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Conserved domains on  [gi|2074816303|ref|NP_001382628|]
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endoribonuclease Dicer isoform 11 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 42-239 1.61e-105

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer 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: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 311.89  E-value: 1.61e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  42 YTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELSYQIRGdFSRNGKRTVFLVNSANQVAQQVSAVRTHSDLKV 121
Cdd:cd18034     1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRK-EKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 122 GEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENC---PS 198
Cdd:cd18034    80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTS 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2074816303 199 CPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 239
Cdd:cd18034   160 RPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 271-365 2.87e-24

Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a central role in RNA interference by breaking down RNA molecules into fragments of about 22 nucleotides (miRNAs and siRNAs). Loading of RNA onto Dicer and the enzymatic cleavage are supported by dsRNA-binding proteins, including trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). Together with Argonaute, this constitutes the RNA-induced silencing complex (RISC) which functions to load the small RNA fragments onto Argonaute. The Partner-binding domain of Dicer is responsible for interactions with the dsRNA-binding proteins. This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases.


:

Pssm-ID: 277191  Cd Length: 104  Bit Score: 96.59  E-value: 2.87e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 271 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 341
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                          90       100
                  ....*....|....*....|....
gi 2074816303 342 RKFLLFTDTFLRKIHALCEEHFSP 365
Cdd:cd15903    81 RLFLRYVITQLRKIRKLLEDEMKN 104
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 372-458 4.03e-04

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd18802:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 142  Bit Score: 40.65  E-value: 4.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 372 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 451
Cdd:cd18802     4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35


                  ....*..
gi 2074816303 452 YTAVVLN 458
Cdd:cd18802    36 ATAVVLS 42
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 42-239 1.61e-105

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer 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: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 311.89  E-value: 1.61e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  42 YTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELSYQIRGdFSRNGKRTVFLVNSANQVAQQVSAVRTHSDLKV 121
Cdd:cd18034     1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRK-EKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 122 GEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENC---PS 198
Cdd:cd18034    80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTS 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2074816303 199 CPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 239
Cdd:cd18034   160 RPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 271-365 2.87e-24

Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a central role in RNA interference by breaking down RNA molecules into fragments of about 22 nucleotides (miRNAs and siRNAs). Loading of RNA onto Dicer and the enzymatic cleavage are supported by dsRNA-binding proteins, including trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). Together with Argonaute, this constitutes the RNA-induced silencing complex (RISC) which functions to load the small RNA fragments onto Argonaute. The Partner-binding domain of Dicer is responsible for interactions with the dsRNA-binding proteins. This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases.


Pssm-ID: 277191  Cd Length: 104  Bit Score: 96.59  E-value: 2.87e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 271 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 341
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                          90       100
                  ....*....|....*....|....
gi 2074816303 342 RKFLLFTDTFLRKIHALCEEHFSP 365
Cdd:cd15903    81 RLFLRYVITQLRKIRKLLEDEMKN 104
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
44-226 8.46e-23

ERCC4-related helicase [Replication, recombination and repair];


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 101.73  E-value: 8.46e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  44 PRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELsyqirgdFSRNGKRTVFLVNS---ANQVAQQVSAVRTHSDLK 120
Cdd:COG1111     4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER-------LHKKGGKVLFLAPTkplVEQHAEFFKEALNIPEDE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 121 VGEYSNlEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCP 200
Cdd:COG1111    77 IVVFTG-EVSPEKRKELWE----KARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDP 151

                         170       180
                  ....*....|....*....|....*.
gi 2074816303 201 RILGLTASILNgkcDPEELEEKIQKL 226
Cdd:COG1111   152 LILGMTASPGS---DEEKIEEVCENL 174
DEXDc smart00487
DEAD-like helicases superfamily;
40-242 1.06e-22

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 95.25  E-value: 1.06e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303   40 NIYTPRKYQVELLEAALD--HNTIVCLNTGSGKTFIAVLLTKELSYqirgdfSRNGKRTVFLVNSANQVAQQVSAVRTHS 117
Cdd:smart00487   5 GFEPLRPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPALEALK------RGKGGRVLVLVPTRELAEQWAEELKKLG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  118 DLKVGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCP 197
Cdd:smart00487  79 PSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLP 158

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 2074816303  198 SCPRILGLTASILNgkcDPEELEEKIQKLEKILKSNAETATDLVV 242
Cdd:smart00487 159 KNVQLLLLSATPPE---EIENLLELFLNDPVFIDVGFTPLEPIEQ 200
PRK13766 PRK13766
Hef nuclease; Provisional
 37-223 9.59e-18

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 86.08  E-value: 9.59e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  37 IHDNIYTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELsyqirgdFSRNGKRTVFLVNSANQVAQQVSAVRTH 116
Cdd:PRK13766    9 IKPNTIEARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAER-------LHKKGGKVLILAPTKPLVEQHAEFFRKF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 117 SDLKVGEYSNL--EVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPY----REIM 190
Cdd:PRK13766   82 LNIPEEKIVVFtgEVSPEKRAELWE----KAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYvyiaERYH 157

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2074816303 191 KLCENcpscPRILGLTASilngkcdPEELEEKI 223
Cdd:PRK13766  158 EDAKN----PLVLGLTAS-------PGSDEEKI 179
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 45-221 1.34e-13

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: 68.42  E-value: 1.34e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  45 RKYQVELLEAAL-DHNTIVCLNTGSGKTFIAVL-LTKELsyqirgDFSRNGKRTVFLV---NSANQVAQQVSavrthsdl 119
Cdd:pfam00270   1 TPIQAEAIPAILeGRDVLVQAPTGSGKTLAFLLpALEAL------DKLDNGPQALVLAptrELAEQIYEELK-------- 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 120 KVGEYSNLEVNASWT-KERWNQ--EFTKHQVLIMTCYVALNVLKNGYLsLSDINLLVFDECHLaILDHPYREIMKLC-EN 195
Cdd:pfam00270  67 KLGKGLGLKVASLLGgDSRKEQleKLKGPDILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHR-LLDMGFGPDLEEIlRR 144

                         170       180
                  ....*....|....*....|....*.
gi 2074816303 196 CPSCPRILGLTASIlngkcdPEELEE 221
Cdd:pfam00270 145 LPKKRQILLLSATL------PRNLED 164
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 372-458 4.03e-04

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains 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: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 40.65  E-value: 4.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 372 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 451
Cdd:cd18802     4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35


                  ....*..
gi 2074816303 452 YTAVVLN 458
Cdd:cd18802    36 ATAVVLS 42
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 42-239 1.61e-105

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer 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: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 311.89  E-value: 1.61e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  42 YTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELSYQIRGdFSRNGKRTVFLVNSANQVAQQVSAVRTHSDLKV 121
Cdd:cd18034     1 FTPRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRK-EKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 122 GEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENC---PS 198
Cdd:cd18034    80 GEYSGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTS 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2074816303 199 CPRILGLTASILNGKCDPEELEEKIQKLEKILKSNAETATD 239
Cdd:cd18034   160 RPRILGLTASPVNGKGDPKSVEKKIQQLEELLNSTIKTVSD 200
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 42-238 9.71e-69

DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family 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: 350685 [Multi-domain]  Cd Length: 201  Bit Score: 217.69  E-value: 9.71e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  42 YTPRKYQVELLEAAL-DHNTIVCLNTGSGKTFIAVLLTKELSYQIRgdfSRNGKRTVFLVNSANQVAQQVSAVRTHSD-- 118
Cdd:cd17927     1 FKPRNYQLELAQPALkGKNTIICLPTGSGKTFVAVLICEHHLKKFP---AGRKGKVVFLANKVPLVEQQKEVFRKHFErp 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 119 -LKVGEYSNlevnASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYL-SLSDINLLVFDECHLAILDHPYREIMKLCENC 196
Cdd:cd17927    78 gYKVTGLSG----DTSENVSVEQIVESSDVIIVTPQILVNDLKSGTIvSLSDFSLLVFDECHNTTKNHPYNEIMFRYLDQ 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2074816303 197 PS-----CPRILGLTASILNGKC-DPEELEEKIQKLEKILKSNAETAT 238
Cdd:cd17927   154 KLgssgpLPQILGLTASPGVGGAkNTEEALEHICKLCANLDISVIATV 201
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 43-226 7.63e-27

DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) 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: 350794 [Multi-domain]  Cd Length: 204  Bit Score: 107.18  E-value: 7.63e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  43 TPRKYQVELLEAALD-HNTIVCLNTGSGKTFIAVLLTKElSYQIRGDFSRNGkRTVFLVNSANQVAQQvSAVRTHSDLKV 121
Cdd:cd18036     2 ELRNYQLELVLPALRgKNTIICAPTGSGKTRVAVYICRH-HLEKRRSAGEKG-RVVVLVNKVPLVEQQ-LEKFFKYFRKG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 122 GEYSNLEvNASWTKERWNQEFTKHQVLIMTCYVALNVLKNG----YLSLSDINLLVFDECHLAILDHPYREIM------K 191
Cdd:cd18036    79 YKVTGLS-GDSSHKVSFGQIVKASDVIICTPQILINNLLSGreeeRVYLSDFSLLIFDECHHTQKEHPYNKIMrmyldkK 157

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2074816303 192 LCENCPScPRILGLTASI-LNGKCDPEELEEKIQKL 226
Cdd:cd18036   158 LSSQGPL-PQILGLTASPgVGGARSFEEALEHILKL 192
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 271-365 2.87e-24

Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a central role in RNA interference by breaking down RNA molecules into fragments of about 22 nucleotides (miRNAs and siRNAs). Loading of RNA onto Dicer and the enzymatic cleavage are supported by dsRNA-binding proteins, including trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). Together with Argonaute, this constitutes the RNA-induced silencing complex (RISC) which functions to load the small RNA fragments onto Argonaute. The Partner-binding domain of Dicer is responsible for interactions with the dsRNA-binding proteins. This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases.


Pssm-ID: 277191  Cd Length: 104  Bit Score: 96.59  E-value: 2.87e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 271 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 341
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                          90       100
                  ....*....|....*....|....
gi 2074816303 342 RKFLLFTDTFLRKIHALCEEHFSP 365
Cdd:cd15903    81 RLFLRYVITQLRKIRKLLEDEMKN 104
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
44-226 8.46e-23

ERCC4-related helicase [Replication, recombination and repair];


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 101.73  E-value: 8.46e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  44 PRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELsyqirgdFSRNGKRTVFLVNS---ANQVAQQVSAVRTHSDLK 120
Cdd:COG1111     4 RRLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAER-------LHKKGGKVLFLAPTkplVEQHAEFFKEALNIPEDE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 121 VGEYSNlEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCP 200
Cdd:COG1111    77 IVVFTG-EVSPEKRKELWE----KARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDP 151

                         170       180
                  ....*....|....*....|....*.
gi 2074816303 201 RILGLTASILNgkcDPEELEEKIQKL 226
Cdd:COG1111   152 LILGMTASPGS---DEEKIEEVCENL 174
DEXDc smart00487
DEAD-like helicases superfamily;
40-242 1.06e-22

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 95.25  E-value: 1.06e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303   40 NIYTPRKYQVELLEAALD--HNTIVCLNTGSGKTFIAVLLTKELSYqirgdfSRNGKRTVFLVNSANQVAQQVSAVRTHS 117
Cdd:smart00487   5 GFEPLRPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPALEALK------RGKGGRVLVLVPTRELAEQWAEELKKLG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  118 DLKVGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCP 197
Cdd:smart00487  79 PSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLP 158

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 2074816303  198 SCPRILGLTASILNgkcDPEELEEKIQKLEKILKSNAETATDLVV 242
Cdd:smart00487 159 KNVQLLLLSATPPE---EIENLLELFLNDPVFIDVGFTPLEPIEQ 200
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 45-226 1.08e-22

DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA), and Holliday junction substrates. Its ATP-dependent DNA branch migration activity can process branched DNA structures such as a movable replication fork. This activity is strongly stimulated in the presence of CENPS and CENPX. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, it strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA. FANCM 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: 350791 [Multi-domain]  Cd Length: 182  Bit Score: 94.70  E-value: 1.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  45 RKYQVELLEAALDHNTIVCLNTGSGKTFIA--VLLtkelsyqirgDFSR---NGKrTVFLVNSANQVAQQVSAVrtHSDL 119
Cdd:cd18033     4 RDYQFTIVQKALFQNTLVALPTGLGKTFIAavVML----------NYYRwfpKGK-IVFMAPTKPLVSQQIEAC--YKIT 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 120 KVGEYSNLEVNASWTKERWNQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSC 199
Cdd:cd18033    71 GIPSSQTAELTGSVPPTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQVVRELMRYNSH 150

                         170       180
                  ....*....|....*....|....*..
gi 2074816303 200 PRILGLTASILNgkcDPEELEEKIQKL 226
Cdd:cd18033   151 FRILALTATPGS---KLEAVQQVIDNL 174
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 44-226 3.17e-22

DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called DEAD box protein 58 (DDX58), is a pathogen-recognition receptor that recognizes viral 5'-triphosphates carrying double-stranded RNA. Upon binding to these microbe-associated molecular patterns (MAMPs), RIG-I forms oligomers and promotes downstream processes that result in type I interferon production and induction of an antiviral state. The optimal ligand for RIG-I has been found to be base-paired or double-stranded RNA (dsRNA) molecules containing a 5' triphosphate (5'-ppp-dsRNA). RIG-I contains two N-terminal caspase activation and recruitment domains (CARDs), which are required for interaction with IPS-1, a superfamily 2 helicase/translocase/ATPase (SF2) domain and a C-terminal regulatory/repressor domain (RD). RIG-I 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: 350831 [Multi-domain]  Cd Length: 202  Bit Score: 94.12  E-value: 3.17e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  44 PRKYQVELLEAALD-HNTIVCLNTGSGKTFIAVLLTKelsYQIRgDFSRNGK-RTVFLVNSANQVAQQVSAVRTH---SD 118
Cdd:cd18073     3 PRNYQLELALPAMKgKNTIICAPTGCGKTFVSLLICE---HHLK-KFPQGQKgKVVFFATKVPVYEQQKSVFSKYferHG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 119 LKV----GEYSNLeVNASWTKErwnqeftKHQVLIMTCYVALNVLKNGYL-SLSDINLLVFDECHLAILDHPYREIM--- 190
Cdd:cd18073    79 YRVtgisGATAEN-VPVEQIIE-------NNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSGNHPYNMIMfry 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2074816303 191 ---KLCENCPSCPRILGLTASILNGKC-DPEELEEKIQKL 226
Cdd:cd18073   151 ldqKLGGSSGPLPQIIGLTASVGVGDAkNTDEALDYICKL 190
helicase_insert_domain cd12088
helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a ...
 271-362 8.73e-22

helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases, like archaeal Hef helicase, MDA5-like helicases and FancM-like helicases. The exact function of this domain is unknown, but seems to play a role in interaction with nucleotides and/or the stabilization of the nucleotide complex.


Pssm-ID: 277187  Cd Length: 82  Bit Score: 89.07  E-value: 8.73e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 271 LMELEEALNFINDCNIsvhskerDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHeqeELHRKFLLFTDT 350
Cdd:cd12088     1 KMILSQLLRDTESLLK-------LLYTAHLRKLNDALELLEDAGIWDALKYIKMFFTEVREGIFD---ELERKLTLRFDE 70

                          90
                  ....*....|..
gi 2074816303 351 FLRKIHALCEEH 362
Cdd:cd12088    71 KLQKLIALSRDP 82
PRK13766 PRK13766
Hef nuclease; Provisional
 37-223 9.59e-18

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 86.08  E-value: 9.59e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  37 IHDNIYTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELsyqirgdFSRNGKRTVFLVNSANQVAQQVSAVRTH 116
Cdd:PRK13766    9 IKPNTIEARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAER-------LHKKGGKVLILAPTKPLVEQHAEFFRKF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 117 SDLKVGEYSNL--EVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPY----REIM 190
Cdd:PRK13766   82 LNIPEEKIVVFtgEVSPEKRAELWE----KAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYvyiaERYH 157

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2074816303 191 KLCENcpscPRILGLTASilngkcdPEELEEKI 223
Cdd:PRK13766  158 EDAKN----PLVLGLTAS-------PGSDEEKI 179
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 44-226 3.55e-14

DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef 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: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 70.62  E-value: 3.55e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  44 PRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLtkelsyqIRGDFSRNGKRTVFLVNSANQVAQQVSAVRT--HSDLKV 121
Cdd:cd18035     3 RRLYQVLIAAVALNGNTLIVLPTGLGKTIIAILV-------AADRLTKKGGKVLILAPSRPLVEQHAENLKRvlNIPDKI 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 122 GEYSNlEVNASWTKERWNqeftKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPR 201
Cdd:cd18035    76 TSLTG-EVKPEERAERWD----ASKIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGNYAYVYIAHRYKREANNPL 150

                         170       180
                  ....*....|....*....|....*
gi 2074816303 202 ILGLTASilnGKCDPEELEEKIQKL 226
Cdd:cd18035   151 ILGLTAS---PGSDKEKIMEICENL 172
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 46-219 3.55e-14

DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong 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: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 70.37  E-value: 3.55e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  46 KYQVELLEAAL--DHNTIVCLNTGSGKTFIAVLLtkelsyqIRGDFSRNGKRTVFLVNS---ANQVAQQVSAVRTHSDLK 120
Cdd:cd17921     4 PIQREALRALYlsGDSVLVSAPTSSGKTLIAELA-------ILRALATSGGKAVYIAPTralVNQKEADLRERFGPLGKN 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 121 VGE-YSNLEVNASWTKERwnqeftkhQVLIMTcYVALNVL--KNGYLSLSDINLLVFDECHL-------AILDHPYREIM 190
Cdd:cd17921    77 VGLlTGDPSVNKLLLAEA--------DILVAT-PEKLDLLlrNGGERLIQDVRLVVVDEAHLigdgergVVLELLLSRLL 147

                         170       180
                  ....*....|....*....|....*....
gi 2074816303 191 KLCENCpscpRILGLTASILNgkcdPEEL 219
Cdd:cd17921   148 RINKNA----RFVGLSATLPN----AEDL 168
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 45-208 5.28e-14

DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 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: 350833 [Multi-domain]  Cd Length: 200  Bit Score: 70.66  E-value: 5.28e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  45 RKYQVELLEAALD-HNTIVCLNTGSGKTFIAVLLTKelsyqiRGDFSRNGKRTVFLVNSANQVAQQVSAVRTHSDlkvGE 123
Cdd:cd18075     4 HGYQWEVVAPALRgKNSIIWLPTGAGKTRAAVYVAR------RHLETKRGAKVAVLVNKVHLVDQHLEKEFHVLL---DK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 124 YSNLEVNA-SWTKERWNQEFTKHQVLIMTCYVALNVLKNG----YLSLSDINLLVFDECHLAILDHPYREIM------KL 192
Cdd:cd18075    75 YTVTAISGdSSHKCFFGQLARGSDVVICTAQILQNALLSGeeeaHVELTDFSLLVIDECHHTHKEAVYNKIMlsylekKL 154

                         170
                  ....*....|....*.
gi 2074816303 193 CENCPsCPRILGLTAS 208
Cdd:cd18075   155 SRQGD-LPQILGLTAS 169
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 45-221 1.34e-13

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: 68.42  E-value: 1.34e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  45 RKYQVELLEAAL-DHNTIVCLNTGSGKTFIAVL-LTKELsyqirgDFSRNGKRTVFLV---NSANQVAQQVSavrthsdl 119
Cdd:pfam00270   1 TPIQAEAIPAILeGRDVLVQAPTGSGKTLAFLLpALEAL------DKLDNGPQALVLAptrELAEQIYEELK-------- 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 120 KVGEYSNLEVNASWT-KERWNQ--EFTKHQVLIMTCYVALNVLKNGYLsLSDINLLVFDECHLaILDHPYREIMKLC-EN 195
Cdd:pfam00270  67 KLGKGLGLKVASLLGgDSRKEQleKLKGPDILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHR-LLDMGFGPDLEEIlRR 144

                         170       180
                  ....*....|....*....|....*.
gi 2074816303 196 CPSCPRILGLTASIlngkcdPEELEE 221
Cdd:pfam00270 145 LPKKRQILLLSATL------PRNLED 164
ResIII pfam04851
Type III restriction enzyme, res subunit;
41-207 5.87e-13

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 66.54  E-value: 5.87e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  41 IYTPRKYQVE----LLEAALDHNTIVCLN--TGSGKTFIAVLLTKELSYqirgdfSRNGKRTVFLVNSANQVAQQvsavr 114
Cdd:pfam04851   1 KLELRPYQIEaienLLESIKNGQKRGLIVmaTGSGKTLTAAKLIARLFK------KGPIKKVLFLVPRKDLLEQA----- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 115 thsdlkVGEYSNLEVNASWTKERWNQEFTKHQV----LIMTCYVALNV-LKNGYLSLSD--INLLVFDECHLAILDHpYR 187
Cdd:pfam04851  70 ------LEEFKKFLPNYVEIGEIISGDKKDESVddnkIVVTTIQSLYKaLELASLELLPdfFDVIIIDEAHRSGASS-YR 142

                         170       180
                  ....*....|....*....|
gi 2074816303 188 EIMKLCencpSCPRILGLTA 207
Cdd:pfam04851 143 NILEYF----KPAFLLGLTA 158
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
42-207 3.45e-12

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 68.51  E-value: 3.45e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  42 YTPRKYQVELLEAALDHNT------IVCLNTGSGKTFIAVLLTKELsyqirgdfsRNGKRTVFLVNSANQVAQqvsavrT 115
Cdd:COG1061    79 FELRPYQQEALEALLAALErgggrgLVVAPTGTGKTVLALALAAEL---------LRGKRVLVLVPRRELLEQ------W 143

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 116 HSDLKvgEYSNLEVNASWTKERWNQ-EFTKHQVLIMtcYVALNVLKNgylslsDINLLVFDECHLAILDHpYREIMKLCE 194
Cdd:COG1061   144 AEELR--RFLGDPLAGGGKKDSDAPiTVATYQSLAR--RAHLDELGD------RFGLVIIDEAHHAGAPS-YRRILEAFP 212

                         170
                  ....*....|...
gi 2074816303 195 ncpsCPRILGLTA 207
Cdd:COG1061   213 ----AAYRLGLTA 221
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
48-221 8.03e-12

Replicative superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 67.23  E-value: 8.03e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  48 QVELLEAAL--DHNTIVCLNTGSGKTFIAVL-LTKELsyqirgdfsRNGKRTVFLVNS---ANQVAQQVSAVRTHSDLKV 121
Cdd:COG1204    27 QAEALEAGLleGKNLVVSAPTASGKTLIAELaILKAL---------LNGGKALYIVPLralASEKYREFKRDFEELGIKV 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 122 GE-YSNLEVNASWTKERwnqeftkhQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLaiLDHPYR----EIM--KLCE 194
Cdd:COG1204    98 GVsTGDYDSDDEWLGRY--------DILVATPEKLDSLLRNGPSWLRDVDLVVVDEAHL--IDDESRgptlEVLlaRLRR 167

                         170       180
                  ....*....|....*....|....*..
gi 2074816303 195 NCPScPRILGLTASILNgkcdPEELEE 221
Cdd:COG1204   168 LNPE-AQIVALSATIGN----AEEIAE 189
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 44-208 9.27e-12

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: 62.71  E-value: 9.27e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  44 PRKYQVELLEAALDHNT----IVCLNTGSGKTFIAVLLTKELSYqirgdfsrngKRTVFLVNSANQVAQqvsavrthsdl 119
Cdd:cd17926     1 LRPYQEEALEAWLAHKNnrrgILVLPTGSGKTLTALALIAYLKE----------LRTLIVVPTDALLDQ----------- 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 120 kvgeysnlevnaswTKERWNQEFTKHQVLIMTC-----------YVAL-----NVLKNGYLSLSDINLLVFDECHLAild 183
Cdd:cd17926    60 --------------WKERFEDFLGDSSIGLIGGgkkkdfddanvVVATyqslsNLAEEEKDLFDQFGLLIVDEAHHL--- 122

                         170       180
                  ....*....|....*....|....*...
gi 2074816303 184 hP---YREIMKLCEncpsCPRILGLTAS 208
Cdd:cd17926   123 -PaktFSEILKELN----AKYRLGLTAT 145
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 43-226 5.47e-11

DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma differentiation-associated protein 5 or Mda5 and IFIH1) is a viral double-stranded RNA (dsRNA) receptor that shares sequence similarity and signaling pathways with RIG-I, yet plays essential functions in antiviral immunity through distinct specificity for viral RNA. RLR-2 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA. RLR-2 uses direct protein-protein contacts to stack along dsRNA in a head-to-tail arrangement. The signaling domain (tandem CARD), which decorates the outside of the core RLR-2 filament, also has an intrinsic propensity to oligomerize into an elongated structure that activates the signaling adaptor, MAVS. RLR-2 uses long dsRNA as a signaling platform to cooperatively assemble the core filament, which in turn promotes stochastic assembly of the tandem CARD oligomers for signaling. LGP2 appears to positively and negatively regulate RLR-2 and RIG-I signaling, respectively. RLR-2 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: 350832 [Multi-domain]  Cd Length: 216  Bit Score: 62.19  E-value: 5.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  43 TPRKYQVELLEAALD-HNTIVCLNTGSGKTFIAVLLTKELSYQIRGDfSRNGKrTVFLVNSANQVAQQVSA-----VRTH 116
Cdd:cd18074     2 TLRDYQMEVAKPALEgKNIIICLPTGSGKTRVAVYITKDHLDKKRKA-SEPGK-VIVLVNKVPLVEQHYRKefnpfLKHW 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 117 SDLkVGEYSNLEVNASWTKerwnqEFTKHQVLIMTCYVALNVLKNGY------LSLSDINLLVFDECHLAILDHPYREIM 190
Cdd:cd18074    80 YQV-IGLSGDSQLKISFPE-----VVKRYDVIICTAQILENSLLNATeeedegVQLSDFSLIIIDECHHTQKEAVYNNIM 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2074816303 191 KLC------------ENCPSC--PRILGLTASI-LNGKCDPEELEEKIQKL 226
Cdd:cd18074   154 RRYlkqkiknrkqkkENKPLIplPQILGLTASPgVGGAKNNKKAEEHILKI 204
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 58-207 1.77e-09

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: 56.26  E-value: 1.77e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  58 HNTIVCLNTGSGKTFIAVLltkelsyQIRGDFSRNGKRTVFLV---NSANQVAQQVSAVRTHsDLKVGEYsnleVNASWT 134
Cdd:cd00046     2 ENVLITAPTGSGKTLAALL-------AALLLLLKKGKKVLVLVptkALALQTAERLRELFGP-GIRVAVL----VGGSSA 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 135 KERWNQEFTKHQVLIMTC-YVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCE------NCpscpRILGLTA 207
Cdd:cd00046    70 EEREKNKLGDADIIIATPdMLLNLLLREDRLFLKDLKLIIVDEAHALLIDSRGALILDLAVrkaglkNA----QVILLSA 145
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 44-207 1.98e-09

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs 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: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 56.42  E-value: 1.98e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  44 PRKYQVELLEA---ALDHNT---IVCLNTGSGKTFIAVLLTKELSyqirgdFSRNGKRTVFLVNSANQVAQQVSAVRTH- 116
Cdd:cd18032     1 PRYYQQEAIEAleeAREKGQrraLLVMATGTGKTYTAAFLIKRLL------EANRKKRILFLAHREELLEQAERSFKEVl 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 117 SDLKVGEYSNLEVNASWTKerwnqeftkhqVLIMTcYVALNvlKNGYLSLSDIN---LLVFDECHLAILDHpYREIMKLC 193
Cdd:cd18032    75 PDGSFGNLKGGKKKPDDAR-----------VVFAT-VQTLN--KRKRLEKFPPDyfdLIIIDEAHHAIASS-YRKILEYF 139

                         170
                  ....*....|....
gi 2074816303 194 ENCPscprILGLTA 207
Cdd:cd18032   140 EPAF----LLGLTA 149
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 48-221 1.23e-05

DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong 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: 350786 [Multi-domain]  Cd Length: 177  Bit Score: 45.79  E-value: 1.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  48 QVELLEAAL--DHNTIVCLNTGSGKTFIAVL-LTKELSyqirgdfsrNGKRTVFLV---NSANQVAQQVSAVRTHS---D 118
Cdd:cd18028     6 QAEAVRAGLlkGENLLISIPTASGKTLIAEMaMVNTLL---------EGGKALYLVplrALASEKYEEFKKLEEIGlkvG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 119 LKVGEYSnlevnaswTKERWNQEFtkhQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLaiLDHPYRE------IMKL 192
Cdd:cd18028    77 ISTGDYD--------EDDEWLGDY---DIIVATYEKFDSLLRHSPSWLRDVGVVVVDEIHL--ISDEERGptlesiVARL 143

                         170       180
                  ....*....|....*....|....*....
gi 2074816303 193 CENCPSCpRILGLTASILNgkcdPEELEE 221
Cdd:cd18028   144 RRLNPNT-QIIGLSATIGN----PDELAE 167
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 34-228 3.38e-05

DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350669 [Multi-domain]  Cd Length: 196  Bit Score: 44.74  E-value: 3.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  34 QEAIHD-NIYTPRKYQVELLEAALD-HNTIVCLNTGSGKT--FIAVLLTKeLSYQIRGdfSRNGKRTVFLVNS---ANQV 106
Cdd:cd00268     2 LKALKKlGFEKPTPIQAQAIPLILSgRDVIGQAQTGSGKTlaFLLPILEK-LLPEPKK--KGRGPQALVLAPTrelAMQI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 107 AQQVSAVRTHSDLKVgeysnlevnASWT----KERWNQEFTKH-QVLIMTCYVALNVLKNGYLSLSDINLLVFDEchlA- 180
Cdd:cd00268    79 AEVARKLGKGTGLKV---------AAIYggapIKKQIEALKKGpDIVVGTPGRLLDLIERGKLDLSNVKYLVLDE---Ad 146

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2074816303 181 -ILDHPYREIM-KLCENCPSCPRILGLTASIlngkcdPEELEEKIQKLEK 228
Cdd:cd00268   147 rMLDMGFEEDVeKILSALPKDRQTLLFSATL------PEEVKELAKKFLK 190
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 372-458 4.03e-04

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains 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: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 40.65  E-value: 4.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 372 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 451
Cdd:cd18802     4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35


                  ....*..
gi 2074816303 452 YTAVVLN 458
Cdd:cd18802    36 ATAVVLS 42
DEADc_DDX47 cd17954
DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can ...
 43-116 4.95e-04

DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can shuttle between the nucleus and the cytoplasm, and has an RNA-independent ATPase activity. DX47 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350712 [Multi-domain]  Cd Length: 203  Bit Score: 41.15  E-value: 4.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  43 TPRKYQVELLEAALDHNTIVCL-NTGSGKT-----------------FIAVLL--TKELSYQIRGDFSRNGK----RTVF 98
Cdd:cd17954    22 KPTKIQEEAIPVALQGRDIIGLaETGSGKTaafalpilqallenpqrFFALVLapTRELAQQISEQFEALGSsiglKSAV 101

                          90
                  ....*....|....*....
gi 2074816303  99 LVNSANQVAQQVS-AVRTH 116
Cdd:cd17954   102 LVGGMDMMAQAIAlAKKPH 120
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 44-231 7.58e-04

DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an IFN-inducible cytoplasmic helicase that plays a role in RIG-I-mediated type I interferon (IFN) nuclease-mediated viral RNA degradation. DDX60 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: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 40.43  E-value: 7.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  44 PRKYQVELLEAaLDHN--TIVCLNTGSGKTFIAVlltkelsYQIRGDFSRNGKRTVFLVNSA----NQVAQQVSAVRTHS 117
Cdd:cd18025     2 PDAWQRELLDI-VDRResALIVAPTSSGKTFISY-------YCMEKVLRESDDGVVVYVAPTkalvNQVVAEVYARFSKK 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 118 DLKVGEYsnleVNASWTKERWNQEFTKHQVLImTCYVALNVLkngYLSLSD------INLLVFDECHL--AILDHPYREI 189
Cdd:cd18025    74 YPPSGKS----LWGVFTRDYRHNNPMNCQVLI-TVPECLEIL---LLSPHNaswvprIKYVIFDEIHSigQSEDGAVWEQ 145

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2074816303 190 MKLCENCPscprILGLTASILNgkcdPEELEEKIQKLEKILK 231
Cdd:cd18025   146 LLLLIPCP----FLALSATIGN----PQKFHEWLQSVQRARK 179
DEXHc_RecQ cd17920
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ...
 43-226 1.67e-03

DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region.


Pssm-ID: 350678 [Multi-domain]  Cd Length: 200  Bit Score: 39.44  E-value: 1.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  43 TPRKYQVELLEAALDH-NTIVCLNTGSGKTFI----AVLLTKE-------LSY---QIRGdFSRNGKRTVFLvNSANQVA 107
Cdd:cd17920    12 EFRPGQLEAINAVLAGrDVLVVMPTGGGKSLCyqlpALLLDGVtlvvsplISLmqdQVDR-LQQLGIRAAAL-NSTLSPE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 108 QQVSAVRthsDLKVGEYSNLEVnaswTKER-WNQEFtkhqvlimtcyvaLNVLKNGYlSLSDINLLVFDECHLaILD--H 184
Cdd:cd17920    90 EKREVLL---RIKNGQYKLLYV----TPERlLSPDF-------------LELLQRLP-ERKRLALIVVDEAHC-VSQwgH 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2074816303 185 ---P-YREIMKLCENCPSCPrILGLTASilngkCDPEELEEKIQKL 226
Cdd:cd17920   148 dfrPdYLRLGRLRRALPGVP-ILALTAT-----ATPEVREDILKRL 187
DEADc_DDX28 cd17948
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ...
 40-197 1.85e-03

DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350706 [Multi-domain]  Cd Length: 231  Bit Score: 39.66  E-value: 1.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  40 NIYTPRKYQVELLEAALDHNTIVC-LNTGSGKT--FIAVLLTKELSYQIRGDFSRNGKRTVFLVNSaNQVAQQVSAVRTh 116
Cdd:cd17948     9 GITKPTTVQKQGIPSILRGRNTLCaAETGSGKTltYLLPIIQRLLRYKLLAEGPFNAPRGLVITPS-RELAEQIGSVAQ- 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 117 sdlKVGEYSNLEVN---ASWTKERW-NQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHlAILDHPYREIM-K 191
Cdd:cd17948    87 ---SLTEGLGLKVKvitGGRTKRQIrNPHFEEVDILVATPGALSKLLTSRIYSLEQLRHLVLDEAD-TLLDDSFNEKLsH 162


                  ....*.
gi 2074816303 192 LCENCP 197
Cdd:cd17948   163 FLRRFP 168
HsdR COG4096
Type I site-specific restriction endonuclease, part of a restriction-modification system ...
 33-108 2.84e-03

Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];


Pssm-ID: 443272 [Multi-domain]  Cd Length: 806  Bit Score: 40.21  E-value: 2.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  33 QQEAIHDNIyTPRKYQVE----LLEA-ALDHNTI-VCLNTGSGKTFIAVLLTKELsyqIRgdfSRNGKRTVFLVNSANQV 106
Cdd:COG4096   149 ATEPYNDGI-ALRYYQIEairrVEEAiAKGQRRAlLVMATGTGKTRTAIALIYRL---LK---AGRAKRILFLADRNALV 221


                  ..
gi 2074816303 107 AQ 108
Cdd:COG4096   222 DQ 223
DEXHc_Brr2_1 cd18019
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ...
 30-211 6.66e-03

N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 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: 350777 [Multi-domain]  Cd Length: 214  Bit Score: 38.12  E-value: 6.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303  30 LP-WQQEAIhDNIYTPRKYQVELLEAAL--DHNTIVCLNTGSGKTFIAVL-LTKELSYQIRGDFSRNGK--RTVFLVNSA 103
Cdd:cd18019     4 LPdWAQPAF-EGFKSLNRIQSKLFPAAFetDENLLLCAPTGAGKTNVALLtILREIGKHRNPDGTINLDafKIVYIAPMK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816303 104 NQVAQQV---SAVRTHSDLKVGEysnLEVNASWTKErwnqEFTKHQVLIMTCYVALNVLKNG----YLSLsdINLLVFDE 176
Cdd:cd18019    83 ALVQEMVgnfSKRLAPYGITVAE---LTGDQQLTKE----QISETQIIVTTPEKWDIITRKSgdrtYTQL--VRLIIIDE 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2074816303 177 CHL----------AILDHPYREIMKLCENCpscpRILGLTASILN 211
Cdd:cd18019   154 IHLlhddrgpvleSIVARTIRQIEQTQEYV----RLVGLSATLPN 194
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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