NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|807215767|gb|KKD37904|]
View 

hypothetical protein WN50_11775 [Limnoraphis robusta CS-951]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
AAA_19 pfam13245
AAA domain;
1-101 2.73e-44

AAA domain;


:

Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 142.74  E-value: 2.73e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767    1 MAAYSKILILTGGPGCGKTFTTATIVELWKAMG---RTILLGAPTGRAAQRLGEMTKLPAKTLHRLLEFDPK-TMNFSRD 76
Cdd:pfam13245   7 TALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvsFPILLAAPTGRAAKRLSERTGLPASTIHRLLGFDDLeAGGFLRD 86

                          90       100
                  ....*....|....*....|....*
gi 807215767   77 RDHPLDCDALIVDETSMLDIFLAYS 101
Cdd:pfam13245  87 EEEPLDGDLLIVDEFSMVDLPLAYR 111
 
Name Accession Description Interval E-value
AAA_19 pfam13245
AAA domain;
1-101 2.73e-44

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 142.74  E-value: 2.73e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767    1 MAAYSKILILTGGPGCGKTFTTATIVELWKAMG---RTILLGAPTGRAAQRLGEMTKLPAKTLHRLLEFDPK-TMNFSRD 76
Cdd:pfam13245   7 TALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvsFPILLAAPTGRAAKRLSERTGLPASTIHRLLGFDDLeAGGFLRD 86

                          90       100
                  ....*....|....*....|....*
gi 807215767   77 RDHPLDCDALIVDETSMLDIFLAYS 101
Cdd:pfam13245  87 EEEPLDGDLLIVDEFSMVDLPLAYR 111
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 1-101 5.07e-43

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: 140.00  E-value: 5.07e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767   1 MAAYSKILILTGGPGCGKTFTTATIVELWKAMGRTILLGAPTGRAAQRLGEMTKLPAKTLHRLLEFDPKTMNFSRDRDHP 80
Cdd:cd17933    8 LVLRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRLSESTGIEASTIHRLLGINPGGGGFYYNEENP 87

                         90       100
                 ....*....|....*....|.
gi 807215767  81 LDCDALIVDETSMLDIFLAYS 101
Cdd:cd17933   88 LDADLLIVDEASMVDTRLMAA 108
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 5-100 1.01e-39

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: 140.11  E-value: 1.01e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767   5 SKILILTGGPGCGKTFTTATIVELWKAMGRTILLGAPTGRAAQRLGEMTKLPAKTLHRLLEFDPKTMNFSRDRDHPL-DC 83
Cdd:COG0507  140 RRVSVLTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRLSESTGIEARTIHRLLGLRPDSGRFRHNRDNPLtPA 219

                         90
                 ....*....|....*..
gi 807215767  84 DALIVDETSMLDIFLAY 100
Cdd:COG0507  220 DLLVVDEASMVDTRLMA 236
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 2-104 3.66e-30

helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 114.88  E-value: 3.66e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767    2 AAYSKILILTGGPGCGKTFTTATIVELWKAMGR--TILLGAPTGRAAQRLGEMTKLPAKTLHRLLEFDPKTMNFSRDRDh 79
Cdd:TIGR01448 335 AIQHKVVILTGGPGTGKTTITRAIIELAEELGGllPVGLAAPTGRAAKRLGEVTGLTASTIHRLLGYGPDTFRHNHLED- 413

                          90       100
                  ....*....|....*....|....*
gi 807215767   80 PLDCDALIVDETSMLDIFLAYSQIS 104
Cdd:TIGR01448 414 PIDCDLLIVDESSMMDTWLALSLLA 438
recD PRK10875
exodeoxyribonuclease V subunit alpha;
2-95 2.03e-19

exodeoxyribonuclease V subunit alpha;


Pssm-ID: 236783 [Multi-domain]  Cd Length: 615  Bit Score: 84.22  E-value: 2.03e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767   2 AAYSKILILTGGPGCGKTFTTA----TIVELWKAMGRTILLGAPTGRAAQRLGE-----MTKLP------------AKTL 60
Cdd:PRK10875 164 ALTRRISVISGGPGTGKTTTVAkllaALIQLADGERCRIRLAAPTGKAAARLTEslgkaLRQLPltdeqkkripeeASTL 243

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 807215767  61 HRLLEFDPKTMNFSRDRDHPLDCDALIVDETSMLD 95
Cdd:PRK10875 244 HRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMVD 278
 
Name Accession Description Interval E-value
AAA_19 pfam13245
AAA domain;
1-101 2.73e-44

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 142.74  E-value: 2.73e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767    1 MAAYSKILILTGGPGCGKTFTTATIVELWKAMG---RTILLGAPTGRAAQRLGEMTKLPAKTLHRLLEFDPK-TMNFSRD 76
Cdd:pfam13245   7 TALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvsFPILLAAPTGRAAKRLSERTGLPASTIHRLLGFDDLeAGGFLRD 86

                          90       100
                  ....*....|....*....|....*
gi 807215767   77 RDHPLDCDALIVDETSMLDIFLAYS 101
Cdd:pfam13245  87 EEEPLDGDLLIVDEFSMVDLPLAYR 111
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 1-101 5.07e-43

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: 140.00  E-value: 5.07e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767   1 MAAYSKILILTGGPGCGKTFTTATIVELWKAMGRTILLGAPTGRAAQRLGEMTKLPAKTLHRLLEFDPKTMNFSRDRDHP 80
Cdd:cd17933    8 LVLRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRLSESTGIEASTIHRLLGINPGGGGFYYNEENP 87

                         90       100
                 ....*....|....*....|.
gi 807215767  81 LDCDALIVDETSMLDIFLAYS 101
Cdd:cd17933   88 LDADLLIVDEASMVDTRLMAA 108
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 5-100 1.01e-39

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: 140.11  E-value: 1.01e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767   5 SKILILTGGPGCGKTFTTATIVELWKAMGRTILLGAPTGRAAQRLGEMTKLPAKTLHRLLEFDPKTMNFSRDRDHPL-DC 83
Cdd:COG0507  140 RRVSVLTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRLSESTGIEARTIHRLLGLRPDSGRFRHNRDNPLtPA 219

                         90
                 ....*....|....*..
gi 807215767  84 DALIVDETSMLDIFLAY 100
Cdd:COG0507  220 DLLVVDEASMVDTRLMA 236
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 2-104 3.66e-30

helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 114.88  E-value: 3.66e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767    2 AAYSKILILTGGPGCGKTFTTATIVELWKAMGR--TILLGAPTGRAAQRLGEMTKLPAKTLHRLLEFDPKTMNFSRDRDh 79
Cdd:TIGR01448 335 AIQHKVVILTGGPGTGKTTITRAIIELAEELGGllPVGLAAPTGRAAKRLGEVTGLTASTIHRLLGYGPDTFRHNHLED- 413

                          90       100
                  ....*....|....*....|....*
gi 807215767   80 PLDCDALIVDETSMLDIFLAYSQIS 104
Cdd:TIGR01448 414 PIDCDLLIVDESSMMDTWLALSLLA 438
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 7-99 1.52e-20

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 83.38  E-value: 1.52e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767    7 ILILTGGPGCGKTFTTATIVELWKAMGRTILLGAPTGRAAQRLGEMTKLPAKTLHRLLefdpkTMNFSRDRDHPLDCdaL 86
Cdd:pfam13604  20 VAVLVGPAGTGKTTALKALREAWEAAGYRVIGLAPTGRAAKVLGEELGIPADTIAKLL-----HRLGGRAGLDPGTL--L 92

                          90
                  ....*....|...
gi 807215767   87 IVDETSMLDIFLA 99
Cdd:pfam13604  93 IVDEAGMVGTRQM 105
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 2-101 5.36e-20

exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273631 [Multi-domain]  Cd Length: 582  Bit Score: 85.97  E-value: 5.36e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767    2 AAYSKILILTGGPGCGKTFTTA----TIVELWKAMGR-TILLGAPTGRAAQRLGE-----MTKLP------------AKT 59
Cdd:TIGR01447 156 ALKSNFSLITGGPGTGKTTTVArlllALVKQSPKQGKlRIALAAPTGKAAARLAEslrkaVKNLAaaealiaalpseAVT 235

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 807215767   60 LHRLLEFDPKTMNFSRDRDHPLDCDALIVDETSMLDIFLAYS 101
Cdd:TIGR01447 236 IHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMVDLPLMAK 277
recD PRK10875
exodeoxyribonuclease V subunit alpha;
2-95 2.03e-19

exodeoxyribonuclease V subunit alpha;


Pssm-ID: 236783 [Multi-domain]  Cd Length: 615  Bit Score: 84.22  E-value: 2.03e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767   2 AAYSKILILTGGPGCGKTFTTA----TIVELWKAMGRTILLGAPTGRAAQRLGE-----MTKLP------------AKTL 60
Cdd:PRK10875 164 ALTRRISVISGGPGTGKTTTVAkllaALIQLADGERCRIRLAAPTGKAAARLTEslgkaLRQLPltdeqkkripeeASTL 243

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 807215767  61 HRLLEFDPKTMNFSRDRDHPLDCDALIVDETSMLD 95
Cdd:PRK10875 244 HRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMVD 278
DEXSc_Pif1_like cd18037
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ...
 10-95 4.69e-10

DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350795 [Multi-domain]  Cd Length: 183  Bit Score: 55.72  E-value: 4.69e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 807215767  10 LTGGPGCGKTFTTATIVELWKAMGRTILLGAPTGRAAQRLGEMT----------KLPAKTLHRLLEFDPKTMNfsrdrdH 79
Cdd:cd18037   17 FTGSAGTGKSYLLRRIIRALPSRPKRVAVTASTGIAACNIGGTTlhsfagiglgSEPAEDLLERVKRSPYLVQ------R 90

                         90
                 ....*....|....*.
gi 807215767  80 PLDCDALIVDETSMLD 95
Cdd:cd18037   91 WRKCDVLIIDEISMLD 106
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 7-51 3.22e-04

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 38.62  E-value: 3.22e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 807215767   7 ILILTGGPGCGKTFTTATIVELWKAMGRT----ILLGAPTGRAAQRLGE 51
Cdd:cd17914    1 LSLIQGPPGTGKTRVLVKIVAALMQNKNGepgrILLVTPTNKAAAQLDN 49
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 12-51 5.16e-04

DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 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: 350797 [Multi-domain]  Cd Length: 234  Bit Score: 39.15  E-value: 5.16e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 807215767  12 GGPGCGKTFTTATIV-ELWKAMGRTILLGAPTGRAAQRLGE 51
Cdd:cd18039   23 GPPGTGKTVTSATIVyHLVKQGNGPVLVCAPSNVAVDQLTE 63
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH