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Conserved domains on  [gi|242821605|ref|XP_002487714|]
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gag/polymerase/env polyprotein, putative [Talaromyces stipitatus ATCC 10500]

Protein Classification

reverse transcriptase family protein( domain architecture ID 10108258)

reverse transcriptase family protein may be an RNA-directed DNA polymerase that catalyzes DNA replication from an RNA template of retrotransposons or retrons

CATH:  3.10.10.10
EC:  2.7.7.-
Gene Ontology:  GO:0016779|GO:0003676
PubMed:  1698615
SCOP:  4002796

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 242-418 1.07e-89

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: 270.62  E-value: 1.07e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605 242 GFIRPSKSPAASPILFVPKKDGTLRLCVDYRGLNKVTIKNRYLLPLMGEILDYINGAKVFSKINLKDAYYHIRIRPGDKW 321
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605 322 KTAFRTRYGHYKYLVMLFGLTNAPAAFQGYINQALRGLVDDFYIIYLDDILIFSKTKEEHTEHLRLICERLQTAELYAKP 401
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 242821605 402 SKCQFYQNKIEFLGFII 418
Cdd:cd01647  161 EKCEFGVPEVEFLGHIV 177
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 242-418 1.07e-89

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: 270.62  E-value: 1.07e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605 242 GFIRPSKSPAASPILFVPKKDGTLRLCVDYRGLNKVTIKNRYLLPLMGEILDYINGAKVFSKINLKDAYYHIRIRPGDKW 321
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605 322 KTAFRTRYGHYKYLVMLFGLTNAPAAFQGYINQALRGLVDDFYIIYLDDILIFSKTKEEHTEHLRLICERLQTAELYAKP 401
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 242821605 402 SKCQFYQNKIEFLGFII 418
Cdd:cd01647  161 EKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 258-418 8.03e-33

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: 122.80  E-value: 8.03e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605  258 VPKKD-GTLRLC----VDYRGLNKVTIKNRYLLPLMGE-------ILDYINGAKVFSKINLKDAYYHIRIRPGDKWKTAF 325
Cdd:pfam00078   1 IPKKGkGKYRPIsllsIDYKALNKIIVKRLKPENLDSPpqpgfrpGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605  326 RTR-----------YGHYKYLVMLFGLTNAPAAFQGYINQALRGL---VDDFYIIYLDDILIFSKTKEEHTEHLRLICER 391
Cdd:pfam00078  81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                         170       180
                  ....*....|....*....|....*....
gi 242821605  392 LQTAELYAKPSKCQFY--QNKIEFLGFII 418
Cdd:pfam00078 161 LKESGLKINPEKTQFFlkSKEVKYLGVTL 189
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 242-418 1.07e-89

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: 270.62  E-value: 1.07e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605 242 GFIRPSKSPAASPILFVPKKDGTLRLCVDYRGLNKVTIKNRYLLPLMGEILDYINGAKVFSKINLKDAYYHIRIRPGDKW 321
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605 322 KTAFRTRYGHYKYLVMLFGLTNAPAAFQGYINQALRGLVDDFYIIYLDDILIFSKTKEEHTEHLRLICERLQTAELYAKP 401
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 242821605 402 SKCQFYQNKIEFLGFII 418
Cdd:cd01647  161 EKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 258-418 8.03e-33

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: 122.80  E-value: 8.03e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605  258 VPKKD-GTLRLC----VDYRGLNKVTIKNRYLLPLMGE-------ILDYINGAKVFSKINLKDAYYHIRIRPGDKWKTAF 325
Cdd:pfam00078   1 IPKKGkGKYRPIsllsIDYKALNKIIVKRLKPENLDSPpqpgfrpGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605  326 RTR-----------YGHYKYLVMLFGLTNAPAAFQGYINQALRGL---VDDFYIIYLDDILIFSKTKEEHTEHLRLICER 391
Cdd:pfam00078  81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                         170       180
                  ....*....|....*....|....*....
gi 242821605  392 LQTAELYAKPSKCQFY--QNKIEFLGFII 418
Cdd:pfam00078 161 LKESGLKINPEKTQFFlkSKEVKYLGVTL 189
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 221-418 9.57e-27

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


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 106.98  E-value: 9.57e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605 221 YPLSRAELEVLQYYLQENLKKGFIRPSKSPAASPILFVPKKDGTLRLCVDYRGLNKVTIKnryllplMGEI------LDY 294
Cdd:cd01645    7 WPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQD-------MGALqpglphPAA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605 295 INGAKVFSKINLKDAYYHIRIRPGDKWKTAF-------RTRYGHYKYLVMLFGLTNAPAAFQGYINQALRGLVD---DFY 364
Cdd:cd01645   80 LPKGWPLIVLDLKDCFFSIPLHPDDRERFAFtvpsinnKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKqypDIV 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 242821605 365 II-YLDDILIFSKTKEEHTEHLRLICERLQTAELYAKPSKCQfYQNKIEFLGFII 418
Cdd:cd01645  160 IYhYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQ-KEPPFQYLGYEL 213
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 221-418 2.39e-24

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: 100.11  E-value: 2.39e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605 221 YPLSRAELEVLQYYLQENLKKGFIRPSKSPAASPILFVPKKDG-TLRLCVDYRGLNKVTIKNRYLLPLMGEILDYINGA- 298
Cdd:cd03715    7 YPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLPPKh 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605 299 KVFSKINLKDAYYHIRIRPGDKWKTAFRTRYGHYKYLVMLFGLTNAPAAFqgyiNQALRGLVDDF--------YIIYLDD 370
Cdd:cd03715   87 QWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLF----HEALARDLAPFplehegtiLLQYVDD 162

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 242821605 371 ILIFSKTKEEHTEHLRLICERLQTAELYAKPSKCQFYQNKIEFLGFII 418
Cdd:cd03715  163 LLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 304-418 6.11e-10

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


Pssm-ID: 239684 [Multi-domain]  Cd Length: 119  Bit Score: 56.58  E-value: 6.11e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605 304 INLKDAYYHIRIRPGDKWKTAFRTRYGHYKYLVMLFGLTNAPAAFQGYINQALRGLVDDFY--IIYLDDILIFS---KTK 378
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVriFSYLDDLLIIAssiKTS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 242821605 379 EEHTEHLRLIceRLQTAELYAKPSKCQFY-QNKIEFLGFII 418
Cdd:cd03714   81 EAVLRHLRAT--LLANLGFTLNLEKSKLGpTQRITFLGLEL 119
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 339-418 2.44e-05

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


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 43.11  E-value: 2.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242821605 339 FGLTNAPAAFQGYINQ----ALRGLVDDFYIIYLDDILIFSKTkEEHTEHLRLICERLQTAELYAKPSKCQFY--QNKIE 412
Cdd:cd00304   14 QGSPLSPALANLYMEKleapILKQLLDITLIRYVDDLVVIAKS-EQQAVKKRELEEFLARLGLNLSDEKTQFTekEKKFK 92


                 ....*.
gi 242821605 413 FLGFII 418
Cdd:cd00304   93 FLGILV 98
 
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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