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Conserved domains on  [gi|14524376|gb|AAK65868|]
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conserved hypothetical protein (plasmid) [Sinorhizobium meliloti 1021]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 11439953)

DEAD/DEAH box helicase is involved in ATP-dependent RNA or DNA unwinding; similar to Sulfolobus solfataricus ATP-dependent DNA helicase Hel308

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXDc smart00487
DEAD-like helicases superfamily;
34-172 1.19e-10

DEAD-like helicases superfamily;


:

Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 61.74  E-value: 1.19e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376     34 PLRPAQEAVLGDWFKNYggdvsggskRDVIIKLHTGQGKTLIGLL-ILQSRLNDNRRPCVYLCPDNFLIEQTCEQASQFG 112
Cdd:smart00487   8 PLRPYQKEAIEALLSGL---------RDVILAAPTGSGKTLAALLpALEALKRGKGGRVLVLVPTRELAEQWAEELKKLG 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376    113 IK---------VSTVEDDLPDDFLAGKS-ILVTSVQKLFNGLTKFGLHRqsIEIDTILMDDAHACSDRIR 172
Cdd:smart00487  79 PSlglkvvglyGGDSKREQLRKLESGKTdILVTTPGRLLDLLENDKLSL--SNVDLVILDEAHRLLDGGF 146
Helicase_C_2 super family cl48175
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.
 409-472 5.71e-05

Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.


The actual alignment was detected with superfamily member pfam13307:

Pssm-ID: 463840 [Multi-domain]  Cd Length: 168  Bit Score: 44.48  E-value: 5.71e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 14524376   409 GIDLPDNTCRVLVFDSRPFsENLTD---------LYQEHCRPESEATLMRTIRSIEQGMGRSVRGEKDYSVVV 472
Cdd:pfam13307  75 GIDFPGDLLRAVIIVGLPF-PNPDDpvveakreyLDSKGGNPFNEWYLPQAVRAVNQAIGRLIRHENDYGAIV 146
 
Name Accession Description Interval E-value
DEXDc smart00487
DEAD-like helicases superfamily;
34-172 1.19e-10

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 61.74  E-value: 1.19e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376     34 PLRPAQEAVLGDWFKNYggdvsggskRDVIIKLHTGQGKTLIGLL-ILQSRLNDNRRPCVYLCPDNFLIEQTCEQASQFG 112
Cdd:smart00487   8 PLRPYQKEAIEALLSGL---------RDVILAAPTGSGKTLAALLpALEALKRGKGGRVLVLVPTRELAEQWAEELKKLG 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376    113 IK---------VSTVEDDLPDDFLAGKS-ILVTSVQKLFNGLTKFGLHRqsIEIDTILMDDAHACSDRIR 172
Cdd:smart00487  79 PSlglkvvglyGGDSKREQLRKLESGKTdILVTTPGRLLDLLENDKLSL--SNVDLVILDEAHRLLDGGF 146
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 61-174 1.21e-09

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 57.41  E-value: 1.21e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376  61 DVIIKLHTGQGKTLIGLLILQSRLNDNRRPCVYLCPDNFLIEQTCE---QASQFGIKVSTV---EDDLPDDFLAGKS--I 132
Cdd:cd00046   3 NVLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAErlrELFGPGIRVAVLvggSSAEEREKNKLGDadI 82

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 14524376 133 LVTSVQKLFNGLTKFGLHRQSiEIDTILMDDAHACSDRIRDA 174
Cdd:cd00046  83 IIATPDMLLNLLLREDRLFLK-DLKLIIVDEAHALLIDSRGA 123
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 58-169 6.18e-06

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 47.24  E-value: 6.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376    58 SKRDVIIKLHTGQGKTLIGLL-ILQS-RLNDNRRPCVYLCPDNFLIEQTCEQASQF----GIKVSTVE--DDLPDDF--L 127
Cdd:pfam00270  13 EGRDVLVQAPTGSGKTLAFLLpALEAlDKLDNGPQALVLAPTRELAEQIYEELKKLgkglGLKVASLLggDSRKEQLekL 92

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 14524376   128 AGKSILVTSVQKLFNGLTKFGLHRQsieIDTILMDDAHACSD 169
Cdd:pfam00270  93 KGPDILVGTPGRLLDLLQERKLLKN---LKLLVLDEAHRLLD 131
Helicase_C_2 pfam13307
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.
 409-472 5.71e-05

Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.


Pssm-ID: 463840 [Multi-domain]  Cd Length: 168  Bit Score: 44.48  E-value: 5.71e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 14524376   409 GIDLPDNTCRVLVFDSRPFsENLTD---------LYQEHCRPESEATLMRTIRSIEQGMGRSVRGEKDYSVVV 472
Cdd:pfam13307  75 GIDFPGDLLRAVIIVGLPF-PNPDDpvveakreyLDSKGGNPFNEWYLPQAVRAVNQAIGRLIRHENDYGAIV 146
PTZ00110 PTZ00110
helicase; Provisional
 58-113 8.72e-03

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 39.76  E-value: 8.72e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 14524376   58 SKRDVIIKLHTGQGKTLIGLL-----IL-QSRLNDNRRP-CVYLCPDNFLIEQTCEQASQFGI 113
Cdd:PTZ00110 166 SGRDMIGIAETGSGKTLAFLLpaivhINaQPLLRYGDGPiVLVLAPTRELAEQIREQCNKFGA 228
 
Name Accession Description Interval E-value
DEXDc smart00487
DEAD-like helicases superfamily;
34-172 1.19e-10

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 61.74  E-value: 1.19e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376     34 PLRPAQEAVLGDWFKNYggdvsggskRDVIIKLHTGQGKTLIGLL-ILQSRLNDNRRPCVYLCPDNFLIEQTCEQASQFG 112
Cdd:smart00487   8 PLRPYQKEAIEALLSGL---------RDVILAAPTGSGKTLAALLpALEALKRGKGGRVLVLVPTRELAEQWAEELKKLG 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376    113 IK---------VSTVEDDLPDDFLAGKS-ILVTSVQKLFNGLTKFGLHRqsIEIDTILMDDAHACSDRIR 172
Cdd:smart00487  79 PSlglkvvglyGGDSKREQLRKLESGKTdILVTTPGRLLDLLENDKLSL--SNVDLVILDEAHRLLDGGF 146
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 61-174 1.21e-09

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 57.41  E-value: 1.21e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376  61 DVIIKLHTGQGKTLIGLLILQSRLNDNRRPCVYLCPDNFLIEQTCE---QASQFGIKVSTV---EDDLPDDFLAGKS--I 132
Cdd:cd00046   3 NVLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAErlrELFGPGIRVAVLvggSSAEEREKNKLGDadI 82

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 14524376 133 LVTSVQKLFNGLTKFGLHRQSiEIDTILMDDAHACSDRIRDA 174
Cdd:cd00046  83 IIATPDMLLNLLLREDRLFLK-DLKLIIVDEAHALLIDSRGA 123
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 56-172 1.70e-07

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: 52.26  E-value: 1.70e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376  56 GGSKRDVIIKLHTGQGKTLIGLLILQSRLNDNRRPCVYLCPDNFLIEQTC----EQASQFGIKVS--TVEDDLPDDFLAG 129
Cdd:cd17921  14 YLSGDSVLVSAPTSSGKTLIAELAILRALATSGGKAVYIAPTRALVNQKEadlrERFGPLGKNVGllTGDPSVNKLLLAE 93

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 14524376 130 KSILVTsVQKLFNGLTKFGLHRQSIEIDTILMDDAHACSDRIR 172
Cdd:cd17921  94 ADILVA-TPEKLDLLLRNGGERLIQDVRLVVVDEAHLIGDGER 135
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 35-165 3.45e-07

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part 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: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 50.38  E-value: 3.45e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376  35 LRPAQEAVLGDWFKNYGGDvsGGskrdvIIKLHTGQGKTLIGLLILQSRLNdnrRPCVYLCPDNFLIEQTCEQASQFGIK 114
Cdd:cd17926   1 LRPYQEEALEAWLAHKNNR--RG-----ILVLPTGSGKTLTALALIAYLKE---LRTLIVVPTDALLDQWKERFEDFLGD 70

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 14524376 115 VST-VEDDLPDDFLAGKSILVTSVQKLFNGL--TKFGLHRQSIeidtILMDDAH 165
Cdd:cd17926  71 SSIgLIGGGKKKDFDDANVVVATYQSLSNLAeeEKDLFDQFGL----LIVDEAH 120
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 59-167 2.74e-06

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer 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: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 48.80  E-value: 2.74e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376  59 KRDVIIKLHTGQGKTLIG-LLI-----LQSRLNDNRRPCVYLCPDNFLIEQTCEQ-ASQFGIKVSTVEDDLPDDFLAGKS 131
Cdd:cd18034  16 KRNTIVVLPTGSGKTLIAvMLIkemgeLNRKEKNPKKRAVFLVPTVPLVAQQAEAiRSHTDLKVGEYSGEMGVDKWTKER 95

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 14524376 132 ---------ILVTSVQKLFNGLTKFGLhrqSIE-IDTILMDDAHAC 167
Cdd:cd18034  96 wkeelekydVLVMTAQILLDALRHGFL---SLSdINLLIFDECHHA 138
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 58-169 6.18e-06

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 47.24  E-value: 6.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376    58 SKRDVIIKLHTGQGKTLIGLL-ILQS-RLNDNRRPCVYLCPDNFLIEQTCEQASQF----GIKVSTVE--DDLPDDF--L 127
Cdd:pfam00270  13 EGRDVLVQAPTGSGKTLAFLLpALEAlDKLDNGPQALVLAPTRELAEQIYEELKKLgkglGLKVASLLggDSRKEQLekL 92

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 14524376   128 AGKSILVTSVQKLFNGLTKFGLHRQsieIDTILMDDAHACSD 169
Cdd:pfam00270  93 KGPDILVGTPGRLLDLLQERKLLKN---LKLLVLDEAHRLLD 131
Helicase_C_2 pfam13307
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.
 409-472 5.71e-05

Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.


Pssm-ID: 463840 [Multi-domain]  Cd Length: 168  Bit Score: 44.48  E-value: 5.71e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 14524376   409 GIDLPDNTCRVLVFDSRPFsENLTD---------LYQEHCRPESEATLMRTIRSIEQGMGRSVRGEKDYSVVV 472
Cdd:pfam13307  75 GIDFPGDLLRAVIIVGLPF-PNPDDpvveakreyLDSKGGNPFNEWYLPQAVRAVNQAIGRLIRHENDYGAIV 146
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 35-172 3.19e-04

DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type 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: 350786 [Multi-domain]  Cd Length: 177  Bit Score: 42.32  E-value: 3.19e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14524376  35 LRPAQ-EAVLGDWFKNyggdvsggskRDVIIKLHTGQGKTLIGLLILQSRLNDNRRpCVYLCPDNFLIEQTCEQASQF-- 111
Cdd:cd18028   2 LYPPQaEAVRAGLLKG----------ENLLISIPTASGKTLIAEMAMVNTLLEGGK-ALYLVPLRALASEKYEEFKKLee 70

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 14524376 112 -GIKV--STVEDDLPDDFLAGKSILVTSVQKlFNGLTKfglHRQSI--EIDTILMDDAHACSDRIR 172
Cdd:cd18028  71 iGLKVgiSTGDYDEDDEWLGDYDIIVATYEK-FDSLLR---HSPSWlrDVGVVVVDEIHLISDEER 132
PTZ00110 PTZ00110
helicase; Provisional
 58-113 8.72e-03

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 39.76  E-value: 8.72e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 14524376   58 SKRDVIIKLHTGQGKTLIGLL-----IL-QSRLNDNRRP-CVYLCPDNFLIEQTCEQASQFGI 113
Cdd:PTZ00110 166 SGRDMIGIAETGSGKTLAFLLpaivhINaQPLLRYGDGPiVLVLAPTRELAEQIREQCNKFGA 228
 
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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