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Conserved domains on  [gi|1057722588|gb|AOE48155|]
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hypothetical protein [Eumigus monticolus]

Protein Classification

reverse transcriptase family protein( domain architecture ID 10226058)

reverse transcriptase family protein such as RNA-directed DNA polymerase that catalyzes DNA replication from an RNA template; contains an exonuclease-endonuclease phosphatase (EEP) domain and may be a fragment of a retrovirus-related Pol polyprotein

CATH:  3.10.10.10
EC:  2.7.7.49
Gene Ontology:  GO:0003964
PubMed:  1698615
SCOP:  4002796

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 439-719 3.66e-59

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: 201.75  E-value: 3.66e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 439 DSLIVPIFKKGDRTDCNNYRGISLLSCLGKLIARILANRILSLVEKILPESQCGFRPSRGTTDLIFTARQLQEKCREQNR 518
Cdd:cd01650     1 KARIILIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEENILPNQFGFRPGRSTTDAILLLREVIEKAKEKKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 519 PLYIAFIDLSKAFDSVNRAALWKILalygfppkfitilrllytdvtatvisndaagdpfhintGVKQGCVIAPTLFSLYV 598
Cdd:cd01650    81 SLVLVFLDFEKAFDSVDHEFLLKAL--------------------------------------GVRQGDPLSPLLFNLAL 122

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 599 atvmqlikDDLPSGIQityrmdgKLFNLSRLKARTRTssaalveLQYADDNAVVAQS-EEDLVKILNAFSSAYKKIGLKL 677
Cdd:cd01650   123 --------DDLLRLLN-------KEEEIKLGGPGITH-------LAYADDIVLFSEGkSRKLQELLQRLQEWSKESGLKI 180

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1057722588 678 NTNKTQILyqPAPGQGLRNINVTIDGVRLQEVNTFPYLGSIL 719
Cdd:cd01650   181 NPSKSKVM--LIGNKKKRLKDITLNGTPIEAVETFKYLGVTI 220
EEP super family cl00490
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 1-159 1.36e-22

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


The actual alignment was detected with superfamily member cd09076:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 236  Bit Score: 97.81  E-value: 1.36e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588   1 MTLRLRLNGnKHVTVVSAYAPTlGSDDDIKEKFYSDLDNILSNINRQDKIILLGDFNARVGKDYKvwngviGKEGVGSVN 80
Cdd:cd09076    89 IMVRFKIKG-KRLTIINVYAPT-ARDEEEKEEFYDQLQDVLDKVPRHDTLIIGGDFNAVLGPKDD------GRKGLDKRN 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588  81 SNGIRLLSK-CAEHGLVitnTIFRQKNRFKT--SWQHPRSKHWHLIDYVIVRKEDLrdVLITKAMTGaDDCWTDHRLIRS 157
Cdd:cd09076   161 ENGERALSAlIEEHDLV---DVWRENNPKTReyTWRSPDHGSRSRIDRILVSKRLR--VKVKKTKIT-PGAGSDHRLVTL 234


                  ..
gi 1057722588 158 VM 159
Cdd:cd09076   235 KL 236
 
Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 439-719 3.66e-59

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: 201.75  E-value: 3.66e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 439 DSLIVPIFKKGDRTDCNNYRGISLLSCLGKLIARILANRILSLVEKILPESQCGFRPSRGTTDLIFTARQLQEKCREQNR 518
Cdd:cd01650     1 KARIILIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEENILPNQFGFRPGRSTTDAILLLREVIEKAKEKKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 519 PLYIAFIDLSKAFDSVNRAALWKILalygfppkfitilrllytdvtatvisndaagdpfhintGVKQGCVIAPTLFSLYV 598
Cdd:cd01650    81 SLVLVFLDFEKAFDSVDHEFLLKAL--------------------------------------GVRQGDPLSPLLFNLAL 122

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 599 atvmqlikDDLPSGIQityrmdgKLFNLSRLKARTRTssaalveLQYADDNAVVAQS-EEDLVKILNAFSSAYKKIGLKL 677
Cdd:cd01650   123 --------DDLLRLLN-------KEEEIKLGGPGITH-------LAYADDIVLFSEGkSRKLQELLQRLQEWSKESGLKI 180

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1057722588 678 NTNKTQILyqPAPGQGLRNINVTIDGVRLQEVNTFPYLGSIL 719
Cdd:cd01650   181 NPSKSKVM--LIGNKKKRLKDITLNGTPIEAVETFKYLGVTI 220
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 447-688 8.56e-31

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: 119.71  E-value: 8.56e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 447 KKGDrtdcNNYRGISLLSCLGKLIARILANRILSlvEKILPESQCGFRPSrgttdliftARQLQEKCreqnrplYIAFID 526
Cdd:pfam00078   3 KKGK----GKYRPISLLSIDYKALNKIIVKRLKP--ENLDSPPQPGFRPG---------LAKLKKAK-------WFLKLD 60

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 527 LSKAFDSVNRAALWKILALYGFPPKFITIlrllytdvtatvisNDAAGDPFHINTGVKQGCVIAPTLFSLYVATVMQlik 606
Cdd:pfam00078  61 LKKAFDQVPLDELDRKLTAFTTPPININW--------------NGELSGGRYEWKGLPQGLVLSPALFQLFMNELLR--- 123

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 607 dDLPSGIQITYrmdgklfnlsrlkartrtssaalveLQYADDNAVVAQSEEDLVKILNAFSSAYKKIGLKLNTNKTQILY 686
Cdd:pfam00078 124 -PLRKRAGLTL-------------------------VRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFL 177


                  ..
gi 1057722588 687 QP 688
Cdd:pfam00078 178 KS 179
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 1-159 1.36e-22

Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197310 [Multi-domain]  Cd Length: 236  Bit Score: 97.81  E-value: 1.36e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588   1 MTLRLRLNGnKHVTVVSAYAPTlGSDDDIKEKFYSDLDNILSNINRQDKIILLGDFNARVGKDYKvwngviGKEGVGSVN 80
Cdd:cd09076    89 IMVRFKIKG-KRLTIINVYAPT-ARDEEEKEEFYDQLQDVLDKVPRHDTLIIGGDFNAVLGPKDD------GRKGLDKRN 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588  81 SNGIRLLSK-CAEHGLVitnTIFRQKNRFKT--SWQHPRSKHWHLIDYVIVRKEDLrdVLITKAMTGaDDCWTDHRLIRS 157
Cdd:cd09076   161 ENGERALSAlIEEHDLV---DVWRENNPKTReyTWRSPDHGSRSRIDRILVSKRLR--VKVKKTKIT-PGAGSDHRLVTL 234


                  ..
gi 1057722588 158 VM 159
Cdd:cd09076   235 KL 236
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
394-686 3.45e-09

Retron-type reverse transcriptase [Mobilome: prophages, transposons];


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 60.09  E-value: 3.45e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 394 RRHKATGCDGIPAEALkegGEELIRHIHDLIVKIWKTEEMPADFRdslIVPIFKKGDRTdcnnyRGISLLSCLGKLIARI 473
Cdd:COG3344    40 ANKGAAGIDGVTVEDF---EEYLEENLYDLRERLRSGSYRPQPVR---RVEIPKPDGGV-----RPLGIPTVRDRVVQQA 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 474 LANRILSLVEKILPESQCGFRPSRGTTDLIftaRQLQEKCREQNRplYIAFIDLSKAFDSVNRAALWKILAlygfppKFI 553
Cdd:COG3344   109 VKQVLEPIFEPDFSDSSYGFRPGRSAHDAL---KKAREYINEGYR--WVVDADIKKFFDNVDHDLLMKRLR------RRI 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 554 T---ILRLLYTDVTATVISNDAAGDPfhiNTGVKQGCVIAPTLFSLYVatvmqlikDDLpsgiqityrmDgklfnlSRLK 630
Cdd:COG3344   178 KdkrVLRLIRRWLKAGVMEDGVVEER---EEGTPQGGPLSPLLANIYL--------HEL----------D------KELE 230

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1057722588 631 ARtrtsSAALVelQYADDNAVVAQSEEDLVKILNAFSSAYKKIGLKLNTNKTQILY 686
Cdd:COG3344   231 RR----GHRFV--RYADDFVILCRSKRAAERVLESLTERLEKLGLELNPEKTRIVR 280
Exo_endo_phos_2 pfam14529
Endonuclease-reverse transcriptase; This domain represents the endonuclease region of ...
 13-156 3.70e-06

Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.


Pssm-ID: 434019 [Multi-domain]  Cd Length: 118  Bit Score: 46.97  E-value: 3.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588  13 VTVVSAYAPtlgsDDDIKEKFYSDLDNILSNINRQdKIILLGDFNARvgkdYKVWNGVIGKegvgsvNSNGIRLLSKCAE 92
Cdd:pfam14529   1 ILIISVYCP----PSDQLRNLLDTLEDILRSLDRP-PIIIGGDFNAH----HPLWGSNSTD------VSRGEELIEFLNE 65

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1057722588  93 HGLVITNTifrqkNRFKTSWQHPRSKHWhlIDYVIVRKEDLRDVLITkamtgADDCWT-DHRLIR 156
Cdd:pfam14529  66 HGLNLLNL-----PKSGPTFISSNGDST--IDLTLTSDPLAVRVLSD-----LGPDSGsDHRPIA 118
 
Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 439-719 3.66e-59

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: 201.75  E-value: 3.66e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 439 DSLIVPIFKKGDRTDCNNYRGISLLSCLGKLIARILANRILSLVEKILPESQCGFRPSRGTTDLIFTARQLQEKCREQNR 518
Cdd:cd01650     1 KARIILIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEENILPNQFGFRPGRSTTDAILLLREVIEKAKEKKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 519 PLYIAFIDLSKAFDSVNRAALWKILalygfppkfitilrllytdvtatvisndaagdpfhintGVKQGCVIAPTLFSLYV 598
Cdd:cd01650    81 SLVLVFLDFEKAFDSVDHEFLLKAL--------------------------------------GVRQGDPLSPLLFNLAL 122

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 599 atvmqlikDDLPSGIQityrmdgKLFNLSRLKARTRTssaalveLQYADDNAVVAQS-EEDLVKILNAFSSAYKKIGLKL 677
Cdd:cd01650   123 --------DDLLRLLN-------KEEEIKLGGPGITH-------LAYADDIVLFSEGkSRKLQELLQRLQEWSKESGLKI 180

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1057722588 678 NTNKTQILyqPAPGQGLRNINVTIDGVRLQEVNTFPYLGSIL 719
Cdd:cd01650   181 NPSKSKVM--LIGNKKKRLKDITLNGTPIEAVETFKYLGVTI 220
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 447-688 8.56e-31

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: 119.71  E-value: 8.56e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 447 KKGDrtdcNNYRGISLLSCLGKLIARILANRILSlvEKILPESQCGFRPSrgttdliftARQLQEKCreqnrplYIAFID 526
Cdd:pfam00078   3 KKGK----GKYRPISLLSIDYKALNKIIVKRLKP--ENLDSPPQPGFRPG---------LAKLKKAK-------WFLKLD 60

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 527 LSKAFDSVNRAALWKILALYGFPPKFITIlrllytdvtatvisNDAAGDPFHINTGVKQGCVIAPTLFSLYVATVMQlik 606
Cdd:pfam00078  61 LKKAFDQVPLDELDRKLTAFTTPPININW--------------NGELSGGRYEWKGLPQGLVLSPALFQLFMNELLR--- 123

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 607 dDLPSGIQITYrmdgklfnlsrlkartrtssaalveLQYADDNAVVAQSEEDLVKILNAFSSAYKKIGLKLNTNKTQILY 686
Cdd:pfam00078 124 -PLRKRAGLTL-------------------------VRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFL 177


                  ..
gi 1057722588 687 QP 688
Cdd:pfam00078 178 KS 179
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 1-159 1.36e-22

Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197310 [Multi-domain]  Cd Length: 236  Bit Score: 97.81  E-value: 1.36e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588   1 MTLRLRLNGnKHVTVVSAYAPTlGSDDDIKEKFYSDLDNILSNINRQDKIILLGDFNARVGKDYKvwngviGKEGVGSVN 80
Cdd:cd09076    89 IMVRFKIKG-KRLTIINVYAPT-ARDEEEKEEFYDQLQDVLDKVPRHDTLIIGGDFNAVLGPKDD------GRKGLDKRN 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588  81 SNGIRLLSK-CAEHGLVitnTIFRQKNRFKT--SWQHPRSKHWHLIDYVIVRKEDLrdVLITKAMTGaDDCWTDHRLIRS 157
Cdd:cd09076   161 ENGERALSAlIEEHDLV---DVWRENNPKTReyTWRSPDHGSRSRIDRILVSKRLR--VKVKKTKIT-PGAGSDHRLVTL 234


                  ..
gi 1057722588 158 VM 159
Cdd:cd09076   235 KL 236
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
394-686 3.45e-09

Retron-type reverse transcriptase [Mobilome: prophages, transposons];


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 60.09  E-value: 3.45e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 394 RRHKATGCDGIPAEALkegGEELIRHIHDLIVKIWKTEEMPADFRdslIVPIFKKGDRTdcnnyRGISLLSCLGKLIARI 473
Cdd:COG3344    40 ANKGAAGIDGVTVEDF---EEYLEENLYDLRERLRSGSYRPQPVR---RVEIPKPDGGV-----RPLGIPTVRDRVVQQA 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 474 LANRILSLVEKILPESQCGFRPSRGTTDLIftaRQLQEKCREQNRplYIAFIDLSKAFDSVNRAALWKILAlygfppKFI 553
Cdd:COG3344   109 VKQVLEPIFEPDFSDSSYGFRPGRSAHDAL---KKAREYINEGYR--WVVDADIKKFFDNVDHDLLMKRLR------RRI 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 554 T---ILRLLYTDVTATVISNDAAGDPfhiNTGVKQGCVIAPTLFSLYVatvmqlikDDLpsgiqityrmDgklfnlSRLK 630
Cdd:COG3344   178 KdkrVLRLIRRWLKAGVMEDGVVEER---EEGTPQGGPLSPLLANIYL--------HEL----------D------KELE 230

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1057722588 631 ARtrtsSAALVelQYADDNAVVAQSEEDLVKILNAFSSAYKKIGLKLNTNKTQILY 686
Cdd:COG3344   231 RR----GHRFV--RYADDFVILCRSKRAAERVLESLTERLEKLGLELNPEKTRIVR 280
Exo_endo_phos_2 pfam14529
Endonuclease-reverse transcriptase; This domain represents the endonuclease region of ...
 13-156 3.70e-06

Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.


Pssm-ID: 434019 [Multi-domain]  Cd Length: 118  Bit Score: 46.97  E-value: 3.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588  13 VTVVSAYAPtlgsDDDIKEKFYSDLDNILSNINRQdKIILLGDFNARvgkdYKVWNGVIGKegvgsvNSNGIRLLSKCAE 92
Cdd:pfam14529   1 ILIISVYCP----PSDQLRNLLDTLEDILRSLDRP-PIIIGGDFNAH----HPLWGSNSTD------VSRGEELIEFLNE 65

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1057722588  93 HGLVITNTifrqkNRFKTSWQHPRSKHWhlIDYVIVRKEDLRDVLITkamtgADDCWT-DHRLIR 156
Cdd:pfam14529  66 HGLNLLNL-----PKSGPTFISSNGDST--IDLTLTSDPLAVRVLSD-----LGPDSGsDHRPIA 118
RT_Bac_retron_II cd03487
RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 468-706 1.43e-04

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: 44.10  E-value: 1.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 468 KLIARILANRILSLVEkiLPESQCGFRPSRGttdlIFTARQLQEKCReqnrplYIAFIDLSKAFDSVNRAALWKILALYG 547
Cdd:cd03487    17 KAIQRKILSNLLSKLP--VHDAAHGFVKGRS----IITNAKPHCGAK------YVLKLDIKDFFPSITFERVRGVFRSLG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 548 FPPKFI-TILRLLYTdvtatvisndaagdpfhINTGVKQGcviAPTlfSLYVAT-VMqlikddlpsgiqitYRMDGKLFN 625
Cdd:cd03487    85 YFSPDVaTILAKLCT-----------------YNGHLPQG---APT--SPALSNlVF--------------RKLDERLSK 128

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588 626 LSRLKARTRTssaalvelQYADDNAVVAQSEEDLV--KILNAFSSAYKKIGLKLNTNKTQILYQPAPgQGLRNINVTIDG 703
Cdd:cd03487   129 LAKSNGLTYT--------RYADDITFSSNKKLKEAldKLLEIIRSILSEEGFKINKSKTRISSKGSR-QIVTGLVVNNGK 199


                  ...
gi 1057722588 704 VRL 706
Cdd:cd03487   200 PSL 202
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 645-685 9.94e-04

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: 40.78  E-value: 9.94e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1057722588 645 YADDNAVVAQSEEDLVKILNAFSSAYKKIGLKLNTNKTQIL 685
Cdd:cd01646    88 YVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEIL 128
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 11-100 1.51e-03

Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197311 [Multi-domain]  Cd Length: 205  Bit Score: 41.12  E-value: 1.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588  11 KHVTVVSAYAPTLGSDDDIKEkFYSDLDNILSNINRqdKIILLGDFNARVGKdykvWNGVIGkegvgsvNSNGIRLLSKC 90
Cdd:cd09077    81 GGITVVSCYAPPSESLEEFEE-YLENLVRIVRGLSR--PVIIGGDFNAWSPA----WGSKRT-------DRRGRLLEDWI 146

                          90
                  ....*....|
gi 1057722588  91 AEHGLVITNT 100
Cdd:cd09077   147 ANLGLVLLND 156
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 11-148 4.32e-03

Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197307 [Multi-domain]  Cd Length: 251  Bit Score: 39.96  E-value: 4.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1057722588  11 KHVTVVSAYAPTLGSDD---DIKEKFYSDLDNILSNINRQDK-IILLGDFN-ARVGKDYKVWNGVIGKEGVGSVNSNGI- 84
Cdd:cd09073    99 DDFYLINVYFPNGGRGLerlDYKLRFYEAFLEFLEKLRKRGKpVVICGDFNvAHEEIDLARPKKNEKNAGFTPEERAWFd 178

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1057722588  85 RLLSKcaehGLVITNTIFRQKNRFKTSWQ---HPRSKH--WHlIDYVIVR---KEDLRDVLITKAMTGADDC 148
Cdd:cd09073   179 KLLSL----GYVDTFRHFHPEPGAYTWWSyrgNARERNvgWR-IDYFLVSeelAEKVKDSGILSKVKGSDHA 245
 
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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