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Conserved domains on  [gi|2074816284|ref|NP_001382627|]
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endoribonuclease Dicer isoform 10 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 237-429 1.00e-55

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: 185.10  E-value: 1.00e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 237 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 316
Cdd:cd18802     4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 317 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 396
Cdd:cd18802    36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2074816284 397 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 429
Cdd:cd18802   110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 12-104 1.50e-42

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd18034:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 200  Bit Score: 152.04  E-value: 1.50e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENC---PSCPRILGLTASILNGKCDPEELEEKI 88
Cdd:cd18034   105 VLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTSRPRILGLTASPVNGKGDPKSVEKKI 184

                          90
                  ....*....|....*.
gi 2074816284  89 QKLEKILKSNAETATD 104
Cdd:cd18034   185 QQLEELLNSTIKTVSD 200
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 495-583 1.30e-32

Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners.


:

Pssm-ID: 460900  Cd Length: 89  Bit Score: 120.29  E-value: 1.30e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 495 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 574
Cdd:pfam03368   1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                  ....*....
gi 2074816284 575 DHLMPVGKE 583
Cdd:pfam03368  80 DHLLPLTKK 88
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 136-230 2.92e-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: 97.36  E-value: 2.92e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 136 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 206
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                          90       100
                  ....*....|....*....|....
gi 2074816284 207 RKFLLFTDTFLRKIHALCEEHFSP 230
Cdd:cd15903    81 RLFLRYVITQLRKIRKLLEDEMKN 104
 
Name Accession Description Interval E-value
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 237-429 1.00e-55

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: 185.10  E-value: 1.00e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 237 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 316
Cdd:cd18802     4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 317 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 396
Cdd:cd18802    36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2074816284 397 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 429
Cdd:cd18802   110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 12-104 1.50e-42

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: 152.04  E-value: 1.50e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENC---PSCPRILGLTASILNGKCDPEELEEKI 88
Cdd:cd18034   105 VLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTSRPRILGLTASPVNGKGDPKSVEKKI 184

                          90
                  ....*....|....*.
gi 2074816284  89 QKLEKILKSNAETATD 104
Cdd:cd18034   185 QQLEELLNSTIKTVSD 200
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 495-583 1.30e-32

Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners.


Pssm-ID: 460900  Cd Length: 89  Bit Score: 120.29  E-value: 1.30e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 495 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 574
Cdd:pfam03368   1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                  ....*....
gi 2074816284 575 DHLMPVGKE 583
Cdd:pfam03368  80 DHLLPLTKK 88
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 136-230 2.92e-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: 97.36  E-value: 2.92e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 136 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 206
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                          90       100
                  ....*....|....*....|....
gi 2074816284 207 RKFLLFTDTFLRKIHALCEEHFSP 230
Cdd:cd15903    81 RLFLRYVITQLRKIRKLLEDEMKN 104
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
12-417 3.90e-21

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 97.88  E-value: 3.90e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPRILGLTASilngkcdPEELEEKIQKL 91
Cdd:COG1111    98 IIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDPLILGMTAS-------PGSDEEKIEEV 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  92 EKILK-SNAETATDlvvldrytSQPceivvDCGPFT-DRSGLYERLLM--ELEEALNFIN-----------DCNISVHSK 156
Cdd:COG1111   171 CENLGiENVEVRTE--------EDP-----DVAPYVhDTEVEWIRVELpeELKEIRDLLNevlddrlkklkELGVIVSTS 237

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 157 ERDST--------LISKQILSDCRAVLVVLGPwcadkVAGMM-------------VRELQKYIKhEQEELHRKFL----- 210
Cdd:COG1111   238 PDLSKkdllalqkKLQRRIREDDSEGYRAISI-----LAEALklrhalelletqgVEALLRYLE-RLEEEARSSGgskas 311

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 211 --LFTDTFLRKIHALCE----EHfspasldlkfvtPKVIKLLEILRKYKpyerqqfesvewynNRNQDNYVswsdseddd 284
Cdd:COG1111   312 krLVSDPRFRKAMRLAEeadiEH------------PKLSKLREILKEQL--------------GTNPDSRI--------- 356

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 285 edeeieekekpetnfpspftnilcgIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGHGIGKNQPRNKQmeaefR 364
Cdd:COG1111   357 -------------------------IVFTQYRDTAEMIVEFLSEPG--------IKAGRFVGQASKEGDKGLTQ-----K 398

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2074816284 365 KQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDL-PTEYRSyVQSKGR 417
Cdd:COG1111   399 EQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGR 451
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 366-418 1.97e-14

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: 69.55  E-value: 1.97e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2074816284 366 QEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 418
Cdd:pfam00271  53 REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
PRK13766 PRK13766
Hef nuclease; Provisional
 12-418 2.95e-14

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 76.07  E-value: 2.95e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPY----REIMKLCENcpscPRILGLTASilNGKcDPEELEEK 87
Cdd:PRK13766  110 VIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYvyiaERYHEDAKN----PLVLGLTAS--PGS-DEEKIKEV 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  88 IQKLeKIlkSNAE--TATDLVVlDRYTSqpcEIVVDcgpftdrsglYERLLM--ELEEALNFINDCnisvhSKERdstli 163
Cdd:PRK13766  183 CENL-GI--EHVEvrTEDDPDV-KPYVH---KVKIE----------WVRVELpeELKEIRDLLNEA-----LKDR----- 235

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 164 sKQILSDCRaVLVVLGPWCADK-VAGMMvRELQKYIKHEQEEL--------------HRKFLLFT---DTFLRKIHALCE 225
Cdd:PRK13766  236 -LKKLKELG-VIVSISPDVSKKeLLGLQ-KKLQQEIANDDSEGyeaisilaeamklrHAVELLETqgvEALRRYLERLRE 312

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 226 EHFSPAS--------LDLKF------------VTPKVIKLLEILRKykpyerqQFEsvewynnRNQDNYVswsdseddde 285
Cdd:PRK13766  313 EARSSGGskaskrlvEDPRFrkavrkakeldiEHPKLEKLREIVKE-------QLG-------KNPDSRI---------- 368

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 286 deeieekekpetnfpspftnilcgIIFVERRYTA-VVLNRLIKEagkqdpelayissNFITGHGIGKNQPRN-KQMEAef 363
Cdd:PRK13766  369 ------------------------IVFTQYRDTAeKIVDLLEKE-------------GIKAVRFVGQASKDGdKGMSQ-- 409

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2074816284 364 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 418
Cdd:PRK13766  410 KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS-IQRKGRT 464
HELICc smart00490
helicase superfamily c-terminal domain;
364-418 6.07e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.54  E-value: 6.07e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816284  364 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 418
Cdd:smart00490  24 EEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
DEXDc smart00487
DEAD-like helicases superfamily;
12-107 1.68e-08

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 54.81  E-value: 1.68e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284   12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPRILGLTASILNgkcDPEELEEKIQKL 91
Cdd:smart00487 108 ILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPE---EIENLLELFLND 184

                           90
                   ....*....|....*.
gi 2074816284   92 EKILKSNAETATDLVV 107
Cdd:smart00487 185 PVFIDVGFTPLEPIEQ 200
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 12-86 7.59e-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: 40.69  E-value: 7.59e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2074816284  12 VLIMTCYVALNVLKNGYLsLSDINLLVFDECHLaILDHPYREIMKLC-ENCPSCPRILGLTASIlngkcdPEELEE 86
Cdd:pfam00270  97 ILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHR-LLDMGFGPDLEEIlRRLPKKRQILLLSATL------PRNLED 164
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
12-86 5.31e-03

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 39.88  E-value: 5.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLaiLDHPYR----EIM--KLCENCPScPRILGLTASILNgkcdPEELE 85
Cdd:COG1204   116 ILVATPEKLDSLLRNGPSWLRDVDLVVVDEAHL--IDDESRgptlEVLlaRLRRLNPE-AQIVALSATIGN----AEEIA 188


                  .
gi 2074816284  86 E 86
Cdd:COG1204   189 E 189
 
Name Accession Description Interval E-value
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 237-429 1.00e-55

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: 185.10  E-value: 1.00e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 237 FVTPKVIKLLEILRKYKPYerqqfesvewynnrnqdnyvswsdsedddedeeieekekpetnfpspfTNILCGIIFVERR 316
Cdd:cd18802     4 VVIPKLQKLIEILREYFPK------------------------------------------------TPDFRGIIFVERR 35

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 317 YTAVVLNRLIKEAGKqdpELAYISSNFITGHGIGKNqprNKQMEAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKC 396
Cdd:cd18802    36 ATAVVLSRLLKEHPS---TLAFIRCGFLIGRGNSSQ---RKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2074816284 397 NLVVRFDLPTEYRSYVQSKGRARAPISNYIMLA 429
Cdd:cd18802   110 NLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 12-104 1.50e-42

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: 152.04  E-value: 1.50e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENC---PSCPRILGLTASILNGKCDPEELEEKI 88
Cdd:cd18034   105 VLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLegrTSRPRILGLTASPVNGKGDPKSVEKKI 184

                          90
                  ....*....|....*.
gi 2074816284  89 QKLEKILKSNAETATD 104
Cdd:cd18034   185 QQLEELLNSTIKTVSD 200
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 495-583 1.30e-32

Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners.


Pssm-ID: 460900  Cd Length: 89  Bit Score: 120.29  E-value: 1.30e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 495 AIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRaSIVGPPMSCVRLAERVVALICCEKLHKIGELD 574
Cdd:pfam03368   1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLR-SIEGPPWRSKKLAKRSAAFEACKALHKAGLLD 79


                  ....*....
gi 2074816284 575 DHLMPVGKE 583
Cdd:pfam03368  80 DHLLPLTKK 88
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 12-103 4.15e-30

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: 117.53  E-value: 4.15e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYL-SLSDINLLVFDECHLAILDHPYREIMKLCENCPS-----CPRILGLTASILNGKC-DPEEL 84
Cdd:cd17927   103 VIIVTPQILVNDLKSGTIvSLSDFSLLVFDECHNTTKNHPYNEIMFRYLDQKLgssgpLPQILGLTASPGVGGAkNTEEA 182

                          90
                  ....*....|....*....
gi 2074816284  85 EEKIQKLEKILKSNAETAT 103
Cdd:cd17927   183 LEHICKLCANLDISVIATV 201
Dicer_PBD cd15903
Partner-binding domain of the endoribonuclease Dicer; The endoribonuclease Dicer plays a ...
 136-230 2.92e-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: 97.36  E-value: 2.92e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 136 LMELEEALNFINDCNISVHS---------KERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELH 206
Cdd:cd15903     1 LSLLDEIIEFLNDCKLFDPEvyiesllldRDPDPKKKLKNILNDILYVLDELGPWGASKAALAFIIQLEKLKKKSTDEKH 80

                          90       100
                  ....*....|....*....|....
gi 2074816284 207 RKFLLFTDTFLRKIHALCEEHFSP 230
Cdd:cd15903    81 RLFLRYVITQLRKIRKLLEDEMKN 104
helicase_insert_domain cd12088
helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a ...
 136-227 3.25e-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: 90.99  E-value: 3.25e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 136 LMELEEALNFINDCNIsvhskerDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHeqeELHRKFLLFTDT 215
Cdd:cd12088     1 KMILSQLLRDTESLLK-------LLYTAHLRKLNDALELLEDAGIWDALKYIKMFFTEVREGIFD---ELERKLTLRFDE 70

                          90
                  ....*....|..
gi 2074816284 216 FLRKIHALCEEH 227
Cdd:cd12088    71 KLQKLIALSRDP 82
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
12-417 3.90e-21

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 97.88  E-value: 3.90e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPRILGLTASilngkcdPEELEEKIQKL 91
Cdd:COG1111    98 IIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDPLILGMTAS-------PGSDEEKIEEV 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  92 EKILK-SNAETATDlvvldrytSQPceivvDCGPFT-DRSGLYERLLM--ELEEALNFIN-----------DCNISVHSK 156
Cdd:COG1111   171 CENLGiENVEVRTE--------EDP-----DVAPYVhDTEVEWIRVELpeELKEIRDLLNevlddrlkklkELGVIVSTS 237

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 157 ERDST--------LISKQILSDCRAVLVVLGPwcadkVAGMM-------------VRELQKYIKhEQEELHRKFL----- 210
Cdd:COG1111   238 PDLSKkdllalqkKLQRRIREDDSEGYRAISI-----LAEALklrhalelletqgVEALLRYLE-RLEEEARSSGgskas 311

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 211 --LFTDTFLRKIHALCE----EHfspasldlkfvtPKVIKLLEILRKYKpyerqqfesvewynNRNQDNYVswsdseddd 284
Cdd:COG1111   312 krLVSDPRFRKAMRLAEeadiEH------------PKLSKLREILKEQL--------------GTNPDSRI--------- 356

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 285 edeeieekekpetnfpspftnilcgIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGHGIGKNQPRNKQmeaefR 364
Cdd:COG1111   357 -------------------------IVFTQYRDTAEMIVEFLSEPG--------IKAGRFVGQASKEGDKGLTQ-----K 398

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2074816284 365 KQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDL-PTEYRSyVQSKGR 417
Cdd:COG1111   399 EQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPvPSEIRS-IQRKGR 451
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 366-418 1.97e-14

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: 69.55  E-value: 1.97e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2074816284 366 QEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 418
Cdd:pfam00271  53 REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
PRK13766 PRK13766
Hef nuclease; Provisional
 12-418 2.95e-14

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 76.07  E-value: 2.95e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPY----REIMKLCENcpscPRILGLTASilNGKcDPEELEEK 87
Cdd:PRK13766  110 VIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYvyiaERYHEDAKN----PLVLGLTAS--PGS-DEEKIKEV 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  88 IQKLeKIlkSNAE--TATDLVVlDRYTSqpcEIVVDcgpftdrsglYERLLM--ELEEALNFINDCnisvhSKERdstli 163
Cdd:PRK13766  183 CENL-GI--EHVEvrTEDDPDV-KPYVH---KVKIE----------WVRVELpeELKEIRDLLNEA-----LKDR----- 235

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 164 sKQILSDCRaVLVVLGPWCADK-VAGMMvRELQKYIKHEQEEL--------------HRKFLLFT---DTFLRKIHALCE 225
Cdd:PRK13766  236 -LKKLKELG-VIVSISPDVSKKeLLGLQ-KKLQQEIANDDSEGyeaisilaeamklrHAVELLETqgvEALRRYLERLRE 312

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 226 EHFSPAS--------LDLKF------------VTPKVIKLLEILRKykpyerqQFEsvewynnRNQDNYVswsdseddde 285
Cdd:PRK13766  313 EARSSGGskaskrlvEDPRFrkavrkakeldiEHPKLEKLREIVKE-------QLG-------KNPDSRI---------- 368

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 286 deeieekekpetnfpspftnilcgIIFVERRYTA-VVLNRLIKEagkqdpelayissNFITGHGIGKNQPRN-KQMEAef 363
Cdd:PRK13766  369 ------------------------IVFTQYRDTAeKIVDLLEKE-------------GIKAVRFVGQASKDGdKGMSQ-- 409

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2074816284 364 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 418
Cdd:PRK13766  410 KEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEIRS-IQRKGRT 464
HELICc smart00490
helicase superfamily c-terminal domain;
364-418 6.07e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.54  E-value: 6.07e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816284  364 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 418
Cdd:smart00490  24 EEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 310-418 6.16e-12

C-terminal helicase domain of Fanconi anemia group M family helicases; 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. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef 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: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 63.53  E-value: 6.16e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 310 IIFVERRYTAvvlNRLIKEAGKQDPELAyiSSNFItGHGIGKNQPRNKQMEaefrkQEEVLRKFRAHETNLLIATSIVEE 389
Cdd:cd18801    34 IIFSEFRDSA---EEIVNFLSKIRPGIR--ATRFI-GQASGKSSKGMSQKE-----QKEVIEQFRKGGYNVLVATSIGEE 102

                          90       100       110
                  ....*....|....*....|....*....|
gi 2074816284 390 GVDIPKCNLVVRFD-LPTEYRSyVQSKGRA 418
Cdd:cd18801   103 GLDIGEVDLIICYDaSPSPIRM-IQRMGRT 131
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 12-91 1.23e-11

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: 64.42  E-value: 1.23e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNG----YLSLSDINLLVFDECHLAILDHPYREIM------KLCENCPScPRILGLTASI-LNGKCD 80
Cdd:cd18036   103 VIICTPQILINNLLSGreeeRVYLSDFSLLIFDECHHTQKEHPYNKIMrmyldkKLSSQGPL-PQILGLTASPgVGGARS 181

                          90
                  ....*....|.
gi 2074816284  81 PEELEEKIQKL 91
Cdd:cd18036   182 FEEALEHILKL 192
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 310-420 3.02e-11

C-terminal helicase domain of the 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. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 60.98  E-value: 3.02e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 310 IIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVEE 389
Cdd:cd18787    31 IIFVNTKKRVDRLAELLEELG--------IKVAAL--HG-DLSQ----------EERERALKKFRSGKVRVLVATDVAAR 89

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2074816284 390 GVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA 420
Cdd:cd18787    90 GLDIPGVDHVINYDLPRDAEDYVHRIGRtGRA 121
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 12-91 3.29e-11

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: 62.92  E-value: 3.29e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYL-SLSDINLLVFDECHLAILDHPYREIM------KLCENCPSCPRILGLTASILNGKC-DPEE 83
Cdd:cd18073   103 IIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSGNHPYNMIMfryldqKLGGSSGPLPQIIGLTASVGVGDAkNTDE 182


                  ....*...
gi 2074816284  84 LEEKIQKL 91
Cdd:cd18073   183 ALDYICKL 190
DEXDc smart00487
DEAD-like helicases superfamily;
12-107 1.68e-08

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 54.81  E-value: 1.68e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284   12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPRILGLTASILNgkcDPEELEEKIQKL 91
Cdd:smart00487 108 ILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPE---EIENLLELFLND 184

                           90
                   ....*....|....*.
gi 2074816284   92 EKILKSNAETATDLVV 107
Cdd:smart00487 185 PVFIDVGFTPLEPIEQ 200
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
309-454 1.72e-08

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 57.08  E-value: 1.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 309 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFItgHGiGKNQprnkqmeaefRKQEEVLRKFRAHETNLLIATSIVE 388
Cdd:COG0513   244 AIVFCNTKRGADRLAEKLQKRG--------ISAAAL--HG-DLSQ----------GQRERALDAFRNGKIRVLVATDVAA 302

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2074816284 389 EGVDIPKCNLVVRFDLPTEYRSYV---------QSKGRArapisnyIMLADtdkiksfEEDLKTYKAIEKILRNK 454
Cdd:COG0513   303 RGIDIDDVSHVINYDLPEDPEDYVhrigrtgraGAEGTA-------ISLVT-------PDERRLLRAIEKLIGQK 363
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 377-418 2.89e-08

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: 51.17  E-value: 2.89e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2074816284 377 ETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 418
Cdd:cd18785    22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRA 63
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 358-449 9.58e-07

C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. 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: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 48.80  E-value: 9.58e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 358 QMEAEfrKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADT 431
Cdd:cd18792    69 KMTED--EKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIiedadRFGLSQLH----QLRGRvGRGKHQSYCYLLYP 142

                          90
                  ....*....|....*...
gi 2074816284 432 DKIKSFEEDLKTYKAIEK 449
Cdd:cd18792   143 DPKKLTETAKKRLRAIAE 160
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 12-91 2.46e-06

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: 48.09  E-value: 2.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPRILGLTASILNgkcDPEELEEKIQKL 91
Cdd:cd18033    98 VFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQVVRELMRYNSHFRILALTATPGS---KLEAVQQVIDNL 174
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
309-418 5.37e-06

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 49.25  E-value: 5.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 309 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGhgigknqprnkQMEAEFRkqEEVLRKFRAHETNLLIATSIVE 388
Cdd:COG1061   308 TLVFCSSVDHAEALAELLNEAG--------IRAAVVTG-----------DTPKKER--EEILEAFRDGELRILVTVDVLN 366

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2074816284 389 EGVDIPKCNLVV--RfdlPTEYRS-YVQSKGRA 418
Cdd:COG1061   367 EGVDVPRLDVAIllR---PTGSPReFIQRLGRG 396
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 12-91 5.65e-06

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: 47.12  E-value: 5.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCENCPSCPRILGLTASilnGKCDPEELEEKIQKL 91
Cdd:cd18035    96 IIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGNYAYVYIAHRYKREANNPLILGLTAS---PGSDKEKIMEICENL 172
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 325-436 1.31e-05

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase 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: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 45.80  E-value: 1.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 325 LIKEAGKQDPELA-----YISSNFITGHGIGKNQPRNKQMEaefrkQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLV 399
Cdd:cd18811    35 LIEESEKLDLKAAvamyeYLKERFRPELNVGLLHGRLKSDE-----KDAVMAEFREGEVDILVSTTVIEVGVDVPNATVM 109

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2074816284 400 V-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADTDKIKS 436
Cdd:cd18811   110 ViedaeRFGLSQLH----QLRGRvGRGDHQSYCLLVYKDPLTE 148
PTZ00424 PTZ00424
helicase 45; Provisional
 364-443 1.53e-05

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 47.51  E-value: 1.53e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 364 RKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA----RAPIS-NYIMLADTDKIKSFE 438
Cdd:PTZ00424  304 KDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSgrfgRKGVAiNFVTPDDIEQLKEIE 383


                  ....*
gi 2074816284 439 EDLKT 443
Cdd:PTZ00424  384 RHYNT 388
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 309-459 1.60e-05

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 47.63  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 309 GIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFITGhgigknqprnkqmEAEFRKQEEVLRKFRAHETNLLIATSIVE 388
Cdd:PRK11192  248 SIVFVRTRERVHELAGWLRKAG--------INCCYLEG-------------EMVQAKRNEAIKRLTDGRVNVLVATDVAA 306

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 389 EGVDIPKCNLVVRFDLPTEYRSYVQSKGR-ARA-----PIS-----NYIMLadtDKIKSF-EEDLK---------TYKAI 447
Cdd:PRK11192  307 RGIDIDDVSHVINFDMPRSADTYLHRIGRtGRAgrkgtAISlveahDHLLL---GKIERYiEEPLKarvidelrpKTKAP 383

                         170
                  ....*....|..
gi 2074816284 448 EKILRNKCSKSV 459
Cdd:PRK11192  384 SEKKTGKPSKKV 395
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 367-404 1.92e-05

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 47.84  E-value: 1.92e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2074816284 367 EEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDL 404
Cdd:PRK10917  521 DAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVienaeRFGL 563
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 309-418 2.88e-05

C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins 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: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 43.70  E-value: 2.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 309 GIIFVERRYTAVVLNRLIKEAGkqdPELAYISSNFItghgigknqprnkqmeAEFRKQEEVLR-KFRAHETNLLIATSIV 387
Cdd:cd18799     9 TLIFCVSIEHAEFMAEAFNEAG---IDAVALNSDYS----------------DRERGDEALILlFFGELKPPILVTVDLL 69

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2074816284 388 EEGVDIPKCNLVVrFDLPTEYRS-YVQSKGRA 418
Cdd:cd18799    70 TTGVDIPEVDNVV-FLRPTESRTlFLQMLGRG 100
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 12-73 4.03e-05

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: 44.85  E-value: 4.03e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2074816284  12 VLIMTCYVALNVLKNG----YLSLSDINLLVFDECHLAILDHPYREIM------KLCENCPsCPRILGLTAS 73
Cdd:cd18075    99 VVICTAQILQNALLSGeeeaHVELTDFSLLVIDECHHTHKEAVYNKIMlsylekKLSRQGD-LPQILGLTAS 169
PTZ00110 PTZ00110
helicase; Provisional
 364-442 1.04e-04

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 45.15  E-value: 1.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 364 RKQEE---VLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQ---SKGRARAPISNYIMLAdTDKIKSF 437
Cdd:PTZ00110  411 KKQEErtwVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHrigRTGRAGAKGASYTFLT-PDKYRLA 489


                  ....*
gi 2074816284 438 EEDLK 442
Cdd:PTZ00110  490 RDLVK 494
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
367-394 1.16e-04

RecG-like helicase [Replication, recombination and repair];


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 45.04  E-value: 1.16e-04
                          10        20
                  ....*....|....*....|....*...
gi 2074816284 367 EEVLRKFRAHETNLLIATSIVEEGVDIP 394
Cdd:COG1200   519 DAVMAAFKAGEIDVLVATTVIEVGVDVP 546
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 356-417 1.53e-04

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 44.84  E-value: 1.53e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2074816284 356 NKQMEAEFRkqEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGR 417
Cdd:PRK11634  276 NGDMNQALR--EQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGR 335
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 368-448 4.58e-04

C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase 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: 350177 [Multi-domain]  Cd Length: 171  Bit Score: 41.46  E-value: 4.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 368 EVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTE-----YRSYVQSKGRA-RAPISNYIMLAD--TDKIKsfee 439
Cdd:cd18790    68 EIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEgflrsETSLIQTIGRAaRNVNGKVILYADkiTDSMQ---- 143


                  ....*....
gi 2074816284 440 dlktyKAIE 448
Cdd:cd18790   144 -----KAIE 147
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 358-449 5.68e-04

C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a DEAD-like helicase 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: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 40.79  E-value: 5.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 358 QMEAEfrKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVV-----RFDLPTEYrsyvQSKGR-ARAPISNYIMLADT 431
Cdd:cd18810    60 QMTEN--ELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIieradKFGLAQLY----QLRGRvGRSKERAYAYFLYP 133

                          90
                  ....*....|....*...
gi 2074816284 432 DKIKSFEEDLKTYKAIEK 449
Cdd:cd18810   134 DQKKLTEDALKRLEAIQE 151
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 12-86 7.59e-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: 40.69  E-value: 7.59e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2074816284  12 VLIMTCYVALNVLKNGYLsLSDINLLVFDECHLaILDHPYREIMKLC-ENCPSCPRILGLTASIlngkcdPEELEE 86
Cdd:pfam00270  97 ILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHR-LLDMGFGPDLEEIlRRLPKKRQILLLSATL------PRNLED 164
Mfd COG1197
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
 343-397 8.99e-04

Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];


Pssm-ID: 440810 [Multi-domain]  Cd Length: 1130  Bit Score: 42.36  E-value: 8.99e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2074816284  343 FITGHGigknqprnkQMEAefRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCN 397
Cdd:COG1197    824 IAVAHG---------QMSE--RELERVMLDFYEGEFDVLVCTTIIETGIDIPNAN 867
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 360-418 1.56e-03

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 41.31  E-value: 1.56e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2074816284 360 EAEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 418
Cdd:PLN00206  401 EKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRA 459
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 320-393 2.94e-03

CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 40.45  E-value: 2.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 320 VVLN---------RLIKEAGKqDPELAYISSNFITGHgigknqprnkqmeaefRKQ--EEVLRKFRAHETNLLIATSIVE 388
Cdd:COG1203   371 VIVNtvkdaqelyEALKEKLP-DEEVYLLHSRFCPAD----------------RSEieKEIKERLERGKPCILVSTQVVE 433


                  ....*
gi 2074816284 389 EGVDI 393
Cdd:COG1203   434 AGVDI 438
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
12-86 5.31e-03

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 39.88  E-value: 5.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284  12 VLIMTCYVALNVLKNGYLSLSDINLLVFDECHLaiLDHPYR----EIM--KLCENCPScPRILGLTASILNgkcdPEELE 85
Cdd:COG1204   116 ILVATPEKLDSLLRNGPSWLRDVDLVVVDEAHL--IDDESRgptlEVLlaRLRRLNPE-AQIVALSATIGN----AEEIA 188


                  .
gi 2074816284  86 E 86
Cdd:COG1204   189 E 189
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 308-418 5.41e-03

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. 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: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 37.57  E-value: 5.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2074816284 308 CGIIFVERRYTAVVLNRLIKEAGkqdpelayISSNFiTGHGIGKNQprnkqmeaefrkQEEVLRKFRAHETNLLIATSIV 387
Cdd:cd18794    32 SGIIYCLSRKECEQVAARLQSKG--------ISAAA-YHAGLEPSD------------RRDVQRKWLRDKIQVIVATVAF 90

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2074816284 388 EEGVDIPKCNLVVRFDLPTEYRSYVQSKGRA 418
Cdd:cd18794    91 GMGIDKPDVRFVIHYSLPKSMESYYQESGRA 121
 
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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