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Conserved domains on  [gi|7019867|dbj|BAA90901|]
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unnamed protein product [Homo sapiens]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 1000858)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA; similar to Homo sapiens exosome RNA helicase MTR4 and Arabidopsis thaliana chloroplastic DExH-box ATP-dependent RNA helicase DExH15

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
BRR2 super family cl34180
Replicative superfamily II helicase [Replication, recombination and repair];
1-121 5.25e-04

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


The actual alignment was detected with superfamily member COG1204:

Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 42.19  E-value: 5.25e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7019867    1 MSGRAGRRGQDLMGDVYFFDIPFPKIGKL----IKSNVPELRGHfpLSITLVLRLMLLASKGDDPEDAKAKVLSVLKHSL 76
Cdd:COG1204 368 MAGRAGRPGYDPYGEAILVAKSSDEADELferyILGEPEPIRSK--LANESALRTHLLALIASGFANSREELLDFLENTF 445

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 7019867   77 LSFKQPrvMDMLKLYFLFSLQFLVKEGYLDQEGN---PMGFAGLVSHL 121
Cdd:COG1204 446 YAYQYD--KGDLEEVVDDALEFLLENGFIEEDGDrlrATKLGKLVSRL 491
 
Name Accession Description Interval E-value
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
1-121 5.25e-04

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 42.19  E-value: 5.25e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7019867    1 MSGRAGRRGQDLMGDVYFFDIPFPKIGKL----IKSNVPELRGHfpLSITLVLRLMLLASKGDDPEDAKAKVLSVLKHSL 76
Cdd:COG1204 368 MAGRAGRPGYDPYGEAILVAKSSDEADELferyILGEPEPIRSK--LANESALRTHLLALIASGFANSREELLDFLENTF 445

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 7019867   77 LSFKQPrvMDMLKLYFLFSLQFLVKEGYLDQEGN---PMGFAGLVSHL 121
Cdd:COG1204 446 YAYQYD--KGDLEEVVDDALEFLLENGFIEEDGDrlrATKLGKLVSRL 491
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 1-19 2.74e-03

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: 37.92  E-value: 2.74e-03
                        10
                ....*....|....*....
gi 7019867    1 MSGRAGRRGQDLMGDVYFF 19
Cdd:cd18795 134 MIGRAGRPGFDTRGEAIIM 152
 
Name Accession Description Interval E-value
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
1-121 5.25e-04

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 42.19  E-value: 5.25e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7019867    1 MSGRAGRRGQDLMGDVYFFDIPFPKIGKL----IKSNVPELRGHfpLSITLVLRLMLLASKGDDPEDAKAKVLSVLKHSL 76
Cdd:COG1204 368 MAGRAGRPGYDPYGEAILVAKSSDEADELferyILGEPEPIRSK--LANESALRTHLLALIASGFANSREELLDFLENTF 445

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 7019867   77 LSFKQPrvMDMLKLYFLFSLQFLVKEGYLDQEGN---PMGFAGLVSHL 121
Cdd:COG1204 446 YAYQYD--KGDLEEVVDDALEFLLENGFIEEDGDrlrATKLGKLVSRL 491
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 1-19 2.74e-03

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: 37.92  E-value: 2.74e-03
                        10
                ....*....|....*....
gi 7019867    1 MSGRAGRRGQDLMGDVYFF 19
Cdd:cd18795 134 MIGRAGRPGFDTRGEAIIM 152
 
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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