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Conserved domains on  [gi|805821995|ref|XP_012151024|]
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PREDICTED: LOW QUALITY PROTEIN: uncharacterized protein LOC105663869 [Megachile rotundata]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 253-434 2.73e-80

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


:

Pssm-ID: 238825  Cd Length: 177  Bit Score: 262.15  E-value: 2.73e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  253 GIIRESNSPFNSPLWIVPKKpdasgKKKWRLVIDYRKLNERTKQDSYPLPLIDEILDKLGNAKYFSAFDLASGFHQIGMR 332
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKK-----DGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLA 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  333 EKDKSKTAFSTTDGHYEYNRMPFGLKNAPATFQRMMNNGLRGLIGNTCFVYMDDIIVFGTTLEEHNRNLQILLERLSKCG 412
Cdd:cd01647    76 EESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAG 155

                         170       180
                  ....*....|....*....|..
gi 805821995  413 LKLQPDKCEYLKPELSYLGHII 434
Cdd:cd01647   156 LKLNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 528-646 1.04e-63

Ty3/Gypsy 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 eukaryotes. 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. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


:

Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 212.35  E-value: 1.04e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  528 ILTTDASNEAIGAVLSQGII-GQDRPIAYASRTLNKAERNYSTTEKELLAIVW*IKHFHQYLYGRKFKIITDHKPLTWVM 606
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 805821995  607 NVKDPTSRLMRWRMKLEEYDYEIIYKKGKSNANADALSRI 646
Cdd:cd09274    81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 785-838 1.58e-15

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: 72.66  E-value: 1.58e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 805821995   785 QEEKERLIKSVHEStiGGHQGVERTLQRLRTMYNWSGITKDVENFIKKCEVCQR 838
Cdd:pfam17921    3 KSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQR 54
transpos_IS481 super family cl41329
IS481 family transposase; null
 835-965 3.35e-15

IS481 family transposase; null


The actual alignment was detected with superfamily member NF033577:

Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 78.40  E-value: 3.35e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  835 VCQRERLKYTANRPPPGTPDVP---SKPNDKVSLDT--IGPLPsNRKYRYILVIQDYLTRYVQLAPLKTKTpKEVAENFW 909
Cdd:NF033577  100 ILRRHGLSRLRALDRKTGKVKRyerAHPGELWHIDIkkLGRIP-DVGRLYLHTAIDDHSRFAYAELYPDET-AETAADFL 177

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  910 TYYCQIFGV-LKEILTDNGLEFRGE---FQEFVEEkLRIKHTTTAVYHPQSNGKNERTHK 965
Cdd:NF033577  178 RRAFAEHGIpIRRVLTDNGSEFRSRahgFELALAE-LGIEHRRTRPYHPQTNGKVERFHR 236
Baculo_F super family cl13666
Baculovirus F protein; This protein is found in a variety of baculoviruses. It is known as the ...
 1003-1410 3.33e-14

Baculovirus F protein; This protein is found in a variety of baculoviruses. It is known as the F protein. Matches to this family are additionally found in some presumed transposons.


The actual alignment was detected with superfamily member pfam12259:

Pssm-ID: 371998  Cd Length: 606  Bit Score: 78.08  E-value: 3.33e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1003 IDREEII-ITPIDTKKSIYLEHIKEAQLYHDTWKVTVGIEYRHLQDEIRLLVLHTNQLAKR--CNEIDPCLSKQriILQQ 1079
Cdd:pfam12259   17 IDIDDYItVTPLPHTSGLYYEPINKLQFVVNTWSFVIEIDHGVLFDRLNELKNLTNKLLQRikSKNLANCTSKG--IIQR 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1080 ERNKRLN------------LELKSLRKFMGHI----------QRRGL-LNAVGEGMKILFGTMTASDAEyynnELDKL-- 1134
Cdd:pfam12259   95 ELNYIINtkivnlvethnsIDFKLPHKGEHPKlrlpkrvrkrRKRGLaLNFVGRVDKYLFGVMDDNDAH----LLHELan 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1135 REDNIKIAHLVRNQTTILLHKIQDNLgTYKFIQQQTDK---LNINFVLLQnatkeeifnleidETLADYIFLYhdvsmtm 1211
Cdd:pfam12259  171 TENSLNYRVKQLTDELIKLAEYVEHK-RHCIERQEDDSceyLERKLNLLK-------------DQLNEIESLY------- 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1212 QKLQEAIVDGKHGIVHPTILPPSELFEAMRNTT----KFEKFPVPLKEEY-YGILLDTSEISITLTNE-KLIYNLRIPIL 1285
Cdd:pfam12259  230 NKLDRAVDDALSNKLSSLIITPERLLDEMKNVDshlpDKETWPVPLTLDNmHTLINNVINCHVFLTPDrKLMFIIEVPLV 309

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1286 EEDVYTLYRPIALPiysYIQGYSVYNVefeyILlnkPHTEFIPINE--------EEKAQFKTVVNQYVIQRKHPNYLTSS 1357
Cdd:pfam12259  310 DKTKFDLYKVVPIP---FCNKNRKCAF----IV---PDSKYIGFSSnrrnyvrlDDTSTCKQTNDNTLCYKSMTSYTSNY 379

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 805821995  1358 SNACLIELLLKKN------QECSQKYIKLQGILFIQLSTDQDWIVIAPKKEQVHIICEN 1410
Cdd:pfam12259  380 ASLCDIKIFLNNRkdidvsKDCDVRAGKFDSEIFYPINNYNRWLYVLQKDTDLNFDCGT 438
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 253-434 2.73e-80

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 262.15  E-value: 2.73e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  253 GIIRESNSPFNSPLWIVPKKpdasgKKKWRLVIDYRKLNERTKQDSYPLPLIDEILDKLGNAKYFSAFDLASGFHQIGMR 332
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKK-----DGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLA 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  333 EKDKSKTAFSTTDGHYEYNRMPFGLKNAPATFQRMMNNGLRGLIGNTCFVYMDDIIVFGTTLEEHNRNLQILLERLSKCG 412
Cdd:cd01647    76 EESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAG 155

                         170       180
                  ....*....|....*....|..
gi 805821995  413 LKLQPDKCEYLKPELSYLGHII 434
Cdd:cd01647   156 LKLNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 528-646 1.04e-63

Ty3/Gypsy 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 eukaryotes. 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. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 212.35  E-value: 1.04e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  528 ILTTDASNEAIGAVLSQGII-GQDRPIAYASRTLNKAERNYSTTEKELLAIVW*IKHFHQYLYGRKFKIITDHKPLTWVM 606
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 805821995  607 NVKDPTSRLMRWRMKLEEYDYEIIYKKGKSNANADALSRI 646
Cdd:cd09274    81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 522-624 2.21e-51

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 176.55  E-value: 2.21e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995   522 DWNKTFILTTDASNEAIGAVLSQ-GIIGQDRPIAYASRTLNKAERNYSTTEKELLAIVW*IKHFHQYLYGRKFKIITDHK 600
Cdd:pfam17917    1 DPSKPFILETDASDYGIGAVLSQkDEDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHK 80

                           90       100
                   ....*....|....*....|....
gi 805821995   601 PLTWVMNVKDPTSRLMRWRMKLEE 624
Cdd:pfam17917   81 PLKYLFTPKELNGRLARWALFLQE 104
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 269-434 7.16e-44

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 158.23  E-value: 7.16e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995   269 VPKKpdasGKKKWRLV----IDYRKLNERTKQ-------DSYPLPLIDEILDKLGNAKYFSAFDLASGFHQIGMREKDKS 337
Cdd:pfam00078    1 IPKK----GKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995   338 KTAFST-----------TDGHYEYNRMPFGLKNAPATFQRMMN---NGLRGLIGNTCFVYMDDIIVFGTTLEEHNRNLQI 403
Cdd:pfam00078   77 LTAFTTppininwngelSGGRYEWKGLPQGLVLSPALFQLFMNellRPLRKRAGLTLVRYADDILIFSKSEEEHQEALEE 156

                          170       180       190
                   ....*....|....*....|....*....|...
gi 805821995   404 LLERLSKCGLKLQPDKCE--YLKPELSYLGHII 434
Cdd:pfam00078  157 VLEWLKESGLKINPEKTQffLKSKEVKYLGVTL 189
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 785-838 1.58e-15

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: 72.66  E-value: 1.58e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 805821995   785 QEEKERLIKSVHEStiGGHQGVERTLQRLRTMYNWSGITKDVENFIKKCEVCQR 838
Cdd:pfam17921    3 KSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQR 54
transpos_IS481 NF033577
IS481 family transposase; null
 835-965 3.35e-15

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 78.40  E-value: 3.35e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  835 VCQRERLKYTANRPPPGTPDVP---SKPNDKVSLDT--IGPLPsNRKYRYILVIQDYLTRYVQLAPLKTKTpKEVAENFW 909
Cdd:NF033577  100 ILRRHGLSRLRALDRKTGKVKRyerAHPGELWHIDIkkLGRIP-DVGRLYLHTAIDDHSRFAYAELYPDET-AETAADFL 177

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  910 TYYCQIFGV-LKEILTDNGLEFRGE---FQEFVEEkLRIKHTTTAVYHPQSNGKNERTHK 965
Cdd:NF033577  178 RRAFAEHGIpIRRVLTDNGSEFRSRahgFELALAE-LGIEHRRTRPYHPQTNGKVERFHR 236
Baculo_F pfam12259
Baculovirus F protein; This protein is found in a variety of baculoviruses. It is known as the ...
 1003-1410 3.33e-14

Baculovirus F protein; This protein is found in a variety of baculoviruses. It is known as the F protein. Matches to this family are additionally found in some presumed transposons.


Pssm-ID: 371998  Cd Length: 606  Bit Score: 78.08  E-value: 3.33e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1003 IDREEII-ITPIDTKKSIYLEHIKEAQLYHDTWKVTVGIEYRHLQDEIRLLVLHTNQLAKR--CNEIDPCLSKQriILQQ 1079
Cdd:pfam12259   17 IDIDDYItVTPLPHTSGLYYEPINKLQFVVNTWSFVIEIDHGVLFDRLNELKNLTNKLLQRikSKNLANCTSKG--IIQR 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1080 ERNKRLN------------LELKSLRKFMGHI----------QRRGL-LNAVGEGMKILFGTMTASDAEyynnELDKL-- 1134
Cdd:pfam12259   95 ELNYIINtkivnlvethnsIDFKLPHKGEHPKlrlpkrvrkrRKRGLaLNFVGRVDKYLFGVMDDNDAH----LLHELan 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1135 REDNIKIAHLVRNQTTILLHKIQDNLgTYKFIQQQTDK---LNINFVLLQnatkeeifnleidETLADYIFLYhdvsmtm 1211
Cdd:pfam12259  171 TENSLNYRVKQLTDELIKLAEYVEHK-RHCIERQEDDSceyLERKLNLLK-------------DQLNEIESLY------- 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1212 QKLQEAIVDGKHGIVHPTILPPSELFEAMRNTT----KFEKFPVPLKEEY-YGILLDTSEISITLTNE-KLIYNLRIPIL 1285
Cdd:pfam12259  230 NKLDRAVDDALSNKLSSLIITPERLLDEMKNVDshlpDKETWPVPLTLDNmHTLINNVINCHVFLTPDrKLMFIIEVPLV 309

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1286 EEDVYTLYRPIALPiysYIQGYSVYNVefeyILlnkPHTEFIPINE--------EEKAQFKTVVNQYVIQRKHPNYLTSS 1357
Cdd:pfam12259  310 DKTKFDLYKVVPIP---FCNKNRKCAF----IV---PDSKYIGFSSnrrnyvrlDDTSTCKQTNDNTLCYKSMTSYTSNY 379

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 805821995  1358 SNACLIELLLKKN------QECSQKYIKLQGILFIQLSTDQDWIVIAPKKEQVHIICEN 1410
Cdd:pfam12259  380 ASLCDIKIFLNNRkdidvsKDCDVRAGKFDSEIFYPINNYNRWLYVLQKDTDLNFDCGT 438
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 859-954 1.50e-08

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: 53.86  E-value: 1.50e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995   859 PNDKVSLD-TIGPLPSNRKYRYILVIQDYLTRYVQLAPLKTKTPKEVAENFWTYYCQIFG-VLKEILTDNGLEFRG-EFQ 935
Cdd:pfam00665    1 PNQLWQGDfTYIRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSkAFR 80

                           90
                   ....*....|....*....
gi 805821995   936 EFVEEkLRIKHTTTAVYHP 954
Cdd:pfam00665   81 EFLKD-LGIKPSFSRPGNP 98
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
866-965 1.47e-06

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 52.58  E-value: 1.47e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  866 DTIgpLPSNRKyRYILVIQDYLTRYVQLAPLKTKTPKEVAENF--WTYYCQIFgVLKEILTDNGLEFRGEFQefVEEKLR 943
Cdd:COG2826   178 DLI--IGKRGK-SALLTLVERKSRFVILLKLPDKTAESVADALirLLRKLPAF-LRKSITTDNGKEFADHKE--IEAALG 251

                          90       100
                  ....*....|....*....|..
gi 805821995  944 IKHTTTAVYHPQSNGKNERTHK 965
Cdd:COG2826   252 IKVYFADPYSPWQRGTNENTNG 273
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 253-434 2.73e-80

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 262.15  E-value: 2.73e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  253 GIIRESNSPFNSPLWIVPKKpdasgKKKWRLVIDYRKLNERTKQDSYPLPLIDEILDKLGNAKYFSAFDLASGFHQIGMR 332
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKK-----DGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLA 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  333 EKDKSKTAFSTTDGHYEYNRMPFGLKNAPATFQRMMNNGLRGLIGNTCFVYMDDIIVFGTTLEEHNRNLQILLERLSKCG 412
Cdd:cd01647    76 EESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAG 155

                         170       180
                  ....*....|....*....|..
gi 805821995  413 LKLQPDKCEYLKPELSYLGHII 434
Cdd:cd01647   156 LKLNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 528-646 1.04e-63

Ty3/Gypsy 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 eukaryotes. 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. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 212.35  E-value: 1.04e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  528 ILTTDASNEAIGAVLSQGII-GQDRPIAYASRTLNKAERNYSTTEKELLAIVW*IKHFHQYLYGRKFKIITDHKPLTWVM 606
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 805821995  607 NVKDPTSRLMRWRMKLEEYDYEIIYKKGKSNANADALSRI 646
Cdd:cd09274    81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 522-624 2.21e-51

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 176.55  E-value: 2.21e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995   522 DWNKTFILTTDASNEAIGAVLSQ-GIIGQDRPIAYASRTLNKAERNYSTTEKELLAIVW*IKHFHQYLYGRKFKIITDHK 600
Cdd:pfam17917    1 DPSKPFILETDASDYGIGAVLSQkDEDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHK 80

                           90       100
                   ....*....|....*....|....
gi 805821995   601 PLTWVMNVKDPTSRLMRWRMKLEE 624
Cdd:pfam17917   81 PLKYLFTPKELNGRLARWALFLQE 104
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
497-595 4.21e-48

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 166.91  E-value: 4.21e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995   497 WENEEQNAFDTLRNALCEEPILIYPDWNKTFILTTDASNEAIGAVLSQGII-GQDRPIAYASRTLNKAERNYSTTEKELL 575
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDdGGERPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 805821995   576 AIVW*IKHFHQYLYGRKFKI 595
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 269-434 7.16e-44

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 158.23  E-value: 7.16e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995   269 VPKKpdasGKKKWRLV----IDYRKLNERTKQ-------DSYPLPLIDEILDKLGNAKYFSAFDLASGFHQIGMREKDKS 337
Cdd:pfam00078    1 IPKK----GKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995   338 KTAFST-----------TDGHYEYNRMPFGLKNAPATFQRMMN---NGLRGLIGNTCFVYMDDIIVFGTTLEEHNRNLQI 403
Cdd:pfam00078   77 LTAFTTppininwngelSGGRYEWKGLPQGLVLSPALFQLFMNellRPLRKRAGLTLVRYADDILIFSKSEEEHQEALEE 156

                          170       180       190
                   ....*....|....*....|....*....|...
gi 805821995   404 LLERLSKCGLKLQPDKCE--YLKPELSYLGHII 434
Cdd:pfam00078  157 VLEWLKESGLKINPEKTQffLKSKEVKYLGVTL 189
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 226-434 7.69e-37

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 139.02  E-value: 7.69e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  226 PIHTRQYRFPPIHQEEIANQVKKMLKEGIIRESNSPFNSPLWIVPKkpdaSGKKKWRLVIDYRKLNERTKQDSYPLPLID 305
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKK----PGGNDYRMVQDLRLVNQAVLPIHPAVPNPY 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  306 EILDKLGNA-KYFSAFDLASGFHQIGMREKDKSKTAFSTTDGHYEYNRMPFGLKNAPATFqrmmNNGLRGLI-------- 376
Cdd:cd03715    77 TLLSLLPPKhQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLF----HEALARDLapfplehe 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 805821995  377 GNTCFVYMDDIIVFGTTLEEHNRNLQILLERLSKCGLKLQPDKCEYLKPELSYLGHII 434
Cdd:cd03715   153 GTILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 226-434 2.02e-25

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 106.21  E-value: 2.02e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  226 PIHTRQYRFPPIHQEEIANQVKKMLKEGIIRESNSPFNSPLWIVPKKpdaSGkkKWRLVIDYRKLNERTK-----QDSYP 300
Cdd:cd01645     1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKK---SG--KWRLLHDLRAVNAQTQdmgalQPGLP 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  301 LPLIdeildkLGNAKYFSAFDLASGFHQIGMREKDKSKTAFS-------TTDGHYEYNRMPFGLKNAPATFQRMMNNGLR 373
Cdd:cd01645    76 HPAA------LPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTvpsinnkGPAKRYQWKVLPQGMKNSPTICQSFVAQALE 149

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 805821995  374 GLIG---NTCFV-YMDDIIVFGTTLEEHNRNLQILLERLSKCGLKLQPDKCEyLKPELSYLGHII 434
Cdd:cd01645   150 PFRKqypDIVIYhYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQ-KEPPFQYLGYEL 213
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 785-838 1.58e-15

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: 72.66  E-value: 1.58e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 805821995   785 QEEKERLIKSVHEStiGGHQGVERTLQRLRTMYNWSGITKDVENFIKKCEVCQR 838
Cdd:pfam17921    3 KSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQR 54
transpos_IS481 NF033577
IS481 family transposase; null
 835-965 3.35e-15

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 78.40  E-value: 3.35e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  835 VCQRERLKYTANRPPPGTPDVP---SKPNDKVSLDT--IGPLPsNRKYRYILVIQDYLTRYVQLAPLKTKTpKEVAENFW 909
Cdd:NF033577  100 ILRRHGLSRLRALDRKTGKVKRyerAHPGELWHIDIkkLGRIP-DVGRLYLHTAIDDHSRFAYAELYPDET-AETAADFL 177

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  910 TYYCQIFGV-LKEILTDNGLEFRGE---FQEFVEEkLRIKHTTTAVYHPQSNGKNERTHK 965
Cdd:NF033577  178 RRAFAEHGIpIRRVLTDNGSEFRSRahgFELALAE-LGIEHRRTRPYHPQTNGKVERFHR 236
Baculo_F pfam12259
Baculovirus F protein; This protein is found in a variety of baculoviruses. It is known as the ...
 1003-1410 3.33e-14

Baculovirus F protein; This protein is found in a variety of baculoviruses. It is known as the F protein. Matches to this family are additionally found in some presumed transposons.


Pssm-ID: 371998  Cd Length: 606  Bit Score: 78.08  E-value: 3.33e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1003 IDREEII-ITPIDTKKSIYLEHIKEAQLYHDTWKVTVGIEYRHLQDEIRLLVLHTNQLAKR--CNEIDPCLSKQriILQQ 1079
Cdd:pfam12259   17 IDIDDYItVTPLPHTSGLYYEPINKLQFVVNTWSFVIEIDHGVLFDRLNELKNLTNKLLQRikSKNLANCTSKG--IIQR 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1080 ERNKRLN------------LELKSLRKFMGHI----------QRRGL-LNAVGEGMKILFGTMTASDAEyynnELDKL-- 1134
Cdd:pfam12259   95 ELNYIINtkivnlvethnsIDFKLPHKGEHPKlrlpkrvrkrRKRGLaLNFVGRVDKYLFGVMDDNDAH----LLHELan 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1135 REDNIKIAHLVRNQTTILLHKIQDNLgTYKFIQQQTDK---LNINFVLLQnatkeeifnleidETLADYIFLYhdvsmtm 1211
Cdd:pfam12259  171 TENSLNYRVKQLTDELIKLAEYVEHK-RHCIERQEDDSceyLERKLNLLK-------------DQLNEIESLY------- 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1212 QKLQEAIVDGKHGIVHPTILPPSELFEAMRNTT----KFEKFPVPLKEEY-YGILLDTSEISITLTNE-KLIYNLRIPIL 1285
Cdd:pfam12259  230 NKLDRAVDDALSNKLSSLIITPERLLDEMKNVDshlpDKETWPVPLTLDNmHTLINNVINCHVFLTPDrKLMFIIEVPLV 309

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1286 EEDVYTLYRPIALPiysYIQGYSVYNVefeyILlnkPHTEFIPINE--------EEKAQFKTVVNQYVIQRKHPNYLTSS 1357
Cdd:pfam12259  310 DKTKFDLYKVVPIP---FCNKNRKCAF----IV---PDSKYIGFSSnrrnyvrlDDTSTCKQTNDNTLCYKSMTSYTSNY 379

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 805821995  1358 SNACLIELLLKKN------QECSQKYIKLQGILFIQLSTDQDWIVIAPKKEQVHIICEN 1410
Cdd:pfam12259  380 ASLCDIKIFLNNRkdidvsKDCDVRAGKFDSEIFYPINNYNRWLYVLQKDTDLNFDCGT 438
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 320-431 4.84e-09

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.


Pssm-ID: 239684 [Multi-domain]  Cd Length: 119  Bit Score: 56.20  E-value: 4.84e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  320 FDLASGFHQIGMREKDKSKTAFSTTDGHYEYNRMPFGLKNAPATFQRMMNNGLRGL--IGNTCFVYMDDIIVFG---TTL 394
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLrlLGVRIFSYLDDLLIIAssiKTS 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 805821995  395 EEHNRNLQILLerLSKCGLKLQPDKCE-YLKPELSYLG 431
Cdd:cd03714    81 EAVLRHLRATL--LANLGFTLNLEKSKlGPTQRITFLG 116
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 859-954 1.50e-08

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: 53.86  E-value: 1.50e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995   859 PNDKVSLD-TIGPLPSNRKYRYILVIQDYLTRYVQLAPLKTKTPKEVAENFWTYYCQIFG-VLKEILTDNGLEFRG-EFQ 935
Cdd:pfam00665    1 PNQLWQGDfTYIRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSkAFR 80

                           90
                   ....*....|....*....
gi 805821995   936 EFVEEkLRIKHTTTAVYHP 954
Cdd:pfam00665   81 EFLKD-LGIKPSFSRPGNP 98
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 528-646 3.79e-07

DIRS1 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 eukaryotes. 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. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 50.74  E-value: 3.79e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  528 ILTTDASNEAIGAVLSqgiigqdrpIAYASRTLNKAERNYSTTEKELLAIVW*IKHFHQYLYGRKFKIITDHKPLTWVMN 607
Cdd:cd09275     1 VLFTDASLSGWGAYLL---------NSRAHGPWSADERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTTAVAYIN 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 805821995  608 -----VKDPTSRLMR----WRMKLEEydyEI--IYKKGKSNANADALSRI 646
Cdd:cd09275    72 kqggtSSPPLLALARqillWCEQRNI---WLraSHIPGVLNTEADRLSRL 118
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
866-965 1.47e-06

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 52.58  E-value: 1.47e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  866 DTIgpLPSNRKyRYILVIQDYLTRYVQLAPLKTKTPKEVAENF--WTYYCQIFgVLKEILTDNGLEFRGEFQefVEEKLR 943
Cdd:COG2826   178 DLI--IGKRGK-SALLTLVERKSRFVILLKLPDKTAESVADALirLLRKLPAF-LRKSITTDNGKEFADHKE--IEAALG 251

                          90       100
                  ....*....|....*....|..
gi 805821995  944 IKHTTTAVYHPQSNGKNERTHK 965
Cdd:COG2826   252 IKVYFADPYSPWQRGTNENTNG 273
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 320-434 6.98e-05

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 43.49  E-value: 6.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  320 FDLASGFHQIgmrekdksktafsttdghyeynRMPFGLKNAPATFQRMMNN----GLRGLIGNTCFVYMDDIIVFGtTLE 395
Cdd:cd00304     1 FDVKSFFTSI----------------------PLPQGSPLSPALANLYMEKleapILKQLLDITLIRYVDDLVVIA-KSE 57

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 805821995  396 EHNRNLQILLERLSKCGLKLQPDKC--EYLKPELSYLGHII 434
Cdd:cd00304    58 QQAVKKRELEEFLARLGLNLSDEKTqfTEKEKKFKFLGILV 98
Gypsy pfam07253
Gypsy protein; This family consists of several Gypsy/Env proteins from Drosophila and ...
 1048-1321 6.07e-03

Gypsy protein; This family consists of several Gypsy/Env proteins from Drosophila and Ceratitis fruit fly species. Gypsy is an endogenous retrovirus of Drosophila melanogaster. Phylogenetic studies suggest that occasional horizontal transfer events of gypsy occur between Drosophila species. Gypsy possesses infective properties associated with the products of the envelope gene that might be at the origin of these interspecies transfers. This family contains many members with full-length matches; however, it also includes a number of very short sequences and short matches of sequences with other unrelated domains on them, which cannot be excluded. These matches may represent remnants of once-functional genes.


Pssm-ID: 254125  Cd Length: 472  Bit Score: 41.38  E-value: 6.07e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1048 EIRLLVLHTNQLAKRCNEIDPCLSKQRIILQQERNKRLNLELKSLRKFMG----HIQRRGLLNAVGEGMKILFGTMTASD 1123
Cdd:pfam07253   23 DQRLYLRHSSNISEYRSVIDETDMLSDSFPQSHMRKLLQVDTDHLRTMLSvlevHHRIARSLDFLGTALKVVAGTPDADD 102

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1124 AEYYNNELDKLREDNikiahlvRNQTTIllhkiqdNLGTYKFIQQQTDKLNinfVLLQNATKEEIFNLEIDETLADYIFL 1203
Cdd:pfam07253  103 LNKIKNTEAQLVEAN-------NNQIFI-------NSETQKQINKLTDTIN---KILQSRKGDLVDTPHLYETLLARNRI 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805821995  1204 yhdVSMTMQKLQEAIVDGKHGIVHPTILPPSELfeamRNTTKFEKFPVPLKEeyygiLLDTSEISITLTNEKLIYNLRIP 1283
Cdd:pfam07253  166 ---IKEEIQNLKLTITLAKLNIVNPTILDHADL----ESLVEENKENTPIVE-----LLEAAKIKVLQSENIIHIIIKYP 233

                          250       260       270
                   ....*....|....*....|....*....|....*...
gi 805821995  1284 ILEEDVYTlyrpiaLPIYSYIQGYSVYNVEFEYILLNK 1321
Cdd:pfam07253  234 KVTFECNK------VIIYPVSHQDTILRLKENTVAECE 265
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 364-424 6.23e-03

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.


Pssm-ID: 238827 [Multi-domain]  Cd Length: 220  Bit Score: 40.35  E-value: 6.23e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 805821995  364 FQRMMNNGLRGLIGN---TCFVYMDDIIVFGTTLEEH-NRNLQILLERLSKCGLKLQPDKCEYLK 424
Cdd:cd01650   125 LLRLLNKEEEIKLGGpgiTHLAYADDIVLFSEGKSRKlQELLQRLQEWSKESGLKINPSKSKVML 189
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 375-430 7.70e-03

RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.


Pssm-ID: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 39.23  E-value: 7.70e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 805821995  375 LIGNTCFV-YMDDIIVFGTTLEEHNRNLQILLERLSKCGLKLQPDKCEYL--------KPELSYL 430
Cdd:cd01646    79 KLKGVDYVrYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILplpegtasKDFLGYR 143
 
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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