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Conserved domains on  [gi|994732|gb|AAC78249|]
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polymerase [Rat leukemia virus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 109-249 1.46e-49

Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


:

Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 169.06  E-value: 1.46e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   109 TWYTDGSSYlvngeqKAGAAVTTEDKVIWASALPVGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAFATAHIHGEIYR 188
Cdd:cd09273   1 TVFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 994732   189 RRGLLtsegKDIKNKTEILALLAALFLPKRLSIIHCPGHQKGHSPEARGNRLADVSAREAA 249
Cdd:cd09273  75 ERGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 586-669 8.56e-37

Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail.


:

Pssm-ID: 436671  Cd Length: 83  Bit Score: 132.26  E-value: 8.56e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     586 HPFQIGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHASHAKAARPEETADHNIApqTWKAQRT-QNPLK 664
Cdd:pfam18697   1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHAVLEDFIP--SWQVQKDrDNPLK 78


                  ....*
gi 994732     665 LRFSR 669
Cdd:pfam18697  79 LRLRR 83
zf-H2C2 super family cl07828
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 275-366 7.37e-28

H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters.


The actual alignment was detected with superfamily member pfam16721:

Pssm-ID: 447530  Cd Length: 96  Bit Score: 107.51  E-value: 7.37e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     275 YTTEDTKLLQKMGAVWCPQLKRWVYTGKTVMPTKMTFELISYLHKLTHLGLKKMKTLLRREEIDTYLLGRDQALREVTES 354
Cdd:pfam16721   5 YTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNITET 84

                          90
                  ....*....|..
gi 994732     355 CRACAQVNPGKA 366
Cdd:pfam16721  85 CKACAQVNASKS 96
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 379-474 8.54e-24

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 95.84  E-value: 8.54e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     379 PGTHWEIDFTEIK-PGMYGHKYLLVFIDTFSGWVEAFPTKHETAKVVTKKLLEEIFPRYG-MPQVLGSDNGPAFVSQVSQ 456
Cdd:pfam00665   1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 994732     457 LVAKLLGIDWKLHCAYRP 474
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
 
Name Accession Description Interval E-value
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 109-249 1.46e-49

Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 169.06  E-value: 1.46e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   109 TWYTDGSSYlvngeqKAGAAVTTEDKVIWASALPVGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAFATAHIHGEIYR 188
Cdd:cd09273   1 TVFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 994732   189 RRGLLtsegKDIKNKTEILALLAALFLPKRLSIIHCPGHQKGHSPEARGNRLADVSAREAA 249
Cdd:cd09273  75 ERGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 586-669 8.56e-37

Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail.


Pssm-ID: 436671  Cd Length: 83  Bit Score: 132.26  E-value: 8.56e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     586 HPFQIGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHASHAKAARPEETADHNIApqTWKAQRT-QNPLK 664
Cdd:pfam18697   1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHAVLEDFIP--SWQVQKDrDNPLK 78


                  ....*
gi 994732     665 LRFSR 669
Cdd:pfam18697  79 LRLRR 83
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 105-249 1.49e-30

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 116.71  E-value: 1.49e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     105 DADHTWYTDGSSylvNGEQKAG--AAVTTEDKVIWASALPVGTSAQRAELIALTQALK-MAEGKRLNVYTDSRYAFATAH 181
Cdd:pfam00075   1 PKAVTVYTDGSC---LGNPGPGgaGAVLYRGHENISAPLPGRTTNNRAELQAVIEALKaLKSPSKVNIYTDSQYVIGGIT 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     182 --IHGEIYRRRGlLTSEGKDIKNKtEILALLAALFLPKRLSIIHCPGHqKGHSpearGNRLADVSAREAA 249
Cdd:pfam00075  78 qwVHGWKKNGWP-TTSEGKPVKNK-DLWQLLKALCKKHQVYWQWVKGH-AGNP----GNEMADRLAKQGA 140
zf-H3C2 pfam16721
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ...
 275-366 7.37e-28

Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers found on Gag-Pol polyproteins from mouse retroviruses. Added to clan to resolve overlaps with zf-H2C2, but neither are true members.


Pssm-ID: 293326  Cd Length: 96  Bit Score: 107.51  E-value: 7.37e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     275 YTTEDTKLLQKMGAVWCPQLKRWVYTGKTVMPTKMTFELISYLHKLTHLGLKKMKTLLRREEIDTYLLGRDQALREVTES 354
Cdd:pfam16721   5 YTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNITET 84

                          90
                  ....*....|..
gi 994732     355 CRACAQVNPGKA 366
Cdd:pfam16721  85 CKACAQVNASKS 96
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 379-474 8.54e-24

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 95.84  E-value: 8.54e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     379 PGTHWEIDFTEIK-PGMYGHKYLLVFIDTFSGWVEAFPTKHETAKVVTKKLLEEIFPRYG-MPQVLGSDNGPAFVSQVSQ 456
Cdd:pfam00665   1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 994732     457 LVAKLLGIDWKLHCAYRP 474
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 377-489 1.24e-14

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 74.93  E-value: 1.24e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732    377 HRPGTHWEIDFTEIKPGMY-GHKYLLVFIDTFSGWVEAFPTKHETAkVVTKKLLEEIFPRYGMP--QVLgSDNGPAFVSQ 453
Cdd:NF033577 125 AHPGELWHIDIKKLGRIPDvGRLYLHTAIDDHSRFAYAELYPDETA-ETAADFLRRAFAEHGIPirRVL-TDNGSEFRSR 202

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 994732    454 VSQLVAKL--LGIDWKLHCAYRPQSSGQVERMNRTIKE 489
Cdd:NF033577 203 AHGFELALaeLGIEHRRTRPYHPQTNGKVERFHRTLKD 240
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
111-249 2.23e-09

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 56.01  E-value: 2.23e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   111 YTDGSSyLVN----GeqkAGAAVTTEDKVIWASA-LPVGTSaQRAELIALTQALKMAE---GKRLNVYTDSRYAF--ATA 180
Cdd:COG0328   6 YTDGAC-RGNpgpgG---WGAVIRYGGEEKELSGgLGDTTN-NRAELTALIAALEALKelgPCEVEIYTDSQYVVnqITG 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 994732   181 HIHGEiyRRRGLltsegKDIKNKtEILALLAALFLPKRLSIIHCPGHQkGHspeaRGNRLADVSAREAA 249
Cdd:COG0328  81 WIHGW--KKNGW-----KPVKNP-DLWQRLDELLARHKVTFEWVKGHA-GH----PGNERADALANKAL 136
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
312-489 3.92e-09

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 58.63  E-value: 3.92e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   312 ELISYLHKLTH-LGLKKMKTLLRREEIdtyLLGRDQALREVTESCRACAQVNPGKAKIGQGVRPRGH--------RPGTH 382
Cdd:COG2801  75 ERIKEIFAESPrYGYRRITAELRREGI---AVNRKRVRRLMRELGLQARRRRKKKYTTYSGHGGPIApnllftatAPNQV 151

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   383 WEIDFTEIKpgMYGHK-YLLVFIDTFS----GWVEAfptKHETAKVVtKKLLEEIFPRYGMPQ--VLGSDNGPAFVSQVS 455
Cdd:COG2801 152 WVTDITYIP--TAEGWlYLAAVIDLFSreivGWSVS---DSMDAELV-VDALEMAIERRGPPKplILHSDNGSQYTSKAY 225

                       170       180       190
                ....*....|....*....|....*....|....
gi 994732   456 QLVAKLLGIDWKLHCAYRPQSSGQVERMNRTIKE 489
Cdd:COG2801 226 QELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 399-489 6.80e-07

ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes several apparently unrelated families of transposases. Members of this family resemble the transposases of ISNCY family elements such as IS1202, ISTde1, ISKpn21, and ISCARN1.


Pssm-ID: 468103 [Multi-domain]  Cd Length: 367  Bit Score: 52.10  E-value: 6.80e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732    399 YLLVFID--TfSGWVEAFPTKHETAK---VVTKKLLEeifpRYGMPQVLGSDNGPAFVSQVSQLVAKL------------ 461
Cdd:NF033594 148 TLLVAIDdaT-GRLMGLRFVESESTFgyfEVTRQYLE----KHGKPVAFYSDKHSVFRVNEEELAGKGdgltqfgralke 222

                         90       100       110
                 ....*....|....*....|....*....|...
gi 994732    462 LGIDWKlhCAYRPQSSGQVERMNRT-----IKE 489
Cdd:NF033594 223 LGIEII--CANSPQAKGRVERANQTlqdrlVKE 253
 
Name Accession Description Interval E-value
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 109-249 1.46e-49

Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 169.06  E-value: 1.46e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   109 TWYTDGSSYlvngeqKAGAAVTTEDKVIWASALPVGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAFATAHIHGEIYR 188
Cdd:cd09273   1 TVFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 994732   189 RRGLLtsegKDIKNKTEILALLAALFLPKRLSIIHCPGHQKGHSPEARGNRLADVSAREAA 249
Cdd:cd09273  75 ERGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 586-669 8.56e-37

Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail.


Pssm-ID: 436671  Cd Length: 83  Bit Score: 132.26  E-value: 8.56e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     586 HPFQIGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHASHAKAARPEETADHNIApqTWKAQRT-QNPLK 664
Cdd:pfam18697   1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHAVLEDFIP--SWQVQKDrDNPLK 78


                  ....*
gi 994732     665 LRFSR 669
Cdd:pfam18697  79 LRLRR 83
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 105-249 1.49e-30

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 116.71  E-value: 1.49e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     105 DADHTWYTDGSSylvNGEQKAG--AAVTTEDKVIWASALPVGTSAQRAELIALTQALK-MAEGKRLNVYTDSRYAFATAH 181
Cdd:pfam00075   1 PKAVTVYTDGSC---LGNPGPGgaGAVLYRGHENISAPLPGRTTNNRAELQAVIEALKaLKSPSKVNIYTDSQYVIGGIT 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     182 --IHGEIYRRRGlLTSEGKDIKNKtEILALLAALFLPKRLSIIHCPGHqKGHSpearGNRLADVSAREAA 249
Cdd:pfam00075  78 qwVHGWKKNGWP-TTSEGKPVKNK-DLWQLLKALCKKHQVYWQWVKGH-AGNP----GNEMADRLAKQGA 140
zf-H3C2 pfam16721
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ...
 275-366 7.37e-28

Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers found on Gag-Pol polyproteins from mouse retroviruses. Added to clan to resolve overlaps with zf-H2C2, but neither are true members.


Pssm-ID: 293326  Cd Length: 96  Bit Score: 107.51  E-value: 7.37e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     275 YTTEDTKLLQKMGAVWCPQLKRWVYTGKTVMPTKMTFELISYLHKLTHLGLKKMKTLLRREEIDTYLLGRDQALREVTES 354
Cdd:pfam16721   5 YTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNITET 84

                          90
                  ....*....|..
gi 994732     355 CRACAQVNPGKA 366
Cdd:pfam16721  85 CKACAQVNASKS 96
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 379-474 8.54e-24

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 95.84  E-value: 8.54e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732     379 PGTHWEIDFTEIK-PGMYGHKYLLVFIDTFSGWVEAFPTKHETAKVVTKKLLEEIFPRYG-MPQVLGSDNGPAFVSQVSQ 456
Cdd:pfam00665   1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 994732     457 LVAKLLGIDWKLHCAYRP 474
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 111-250 4.58e-17

Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos.


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 78.38  E-value: 4.58e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   111 YTDGSSyLVNGEQ--KAGAAVTTEDKVIWASALPVGTSAQ---RAELIALTQALKMA---EGKRLNVYTDSRYAFATAHI 182
Cdd:cd09280   3 YTDGSC-LNNGKPgaRAGIGVYFGPGDPRNVSEPLPGRKQtnnRAELLAVIHALEQApeeGIRKLEIRTDSKYAINCITK 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 994732   183 HGEIYRRRGLLTSEGKDIKNKTEILA-LLAALFLPKRLSIIHCPGHQKGHspearGNRLADVSAREAAM 250
Cdd:cd09280  82 WIPKWKKNGWKTSKGKPVKNQDLIKElDKLLRKRGIKVKFEHVKGHSGDP-----GNEEADRLAREGAD 145
transpos_IS481 NF033577
IS481 family transposase; null
 377-489 1.24e-14

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 74.93  E-value: 1.24e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732    377 HRPGTHWEIDFTEIKPGMY-GHKYLLVFIDTFSGWVEAFPTKHETAkVVTKKLLEEIFPRYGMP--QVLgSDNGPAFVSQ 453
Cdd:NF033577 125 AHPGELWHIDIKKLGRIPDvGRLYLHTAIDDHSRFAYAELYPDETA-ETAADFLRRAFAEHGIPirRVL-TDNGSEFRSR 202

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 994732    454 VSQLVAKL--LGIDWKLHCAYRPQSSGQVERMNRTIKE 489
Cdd:NF033577 203 AHGFELALaeLGIEHRRTRPYHPQTNGKVERFHRTLKD 240
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 111-249 1.82e-12

RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 65.20  E-value: 1.82e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   111 YTDGSSylVNGEQKAG--AAVTTEDKVIWASALPVGTSAQRAELIALTQALKMA-EGKRLNVYTDSRYAF--ATAHIHGe 185
Cdd:cd09278   5 YTDGAC--LGNPGPGGwaAVIRYGDHEKELSGGEPGTTNNRMELTAAIEALEALkEPCPVTIYTDSQYVIngITKWIKG- 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 994732   186 iYRRRGLLTSEGKDIKNKtEILALLAALFLPKRLSIIHCPGHQkGHspeaRGNRLADVSAREAA 249
Cdd:cd09278  82 -WKKNGWKTADGKPVKNR-DLWQELDALLAGHKVTWEWVKGHA-GH----PGNERADRLANKAA 138
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 318-359 3.54e-11

H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters.


Pssm-ID: 430537  Cd Length: 39  Bit Score: 58.11  E-value: 3.54e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 994732     318 HKLTHLGLKKMKTLLRREeidTYLLGRDQALREVTESCRACA 359
Cdd:pfam09337   1 HALTHLGINKLTALLARK---YHWLGIKETVSEVISSCVACQ 39
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 110-246 9.87e-11

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 59.64  E-value: 9.87e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   110 WYTDGSSylVNGEQKAGAAVT---TEDKVIWASALPVGT-SAQRAELIALTQALKMA---EGKRLNVYTDSRYAFATahI 182
Cdd:cd06222   1 INVDGSC--RGNPGPAGIGGVlrdHEGGWLGGFALKIGApTALEAELLALLLALELAldlGYLKVIIESDSKYVVDL--I 76

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 994732   183 HGEIYRRrglltsegkdIKNKTEILALLAALFLPKRLSIIHCPGHqkghspearGNRLADVSAR 246
Cdd:cd06222  77 NSGSFKW----------SPNILLIEDILLLLSRFWSVKISHVPRE---------GNQVADALAK 121
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 111-249 8.28e-10

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 57.23  E-value: 8.28e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   111 YTDGSSYlvngEQKAGAAVTTEDKVIWAS---ALPVGTSAQRAELIALTQALKMA-----EGKRLNVYTDSRYAFATahi 182
Cdd:cd09276   3 YTDGSKL----EGSVGAGFVIYRGGEVISrsyRLGTHASVFDAELEAILEALELAlatarRARKVTIFTDSQSALQA--- 75

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 994732   183 hgeIYRRRglltSEGKDIKNKTEILALLAALFLPKRLSIIHCPGHQkghspEARGNRLADVSAREAA 249
Cdd:cd09276  76 ---LRNPR----RSSGQVILIRILRLLRLLKAKGVKVRLRWVPGHV-----GIEGNEAADRLAKEAA 130
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
111-249 2.23e-09

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 56.01  E-value: 2.23e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   111 YTDGSSyLVN----GeqkAGAAVTTEDKVIWASA-LPVGTSaQRAELIALTQALKMAE---GKRLNVYTDSRYAF--ATA 180
Cdd:COG0328   6 YTDGAC-RGNpgpgG---WGAVIRYGGEEKELSGgLGDTTN-NRAELTALIAALEALKelgPCEVEIYTDSQYVVnqITG 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 994732   181 HIHGEiyRRRGLltsegKDIKNKtEILALLAALFLPKRLSIIHCPGHQkGHspeaRGNRLADVSAREAA 249
Cdd:COG0328  81 WIHGW--KKNGW-----KPVKNP-DLWQRLDELLARHKVTFEWVKGHA-GH----PGNERADALANKAL 136
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
312-489 3.92e-09

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 58.63  E-value: 3.92e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   312 ELISYLHKLTH-LGLKKMKTLLRREEIdtyLLGRDQALREVTESCRACAQVNPGKAKIGQGVRPRGH--------RPGTH 382
Cdd:COG2801  75 ERIKEIFAESPrYGYRRITAELRREGI---AVNRKRVRRLMRELGLQARRRRKKKYTTYSGHGGPIApnllftatAPNQV 151

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   383 WEIDFTEIKpgMYGHK-YLLVFIDTFS----GWVEAfptKHETAKVVtKKLLEEIFPRYGMPQ--VLGSDNGPAFVSQVS 455
Cdd:COG2801 152 WVTDITYIP--TAEGWlYLAAVIDLFSreivGWSVS---DSMDAELV-VDALEMAIERRGPPKplILHSDNGSQYTSKAY 225

                       170       180       190
                ....*....|....*....|....*....|....
gi 994732   456 QLVAKLLGIDWKLHCAYRPQSSGQVERMNRTIKE 489
Cdd:COG2801 226 QELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 399-489 6.80e-07

ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes several apparently unrelated families of transposases. Members of this family resemble the transposases of ISNCY family elements such as IS1202, ISTde1, ISKpn21, and ISCARN1.


Pssm-ID: 468103 [Multi-domain]  Cd Length: 367  Bit Score: 52.10  E-value: 6.80e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732    399 YLLVFID--TfSGWVEAFPTKHETAK---VVTKKLLEeifpRYGMPQVLGSDNGPAFVSQVSQLVAKL------------ 461
Cdd:NF033594 148 TLLVAIDdaT-GRLMGLRFVESESTFgyfEVTRQYLE----KHGKPVAFYSDKHSVFRVNEEELAGKGdgltqfgralke 222

                         90       100       110
                 ....*....|....*....|....*....|...
gi 994732    462 LGIDWKlhCAYRPQSSGQVERMNRT-----IKE 489
Cdd:NF033594 223 LGIEII--CANSPQAKGRVERANQTlqdrlVKE 253
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
378-493 7.71e-05

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 45.26  E-value: 7.71e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 994732   378 RPGtHWEIDfteIKPGMYGHKYLLVFIDTFSGWVEAFPTKHETAKVVTKKL--LEEIFPRYgMPQVLGSDNGPAFVSqvS 455
Cdd:COG2826 171 EPG-HWEGD---LIIGKRGKSALLTLVERKSRFVILLKLPDKTAESVADALirLLRKLPAF-LRKSITTDNGKEFAD--H 243

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 994732   456 QLVAKLLGIDwklhcAY--RPQSS---GQVERMNRTIKETLSK 493
Cdd:COG2826 244 KEIEAALGIK-----VYfaDPYSPwqrGTNENTNGLLRQYFPK 281
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 306-363 5.51e-04

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 38.38  E-value: 5.51e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 994732     306 PTKMTFELISYLHKLT-HLGLKKMKTLLRReeiDTYLLGRDQALREVTESCRACAQVNP 363
Cdd:pfam17921   2 PKSLRKEILKEAHDSGgHLGIEKTLARLRR---RYWWPGMRKDVKKYVKSCETCQRRKP 57
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 111-174 9.29e-04

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 39.76  E-value: 9.29e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 994732   111 YTDGSSYLVNGEQKAGAAVTTEDKVIWASALPVGTSAQ--RAELIALTQALKMAEG---KRLNVYTDSR 174
Cdd:cd09279   4 YFDGASRGNPGPAGAGVVIYSPGGEVLELSERLGFPATnnEAEYEALIAGLELALElgaEKLEIYGDSQ 72
 
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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