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Conserved domains on  [gi|1063722547|ref|NP_001328228|]
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ATP-dependent RNA helicase [Arabidopsis thaliana]

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 ...
 89-230 1.13e-86

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: 264.81  E-value: 1.13e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547  89 RKVILHVGPTNSGKTYSALKHLEQSSSGVYCGPLRLLAWEVAKRLNKANVPCDLITGQEKDLVEGATHKAVTVEMADVTS 168
Cdd:cd17913     1 RKIIFHAGPTNSGKTYHALQRLKSAKSGVYCGPLRLLAWEVYERLNAEGVPCDLVTGQERREVEGATHVSCTVEMASISE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063722547 169 VYDCAIIDEIQMVGCKQRGFAFTRALLGIAADELHLCGDPAVVPLVEDILKVTGDDVEVHTY 230
Cdd:cd17913    81 PYDVAVIDEIQMIGDPQRGWAWTRALLGLPAEEIHLCGDPSALPLVRKLAETTGDELEVREY 142
SF2_C_suv3 cd18805
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene ...
 234-368 5.85e-74

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: 231.68  E-value: 5.85e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 234 SPLVPLKVPVSSVSSIKTGDCLVTFSRKDIYAYKKTIERAGKHLCSVVYGSLPPETRTAQATRFNDETNDFDVLVASDAI 313
Cdd:cd18805     1 TPLSVESKPLGSLRNLRPGDCVVAFSRKDIFSLKREIEKRTGLKCAVIYGALPPETRRQQARLFNDPESGYDVLVASDAI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063722547 314 GMGLNLNISRIIFSTLQKYDGSETRDLTVSEIKQIAGRAGRFQSKFPIGEVTCLH 368
Cdd:cd18805    81 GMGLNLNIRRVIFSSLSKFDGNEMRPLSPSEVKQIAGRAGRFGSHFPEGEVTTLR 135
SUV3_C pfam12513
Mitochondrial degradasome RNA helicase subunit C terminal; This domain family is found in ...
 505-551 8.39e-14

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: 65.61  E-value: 8.39e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063722547 505 KELESIHKVLDLYVWLSLRLEDSFPDREVAASQKSICNLLIEQFLEG 551
Cdd:pfam12513   1 ERLESLHKVLDLYLWLSYRFPEVFPDRELAEELKKLVEEKIEEGLER 47
Suv3_C_1 super family cl39526
Suv3 C-terminal domain 1; This domain is found in Suv3 present in Homo sapiens. Suv3 is an ...
 439-479 1.36e-05

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.


The actual alignment was detected with superfamily member pfam18147:

Pssm-ID: 436308  Cd Length: 41  Bit Score: 42.04  E-value: 1.36e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063722547 439 AAIVDELPLGLQEKYLFVVSPVDVNDEISGQGLAQFAQNFS 479
Cdd:pfam18147   1 ADLIQPVPLSLRDRYTFCMAPVNTRDPKAVAALVEFARCYA 41
 
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 ...
 89-230 1.13e-86

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: 264.81  E-value: 1.13e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547  89 RKVILHVGPTNSGKTYSALKHLEQSSSGVYCGPLRLLAWEVAKRLNKANVPCDLITGQEKDLVEGATHKAVTVEMADVTS 168
Cdd:cd17913     1 RKIIFHAGPTNSGKTYHALQRLKSAKSGVYCGPLRLLAWEVYERLNAEGVPCDLVTGQERREVEGATHVSCTVEMASISE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063722547 169 VYDCAIIDEIQMVGCKQRGFAFTRALLGIAADELHLCGDPAVVPLVEDILKVTGDDVEVHTY 230
Cdd:cd17913    81 PYDVAVIDEIQMIGDPQRGWAWTRALLGLPAEEIHLCGDPSALPLVRKLAETTGDELEVREY 142
SF2_C_suv3 cd18805
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene ...
 234-368 5.85e-74

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: 231.68  E-value: 5.85e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 234 SPLVPLKVPVSSVSSIKTGDCLVTFSRKDIYAYKKTIERAGKHLCSVVYGSLPPETRTAQATRFNDETNDFDVLVASDAI 313
Cdd:cd18805     1 TPLSVESKPLGSLRNLRPGDCVVAFSRKDIFSLKREIEKRTGLKCAVIYGALPPETRRQQARLFNDPESGYDVLVASDAI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063722547 314 GMGLNLNISRIIFSTLQKYDGSETRDLTVSEIKQIAGRAGRFQSKFPIGEVTCLH 368
Cdd:cd18805    81 GMGLNLNIRRVIFSSLSKFDGNEMRPLSPSEVKQIAGRAGRFGSHFPEGEVTTLR 135
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
88-354 4.26e-27

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 116.19  E-value: 4.26e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547  88 KRKVILHVGPTNSGKTYSAL----KHLEQSSSGVYCGPLRLLAWE----VAKRLNKANVpcDLITGqekDLVE--GATHK 157
Cdd:COG4581    39 AGRSVLVAAPTGSGKTLVAEfaifLALARGRRSFYTAPIKALSNQkffdLVERFGAENV--GLLTG---DASVnpDAPIV 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 158 AVTVEM---------ADVTSVyDCAIIDEIQMVGCKQRGFAFTRALLGIAADELHLC-----GDpaVVPLVEDILKVTGD 223
Cdd:COG4581   114 VMTTEIlrnmlyregADLEDV-GVVVMDEFHYLADPDRGWVWEEPIIHLPARVQLVLlsatvGN--AEEFAEWLTRVRGE 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 224 DVEVHTYERLSPLVP-----------------LKVPVS---SVSSIKTGDCL----VTFSRKD----------------- 262
Cdd:COG4581   191 TAVVVSEERPVPLEFhylvtprlfplfrvnpeLLRPPSrheVIEELDRGGLLpaivFIFSRRGcdeaaqqllsarlttke 270

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 263 ----IYA------------YKKTIERAGKHLCSVVYGSLPPETRTAQATRFndETNDFDVLVASDAIGMGLNLNISRIIF 326
Cdd:COG4581   271 eraeIREaidefaedfsvlFGKTLSRLLRRGIAVHHAGMLPKYRRLVEELF--QAGLLKVVFATDTLAVGINMPARTVVF 348

                         330       340
                  ....*....|....*....|....*...
gi 1063722547 327 STLQKYDGSETRDLTVSEIKQIAGRAGR 354
Cdd:COG4581   349 TKLSKFDGERHRPLTAREFHQIAGRAGR 376
SUV3_C pfam12513
Mitochondrial degradasome RNA helicase subunit C terminal; This domain family is found in ...
 505-551 8.39e-14

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: 65.61  E-value: 8.39e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063722547 505 KELESIHKVLDLYVWLSLRLEDSFPDREVAASQKSICNLLIEQFLEG 551
Cdd:pfam12513   1 ERLESLHKVLDLYLWLSYRFPEVFPDRELAEELKKLVEEKIEEGLER 47
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 246-355 5.08e-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: 65.31  E-value: 5.08e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 246 VSSIKTGDCLVtFSRKDIYAYKKTIERAGKHLCSVVYGSLPPETRTAQATRFNDetNDFDVLVASDAIGMGLNL-NISRI 324
Cdd:pfam00271  10 LKKERGGKVLI-FSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRK--GKIDVLVATDVAERGLDLpDVDLV 86

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1063722547 325 IFstlqkYDGsetrDLTVSEIKQIAGRAGRF 355
Cdd:pfam00271  87 IN-----YDL----PWNPASYIQRIGRAGRA 108
HELICc smart00490
helicase superfamily c-terminal domain;
272-355 2.11e-11

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 59.92  E-value: 2.11e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547  272 RAGKHLCSVVYGSLPPETRTAQATRFNDetNDFDVLVASDAIGMGLNL-NISRIIFstlqkYDgsetRDLTVSEIKQIAG 350
Cdd:smart00490   8 KELGIKVARLHGGLSQEEREEILDKFNN--GKIKVLVATDVAERGLDLpGVDLVII-----YD----LPWSPASYIQRIG 76


                   ....*
gi 1063722547  351 RAGRF 355
Cdd:smart00490  77 RAGRA 81
Suv3_C_1 pfam18147
Suv3 C-terminal domain 1; This domain is found in Suv3 present in Homo sapiens. Suv3 is an ...
 439-479 1.36e-05

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: 42.04  E-value: 1.36e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063722547 439 AAIVDELPLGLQEKYLFVVSPVDVNDEISGQGLAQFAQNFS 479
Cdd:pfam18147   1 ADLIQPVPLSLRDRYTFCMAPVNTRDPKAVAALVEFARCYA 41
PRK02362 PRK02362
ATP-dependent DNA helicase;
285-354 8.30e-04

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 42.25  E-value: 8.30e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063722547 285 LPPETRTAQATRFNDetNDFDVLVASDAIGMGLNLNISRIIFSTLQKYDGSE-TRDLTVSEIKQIAGRAGR 354
Cdd:PRK02362  313 LSREHRELVEDAFRD--RLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAgMQPIPVLEYHQMAGRAGR 381
DEXDc smart00487
DEAD-like helicases superfamily;
87-187 2.59e-03

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 39.40  E-value: 2.59e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547   87 KKRKVILHVGPTNSGKT----YSALKHLEQSSSG--VYCGPLRLLAWEVAKRLNK-----ANVPCDLITG-----QEKDL 150
Cdd:smart00487  22 SGLRDVILAAPTGSGKTlaalLPALEALKRGKGGrvLVLVPTRELAEQWAEELKKlgpslGLKVVGLYGGdskreQLRKL 101

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1063722547  151 VEGATH-KAVTVEMAD--------VTSVYDCAIIDEIQMVGCKQRG 187
Cdd:smart00487 102 ESGKTDiLVTTPGRLLdllendklSLSNVDLVILDEAHRLLDGGFG 147
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 279-319 2.60e-03

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 40.59  E-value: 2.60e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063722547 279 SVVYGSLPPETRTAQATRFNDETNDFDVLVASDAIGMGLNL 319
Cdd:COG0553   577 AYLHGGTSAEERDELVDRFQEGPEAPVFLISLKAGGEGLNL 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 ...
 89-230 1.13e-86

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: 264.81  E-value: 1.13e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547  89 RKVILHVGPTNSGKTYSALKHLEQSSSGVYCGPLRLLAWEVAKRLNKANVPCDLITGQEKDLVEGATHKAVTVEMADVTS 168
Cdd:cd17913     1 RKIIFHAGPTNSGKTYHALQRLKSAKSGVYCGPLRLLAWEVYERLNAEGVPCDLVTGQERREVEGATHVSCTVEMASISE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063722547 169 VYDCAIIDEIQMVGCKQRGFAFTRALLGIAADELHLCGDPAVVPLVEDILKVTGDDVEVHTY 230
Cdd:cd17913    81 PYDVAVIDEIQMIGDPQRGWAWTRALLGLPAEEIHLCGDPSALPLVRKLAETTGDELEVREY 142
SF2_C_suv3 cd18805
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene ...
 234-368 5.85e-74

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: 231.68  E-value: 5.85e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 234 SPLVPLKVPVSSVSSIKTGDCLVTFSRKDIYAYKKTIERAGKHLCSVVYGSLPPETRTAQATRFNDETNDFDVLVASDAI 313
Cdd:cd18805     1 TPLSVESKPLGSLRNLRPGDCVVAFSRKDIFSLKREIEKRTGLKCAVIYGALPPETRRQQARLFNDPESGYDVLVASDAI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063722547 314 GMGLNLNISRIIFSTLQKYDGSETRDLTVSEIKQIAGRAGRFQSKFPIGEVTCLH 368
Cdd:cd18805    81 GMGLNLNIRRVIFSSLSKFDGNEMRPLSPSEVKQIAGRAGRFGSHFPEGEVTTLR 135
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
88-354 4.26e-27

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 116.19  E-value: 4.26e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547  88 KRKVILHVGPTNSGKTYSAL----KHLEQSSSGVYCGPLRLLAWE----VAKRLNKANVpcDLITGqekDLVE--GATHK 157
Cdd:COG4581    39 AGRSVLVAAPTGSGKTLVAEfaifLALARGRRSFYTAPIKALSNQkffdLVERFGAENV--GLLTG---DASVnpDAPIV 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 158 AVTVEM---------ADVTSVyDCAIIDEIQMVGCKQRGFAFTRALLGIAADELHLC-----GDpaVVPLVEDILKVTGD 223
Cdd:COG4581   114 VMTTEIlrnmlyregADLEDV-GVVVMDEFHYLADPDRGWVWEEPIIHLPARVQLVLlsatvGN--AEEFAEWLTRVRGE 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 224 DVEVHTYERLSPLVP-----------------LKVPVS---SVSSIKTGDCL----VTFSRKD----------------- 262
Cdd:COG4581   191 TAVVVSEERPVPLEFhylvtprlfplfrvnpeLLRPPSrheVIEELDRGGLLpaivFIFSRRGcdeaaqqllsarlttke 270

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 263 ----IYA------------YKKTIERAGKHLCSVVYGSLPPETRTAQATRFndETNDFDVLVASDAIGMGLNLNISRIIF 326
Cdd:COG4581   271 eraeIREaidefaedfsvlFGKTLSRLLRRGIAVHHAGMLPKYRRLVEELF--QAGLLKVVFATDTLAVGINMPARTVVF 348

                         330       340
                  ....*....|....*....|....*...
gi 1063722547 327 STLQKYDGSETRDLTVSEIKQIAGRAGR 354
Cdd:COG4581   349 TKLSKFDGERHRPLTAREFHQIAGRAGR 376
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
97-354 7.85e-14

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 74.16  E-value: 7.85e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547  97 PTNSGKT----YSALKHLEQSSSGVYCGPLRLLAWEVAKRLNKA----NVPCDLITGqEKDLVEGATHKA----VTVEMA 164
Cdd:COG1204    46 PTASGKTliaeLAILKALLNGGKALYIVPLRALASEKYREFKRDfeelGIKVGVSTG-DYDSDDEWLGRYdilvATPEKL 124

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 165 D---------VTSVyDCAIIDEIQMVGCKQRGF----AFTRAllgiaadeLHLCGDP------AVVPLVEDILKVTGDDV 225
Cdd:COG1204   125 DsllrngpswLRDV-DLVVVDEAHLIDDESRGPtlevLLARL--------RRLNPEAqivalsATIGNAEEIAEWLDAEL 195

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 226 EVHTYerlSPlVPLKVPVSSVSSIKTGD----------------------CLVtF--SRKDIYAY-KKTIERAGKHLCSV 280
Cdd:COG1204   196 VKSDW---RP-VPLNEGVLYDGVLRFDDgsrrskdptlalaldlleeggqVLV-FvsSRRDAESLaKKLADELKRRLTPE 270

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 281 V-----------------------------------YGSLPPETRTAQATRFndETNDFDVLVASDAIGMGLNLNISRII 325
Cdd:COG1204   271 EreeleelaeellevseethtnekladclekgvafhHAGLPSELRRLVEDAF--REGLIKVLVATPTLAAGVNLPARRVI 348

                         330       340
                  ....*....|....*....|....*....
gi 1063722547 326 FSTLqKYDGSEtrDLTVSEIKQIAGRAGR 354
Cdd:COG1204   349 IRDT-KRGGMV--PIPVLEFKQMAGRAGR 374
SUV3_C pfam12513
Mitochondrial degradasome RNA helicase subunit C terminal; This domain family is found in ...
 505-551 8.39e-14

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: 65.61  E-value: 8.39e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063722547 505 KELESIHKVLDLYVWLSLRLEDSFPDREVAASQKSICNLLIEQFLEG 551
Cdd:pfam12513   1 ERLESLHKVLDLYLWLSYRFPEVFPDRELAEELKKLVEEKIEEGLER 47
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 246-355 5.08e-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: 65.31  E-value: 5.08e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547 246 VSSIKTGDCLVtFSRKDIYAYKKTIERAGKHLCSVVYGSLPPETRTAQATRFNDetNDFDVLVASDAIGMGLNL-NISRI 324
Cdd:pfam00271  10 LKKERGGKVLI-FSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRK--GKIDVLVATDVAERGLDLpDVDLV 86

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1063722547 325 IFstlqkYDGsetrDLTVSEIKQIAGRAGRF 355
Cdd:pfam00271  87 IN-----YDL----PWNPASYIQRIGRAGRA 108
HELICc smart00490
helicase superfamily c-terminal domain;
272-355 2.11e-11

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 59.92  E-value: 2.11e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547  272 RAGKHLCSVVYGSLPPETRTAQATRFNDetNDFDVLVASDAIGMGLNL-NISRIIFstlqkYDgsetRDLTVSEIKQIAG 350
Cdd:smart00490   8 KELGIKVARLHGGLSQEEREEILDKFNN--GKIKVLVATDVAERGLDLpGVDLVII-----YD----LPWSPASYIQRIG 76


                   ....*
gi 1063722547  351 RAGRF 355
Cdd:smart00490  77 RAGRA 81
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 306-354 2.53e-10

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: 59.10  E-value: 2.53e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063722547 306 VLVASDAIGMGLNLNISRIIFSTLQKYDGSETRDLTVSEIKQIAGRAGR 354
Cdd:cd18795    92 VLVATSTLAAGVNLPARTVIIKGTQRYDGKGYRELSPLEYLQMIGRAGR 140
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 97-187 4.09e-06

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: 47.26  E-value: 4.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547  97 PTNSGKT----YSALKHLEQS-SSGVYCGPLRLLAWEVAKRLNK----ANVPCDLITG--QEKDLVEGATHKAV-TVEMA 164
Cdd:cd17921    25 PTSSGKTliaeLAILRALATSgGKAVYIAPTRALVNQKEADLRErfgpLGKNVGLLTGdpSVNKLLLAEADILVaTPEKL 104

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1063722547 165 DVTSVY---------DCAIIDEIQMVGCKQRG 187
Cdd:cd17921   105 DLLLRNggerliqdvRLVVVDEAHLIGDGERG 136
Suv3_C_1 pfam18147
Suv3 C-terminal domain 1; This domain is found in Suv3 present in Homo sapiens. Suv3 is an ...
 439-479 1.36e-05

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: 42.04  E-value: 1.36e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063722547 439 AAIVDELPLGLQEKYLFVVSPVDVNDEISGQGLAQFAQNFS 479
Cdd:pfam18147   1 ADLIQPVPLSLRDRYTFCMAPVNTRDPKAVAALVEFARCYA 41
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 283-319 1.64e-05

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: 44.77  E-value: 1.64e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1063722547 283 GSLPPETRTAQATRFNDETNDFDVLVASDAIGMGLNL 319
Cdd:cd18793    59 GSTSSKERQKLVDRFNEDPDIRVFLLSTKAGGVGLNL 95
DEAD-like_helicase_N cd17912
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 92-208 7.56e-05

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: 41.35  E-value: 7.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547  92 ILHVGPTNSGKTYSALKHLEQ----SSSGVYCGPLRLLAWEvakrlnkanvpcdlitgqekdlvegathkavtvemadvt 167
Cdd:cd17912     2 ILHLGPTGSGKTLVAIQKIASamssGKSVLVVTPTKLLAHE--------------------------------------- 42

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1063722547 168 svyDCAIIDEIQMVGCKQRG-FAFTRALLGIAADELHLCGDP 208
Cdd:cd17912    43 ---ILIVIDEIQ*ILDPAAGwAWATRALLGLKAEKVIGVGAT 81
PRK02362 PRK02362
ATP-dependent DNA helicase;
285-354 8.30e-04

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 42.25  E-value: 8.30e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063722547 285 LPPETRTAQATRFNDetNDFDVLVASDAIGMGLNLNISRIIFSTLQKYDGSE-TRDLTVSEIKQIAGRAGR 354
Cdd:PRK02362  313 LSREHRELVEDAFRD--RLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAgMQPIPVLEYHQMAGRAGR 381
DEXDc smart00487
DEAD-like helicases superfamily;
87-187 2.59e-03

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 39.40  E-value: 2.59e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063722547   87 KKRKVILHVGPTNSGKT----YSALKHLEQSSSG--VYCGPLRLLAWEVAKRLNK-----ANVPCDLITG-----QEKDL 150
Cdd:smart00487  22 SGLRDVILAAPTGSGKTlaalLPALEALKRGKGGrvLVLVPTRELAEQWAEELKKlgpslGLKVVGLYGGdskreQLRKL 101

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1063722547  151 VEGATH-KAVTVEMAD--------VTSVYDCAIIDEIQMVGCKQRG 187
Cdd:smart00487 102 ESGKTDiLVTTPGRLLdllendklSLSNVDLVILDEAHRLLDGGFG 147
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 279-319 2.60e-03

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 40.59  E-value: 2.60e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063722547 279 SVVYGSLPPETRTAQATRFNDETNDFDVLVASDAIGMGLNL 319
Cdd:COG0553   577 AYLHGGTSAEERDELVDRFQEGPEAPVFLISLKAGGEGLNL 617
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 306-354 8.83e-03

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: 35.37  E-value: 8.83e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063722547 306 VLVASDAIGMGL-NLNISRIIFstlqkYDGSETRdltvSEIKQIAGRAGR 354
Cdd:cd18785    25 ILVATNVLGEGIdVPSLDTVIF-----FDPPSSA----ASYIQRVGRAGR 65
 
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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