in extrarenal tissues. In contrast, TRPV6 has a broader expression pattern such as expression in the intestine, kidney, placenta, epididymis, exocrine tissues, and a few other tissues. Pssm-ID: 411976 [Multi-domain] Cd Length: 609 Bit Score: 45.39 E-value: 5.25e-04
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| LY | smart00135 | Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) ... |
2163-2205 | 5.83e-04 | ||||||||
Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin. Pssm-ID: 214531 [Multi-domain] Cd Length: 43 Bit Score: 39.89 E-value: 5.83e-04
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
430-541 | 7.35e-04 | ||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 45.52 E-value: 7.35e-04
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| Name | Accession | Description | Interval | E-value | ||||||||
| DEXHc_SMARCA4 | cd18062 | DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ... |
720-970 | 5.60e-171 | ||||||||
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: 525.76 E-value: 5.60e-171
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| DEXHc_SMARCA2_SMARCA4 | cd17996 | DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ... |
740-970 | 2.79e-166 | ||||||||
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: 511.53 E-value: 2.79e-166
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| DEXHc_SMARCA2 | cd18063 | DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent ... |
720-970 | 6.26e-163 | ||||||||
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: 502.67 E-value: 6.26e-163
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| PLN03142 | PLN03142 | Probable chromatin-remodeling complex ATPase chain; Provisional |
739-1216 | 2.35e-158 | ||||||||
Probable chromatin-remodeling complex ATPase chain; Provisional Pssm-ID: 215601 [Multi-domain] Cd Length: 1033 Bit Score: 520.90 E-value: 2.35e-158
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| AP-1_Mu1B_Cterm | cd09259 | C-terminal domain of medium Mu1B subunit in epithelial cell-specific clathrin-associated ... |
2527-2741 | 5.80e-142 | ||||||||
C-terminal domain of medium Mu1B subunit in epithelial cell-specific clathrin-associated adaptor protein (AP) complex AP-1; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1B subunit encoded by ap1m2 gene exclusively expressed in polarized epithelial cells. Epithelial cell-specific AP-1 is used to sort proteins to the basolateral plasma membrane, which involves the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). The phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1B subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic reside-binding. Besides, AP-1 mu1B subunit mediates the basolateral recycling of low-density lipoprotein receptor (LDLR) and transferrin receptor (TfR) from the sorting endosomes, where the basolateral sorting signal does not belong to the tyrosine-based signals. Thus, the binding site in mu1B subunit of AP-1 for the signals of LDLR and TfR might be distinct from that for YXXPhi signals. Pssm-ID: 271167 Cd Length: 268 Bit Score: 443.31 E-value: 5.80e-142
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| AP-1_Mu1_Cterm | cd09250 | C-terminal domain of medium Mu1 subunit in clathrin-associated adaptor protein (AP) complex ... |
2527-2741 | 8.25e-130 | ||||||||
C-terminal domain of medium Mu1 subunit in clathrin-associated adaptor protein (AP) complex AP-1; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1 subunit, which includes two closely related homologs, mu1A (encoded by ap1m1) and mu1B (encoded by ap1m2). Mu1A is ubiquitously expressed, but mu1B is expressed exclusively in polarized epithelial cells. AP-1 has been implicated in bi-directional transport between the trans-Golgi network (TGN) and endosomes. It plays an essential role in the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). Epithelial cell-specific AP-1 is also involved in sorting to the basolateral surface of polarized epithelial cells. Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). Phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Pssm-ID: 271158 Cd Length: 272 Bit Score: 408.91 E-value: 8.25e-130
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| AP-1_Mu1A_Cterm | cd09258 | C-terminal domain of medium Mu1A subunit in ubiquitously expressed clathrin-associated adaptor ... |
2526-2741 | 1.03e-125 | ||||||||
C-terminal domain of medium Mu1A subunit in ubiquitously expressed clathrin-associated adaptor protein (AP) complex AP-1; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1A subunit encoded by ap1m1 gene, which is ubiquitously expressed in all mammalian tissues and cells. AP-1 has been implicated in bidirectional transport between the trans-Golgi network (TGN) and endosomes. It is involved in the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). The ubiquitous AP-1 is recruited to the TGN membrane, as well as to immature secretory granules. Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). Phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1A subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Pssm-ID: 271166 Cd Length: 270 Bit Score: 396.95 E-value: 1.03e-125
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
739-1200 | 2.54e-121 | ||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 401.14 E-value: 2.54e-121
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| SNF2-rel_dom | pfam00176 | SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
746-1041 | 4.89e-115 | ||||||||
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: 367.01 E-value: 4.89e-115
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| DEXHc_SMARCA1_SMARCA5 | cd17997 | DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ... |
740-970 | 1.81e-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: 302.32 E-value: 1.81e-93
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| DEXHc_HELLS_SMARCA6 | cd18009 | DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ... |
740-970 | 1.16e-91 | ||||||||
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: 297.76 E-value: 1.16e-91
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| DEXQc_SRCAP | cd18003 | DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ... |
743-968 | 1.94e-82 | ||||||||
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: 270.76 E-value: 1.94e-82
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| AP-2_Mu2_Cterm | cd09251 | C-terminal domain of medium Mu2 subunit in ubiquitously expressed clathrin-associated adaptor ... |
2539-2741 | 1.31e-80 | ||||||||
C-terminal domain of medium Mu2 subunit in ubiquitously expressed clathrin-associated adaptor protein (AP) complex AP-2; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, -2, -3, and -4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 2 (AP-2) medium mu2 subunit. Mu2 is ubiquitously expressed in mammals. In higher eukaryotes, AP-2 plays a critical role in clathrin-mediated endocytosis from the plasma membrane in different cells. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-2. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-2 mu2 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Since the Y-X-X-Phi binding site is buried in the core structure of AP-2, a phosphorylation induced conformational change is required when the cargo molecules binds to AP-2. In addition, the C-terminal domain of mu2 subunit has been shown to bind other molecules. For instance, it can bind phosphoinositides, in particular PI[4,5]P2, which might be involved in the recognition process of the tyrosine-based signals. It can also interact with synaptotagmins, a family of important modulators of calcium-dependent neurosecretion within the synaptic vesicle (SV) membrane. Since many of the other endocytic adaptors responsible for biogenesis of synaptic vesicles exist, in the absence of AP-2, clathrin-mediated endocytosis can still occur. However, the cells may not survive in the complete absence of clathrin as well as AP-2. Pssm-ID: 271159 Cd Length: 263 Bit Score: 267.15 E-value: 1.31e-80
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| DEXHc_Snf | cd17919 | DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
743-919 | 2.09e-80 | ||||||||
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: 263.27 E-value: 2.09e-80
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| DEXHc_CHD1_2 | cd17993 | DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ... |
742-968 | 6.63e-80 | ||||||||
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: 263.45 E-value: 6.63e-80
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| Adap_comp_sub | pfam00928 | Adaptor complexes medium subunit family; This family also contains members which are coatomer ... |
2530-2741 | 8.84e-79 | ||||||||
Adaptor complexes medium subunit family; This family also contains members which are coatomer subunits. Pssm-ID: 395742 Cd Length: 259 Bit Score: 261.85 E-value: 8.84e-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; ... |
743-968 | 5.72e-77 | ||||||||
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: 255.25 E-value: 5.72e-77
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| DEXHc_SMARCA5 | cd18064 | DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ... |
741-980 | 1.74e-74 | ||||||||
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: 248.81 E-value: 1.74e-74
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| DEXHc_SMARCA1 | cd18065 | DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ... |
741-970 | 3.07e-72 | ||||||||
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: 241.85 E-value: 3.07e-72
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| DEXQc_INO80 | cd18002 | DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ... |
743-968 | 8.40e-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: 8.40e-66
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| DEXQc_arch_SWI2_SNF2 | cd18012 | DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ... |
739-970 | 1.46e-62 | ||||||||
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: 213.58 E-value: 1.46e-62
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| DEXHc_CHD2 | cd18054 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ... |
742-968 | 3.25e-62 | ||||||||
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: 213.33 E-value: 3.25e-62
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| Bromo_SNF2L2 | cd05516 | Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ... |
1410-1516 | 8.13e-62 | ||||||||
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: 206.89 E-value: 8.13e-62
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| AP_MHD_Cterm | cd07954 | C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); ... |
2543-2723 | 7.18e-61 | ||||||||
C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an endocytic adaptor syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related proteins. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. Stonins have been characterized as clathrin-dependent AP-2 mu chain related factors and may act as cargo-specific sorting adaptors in endocytosis. Coat protein complex I (COPI)-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. MuD is distantly related to the C-terminal domain of mu2 subunit of AP-2. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress responses. It shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, FCHo1/2, which represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein SGIP1 does have a C-terminal MHD and has been classified into this family as well. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15. Pssm-ID: 271157 Cd Length: 245 Bit Score: 209.95 E-value: 7.18e-61
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| DEXHc_CHD1L | cd18006 | DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ... |
743-968 | 4.11e-60 | ||||||||
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: 206.52 E-value: 4.11e-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; ... |
743-968 | 5.75e-57 | ||||||||
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: 196.51 E-value: 5.75e-57
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| AP-4_Mu4_Cterm | cd09253 | C-terminal domain of medium Mu4 subunit in adaptor protein (AP) complex AP-4; AP complexes ... |
2533-2722 | 1.22e-54 | ||||||||
C-terminal domain of medium Mu4 subunit in adaptor protein (AP) complex AP-4; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 4 (AP-4) medium mu4 subunit. AP-4 plays a role in signal-mediated trafficking of integral membrane proteins in mammalian cells. Unlike other AP complexes, AP-4 is found only in mammals and plants. It is believed to be part of a nonclathrin coat, since it might function independently of clathrin, a scaffolding protein participating in the formation of coated vesicles. Recruitment of AP-4 to the trans-Golgi network (TGN) membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1) or a related protein. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. One of the most important sorting signals binding to mu subunits of AP complexes are tyrosine-based endocytotic signals, which are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. However, AP-4 does not bind most canonical tyrosine-based signals except for two naturally occurring ones from the lysosomal membrane proteins CD63 and LAMP-2a. It binds YX [FYL][FL]E motif, where X can be any residue, from the cytosolic tails of amyloid precursor protein (APP) family members in a distinct way. Pssm-ID: 271161 Cd Length: 271 Bit Score: 192.79 E-value: 1.22e-54
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| DEXHc_SMARCAD1 | cd17998 | DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ... |
743-922 | 5.18e-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: 187.98 E-value: 5.18e-54
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| SF2_C_SNF | cd18793 | C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
1068-1189 | 2.08e-52 | ||||||||
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: 181.14 E-value: 2.08e-52
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| DEXHc_CHD1 | cd18053 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ... |
742-968 | 3.11e-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: 181.79 E-value: 3.11e-51
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| DEXHc_CHD6 | cd18058 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ... |
743-968 | 6.49e-51 | ||||||||
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: 180.24 E-value: 6.49e-51
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| DEXHc_ERCC6 | cd18000 | DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ... |
743-919 | 2.64e-50 | ||||||||
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: 177.52 E-value: 2.64e-50
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| DEXHc_Mot1 | cd17999 | DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ... |
743-968 | 3.95e-49 | ||||||||
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: 175.62 E-value: 3.95e-49
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| DEXHc_CHD5 | cd18057 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ... |
743-968 | 5.42e-49 | ||||||||
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: 175.25 E-value: 5.42e-49
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| DEXHc_CHD3 | cd18055 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ... |
743-968 | 1.90e-48 | ||||||||
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: 173.66 E-value: 1.90e-48
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| DEXHc_CHD7 | cd18059 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ... |
743-968 | 2.78e-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: 172.91 E-value: 2.78e-48
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| DEXHc_ERCC6L | cd18001 | DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ... |
743-968 | 2.92e-48 | ||||||||
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: 172.94 E-value: 2.92e-48
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| DEXHc_CHD8 | cd18060 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ... |
743-968 | 8.38e-48 | ||||||||
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: 171.39 E-value: 8.38e-48
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| AP-3_Mu3_Cterm | cd09252 | C-terminal domain of medium Mu3 subunit in adaptor protein (AP) complex AP-3; AP complexes ... |
2530-2722 | 1.31e-47 | ||||||||
C-terminal domain of medium Mu3 subunit in adaptor protein (AP) complex AP-3; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 3 (AP-3) medium mu3 subunit, which includes two closely related homologs, mu3A (P47A, encoded by ap3m1) and mu1B (P47B, encoded by ap3m2). Mu3A is ubiquitously expressed, but mu3B is specifically expressed in neurons and neuroendocrine cells. AP-3 is particularly important for targeting integral membrane proteins to lysosomes and lysome-related organelles at trans-Golgi network (TGN) and/or endosomes, such as the yeast vacuole, fly pigment granules and mammalian melanosomes, platelet dense bodies and the secretory lysosomes of cytotoxic T lymphocytes. Unlike AP-1 and AP-2, which function in conjunction with clathrin which is a scaffolding protein participating in the formation of coated vesicles, the nature of the outer shell of AP-3 containing coats remains to be elucidated. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-3 mu3 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Pssm-ID: 271160 Cd Length: 251 Bit Score: 172.00 E-value: 1.31e-47
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| AP1_Mu_N | cd14835 | AP-1 complex subunit mu N-terminal domain; AP-1 complex mu subunit is part of the ... |
2429-2515 | 2.80e-47 | ||||||||
AP-1 complex subunit mu N-terminal domain; AP-1 complex mu subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large gamma-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In the case of AP-1 the coat protein is clathrin. AP-1 binds the phospholipid PI(4)P which plays a role in its localisation to the trans-Golgi network (TGN)/endosome. The mu subunit is comprised of an N-terminal longin domain followed by a C-terminal domain which is involved in the binding of the Y-X-X-Phi sorting signal. Pssm-ID: 341439 Cd Length: 139 Bit Score: 166.57 E-value: 2.80e-47
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| DEXHc_ERCC6L2 | cd18005 | DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ... |
743-968 | 1.31e-46 | ||||||||
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: 168.71 E-value: 1.31e-46
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| DEXHc_CHD4 | cd18056 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ... |
743-968 | 9.74e-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: 9.74e-46
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| DEXHc_CHD9 | cd18061 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ... |
743-968 | 1.44e-43 | ||||||||
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: 159.40 E-value: 1.44e-43
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| DEXHc_RAD54 | cd18004 | DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ... |
743-968 | 1.91e-42 | ||||||||
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: 156.68 E-value: 1.91e-42
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| DEXDc_SHPRH-like | cd18008 | DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ... |
743-968 | 3.18e-41 | ||||||||
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: 153.21 E-value: 3.18e-41
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| DEXHc_ATRX-like | cd18007 | DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ... |
743-956 | 2.77e-37 | ||||||||
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350765 [Multi-domain] Cd Length: 239 Bit Score: 141.66 E-value: 2.77e-37
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| ANKYR | COG0666 | Ankyrin repeat [Signal transduction mechanisms]; |
2763-2919 | 7.92e-32 | ||||||||
Ankyrin repeat [Signal transduction mechanisms]; Pssm-ID: 440430 [Multi-domain] Cd Length: 289 Bit Score: 127.76 E-value: 7.92e-32
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| DEXHc_HLTF1_SMARC3 | cd18071 | DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ... |
743-968 | 1.10e-31 | ||||||||
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: 125.66 E-value: 1.10e-31
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| BROMO | smart00297 | bromo domain; |
1408-1516 | 1.20e-31 | ||||||||
bromo domain; Pssm-ID: 197636 [Multi-domain] Cd Length: 107 Bit Score: 120.46 E-value: 1.20e-31
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
742-931 | 3.85e-31 | ||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 122.60 E-value: 3.85e-31
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| DEXHc_RAD54B | cd18066 | DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ... |
743-968 | 1.68e-30 | ||||||||
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: 122.26 E-value: 1.68e-30
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| Bromo_polybromo_V | cd05515 | Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ... |
1410-1514 | 9.10e-30 | ||||||||
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: 115.09 E-value: 9.10e-30
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| Bromo_SNF2 | cd05519 | Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ... |
1410-1510 | 9.38e-29 | ||||||||
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: 112.43 E-value: 9.38e-29
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| DEXHc_RAD54A | cd18067 | DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ... |
743-968 | 3.97e-28 | ||||||||
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: 115.64 E-value: 3.97e-28
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| SnAC | pfam14619 | Snf2-ATP coupling, chromatin remodelling complex; This domain appears to play a crucial role ... |
1273-1340 | 4.10e-28 | ||||||||
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: 109.27 E-value: 4.10e-28
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| Bromodomain | cd04369 | Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ... |
1410-1512 | 8.68e-28 | ||||||||
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: 109.38 E-value: 8.68e-28
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| DEXHc_HARP_SMARCAL1 | cd18010 | DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ... |
743-956 | 1.59e-26 | ||||||||
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: 109.99 E-value: 1.59e-26
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| ANKYR | COG0666 | Ankyrin repeat [Signal transduction mechanisms]; |
2749-2914 | 2.31e-26 | ||||||||
Ankyrin repeat [Signal transduction mechanisms]; Pssm-ID: 440430 [Multi-domain] Cd Length: 289 Bit Score: 111.97 E-value: 2.31e-26
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| HSA | smart00573 | domain in helicases and associated with SANT domains; |
453-525 | 3.92e-26 | ||||||||
domain in helicases and associated with SANT domains; Pssm-ID: 214727 [Multi-domain] Cd Length: 73 Bit Score: 103.63 E-value: 3.92e-26
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| AP-3_Mu3A_Cterm | cd09260 | C-terminal domain of medium Mu3A subunit in ubiquitously expressed adaptor protein (AP) ... |
2530-2718 | 1.36e-25 | ||||||||
C-terminal domain of medium Mu3A subunit in ubiquitously expressed adaptor protein (AP) complex AP-3; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 3 (AP-3) medium mu3A subunit encoded by ap3m1gene. Mu3A is ubiquitously expressed in all mammalian tissues and cells. It appears to be localized to the trans-Golgi network (TGN) and/or endosomes and participates in trafficking to the vacuole/lysosome in yeast, flies, and mammals. Unlike AP-1 and AP-2, which function in conjunction with clathrin which is a scaffolding protein participating in the formation of coated vesicles, the nature of the outer shell of ubiquitous AP-3 containing coats remains to be elucidated. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-3 mu3A subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Pssm-ID: 211371 Cd Length: 254 Bit Score: 108.65 E-value: 1.36e-25
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| DEXHc_ARIP4 | cd18069 | DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called ... |
743-956 | 2.10e-25 | ||||||||
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: 107.21 E-value: 2.10e-25
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| AP-3_Mu3B_Cterm | cd09261 | C-terminal domain of medium Mu3B subunit in neuron-specific adaptor protein (AP) complex AP-3; ... |
2530-2718 | 4.10e-25 | ||||||||
C-terminal domain of medium Mu3B subunit in neuron-specific adaptor protein (AP) complex AP-3; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 3 (AP-3) medium mu3B subunit encoded by ap3m2 gene. Mu3B is specifically expressed in neurons and neuroendocrine cells. Neuron-specific AP-3 appears to be involved in synaptic vesicle biogenesis from endosomes in neurons and plays an important role in synaptic transmission in the central nervous system. Unlike AP-1 and AP-2, which function in conjunction with clathrin which is a scaffolding protein participating in the formation of coated vesicles, the nature of the outer shell of neuron-specific AP-3 containing coats remains to be elucidated. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-3 mu3B subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Pssm-ID: 211372 Cd Length: 254 Bit Score: 107.05 E-value: 4.10e-25
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| Bromo_polybromo_IV | cd05518 | Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ... |
1412-1515 | 1.35e-24 | ||||||||
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: 100.21 E-value: 1.35e-24
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
1069-1178 | 2.18e-24 | ||||||||
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: 99.98 E-value: 2.18e-24
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| AP-like_stonins_MHD | cd09255 | Mu homology domain (MHD) of adaptor-like proteins (AP-like), stonins; A small family of ... |
2533-2722 | 1.79e-23 | ||||||||
Mu homology domain (MHD) of adaptor-like proteins (AP-like), stonins; A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonins, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonins is unable to recognize tyrosine-based endocytic sorting signals. To data, little is known about the localization and function of stonin 1. Stonin 2, also known as stoned B, acts as an AP-2-dependent synaptotagmin-specific sorting adaptors for SV endocytosis. Stoned A is not a stonin. It is structurally unrelated to the adaptins and does not appear to have mammalian homologs. It is not included in this family. Pssm-ID: 271163 [Multi-domain] Cd Length: 315 Bit Score: 104.03 E-value: 1.79e-23
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| HSA | pfam07529 | HSA domain; This domain is predicted to bind DNA and is often found associated with helicases. ... |
454-520 | 5.52e-23 | ||||||||
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: 94.56 E-value: 5.52e-23
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| Bromo_polybromo_II | cd05517 | Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ... |
1428-1510 | 1.05e-22 | ||||||||
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: 94.81 E-value: 1.05e-22
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| Bromo_polybromo_I | cd05524 | Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ... |
1417-1516 | 8.04e-22 | ||||||||
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: 92.78 E-value: 8.04e-22
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| DEXHc_ATRX | cd18068 | DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ... |
764-956 | 7.98e-21 | ||||||||
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: 94.57 E-value: 7.98e-21
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| DEXHc_TTF2 | cd18072 | DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ... |
743-968 | 8.26e-21 | ||||||||
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: 94.08 E-value: 8.26e-21
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| AP_Mu_N | cd14828 | AP complex subunit mu N-terminal domain; AP complex mu subunits are part of the ... |
2429-2510 | 5.80e-20 | ||||||||
AP complex subunit mu N-terminal domain; AP complex mu subunits are part of the heterotetrameric adaptor protein (AP) complex which consists of one large subunit (alpha-, gamma-, delta- or epsilon), one beta-, one mu-, and one sigma-subunit. In general, AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In most cases the coat protein is clathrin (AP1 and AP2 complex), but some of the other members of the AP complex family are associated with nonclathrin coats. The mu subunit is comprised of an N-terminal longin domain followed by a C-terminal domain which is involved in the binding of the Y-X-X-Phi sorting signal. Pssm-ID: 341432 Cd Length: 136 Bit Score: 88.41 E-value: 5.80e-20
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| Bromo_polybromo_III | cd05520 | Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ... |
1430-1508 | 8.79e-20 | ||||||||
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: 86.62 E-value: 8.79e-20
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| DEXDc_RapA | cd18011 | DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
765-922 | 1.53e-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: 89.66 E-value: 1.53e-19
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| AP2_Mu_N | cd14836 | AP-2 complex subunit mu N-terminal domain; AP-2 complex mu subunit is part of the ... |
2463-2514 | 4.65e-19 | ||||||||
AP-2 complex subunit mu N-terminal domain; AP-2 complex mu subunit is part of the heterotetrameric adaptor protein (AP)-2 complex which consists of one large alpha-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In the case of AP-2 the coat protein is clathrin. AP-2 binds the phospholipid PI(4,5)P2 which is important for its localisation to the plasma membrane. The mu subunit is comprised of an N-terminal longin domain followed by a C-terminal domain which is involved in the binding of the Y-X-X-Phi sorting signal. Pssm-ID: 341440 Cd Length: 140 Bit Score: 86.04 E-value: 4.65e-19
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
1100-1178 | 1.32e-18 | ||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 82.64 E-value: 1.32e-18
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| COG5076 | COG5076 | Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ... |
1366-1518 | 2.32e-18 | ||||||||
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]; Pssm-ID: 227408 [Multi-domain] Cd Length: 371 Bit Score: 89.86 E-value: 2.32e-18
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| Bromodomain | pfam00439 | Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ... |
1414-1502 | 2.76e-18 | ||||||||
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: 81.59 E-value: 2.76e-18
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| Bromo_Rsc1_2_I | cd05521 | Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ... |
1410-1507 | 2.16e-17 | ||||||||
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: 80.06 E-value: 2.16e-17
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| ANKYR | COG0666 | Ankyrin repeat [Signal transduction mechanisms]; |
2768-2900 | 2.51e-16 | ||||||||
Ankyrin repeat [Signal transduction mechanisms]; Pssm-ID: 440430 [Multi-domain] Cd Length: 289 Bit Score: 82.31 E-value: 2.51e-16
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| Bromo_Rsc1_2_II | cd05522 | Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ... |
1413-1512 | 3.28e-16 | ||||||||
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: 76.51 E-value: 3.28e-16
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| ANKYR | COG0666 | Ankyrin repeat [Signal transduction mechanisms]; |
2748-2914 | 5.59e-16 | ||||||||
Ankyrin repeat [Signal transduction mechanisms]; Pssm-ID: 440430 [Multi-domain] Cd Length: 289 Bit Score: 81.15 E-value: 5.59e-16
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| BRK | pfam07533 | BRK domain; The function of this domain is unknown. It is often found associated with ... |
605-648 | 1.89e-15 | ||||||||
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: 72.16 E-value: 1.89e-15
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| AP_longin-like | cd14823 | Longin-like domains of AP complex subunits; AP complex sigma subunits are part of the ... |
2429-2507 | 4.62e-15 | ||||||||
Longin-like domains of AP complex subunits; AP complex sigma subunits are part of the heterotetrameric adaptor protein (AP) complex which consists of one large subunit (alpha-, gamma-, delta- or epsilon), one beta-, one mu-, and one sigma-subunit. In general, AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In most cases the coat protein is clathrin (AP1 and AP2 complex), but some of the other members of the AP complex family are associated with nonclathrin coats. The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals. Pssm-ID: 341427 Cd Length: 131 Bit Score: 74.09 E-value: 4.62e-15
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| QLQ | pfam08880 | QLQ; The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found ... |
175-209 | 5.80e-15 | ||||||||
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: 70.44 E-value: 5.80e-15
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| AP3_Mu_N | cd14837 | AP-3 complex subunit mu N-terminal domain; AP-3 complex mu subunit is part of the ... |
2463-2508 | 1.22e-14 | ||||||||
AP-3 complex subunit mu N-terminal domain; AP-3 complex mu subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large delta-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. AP-3 binds the coat protein clathrin and the phospholipid PI(3)P and it is localized in the endosome. The mu subunit is comprised of an N-terminal longin domain followed by a C-terminal domain which is involved in the binding of the Y-X-X-Phi sorting signal. Pssm-ID: 341441 Cd Length: 139 Bit Score: 73.32 E-value: 1.22e-14
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| BRK | smart00592 | domain in transcription and CHROMO domain helicases; |
606-650 | 2.48e-14 | ||||||||
domain in transcription and CHROMO domain helicases; Pssm-ID: 197800 Cd Length: 45 Bit Score: 69.30 E-value: 2.48e-14
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| DEXQc_SHPRH | cd18070 | DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ... |
743-917 | 4.33e-14 | ||||||||
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: 75.07 E-value: 4.33e-14
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1679-1713 | 4.63e-14 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 68.00 E-value: 4.63e-14
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1596-1628 | 1.50e-13 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 66.50 E-value: 1.50e-13
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1763-1797 | 2.02e-13 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 66.46 E-value: 2.02e-13
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| DEXQc_bact_SNF2 | cd18013 | DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ... |
743-933 | 2.17e-13 | ||||||||
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: 72.00 E-value: 2.17e-13
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1677-1713 | 3.49e-13 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 65.73 E-value: 3.49e-13
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| Ank_2 | pfam12796 | Ankyrin repeats (3 copies); |
2808-2882 | 4.04e-13 | ||||||||
Ankyrin repeats (3 copies); Pssm-ID: 463710 [Multi-domain] Cd Length: 91 Bit Score: 67.45 E-value: 4.04e-13
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| AP4_Mu_N | cd14838 | AP-4 complex subunit mu N-terminal domain; AP-4 complex mu subunit is part of the ... |
2460-2511 | 4.41e-13 | ||||||||
AP-4 complex subunit mu N-terminal domain; AP-4 complex mu subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large epsilon-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. AP-4 does not bind the coat protein clathrin, it is associated with nonclathrin coats. Its phospholipid binding partner is unknown and it is localized in the trans-Golgi network (TGN). The mu subunit is comprised of an N-terminal longin domain followed by a C-terminal domain which is involved in the binding of the Y-X-X-Phi sorting signal. Pssm-ID: 341442 Cd Length: 137 Bit Score: 68.73 E-value: 4.41e-13
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1717-1749 | 4.83e-13 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 65.35 E-value: 4.83e-13
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1679-1710 | 7.21e-13 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 64.58 E-value: 7.21e-13
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1717-1754 | 7.92e-13 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 64.58 E-value: 7.92e-13
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1718-1754 | 2.39e-12 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 63.38 E-value: 2.39e-12
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1763-1794 | 3.21e-12 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 62.65 E-value: 3.21e-12
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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 ... |
175-208 | 3.50e-12 | ||||||||
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: 62.94 E-value: 3.50e-12
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1597-1629 | 3.85e-12 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 62.61 E-value: 3.85e-12
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| Bromo_gcn5_like | cd05509 | Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ... |
1437-1518 | 7.42e-12 | ||||||||
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: 64.11 E-value: 7.42e-12
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| Ldl_recept_b | pfam00058 | Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif ... |
2096-2136 | 8.04e-12 | ||||||||
Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure. Pssm-ID: 459654 Cd Length: 42 Bit Score: 61.79 E-value: 8.04e-12
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| Bromo_ASH1 | cd05525 | Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ... |
1410-1514 | 9.23e-12 | ||||||||
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: 63.95 E-value: 9.23e-12
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| Ank_2 | pfam12796 | Ankyrin repeats (3 copies); |
2835-2914 | 1.22e-11 | ||||||||
Ankyrin repeats (3 copies); Pssm-ID: 463710 [Multi-domain] Cd Length: 91 Bit Score: 63.21 E-value: 1.22e-11
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1801-1836 | 1.47e-11 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 61.11 E-value: 1.47e-11
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| LY | smart00135 | Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) ... |
2034-2075 | 1.96e-11 | ||||||||
Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin. Pssm-ID: 214531 [Multi-domain] Cd Length: 43 Bit Score: 60.69 E-value: 1.96e-11
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1802-1836 | 2.94e-11 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 60.30 E-value: 2.94e-11
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| Bromo_Acf1_like | cd05504 | Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ... |
1437-1509 | 5.13e-11 | ||||||||
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: 62.03 E-value: 5.13e-11
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| Ank_2 | pfam12796 | Ankyrin repeats (3 copies); |
2771-2860 | 6.80e-11 | ||||||||
Ankyrin repeats (3 copies); Pssm-ID: 463710 [Multi-domain] Cd Length: 91 Bit Score: 60.90 E-value: 6.80e-11
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1762-1797 | 8.04e-11 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 58.80 E-value: 8.04e-11
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| AP_stonin-1_MHD | cd09262 | Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned ... |
2539-2722 | 1.35e-10 | ||||||||
Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned B-like factor); A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are the only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonin 1, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonin-1 is unable to recognize tyrosine-based endocytic sorting signals. To data, little is known about the localization and function of stonin-1. Pssm-ID: 271168 Cd Length: 314 Bit Score: 65.35 E-value: 1.35e-10
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| Bromo_BDF1_2_II | cd05499 | Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ... |
1441-1512 | 2.10e-10 | ||||||||
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: 59.99 E-value: 2.10e-10
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| AP_stonin-2_MHD | cd09263 | Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-2; A small family of ... |
2536-2722 | 5.44e-10 | ||||||||
Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-2; A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are the only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonin 2, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonin-2 is unable to recognize tyrosine-based endocytic sorting signals. It acts as an AP-2-dependent synaptotagmin-specific sorting adaptor for SV endocytosis. Pssm-ID: 271169 Cd Length: 318 Bit Score: 63.50 E-value: 5.44e-10
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| EGF_CA | smart00179 | Calcium-binding EGF-like domain; |
1920-1950 | 5.65e-10 | ||||||||
Calcium-binding EGF-like domain; Pssm-ID: 214542 [Multi-domain] Cd Length: 39 Bit Score: 56.49 E-value: 5.65e-10
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| Bromo_AAA | cd05528 | Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ... |
1445-1492 | 5.69e-10 | ||||||||
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: 58.91 E-value: 5.69e-10
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| Med15 | pfam09606 | ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ... |
19-351 | 6.25e-10 | ||||||||
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 65.03 E-value: 6.25e-10
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1801-1833 | 7.26e-10 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 56.10 E-value: 7.26e-10
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| FXa_inhibition | pfam14670 | Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is ... |
1884-1918 | 9.57e-10 | ||||||||
Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442. Pssm-ID: 464251 [Multi-domain] Cd Length: 36 Bit Score: 55.71 E-value: 9.57e-10
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| PTZ00322 | PTZ00322 | 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional |
2803-2921 | 1.17e-09 | ||||||||
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional Pssm-ID: 140343 [Multi-domain] Cd Length: 664 Bit Score: 64.15 E-value: 1.17e-09
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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 ... |
1408-1512 | 1.63e-09 | ||||||||
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: 58.12 E-value: 1.63e-09
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| SOBP | pfam15279 | Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual ... |
102-320 | 2.26e-09 | ||||||||
Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual disability. It carries a zinc-finger of the zf-C2H2 type at the N-terminus, and a highly characteriztic C-terminal PhPhPhPhPhPh motif. The deduced 873-amino acid protein contains an N-terminal nuclear localization signal (NLS), followed by 2 FCS-type zinc finger motifs, a proline-rich region (PR1), a putative RNA-binding motif region, and a C-terminal NLS embedded in a second proline-rich motif. SOBP is expressed in various human tissues, including developing mouse brain at embryonic day 14. In postnatal and adult mouse brain SOBP is expressed in all neurons, with intense staining in the limbic system. Highest expression is in layer V cortical neurons, hippocampus, pyriform cortex, dorsomedial nucleus of thalamus, amygdala, and hypothalamus. Postnatal expression of SOBP in the limbic system corresponds to a time of active synaptogenesis. the family is also referred to as Jackson circler, JXC1. In seven affected siblings from a consanguineous Israeli Arab family with mental retardation, anterior maxillary protrusion, and strabismus mutations were found in this protein. Pssm-ID: 464609 [Multi-domain] Cd Length: 325 Bit Score: 61.75 E-value: 2.26e-09
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1638-1674 | 3.14e-09 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 54.52 E-value: 3.14e-09
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1596-1629 | 3.21e-09 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 54.56 E-value: 3.21e-09
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| EGF_CA | cd00054 | Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular ... |
1920-1950 | 4.21e-09 | ||||||||
Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements. Pssm-ID: 238011 Cd Length: 38 Bit Score: 54.18 E-value: 4.21e-09
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| PHA02874 | PHA02874 | ankyrin repeat protein; Provisional |
2766-2914 | 4.22e-09 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 165205 [Multi-domain] Cd Length: 434 Bit Score: 61.52 E-value: 4.22e-09
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| PHA03095 | PHA03095 | ankyrin-like protein; Provisional |
2776-2914 | 4.73e-09 | ||||||||
ankyrin-like protein; Provisional Pssm-ID: 222980 [Multi-domain] Cd Length: 471 Bit Score: 61.58 E-value: 4.73e-09
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| Bromo_brd7_like | cd05513 | Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ... |
1447-1499 | 7.80e-09 | ||||||||
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: 55.49 E-value: 7.80e-09
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1840-1874 | 1.21e-08 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 52.64 E-value: 1.21e-08
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| Bromo_brd1_like | cd05512 | Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ... |
1435-1506 | 1.24e-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: 54.71 E-value: 1.24e-08
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| LY | smart00135 | Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) ... |
2077-2119 | 1.38e-08 | ||||||||
Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin. Pssm-ID: 214531 [Multi-domain] Cd Length: 43 Bit Score: 52.60 E-value: 1.38e-08
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| Bromo_tif1_like | cd05502 | Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ... |
1431-1516 | 1.65e-08 | ||||||||
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: 54.60 E-value: 1.65e-08
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| LDLa | cd00112 | Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ... |
1844-1874 | 1.67e-08 | ||||||||
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure Pssm-ID: 238060 Cd Length: 35 Bit Score: 52.21 E-value: 1.67e-08
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| Bromo_brd8_like | cd05507 | Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ... |
1414-1492 | 2.24e-08 | ||||||||
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: 54.29 E-value: 2.24e-08
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| Ldl_recept_a | pfam00057 | Low-density lipoprotein receptor domain class A; |
1636-1674 | 2.65e-08 | ||||||||
Low-density lipoprotein receptor domain class A; Pssm-ID: 395011 Cd Length: 37 Bit Score: 51.87 E-value: 2.65e-08
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| ANKYR | COG0666 | Ankyrin repeat [Signal transduction mechanisms]; |
2777-2914 | 2.72e-08 | ||||||||
Ankyrin repeat [Signal transduction mechanisms]; Pssm-ID: 440430 [Multi-domain] Cd Length: 289 Bit Score: 58.04 E-value: 2.72e-08
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1846-1874 | 2.73e-08 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 51.87 E-value: 2.73e-08
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
102-351 | 2.82e-08 | ||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 59.95 E-value: 2.82e-08
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| Atrophin-1 | pfam03154 | Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ... |
98-334 | 3.07e-08 | ||||||||
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: 59.78 E-value: 3.07e-08
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| PHA02874 | PHA02874 | ankyrin repeat protein; Provisional |
2816-2882 | 4.63e-08 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 165205 [Multi-domain] Cd Length: 434 Bit Score: 58.44 E-value: 4.63e-08
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
763-901 | 5.01e-08 | ||||||||
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: 54.33 E-value: 5.01e-08
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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 ... |
1441-1510 | 5.81e-08 | ||||||||
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: 53.05 E-value: 5.81e-08
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| Bromo_TFIID | cd05511 | Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ... |
1444-1496 | 7.01e-08 | ||||||||
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: 53.04 E-value: 7.01e-08
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| Atrophin-1 | pfam03154 | Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ... |
27-464 | 7.71e-08 | ||||||||
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: 58.24 E-value: 7.71e-08
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| PHA02874 | PHA02874 | ankyrin repeat protein; Provisional |
2792-2902 | 7.85e-08 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 165205 [Multi-domain] Cd Length: 434 Bit Score: 57.67 E-value: 7.85e-08
|
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| PHA02875 | PHA02875 | ankyrin repeat protein; Provisional |
2768-2924 | 8.92e-08 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 165206 [Multi-domain] Cd Length: 413 Bit Score: 57.31 E-value: 8.92e-08
|
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| Bromo_BAZ2A_B_like | cd05503 | Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ... |
1444-1511 | 1.14e-07 | ||||||||
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: 51.99 E-value: 1.14e-07
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| Drf_FH1 | pfam06346 | Formin Homology Region 1; This region is found in some of the Diaphanous related formins (Drfs) ... |
102-297 | 1.45e-07 | ||||||||
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: 53.34 E-value: 1.45e-07
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| Ldl_recept_b | pfam00058 | Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif ... |
2053-2093 | 1.49e-07 | ||||||||
Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure. Pssm-ID: 459654 Cd Length: 42 Bit Score: 49.85 E-value: 1.49e-07
|
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| PLN03192 | PLN03192 | Voltage-dependent potassium channel; Provisional |
2802-2914 | 1.63e-07 | ||||||||
Voltage-dependent potassium channel; Provisional Pssm-ID: 215625 [Multi-domain] Cd Length: 823 Bit Score: 57.19 E-value: 1.63e-07
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| Ank_5 | pfam13857 | Ankyrin repeats (many copies); |
2849-2902 | 1.81e-07 | ||||||||
Ankyrin repeats (many copies); Pssm-ID: 433530 [Multi-domain] Cd Length: 56 Bit Score: 50.04 E-value: 1.81e-07
|
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| Bromo_BDF1_2_I | cd05500 | Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ... |
1441-1509 | 2.58e-07 | ||||||||
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: 51.16 E-value: 2.58e-07
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
357-570 | 2.95e-07 | ||||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 56.48 E-value: 2.95e-07
|
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
742-902 | 3.82e-07 | ||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 52.29 E-value: 3.82e-07
|
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
102-356 | 4.57e-07 | ||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 56.10 E-value: 4.57e-07
|
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| Ank_5 | pfam13857 | Ankyrin repeats (many copies); |
2816-2870 | 5.32e-07 | ||||||||
Ankyrin repeats (many copies); Pssm-ID: 433530 [Multi-domain] Cd Length: 56 Bit Score: 48.88 E-value: 5.32e-07
|
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| LDLa | smart00192 | Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ... |
1637-1671 | 5.58e-07 | ||||||||
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. Pssm-ID: 197566 Cd Length: 33 Bit Score: 48.01 E-value: 5.58e-07
|
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
743-902 | 7.89e-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: 51.15 E-value: 7.89e-07
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| Bromo_WDR9_II | cd05496 | Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ... |
1434-1516 | 9.16e-07 | ||||||||
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: 50.15 E-value: 9.16e-07
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
87-356 | 1.06e-06 | ||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 54.94 E-value: 1.06e-06
|
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| PHA03095 | PHA03095 | ankyrin-like protein; Provisional |
2773-2888 | 1.19e-06 | ||||||||
ankyrin-like protein; Provisional Pssm-ID: 222980 [Multi-domain] Cd Length: 471 Bit Score: 53.88 E-value: 1.19e-06
|
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| PHA03378 | PHA03378 | EBNA-3B; Provisional |
97-349 | 1.25e-06 | ||||||||
EBNA-3B; Provisional Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 54.30 E-value: 1.25e-06
|
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| EGF_CA | pfam07645 | Calcium-binding EGF domain; |
1920-1948 | 1.82e-06 | ||||||||
Calcium-binding EGF domain; Pssm-ID: 429571 Cd Length: 32 Bit Score: 46.46 E-value: 1.82e-06
|
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| Atrophin-1 | pfam03154 | Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ... |
37-467 | 2.28e-06 | ||||||||
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: 53.62 E-value: 2.28e-06
|
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| PHA03100 | PHA03100 | ankyrin repeat protein; Provisional |
2815-2882 | 3.58e-06 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 222984 [Multi-domain] Cd Length: 422 Bit Score: 52.36 E-value: 3.58e-06
|
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| FXa_inhibition | pfam14670 | Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is ... |
2241-2278 | 3.82e-06 | ||||||||
Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442. Pssm-ID: 464251 [Multi-domain] Cd Length: 36 Bit Score: 45.70 E-value: 3.82e-06
|
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| MISS | pfam15822 | MAPK-interacting and spindle-stabilising protein-like; MISS is a family of eukaryotic ... |
101-353 | 4.39e-06 | ||||||||
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: 50.76 E-value: 4.39e-06
|
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
358-570 | 5.58e-06 | ||||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 52.25 E-value: 5.58e-06
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| LY | smart00135 | Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) ... |
2122-2160 | 6.17e-06 | ||||||||
Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin. Pssm-ID: 214531 [Multi-domain] Cd Length: 43 Bit Score: 45.29 E-value: 6.17e-06
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| Ldl_recept_b | pfam00058 | Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif ... |
2140-2182 | 6.20e-06 | ||||||||
Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure. Pssm-ID: 459654 Cd Length: 42 Bit Score: 45.23 E-value: 6.20e-06
|
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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 ... |
1445-1517 | 7.02e-06 | ||||||||
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: 47.03 E-value: 7.02e-06
|
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| PHA03100 | PHA03100 | ankyrin repeat protein; Provisional |
2809-2882 | 7.26e-06 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 222984 [Multi-domain] Cd Length: 422 Bit Score: 51.20 E-value: 7.26e-06
|
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| Bromo_plant1 | cd05506 | Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ... |
1441-1509 | 8.14e-06 | ||||||||
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: 46.55 E-value: 8.14e-06
|
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
358-543 | 8.40e-06 | ||||||||
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: 50.69 E-value: 8.40e-06
|
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| Pro-rich | pfam15240 | Proline-rich protein; This family includes several eukaryotic proline-rich proteins. |
149-272 | 9.46e-06 | ||||||||
Proline-rich protein; This family includes several eukaryotic proline-rich proteins. Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 48.50 E-value: 9.46e-06
|
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
740-902 | 9.64e-06 | ||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 51.18 E-value: 9.64e-06
|
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| Pro-rich | pfam15240 | Proline-rich protein; This family includes several eukaryotic proline-rich proteins. |
209-356 | 9.83e-06 | ||||||||
Proline-rich protein; This family includes several eukaryotic proline-rich proteins. Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 48.50 E-value: 9.83e-06
|
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| EGF_CA | smart00179 | Calcium-binding EGF-like domain; |
1880-1919 | 1.00e-05 | ||||||||
Calcium-binding EGF-like domain; Pssm-ID: 214542 [Multi-domain] Cd Length: 39 Bit Score: 44.55 E-value: 1.00e-05
|
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
358-552 | 1.05e-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: 50.30 E-value: 1.05e-05
|
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| NHL | cd05819 | NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in ... |
1997-2221 | 1.13e-05 | ||||||||
NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. The repeats have a catalytic activity in Peptidyl-glycine alpha-amidating monooxygenase; proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Tripartite motif-containing protein 32 interacts with the activation domain of Tat. This interaction is mediated by the NHL repeats. Pssm-ID: 271320 [Multi-domain] Cd Length: 269 Bit Score: 49.62 E-value: 1.13e-05
|
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| NHL | cd05819 | NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in ... |
1997-2150 | 1.15e-05 | ||||||||
NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. The repeats have a catalytic activity in Peptidyl-glycine alpha-amidating monooxygenase; proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Tripartite motif-containing protein 32 interacts with the activation domain of Tat. This interaction is mediated by the NHL repeats. Pssm-ID: 271320 [Multi-domain] Cd Length: 269 Bit Score: 49.62 E-value: 1.15e-05
|
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| Bromo_WSTF_like | cd05505 | Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ... |
1412-1498 | 1.30e-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: 45.99 E-value: 1.30e-05
|
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| PHA03100 | PHA03100 | ankyrin repeat protein; Provisional |
2815-2914 | 1.41e-05 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 222984 [Multi-domain] Cd Length: 422 Bit Score: 50.43 E-value: 1.41e-05
|
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| Ank_4 | pfam13637 | Ankyrin repeats (many copies); |
2832-2882 | 1.45e-05 | ||||||||
Ankyrin repeats (many copies); Pssm-ID: 372654 [Multi-domain] Cd Length: 54 Bit Score: 44.57 E-value: 1.45e-05
|
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| YvrE | COG3386 | Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]; Sugar lactone lactonase ... |
2032-2175 | 1.54e-05 | ||||||||
Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]; Sugar lactone lactonase YvrE is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway Pssm-ID: 442613 [Multi-domain] Cd Length: 266 Bit Score: 49.12 E-value: 1.54e-05
|
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| DDXDc_reverse_gyrase | cd17924 | DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
771-870 | 2.13e-05 | ||||||||
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350682 [Multi-domain] Cd Length: 189 Bit Score: 47.71 E-value: 2.13e-05
|
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| PHA03377 | PHA03377 | EBNA-3C; Provisional |
100-337 | 2.39e-05 | ||||||||
EBNA-3C; Provisional Pssm-ID: 177614 [Multi-domain] Cd Length: 1000 Bit Score: 50.05 E-value: 2.39e-05
|
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
97-297 | 2.45e-05 | ||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 50.32 E-value: 2.45e-05
|
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| DR0291 | COG1579 | Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ... |
393-566 | 3.04e-05 | ||||||||
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only]; Pssm-ID: 441187 [Multi-domain] Cd Length: 236 Bit Score: 48.00 E-value: 3.04e-05
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| Ldl_recept_b | pfam00058 | Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif ... |
2183-2223 | 3.42e-05 | ||||||||
Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure. Pssm-ID: 459654 Cd Length: 42 Bit Score: 43.30 E-value: 3.42e-05
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| PHA02878 | PHA02878 | ankyrin repeat protein; Provisional |
2778-2871 | 4.03e-05 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 222939 [Multi-domain] Cd Length: 477 Bit Score: 49.11 E-value: 4.03e-05
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| EGF_CA | cd00054 | Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular ... |
1880-1919 | 4.10e-05 | ||||||||
Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements. Pssm-ID: 238011 Cd Length: 38 Bit Score: 43.01 E-value: 4.10e-05
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| Bromo_SPT7_like | cd05510 | Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ... |
1434-1492 | 4.44e-05 | ||||||||
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: 45.12 E-value: 4.44e-05
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| PHA03100 | PHA03100 | ankyrin repeat protein; Provisional |
2779-2914 | 4.60e-05 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 222984 [Multi-domain] Cd Length: 422 Bit Score: 48.51 E-value: 4.60e-05
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| PHA03378 | PHA03378 | EBNA-3B; Provisional |
94-341 | 4.88e-05 | ||||||||
EBNA-3B; Provisional Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 49.30 E-value: 4.88e-05
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
1131-1179 | 4.97e-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: 43.85 E-value: 4.97e-05
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| Ank_4 | pfam13637 | Ankyrin repeats (many copies); |
2805-2850 | 5.95e-05 | ||||||||
Ankyrin repeats (many copies); Pssm-ID: 372654 [Multi-domain] Cd Length: 54 Bit Score: 43.03 E-value: 5.95e-05
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| EGF | cd00053 | Epidermal growth factor domain, found in epidermal growth factor (EGF) presents in a large ... |
1923-1950 | 6.94e-05 | ||||||||
Epidermal growth factor domain, found in epidermal growth factor (EGF) presents in a large number of proteins, mostly animal; the list of proteins currently known to contain one or more copies of an EGF-like pattern is large and varied; the functional significance of EGF-like domains in what appear to be unrelated proteins is not yet clear; a common feature is that these repeats are found in the extracellular domain of membrane-bound proteins or in proteins known to be secreted (exception: prostaglandin G/H synthase); the domain includes six cysteine residues which have been shown to be involved in disulfide bonds; the main structure is a two-stranded beta-sheet followed by a loop to a C-terminal short two-stranded sheet; Subdomains between the conserved cysteines vary in length; the region between the 5th and 6th cysteine contains two conserved glycines of which at least one is present in most EGF-like domains; a subset of these bind calcium. Pssm-ID: 238010 Cd Length: 36 Bit Score: 42.08 E-value: 6.94e-05
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| Bromo_polybromo_VI | cd05526 | Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which ... |
1428-1518 | 7.60e-05 | ||||||||
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: 44.28 E-value: 7.60e-05
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| NHL_like_6 | cd14962 | Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ... |
2002-2102 | 7.89e-05 | ||||||||
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. Pssm-ID: 271332 [Multi-domain] Cd Length: 271 Bit Score: 47.20 E-value: 7.89e-05
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
363-569 | 8.14e-05 | ||||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 48.53 E-value: 8.14e-05
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| PHA03100 | PHA03100 | ankyrin repeat protein; Provisional |
2779-2861 | 8.35e-05 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 222984 [Multi-domain] Cd Length: 422 Bit Score: 47.74 E-value: 8.35e-05
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| PHA02876 | PHA02876 | ankyrin repeat protein; Provisional |
2796-2892 | 9.74e-05 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 165207 [Multi-domain] Cd Length: 682 Bit Score: 48.14 E-value: 9.74e-05
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| YncE | COG3391 | DNA-binding beta-propeller fold protein YncE [General function prediction only]; |
1996-2147 | 1.61e-04 | ||||||||
DNA-binding beta-propeller fold protein YncE [General function prediction only]; Pssm-ID: 442618 [Multi-domain] Cd Length: 237 Bit Score: 45.84 E-value: 1.61e-04
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| EGF | smart00181 | Epidermal growth factor-like domain; |
1923-1953 | 1.66e-04 | ||||||||
Epidermal growth factor-like domain; Pssm-ID: 214544 Cd Length: 35 Bit Score: 40.96 E-value: 1.66e-04
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| Med15 | pfam09606 | ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ... |
32-220 | 1.91e-04 | ||||||||
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 46.93 E-value: 1.91e-04
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| DUF4670 | pfam15709 | Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ... |
406-552 | 1.96e-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: 46.87 E-value: 1.96e-04
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| PHA03264 | PHA03264 | envelope glycoprotein D; Provisional |
174-328 | 2.70e-04 | ||||||||
envelope glycoprotein D; Provisional Pssm-ID: 223029 [Multi-domain] Cd Length: 416 Bit Score: 46.15 E-value: 2.70e-04
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| PHA03307 | PHA03307 | transcriptional regulator ICP4; Provisional |
36-260 | 3.23e-04 | ||||||||
transcriptional regulator ICP4; Provisional Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 46.70 E-value: 3.23e-04
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| EnvC | COG4942 | Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ... |
381-652 | 3.92e-04 | ||||||||
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: 45.53 E-value: 3.92e-04
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
771-902 | 4.14e-04 | ||||||||
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 43.39 E-value: 4.14e-04
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
392-594 | 4.35e-04 | ||||||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 45.91 E-value: 4.35e-04
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| NHL | cd05819 | NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in ... |
1992-2106 | 4.37e-04 | ||||||||
NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. The repeats have a catalytic activity in Peptidyl-glycine alpha-amidating monooxygenase; proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Tripartite motif-containing protein 32 interacts with the activation domain of Tat. This interaction is mediated by the NHL repeats. Pssm-ID: 271320 [Multi-domain] Cd Length: 269 Bit Score: 45.00 E-value: 4.37e-04
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| PABP-1234 | TIGR01628 | polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ... |
178-424 | 4.44e-04 | ||||||||
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range. Pssm-ID: 130689 [Multi-domain] Cd Length: 562 Bit Score: 45.95 E-value: 4.44e-04
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| PRKCSH-like | pfam12999 | Glucosidase II beta subunit-like; The sequences found in this family are similar to a region ... |
1683-1763 | 4.80e-04 | ||||||||
Glucosidase II beta subunit-like; The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II, which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyzes the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. Pssm-ID: 372423 [Multi-domain] Cd Length: 176 Bit Score: 43.62 E-value: 4.80e-04
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
16-334 | 5.23e-04 | ||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 46.08 E-value: 5.23e-04
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| TRPV5-6 | cd22192 | Transient Receptor Potential channel, Vanilloid subfamily (TRPV), types 5 and 6; TRPV5 and ... |
2771-2901 | 5.25e-04 | ||||||||
Transient Receptor Potential channel, Vanilloid subfamily (TRPV), types 5 and 6; TRPV5 and TRPV6 (TRPV5/6) are two homologous members within the vanilloid subfamily of the transient receptor potential (TRP) family. TRPV5 and TRPV6 show only 30-40% homology with other members of the TRP family and have unique properties that differentiates them from other TRP channels. They mediate calcium uptake in epithelia and their expression is dramatically increased in numerous types of cancer. The structure of TRPV5/6 shows the typical topology features of all TRP family members, such as six transmembrane regions, a short hydrophobic stretch between transmembrane segments 5 and 6, which is predicted to form the Ca2+ pore, and large intracellular N- and C-terminal domains. The N-terminal domain of TRPV5/6 contains three ankyrin repeats. This structural element is present in several proteins and plays a role in protein-protein interactions. The N- and C-terminal tails of TRPV5/6 each contain an internal PDZ motif which can function as part of a molecular scaffold via interaction with PDZ-domain containing proteins. A major difference between the properties of TRPV5 and TRPV6 is in their tissue distribution: TRPV5 is predominantly expressed in the distal convoluted tubules (DCT) and connecting tubules (CNT) of the kidney, with limited expression in extrarenal tissues. In contrast, TRPV6 has a broader expression pattern such as expression in the intestine, kidney, placenta, epididymis, exocrine tissues, and a few other tissues. Pssm-ID: 411976 [Multi-domain] Cd Length: 609 Bit Score: 45.39 E-value: 5.25e-04
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| Bromo_cbp_like | cd05495 | Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ... |
1441-1512 | 5.39e-04 | ||||||||
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: 41.66 E-value: 5.39e-04
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| LY | smart00135 | Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) ... |
2163-2205 | 5.83e-04 | ||||||||
Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin. Pssm-ID: 214531 [Multi-domain] Cd Length: 43 Bit Score: 39.89 E-value: 5.83e-04
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| PHA02876 | PHA02876 | ankyrin repeat protein; Provisional |
2784-2870 | 5.93e-04 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 165207 [Multi-domain] Cd Length: 682 Bit Score: 45.44 E-value: 5.93e-04
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| EGF | smart00181 | Epidermal growth factor-like domain; |
1883-1919 | 6.27e-04 | ||||||||
Epidermal growth factor-like domain; Pssm-ID: 214544 Cd Length: 35 Bit Score: 39.42 E-value: 6.27e-04
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
357-529 | 6.49e-04 | ||||||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 45.14 E-value: 6.49e-04
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| NHL_like_5 | cd14963 | Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ... |
2014-2104 | 7.18e-04 | ||||||||
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. Pssm-ID: 271333 [Multi-domain] Cd Length: 268 Bit Score: 44.20 E-value: 7.18e-04
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
430-541 | 7.35e-04 | ||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 45.52 E-value: 7.35e-04
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| Ank | pfam00023 | Ankyrin repeat; Ankyrins are multifunctional adaptors that link specific proteins to the ... |
2798-2828 | 7.78e-04 | ||||||||
Ankyrin repeat; Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities. Repeats 13-24 are especially active, with known sites of interaction for the Na/K ATPase, Cl/HCO(3) anion exchanger, voltage-gated sodium channel, clathrin heavy chain and L1 family cell adhesion molecules. The ANK repeats are found to form a contiguous spiral stack such that ion transporters like the anion exchanger associate in a large central cavity formed by the ANK repeat spiral, while clathrin and cell adhesion molecules associate with specific regions outside this cavity. Pssm-ID: 459634 [Multi-domain] Cd Length: 34 Bit Score: 39.19 E-value: 7.78e-04
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| DUF5401 | pfam17380 | Family of unknown function (DUF5401); This is a family of unknown function found in ... |
328-549 | 9.01e-04 | ||||||||
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: 44.73 E-value: 9.01e-04
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| PRK07764 | PRK07764 | DNA polymerase III subunits gamma and tau; Validated |
84-328 | 9.75e-04 | ||||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 44.98 E-value: 9.75e-04
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
364-569 | 1.05e-03 | ||||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 44.93 E-value: 1.05e-03
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
360-569 | 1.34e-03 | ||||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 44.67 E-value: 1.34e-03
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| AP_MuD_MHD | cd09256 | Mu-homology domain (MHD) of a adaptor protein (AP) encoded by mu-2 related death-inducing gene, ... |
2566-2722 | 1.42e-03 | ||||||||
Mu-homology domain (MHD) of a adaptor protein (AP) encoded by mu-2 related death-inducing gene, MuD (also known as MUDENG); This family corresponds to the MHD found in a protein encoded by MuD (also known as Adapter-related protein complex 5 subunit mu-1), which is distantly related to the C-terminal domain of the mu2 subunit of AP complexes that participates in clathrin-mediated endocytosis. MuD is evolutionary conserved from mammals to amphibians. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Pssm-ID: 271164 Cd Length: 276 Bit Score: 43.14 E-value: 1.42e-03
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| PHA02878 | PHA02878 | ankyrin repeat protein; Provisional |
2748-2875 | 1.45e-03 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 222939 [Multi-domain] Cd Length: 477 Bit Score: 44.10 E-value: 1.45e-03
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| cEGF | pfam12662 | Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved ... |
1904-1923 | 1.48e-03 | ||||||||
Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteriztic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue. Pssm-ID: 463661 Cd Length: 22 Bit Score: 38.16 E-value: 1.48e-03
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| Ank_5 | pfam13857 | Ankyrin repeats (many copies); |
2783-2835 | 1.49e-03 | ||||||||
Ankyrin repeats (many copies); Pssm-ID: 433530 [Multi-domain] Cd Length: 56 Bit Score: 38.87 E-value: 1.49e-03
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| NHL | cd05819 | NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in ... |
2038-2195 | 1.64e-03 | ||||||||
NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. The repeats have a catalytic activity in Peptidyl-glycine alpha-amidating monooxygenase; proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Tripartite motif-containing protein 32 interacts with the activation domain of Tat. This interaction is mediated by the NHL repeats. Pssm-ID: 271320 [Multi-domain] Cd Length: 269 Bit Score: 43.08 E-value: 1.64e-03
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| YncE | COG3391 | DNA-binding beta-propeller fold protein YncE [General function prediction only]; |
2052-2204 | 1.71e-03 | ||||||||
DNA-binding beta-propeller fold protein YncE [General function prediction only]; Pssm-ID: 442618 [Multi-domain] Cd Length: 237 Bit Score: 42.76 E-value: 1.71e-03
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| EGF | cd00053 | Epidermal growth factor domain, found in epidermal growth factor (EGF) presents in a large ... |
1883-1919 | 1.73e-03 | ||||||||
Epidermal growth factor domain, found in epidermal growth factor (EGF) presents in a large number of proteins, mostly animal; the list of proteins currently known to contain one or more copies of an EGF-like pattern is large and varied; the functional significance of EGF-like domains in what appear to be unrelated proteins is not yet clear; a common feature is that these repeats are found in the extracellular domain of membrane-bound proteins or in proteins known to be secreted (exception: prostaglandin G/H synthase); the domain includes six cysteine residues which have been shown to be involved in disulfide bonds; the main structure is a two-stranded beta-sheet followed by a loop to a C-terminal short two-stranded sheet; Subdomains between the conserved cysteines vary in length; the region between the 5th and 6th cysteine contains two conserved glycines of which at least one is present in most EGF-like domains; a subset of these bind calcium. Pssm-ID: 238010 Cd Length: 36 Bit Score: 38.23 E-value: 1.73e-03
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| Med15 | pfam09606 | ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ... |
180-351 | 1.96e-03 | ||||||||
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 43.84 E-value: 1.96e-03
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
360-569 | 2.09e-03 | ||||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 43.77 E-value: 2.09e-03
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| PHA02876 | PHA02876 | ankyrin repeat protein; Provisional |
2809-2914 | 2.78e-03 | ||||||||
ankyrin repeat protein; Provisional Pssm-ID: 165207 [Multi-domain] Cd Length: 682 Bit Score: 43.13 E-value: 2.78e-03
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| PHA03377 | PHA03377 | EBNA-3C; Provisional |
92-339 | 3.08e-03 | ||||||||
EBNA-3C; Provisional Pssm-ID: 177614 [Multi-domain] Cd Length: 1000 Bit Score: 43.12 E-value: 3.08e-03
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
358-540 | 3.29e-03 | ||||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 43.13 E-value: 3.29e-03
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| FXa_inhibition | pfam14670 | Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is ... |
1930-1958 | 3.36e-03 | ||||||||
Coagulation Factor Xa inhibitory site; This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442. Pssm-ID: 464251 [Multi-domain] Cd Length: 36 Bit Score: 37.22 E-value: 3.36e-03
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| PHA03095 | PHA03095 | ankyrin-like protein; Provisional |
2794-2907 | 3.79e-03 | ||||||||
ankyrin-like protein; Provisional Pssm-ID: 222980 [Multi-domain] Cd Length: 471 Bit Score: 42.70 E-value: 3.79e-03
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| PHA03379 | PHA03379 | EBNA-3A; Provisional |
102-351 | 4.70e-03 | ||||||||
EBNA-3A; Provisional Pssm-ID: 223066 [Multi-domain] Cd Length: 935 Bit Score: 42.74 E-value: 4.70e-03
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| Myosin_tail_1 | pfam01576 | Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ... |
366-567 | 5.39e-03 | ||||||||
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament. Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 42.47 E-value: 5.39e-03
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| SSDP | pfam04503 | Single-stranded DNA binding protein, SSDP; This is a family of eukaryotic single-stranded DNA ... |
157-344 | 5.53e-03 | ||||||||
Single-stranded DNA binding protein, SSDP; This is a family of eukaryotic single-stranded DNA binding proteins with specificity to a pyrimidine-rich element found in the promoter region of the alpha2(I) collagen gene. Pssm-ID: 461334 [Multi-domain] Cd Length: 293 Bit Score: 41.48 E-value: 5.53e-03
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| DUF4670 | pfam15709 | Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ... |
433-562 | 5.89e-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: 42.25 E-value: 5.89e-03
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| EGF_3 | pfam12947 | EGF domain; This family includes a variety of EGF-like domain homologs. This family includes ... |
1924-1952 | 6.00e-03 | ||||||||
EGF domain; This family includes a variety of EGF-like domain homologs. This family includes the C-terminal domain of the malaria parasite MSP1 protein. Pssm-ID: 463759 [Multi-domain] Cd Length: 36 Bit Score: 36.81 E-value: 6.00e-03
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| Atrophin-1 | pfam03154 | Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ... |
205-359 | 7.02e-03 | ||||||||
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: 42.06 E-value: 7.02e-03
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| PHA02682 | PHA02682 | ORF080 virion core protein; Provisional |
236-441 | 7.48e-03 | ||||||||
ORF080 virion core protein; Provisional Pssm-ID: 177464 [Multi-domain] Cd Length: 280 Bit Score: 41.00 E-value: 7.48e-03
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| PLN03192 | PLN03192 | Voltage-dependent potassium channel; Provisional |
2764-2822 | 7.75e-03 | ||||||||
Voltage-dependent potassium channel; Provisional Pssm-ID: 215625 [Multi-domain] Cd Length: 823 Bit Score: 41.78 E-value: 7.75e-03
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
400-565 | 9.15e-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: 41.06 E-value: 9.15e-03
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