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Conserved domains on  [gi|495120839|ref|WP_007845654|]
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MULTISPECIES: group II intron reverse transcriptase/maturase [Bacteria]

Protein Classification

group II intron reverse transcriptase/maturase( domain architecture ID 12152919)

group II intron reverse transcriptase/maturase; group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 62-412 2.76e-160

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]


:

Pssm-ID: 275209 [Multi-domain]  Cd Length: 354  Bit Score: 460.39  E-value: 2.76e-160
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839   62 AKALAVKRVTSNSGsdTAGVDKVKWSTPNARF-----KAIGELKRRGYKPQPLKRVNIKKSNGKLRPLGIPTMKDRAMQA 136
Cdd:TIGR04416   3 NLLLAYKRVKANKG--AAGVDGVTIEDFEEYLeenlyKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRVVQQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  137 LYLLALEPVSETTADSNSYGFRKERSTRDAREQCFCVLAKKAspEWIMEGDIKGCFDHISHEWLLNNI---PMDKVML-- 211
Cdd:TIGR04416  81 AVKQVLEPIFEPDFSENSYGFRPGRSAHDAIAKARKRLNRGY--RWVVDADIKGFFDNINHDLLMKAVarrISDKRVLrl 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  212 -RKWLKCGFVFNKELFPTEEGTPQGGIISPTLANMTLDGLQTMLAEKYHkkfvnrkttyypKVHLVRYADDFIITGRSKE 290
Cdd:TIGR04416 159 iRRWLKAGVMEDGEVQETEEGTPQGGVISPLLANIYLHYLDDEWEKRGY------------KVRFVRYADDFVILCRSKE 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  291 ALEEIKPLVVDFLKERGLTLSEEKTKITHI-DDGFDFLGYNIRK-----YKGVLLIKPSKKSLKKFMQKIRGIIDSNKGS 364
Cdd:TIGR04416 227 AAERVLEALTKRLEELGLELNPEKTKIVHCkDGGFDFLGFTFRKrksknGKGKLLIKPSKKAVKKFKEKIRELTKRRRGL 306

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 495120839  365 KQESLIRLLNPVITGWVNYYKNCVASDTFRKADYLIFEKLWQWAKRRH 412
Cdd:TIGR04416 307 SLEELIKKLNPILRGWANYFGIANSSRTFSKLDHWIRRRLRRWLRKKW 354
RVT_N pfam13655
N-terminal domain of reverse transcriptase; This domain is found at the N-terminus of ...
 18-99 5.75e-36

N-terminal domain of reverse transcriptase; This domain is found at the N-terminus of bacterial reverse transcriptases.


:

Pssm-ID: 433382  Cd Length: 83  Bit Score: 128.76  E-value: 5.75e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839   18 WESIDWNKCEIAVNKLQARIVKAQKAGKHGRVKSLQWVLTHSFYAKALAVKRVT-SNSGSDTAGVDKVKWSTPNARFKAI 96
Cdd:pfam13655   1 WKSIDWKKVERNVFKLQKRIYKASQEGDWRKVRRLQKLLTRSFSAKLLAVRRVTqENQGKKTAGVDGVKWLTPKQRLELV 80


                  ...
gi 495120839   97 GEL 99
Cdd:pfam13655  81 LSL 83
 
Name Accession Description Interval E-value
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 62-412 2.76e-160

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]


Pssm-ID: 275209 [Multi-domain]  Cd Length: 354  Bit Score: 460.39  E-value: 2.76e-160
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839   62 AKALAVKRVTSNSGsdTAGVDKVKWSTPNARF-----KAIGELKRRGYKPQPLKRVNIKKSNGKLRPLGIPTMKDRAMQA 136
Cdd:TIGR04416   3 NLLLAYKRVKANKG--AAGVDGVTIEDFEEYLeenlyKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRVVQQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  137 LYLLALEPVSETTADSNSYGFRKERSTRDAREQCFCVLAKKAspEWIMEGDIKGCFDHISHEWLLNNI---PMDKVML-- 211
Cdd:TIGR04416  81 AVKQVLEPIFEPDFSENSYGFRPGRSAHDAIAKARKRLNRGY--RWVVDADIKGFFDNINHDLLMKAVarrISDKRVLrl 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  212 -RKWLKCGFVFNKELFPTEEGTPQGGIISPTLANMTLDGLQTMLAEKYHkkfvnrkttyypKVHLVRYADDFIITGRSKE 290
Cdd:TIGR04416 159 iRRWLKAGVMEDGEVQETEEGTPQGGVISPLLANIYLHYLDDEWEKRGY------------KVRFVRYADDFVILCRSKE 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  291 ALEEIKPLVVDFLKERGLTLSEEKTKITHI-DDGFDFLGYNIRK-----YKGVLLIKPSKKSLKKFMQKIRGIIDSNKGS 364
Cdd:TIGR04416 227 AAERVLEALTKRLEELGLELNPEKTKIVHCkDGGFDFLGFTFRKrksknGKGKLLIKPSKKAVKKFKEKIRELTKRRRGL 306

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 495120839  365 KQESLIRLLNPVITGWVNYYKNCVASDTFRKADYLIFEKLWQWAKRRH 412
Cdd:TIGR04416 307 SLEELIKKLNPILRGWANYFGIANSSRTFSKLDHWIRRRLRRWLRKKW 354
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 110-331 1.76e-97

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: 295.26  E-value: 1.76e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 110 KRVNIKKSNGKLRPLGIPTMKDRAMQALYLLALEPVSETTADSNSYGFRKERSTRDAREQCFcvLAKKASPEWIMEGDIK 189
Cdd:cd01651    1 RRVYIPKPNGKKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDALKAIR--RNVKGGYTWVIEGDIK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 190 GCFDHISHEWLLNNIPMD----KVML--RKWLKCGFVFNKELFPTEEGTPQGGIISPTLANMTLDGLQTMLAEKYHKKFV 263
Cdd:cd01651   79 GFFDNIDHDLLLKILKRRigdkRVLRliRKWLKAGVLEDGKLVETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYYD 158

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495120839 264 NRKtTYYPKVHLVRYADDFIITGRSKEALEEIKPLVVDFLKERGLTLSEEKTKITHI-DDGFDFLGYNI 331
Cdd:cd01651  159 TSD-PKFRRLRYVRYADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRITHFkSEGFDFLGFTF 226
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
34-435 3.12e-79

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 255.39  E-value: 3.12e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  34 QARIVKAQKAGKHGRVKSLQ-WVLTHSFYAKALavKRVTSNSGSdtAGVDKVKWstpnARFKA---------IGELKRRG 103
Cdd:COG3344    3 LRRITEKAKPDPGARFTSLLeKILSRENLLEAY--KRVKANKGA--AGIDGVTV----EDFEEyleenlydlRERLRSGS 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 104 YKPQPLKRVNIKKSNGKLRPLGIPTMKDR-AMQALyLLALEPVSETTADSNSYGFRKERSTRDAREQCFCVLAKKasPEW 182
Cdd:COG3344   75 YRPQPVRRVEIPKPDGGVRPLGIPTVRDRvVQQAV-KQVLEPIFEPDFSDSSYGFRPGRSAHDALKKAREYINEG--YRW 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 183 IMEGDIKGCFDHISHEWLLNNIPM---DKVML---RKWLKCGFVFNKELFPTEEGTPQGGIISPTLANMTLDGLQTMLAE 256
Cdd:COG3344  152 VVDADIKKFFDNVDHDLLMKRLRRrikDKRVLrliRRWLKAGVMEDGVVEEREEGTPQGGPLSPLLANIYLHELDKELER 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 257 KYHKkfvnrkttyypkvhLVRYADDFIITGRSKEALEEIKPLVVDFLKERGLTLSEEKTKITHIDDGFDFLGYNIRKYKG 336
Cdd:COG3344  232 RGHR--------------FVRYADDFVILCRSKRAAERVLESLTERLEKLGLELNPEKTRIVRPGDGFKFLGFSFRRGKG 297

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 337 VLLIKPSKKSLKKFMQKIRGIIDSNKGSKQESLIRLLNPVITGWVNYYKNCVAS-------DTFRKADYLIFEKLWQWAK 409
Cdd:COG3344  298 LGFKFRPRKSKRKKKRKRRRRTRRRSRKRRRRIRRLLRRLLLGWRRYLLLAELKrllnallRGRRRYYRRLWRKRRKKLR 377

                        410       420
                 ....*....|....*....|....*.
gi 495120839 410 RRHPKKGKYWIADRYFTRVKNRNWCF 435
Cdd:COG3344  378 RRLRLLLLRRARRRRAKRRARGRKRR 403
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 115-331 3.42e-41

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: 147.06  E-value: 3.42e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  115 KKSNGKLRPLGIPTMKDRAMQALYLLALEPvsETTADSNSYGFRKerstrdareqcfcVLAKKASPEWIMEGDIKGCFDH 194
Cdd:pfam00078   3 KKGKGKYRPISLLSIDYKALNKIIVKRLKP--ENLDSPPQPGFRP-------------GLAKLKKAKWFLKLDLKKAFDQ 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  195 ISHEWLLNNIPMDKV--MLRKWLKCgfvfNKELFPTEEGTPQGGIISPTLANMTLDGLQTMLAEKYhkkfvnrkttyypK 272
Cdd:pfam00078  68 VPLDELDRKLTAFTTppININWNGE----LSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-------------G 130

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 495120839  273 VHLVRYADDFIITGRSKEALEEIKPLVVDFLKERGLTLSEEKTKITHIDDGFDFLGYNI 331
Cdd:pfam00078 131 LTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFLKSKEVKYLGVTL 189
RVT_N pfam13655
N-terminal domain of reverse transcriptase; This domain is found at the N-terminus of ...
 18-99 5.75e-36

N-terminal domain of reverse transcriptase; This domain is found at the N-terminus of bacterial reverse transcriptases.


Pssm-ID: 433382  Cd Length: 83  Bit Score: 128.76  E-value: 5.75e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839   18 WESIDWNKCEIAVNKLQARIVKAQKAGKHGRVKSLQWVLTHSFYAKALAVKRVT-SNSGSDTAGVDKVKWSTPNARFKAI 96
Cdd:pfam13655   1 WKSIDWKKVERNVFKLQKRIYKASQEGDWRKVRRLQKLLTRSFSAKLLAVRRVTqENQGKKTAGVDGVKWLTPKQRLELV 80


                  ...
gi 495120839   97 GEL 99
Cdd:pfam13655  81 LSL 83
 
Name Accession Description Interval E-value
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 62-412 2.76e-160

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]


Pssm-ID: 275209 [Multi-domain]  Cd Length: 354  Bit Score: 460.39  E-value: 2.76e-160
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839   62 AKALAVKRVTSNSGsdTAGVDKVKWSTPNARF-----KAIGELKRRGYKPQPLKRVNIKKSNGKLRPLGIPTMKDRAMQA 136
Cdd:TIGR04416   3 NLLLAYKRVKANKG--AAGVDGVTIEDFEEYLeenlyKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRVVQQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  137 LYLLALEPVSETTADSNSYGFRKERSTRDAREQCFCVLAKKAspEWIMEGDIKGCFDHISHEWLLNNI---PMDKVML-- 211
Cdd:TIGR04416  81 AVKQVLEPIFEPDFSENSYGFRPGRSAHDAIAKARKRLNRGY--RWVVDADIKGFFDNINHDLLMKAVarrISDKRVLrl 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  212 -RKWLKCGFVFNKELFPTEEGTPQGGIISPTLANMTLDGLQTMLAEKYHkkfvnrkttyypKVHLVRYADDFIITGRSKE 290
Cdd:TIGR04416 159 iRRWLKAGVMEDGEVQETEEGTPQGGVISPLLANIYLHYLDDEWEKRGY------------KVRFVRYADDFVILCRSKE 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  291 ALEEIKPLVVDFLKERGLTLSEEKTKITHI-DDGFDFLGYNIRK-----YKGVLLIKPSKKSLKKFMQKIRGIIDSNKGS 364
Cdd:TIGR04416 227 AAERVLEALTKRLEELGLELNPEKTKIVHCkDGGFDFLGFTFRKrksknGKGKLLIKPSKKAVKKFKEKIRELTKRRRGL 306

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 495120839  365 KQESLIRLLNPVITGWVNYYKNCVASDTFRKADYLIFEKLWQWAKRRH 412
Cdd:TIGR04416 307 SLEELIKKLNPILRGWANYFGIANSSRTFSKLDHWIRRRLRRWLRKKW 354
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 110-331 1.76e-97

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: 295.26  E-value: 1.76e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 110 KRVNIKKSNGKLRPLGIPTMKDRAMQALYLLALEPVSETTADSNSYGFRKERSTRDAREQCFcvLAKKASPEWIMEGDIK 189
Cdd:cd01651    1 RRVYIPKPNGKKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDALKAIR--RNVKGGYTWVIEGDIK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 190 GCFDHISHEWLLNNIPMD----KVML--RKWLKCGFVFNKELFPTEEGTPQGGIISPTLANMTLDGLQTMLAEKYHKKFV 263
Cdd:cd01651   79 GFFDNIDHDLLLKILKRRigdkRVLRliRKWLKAGVLEDGKLVETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYYD 158

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495120839 264 NRKtTYYPKVHLVRYADDFIITGRSKEALEEIKPLVVDFLKERGLTLSEEKTKITHI-DDGFDFLGYNI 331
Cdd:cd01651  159 TSD-PKFRRLRYVRYADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRITHFkSEGFDFLGFTF 226
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
34-435 3.12e-79

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 255.39  E-value: 3.12e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  34 QARIVKAQKAGKHGRVKSLQ-WVLTHSFYAKALavKRVTSNSGSdtAGVDKVKWstpnARFKA---------IGELKRRG 103
Cdd:COG3344    3 LRRITEKAKPDPGARFTSLLeKILSRENLLEAY--KRVKANKGA--AGIDGVTV----EDFEEyleenlydlRERLRSGS 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 104 YKPQPLKRVNIKKSNGKLRPLGIPTMKDR-AMQALyLLALEPVSETTADSNSYGFRKERSTRDAREQCFCVLAKKasPEW 182
Cdd:COG3344   75 YRPQPVRRVEIPKPDGGVRPLGIPTVRDRvVQQAV-KQVLEPIFEPDFSDSSYGFRPGRSAHDALKKAREYINEG--YRW 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 183 IMEGDIKGCFDHISHEWLLNNIPM---DKVML---RKWLKCGFVFNKELFPTEEGTPQGGIISPTLANMTLDGLQTMLAE 256
Cdd:COG3344  152 VVDADIKKFFDNVDHDLLMKRLRRrikDKRVLrliRRWLKAGVMEDGVVEEREEGTPQGGPLSPLLANIYLHELDKELER 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 257 KYHKkfvnrkttyypkvhLVRYADDFIITGRSKEALEEIKPLVVDFLKERGLTLSEEKTKITHIDDGFDFLGYNIRKYKG 336
Cdd:COG3344  232 RGHR--------------FVRYADDFVILCRSKRAAERVLESLTERLEKLGLELNPEKTRIVRPGDGFKFLGFSFRRGKG 297

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 337 VLLIKPSKKSLKKFMQKIRGIIDSNKGSKQESLIRLLNPVITGWVNYYKNCVAS-------DTFRKADYLIFEKLWQWAK 409
Cdd:COG3344  298 LGFKFRPRKSKRKKKRKRRRRTRRRSRKRRRRIRRLLRRLLLGWRRYLLLAELKrllnallRGRRRYYRRLWRKRRKKLR 377

                        410       420
                 ....*....|....*....|....*.
gi 495120839 410 RRHPKKGKYWIADRYFTRVKNRNWCF 435
Cdd:COG3344  378 RRLRLLLLRRARRRRAKRRARGRKRR 403
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 115-331 3.42e-41

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: 147.06  E-value: 3.42e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  115 KKSNGKLRPLGIPTMKDRAMQALYLLALEPvsETTADSNSYGFRKerstrdareqcfcVLAKKASPEWIMEGDIKGCFDH 194
Cdd:pfam00078   3 KKGKGKYRPISLLSIDYKALNKIIVKRLKP--ENLDSPPQPGFRP-------------GLAKLKKAKWFLKLDLKKAFDQ 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  195 ISHEWLLNNIPMDKV--MLRKWLKCgfvfNKELFPTEEGTPQGGIISPTLANMTLDGLQTMLAEKYhkkfvnrkttyypK 272
Cdd:pfam00078  68 VPLDELDRKLTAFTTppININWNGE----LSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-------------G 130

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 495120839  273 VHLVRYADDFIITGRSKEALEEIKPLVVDFLKERGLTLSEEKTKITHIDDGFDFLGYNI 331
Cdd:pfam00078 131 LTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFLKSKEVKYLGVTL 189
RVT_N pfam13655
N-terminal domain of reverse transcriptase; This domain is found at the N-terminus of ...
 18-99 5.75e-36

N-terminal domain of reverse transcriptase; This domain is found at the N-terminus of bacterial reverse transcriptases.


Pssm-ID: 433382  Cd Length: 83  Bit Score: 128.76  E-value: 5.75e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839   18 WESIDWNKCEIAVNKLQARIVKAQKAGKHGRVKSLQWVLTHSFYAKALAVKRVT-SNSGSDTAGVDKVKWSTPNARFKAI 96
Cdd:pfam13655   1 WKSIDWKKVERNVFKLQKRIYKASQEGDWRKVRRLQKLLTRSFSAKLLAVRRVTqENQGKKTAGVDGVKWLTPKQRLELV 80


                  ...
gi 495120839   97 GEL 99
Cdd:pfam13655  81 LSL 83
GIIM pfam08388
Group II intron, maturase-specific domain; This region is found mainly in various bacterial ...
 347-425 3.20e-26

Group II intron, maturase-specific domain; This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing.


Pssm-ID: 429966 [Multi-domain]  Cd Length: 80  Bit Score: 101.89  E-value: 3.20e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839  347 LKKFMQKIRGII-DSNKGSKQESLIRLLNPVITGWVNYYKNCVASDTFRKADYLIFEKLWQWAKRRHPKKGKYWIADRYF 425
Cdd:pfam08388   1 VKRFKRKIRELTlRSHKGLSLEDLIRKLNPIIRGWANYFRHVVSKRTFSKLDHWIRRRLRRWAWRRHKRKKRRWILRKYW 80
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 142-320 1.26e-13

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: 70.40  E-value: 1.26e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 142 LEPVSETTADSNSYGFRKERSTRDAreqcfcVLAKKaspEWIMEG------------DIKGCFDHISHEWLLNNIpmdkv 209
Cdd:cd01650   40 LRPVLEENILPNQFGFRPGRSTTDA------ILLLR---EVIEKAkekkkslvlvflDFEKAFDSVDHEFLLKAL----- 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 210 mlrkwlkcgfvfnkelfpteeGTPQGGIISPTLANMTLDGLQTMLAEKYHKKFVNRKTTYypkvhlVRYADDFIITGRSK 289
Cdd:cd01650  106 ---------------------GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITH------LAYADDIVLFSEGK 158

                        170       180       190
                 ....*....|....*....|....*....|..
gi 495120839 290 E-ALEEIKPLVVDFLKERGLTLSEEKTKITHI 320
Cdd:cd01650  159 SrKLQELLQRLQEWSKESGLKINPSKSKVMLI 190
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 187-343 2.30e-13

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: 67.74  E-value: 2.30e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 187 DIKGCFDHISHE---WLLNNIPMDKVMLRKW-LKCGFVFNKELFPTEEGT---PQGGIISPTLANMTLDGLQTMLAEKYh 259
Cdd:cd01646    2 DISNFYDSIYTHslpWALHGKIKAKQLLKLLrLLGNLLDLLLLSSQYGQTnglPIGPLTSRFLANIYLNDVDHELKSKL- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 260 kkfvnrkttyyPKVHLVRYADDFIITGRSKEALEEIKPLVVDFLKERGLTLSEEKTKITHIDDGFDFLGYNIRKYKGVLL 339
Cdd:cd01646   81 -----------KGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILPLPEGTASKDFLGYRFSPILL 149


                 ....
gi 495120839 340 IKPS 343
Cdd:cd01646  150 IKSS 153
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 223-331 1.07e-10

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: 58.52  E-value: 1.07e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 223 KELFPTEEgTPQGGIISPTLANMTLDGLQTMLAEKYHKKFvnrkttyypkvhLVRYADDFIITGRSKEAlEEIKPLVVDF 302
Cdd:cd00304    4 KSFFTSIP-LPQGSPLSPALANLYMEKLEAPILKQLLDIT------------LIRYVDDLVVIAKSEQQ-AVKKRELEEF 69

                         90       100
                 ....*....|....*....|....*....
gi 495120839 303 LKERGLTLSEEKTKITHIDDGFDFLGYNI 331
Cdd:cd00304   70 LARLGLNLSDEKTQFTEKEKKFKFLGILV 98
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 233-331 4.94e-08

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: 53.44  E-value: 4.94e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 233 PQGGIISPTLANMTLDglQTMlaEKYHKKfvnrkttyYPKVHLVRYADDFIITGRSKEALEEIKPLVVDFLKERGLTLSE 312
Cdd:cd01645  130 PQGMKNSPTICQSFVA--QAL--EPFRKQ--------YPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPP 197

                         90
                 ....*....|....*....
gi 495120839 313 EKTKithIDDGFDFLGYNI 331
Cdd:cd01645  198 EKVQ---KEPPFQYLGYEL 213
TERT cd01648
TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that ...
 186-331 2.31e-06

TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at the chromosome ends protects against the erosion of gene-encoding DNA. Telomerase is not normally expressed in somatic cells. It has been suggested that exogenous TERT may extend the lifespan of, or even immortalize, the cell. However, recent studies have shown that telomerase activity can be induced by a number of oncogenes. Conversely, the oncogene c-myc can be activated in human TERT immortalized cells. Sequence comparisons place the telomerase proteins in the RT family but reveal hallmarks that distinguish them from retroviral and retrotransposon relatives.


Pssm-ID: 238826  Cd Length: 119  Bit Score: 46.87  E-value: 2.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 186 GDIKGCFDHISHEWLLNnipmdkvmlrkwlkcgfvfnkelfpteEGTPQGGIISPTLANMTLDglqTMLAEKYHKKFVNR 265
Cdd:cd01648    1 TDIKKCYDSIPQYYRQK---------------------------VGIPQGSPLSSLLCSLYYA---DLENKYLSFLDVID 50

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495120839 266 KTTYypkvhLVRYADDFI-ITGRSKEALEEIKPLVVDFLKERGLTLSEEKTKIT------HIDDGFDFLGYNI 331
Cdd:cd01648   51 KDSL-----LLRLVDDFLlITTSLDKAIKFLNLLLRGFINQYKTFVNFDKTQINfsfaqlDSSDLIPWCGLLI 118
RT_Bac_retron_II cd03487
RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 116-317 8.76e-06

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: 46.80  E-value: 8.76e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 116 KSNGKLRPLGIPTMKDRAMQ---ALYLLALEPVSEttadsNSYGFRKERSTRDAreqcfcvlAKK-ASPEWIMEGDIKGC 191
Cdd:cd03487    1 KKNGGFRTIYAPKPELKAIQrkiLSNLLSKLPVHD-----AAHGFVKGRSIITN--------AKPhCGAKYVLKLDIKDF 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 192 FDHISHEwllnnipmdkvMLRKWLKCGFVFNKEL------FPTEEGT-PQGGIISPTLANMT---LDGLQTMLAEKYHkk 261
Cdd:cd03487   68 FPSITFE-----------RVRGVFRSLGYFSPDVatilakLCTYNGHlPQGAPTSPALSNLVfrkLDERLSKLAKSNG-- 134

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495120839 262 fvnrkttyypkVHLVRYADDFIITGR------SKEALEEIKPLvvdfLKERGLTLSEEKTKI 317
Cdd:cd03487  135 -----------LTYTRYADDITFSSNkklkeaLDKLLEIIRSI----LSEEGFKINKSKTRI 181
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 233-329 7.73e-04

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: 41.18  E-value: 7.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495120839 233 PQGGIISPTLANMTLdglqtmlaekyhKKFVNRKTTYYPKVHLVRYADDFIITGRSKEALEEIKPLVVDFLKERGLTLSe 312
Cdd:cd03715  126 PQGFKNSPTLFHEAL------------ARDLAPFPLEHEGTILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVS- 192

                         90
                 ....*....|....*..
gi 495120839 313 eKTKITHIDDGFDFLGY 329
Cdd:cd03715  193 -PKKAQICRAEVKFLGV 208
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 278-331 7.28e-03

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: 37.57  E-value: 7.28e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495120839 278 YADDFIITGRSKEALEEIKPLVVDFLKERGLTLSEEKTKItHIDDGfDFLGYNI 331
Cdd:cd01647  126 YLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEF-GVPEV-EFLGHIV 177
 
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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