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Conserved domains on  [gi|137606|sp|P11107|]
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RecName: Full=Probable helicase D10; AltName: Full=Protein D10

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 11437332)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA

CATH:  1.20.1320.20|3.40.50.300
EC:  3.6.4.-
Gene Ontology:  GO:0005524|GO:0004386|GO:0003676
PubMed:  20206133
SCOP:  3002019

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
47-406 2.03e-53

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


:

Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 187.92  E-value: 2.03e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606    47 AKEIKWIPITRLDLLDAKGIKYELVDKRTLAPVD-IPKPKFKLREEdQ-------LPIYEECDDTCIINGKPGFGKTILA 118
Cdd:COG1061  39 RLAIKEGTREDGRRLPEEDTERELAEAEALEAGDeASGTSFELRPY-QqealealLAALERGGGRGLVVAPTGTGKTVLA 117

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   119 LALAYKF--GQKTLVICTNTSIREMWAAEVRKWFGFEPGiiGSGKYNIDPPIVVSNIQTVNKHA--NNLSKVFGTVIVDE 194
Cdd:COG1061 118 LALAAELlrGKRVLVLVPRRELLEQWAEELRRFLGDPLA--GGGKKDSDAPITVATYQSLARRAhlDELGDRFGLVIIDE 195

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   195 VHHCVATTFTNFLEISCARYKIGLSGTLKRKDGLQVMFKDFFGyKIFSPPV-----NNTVAPtIHRYSVPVELSGNQNVP 269
Cdd:COG1061 196 AHHAGAPSYRRILEAFPAAYRLGLTATPFRSDGREILLFLFDG-IVYEYSLkeaieDGYLAP-PEYYGIRVDLTDERAEY 273

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   270 WALRAND----VYNHPEYRETIINLAHLYVNmGHKVLIVSDRTELIQTILEALTQRGVTTYEIIGATHLDDRLKIQEDIA 345
Cdd:COG1061 274 DALSERLrealAADAERKDKILRELLREHPD-DRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFR 352

                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 137606   346 KGGPCVLaAAQSIFSEGISLNELSCLIMGSLINNESLIEQLAGRVQRIVEGKLDPIVVDLI 406
Cdd:COG1061 353 DGELRIL-VTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRGLRPAPGKEDALVYDFV 412
 
Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
47-406 2.03e-53

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 187.92  E-value: 2.03e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606    47 AKEIKWIPITRLDLLDAKGIKYELVDKRTLAPVD-IPKPKFKLREEdQ-------LPIYEECDDTCIINGKPGFGKTILA 118
Cdd:COG1061  39 RLAIKEGTREDGRRLPEEDTERELAEAEALEAGDeASGTSFELRPY-QqealealLAALERGGGRGLVVAPTGTGKTVLA 117

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   119 LALAYKF--GQKTLVICTNTSIREMWAAEVRKWFGFEPGiiGSGKYNIDPPIVVSNIQTVNKHA--NNLSKVFGTVIVDE 194
Cdd:COG1061 118 LALAAELlrGKRVLVLVPRRELLEQWAEELRRFLGDPLA--GGGKKDSDAPITVATYQSLARRAhlDELGDRFGLVIIDE 195

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   195 VHHCVATTFTNFLEISCARYKIGLSGTLKRKDGLQVMFKDFFGyKIFSPPV-----NNTVAPtIHRYSVPVELSGNQNVP 269
Cdd:COG1061 196 AHHAGAPSYRRILEAFPAAYRLGLTATPFRSDGREILLFLFDG-IVYEYSLkeaieDGYLAP-PEYYGIRVDLTDERAEY 273

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   270 WALRAND----VYNHPEYRETIINLAHLYVNmGHKVLIVSDRTELIQTILEALTQRGVTTYEIIGATHLDDRLKIQEDIA 345
Cdd:COG1061 274 DALSERLrealAADAERKDKILRELLREHPD-DRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFR 352

                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 137606   346 KGGPCVLaAAQSIFSEGISLNELSCLIMGSLINNESLIEQLAGRVQRIVEGKLDPIVVDLI 406
Cdd:COG1061 353 DGELRIL-VTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRGLRPAPGKEDALVYDFV 412
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 105-222 8.85e-23

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: 93.91  E-value: 8.85e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   105 IINGKPGFGKTILALAL-AYKFGQKTLVICTNTSIREMWAAEVRKWFGFEP-GIIGSG--KYNIDPPIVVSNIQTVNKHA 180
Cdd:cd17926  22 ILVLPTGSGKTLTALALiAYLKELRTLIVVPTDALLDQWKERFEDFLGDSSiGLIGGGkkKDFDDANVVVATYQSLSNLA 101

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 137606   181 NNLSKV---FGTVIVDEVHHCVATTFTNFLEISCARYKIGLSGTL 222
Cdd:cd17926 102 EEEKDLfdqFGLLIVDEAHHLPAKTFSEILKELNAKYRLGLTATP 146
ResIII pfam04851
Type III restriction enzyme, res subunit;
105-224 1.01e-14

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 71.55  E-value: 1.01e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606     105 IINGKPGFGKTILALALAYKF-----GQKTLVICTNTSIREMWAAEVRKWFGFE---PGIIGSGKYNIDP---PIVVSNI 173
Cdd:pfam04851  27 LIVMATGSGKTLTAAKLIARLfkkgpIKKVLFLVPRKDLLEQALEEFKKFLPNYveiGEIISGDKKDESVddnKIVVTTI 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 137606     174 QTVNKHANNLSKV-----FGTVIVDEVHHCVATTFTNFLEISCARYKIGLSGTLKR 224
Cdd:pfam04851 107 QSLYKALELASLEllpdfFDVIIIDEAHRSGASSYRNILEYFKPAFLLGLTATPER 162
uvsW PHA02558
UvsW helicase; Provisional
 100-406 1.66e-13

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 72.35  E-value: 1.66e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606    100 CDDTCIINGKPGFGKTILALALAYKFGQ----KTLVICTNTSIREMWA---AEVRkWF--GFEPGIIGSGKYNIDPPIVV 170
Cdd:PHA02558 128 KNNRRLLNLPTSAGKSLIQYLLSRYYLEnyegKVLIIVPTTSLVTQMIddfVDYR-LFprEAMHKIYSGTAKDTDAPIVV 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606    171 SNIQTVNKHANNLSKVFGTVIVDEVHHCVATTFTNFLE--ISCaRYKIGLSGTLK--RKDGLQVMfkDFFGyKIFSP--- 243
Cdd:PHA02558 207 STWQSAVKQPKEWFDQFGMVIVDECHLFTGKSLTSIITklDNC-KFKFGLTGSLRdgKANILQYV--GLFG-DIFKPvtt 282

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606    244 -------PVNNTVAPTIH-RYSvPVELSGNQNVPWALRANDVYNHPEYRETIINLAHLYVNMGHKVLIVSDRTELIQTIL 315
Cdd:PHA02558 283 sqlmeegQVTDLKINSIFlRYP-DEDRVKLKGEDYQEEIKYITSHTKRNKWIANLALKLAKKGENTFVMFKYVEHGKPLY 361

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606    316 EALTQRGVTTYEIIGATHLDDRLKIQEDIAKGGPCVLAAAQSIFSEGISLNELSCLIMGSLINNESLIEQLAGRVQRIVE 395
Cdd:PHA02558 362 EMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHG 441

                        330
                 ....*....|.
gi 137606    396 GKLDPIVVDLI 406
Cdd:PHA02558 442 SKSIATVWDII 452
DEXDc smart00487
DEAD-like helicases superfamily;
94-222 1.21e-12

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 66.75  E-value: 1.21e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606       94 LPIYEECDDTCIINGKPGFGKTILALALAYKFGQ-----KTLVICTNTSIREMWAAEVRKWFGFEPG----IIGSGKYNI 164
Cdd:smart00487  17 IEALLSGLRDVILAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLkvvgLYGGDSKRE 96

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 137606      165 D--------PPIVVSNIQTVNKHANNLSKV---FGTVIVDEVHHCVATTFTNFLEISC-----ARYKIGLSGTL 222
Cdd:smart00487  97 QlrklesgkTDILVTTPGRLLDLLENDKLSlsnVDLVILDEAHRLLDGGFGDQLEKLLkllpkNVQLLLLSATP 170
 
Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
47-406 2.03e-53

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 187.92  E-value: 2.03e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606    47 AKEIKWIPITRLDLLDAKGIKYELVDKRTLAPVD-IPKPKFKLREEdQ-------LPIYEECDDTCIINGKPGFGKTILA 118
Cdd:COG1061  39 RLAIKEGTREDGRRLPEEDTERELAEAEALEAGDeASGTSFELRPY-QqealealLAALERGGGRGLVVAPTGTGKTVLA 117

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   119 LALAYKF--GQKTLVICTNTSIREMWAAEVRKWFGFEPGiiGSGKYNIDPPIVVSNIQTVNKHA--NNLSKVFGTVIVDE 194
Cdd:COG1061 118 LALAAELlrGKRVLVLVPRRELLEQWAEELRRFLGDPLA--GGGKKDSDAPITVATYQSLARRAhlDELGDRFGLVIIDE 195

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   195 VHHCVATTFTNFLEISCARYKIGLSGTLKRKDGLQVMFKDFFGyKIFSPPV-----NNTVAPtIHRYSVPVELSGNQNVP 269
Cdd:COG1061 196 AHHAGAPSYRRILEAFPAAYRLGLTATPFRSDGREILLFLFDG-IVYEYSLkeaieDGYLAP-PEYYGIRVDLTDERAEY 273

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   270 WALRAND----VYNHPEYRETIINLAHLYVNmGHKVLIVSDRTELIQTILEALTQRGVTTYEIIGATHLDDRLKIQEDIA 345
Cdd:COG1061 274 DALSERLrealAADAERKDKILRELLREHPD-DRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFR 352

                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 137606   346 KGGPCVLaAAQSIFSEGISLNELSCLIMGSLINNESLIEQLAGRVQRIVEGKLDPIVVDLI 406
Cdd:COG1061 353 DGELRIL-VTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRGLRPAPGKEDALVYDFV 412
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 105-222 8.85e-23

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: 93.91  E-value: 8.85e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   105 IINGKPGFGKTILALAL-AYKFGQKTLVICTNTSIREMWAAEVRKWFGFEP-GIIGSG--KYNIDPPIVVSNIQTVNKHA 180
Cdd:cd17926  22 ILVLPTGSGKTLTALALiAYLKELRTLIVVPTDALLDQWKERFEDFLGDSSiGLIGGGkkKDFDDANVVVATYQSLSNLA 101

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 137606   181 NNLSKV---FGTVIVDEVHHCVATTFTNFLEISCARYKIGLSGTL 222
Cdd:cd17926 102 EEEKDLfdqFGLLIVDEAHHLPAKTFSEILKELNAKYRLGLTATP 146
ResIII pfam04851
Type III restriction enzyme, res subunit;
105-224 1.01e-14

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 71.55  E-value: 1.01e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606     105 IINGKPGFGKTILALALAYKF-----GQKTLVICTNTSIREMWAAEVRKWFGFE---PGIIGSGKYNIDP---PIVVSNI 173
Cdd:pfam04851  27 LIVMATGSGKTLTAAKLIARLfkkgpIKKVLFLVPRKDLLEQALEEFKKFLPNYveiGEIISGDKKDESVddnKIVVTTI 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 137606     174 QTVNKHANNLSKV-----FGTVIVDEVHHCVATTFTNFLEISCARYKIGLSGTLKR 224
Cdd:pfam04851 107 QSLYKALELASLEllpdfFDVIIIDEAHRSGASSYRNILEYFKPAFLLGLTATPER 162
uvsW PHA02558
UvsW helicase; Provisional
 100-406 1.66e-13

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 72.35  E-value: 1.66e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606    100 CDDTCIINGKPGFGKTILALALAYKFGQ----KTLVICTNTSIREMWA---AEVRkWF--GFEPGIIGSGKYNIDPPIVV 170
Cdd:PHA02558 128 KNNRRLLNLPTSAGKSLIQYLLSRYYLEnyegKVLIIVPTTSLVTQMIddfVDYR-LFprEAMHKIYSGTAKDTDAPIVV 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606    171 SNIQTVNKHANNLSKVFGTVIVDEVHHCVATTFTNFLE--ISCaRYKIGLSGTLK--RKDGLQVMfkDFFGyKIFSP--- 243
Cdd:PHA02558 207 STWQSAVKQPKEWFDQFGMVIVDECHLFTGKSLTSIITklDNC-KFKFGLTGSLRdgKANILQYV--GLFG-DIFKPvtt 282

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606    244 -------PVNNTVAPTIH-RYSvPVELSGNQNVPWALRANDVYNHPEYRETIINLAHLYVNMGHKVLIVSDRTELIQTIL 315
Cdd:PHA02558 283 sqlmeegQVTDLKINSIFlRYP-DEDRVKLKGEDYQEEIKYITSHTKRNKWIANLALKLAKKGENTFVMFKYVEHGKPLY 361

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606    316 EALTQRGVTTYEIIGATHLDDRLKIQEDIAKGGPCVLAAAQSIFSEGISLNELSCLIMGSLINNESLIEQLAGRVQRIVE 395
Cdd:PHA02558 362 EMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHG 441

                        330
                 ....*....|.
gi 137606    396 GKLDPIVVDLI 406
Cdd:PHA02558 442 SKSIATVWDII 452
DEXDc smart00487
DEAD-like helicases superfamily;
94-222 1.21e-12

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 66.75  E-value: 1.21e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606       94 LPIYEECDDTCIINGKPGFGKTILALALAYKFGQ-----KTLVICTNTSIREMWAAEVRKWFGFEPG----IIGSGKYNI 164
Cdd:smart00487  17 IEALLSGLRDVILAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLkvvgLYGGDSKRE 96

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 137606      165 D--------PPIVVSNIQTVNKHANNLSKV---FGTVIVDEVHHCVATTFTNFLEISC-----ARYKIGLSGTL 222
Cdd:smart00487  97 QlrklesgkTDILVTTPGRLLDLLENDKLSlsnVDLVILDEAHRLLDGGFGDQLEKLLkllpkNVQLLLLSATP 170
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 111-231 1.31e-12

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members 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: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 65.66  E-value: 1.31e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   111 GFGKTILALALAYKF-----GQKTLVICTNTSIREMWAAEVRKWFGF-EPGIIGSGKYNI-DPPIVVSNIQTVNK--HAN 181
Cdd:cd18032  30 GTGKTYTAAFLIKRLleanrKKRILFLAHREELLEQAERSFKEVLPDgSFGNLKGGKKKPdDARVVFATVQTLNKrkRLE 109

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 137606   182 NLSK-VFGTVIVDEVHHCVATTFTNFLEISCARYKIGLSGTLKRKDGLQVM 231
Cdd:cd18032 110 KFPPdYFDLIIIDEAHHAIASSYRKILEYFEPAFLLGLTATPERTDGLDTY 160
DEXHc_XPB cd18029
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ...
 111-227 1.54e-12

DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription factor complex helicase XPB subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB 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: 350787 [Multi-domain]  Cd Length: 169  Bit Score: 65.40  E-value: 1.54e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   111 GFGKTILALALAYKFGQKTLVICTNTSIREMWAAEVRKWFGFEPGIIG---SGKYNI--DPPIVVSNIQTV------NKH 179
Cdd:cd18029  36 GAGKTLVGITAACTIKKSTLVLCTSAVSVEQWRRQFLDWTTIDDEQIGrftSDKKEIfpEAGVTVSTYSMLantrkrSPE 115

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 137606   180 A----NNLSKV-FGTVIVDEVHHCVATTFTNFLEISCARYKIGLSGTLKRKDG 227
Cdd:cd18029 116 SekfmEFITEReWGLIILDEVHVVPAPMFRRVLTLQKAHCKLGLTATLVREDD 168
DEXHc_HARP_SMARCAL1 cd18010
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ...
 104-221 1.56e-11

DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1, also known as HARP) is recruited to stalled replication forks to promote repair and helps restart replication. It plays a role in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress. Mutations cause Schimke Immunoosseous Dysplasia. SMARCAL1 is 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: 350768 [Multi-domain]  Cd Length: 213  Bit Score: 63.38  E-value: 1.56e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   104 CIINGKPGFGKTILALALAYKFGQK-TLVICTNTSIREMWAAEVRKWFGFEP----GIIGSGK---YNIDPPIVVSNIQT 175
Cdd:cd18010  19 VLIADEMGLGKTVQAIAIAAYYREEwPLLIVCPSSLRLTWADEIERWLPSLPpddiQVIVKSKdglRDGDAKVVIVSYDL 98

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 137606   176 VNKHANNLSKV-FGTVIVDEVHHC---VATTFTNFLEIS-CARYKIGLSGT 221
Cdd:cd18010  99 LRRLEKQLLARkFKVVICDESHYLknsKAKRTKAALPLLkRAKRVILLSGT 149
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 110-221 6.40e-09

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 58.31  E-value: 6.40e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   110 PGFGKTI--LALALAYKF---GQKTLVICTnTSIREMWAAEVRKWFGFEPGIIGSG----KYNIDP----PIVVSNIQTV 176
Cdd:COG0553 269 MGLGKTIqaLALLLELKErglARPVLIVAP-TSLVGNWQRELAKFAPGLRVLVLDGtrerAKGANPfedaDLVITSYGLL 347

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 137606   177 NKHANNLSKV-FGTVIVDEVHHC--VATTFTNFLEISCARYKIGLSGT 221
Cdd:COG0553 348 RRDIELLAAVdWDLVILDEAQHIknPATKRAKAVRALKARHRLALTGT 395
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 282-393 3.39e-08

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: 51.44  E-value: 3.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606     282 EYRETIINLahLYVNMGHKVLIVSDRTELIQT-ILeaLTQRGVTTYEIIGATHLDDRLKIQEDIAKGGPCVLAAAqSIFS 360
Cdd:pfam00271   1 EKLEALLEL--LKKERGGKVLIFSQTKKTLEAeLL--LEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVAT-DVAE 75

                          90       100       110
                  ....*....|....*....|....*....|...
gi 137606     361 EGISLNELSCLIMGSLINNESLIEQLAGRVQRI 393
Cdd:pfam00271  76 RGLDLPDVDLVINYDLPWNPASYIQRIGRAGRA 108
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 104-221 6.25e-08

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: 51.64  E-value: 6.25e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   104 CIINGKPGFGKTILALALAY----KFGQKTLVICTNTSIREMWAAEVRKWFGfePGI---IGSGKYNI---------DPP 167
Cdd:cd00046   4 VLITAPTGSGKTLAALLAALllllKKGKKVLVLVPTKALALQTAERLRELFG--PGIrvaVLVGGSSAeereknklgDAD 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 137606   168 IVVSNIQTVNK----HANNLSKVFGTVIVDEVHHCVATTFTNFLEISCARYK-------IGLSGT 221
Cdd:cd00046  82 IIIATPDMLLNlllrEDRLFLKDLKLIIVDEAHALLIDSRGALILDLAVRKAglknaqvILLSAT 146
HELICc smart00490
helicase superfamily c-terminal domain;
312-393 1.39e-07

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 48.75  E-value: 1.39e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606      312 QTILEALTQRGVTTYEIIGATHLDDRLKIQEDIAKGGPCVLAAAQsIFSEGISLNELSCLIMGSLINNESLIEQLAGRVQ 391
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATD-VAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAG 79


                   ..
gi 137606      392 RI 393
Cdd:smart00490  80 RA 81
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 110-221 3.28e-06

DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins 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: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 47.18  E-value: 3.28e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   110 PGFGKTILALALAY------KFGQKTLVICTNtSIREMWAAEVRKWFGF-----------EPGIIGSGKYNIDPPIVVSN 172
Cdd:cd17919  28 MGLGKTLQAIAFLAyllkegKERGPVLVVCPL-SVLENWEREFEKWTPDlrvvvyhgsqrERAQIRAKEKLDKFDVVLTT 106

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 137606   173 IQTVNKHANNLSKV-FGTVIVDEVHHCV---ATTFTNFLEISCaRYKIGLSGT 221
Cdd:cd17919 107 YETLRRDKASLRKFrWDLVVVDEAHRLKnpkSQLSKALKALRA-KRRLLLTGT 158
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 298-393 3.58e-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: 43.23  E-value: 3.58e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   298 GHKVLIVSDRTELIQTILEALTQRGVTTYEIIGATHLDDRLKIQEDIAKGG--PCVLAAAQSIfSEGISLNELSCLIMGS 375
Cdd:cd18793  27 GEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPdiRVFLLSTKAG-GVGLNLTAANRVILYD 105

                        90
                ....*....|....*...
gi 137606   376 LINNESLIEQLAGRVQRI 393
Cdd:cd18793 106 PWWNPAVEEQAIDRAHRI 123
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 104-221 1.09e-04

DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is 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: 350769 [Multi-domain]  Cd Length: 207  Bit Score: 43.05  E-value: 1.09e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   104 CIINGKPGFGKTILALALAYKF-----GQKTLVICTnTSIREMWAAEVRKWFGFEPGIIGSGKYNI----------DPPI 168
Cdd:cd18011  20 LLLADEVGLGKTIEAGLIIKELllrgdAKRVLILCP-ASLVEQWQDELQDKFGLPFLILDRETAAQlrrlignpfeEFPI 98

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 137606   169 VVSNIQTVnKHANNLSKVF-----GTVIVDEVHHCVATTF------TNFLE--ISCARYKIGLSGT 221
Cdd:cd18011  99 VIVSLDLL-KRSEERRGLLlseewDLVVVDEAHKLRNSGGgketkrYKLGRllAKRARHVLLLTAT 163
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
 104-221 2.73e-04

DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are members 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: 350762 [Multi-domain]  Cd Length: 240  Bit Score: 42.27  E-value: 2.73e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   104 CIINGKPGFGKTILALALAY------KFGQ----KTLVICTNTSIREmWAAEVRKWFGFEPG----IIGSGKYNIDP--- 166
Cdd:cd18004  27 AILADEMGLGKTLQAIALVWtllkqgPYGKptakKALIVCPSSLVGN-WKAEFDKWLGLRRIkvvtADGNAKDVKASldf 105

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 137606   167 -------PIVVSNIQTVNKHANNLSK--VFGTVIVDEVHHC----VATTFTnFLEISCARyKIGLSGT 221
Cdd:cd18004 106 fssastyPVLIISYETLRRHAEKLSKkiSIDLLICDEGHRLknseSKTTKA-LNSLPCRR-RLLLTGT 171
DEXHc_UvsW cd18031
DEXH-box helicase domain of bacteriophage UvsW; Bacteriophage UvsW is part of the WXY system ...
 113-223 8.52e-04

DEXH-box helicase domain of bacteriophage UvsW; Bacteriophage UvsW is part of the WXY system that repairs DNA damage by a process that involves homologous recombination. UvsW 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: 350789 [Multi-domain]  Cd Length: 161  Bit Score: 40.11  E-value: 8.52e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   113 GKTILALALAY----KFGQKTLVICTNTSIremwAAEVR------KWFGFEP---GIIGSGKYNIDPP---IVVSNIQTV 176
Cdd:cd18031  27 GRSLIQALLARyyleNYEGKILIIVPTTAL----TTQMAddfvdyRLFSHAMikkIGGGASKDDKYKNdapVVVGTWQTV 102

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 137606   177 NKHANNLSKVFGTVIVDEVHHCVATTFTNFLE-ISCARYKIGLSGTLK 223
Cdd:cd18031 103 VKQPKEWFSQFGMMMNDECHLATGKSISSIISgLNNCMFKFGLSGSLR 150
DEXHc_ATRX-like cd18007
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
 104-149 1.32e-03

DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They are members 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: 350765 [Multi-domain]  Cd Length: 239  Bit Score: 40.35  E-value: 1.32e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 137606   104 CIINGKPGFGKT------ILALALAYKFGQKTLVICTnTSIREMWAAEVRKW 149
Cdd:cd18007  29 CILAHTMGLGKTlqvitfLHTYLAAAPRRSRPLVLCP-ASTLYNWEDEFKKW 79
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
 104-236 1.39e-03

DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 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: 350763 [Multi-domain]  Cd Length: 245  Bit Score: 40.06  E-value: 1.39e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   104 CIINGKPGFGKTILALALAYKFGQKT--------------------------LVICTNTSIREmWAAEVRKWFGFEPGII 157
Cdd:cd18005  22 GILGDDMGLGKTVQVIAFLAAVLGKTgtrrdrennrprfkkkppassakkpvLIVAPLSVLYN-WKDELDTWGHFEVGVY 100

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   158 GSGKYNIDP---------PIVVSNIQTVNKHANNLSKV-FGTVIVDEVHHC---VATTFTNFLEISCARyKIGLSGTLKR 224
Cdd:cd18005 101 HGSRKDDELegrlkagrlEVVVTTYDTLRRCIDSLNSInWSAVIADEAHRIknpKSKLTQAMKELKCKV-RIGLTGTLLQ 179

                       170       180
                ....*....|....*....|....*...
gi 137606   225 KD----------------GLQVMFKDFF 236
Cdd:cd18005 180 NNmkelwclldwavpgalGSRSQFKKHF 207
DEXHc_RAD54A cd18067
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ...
 98-221 1.49e-03

DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as RAD54L or RAD54, plays a role in homologous recombination related repair of DNA double-strand breaks. RAD54A 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: 350825 [Multi-domain]  Cd Length: 243  Bit Score: 40.15  E-value: 1.49e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606    98 EECDDTCIINGKPGFGKTILALALAYKFGQ----------KTLVICTNTSIREmWAAEVRKWFG--FEPGIIGSGK---- 161
Cdd:cd18067  21 IRGSHGCIMADEMGLGKTLQCITLMWTLLRqspqckpeidKAIVVSPSSLVKN-WANELGKWLGgrLQPLAIDGGSkkei 99

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 137606   162 ------------YNIDPPIVVSNIQTVNKHANNLSKV-FGTVIVDEVHHCVAT---TFTNFLEISCARyKIGLSGT 221
Cdd:cd18067 100 drklvqwasqqgRRVSTPVLIISYETFRLHVEVLQKGeVGLVICDEGHRLKNSdnqTYQALDSLNTQR-RVLLSGT 174
DEXQc_bact_SNF2 cd18013
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ...
 102-221 5.13e-03

DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprise a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. The bacterial SNF2 present in this family are members 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: 350771 [Multi-domain]  Cd Length: 218  Bit Score: 38.10  E-value: 5.13e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 137606   102 DTCIINGKPGFGKTILAL-ALAY----KFGQKTLVICTNTSIREMWAAEVRKWFGFE----PGIIGSGK-----YNIDPP 167
Cdd:cd18013  16 PYCGLFLDMGLGKTVTTLtALSDlqldDFTRRVLVIAPLRVARSTWPDEVEKWNHLRnltvSVAVGTERqrskaANTPAD 95

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 137606   168 IVVSNIQTVNKHANNLSKV--FGTVIVDEvhhcvATTFTNFleiSCARYK------------IGLSGT 221
Cdd:cd18013  96 LYVINRENLKWLVNKSGDPwpFDMVVIDE-----LSSFKSP---RSKRFKalrkvrpvikrlIGLTGT 155
 
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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