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Conserved domains on  [gi|2062403266|gb|QXF79000|]
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helicase DNA B, partial [Phaethon rubricauda]

Protein Classification

DEAD/DEAH box helicase family protein( domain architecture ID 1000205)

DEAD/DEAH box helicase family protein such as a DEAD/DEAH box-containing ATP-dependent helicase, which catalyzes the unwinding of DNA or RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 154-251 4.48e-10

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


The actual alignment was detected with superfamily member cd17933:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 155  Bit Score: 56.79  E-value: 4.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062403266 154 DQVIALERICSNPVTIISGKGGCGKSTIVSCLFHHLKQMEKEVEAAskdfeedleaseewntfdhhcdsenmytkkslnv 233
Cdd:cd17933     1 EQKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLA---------------------------------- 46

                          90
                  ....*....|....*...
gi 2062403266 234 lftAPTGRAASLLTEKTK 251
Cdd:cd17933    47 ---APTGKAAKRLSESTG 61
RecD super family cl33920
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 16-250 7.53e-07

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0507:

Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 49.59  E-value: 7.53e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062403266  16 EMGHTYeDQDELArfVSKYMSIEHAWQS-LEFLKDQNVVIREKKLvFLPHLYKSEKDIAMYIGDLlsKKSWQLDVDVRKI 94
Cdd:COG0507    40 GEGHTF-PLEDLA--AARLLGVAEDIEAaLAALVESGPLVLDGRR-YLTRLLEAEQRLARRLRRL--ARPALDEADVEAA 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062403266  95 LNVPETSREMVDNKmnvtqphemqhlkensadnhnsenhfaekevgstsgsqrkaevdlDQVIALERIC-SNPVTIISGK 173
Cdd:COG0507   114 LAALEPRAGITLSD---------------------------------------------EQREAVALALtTRRVSVLTGG 148

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2062403266 174 GGCGKSTIVSCLFHHLKQMekeveaaskdfeedleaseewntfdhhcdsenmytkkSLNVLFTAPTGRAASLLTEKT 250
Cdd:COG0507   149 AGTGKTTTLRALLAALEAL-------------------------------------GLRVALAAPTGKAAKRLSEST 188
 
Name Accession Description Interval E-value
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 154-251 4.48e-10

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD 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: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 56.79  E-value: 4.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062403266 154 DQVIALERICSNPVTIISGKGGCGKSTIVSCLFHHLKQMEKEVEAAskdfeedleaseewntfdhhcdsenmytkkslnv 233
Cdd:cd17933     1 EQKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLA---------------------------------- 46

                          90
                  ....*....|....*...
gi 2062403266 234 lftAPTGRAASLLTEKTK 251
Cdd:cd17933    47 ---APTGKAAKRLSESTG 61
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 16-250 7.53e-07

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 49.59  E-value: 7.53e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062403266  16 EMGHTYeDQDELArfVSKYMSIEHAWQS-LEFLKDQNVVIREKKLvFLPHLYKSEKDIAMYIGDLlsKKSWQLDVDVRKI 94
Cdd:COG0507    40 GEGHTF-PLEDLA--AARLLGVAEDIEAaLAALVESGPLVLDGRR-YLTRLLEAEQRLARRLRRL--ARPALDEADVEAA 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062403266  95 LNVPETSREMVDNKmnvtqphemqhlkensadnhnsenhfaekevgstsgsqrkaevdlDQVIALERIC-SNPVTIISGK 173
Cdd:COG0507   114 LAALEPRAGITLSD---------------------------------------------EQREAVALALtTRRVSVLTGG 148

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2062403266 174 GGCGKSTIVSCLFHHLKQMekeveaaskdfeedleaseewntfdhhcdsenmytkkSLNVLFTAPTGRAASLLTEKT 250
Cdd:COG0507   149 AGTGKTTTLRALLAALEAL-------------------------------------GLRVALAAPTGKAAKRLSEST 188
CooC COG3640
CO dehydrogenase nickel-insertion accessory protein CooC1 [Posttranslational modification, ...
 170-196 9.17e-04

CO dehydrogenase nickel-insertion accessory protein CooC1 [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 442857 [Multi-domain]  Cd Length: 249  Bit Score: 39.38  E-value: 9.17e-04
                          10        20
                  ....*....|....*....|....*..
gi 2062403266 170 ISGKGGCGKSTIVSCLFHHLKQMEKEV 196
Cdd:COG3640     5 VAGKGGVGKTTLSALLARYLAEKGKPV 31
 
Name Accession Description Interval E-value
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 154-251 4.48e-10

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD 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: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 56.79  E-value: 4.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062403266 154 DQVIALERICSNPVTIISGKGGCGKSTIVSCLFHHLKQMEKEVEAAskdfeedleaseewntfdhhcdsenmytkkslnv 233
Cdd:cd17933     1 EQKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLA---------------------------------- 46

                          90
                  ....*....|....*...
gi 2062403266 234 lftAPTGRAASLLTEKTK 251
Cdd:cd17933    47 ---APTGKAAKRLSESTG 61
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 16-250 7.53e-07

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 49.59  E-value: 7.53e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062403266  16 EMGHTYeDQDELArfVSKYMSIEHAWQS-LEFLKDQNVVIREKKLvFLPHLYKSEKDIAMYIGDLlsKKSWQLDVDVRKI 94
Cdd:COG0507    40 GEGHTF-PLEDLA--AARLLGVAEDIEAaLAALVESGPLVLDGRR-YLTRLLEAEQRLARRLRRL--ARPALDEADVEAA 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062403266  95 LNVPETSREMVDNKmnvtqphemqhlkensadnhnsenhfaekevgstsgsqrkaevdlDQVIALERIC-SNPVTIISGK 173
Cdd:COG0507   114 LAALEPRAGITLSD---------------------------------------------EQREAVALALtTRRVSVLTGG 148

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2062403266 174 GGCGKSTIVSCLFHHLKQMekeveaaskdfeedleaseewntfdhhcdsenmytkkSLNVLFTAPTGRAASLLTEKT 250
Cdd:COG0507   149 AGTGKTTTLRALLAALEAL-------------------------------------GLRVALAAPTGKAAKRLSEST 188
CooC COG3640
CO dehydrogenase nickel-insertion accessory protein CooC1 [Posttranslational modification, ...
 170-196 9.17e-04

CO dehydrogenase nickel-insertion accessory protein CooC1 [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 442857 [Multi-domain]  Cd Length: 249  Bit Score: 39.38  E-value: 9.17e-04
                          10        20
                  ....*....|....*....|....*..
gi 2062403266 170 ISGKGGCGKSTIVSCLFHHLKQMEKEV 196
Cdd:COG3640     5 VAGKGGVGKTTLSALLARYLAEKGKPV 31
SIMIBI_bact_arch cd03110
bacterial and archaeal subfamily of SIMIBI; Uncharacterized bacterial and archaeal subfamily ...
 167-186 2.45e-03

bacterial and archaeal subfamily of SIMIBI; Uncharacterized bacterial and archaeal subfamily of SIMIBI superfamily. Proteins in this superfamily contain an ATP-binding domain and use energy from hydrolysis of ATP to transfer electron or ion. The specific function of this family is unknown.


Pssm-ID: 349764 [Multi-domain]  Cd Length: 246  Bit Score: 38.14  E-value: 2.45e-03
                          10        20
                  ....*....|....*....|
gi 2062403266 167 VTIISGKGGCGKSTIVSCLF 186
Cdd:cd03110     2 IAVLSGKGGTGKTTITANLA 21
Mrp_NBP35 cd02037
Mrp/NBP35 ATP-binding protein family; Mrp/NBP35 ATP-binding family protein are typically ...
 167-196 8.93e-03

Mrp/NBP35 ATP-binding protein family; Mrp/NBP35 ATP-binding family protein are typically iron-sulfur (FeS) cluster scaffolds that function to assemble nascent FeS clusters for transfer to FeS-requiring enzymes. Members include the eukaryotic nucleotide-binding protein 1 (NUBP1) which is a component of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA) machinery and the archael [NiFe] hydrogenase maturation protein HypB which is required for nickel insertion into [NiFe] hydrogenase.


Pssm-ID: 349757 [Multi-domain]  Cd Length: 213  Bit Score: 36.33  E-value: 8.93e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 2062403266 167 VTIISGKGGCGKSTIVSCLFHHLKQMEKEV 196
Cdd:cd02037     3 IAVLSGKGGVGKSTVAVNLALALAKKGYKV 32
 
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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