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Conserved domains on  [gi|2030916631|gb|QUM93285|]
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pol polyprotein, partial [Avian leukosis virus ev/J]

Protein Classification

pol protein( domain architecture ID 10108207)

HIV-1 pol protein containing the retroviral aspartyl protease, reverse transcriptase (RT), RT thumb, RT connection, RNase H, and integrase domains; RT catalyzes the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 18-230 5.55e-138

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: 408.59  E-value: 5.55e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631  18 PVWIDQWPLPEGKLVALTQLVEKELQLGHIEPSLSCWNTPVFVIRKASGSYRLLHDLRAVNAKLVPFGAVQQGAPVLSAL 97
Cdd:cd01645     1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631  98 PRGWPLMVLDLKDCFFSIPLAEQDREAFAFTLPSVNNQAPARRFQWKVLPQGMTCSPTICQLIVGQVLEPLRLKHPSLCM 177
Cdd:cd01645    81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2030916631 178 LHYMDDLLLAASSHDRLETAGEEVISTLERAGFTISPDKVQREPGVQYLGYKL 230
Cdd:cd01645   161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 629-722 3.89e-22

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: 91.61  E-value: 3.89e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 629 PLQIWQTDFTLEPRMAP--RSWLAVTVDTASSAIVVTQHG-RVTSVAAQHHWATAIAVLG-RPKAIKTDNGSCFTSKSTR 704
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSsEMDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 2030916631 705 EWLARWGIAHTTGIPGNS 722
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 446-571 4.19e-19

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.


The actual alignment was detected with superfamily member cd09273:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 131  Bit Score: 84.31  E-value: 4.19e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 446 TVFTDASSS-THKGVVVWREgprweIKEIADL--GASVQQLEARAVAMALLLWPTTPTNVVTDSAFVAKMLLKMGQEGVP 522
Cdd:cd09273     1 TVFTDGSSFkAGYAIVSGTE-----IVEAQPLppGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGIE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2030916631 523 ST-------AAAFILEDALSQRSAMAAVLHVRSHSEVPGFFTEGNDVADSQATFQA 571
Cdd:cd09273    76 RGflksiknLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 579-614 5.98e-12

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


:

Pssm-ID: 426567  Cd Length: 36  Bit Score: 60.85  E-value: 5.98e-12
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2030916631 579 DLHTALHVGPRALSKACNISMQQAREVVQTCPHCNS 614
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
RVT_thumb super family cl06055
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 245-291 9.97e-09

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


The actual alignment was detected with superfamily member pfam06817:

Pssm-ID: 429135  Cd Length: 66  Bit Score: 52.32  E-value: 9.97e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2030916631 245 RIATLWDVQKLVGSLQWLRPALGIPPRLMGPFYEQLRG-SDPNEAREW 291
Cdd:pfam06817  10 HLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGdSDLTSPRTL 57
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 18-230 5.55e-138

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: 408.59  E-value: 5.55e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631  18 PVWIDQWPLPEGKLVALTQLVEKELQLGHIEPSLSCWNTPVFVIRKASGSYRLLHDLRAVNAKLVPFGAVQQGAPVLSAL 97
Cdd:cd01645     1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631  98 PRGWPLMVLDLKDCFFSIPLAEQDREAFAFTLPSVNNQAPARRFQWKVLPQGMTCSPTICQLIVGQVLEPLRLKHPSLCM 177
Cdd:cd01645    81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2030916631 178 LHYMDDLLLAASSHDRLETAGEEVISTLERAGFTISPDKVQREPGVQYLGYKL 230
Cdd:cd01645   161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 61-230 2.08e-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: 158.62  E-value: 2.08e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631  61 IRKAS-GSYRLL----HDLRAVNAKLVP-------FGAVQQGA-PVLSALPRGWPLMVLDLKDCFFSIPLAEQDREAFAF 127
Cdd:pfam00078   1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFrPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 128 TLPSVNN----QAPARRFQWKVLPQGMTCSPTICQLIVGQVLEPLRlKHPSLCMLHYMDDLLLAASSHDRLETAGEEVIS 203
Cdd:pfam00078  81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLR-KRAGLTLVRYADDILIFSKSEEEHQEALEEVLE 159

                         170       180       190
                  ....*....|....*....|....*....|
gi 2030916631 204 TLERAGFTISPDKVQ---REPGVQYLGYKL 230
Cdd:pfam00078 160 WLKESGLKINPEKTQfflKSKEVKYLGVTL 189
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 629-722 3.89e-22

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: 91.61  E-value: 3.89e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 629 PLQIWQTDFTLEPRMAP--RSWLAVTVDTASSAIVVTQHG-RVTSVAAQHHWATAIAVLG-RPKAIKTDNGSCFTSKSTR 704
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSsEMDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 2030916631 705 EWLARWGIAHTTGIPGNS 722
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 446-571 4.19e-19

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: 84.31  E-value: 4.19e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 446 TVFTDASSS-THKGVVVWREgprweIKEIADL--GASVQQLEARAVAMALLLWPTTPTNVVTDSAFVAKMLLKMGQEGVP 522
Cdd:cd09273     1 TVFTDGSSFkAGYAIVSGTE-----IVEAQPLppGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGIE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2030916631 523 ST-------AAAFILEDALSQRSAMAAVLHVRSHSEVPGFFTEGNDVADSQATFQA 571
Cdd:cd09273    76 RGflksiknLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
transpos_IS481 NF033577
IS481 family transposase; null
 633-737 4.41e-13

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 70.70  E-value: 4.41e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 633 WQTDFTLEPRMAPRSWLA--VTVDTASSAIVVTQHGRVTSVAAQHHWATAIAVLG-RPKAIKTDNGSCFTSKST--REWL 707
Cdd:NF033577  131 WHIDIKKLGRIPDVGRLYlhTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGiPIRRVLTDNGSEFRSRAHgfELAL 210

                          90       100       110
                  ....*....|....*....|....*....|
gi 2030916631 708 ARWGIAHTTGIPGNSQGQAMVERANRLLKD 737
Cdd:NF033577  211 AELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 579-614 5.98e-12

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


Pssm-ID: 426567  Cd Length: 36  Bit Score: 60.85  E-value: 5.98e-12
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2030916631 579 DLHTALHVGPRALSKACNISMQQAREVVQTCPHCNS 614
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
628-737 5.27e-11

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 64.79  E-value: 5.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 628 GPLQIWQTDFTlEPRMAP-RSWLAVTVDTASSAIV---VTQHGRVTSVAAqhHWATAIAVLG--RPKAIKTDNGSCFTSK 701
Cdd:COG2801   147 APNQVWVTDIT-YIPTAEgWLYLAAVIDLFSREIVgwsVSDSMDAELVVD--ALEMAIERRGppKPLILHSDNGSQYTSK 223

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2030916631 702 STREWLARWGIAHTTGIPGNSQGQAMVERANRLLKD 737
Cdd:COG2801   224 AYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
transpos_IS3 NF033516
IS3 family transposase;
629-737 1.26e-10

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 64.12  E-value: 1.26e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 629 PLQIWQTDFTlEPRMApRSW--LAVTVDTASSAIV---VTQHGRVTSVAAQhhWATAIAVLGRPKA--IKTDNGSCFTSK 701
Cdd:NF033516  215 PNQVWVTDIT-YIRTA-EGWlyLAVVLDLFSREIVgwsVSTSMSAELVLDA--LEMAIEWRGKPEGliLHSDNGSQYTSK 290

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2030916631 702 STREWLARWGIAHTTGIPGNSQGQAMVERANRLLKD 737
Cdd:NF033516  291 AYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKR 326
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 245-291 9.97e-09

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


Pssm-ID: 429135  Cd Length: 66  Bit Score: 52.32  E-value: 9.97e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2030916631 245 RIATLWDVQKLVGSLQWLRPALGIPPRLMGPFYEQLRG-SDPNEAREW 291
Cdd:pfam06817  10 HLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGdSDLTSPRTL 57
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 628-736 3.78e-05

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 46.40  E-value: 3.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 628 GPLQIWQTDFTLEPRMAPRSWLAVTVDTASSAIV-----VTQHGRVTSVAAQHHWATAiavlGRPKA--IKTDNGSCFTS 700
Cdd:PHA02517  108 RPNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVgwrvsSSMDTDFVLDALEQALWAR----GRPGGliHHSDKGSQYVS 183

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2030916631 701 KSTREWLARWGIAHTTGIPGNSQGQAMVERANRLLK 736
Cdd:PHA02517  184 LAYTQRLKEAGIRASTGSRGDSYDNAPAESINGLYK 219
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 18-230 5.55e-138

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: 408.59  E-value: 5.55e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631  18 PVWIDQWPLPEGKLVALTQLVEKELQLGHIEPSLSCWNTPVFVIRKASGSYRLLHDLRAVNAKLVPFGAVQQGAPVLSAL 97
Cdd:cd01645     1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631  98 PRGWPLMVLDLKDCFFSIPLAEQDREAFAFTLPSVNNQAPARRFQWKVLPQGMTCSPTICQLIVGQVLEPLRLKHPSLCM 177
Cdd:cd01645    81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2030916631 178 LHYMDDLLLAASSHDRLETAGEEVISTLERAGFTISPDKVQREPGVQYLGYKL 230
Cdd:cd01645   161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 18-228 7.67e-45

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: 160.59  E-value: 7.67e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631  18 PVWIDQWPLPEGKLVALTQLVEKELQLGHIEPSLSCWNTPVFVIRKASG-SYRLLHDLRAVNAKLVPFG-AVQQGAPVLS 95
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHpAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631  96 ALPR--GWpLMVLDLKDCFFSIPLAEQDREAFAFTLPSvnnqapaRRFQWKVLPQGMTCSPTICQLIVGQVLEPLRLKHP 173
Cdd:cd03715    81 LLPPkhQW-YTVLDLANAFFSLPLAPDSQPLFAFEWEG-------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHE 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2030916631 174 SLCMLHYMDDLLLAASSHDRLETAGEEVISTLERAGFTISPDKVQR-EPGVQYLGY 228
Cdd:cd03715   153 GTILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQIcRAEVKFLGV 208
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 61-230 2.08e-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: 158.62  E-value: 2.08e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631  61 IRKAS-GSYRLL----HDLRAVNAKLVP-------FGAVQQGA-PVLSALPRGWPLMVLDLKDCFFSIPLAEQDREAFAF 127
Cdd:pfam00078   1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFrPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 128 TLPSVNN----QAPARRFQWKVLPQGMTCSPTICQLIVGQVLEPLRlKHPSLCMLHYMDDLLLAASSHDRLETAGEEVIS 203
Cdd:pfam00078  81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLR-KRAGLTLVRYADDILIFSKSEEEHQEALEEVLE 159

                         170       180       190
                  ....*....|....*....|....*....|
gi 2030916631 204 TLERAGFTISPDKVQ---REPGVQYLGYKL 230
Cdd:pfam00078 160 WLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 45-229 8.52e-28

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: 110.76  E-value: 8.52e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631  45 GHIEPSLSCWNTPVFVIRKASGSYRLLHDLRAVNAKLVpfgavqqgaPVLSALPRGWPLM----------VLDLKDCFFS 114
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTI---------KDRYPLPTIDELLeelagakvfsKLDLRSGYHQ 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 115 IPLAEQDREAFAFTLPSvnnqapaRRFQWKVLPQGMTCSPTICQLIVGQVLEPLRLKhpslCMLHYMDDLLLAASSHDRL 194
Cdd:cd01647    72 IPLAEESRPKTAFRTPF-------GLYEYTRMPFGLKNAPATFQRLMNKILGDLLGD----FVEVYLDDILVYSKTEEEH 140

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2030916631 195 ETAGEEVISTLERAGFTISPDKVQ-REPGVQYLGYK 229
Cdd:cd01647   141 LEHLREVLERLREAGLKLNPEKCEfGVPEVEFLGHI 176
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 629-722 3.89e-22

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: 91.61  E-value: 3.89e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 629 PLQIWQTDFTLEPRMAP--RSWLAVTVDTASSAIVVTQHG-RVTSVAAQHHWATAIAVLG-RPKAIKTDNGSCFTSKSTR 704
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSsEMDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 2030916631 705 EWLARWGIAHTTGIPGNS 722
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 446-571 4.19e-19

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: 84.31  E-value: 4.19e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 446 TVFTDASSS-THKGVVVWREgprweIKEIADL--GASVQQLEARAVAMALLLWPTTPTNVVTDSAFVAKMLLKMGQEGVP 522
Cdd:cd09273     1 TVFTDGSSFkAGYAIVSGTE-----IVEAQPLppGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGIE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2030916631 523 ST-------AAAFILEDALSQRSAMAAVLHVRSHSEVPGFFTEGNDVADSQATFQA 571
Cdd:cd09273    76 RGflksiknLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
transpos_IS481 NF033577
IS481 family transposase; null
 633-737 4.41e-13

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 70.70  E-value: 4.41e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 633 WQTDFTLEPRMAPRSWLA--VTVDTASSAIVVTQHGRVTSVAAQHHWATAIAVLG-RPKAIKTDNGSCFTSKST--REWL 707
Cdd:NF033577  131 WHIDIKKLGRIPDVGRLYlhTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGiPIRRVLTDNGSEFRSRAHgfELAL 210

                          90       100       110
                  ....*....|....*....|....*....|
gi 2030916631 708 ARWGIAHTTGIPGNSQGQAMVERANRLLKD 737
Cdd:NF033577  211 AELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 579-614 5.98e-12

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


Pssm-ID: 426567  Cd Length: 36  Bit Score: 60.85  E-value: 5.98e-12
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2030916631 579 DLHTALHVGPRALSKACNISMQQAREVVQTCPHCNS 614
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 106-230 2.80e-11

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: 61.21  E-value: 2.80e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 106 LDLKDCFFSIPLAEQDREAFAFTLPSvnnqapaRRFQWKVLPQGMTCSPTICQLIVGQVLEPLRLKhpSLCMLHYMDDLL 185
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGFAWQG-------ETYQFKALPFGLSLAPRVFTKVVEALLAPLRLL--GVRIFSYLDDLL 71

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2030916631 186 LAASSHDRLETAGEEVIST-LERAGFTISPDKVQREP--GVQYLGYKL 230
Cdd:cd03714    72 IIASSIKTSEAVLRHLRATlLANLGFTLNLEKSKLGPtqRITFLGLEL 119
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
628-737 5.27e-11

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 64.79  E-value: 5.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 628 GPLQIWQTDFTlEPRMAP-RSWLAVTVDTASSAIV---VTQHGRVTSVAAqhHWATAIAVLG--RPKAIKTDNGSCFTSK 701
Cdd:COG2801   147 APNQVWVTDIT-YIPTAEgWLYLAAVIDLFSREIVgwsVSDSMDAELVVD--ALEMAIERRGppKPLILHSDNGSQYTSK 223

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2030916631 702 STREWLARWGIAHTTGIPGNSQGQAMVERANRLLKD 737
Cdd:COG2801   224 AYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
transpos_IS3 NF033516
IS3 family transposase;
629-737 1.26e-10

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 64.12  E-value: 1.26e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 629 PLQIWQTDFTlEPRMApRSW--LAVTVDTASSAIV---VTQHGRVTSVAAQhhWATAIAVLGRPKA--IKTDNGSCFTSK 701
Cdd:NF033516  215 PNQVWVTDIT-YIRTA-EGWlyLAVVLDLFSREIVgwsVSTSMSAELVLDA--LEMAIEWRGKPEGliLHSDNGSQYTSK 290

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2030916631 702 STREWLARWGIAHTTGIPGNSQGQAMVERANRLLKD 737
Cdd:NF033516  291 AYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKR 326
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 106-230 1.20e-09

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: 56.21  E-value: 1.20e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 106 LDLKDCFFSIPLaeqdreafaftlpsvnnqaparrfqwkvlPQGMTCSPTICQLIVGQVLEPLRLKHPSLCMLHYMDDLL 185
Cdd:cd00304     1 FDVKSFFTSIPL-----------------------------PQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLV 51

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2030916631 186 LAASSHDrLETAGEEVISTLERAGFTISPDKVQ---REPGVQYLGYKL 230
Cdd:cd00304    52 VIAKSEQ-QAVKKRELEEFLARLGLNLSDEKTQfteKEKKFKFLGILV 98
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 245-291 9.97e-09

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


Pssm-ID: 429135  Cd Length: 66  Bit Score: 52.32  E-value: 9.97e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2030916631 245 RIATLWDVQKLVGSLQWLRPALGIPPRLMGPFYEQLRG-SDPNEAREW 291
Cdd:pfam06817  10 HLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGdSDLTSPRTL 57
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 628-736 3.78e-05

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 46.40  E-value: 3.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 628 GPLQIWQTDFTLEPRMAPRSWLAVTVDTASSAIV-----VTQHGRVTSVAAQHHWATAiavlGRPKA--IKTDNGSCFTS 700
Cdd:PHA02517  108 RPNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVgwrvsSSMDTDFVLDALEQALWAR----GRPGGliHHSDKGSQYVS 183

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2030916631 701 KSTREWLARWGIAHTTGIPGNSQGQAMVERANRLLK 736
Cdd:PHA02517  184 LAYTQRLKEAGIRASTGSRGDSYDNAPAESINGLYK 219
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 89-214 1.73e-04

RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.


Pssm-ID: 238822  Cd Length: 213  Bit Score: 43.83  E-value: 1.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631  89 QGAPVLSALP------RGWPLMVL-DLKDCFFSIPLAEQDREAFAFTLPSVNNQAPARRFQWKVLPQGMTCSPTICQLIV 161
Cdd:cd01644    40 KGPDLLNSLFgvllrfRQGKIAVSaDIEKMFHQVKVRPEDRDVLRFLWRKDGDEPKPIEYRMTVVPFGAASAPFLANRAL 119

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2030916631 162 GQVLEplrlKHPSLCML------HYMDDLLLAASSHDRLETAGEEVISTLERAGFTISP 214
Cdd:cd01644   120 KQHAE----DHPHEAAAkiikrnFYVDDILVSTDTLNEAVNVAKRLIALLKKGGFNLRK 174
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 147-228 1.69e-03

RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).


Pssm-ID: 238828 [Multi-domain]  Cd Length: 226  Bit Score: 41.03  E-value: 1.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 147 PQGMTCSPTIC--------QLIVGQVLEPLRLKHPSLCMLH---YMDDLLLAASSHDRLETAGEEVISTLERAGFTISPD 215
Cdd:cd01651   128 PQGGVISPLLAniylheldKFVEEKLKEYYDTSDPKFRRLRyvrYADDFVIGVRGPKEAEEIKELIREFLEELGLELNPE 207

                          90
                  ....*....|....*..
gi 2030916631 216 KVQ----REPGVQYLGY 228
Cdd:cd01651   208 KTRithfKSEGFDFLGF 224
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 106-230 3.57e-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: 38.85  E-value: 3.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 106 LDLKDCFFSIPL------------AEQDREAFAFTLPSVNN-QAPARRFQWKVLPQGmtcsPTICQLIVGQVLEPL--RL 170
Cdd:cd01646     1 LDISNFYDSIYThslpwalhgkikAKQLLKLLRLLGNLLDLlLLSSQYGQTNGLPIG----PLTSRFLANIYLNDVdhEL 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2030916631 171 KHPSLCMLH--YMDDLLLAASSHDRLETAGEEVISTLERAGFTISPDKVQREP------GVQYLGYKL 230
Cdd:cd01646    77 KSKLKGVDYvrYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILPlpegtaSKDFLGYRF 144
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 446-564 6.90e-03

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: 37.58  E-value: 6.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 446 TVFTDASSSTHK---GVVVWREGPRWEIKEIADLGASVQQLEARAVAMALLL-----WPTTPTNVVTDSAFVAKMLLKM- 516
Cdd:cd09276     1 VIYTDGSKLEGSvgaGFVIYRGGEVISRSYRLGTHASVFDAELEAILEALELalataRRARKVTIFTDSQSALQALRNPr 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2030916631 517 ---GQEGVpstAAAFILEDALSQRSAMAAVLHVRSHSEVPgffteGNDVAD 564
Cdd:cd09276    81 rssGQVIL---IRILRLLRLLKAKGVKVRLRWVPGHVGIE-----GNEAAD 123
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 139-216 9.48e-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: 38.43  E-value: 9.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 139 RRFQWKVL--PQGMTCSPT---------ICQLivgQVLEPLRLKHPSLCMLHYMDDLLLAASSHdrlETAGEEVISTLER 207
Cdd:cd01650    98 HEFLLKALgvRQGDPLSPLlfnlalddlLRLL---NKEEEIKLGGPGITHLAYADDIVLFSEGK---SRKLQELLQRLQE 171

                          90
                  ....*....|...
gi 2030916631 208 A----GFTISPDK 216
Cdd:cd01650   172 WskesGLKINPSK 184
RT_Bac_retron_II cd03487
RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 103-216 9.85e-03

RT_Bac_retron_II: 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: 239569 [Multi-domain]  Cd Length: 214  Bit Score: 38.32  E-value: 9.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2030916631 103 LMVLDLKDCFFSIPlAEQDREAFA---FTLPSVnnqapARRFQW-----KVLPQGMTCSPTICQLivgqVLEPL------ 168
Cdd:cd03487    59 VLKLDIKDFFPSIT-FERVRGVFRslgYFSPDV-----ATILAKlctynGHLPQGAPTSPALSNL----VFRKLderlsk 128

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2030916631 169 RLKHPSLCMLHYMDDLLLaaSSHDRLETAGEEVI----STLERAGFTISPDK 216
Cdd:cd03487   129 LAKSNGLTYTRYADDITF--SSNKKLKEALDKLLeiirSILSEEGFKINKSK 178
 
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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