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Conserved domains on  [gi|63087685|emb|CAI92124|]
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SUV3L1 protein [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXQc_Suv3 cd17913
DEXQ-box helicase domain of Suv3; Suppressor of var1 3-like protein (Suv3) is a DNA/RNA ...
 200-345 5.12e-95

DEXQ-box helicase domain of Suv3; Suppressor of var1 3-like protein (Suv3) is a DNA/RNA unwinding enzyme belonging to the class of DexH-box helicases. It localizes predominantly in the mitochondria, where it forms an RNA-degrading complex called mitochondrial degradosome (mtEXO) with exonuclease PNP (polynucleotide phosphorylase), that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. Suv3 plays a role in the RNA surveillance system in mitochondria; it regulates the stability of mature mRNAs, the removal of aberrantly formed mRNAs and the rapid degradation of non coding processing intermediates. It also confers salinity and drought stress tolerance by maintaining both photosynthesis and antioxidant machinery, probably via an increase in plant hormone levels such as gibberellic acid (GA3), the cytokinin zeatin (Z), and indole-3-acetic acid (IAA). Suv3 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: 350671 [Multi-domain]  Cd Length: 142  Bit Score: 292.15  E-value: 5.12e-95
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 200 RKIIFHSGPTNSGKTYHAIQRYLSATSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERLTVEPegkqATHVSCTVEMC 279
Cdd:cd17913   1 RKIIFHAGPTNSGKTYHALQRLKSAKSGVYCGPLRLLAWEVYERLNAEGVPCDLVTGQERREVEG----ATHVSCTVEMA 76

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 63087685 280 NVATPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGESAAINLVSELLYTTGEEVEVQKY 345
Cdd:cd17913  77 SISEPYDVAVIDEIQMIGDPQRGWAWTRALLGLPAEEIHLCGDPSALPLVRKLAETTGDELEVREY 142
SF2_C_suv3 cd18805
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene ...
 349-487 9.34e-79

C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene encodes a DNA and RNA helicase, which is localized in mitochondria and is a subunit of the degradosome complex involved in regulation of RNA surveillance and turnover. SUV3 exhibits DNA and RNA-dependent ATPase, DNA and RNA-binding and DNA and RNA unwinding activities. SUV3 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: 350192 [Multi-domain]  Cd Length: 135  Bit Score: 249.01  E-value: 9.34e-79
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 349 TPISVLDHALESLDNLQPGDCIVCFSKNDIYSVSRQIEIR-GLESAVIYGSLPPGTKLAQARKFNDPNDPCKILVATDAI 427
Cdd:cd18805   1 TPLSVESKPLGSLRNLRPGDCVVAFSRKDIFSLKREIEKRtGLKCAVIYGALPPETRRQQARLFNDPESGYDVLVASDAI 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 428 GMGLNLSIRRIIFYSLIKPSINekgekELEPITTSQALQIAGRAGRFSSHFKEGQVTTMH 487
Cdd:cd18805  81 GMGLNLNIRRVIFSSLSKFDGN-----EMRPLSPSEVKQIAGRAGRFGSHFPEGEVTTLR 135
Suv3_N super family cl39503
Suv3 helical N-terminal domain; This is the N-terminal domain of Suv3 present in Homo sapiens. ...
 62-179 2.02e-57

Suv3 helical N-terminal domain; This is the N-terminal domain of Suv3 present in Homo sapiens. Suv3 is an NTP-dependent RNA/DNA helicase that is necessary for the degradation of mature mtRNAs. Suv3 has been found to interact in vitro with polynucleotide phosphorylase.


The actual alignment was detected with superfamily member pfam18114:

Pssm-ID: 436283  Cd Length: 116  Bit Score: 191.39  E-value: 2.02e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685    62 SLFVPLTVKPqgPSADGDVGAELTRPLDKNEVKKI*DKFYKRQEIQKRSADYGLDARLFHQAFISFRNYIMQSHSLDVDI 141
Cdd:pfam18114   1 DLVVPVKVKP--NVDDADVGEELTGSLDKDSLIKVLDEFARRPAIRQLATENGLNDKLFMQAFSSFREYCLESESLPVDL 78

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 63087685   142 HIVLNDICFSAAHVDGLFPFFLRHAKQIFPVLECKDDL 179
Cdd:pfam18114  79 HILLSDIIKGGGHVDDLFPYFLRHAKQVFPHLECMDDL 116
Suv3_C_1 pfam18147
Suv3 C-terminal domain 1; This domain is found in Suv3 present in Homo sapiens. Suv3 is an ...
 558-598 5.04e-15

Suv3 C-terminal domain 1; This domain is found in Suv3 present in Homo sapiens. Suv3 is an NTP-dependent RNA/DNA helicase that is necessary for the degradation of mature mtRNAs. Suv3 has been found to interact in vitro with polynucleotide phosphorylase. This domain makes up part of the C-terminal domain.


:

Pssm-ID: 436308  Cd Length: 41  Bit Score: 69.39  E-value: 5.04e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 63087685   558 AELIQHIPLSLRVRYVFCTAPINKKQPFVCSSLLQFARQYS 598
Cdd:pfam18147   1 ADLIQPVPLSLRDRYTFCMAPVNTRDPKAVAALVEFARCYA 41
SUV3_C pfam12513
Mitochondrial degradasome RNA helicase subunit C terminal; This domain family is found in ...
 626-672 8.96e-15

Mitochondrial degradasome RNA helicase subunit C terminal; This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00271. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes.


:

Pssm-ID: 463616  Cd Length: 47  Bit Score: 68.70  E-value: 8.96e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 63087685   626 MDLEAVHDVFDLYLWLSYRFIDMFPDSSLVRSLQKELDAIIQEGVHN 672
Cdd:pfam12513   1 ERLESLHKVLDLYLWLSYRFPEVFPDRELAEELKKLVEEKIEEGLER 47
 
Name Accession Description Interval E-value
DEXQc_Suv3 cd17913
DEXQ-box helicase domain of Suv3; Suppressor of var1 3-like protein (Suv3) is a DNA/RNA ...
 200-345 5.12e-95

DEXQ-box helicase domain of Suv3; Suppressor of var1 3-like protein (Suv3) is a DNA/RNA unwinding enzyme belonging to the class of DexH-box helicases. It localizes predominantly in the mitochondria, where it forms an RNA-degrading complex called mitochondrial degradosome (mtEXO) with exonuclease PNP (polynucleotide phosphorylase), that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. Suv3 plays a role in the RNA surveillance system in mitochondria; it regulates the stability of mature mRNAs, the removal of aberrantly formed mRNAs and the rapid degradation of non coding processing intermediates. It also confers salinity and drought stress tolerance by maintaining both photosynthesis and antioxidant machinery, probably via an increase in plant hormone levels such as gibberellic acid (GA3), the cytokinin zeatin (Z), and indole-3-acetic acid (IAA). Suv3 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: 350671 [Multi-domain]  Cd Length: 142  Bit Score: 292.15  E-value: 5.12e-95
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 200 RKIIFHSGPTNSGKTYHAIQRYLSATSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERLTVEPegkqATHVSCTVEMC 279
Cdd:cd17913   1 RKIIFHAGPTNSGKTYHALQRLKSAKSGVYCGPLRLLAWEVYERLNAEGVPCDLVTGQERREVEG----ATHVSCTVEMA 76

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 63087685 280 NVATPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGESAAINLVSELLYTTGEEVEVQKY 345
Cdd:cd17913  77 SISEPYDVAVIDEIQMIGDPQRGWAWTRALLGLPAEEIHLCGDPSALPLVRKLAETTGDELEVREY 142
SF2_C_suv3 cd18805
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene ...
 349-487 9.34e-79

C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene encodes a DNA and RNA helicase, which is localized in mitochondria and is a subunit of the degradosome complex involved in regulation of RNA surveillance and turnover. SUV3 exhibits DNA and RNA-dependent ATPase, DNA and RNA-binding and DNA and RNA unwinding activities. SUV3 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: 350192 [Multi-domain]  Cd Length: 135  Bit Score: 249.01  E-value: 9.34e-79
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 349 TPISVLDHALESLDNLQPGDCIVCFSKNDIYSVSRQIEIR-GLESAVIYGSLPPGTKLAQARKFNDPNDPCKILVATDAI 427
Cdd:cd18805   1 TPLSVESKPLGSLRNLRPGDCVVAFSRKDIFSLKREIEKRtGLKCAVIYGALPPETRRQQARLFNDPESGYDVLVASDAI 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 428 GMGLNLSIRRIIFYSLIKPSINekgekELEPITTSQALQIAGRAGRFSSHFKEGQVTTMH 487
Cdd:cd18805  81 GMGLNLNIRRVIFSSLSKFDGN-----EMRPLSPSEVKQIAGRAGRFGSHFPEGEVTTLR 135
Suv3_N pfam18114
Suv3 helical N-terminal domain; This is the N-terminal domain of Suv3 present in Homo sapiens. ...
 62-179 2.02e-57

Suv3 helical N-terminal domain; This is the N-terminal domain of Suv3 present in Homo sapiens. Suv3 is an NTP-dependent RNA/DNA helicase that is necessary for the degradation of mature mtRNAs. Suv3 has been found to interact in vitro with polynucleotide phosphorylase.


Pssm-ID: 436283  Cd Length: 116  Bit Score: 191.39  E-value: 2.02e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685    62 SLFVPLTVKPqgPSADGDVGAELTRPLDKNEVKKI*DKFYKRQEIQKRSADYGLDARLFHQAFISFRNYIMQSHSLDVDI 141
Cdd:pfam18114   1 DLVVPVKVKP--NVDDADVGEELTGSLDKDSLIKVLDEFARRPAIRQLATENGLNDKLFMQAFSSFREYCLESESLPVDL 78

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 63087685   142 HIVLNDICFSAAHVDGLFPFFLRHAKQIFPVLECKDDL 179
Cdd:pfam18114  79 HILLSDIIKGGGHVDDLFPYFLRHAKQVFPHLECMDDL 116
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
199-506 4.74e-29

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 123.90  E-value: 4.74e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 199 QRKIIFHSGPTNSGKTY---HAIQRYLS-ATSGVYCGPLKLLAHEIFEKSNAA--GVPCDLVTGEErlTVEPEgkqATHV 272
Cdd:COG4581  39 AGRSVLVAAPTGSGKTLvaeFAIFLALArGRRSFYTAPIKALSNQKFFDLVERfgAENVGLLTGDA--SVNPD---APIV 113

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 273 SCTVEMC-NVA-------TPYEVAVIDEIQMIRDPARGWAWTRALLGLcAEEVHLCGESAAIN----LVSELLYTTGEEV 340
Cdd:COG4581 114 VMTTEILrNMLyregadlEDVGVVVMDEFHYLADPDRGWVWEEPIIHL-PARVQLVLLSATVGnaeeFAEWLTRVRGETA 192

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 341 EVQKYER-------------LTPISVLDHAL-------ESLDNLQPGDC----IVCFS---------------------- 374
Cdd:COG4581 193 VVVSEERpvplefhylvtprLFPLFRVNPELlrppsrhEVIEELDRGGLlpaiVFIFSrrgcdeaaqqllsarlttkeer 272

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 375 ----------KNDIYSVSRQIEIRGLES--AVIYGSLPPGTKLAQARKFNDpnDPCKILVATDAIGMGLNLSIRRIIFYS 442
Cdd:COG4581 273 aeireaidefAEDFSVLFGKTLSRLLRRgiAVHHAGMLPKYRRLVEELFQA--GLLKVVFATDTLAVGINMPARTVVFTK 350

                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 63087685 443 LIKpsINekGEKElEPITTSQALQIAGRAGRFSSHfKEGQVTTMHR--DDLALLKDILNRPVDPIQ 506
Cdd:COG4581 351 LSK--FD--GERH-RPLTAREFHQIAGRAGRRGID-TEGHVVVLAPehDDPKKFARLASARPEPLR 410
Suv3_C_1 pfam18147
Suv3 C-terminal domain 1; This domain is found in Suv3 present in Homo sapiens. Suv3 is an ...
 558-598 5.04e-15

Suv3 C-terminal domain 1; This domain is found in Suv3 present in Homo sapiens. Suv3 is an NTP-dependent RNA/DNA helicase that is necessary for the degradation of mature mtRNAs. Suv3 has been found to interact in vitro with polynucleotide phosphorylase. This domain makes up part of the C-terminal domain.


Pssm-ID: 436308  Cd Length: 41  Bit Score: 69.39  E-value: 5.04e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 63087685   558 AELIQHIPLSLRVRYVFCTAPINKKQPFVCSSLLQFARQYS 598
Cdd:pfam18147   1 ADLIQPVPLSLRDRYTFCMAPVNTRDPKAVAALVEFARCYA 41
SUV3_C pfam12513
Mitochondrial degradasome RNA helicase subunit C terminal; This domain family is found in ...
 626-672 8.96e-15

Mitochondrial degradasome RNA helicase subunit C terminal; This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00271. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes.


Pssm-ID: 463616  Cd Length: 47  Bit Score: 68.70  E-value: 8.96e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 63087685   626 MDLEAVHDVFDLYLWLSYRFIDMFPDSSLVRSLQKELDAIIQEGVHN 672
Cdd:pfam12513   1 ERLESLHKVLDLYLWLSYRFPEVFPDRELAEELKKLVEEKIEEGLER 47
HELICc smart00490
helicase superfamily c-terminal domain;
381-474 1.37e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 66.47  E-value: 1.37e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685    381 VSRQIEIRGLESAVIYGSLPPGTKLAQARKFNdpNDPCKILVATDAIGMGLNL-SIRRIIFYSLikpsinekgekelePI 459
Cdd:smart00490   3 LAELLKELGIKVARLHGGLSQEEREEILDKFN--NGKIKVLVATDVAERGLDLpGVDLVIIYDL--------------PW 66

                           90
                   ....*....|....*
gi 63087685    460 TTSQALQIAGRAGRF 474
Cdd:smart00490  67 SPASYIQRIGRAGRA 81
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 356-474 5.17e-13

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: 65.69  E-value: 5.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685   356 HALESLDNLQPGDCIVCFSKNDIYSVSRQIEIR-GLESAVIYGSLPPGTKLAQARKFNDPNdpCKILVATDAIGMGLNL- 433
Cdd:pfam00271   4 EALLELLKKERGGKVLIFSQTKKTLEAELLLEKeGIKVARLHGDLSQEEREEILEDFRKGK--IDVLVATDVAERGLDLp 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 63087685   434 SIRRIIFYSLikpsinekgekelePITTSQALQIAGRAGRF 474
Cdd:pfam00271  82 DVDLVINYDL--------------PWNPASYIQRIGRAGRA 108
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 381-433 9.25e-05

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 45.99  E-value: 9.25e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 63087685 381 VSRQIEIRGLESAVIYGSLPPGTKLAQARKFNDPNDPCKILVATDAIGMGLNL 433
Cdd:COG0553 565 LEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPEAPVFLISLKAGGEGLNL 617
 
Name Accession Description Interval E-value
DEXQc_Suv3 cd17913
DEXQ-box helicase domain of Suv3; Suppressor of var1 3-like protein (Suv3) is a DNA/RNA ...
 200-345 5.12e-95

DEXQ-box helicase domain of Suv3; Suppressor of var1 3-like protein (Suv3) is a DNA/RNA unwinding enzyme belonging to the class of DexH-box helicases. It localizes predominantly in the mitochondria, where it forms an RNA-degrading complex called mitochondrial degradosome (mtEXO) with exonuclease PNP (polynucleotide phosphorylase), that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. Suv3 plays a role in the RNA surveillance system in mitochondria; it regulates the stability of mature mRNAs, the removal of aberrantly formed mRNAs and the rapid degradation of non coding processing intermediates. It also confers salinity and drought stress tolerance by maintaining both photosynthesis and antioxidant machinery, probably via an increase in plant hormone levels such as gibberellic acid (GA3), the cytokinin zeatin (Z), and indole-3-acetic acid (IAA). Suv3 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: 350671 [Multi-domain]  Cd Length: 142  Bit Score: 292.15  E-value: 5.12e-95
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 200 RKIIFHSGPTNSGKTYHAIQRYLSATSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERLTVEPegkqATHVSCTVEMC 279
Cdd:cd17913   1 RKIIFHAGPTNSGKTYHALQRLKSAKSGVYCGPLRLLAWEVYERLNAEGVPCDLVTGQERREVEG----ATHVSCTVEMA 76

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 63087685 280 NVATPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGESAAINLVSELLYTTGEEVEVQKY 345
Cdd:cd17913  77 SISEPYDVAVIDEIQMIGDPQRGWAWTRALLGLPAEEIHLCGDPSALPLVRKLAETTGDELEVREY 142
SF2_C_suv3 cd18805
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene ...
 349-487 9.34e-79

C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene encodes a DNA and RNA helicase, which is localized in mitochondria and is a subunit of the degradosome complex involved in regulation of RNA surveillance and turnover. SUV3 exhibits DNA and RNA-dependent ATPase, DNA and RNA-binding and DNA and RNA unwinding activities. SUV3 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: 350192 [Multi-domain]  Cd Length: 135  Bit Score: 249.01  E-value: 9.34e-79
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 349 TPISVLDHALESLDNLQPGDCIVCFSKNDIYSVSRQIEIR-GLESAVIYGSLPPGTKLAQARKFNDPNDPCKILVATDAI 427
Cdd:cd18805   1 TPLSVESKPLGSLRNLRPGDCVVAFSRKDIFSLKREIEKRtGLKCAVIYGALPPETRRQQARLFNDPESGYDVLVASDAI 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 428 GMGLNLSIRRIIFYSLIKPSINekgekELEPITTSQALQIAGRAGRFSSHFKEGQVTTMH 487
Cdd:cd18805  81 GMGLNLNIRRVIFSSLSKFDGN-----EMRPLSPSEVKQIAGRAGRFGSHFPEGEVTTLR 135
Suv3_N pfam18114
Suv3 helical N-terminal domain; This is the N-terminal domain of Suv3 present in Homo sapiens. ...
 62-179 2.02e-57

Suv3 helical N-terminal domain; This is the N-terminal domain of Suv3 present in Homo sapiens. Suv3 is an NTP-dependent RNA/DNA helicase that is necessary for the degradation of mature mtRNAs. Suv3 has been found to interact in vitro with polynucleotide phosphorylase.


Pssm-ID: 436283  Cd Length: 116  Bit Score: 191.39  E-value: 2.02e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685    62 SLFVPLTVKPqgPSADGDVGAELTRPLDKNEVKKI*DKFYKRQEIQKRSADYGLDARLFHQAFISFRNYIMQSHSLDVDI 141
Cdd:pfam18114   1 DLVVPVKVKP--NVDDADVGEELTGSLDKDSLIKVLDEFARRPAIRQLATENGLNDKLFMQAFSSFREYCLESESLPVDL 78

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 63087685   142 HIVLNDICFSAAHVDGLFPFFLRHAKQIFPVLECKDDL 179
Cdd:pfam18114  79 HILLSDIIKGGGHVDDLFPYFLRHAKQVFPHLECMDDL 116
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
199-506 4.74e-29

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 123.90  E-value: 4.74e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 199 QRKIIFHSGPTNSGKTY---HAIQRYLS-ATSGVYCGPLKLLAHEIFEKSNAA--GVPCDLVTGEErlTVEPEgkqATHV 272
Cdd:COG4581  39 AGRSVLVAAPTGSGKTLvaeFAIFLALArGRRSFYTAPIKALSNQKFFDLVERfgAENVGLLTGDA--SVNPD---APIV 113

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 273 SCTVEMC-NVA-------TPYEVAVIDEIQMIRDPARGWAWTRALLGLcAEEVHLCGESAAIN----LVSELLYTTGEEV 340
Cdd:COG4581 114 VMTTEILrNMLyregadlEDVGVVVMDEFHYLADPDRGWVWEEPIIHL-PARVQLVLLSATVGnaeeFAEWLTRVRGETA 192

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 341 EVQKYER-------------LTPISVLDHAL-------ESLDNLQPGDC----IVCFS---------------------- 374
Cdd:COG4581 193 VVVSEERpvplefhylvtprLFPLFRVNPELlrppsrhEVIEELDRGGLlpaiVFIFSrrgcdeaaqqllsarlttkeer 272

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 375 ----------KNDIYSVSRQIEIRGLES--AVIYGSLPPGTKLAQARKFNDpnDPCKILVATDAIGMGLNLSIRRIIFYS 442
Cdd:COG4581 273 aeireaidefAEDFSVLFGKTLSRLLRRgiAVHHAGMLPKYRRLVEELFQA--GLLKVVFATDTLAVGINMPARTVVFTK 350

                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 63087685 443 LIKpsINekGEKElEPITTSQALQIAGRAGRFSSHfKEGQVTTMHR--DDLALLKDILNRPVDPIQ 506
Cdd:COG4581 351 LSK--FD--GERH-RPLTAREFHQIAGRAGRRGID-TEGHVVVLAPehDDPKKFARLASARPEPLR 410
DEAD-like_helicase_N cd17912
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 202-323 1.20e-17

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


Pssm-ID: 350670 [Multi-domain]  Cd Length: 81  Bit Score: 77.94  E-value: 1.20e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 202 IIFHSGPTNSGKTYHAIQRY----LSATSGVYCGPLKLLAHEIfeksnaagvpcdlvtgeerltvepegkqathvsctve 277
Cdd:cd17912   1 NILHLGPTGSGKTLVAIQKIasamSSGKSVLVVTPTKLLAHEI------------------------------------- 43

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 63087685 278 mcnvatpyeVAVIDEIQMIRDPARGWAW-TRALLGLCAEEVHLCGES 323
Cdd:cd17912  44 ---------LIVIDEIQ*ILDPAAGWAWaTRALLGLKAEKVIGVGAT 81
Suv3_C_1 pfam18147
Suv3 C-terminal domain 1; This domain is found in Suv3 present in Homo sapiens. Suv3 is an ...
 558-598 5.04e-15

Suv3 C-terminal domain 1; This domain is found in Suv3 present in Homo sapiens. Suv3 is an NTP-dependent RNA/DNA helicase that is necessary for the degradation of mature mtRNAs. Suv3 has been found to interact in vitro with polynucleotide phosphorylase. This domain makes up part of the C-terminal domain.


Pssm-ID: 436308  Cd Length: 41  Bit Score: 69.39  E-value: 5.04e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 63087685   558 AELIQHIPLSLRVRYVFCTAPINKKQPFVCSSLLQFARQYS 598
Cdd:pfam18147   1 ADLIQPVPLSLRDRYTFCMAPVNTRDPKAVAALVEFARCYA 41
SUV3_C pfam12513
Mitochondrial degradasome RNA helicase subunit C terminal; This domain family is found in ...
 626-672 8.96e-15

Mitochondrial degradasome RNA helicase subunit C terminal; This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00271. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes.


Pssm-ID: 463616  Cd Length: 47  Bit Score: 68.70  E-value: 8.96e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 63087685   626 MDLEAVHDVFDLYLWLSYRFIDMFPDSSLVRSLQKELDAIIQEGVHN 672
Cdd:pfam12513   1 ERLESLHKVLDLYLWLSYRFPEVFPDRELAEELKKLVEEKIEEGLER 47
HELICc smart00490
helicase superfamily c-terminal domain;
381-474 1.37e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 66.47  E-value: 1.37e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685    381 VSRQIEIRGLESAVIYGSLPPGTKLAQARKFNdpNDPCKILVATDAIGMGLNL-SIRRIIFYSLikpsinekgekelePI 459
Cdd:smart00490   3 LAELLKELGIKVARLHGGLSQEEREEILDKFN--NGKIKVLVATDVAERGLDLpGVDLVIIYDL--------------PW 66

                           90
                   ....*....|....*
gi 63087685    460 TTSQALQIAGRAGRF 474
Cdd:smart00490  67 SPASYIQRIGRAGRA 81
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 356-474 5.17e-13

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: 65.69  E-value: 5.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685   356 HALESLDNLQPGDCIVCFSKNDIYSVSRQIEIR-GLESAVIYGSLPPGTKLAQARKFNDPNdpCKILVATDAIGMGLNL- 433
Cdd:pfam00271   4 EALLELLKKERGGKVLIFSQTKKTLEAELLLEKeGIKVARLHGDLSQEEREEILEDFRKGK--IDVLVATDVAERGLDLp 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 63087685   434 SIRRIIFYSLikpsinekgekelePITTSQALQIAGRAGRF 474
Cdd:pfam00271  82 DVDLVINYDL--------------PWNPASYIQRIGRAGRA 108
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 206-319 6.71e-08

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: 53.03  E-value: 6.71e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 206 SGPTNSGKT---YHAIQRYLsATSG---VYCGPLKLLAHEIF----EKSNAAGVPCDLVTGEERLTVEPEGKqATHVSCT 275
Cdd:cd17921  23 SAPTSSGKTliaELAILRAL-ATSGgkaVYIAPTRALVNQKEadlrERFGPLGKNVGLLTGDPSVNKLLLAE-ADILVAT 100

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 63087685 276 VEMCNVAT---------PYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHL 319
Cdd:cd17921 101 PEKLDLLLrnggerliqDVRLVVVDEAHLIGDGERGVVLELLLSRLLRINKNA 153
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 381-441 2.04e-06

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 47.86  E-value: 2.04e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 63087685 381 VSRQIEIRGLESAVIYGSLPPGTKLAQARKFNDPNDPCKILVATDAIGMGLNLSI-RRIIFY 441
Cdd:cd18793  43 LEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPDIRVFLLSTKAGGVGLNLTAaNRVILY 104
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
206-473 4.57e-06

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 49.89  E-value: 4.57e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 206 SGPTNSGKT---YHAIQRYLsATSG--VYCGPLKLLAHEIFEKSNAA----GVPCDLVTGEeRLTVEPEGKQATHVSCTV 276
Cdd:COG1204  44 SAPTASGKTliaELAILKAL-LNGGkaLYIVPLRALASEKYREFKRDfeelGIKVGVSTGD-YDSDDEWLGRYDILVATP 121

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 277 EMC--------NVATPYEVAVIDEIQMIRDPARG----WAWTRAL--------LGLCA-----EEVhlcgesaAINLVSE 331
Cdd:COG1204 122 EKLdsllrngpSWLRDVDLVVVDEAHLIDDESRGptleVLLARLRrlnpeaqiVALSAtignaEEI-------AEWLDAE 194

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 332 LLYTT------------GEEVEVQKYERLTPISVLDHALESLDnlQPGDCIV-CFSKNDIYSVSRQI------------- 385
Cdd:COG1204 195 LVKSDwrpvplnegvlyDGVLRFDDGSRRSKDPTLALALDLLE--EGGQVLVfVSSRRDAESLAKKLadelkrrltpeer 272

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 386 -EIRGLESAVI-----------------------YGSLPPGTKLAQARKFNDPNdpCKILVATDAIGMGLNLSIRRIIFY 441
Cdd:COG1204 273 eELEELAEELLevseethtnekladclekgvafhHAGLPSELRRLVEDAFREGL--IKVLVATPTLAAGVNLPARRVIIR 350

                       330       340       350
                ....*....|....*....|....*....|..
gi 63087685 442 SLikpsineKGEKElEPITTSQALQIAGRAGR 473
Cdd:COG1204 351 DT-------KRGGM-VPIPVLEFKQMAGRAGR 374
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 365-473 9.11e-06

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 45.66  E-value: 9.11e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 365 QPGDC--IVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQARKFNdpNDPCKILVATDAIGMGLNLS-IRRIIFY 441
Cdd:cd18794  28 HLGGSgiIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKWL--RDKIQVIVATVAFGMGIDKPdVRFVIHY 105

                        90       100       110
                ....*....|....*....|....*....|..
gi 63087685 442 SLikPsinekgeKELEpittsQALQIAGRAGR 473
Cdd:cd18794 106 SL--P-------KSME-----SYYQESGRAGR 123
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 419-483 6.17e-05

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 41.92  E-value: 6.17e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 63087685 419 KILVATDAIGMGL-NLSIRRIIFYSlikpsinekgekelEPITTSQALQIAGRAGRFSShfKEGQV 483
Cdd:cd18785  24 EILVATNVLGEGIdVPSLDTVIFFD--------------PPSSAASYIQRVGRAGRGGK--DEGEV 73
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 381-433 9.25e-05

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 45.99  E-value: 9.25e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 63087685 381 VSRQIEIRGLESAVIYGSLPPGTKLAQARKFNDPNDPCKILVATDAIGMGLNL 433
Cdd:COG0553 565 LEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPEAPVFLISLKAGGEGLNL 617
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 343-433 7.39e-04

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: 40.18  E-value: 7.39e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63087685 343 QKYERLTPISVLDHALESLDNLQPGDCIVCF--SKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQARKFNdpNDPCKI 420
Cdd:cd18787   3 QLYVVVEEEEKKLLLLLLLLEKLKPGKAIIFvnTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFR--SGKVRV 80

                        90
                ....*....|...
gi 63087685 421 LVATDAIGMGLNL 433
Cdd:cd18787  81 LVATDVAARGLDI 93
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 419-473 7.60e-04

C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases 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: 350182 [Multi-domain]  Cd Length: 154  Bit Score: 40.61  E-value: 7.60e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 63087685 419 KILVATDAIGMGLNLSIRRIIFYSLIKpsineKGEKELEPITTSQALQIAGRAGR 473
Cdd:cd18795  91 KVLVATSTLAAGVNLPARTVIIKGTQR-----YDGKGYRELSPLEYLQMIGRAGR 140
 
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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