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Conserved domains on  [gi|63054443|ref|NP_588215|]
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dicer [Schizosaccharomyces pombe]

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 ...
 12-215 1.03e-76

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: 252.19  E-value: 1.03e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   12 LRKYQQDVYNIASKQNTLLVMRTGAGKTLLAVKLIKQKLEEQILIQEsnleHKKISVFLVNKVPLVFQQAEYIRSQLPAK 91
Cdd:cd18034    3 PRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRKEKN----PKKRAVFLVPTVPLVAQQAEAIRSHTDLK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   92 VGMFYGELSIEMSE-QLLTNIILKYNVIVITADLFYLFLARGFLSINDLNLIIFDECHHAIGNDAYARIMNDFYHrakav 170
Cdd:cd18034   79 VGEYSGEMGVDKWTkERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYH----- 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 63054443  171 lSKKHFTLPRIFGMTASPFTGKK--GNLYHRLYQWEQLFDSKAHVVS 215
Cdd:cd18034  154 -LEGRTSRPRILGLTASPVNGKGdpKSVEKKIQQLEELLNSTIKTVS 199
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 344-475 1.04e-57

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: 195.50  E-value: 1.04e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  344 KVFKLLELLKATYRKSDSVRTVIFVERKATAFTLSLFMKT--LNLPNIRAHSFIGHGPSDQGEFS-MTFRRQKDTLHKFK 420
Cdd:cd18802    8 KLQKLIEILREYFPKTPDFRGIIFVERRATAVVLSRLLKEhpSTLAFIRCGFLIGRGNSSQRKRSlMTQRKQKETLDKFR 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 63054443  421 TGKYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVQSRGRARAMASKFLIFL 475
Cdd:cd18802   88 DGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1098-1247 8.56e-36

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


:

Pssm-ID: 238333  Cd Length: 133  Bit Score: 132.35  E-value: 8.56e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443 1098 KLLHLAFIHPSMMSQQGIyENYQQLEFLGDAVLDYIIVQYLYKKYPNATSGELTDYKSFYVCNKSLSYIGFVLNLHKYIQ 1177
Cdd:cd00593    1 SLLLEALTHPSYANEHGR-FNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLR 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443 1178 HESAAMCDAifeyqelieafretasenpwfwfEIDSPKFISDTLEAMICAIFLDSGFSLqSLQFVLPLFL 1247
Cdd:cd00593   80 LGKGEEKSG-----------------------GRLRPKILADVFEALIGAIYLDGGFEA-ARKFLLRLLG 125
RIBOc smart00535
Ribonuclease III family;
912-1045 6.36e-26

Ribonuclease III family;


:

Pssm-ID: 197778  Cd Length: 129  Bit Score: 104.22  E-value: 6.36e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443     912 DTACQALTSAESQLNF-DYDRLEFYGDCFLKLGASITVFLKFPDTQEYQLHFNRKKIISNCNLYKVAIDCELPKY-ALST 989
Cdd:smart00535    1 SLLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFiRLGR 80

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 63054443     990 PLEIRHWCPygfqkstsdkcryavlqklSVKRIADMVEASIGACLLDSGLDSALKI 1045
Cdd:smart00535   81 GEAISGGRD-------------------KPKILADVFEALIGAIYLDSGLEAAREF 117
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 537-625 3.75e-24

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: 97.57  E-value: 3.75e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    537 AVSLLYNFCNTLSRDVYTRYYPTFTAQPCLSGWYCFEVELPKACKVPAAQGSPAKSIRKAKQNAAFIMCLDLIRMGLIDK 616
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLRSIEGPPWRSKKLAKRSAAFEACKALHKAGLLDD 80


                   ....*....
gi 63054443    617 HLKPLDFRR 625
Cdd:pfam03368   81 HLLPLTKKK 89
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 12-215 1.03e-76

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: 252.19  E-value: 1.03e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   12 LRKYQQDVYNIASKQNTLLVMRTGAGKTLLAVKLIKQKLEEQILIQEsnleHKKISVFLVNKVPLVFQQAEYIRSQLPAK 91
Cdd:cd18034    3 PRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRKEKN----PKKRAVFLVPTVPLVAQQAEAIRSHTDLK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   92 VGMFYGELSIEMSE-QLLTNIILKYNVIVITADLFYLFLARGFLSINDLNLIIFDECHHAIGNDAYARIMNDFYHrakav 170
Cdd:cd18034   79 VGEYSGEMGVDKWTkERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYH----- 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 63054443  171 lSKKHFTLPRIFGMTASPFTGKK--GNLYHRLYQWEQLFDSKAHVVS 215
Cdd:cd18034  154 -LEGRTSRPRILGLTASPVNGKGdpKSVEKKIQQLEELLNSTIKTVS 199
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 344-475 1.04e-57

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: 195.50  E-value: 1.04e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  344 KVFKLLELLKATYRKSDSVRTVIFVERKATAFTLSLFMKT--LNLPNIRAHSFIGHGPSDQGEFS-MTFRRQKDTLHKFK 420
Cdd:cd18802    8 KLQKLIEILREYFPKTPDFRGIIFVERRATAVVLSRLLKEhpSTLAFIRCGFLIGRGNSSQRKRSlMTQRKQKETLDKFR 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 63054443  421 TGKYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVQSRGRARAMASKFLIFL 475
Cdd:cd18802   88 DGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
13-463 2.79e-43

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 169.91  E-value: 2.79e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   13 RKYQQDVYNIASKQNTLLVMRTGAGKTLLAVKLIKQKLEEqiliqesnleHKKISVFLVNKVPLVFQQAEYIRSQLPA-- 90
Cdd:COG1111    5 RLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAERLHK----------KGGKVLFLAPTKPLVEQHAEFFKEALNIpe 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   91 -KVGMFYGELSIEMSEQLLTniilKYNVIVITADLFYLFLARGFLSINDLNLIIFDECHHAIGNDAYARIMNDFYHRAKA 169
Cdd:COG1111   75 dEIVVFTGEVSPEKRKELWE----KARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKD 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  170 vlskkhftlPRIFGMTASPFTGKK------GNLY--HRLYQWEQLFDSKAHVVSEN------ELADYF---------CLP 226
Cdd:COG1111  151 ---------PLILGMTASPGSDEEkieevcENLGieNVEVRTEEDPDVAPYVHDTEvewirvELPEELkeirdllneVLD 221

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  227 EESYVMYSNKLVVPPSDSIIKKCEETLQGcKLISR----------AVKTaLAETIDMglwfgeqvwLYLVDFVET----- 291
Cdd:COG1111  222 DRLKKLKELGVIVSTSPDLSKKDLLALQK-KLQRRireddsegyrAISI-LAEALKL---------RHALELLETqgvea 290

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  292 -----KRLKKKALG-------KQLSDDEEL--AIDRLKifvedwknnKYSDNGPripvfdstdvtdKVFKLLELLKATYR 357
Cdd:COG1111  291 llrylERLEEEARSsggskasKRLVSDPRFrkAMRLAE---------EADIEHP------------KLSKLREILKEQLG 349

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  358 KSDSVRTVIFVE-RKatafTLSLFMKTLNLPNIRAHSFIGHGpSDQGEFSMTFRRQKDTLHKFKTGKYNVLIATAVAEEG 436
Cdd:COG1111  350 TNPDSRIIVFTQyRD----TAEMIVEFLSEPGIKAGRFVGQA-SKEGDKGLTQKEQIEILERFRAGEFNVLVATSVAEEG 424

                        490       500       510
                 ....*....|....*....|....*....|....*.
gi 63054443  437 IDVPSCNLV---------IRFnicrtvtqyVQSRGR 463
Cdd:COG1111  425 LDIPEVDLVifyepvpseIRS---------IQRKGR 451
PRK13766 PRK13766
Hef nuclease; Provisional
 13-464 4.83e-37

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 151.18  E-value: 4.83e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    13 RKYQQDVYNIASKQNTLLVMRTGAGKTLLAVKLIKQKLEEqiliqesnleHKKISVFLVNKVPLVFQQAEYIRSQL---P 89
Cdd:PRK13766   17 RLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAERLHK----------KGGKVLILAPTKPLVEQHAEFFRKFLnipE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    90 AKVGMFYGELSIEMSEQLLTniilKYNVI-----VITADLfylfLArGFLSINDLNLIIFDECHHAIGNDAYARIMNDFY 164
Cdd:PRK13766   87 EKIVVFTGEVSPEKRAELWE----KAKVIvatpqVIENDL----IA-GRISLEDVSLLIFDEAHRAVGNYAYVYIAERYH 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   165 HRAKAvlskkhftlPRIFGMTASPFTGKK------GNLYHRlyqweqlfdskaHVVSENE----LADYFC---------- 224
Cdd:PRK13766  158 EDAKN---------PLVLGLTASPGSDEEkikevcENLGIE------------HVEVRTEddpdVKPYVHkvkiewvrve 216

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   225 LPEE-----SYV----------MYSNKLVVPPSDSIIKKCEETLQGcKL----------ISRAVKTaLAETIDMGlwfge 279
Cdd:PRK13766  217 LPEElkeirDLLnealkdrlkkLKELGVIVSISPDVSKKELLGLQK-KLqqeianddseGYEAISI-LAEAMKLR----- 289

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   280 qvwlYLVDFVET----------KRLKKKALGKQLSD-DEELAID-RLKIFVEDWKnnKYSDNGPripvfdstdvtdKVFK 347
Cdd:PRK13766  290 ----HAVELLETqgvealrrylERLREEARSSGGSKaSKRLVEDpRFRKAVRKAK--ELDIEHP------------KLEK 351

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   348 LLELLKATYRKSDSVRTVIFVERKATAFTLSlfmKTLNLPNIRAHSFIGHGPSDQGEfSMTFRRQKDTLHKFKTGKYNVL 427
Cdd:PRK13766  352 LREIVKEQLGKNPDSRIIVFTQYRDTAEKIV---DLLEKEGIKAVRFVGQASKDGDK-GMSQKEQIEILDKFRAGEFNVL 427

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*.
gi 63054443   428 IATAVAEEGIDVPSCNLV---------IRFnicrtvtqyVQSRGRA 464
Cdd:PRK13766  428 VSTSVAEEGLDIPSVDLVifyepvpseIRS---------IQRKGRT 464
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1098-1247 8.56e-36

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 132.35  E-value: 8.56e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443 1098 KLLHLAFIHPSMMSQQGIyENYQQLEFLGDAVLDYIIVQYLYKKYPNATSGELTDYKSFYVCNKSLSYIGFVLNLHKYIQ 1177
Cdd:cd00593    1 SLLLEALTHPSYANEHGR-FNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLR 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443 1178 HESAAMCDAifeyqelieafretasenpwfwfEIDSPKFISDTLEAMICAIFLDSGFSLqSLQFVLPLFL 1247
Cdd:cd00593   80 LGKGEEKSG-----------------------GRLRPKILADVFEALIGAIYLDGGFEA-ARKFLLRLLG 125
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1086-1246 3.83e-33

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 128.29  E-value: 3.83e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443 1086 IEETIGYSFKNKKLLHLAFIHPSMMSQQGIYENYQQLEFLGDAVLDYIIVQYLYKKYPNATSGELTDYKSFYVCNKSLSY 1165
Cdd:COG0571    7 LEERLGYRFKDPELLEQALTHRSYANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443 1166 IGFVLNLHKYIqhesaamcdaIFEYQELIEAFRETASenpwfwfeIdspkfISDTLEAMICAIFLDSGFSlQSLQFVLPL 1245
Cdd:COG0571   87 IARELGLGDYL----------RLGKGEEKSGGRRRPS--------I-----LADAFEALIGAIYLDGGLE-AARKFVLRL 142


                 .
gi 63054443 1246 F 1246
Cdd:COG0571  143 F 143
RIBOc smart00535
Ribonuclease III family;
1098-1253 3.54e-32

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 121.94  E-value: 3.54e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    1098 KLLHLAFIHPSMMSQQgiyENYQQLEFLGDAVLDYIIVQYLYKKYPNATSGELTDYKSFYVCNKSLSYIGFVLNLHKYIQ 1177
Cdd:smart00535    1 SLLLRALTHASYSNEH---EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIR 77

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 63054443    1178 HEsaamcdaifeyqelieafRETASENPWfwfeiDSPKFISDTLEAMICAIFLDSGFSlQSLQFVLPLFLNSLGDA 1253
Cdd:smart00535   78 LG------------------RGEAISGGR-----DKPKILADVFEALIGAIYLDSGLE-AAREFIRDLLGPRLDEL 129
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1086-1246 2.36e-29

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 117.30  E-value: 2.36e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   1086 IEETIGYSFKNKKLLHLAFIHPSMMSQQGIY-ENYQQLEFLGDAVLDYIIVQYLYKKYPNATSGELTDYKSFYVCNKSLS 1164
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHHKDvKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   1165 YIGFVLNLHKYIQHESAAMCDAIFEyqelieafretasenpwfwfeidSPKFISDTLEAMICAIFLDSGFSLqSLQFVLP 1244
Cdd:TIGR02191   81 EVARELGLGDFLLLGKGEEKSGGRR-----------------------RDSILADAFEALIGAIYLDSGLEA-ARKFILK 136


                   ..
gi 63054443   1245 LF 1246
Cdd:TIGR02191  137 LL 138
RIBOc smart00535
Ribonuclease III family;
912-1045 6.36e-26

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 104.22  E-value: 6.36e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443     912 DTACQALTSAESQLNF-DYDRLEFYGDCFLKLGASITVFLKFPDTQEYQLHFNRKKIISNCNLYKVAIDCELPKY-ALST 989
Cdd:smart00535    1 SLLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFiRLGR 80

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 63054443     990 PLEIRHWCPygfqkstsdkcryavlqklSVKRIADMVEASIGACLLDSGLDSALKI 1045
Cdd:smart00535   81 GEAISGGRD-------------------KPKILADVFEALIGAIYLDSGLEAAREF 117
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 916-1055 1.06e-25

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 103.85  E-value: 1.06e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  916 QALT---SAESQLNFDYDRLEFYGDCFLKLGASITVFLKFPDTQEYQLHFNRKKIISNCNLYKVAIDCELPKYALSTPLE 992
Cdd:cd00593    5 EALThpsYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKGE 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 63054443  993 IRHwcpygfqkstsdkcryavLQKLSVKRIADMVEASIGACLLDSGLDSALKICKSLSVGLLD 1055
Cdd:cd00593   85 EKS------------------GGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIE 129
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1120-1233 2.20e-24

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 98.89  E-value: 2.20e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   1120 QQLEFLGDAVLDYIIVQYLYKKYPNATSGELTDYKSFYVCNKSLSYIGFVLNLHKYIQHESAamcDAIFEYQELIEAFRE 1199
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEEL---DIRRRNNALGKGPKR 77

                           90       100       110
                   ....*....|....*....|....*....|....
gi 63054443   1200 TASEnpwfwfeidsPKFISDTLEAMICAIFLDSG 1233
Cdd:pfam00636   78 ADGK----------EKVLADAFEALIGALYLDGG 101
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 537-625 3.75e-24

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: 97.57  E-value: 3.75e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    537 AVSLLYNFCNTLSRDVYTRYYPTFTAQPCLSGWYCFEVELPKACKVPAAQGSPAKSIRKAKQNAAFIMCLDLIRMGLIDK 616
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLRSIEGPPWRSKKLAKRSAAFEACKALHKAGLLDD 80


                   ....*....
gi 63054443    617 HLKPLDFRR 625
Cdd:pfam03368   81 HLLPLTKKK 89
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 343-464 1.00e-19

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: 85.73  E-value: 1.00e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    343 DKVFKLLELLKATYRKsdsvRTVIFVERKATAfTLSLFMKTLNLPNIRAHSfighgpsdqgefSMTFRRQKDTLHKFKTG 422
Cdd:pfam00271    1 EKLEALLELLKKERGG----KVLIFSQTKKTL-EAELLLEKEGIKVARLHG------------DLSQEEREEILEDFRKG 63

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 63054443    423 KYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVQSRGRA 464
Cdd:pfam00271   64 KIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
Ribonuclease_3 pfam00636
Ribonuclease III domain;
930-1038 5.80e-18

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 80.40  E-value: 5.80e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    930 DRLEFYGDCFLKLGASITVFLKFPDTQEYQLHFNRKKIISNCNLYKVAIDCELPKYALSTPLEIRHWcpygFQKSTSDKC 1009
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRR----NNALGKGPK 76

                           90       100
                   ....*....|....*....|....*....
gi 63054443   1010 RyavlQKLSVKRIADMVEASIGACLLDSG 1038
Cdd:pfam00636   77 R----ADGKEKVLADAFEALIGALYLDGG 101
DEXDc smart00487
DEAD-like helicases superfamily;
12-188 1.07e-16

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 80.23  E-value: 1.07e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443      12 LRKYQQDVYNIASK--QNTLLVMRTGAGKTLLAVKLIKQKLEEQiliqesnleHKKISVFLVNKVPLVFQQAEYIR---S 86
Cdd:smart00487    9 LRPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPALEALKRG---------KGGRVLVLVPTRELAEQWAEELKklgP 79

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443      87 QLPAKVGMFYGELSIEMSEQLLTNIilKYNVIVITADLFYLFLARGFLSINDLNLIIFDECHHAIGNDAYARIMNDFYHR 166
Cdd:smart00487   80 SLGLKVVGLYGGDSKREQLRKLESG--KTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLL 157

                           170       180
                    ....*....|....*....|..
gi 63054443     167 AKAvlskkhftlPRIFGMTASP 188
Cdd:smart00487  158 PKN---------VQLLLLSATP 170
ResIII pfam04851
Type III restriction enzyme, res subunit;
12-189 1.09e-16

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 78.87  E-value: 1.09e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443     12 LRKYQQDVYN-----IASKQNT-LLVMRTGAGKTLLAVKLIKQKLEEQiliqesnleHKKISVFLVNKVPLVFQQAEYIR 85
Cdd:pfam04851    4 LRPYQIEAIEnllesIKNGQKRgLIVMATGSGKTLTAAKLIARLFKKG---------PIKKVLFLVPRKDLLEQALEEFK 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443     86 sqlpaKVGMFYGELSIEMSEQLLTNIILKYNVIVITADLFYLFLARGF--LSINDLNLIIFDECHHAIGnDAYARImndf 163
Cdd:pfam04851   75 -----KFLPNYVEIGEIISGDKKDESVDDNKIVVTTIQSLYKALELASleLLPDFFDVIIIDEAHRSGA-SSYRNI---- 144

                          170       180
                   ....*....|....*....|....*.
gi 63054443    164 yhrakavlsKKHFTLPRIFGMTASPF 189
Cdd:pfam04851  145 ---------LEYFKPAFLLGLTATPE 161
HELICc smart00490
helicase superfamily c-terminal domain;
376-464 9.56e-15

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.70  E-value: 9.56e-15
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443     376 TLSLFMKTLNLPNIRAHSfighgpsdqgefSMTFRRQKDTLHKFKTGKYNVLIATAVAEEGIDVPSCNLVIRFNICRTVT 455
Cdd:smart00490    2 ELAELLKELGIKVARLHG------------GLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPA 69


                    ....*....
gi 63054443     456 QYVQSRGRA 464
Cdd:smart00490   70 SYIQRIGRA 78
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
339-469 1.94e-10

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 64.78  E-value: 1.94e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  339 TDVTDKVFKLLELLKATyrksDSVRTVIFVERKATAFTLSlfmKTLNLPNIRAHSFigHGPSDQGEfsmtfrRQKdTLHK 418
Cdd:COG0513  223 VDKRDKLELLRRLLRDE----DPERAIVFCNTKRGADRLA---EKLQKRGISAAAL--HGDLSQGQ------RER-ALDA 286

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 63054443  419 FKTGKYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVqSR-GR-ARAMAS 469
Cdd:COG0513  287 FRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYV-HRiGRtGRAGAE 338
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 349-466 5.16e-09

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 60.34  E-value: 5.16e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   349 LELLKATYRKSDSVRTVIFVERKATAFTLSLFMKTLNLPNirahSFIghgpsdQGEFSMTFRRQkdTLHKFKTGKYNVLI 428
Cdd:PRK11192  233 TALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINC----CYL------EGEMVQAKRNE--AIKRLTDGRVNVLV 300

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 63054443   429 ATAVAEEGIDVPSCNLVIRFNICRTVTQYVQSRGR-ARA 466
Cdd:PRK11192  301 ATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRtGRA 339
 
Name Accession Description Interval E-value
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 12-215 1.03e-76

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: 252.19  E-value: 1.03e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   12 LRKYQQDVYNIASKQNTLLVMRTGAGKTLLAVKLIKQKLEEQILIQEsnleHKKISVFLVNKVPLVFQQAEYIRSQLPAK 91
Cdd:cd18034    3 PRSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNRKEKN----PKKRAVFLVPTVPLVAQQAEAIRSHTDLK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   92 VGMFYGELSIEMSE-QLLTNIILKYNVIVITADLFYLFLARGFLSINDLNLIIFDECHHAIGNDAYARIMNDFYHrakav 170
Cdd:cd18034   79 VGEYSGEMGVDKWTkERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYH----- 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 63054443  171 lSKKHFTLPRIFGMTASPFTGKK--GNLYHRLYQWEQLFDSKAHVVS 215
Cdd:cd18034  154 -LEGRTSRPRILGLTASPVNGKGdpKSVEKKIQQLEELLNSTIKTVS 199
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 344-475 1.04e-57

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: 195.50  E-value: 1.04e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  344 KVFKLLELLKATYRKSDSVRTVIFVERKATAFTLSLFMKT--LNLPNIRAHSFIGHGPSDQGEFS-MTFRRQKDTLHKFK 420
Cdd:cd18802    8 KLQKLIEILREYFPKTPDFRGIIFVERRATAVVLSRLLKEhpSTLAFIRCGFLIGRGNSSQRKRSlMTQRKQKETLDKFR 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 63054443  421 TGKYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVQSRGRARAMASKFLIFL 475
Cdd:cd18802   88 DGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
13-463 2.79e-43

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 169.91  E-value: 2.79e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   13 RKYQQDVYNIASKQNTLLVMRTGAGKTLLAVKLIKQKLEEqiliqesnleHKKISVFLVNKVPLVFQQAEYIRSQLPA-- 90
Cdd:COG1111    5 RLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAERLHK----------KGGKVLFLAPTKPLVEQHAEFFKEALNIpe 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   91 -KVGMFYGELSIEMSEQLLTniilKYNVIVITADLFYLFLARGFLSINDLNLIIFDECHHAIGNDAYARIMNDFYHRAKA 169
Cdd:COG1111   75 dEIVVFTGEVSPEKRKELWE----KARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKD 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  170 vlskkhftlPRIFGMTASPFTGKK------GNLY--HRLYQWEQLFDSKAHVVSEN------ELADYF---------CLP 226
Cdd:COG1111  151 ---------PLILGMTASPGSDEEkieevcENLGieNVEVRTEEDPDVAPYVHDTEvewirvELPEELkeirdllneVLD 221

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  227 EESYVMYSNKLVVPPSDSIIKKCEETLQGcKLISR----------AVKTaLAETIDMglwfgeqvwLYLVDFVET----- 291
Cdd:COG1111  222 DRLKKLKELGVIVSTSPDLSKKDLLALQK-KLQRRireddsegyrAISI-LAEALKL---------RHALELLETqgvea 290

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  292 -----KRLKKKALG-------KQLSDDEEL--AIDRLKifvedwknnKYSDNGPripvfdstdvtdKVFKLLELLKATYR 357
Cdd:COG1111  291 llrylERLEEEARSsggskasKRLVSDPRFrkAMRLAE---------EADIEHP------------KLSKLREILKEQLG 349

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  358 KSDSVRTVIFVE-RKatafTLSLFMKTLNLPNIRAHSFIGHGpSDQGEFSMTFRRQKDTLHKFKTGKYNVLIATAVAEEG 436
Cdd:COG1111  350 TNPDSRIIVFTQyRD----TAEMIVEFLSEPGIKAGRFVGQA-SKEGDKGLTQKEQIEILERFRAGEFNVLVATSVAEEG 424

                        490       500       510
                 ....*....|....*....|....*....|....*.
gi 63054443  437 IDVPSCNLV---------IRFnicrtvtqyVQSRGR 463
Cdd:COG1111  425 LDIPEVDLVifyepvpseIRS---------IQRKGR 451
PRK13766 PRK13766
Hef nuclease; Provisional
 13-464 4.83e-37

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 151.18  E-value: 4.83e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    13 RKYQQDVYNIASKQNTLLVMRTGAGKTLLAVKLIKQKLEEqiliqesnleHKKISVFLVNKVPLVFQQAEYIRSQL---P 89
Cdd:PRK13766   17 RLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAERLHK----------KGGKVLILAPTKPLVEQHAEFFRKFLnipE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    90 AKVGMFYGELSIEMSEQLLTniilKYNVI-----VITADLfylfLArGFLSINDLNLIIFDECHHAIGNDAYARIMNDFY 164
Cdd:PRK13766   87 EKIVVFTGEVSPEKRAELWE----KAKVIvatpqVIENDL----IA-GRISLEDVSLLIFDEAHRAVGNYAYVYIAERYH 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   165 HRAKAvlskkhftlPRIFGMTASPFTGKK------GNLYHRlyqweqlfdskaHVVSENE----LADYFC---------- 224
Cdd:PRK13766  158 EDAKN---------PLVLGLTASPGSDEEkikevcENLGIE------------HVEVRTEddpdVKPYVHkvkiewvrve 216

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   225 LPEE-----SYV----------MYSNKLVVPPSDSIIKKCEETLQGcKL----------ISRAVKTaLAETIDMGlwfge 279
Cdd:PRK13766  217 LPEElkeirDLLnealkdrlkkLKELGVIVSISPDVSKKELLGLQK-KLqqeianddseGYEAISI-LAEAMKLR----- 289

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   280 qvwlYLVDFVET----------KRLKKKALGKQLSD-DEELAID-RLKIFVEDWKnnKYSDNGPripvfdstdvtdKVFK 347
Cdd:PRK13766  290 ----HAVELLETqgvealrrylERLREEARSSGGSKaSKRLVEDpRFRKAVRKAK--ELDIEHP------------KLEK 351

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   348 LLELLKATYRKSDSVRTVIFVERKATAFTLSlfmKTLNLPNIRAHSFIGHGPSDQGEfSMTFRRQKDTLHKFKTGKYNVL 427
Cdd:PRK13766  352 LREIVKEQLGKNPDSRIIVFTQYRDTAEKIV---DLLEKEGIKAVRFVGQASKDGDK-GMSQKEQIEILDKFRAGEFNVL 427

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*.
gi 63054443   428 IATAVAEEGIDVPSCNLV---------IRFnicrtvtqyVQSRGRA 464
Cdd:PRK13766  428 VSTSVAEEGLDIPSVDLVifyepvpseIRS---------IQRKGRT 464
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1098-1247 8.56e-36

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 132.35  E-value: 8.56e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443 1098 KLLHLAFIHPSMMSQQGIyENYQQLEFLGDAVLDYIIVQYLYKKYPNATSGELTDYKSFYVCNKSLSYIGFVLNLHKYIQ 1177
Cdd:cd00593    1 SLLLEALTHPSYANEHGR-FNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLR 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443 1178 HESAAMCDAifeyqelieafretasenpwfwfEIDSPKFISDTLEAMICAIFLDSGFSLqSLQFVLPLFL 1247
Cdd:cd00593   80 LGKGEEKSG-----------------------GRLRPKILADVFEALIGAIYLDGGFEA-ARKFLLRLLG 125
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1086-1246 3.83e-33

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 128.29  E-value: 3.83e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443 1086 IEETIGYSFKNKKLLHLAFIHPSMMSQQGIYENYQQLEFLGDAVLDYIIVQYLYKKYPNATSGELTDYKSFYVCNKSLSY 1165
Cdd:COG0571    7 LEERLGYRFKDPELLEQALTHRSYANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSEETLAE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443 1166 IGFVLNLHKYIqhesaamcdaIFEYQELIEAFRETASenpwfwfeIdspkfISDTLEAMICAIFLDSGFSlQSLQFVLPL 1245
Cdd:COG0571   87 IARELGLGDYL----------RLGKGEEKSGGRRRPS--------I-----LADAFEALIGAIYLDGGLE-AARKFVLRL 142


                 .
gi 63054443 1246 F 1246
Cdd:COG0571  143 F 143
RIBOc smart00535
Ribonuclease III family;
1098-1253 3.54e-32

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 121.94  E-value: 3.54e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    1098 KLLHLAFIHPSMMSQQgiyENYQQLEFLGDAVLDYIIVQYLYKKYPNATSGELTDYKSFYVCNKSLSYIGFVLNLHKYIQ 1177
Cdd:smart00535    1 SLLLRALTHASYSNEH---EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIR 77

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 63054443    1178 HEsaamcdaifeyqelieafRETASENPWfwfeiDSPKFISDTLEAMICAIFLDSGFSlQSLQFVLPLFLNSLGDA 1253
Cdd:smart00535   78 LG------------------RGEAISGGR-----DKPKILADVFEALIGAIYLDSGLE-AAREFIRDLLGPRLDEL 129
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1086-1246 2.36e-29

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 117.30  E-value: 2.36e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   1086 IEETIGYSFKNKKLLHLAFIHPSMMSQQGIY-ENYQQLEFLGDAVLDYIIVQYLYKKYPNATSGELTDYKSFYVCNKSLS 1164
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYANEHHKDvKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   1165 YIGFVLNLHKYIQHESAAMCDAIFEyqelieafretasenpwfwfeidSPKFISDTLEAMICAIFLDSGFSLqSLQFVLP 1244
Cdd:TIGR02191   81 EVARELGLGDFLLLGKGEEKSGGRR-----------------------RDSILADAFEALIGAIYLDSGLEA-ARKFILK 136


                   ..
gi 63054443   1245 LF 1246
Cdd:TIGR02191  137 LL 138
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 12-195 1.37e-26

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: 108.67  E-value: 1.37e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   12 LRKYQQDVYNIASK-QNTLLVMRTGAGKTLLAVKLIKQKLEeqiliQESNLEHKKIsVFLVNKVPLVFQQAEYIRS---Q 87
Cdd:cd17927    3 PRNYQLELAQPALKgKNTIICLPTGSGKTFVAVLICEHHLK-----KFPAGRKGKV-VFLANKVPLVEQQKEVFRKhfeR 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   88 LPAKVGMFYGELSIEMSEQLltnIILKYNVIVITADLFYLFLARG-FLSINDLNLIIFDECHHAIGNDAYARIMNDfYHR 166
Cdd:cd17927   77 PGYKVTGLSGDTSENVSVEQ---IVESSDVIIVTPQILVNDLKSGtIVSLSDFSLLVFDECHNTTKNHPYNEIMFR-YLD 152

                        170       180
                 ....*....|....*....|....*....
gi 63054443  167 AKAVLSKKhftLPRIFGMTASPFTGKKGN 195
Cdd:cd17927  153 QKLGSSGP---LPQILGLTASPGVGGAKN 178
RIBOc smart00535
Ribonuclease III family;
912-1045 6.36e-26

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 104.22  E-value: 6.36e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443     912 DTACQALTSAESQLNF-DYDRLEFYGDCFLKLGASITVFLKFPDTQEYQLHFNRKKIISNCNLYKVAIDCELPKY-ALST 989
Cdd:smart00535    1 SLLLRALTHASYSNEHeHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFiRLGR 80

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 63054443     990 PLEIRHWCPygfqkstsdkcryavlqklSVKRIADMVEASIGACLLDSGLDSALKI 1045
Cdd:smart00535   81 GEAISGGRD-------------------KPKILADVFEALIGAIYLDSGLEAAREF 117
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 916-1055 1.06e-25

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 103.85  E-value: 1.06e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  916 QALT---SAESQLNFDYDRLEFYGDCFLKLGASITVFLKFPDTQEYQLHFNRKKIISNCNLYKVAIDCELPKYALSTPLE 992
Cdd:cd00593    5 EALThpsYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKGE 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 63054443  993 IRHwcpygfqkstsdkcryavLQKLSVKRIADMVEASIGACLLDSGLDSALKICKSLSVGLLD 1055
Cdd:cd00593   85 EKS------------------GGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIE 129
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1120-1233 2.20e-24

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 98.89  E-value: 2.20e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   1120 QQLEFLGDAVLDYIIVQYLYKKYPNATSGELTDYKSFYVCNKSLSYIGFVLNLHKYIQHESAamcDAIFEYQELIEAFRE 1199
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEEL---DIRRRNNALGKGPKR 77

                           90       100       110
                   ....*....|....*....|....*....|....
gi 63054443   1200 TASEnpwfwfeidsPKFISDTLEAMICAIFLDSG 1233
Cdd:pfam00636   78 ADGK----------EKVLADAFEALIGALYLDGG 101
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 537-625 3.75e-24

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: 97.57  E-value: 3.75e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    537 AVSLLYNFCNTLSRDVYTRYYPTFTAQPCLSGWYCFEVELPKACKVPAAQGSPAKSIRKAKQNAAFIMCLDLIRMGLIDK 616
Cdd:pfam03368    1 AISLLNHYCSTLPSDEFTDLRPEYEVTEVEGGKFVCTVTLPINSPLRSIEGPPWRSKKLAKRSAAFEACKALHKAGLLDD 80


                   ....*....
gi 63054443    617 HLKPLDFRR 625
Cdd:pfam03368   81 HLLPLTKKK 89
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
12-551 3.16e-22

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 102.80  E-value: 3.16e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   12 LRKYQQDVYN------IASKQNTLLVMRTGAGKTLLAVKLIKQkleeqiliqesnLEHKKISVFLVNKVPLVFQQAEYIR 85
Cdd:COG1061   81 LRPYQQEALEallaalERGGGRGLVVAPTGTGKTVLALALAAE------------LLRGKRVLVLVPRRELLEQWAEELR 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   86 SQLPAKVGmfyGELSIEmseqlltniiLKYNVIVITADLFYLFLARGFLSiNDLNLIIFDECHHAiGNDAYARIMNdfyh 165
Cdd:COG1061  149 RFLGDPLA---GGGKKD----------SDAPITVATYQSLARRAHLDELG-DRFGLVIIDEAHHA-GAPSYRRILE---- 209

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  166 rakavlskkHFTLPRIFGMTASPFTGKKGNLYhrlyqwEQLFDSKAHVVSENELADyfclpeesyvmysNKLVVPPsdsI 245
Cdd:COG1061  210 ---------AFPAAYRLGLTATPFRSDGREIL------LFLFDGIVYEYSLKEAIE-------------DGYLAPP---E 258

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  246 IKKCEETLQGckliSRAVKTALAETIDmglwfgeqvwlylvdfvetkrlkkkalgKQLSDDEELAIDRLKifvedwknnk 325
Cdd:COG1061  259 YYGIRVDLTD----ERAEYDALSERLR----------------------------EALAADAERKDKILR---------- 296

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  326 ysdngpripvfdstdvtdkvfkllELLKatyRKSDSVRTVIFVERKATAFTLSlfmKTLNLPNIRAHSFIGHGPSDQgef 405
Cdd:COG1061  297 ------------------------ELLR---EHPDDRKTLVFCSSVDHAEALA---ELLNEAGIRAAVVTGDTPKKE--- 343

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  406 smtfRRQKdtLHKFKTGKYNVLIATAVAEEGIDVPSCNLVIrfnICR---TVTQYVQSRGRA-RAMASKfliflntEELL 481
Cdd:COG1061  344 ----REEI--LEAFRDGELRILVTVDVLNEGVDVPRLDVAI---LLRptgSPREFIQRLGRGlRPAPGK-------EDAL 407

                        490       500       510       520       530       540       550
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 63054443  482 IHERILHEEKNLKFALSELSNSNI----FDSLVCEERERVTDDIVYEVGETGALLTGLYAVSLLYNFCNTLSRD 551
Cdd:COG1061  408 VYDFVGNDVPVLEELAKDLRDLAGyrveFLDEEESEELALLIAVKPALEVKGELEEELLEELELLEDALLLVLA 481
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 12-195 3.71e-22

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: 96.01  E-value: 3.71e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   12 LRKYQQDVYNIASK-QNTLLVMRTGAGKTLLAVKLIKQKLEEQiliqESNLEHKKIsVFLVNKVPLVFQQAE----YIRS 86
Cdd:cd18036    3 LRNYQLELVLPALRgKNTIICAPTGSGKTRVAVYICRHHLEKR----RSAGEKGRV-VVLVNKVPLVEQQLEkffkYFRK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   87 QLpaKVGMFYGELSIEMSEQlltNIILKYNVIVITADLFYLFLARG----FLSINDLNLIIFDECHHAIGNDAYARIMND 162
Cdd:cd18036   78 GY--KVTGLSGDSSHKVSFG---QIVKASDVIICTPQILINNLLSGreeeRVYLSDFSLLIFDECHHTQKEHPYNKIMRM 152

                        170       180       190
                 ....*....|....*....|....*....|...
gi 63054443  163 fYHRAKAVLSKKhftLPRIFGMTASPFTGKKGN 195
Cdd:cd18036  153 -YLDKKLSSQGP---LPQILGLTASPGVGGARS 181
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 13-188 4.67e-21

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: 92.19  E-value: 4.67e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   13 RKYQQDVYNIASKQNTLLVMRTGAGKTLLAvklikqkleeqILIQESNLEHKKISV-FLVNKVPLVFQQAEYIRSQL--P 89
Cdd:cd18035    4 RLYQVLIAAVALNGNTLIVLPTGLGKTIIA-----------ILVAADRLTKKGGKVlILAPSRPLVEQHAENLKRVLniP 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   90 AKVGMFYGELSIEMSEQLLTniilKYNVIVITADLFYLFLARGFLSINDLNLIIFDECHHAIGNDAYARIMNDFYHRAKA 169
Cdd:cd18035   73 DKITSLTGEVKPEERAERWD----ASKIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGNYAYVYIAHRYKREANN 148

                        170
                 ....*....|....*....
gi 63054443  170 vlskkhftlPRIFGMTASP 188
Cdd:cd18035  149 ---------PLILGLTASP 158
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 344-475 9.74e-21

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: 89.72  E-value: 9.74e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  344 KVFKLLELLKATYRKSDSV---RTVIFVERKATAFTLSLFMkTLNLPNIRAHSFIGH--GPSDQGefsMTFRRQKDTLHK 418
Cdd:cd18801   10 KLEKLEEIVKEHFKKKQEGsdtRVIIFSEFRDSAEEIVNFL-SKIRPGIRATRFIGQasGKSSKG---MSQKEQKEVIEQ 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 63054443  419 FKTGKYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVQSRGRA-RAMASKFLIFL 475
Cdd:cd18801   86 FRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRTgRKRQGRVVVLL 143
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 343-464 1.00e-19

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: 85.73  E-value: 1.00e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    343 DKVFKLLELLKATYRKsdsvRTVIFVERKATAfTLSLFMKTLNLPNIRAHSfighgpsdqgefSMTFRRQKDTLHKFKTG 422
Cdd:pfam00271    1 EKLEALLELLKKERGG----KVLIFSQTKKTL-EAELLLEKEGIKVARLHG------------DLSQEEREEILEDFRKG 63

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 63054443    423 KYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVQSRGRA 464
Cdd:pfam00271   64 KIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRA 105
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 27-186 3.64e-18

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: 82.45  E-value: 3.64e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   27 NTLLVMRTGAGKTLLAvklikqkleEQILIQESNLEHKKISVFLVNKVpLVFQQAEYIRS--QLPAKVGMFYGELSiemS 104
Cdd:cd00046    3 NVLITAPTGSGKTLAA---------LLAALLLLLKKGKKVLVLVPTKA-LALQTAERLRElfGPGIRVAVLVGGSS---A 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  105 EQLLTNIILKYNVIVITADLFY-LFLARGFLSINDLNLIIFDECHHAIGNDAYARIMnDFYHRakavlsKKHFTLPRIFG 183
Cdd:cd00046   70 EEREKNKLGDADIIIATPDMLLnLLLREDRLFLKDLKLIIVDEAHALLIDSRGALIL-DLAVR------KAGLKNAQVIL 142


                 ...
gi 63054443  184 MTA 186
Cdd:cd00046  143 LSA 145
Ribonuclease_3 pfam00636
Ribonuclease III domain;
930-1038 5.80e-18

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 80.40  E-value: 5.80e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    930 DRLEFYGDCFLKLGASITVFLKFPDTQEYQLHFNRKKIISNCNLYKVAIDCELPKYALSTPLEIRHWcpygFQKSTSDKC 1009
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRR----NNALGKGPK 76

                           90       100
                   ....*....|....*....|....*....
gi 63054443   1010 RyavlQKLSVKRIADMVEASIGACLLDSG 1038
Cdd:pfam00636   77 R----ADGKEKVLADAFEALIGALYLDGG 101
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 341-466 1.07e-17

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: 80.63  E-value: 1.07e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  341 VTDKVFKLLELLKATYRKSDSVRTVIFVERKATAFTLSLFMKTLNlpnIRAHSFigHGpsdqgefSMTFRRQKDTLHKFK 420
Cdd:cd18787    7 VVEEEEKKLLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEELG---IKVAAL--HG-------DLSQEERERALKKFR 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 63054443  421 TGKYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVQsR-GR-ARA 466
Cdd:cd18787   75 SGKVRVLVATDVAARGLDIPGVDHVINYDLPRDAEDYVH-RiGRtGRA 121
DEXDc smart00487
DEAD-like helicases superfamily;
12-188 1.07e-16

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 80.23  E-value: 1.07e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443      12 LRKYQQDVYNIASK--QNTLLVMRTGAGKTLLAVKLIKQKLEEQiliqesnleHKKISVFLVNKVPLVFQQAEYIR---S 86
Cdd:smart00487    9 LRPYQKEAIEALLSglRDVILAAPTGSGKTLAALLPALEALKRG---------KGGRVLVLVPTRELAEQWAEELKklgP 79

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443      87 QLPAKVGMFYGELSIEMSEQLLTNIilKYNVIVITADLFYLFLARGFLSINDLNLIIFDECHHAIGNDAYARIMNDFYHR 166
Cdd:smart00487   80 SLGLKVVGLYGGDSKREQLRKLESG--KTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLL 157

                           170       180
                    ....*....|....*....|..
gi 63054443     167 AKAvlskkhftlPRIFGMTASP 188
Cdd:smart00487  158 PKN---------VQLLLLSATP 170
ResIII pfam04851
Type III restriction enzyme, res subunit;
12-189 1.09e-16

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 78.87  E-value: 1.09e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443     12 LRKYQQDVYN-----IASKQNT-LLVMRTGAGKTLLAVKLIKQKLEEQiliqesnleHKKISVFLVNKVPLVFQQAEYIR 85
Cdd:pfam04851    4 LRPYQIEAIEnllesIKNGQKRgLIVMATGSGKTLTAAKLIARLFKKG---------PIKKVLFLVPRKDLLEQALEEFK 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443     86 sqlpaKVGMFYGELSIEMSEQLLTNIILKYNVIVITADLFYLFLARGF--LSINDLNLIIFDECHHAIGnDAYARImndf 163
Cdd:pfam04851   75 -----KFLPNYVEIGEIISGDKKDESVDDNKIVVTTIQSLYKALELASleLLPDFFDVIIIDEAHRSGA-SSYRNI---- 144

                          170       180
                   ....*....|....*....|....*.
gi 63054443    164 yhrakavlsKKHFTLPRIFGMTASPF 189
Cdd:pfam04851  145 ---------LEYFKPAFLLGLTATPE 161
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 12-196 9.19e-16

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: 77.55  E-value: 9.19e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   12 LRKYQQDVYNIASK-QNTLLVMRTGAGKTLLAVKLIKQKLEeqiliQESNLEHKKIsVFLVNKVPLVFQQA----EYIRS 86
Cdd:cd18073    3 PRNYQLELALPAMKgKNTIICAPTGCGKTFVSLLICEHHLK-----KFPQGQKGKV-VFFATKVPVYEQQKsvfsKYFER 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   87 QLPAKVGMfygelSIEMSEQLLTNIILKYN-VIVITADLFYLFLARGFL-SINDLNLIIFDECHHAIGNDAYARIMNDFY 164
Cdd:cd18073   77 HGYRVTGI-----SGATAENVPVEQIIENNdIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSGNHPYNMIMFRYL 151

                        170       180       190
                 ....*....|....*....|....*....|..
gi 63054443  165 HRAkavLSKKHFTLPRIFGMTASPFTGKKGNL 196
Cdd:cd18073  152 DQK---LGGSSGPLPQIIGLTASVGVGDAKNT 180
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1097-1250 7.60e-15

Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.


Pssm-ID: 434075  Cd Length: 127  Bit Score: 72.59  E-value: 7.60e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   1097 KKLLHLAFIHPSMMsqQGIYENYQQLEFLGDAVLDYIIVQYLYKKyPNATSGELTDYKSFYVCNKSLSYIGFVLNLHKYI 1176
Cdd:pfam14622    1 EELLLQALTHKSYA--NGRKPYNERLEFLGDAVLELSVSEYLFKK-PDLDEGGLTKLRASIVSEESLAEIAREIGLGKYL 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 63054443   1177 QHESAamcdaifeyQELIEAFREtasenpwfwfeidsPKFISDTLEAMICAIFLDSGFSLQSlQFVLPLFLNSL 1250
Cdd:pfam14622   78 RLGKG---------EEETGGSGR--------------ESILADALEALIGAIYLDGGFEVAK-EFILKKILPDL 127
HELICc smart00490
helicase superfamily c-terminal domain;
376-464 9.56e-15

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.70  E-value: 9.56e-15
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443     376 TLSLFMKTLNLPNIRAHSfighgpsdqgefSMTFRRQKDTLHKFKTGKYNVLIATAVAEEGIDVPSCNLVIRFNICRTVT 455
Cdd:smart00490    2 ELAELLKELGIKVARLHG------------GLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPA 69


                    ....*....
gi 63054443     456 QYVQSRGRA 464
Cdd:smart00490   70 SYIQRIGRA 78
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 12-198 2.06e-14

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: 72.21  E-value: 2.06e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   12 LRKYQQD-VYNI-----ASKQNTLLVMRTGAGKTLLAVKLIKQKLEEQiliqesnlEHKKIsVFLVNKVPLVFQQAEYIR 85
Cdd:cd18032    1 PRYYQQEaIEALeeareKGQRRALLVMATGTGKTYTAAFLIKRLLEAN--------RKKRI-LFLAHREELLEQAERSFK 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   86 SQLPAKVGMFYGELSIEMSEqlltniilkYNVIVITAD-LFYLFLARGFlSINDLNLIIFDECHHAIGNdAYARIMndfy 164
Cdd:cd18032   72 EVLPDGSFGNLKGGKKKPDD---------ARVVFATVQtLNKRKRLEKF-PPDYFDLIIIDEAHHAIAS-SYRKIL---- 136

                        170       180       190
                 ....*....|....*....|....*....|....
gi 63054443  165 hrakavlskKHFTLPRIFGMTASPFTGKKGNLYH 198
Cdd:cd18032  137 ---------EYFEPAFLLGLTATPERTDGLDTYE 161
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 12-191 4.76e-14

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: 72.97  E-value: 4.76e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   12 LRKYQQDVYNIA-SKQNTLLVMRTGAGKTLLAVKLIKQKLEEQiliqESNLEHKKIsVFLVNKVPLVFQQaeYIRSQLP- 89
Cdd:cd18074    3 LRDYQMEVAKPAlEGKNIIICLPTGSGKTRVAVYITKDHLDKK----RKASEPGKV-IVLVNKVPLVEQH--YRKEFNPf 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   90 ----AKVGMFYGELSIEMSeqlLTNIILKYNVIVITADLFYLFLARGF------LSINDLNLIIFDECHHAIGNDAYARI 159
Cdd:cd18074   76 lkhwYQVIGLSGDSQLKIS---FPEVVKRYDVIICTAQILENSLLNATeeedegVQLSDFSLIIIDECHHTQKEAVYNNI 152

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 63054443  160 MNDFY-----HRAKAVLSKKHFTLPRIFGMTASPFTG 191
Cdd:cd18074  153 MRRYLkqkikNRKQKKENKPLIPLPQILGLTASPGVG 189
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 12-196 6.84e-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: 71.81  E-value: 6.84e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   12 LRKYQQDVYNIASK-QNTLLVMRTGAGKTLLAVKLIKQKLEEQiliqesnlEHKKIsVFLVNKVPLVFQQAEYIRSQLPA 90
Cdd:cd18075    3 LHGYQWEVVAPALRgKNSIIWLPTGAGKTRAAVYVARRHLETK--------RGAKV-AVLVNKVHLVDQHLEKEFHVLLD 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   91 KVGMfyGELSIEMSEQLLTNIILKYNVIVI-TADLFYLFLARG----FLSINDLNLIIFDECHHAIGNDAYARIMNDFYH 165
Cdd:cd18075   74 KYTV--TAISGDSSHKCFFGQLARGSDVVIcTAQILQNALLSGeeeaHVELTDFSLLVIDECHHTHKEAVYNKIMLSYLE 151

                        170       180       190
                 ....*....|....*....|....*....|.
gi 63054443  166 RAkavLSKKHfTLPRIFGMTASPFTGKKGNL 196
Cdd:cd18075  152 KK---LSRQG-DLPQILGLTASPGTGGATSF 178
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 12-188 6.67e-13

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: 67.33  E-value: 6.67e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   12 LRKYQQD-VYNIASKQNT---LLVMRTGAGKTLLAVKLIKQKLEEQILIqesnlehkkisvfLVNKVPLVFQ-QAEYIRS 86
Cdd:cd17926    1 LRPYQEEaLEAWLAHKNNrrgILVLPTGSGKTLTALALIAYLKELRTLI-------------VVPTDALLDQwKERFEDF 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   87 QLPAKVGMFYGElsiemSEQLLTNIilkyNVIVITADLFYLFLARGFLSINDLNLIIFDECHHaIGNDAYARIMNDFYHr 166
Cdd:cd17926   68 LGDSSIGLIGGG-----KKKDFDDA----NVVVATYQSLSNLAEEEKDLFDQFGLLIVDEAHH-LPAKTFSEILKELNA- 136

                        170       180
                 ....*....|....*....|..
gi 63054443  167 akavlskkhftlPRIFGMTASP 188
Cdd:cd17926  137 ------------KYRLGLTATP 146
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 12-188 3.25e-11

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: 63.50  E-value: 3.25e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   12 LRKYQQDVYNIASKQNTLLVMRTGAGKTLLAVKLI--------KQKLeeqiliqesnlehkkisVFLVNKVPLVFQQAEY 83
Cdd:cd18033    3 LRDYQFTIVQKALFQNTLVALPTGLGKTFIAAVVMlnyyrwfpKGKI-----------------VFMAPTKPLVSQQIEA 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   84 IRsqlpaKVGMFYGELSIEMSEQLLTNIILKY----NVIVITADLFYLFLARGFLSINDLNLIIFDECHHAIGNDAYARI 159
Cdd:cd18033   66 CY-----KITGIPSSQTAELTGSVPPTKRAELwaskRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQV 140

                        170       180
                 ....*....|....*....|....*....
gi 63054443  160 MnDFYHRakavlSKKHFtlpRIFGMTASP 188
Cdd:cd18033  141 V-RELMR-----YNSHF---RILALTATP 160
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 423-475 4.69e-11

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: 60.03  E-value: 4.69e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 63054443  423 KYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVQSRGRA-RAMASKFLIFL 475
Cdd:cd18785   22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAgRGGKDEGEVIL 75
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
339-469 1.94e-10

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 64.78  E-value: 1.94e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  339 TDVTDKVFKLLELLKATyrksDSVRTVIFVERKATAFTLSlfmKTLNLPNIRAHSFigHGPSDQGEfsmtfrRQKdTLHK 418
Cdd:COG0513  223 VDKRDKLELLRRLLRDE----DPERAIVFCNTKRGADRLA---EKLQKRGISAAAL--HGDLSQGQ------RER-ALDA 286

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 63054443  419 FKTGKYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVqSR-GR-ARAMAS 469
Cdd:COG0513  287 FRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYV-HRiGRtGRAGAE 338
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 11-148 5.08e-10

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: 59.97  E-value: 5.08e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   11 LLRKYQQDVYN--IASKQNTLLVMRTGAGKTLLAVKLIKQKLeeqiliqesnLEHKKISVFLVNKVPLVFQQAEYIR--- 85
Cdd:cd17921    1 LLNPIQREALRalYLSGDSVLVSAPTSSGKTLIAELAILRAL----------ATSGGKAVYIAPTRALVNQKEADLRerf 70

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 63054443   86 SQLPAKVGMFYGELSIEMSEqlltniILKYNVIVITADLFYLFL-ARGFLSINDLNLIIFDECH 148
Cdd:cd17921   71 GPLGKNVGLLTGDPSVNKLL------LAEADILVATPEKLDLLLrNGGERLIQDVRLVVVDEAH 128
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 349-466 5.16e-09

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 60.34  E-value: 5.16e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   349 LELLKATYRKSDSVRTVIFVERKATAFTLSLFMKTLNLPNirahSFIghgpsdQGEFSMTFRRQkdTLHKFKTGKYNVLI 428
Cdd:PRK11192  233 TALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINC----CYL------EGEMVQAKRNE--AIKRLTDGRVNVLV 300

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 63054443   429 ATAVAEEGIDVPSCNLVIRFNICRTVTQYVQSRGR-ARA 466
Cdd:PRK11192  301 ATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRtGRA 339
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 13-188 2.77e-08

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: 54.56  E-value: 2.77e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443     13 RKYQQDVYN-IASKQNTLLVMRTGAGKTLLAVKLIkqkleeqilIQESNLEHKKISVFLVnkVP---LVFQQAEYIR--- 85
Cdd:pfam00270    1 TPIQAEAIPaILEGRDVLVQAPTGSGKTLAFLLPA---------LEALDKLDNGPQALVL--APtreLAEQIYEELKklg 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443     86 SQLPAKVGMFYGelSIEMSEQLltNIILKYNVIVIT-ADLFYLFLARGFLSinDLNLIIFDECHHAIGndayarimNDFY 164
Cdd:pfam00270   70 KGLGLKVASLLG--GDSRKEQL--EKLKGPDILVGTpGRLLDLLQERKLLK--NLKLLVLDEAHRLLD--------MGFG 135

                          170       180
                   ....*....|....*....|....
gi 63054443    165 HRAKAVLSKKHFTlPRIFGMTASP 188
Cdd:pfam00270  136 PDLEEILRRLPKK-RQILLLSATL 158
PTZ00110 PTZ00110
helicase; Provisional
 343-504 8.94e-08

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 56.71  E-value: 8.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   343 DKVFKLLELLKATYRksDSVRTVIFVERKATAFTLSlfmKTLNLPNIRAHSFigHGPSDQGEfsmtfRRQkdTLHKFKTG 422
Cdd:PTZ00110  361 EKRGKLKMLLQRIMR--DGDKILIFVETKKGADFLT---KELRLDGWPALCI--HGDKKQEE-----RTW--VLNEFKTG 426

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   423 KYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVQ---SRGRARAMASKFLIFLNTEELLIHE--RILHE-EKNLKFA 496
Cdd:PTZ00110  427 KSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHrigRTGRAGAKGASYTFLTPDKYRLARDlvKVLREaKQPVPPE 506


                  ....*...
gi 63054443   497 LSELSNSN 504
Cdd:PTZ00110  507 LEKLSNER 514
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
 344-446 3.83e-07

C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB 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: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 51.10  E-value: 3.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  344 KVFKLLELLKatyRKSDSVRTVIFVERKATAFTLSlfmKTLNLPNIrahsfigHGPSDQGEfsmtfRRQkdTLHKFKTGK 423
Cdd:cd18789   35 KLRALEELLK---RHEQGDKIIVFTDNVEALYRYA---KRLLKPFI-------TGETPQSE-----REE--ILQNFREGE 94

                         90       100
                 ....*....|....*....|...
gi 63054443  424 YNVLIATAVAEEGIDVPSCNLVI 446
Cdd:cd18789   95 YNTLVVSKVGDEGIDLPEANVAI 117
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 403-504 4.97e-06

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 51.00  E-value: 4.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   403 GEFSMTFRRQkdTLHKFKTGKYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVQSRGR-ARA-MASKFLIFLNTEEl 480
Cdd:PRK11634  277 GDMNQALREQ--TLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRtGRAgRAGRALLFVENRE- 353

                          90       100
                  ....*....|....*....|....*
gi 63054443   481 lihERILHE-EKNLKFALSELSNSN 504
Cdd:PRK11634  354 ---RRLLRNiERTMKLTIPEVELPN 375
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 400-478 2.35e-05

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 48.63  E-value: 2.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   400 SDQGEFSMTFRRqkDTLHKFKTGKYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVQSRGRARAMASK--FLIFLNT 477
Cdd:PLN00206  397 SIHGEKSMKERR--EVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKgtAIVFVNE 474


                  .
gi 63054443   478 E 478
Cdd:PLN00206  475 E 475
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 916-1048 2.50e-05

Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.


Pssm-ID: 434075  Cd Length: 127  Bit Score: 45.24  E-value: 2.50e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    916 QALT--SAESQLNFDYDRLEFYGDCFLKLgASITVFLKFPDTQEYQLHFNRKKIISNCNLYKVAIDCELPKYA-LSTPLE 992
Cdd:pfam14622    6 QALThkSYANGRKPYNERLEFLGDAVLEL-SVSEYLFKKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYLrLGKGEE 84

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 63054443    993 irhwcpygfqkSTSDKCRYAVLqklsvkriADMVEASIGACLLDSGLDSALKICKS 1048
Cdd:pfam14622   85 -----------ETGGSGRESIL--------ADALEALIGAIYLDGGFEVAKEFILK 121
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 395-463 5.89e-05

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: 44.64  E-value: 5.89e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  395 IGHGpsdqgefSMTFRRQKDTLHKFKTGKYNVLIATAVAEEGIDVPSCNLVIRFNICR-TVTQYVQSRGR 463
Cdd:cd18810   56 IAHG-------QMTENELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIIERADKfGLAQLYQLRGR 118
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 362-474 1.71e-04

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: 42.55  E-value: 1.71e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443  362 VRTVIFVERKATAftlsLFMKTLnlpnirahsFIGHGPSDQGEFSMTFRRQ--KDTLHKFKTGKYNVLIATAVA--EEGI 437
Cdd:cd18799    7 IKTLIFCVSIEHA----EFMAEA---------FNEAGIDAVALNSDYSDRErgDEALILLFFGELKPPILVTVDllTTGV 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 63054443  438 DVPSCNLVIRFNICRTVTQYVQSRGRA-RAMASK--FLIF 474
Cdd:cd18799   74 DIPEVDNVVFLRPTESRTLFLQMLGRGlRLHEGKdfFTIL 113
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
2-154 2.16e-04

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 45.66  E-value: 2.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443    2 DISSFLLPQLLRK--------YQQDVYN--IASKQNTLLVMRTGAGKTLLAvklikqkleeQILIQeSNLEHKKISVFLv 71
Cdd:COG1204    5 ELPLEKVIEFLKErgieelypPQAEALEagLLEGKNLVVSAPTASGKTLIA----------ELAIL-KALLNGGKALYI- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   72 nkVPL------VFQQAEYIRSQLPAKVGMFYGElsIEMSEQLLTNiilkYNVIVITADLFYLFLARGFLSINDLNLIIFD 145
Cdd:COG1204   73 --VPLralaseKYREFKRDFEELGIKVGVSTGD--YDSDDEWLGR----YDILVATPEKLDSLLRNGPSWLRDVDLVVVD 144


                 ....*....
gi 63054443  146 ECHHaIGND 154
Cdd:COG1204  145 EAHL-IDDE 152
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
 16-188 2.80e-04

DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA 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: 350687 [Multi-domain]  Cd Length: 178  Bit Score: 43.35  E-value: 2.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   16 QQDVYN-----IASKQNTLLVMRTGAGKTLLAVKLIKQKLEEQiliqesnlehkKISVFLVNKVPLVFQQAEYIRSQLPA 90
Cdd:cd17929    1 QRKAYEaivssLGGFKTFLLHGVTGSGKTEVYIELIEKVLAKG-----------KQVLVLVPEISLTPQLIKRFKKRFGD 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   91 KVGMFYGELS-IEMSEQLLTnIILKYNVIVITadlfylflARG--FLSINDLNLIIFDECHhaigNDAYARIMNDFYH-R 166
Cdd:cd17929   70 KVAVLHSKLSdKERADEWRK-IKRGEAKVVIG--------ARSalFAPFKNLGLIIVDEEH----DSSYKQDSGPRYHaR 136

                        170       180
                 ....*....|....*....|..
gi 63054443  167 AKAVLSKKHFTLPRIFGmTASP 188
Cdd:cd17929  137 DVAIYRAKLENAPVVLG-SATP 157
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 419-463 1.17e-03

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: 41.18  E-value: 1.17e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 63054443  419 FKTGKYNVLIATAVAEEGIDVPSCNLVI-----RFNIcrtvTQYVQSRGR 463
Cdd:cd18811   83 FREGEVDILVSTTVIEVGVDVPNATVMViedaeRFGL----SQLHQLRGR 128
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 22-148 1.67e-03

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: 40.78  E-value: 1.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054443   22 IASKQNTLLVMRTGAGKTLLAvklikqkleeQILIQESNLEHKKiSVFLvnkVPLVFQQAEYIR-----SQLPAKVGMFY 96
Cdd:cd18028   14 LLKGENLLISIPTASGKTLIA----------EMAMVNTLLEGGK-ALYL---VPLRALASEKYEefkklEEIGLKVGIST 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 63054443   97 GELSIEmseqllTNIILKYNVIVITADLFYLFLARGFLSINDLNLIIFDECH 148
Cdd:cd18028   80 GDYDED------DEWLGDYDIIVATYEKFDSLLRHSPSWLRDVGVVVVDEIH 125
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 415-469 1.78e-03

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 42.59  E-value: 1.78e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 63054443   415 TLHKFKTGKYNVLIATAVAEEGIDVPSCNLVIRFNICRTVTQYVQSRGR-ARAMAS 469
Cdd:PRK01297  377 TLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRtGRAGAS 432
PRK10689 PRK10689
transcription-repair coupling factor; Provisional
 395-463 7.72e-03

transcription-repair coupling factor; Provisional


Pssm-ID: 182649 [Multi-domain]  Cd Length: 1147  Bit Score: 40.88  E-value: 7.72e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 63054443   395 IGHGpsdqgefSMTFRRQKDTLHKFKTGKYNVLIATAVAEEGIDVPSCNLVIrfnICRT----VTQYVQSRGR 463
Cdd:PRK10689  840 IGHG-------QMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTII---IERAdhfgLAQLHQLRGR 902
 
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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