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Conserved domains on  [gi|1277955550|gb|ATV93713|]
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polyprotein, partial [Hepacivirus hominis]

Protein Classification

DEAD/DEAH box-containing ATP-dependent helicase( domain architecture ID 1565721)

DEAD/DEAH box-containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA, similar to mitochondrial ATP-dependent RNA helicase MRH4

CATH:  1.10.820.10
EC:  3.6.4.13|3.6.4.12
Gene Ontology:  GO:0005524|GO:0016887|GO:0004386
PubMed:  21779027|20225155

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 148-269 2.91e-44

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd18806:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 145  Bit Score: 150.10  E-value: 2.91e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277955550 148 IEEVALTNDGEIPFYGKALPLamIKGGRHLVFCHSKKKCDELASKLRGMGINAVAFYRGLDVSV---IPTSGDVVVCATD 224
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWIT--IYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1277955550 225 ALMTGFTGDFDSVIDCNVAVEQYVDFSLDPTFsIETRTTPQDAVS 269
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGDFRV-ILTGPVPQTAAS 122
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 10-152 1.71e-41

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 cd17931:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 151  Bit Score: 143.07  E-value: 1.71e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277955550  10 QVGYLHAPTGSGKSTKVPAAYVAQGYS----VLVLNPSVAATLGFGTYMSKAygiDPNIRTGTRTITTGAK--LTYSTYG 83
Cdd:cd17931     2 QLTVLDLHPGAGKTTRVLPQIIREAIKkrlrTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGNeiVDYMCHG 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1277955550  84 KFLaDGGCSGGA---YDVIICDECHAQDATSILGIGTVLDQAETaGVRLTVLATATPPGSITVPH---PNIEEVA 152
Cdd:cd17931    79 TFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
 
Name Accession Description Interval E-value
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 148-269 2.91e-44

C-terminal helicase domain of viral helicase; Viral helicases in this family here 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: 350193 [Multi-domain]  Cd Length: 145  Bit Score: 150.10  E-value: 2.91e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277955550 148 IEEVALTNDGEIPFYGKALPLamIKGGRHLVFCHSKKKCDELASKLRGMGINAVAFYRGLDVSV---IPTSGDVVVCATD 224
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWIT--IYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1277955550 225 ALMTGFTGDFDSVIDCNVAVEQYVDFSLDPTFsIETRTTPQDAVS 269
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGDFRV-ILTGPVPQTAAS 122
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 10-152 1.71e-41

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 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: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 143.07  E-value: 1.71e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277955550  10 QVGYLHAPTGSGKSTKVPAAYVAQGYS----VLVLNPSVAATLGFGTYMSKAygiDPNIRTGTRTITTGAK--LTYSTYG 83
Cdd:cd17931     2 QLTVLDLHPGAGKTTRVLPQIIREAIKkrlrTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGNeiVDYMCHG 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1277955550  84 KFLaDGGCSGGA---YDVIICDECHAQDATSILGIGTVLDQAETaGVRLTVLATATPPGSITVPH---PNIEEVA 152
Cdd:cd17931    79 TFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
DEXDc smart00487
DEAD-like helicases superfamily;
3-141 5.48e-13

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 67.13  E-value: 5.48e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277955550    3 PAVPESYQVGYLHAPTGSGKSTKVPAAYVAQGYS-----VLVLNPSVAATLGFGTYMSKA-----------YGIDPNIRT 66
Cdd:smart00487  18 EALLSGLRDVILAAPTGSGKTLAALLPALEALKRgkggrVLVLVPTRELAEQWAEELKKLgpslglkvvglYGGDSKREQ 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277955550   67 GTRTITTGAKLTYSTYGKF---LADGGCSGGAYDVIICDECH----AQDATSILGIGTVLDQAetagvRLTVLATATPPG 139
Cdd:smart00487  98 LRKLESGKTDILVTTPGRLldlLENDKLSLSNVDLVILDEAHrlldGGFGDQLEKLLKLLPKN-----VQLLLLSATPPE 172


                   ..
gi 1277955550  140 SI 141
Cdd:smart00487 173 EI 174
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
96-147 6.47e-05

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 42.71  E-value: 6.47e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1277955550  96 YDVIICDECHAQDATSILGIG---TVLDQAETAgvrlTVLATATPPGSiTVPHPN 147
Cdd:pfam07652  94 YEVIIMDEAHFTDPASIAARGyisTLVELGEAA----AIFMTATPPGT-SDPFPE 143
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
168-204 2.09e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 39.75  E-value: 2.09e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1277955550 168 LAMIKGGRHLVFCHSKKKCDELASKLRGMGINAVAFY 204
Cdd:COG0513   236 LRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALH 272
 
Name Accession Description Interval E-value
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 148-269 2.91e-44

C-terminal helicase domain of viral helicase; Viral helicases in this family here 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: 350193 [Multi-domain]  Cd Length: 145  Bit Score: 150.10  E-value: 2.91e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277955550 148 IEEVALTNDGEIPFYGKALPLamIKGGRHLVFCHSKKKCDELASKLRGMGINAVAFYRGLDVSV---IPTSGDVVVCATD 224
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWIT--IYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1277955550 225 ALMTGFTGDFDSVIDCNVAVEQYVDFSLDPTFsIETRTTPQDAVS 269
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGDFRV-ILTGPVPQTAAS 122
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 10-152 1.71e-41

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 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: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 143.07  E-value: 1.71e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277955550  10 QVGYLHAPTGSGKSTKVPAAYVAQGYS----VLVLNPSVAATLGFGTYMSKAygiDPNIRTGTRTITTGAK--LTYSTYG 83
Cdd:cd17931     2 QLTVLDLHPGAGKTTRVLPQIIREAIKkrlrTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGNeiVDYMCHG 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1277955550  84 KFLaDGGCSGGA---YDVIICDECHAQDATSILGIGTVLDQAETaGVRLTVLATATPPGSITVPH---PNIEEVA 152
Cdd:cd17931    79 TFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
DEXDc smart00487
DEAD-like helicases superfamily;
3-141 5.48e-13

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 67.13  E-value: 5.48e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277955550    3 PAVPESYQVGYLHAPTGSGKSTKVPAAYVAQGYS-----VLVLNPSVAATLGFGTYMSKA-----------YGIDPNIRT 66
Cdd:smart00487  18 EALLSGLRDVILAAPTGSGKTLAALLPALEALKRgkggrVLVLVPTRELAEQWAEELKKLgpslglkvvglYGGDSKREQ 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277955550   67 GTRTITTGAKLTYSTYGKF---LADGGCSGGAYDVIICDECH----AQDATSILGIGTVLDQAetagvRLTVLATATPPG 139
Cdd:smart00487  98 LRKLESGKTDILVTTPGRLldlLENDKLSLSNVDLVILDEAHrlldGGFGDQLEKLLKLLPKN-----VQLLLLSATPPE 172


                   ..
gi 1277955550  140 SI 141
Cdd:smart00487 173 EI 174
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
96-147 6.47e-05

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 42.71  E-value: 6.47e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1277955550  96 YDVIICDECHAQDATSILGIG---TVLDQAETAgvrlTVLATATPPGSiTVPHPN 147
Cdd:pfam07652  94 YEVIIMDEAHFTDPASIAARGyisTLVELGEAA----AIFMTATPPGT-SDPFPE 143
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 168-208 8.38e-05

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 42.11  E-value: 8.38e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1277955550 168 LAMIKGGRHLVFCHSKKKCDELASKLRGMGINAVAFYRGLD 208
Cdd:cd18787    22 LEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLS 62
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 172-225 1.33e-04

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. 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: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 41.43  E-value: 1.33e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1277955550 172 KGGRHLVFCHSKKKCDELASKLRGMGINAVAFYRGL----DVSVIP---TSGDVVVCATDA 225
Cdd:cd18794    29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRkwlRDKIQVIVATVA 89
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
168-204 2.09e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 39.75  E-value: 2.09e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1277955550 168 LAMIKGGRHLVFCHSKKKCDELASKLRGMGINAVAFY 204
Cdd:COG0513   236 LRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALH 272
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 14-129 3.18e-03

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: 38.31  E-value: 3.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277955550  14 LHAPTGSGKST---KVPAAYVAQGYSVLVLNPSVAATLGfgtyMSKAYGIDpnirtgtrtITTGAKLTYSTYGKFLADGG 90
Cdd:pfam13604  23 LVGPAGTGKTTalkALREAWEAAGYRVIGLAPTGRAAKV----LGEELGIP---------ADTIAKLLHRLGGRAGLDPG 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1277955550  91 csggayDVIICDEchaqdAT--SILGIGTVLDQAETAGVRL 129
Cdd:pfam13604  90 ------TLLIVDE-----AGmvGTRQMARLLKLAEDAGARV 119
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
 8-47 4.52e-03

DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA 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: 350687 [Multi-domain]  Cd Length: 178  Bit Score: 37.57  E-value: 4.52e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1277955550   8 SYQVGYLHAPTGSGKS---TKVPAAYVAQGYSVLVLNPSVAAT 47
Cdd:cd17929    14 GFKTFLLHGVTGSGKTevyIELIEKVLAKGKQVLVLVPEISLT 56
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
177-226 6.13e-03

Superfamily II DNA helicase RecQ [Replication, recombination and repair];


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 38.58  E-value: 6.13e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1277955550 177 LVFCHSKKKCDELASKLRGMGINAVAFYRGLDVSV--------IptSGDV-VVCATDAL 226
Cdd:COG0514   234 IVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 177-198 6.75e-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: 36.76  E-value: 6.75e-03
                          10        20
                  ....*....|....*....|..
gi 1277955550 177 LVFCHSKKKCDELASKLRGMGI 198
Cdd:cd18795    47 LVFCSSRKECEKTAKDLAGIAF 68
 
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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