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Conserved domains on  [gi|2274520711|gb|UTT89831|]
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hypothetical protein NDA17_004223 [Ustilago hordei]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 88-264 3.13e-84

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: 266.38  E-value: 3.13e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711  88 GFIRPSKSPARSPVLFVPKKDGGLRLCVDYRGLNEITVKNRAPLPLIEEQLFLLRKARIYTKLDLRAAYNLIQIAKGDEW 167
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 168 KTAFGTQLGLYEYLVMPFGLANAPAHFQSFINDIFRDIIGVYVVVYLDDFLIFSDTEEVHVKHVTEVLTRLRSNRLFAKL 247
Cdd:cd01647    81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                         170
                  ....*....|....*..
gi 2274520711 248 SKCEFHTKTVEFLGYII 264
Cdd:cd01647   161 EKCEFGVPEVEFLGHIV 177
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
332-411 2.35e-34

RNase H-like domain found in reverse transcriptase;


:

Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 126.46  E-value: 2.35e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 332 EEAQQAFHKLIQAFTSAGVLQHFDYHLPTRLETDASDFAIAGVLKQEHE-GRWHPVAFYSRKMSSAEKNYEIHDKELLAV 410
Cdd:pfam17919   3 EECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDdGGERPIAYASRKLSPAERNYSTTEKELLAI 82


                  .
gi 2274520711 411 Y 411
Cdd:pfam17919  83 V 83
transpos_IS481 super family cl41329
IS481 family transposase; null
 548-668 1.67e-09

IS481 family transposase; null


The actual alignment was detected with superfamily member NF033577:

Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.91  E-value: 1.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 548 IKGLPPsKKYDSKTYdsILVIVNRLTKFAILA--PTHKTVTAKQTAVLLYghmvRLFGYPDHMV-SDRGRQFIS--GAWK 622
Cdd:NF033577  135 IKKLGR-IPDVGRLY--LHTAIDDHSRFAYAElyPDETAETAADFLRRAF----AEHGIPIRRVlTDNGSEFRSraHGFE 207

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2274520711 623 AFAEQMGVKHSLSMAYHPQTDGQTERVNQVIEQ---YLRMYCNYEQ-----DDW 668
Cdd:NF033577  208 LALAELGIEHRRTRPYHPQTNGKVERFHRTLKDefaYARPYESLAElqaalDEW 261
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 88-264 3.13e-84

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: 266.38  E-value: 3.13e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711  88 GFIRPSKSPARSPVLFVPKKDGGLRLCVDYRGLNEITVKNRAPLPLIEEQLFLLRKARIYTKLDLRAAYNLIQIAKGDEW 167
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 168 KTAFGTQLGLYEYLVMPFGLANAPAHFQSFINDIFRDIIGVYVVVYLDDFLIFSDTEEVHVKHVTEVLTRLRSNRLFAKL 247
Cdd:cd01647    81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                         170
                  ....*....|....*..
gi 2274520711 248 SKCEFHTKTVEFLGYII 264
Cdd:cd01647   161 EKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 104-264 4.72e-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: 148.99  E-value: 4.72e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 104 VPKKD-GGLRLC----VDYRGLNEITVK-------NRAPLPLIEEQLFLLRKARIYTKLDLRAAYNLIQIAKGDEWKTAF 171
Cdd:pfam00078   1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 172 GTQL-----------GLYEYLVMPFGLANAPAHFQSFINDIFRDI---IGVYVVVYLDDFLIFSDTEEVHVKHVTEVLTR 237
Cdd:pfam00078  81 TTPPininwngelsgGRYEWKGLPQGLVLSPALFQLFMNELLRPLrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                         170       180
                  ....*....|....*....|....*....
gi 2274520711 238 LRSNRLFAKLSKCEF--HTKTVEFLGYII 264
Cdd:pfam00078 161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
332-411 2.35e-34

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 126.46  E-value: 2.35e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 332 EEAQQAFHKLIQAFTSAGVLQHFDYHLPTRLETDASDFAIAGVLKQEHE-GRWHPVAFYSRKMSSAEKNYEIHDKELLAV 410
Cdd:pfam17919   3 EECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDdGGERPIAYASRKLSPAERNYSTTEKELLAI 82


                  .
gi 2274520711 411 Y 411
Cdd:pfam17919  83 V 83
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 361-411 6.73e-22

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 91.79  E-value: 6.73e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2274520711 361 RLETDASDFAIAGVLKQEHE-GRWHPVAFYSRKMSSAEKNYEIHDKELLAVY 411
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAERNYSTTEKELLAIV 52
transpos_IS481 NF033577
IS481 family transposase; null
 548-668 1.67e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.91  E-value: 1.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 548 IKGLPPsKKYDSKTYdsILVIVNRLTKFAILA--PTHKTVTAKQTAVLLYghmvRLFGYPDHMV-SDRGRQFIS--GAWK 622
Cdd:NF033577  135 IKKLGR-IPDVGRLY--LHTAIDDHSRFAYAElyPDETAETAADFLRRAF----AEHGIPIRRVlTDNGSEFRSraHGFE 207

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2274520711 623 AFAEQMGVKHSLSMAYHPQTDGQTERVNQVIEQ---YLRMYCNYEQ-----DDW 668
Cdd:NF033577  208 LALAELGIEHRRTRPYHPQTNGKVERFHRTLKDefaYARPYESLAElqaalDEW 261
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 553-640 1.15e-08

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 53.09  E-value: 1.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 553 PSKKYDSKTYdsILVIVNRLTKFAILAPTHKTVTAKQT-AVLLYghMVRLFGY-PDHMVSDRGRQFISGAWKAFAEQMGV 630
Cdd:pfam00665  13 RIPGGGGKLY--LLVIVDDFSREILAWALSSEMDAELVlDALER--AIAFRGGvPLIIHSDNGSEYTSKAFREFLKDLGI 88

                          90
                  ....*....|
gi 2274520711 631 KHSLSMAYHP 640
Cdd:pfam00665  89 KPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
610-691 7.25e-05

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 45.53  E-value: 7.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 610 SDRGRQFISGAWKAFAEQMGVKHSLSMAYHPQTDGQTERVNQVIEQ---YLRMYCNYEQddwANlLDTAAFV--YNNT-V 683
Cdd:COG2801   214 SDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYellYRRRFESLEE---AR-EAIEEYIefYNHErP 289


                  ....*....
gi 2274520711 684 HNSIG-VSP 691
Cdd:COG2801   290 HSSLGyLTP 298
transpos_IS30 NF033563
IS30 family transposase;
560-657 6.94e-03

IS30 family transposase;


Pssm-ID: 468088 [Multi-domain]  Cd Length: 267  Bit Score: 39.12  E-value: 6.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 560 KTYDSILVIVNRLTKFAILA--PTHKTVTAKQTAVLLyghmvrLFGYPDHMV----SDRGRQFisGAWKAFAEQMGVK-- 631
Cdd:NF033563  145 KHKSALLTLVERKSRFVILVklPDKTAESVNKALIKL------LKPLPKHLRksitADNGKEF--ARHSEIEEALGIDvy 216

                          90       100
                  ....*....|....*....|....*...
gi 2274520711 632 --HslsmAYHPQTDGQTERVNQVIEQYL 657
Cdd:NF033563  217 faD----PYSPWQRGTNENTNGLLRQYL 240
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 88-264 3.13e-84

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: 266.38  E-value: 3.13e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711  88 GFIRPSKSPARSPVLFVPKKDGGLRLCVDYRGLNEITVKNRAPLPLIEEQLFLLRKARIYTKLDLRAAYNLIQIAKGDEW 167
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 168 KTAFGTQLGLYEYLVMPFGLANAPAHFQSFINDIFRDIIGVYVVVYLDDFLIFSDTEEVHVKHVTEVLTRLRSNRLFAKL 247
Cdd:cd01647    81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                         170
                  ....*....|....*..
gi 2274520711 248 SKCEFHTKTVEFLGYII 264
Cdd:cd01647   161 EKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 104-264 4.72e-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: 148.99  E-value: 4.72e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 104 VPKKD-GGLRLC----VDYRGLNEITVK-------NRAPLPLIEEQLFLLRKARIYTKLDLRAAYNLIQIAKGDEWKTAF 171
Cdd:pfam00078   1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 172 GTQL-----------GLYEYLVMPFGLANAPAHFQSFINDIFRDI---IGVYVVVYLDDFLIFSDTEEVHVKHVTEVLTR 237
Cdd:pfam00078  81 TTPPininwngelsgGRYEWKGLPQGLVLSPALFQLFMNELLRPLrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                         170       180
                  ....*....|....*....|....*....
gi 2274520711 238 LRSNRLFAKLSKCEF--HTKTVEFLGYII 264
Cdd:pfam00078 161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
332-411 2.35e-34

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 126.46  E-value: 2.35e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 332 EEAQQAFHKLIQAFTSAGVLQHFDYHLPTRLETDASDFAIAGVLKQEHE-GRWHPVAFYSRKMSSAEKNYEIHDKELLAV 410
Cdd:pfam17919   3 EECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDdGGERPIAYASRKLSPAERNYSTTEKELLAI 82


                  .
gi 2274520711 411 Y 411
Cdd:pfam17919  83 V 83
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 361-411 6.73e-22

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 91.79  E-value: 6.73e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2274520711 361 RLETDASDFAIAGVLKQEHE-GRWHPVAFYSRKMSSAEKNYEIHDKELLAVY 411
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAERNYSTTEKELLAIV 52
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 355-410 6.75e-22

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


Pssm-ID: 465565  Cd Length: 104  Bit Score: 91.03  E-value: 6.75e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2274520711 355 DYHLPTRLETDASDFAIAGVLKQ-EHEGRWHPVAFYSRKMSSAEKNYEIHDKELLAV 410
Cdd:pfam17917   1 DPSKPFILETDASDYGIGAVLSQkDEDGKERPIAYASRKLTPAERNYSTTEKELLAI 57
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 81-264 5.05e-20

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: 89.33  E-value: 5.05e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711  81 LDENLEKGFIRPSKSPARSPVLFVPKKDGG-LRLCVDYRGLNEITVKNRAPLPLIEEQLFLL-RKARIYTKLDLRAAYNL 158
Cdd:cd03715    21 IQELLEAGILVPCQSPWNTPILPVKKPGGNdYRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLpPKHQWYTVLDLANAFFS 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 159 IQIAKGDEWKTAF---GTQlglYEYLVMPFGLANAPAHFQsfiNDIFRDI-------IGVYVVVYLDDFLIFSDTEEVHV 228
Cdd:cd03715   101 LPLAPDSQPLFAFeweGQQ---YTFTRLPQGFKNSPTLFH---EALARDLapfplehEGTILLQYVDDLLLAADSEEDCL 174

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2274520711 229 KHVTEVLTRLRSNRLFAKLSKCEFHTKTVEFLGYII 264
Cdd:cd03715   175 KGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 62-238 2.49e-18

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: 84.26  E-value: 2.49e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711  62 PQGPLylkgPKEMSE-LRRYLDENLEKGFIRPSKSPARSPVLFVPKKDGGLRLCVDYRGLNEITVknraplPLIEEQLFL 140
Cdd:cd01645     5 KQWPL----TEEKLEaLTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQ------DMGALQPGL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 141 -----LRKARIYTKLDLRAAYNLIQIAKGDEWKTAF----------GTQlglYEYLVMPFGLANAPAHFQSFINDIFRDI 205
Cdd:cd01645    75 phpaaLPKGWPLIVLDLKDCFFSIPLHPDDRERFAFtvpsinnkgpAKR---YQWKVLPQGMKNSPTICQSFVAQALEPF 151

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2274520711 206 IG----VYVVVYLDDFLIFSDTEEVHVKHVTEVLTRL 238
Cdd:cd01645   152 RKqypdIVIYHYMDDILIASDLEGQLREIYEELRQTL 188
transpos_IS481 NF033577
IS481 family transposase; null
 548-668 1.67e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.91  E-value: 1.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 548 IKGLPPsKKYDSKTYdsILVIVNRLTKFAILA--PTHKTVTAKQTAVLLYghmvRLFGYPDHMV-SDRGRQFIS--GAWK 622
Cdd:NF033577  135 IKKLGR-IPDVGRLY--LHTAIDDHSRFAYAElyPDETAETAADFLRRAF----AEHGIPIRRVlTDNGSEFRSraHGFE 207

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2274520711 623 AFAEQMGVKHSLSMAYHPQTDGQTERVNQVIEQ---YLRMYCNYEQ-----DDW 668
Cdd:NF033577  208 LALAELGIEHRRTRPYHPQTNGKVERFHRTLKDefaYARPYESLAElqaalDEW 261
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 553-640 1.15e-08

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 53.09  E-value: 1.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 553 PSKKYDSKTYdsILVIVNRLTKFAILAPTHKTVTAKQT-AVLLYghMVRLFGY-PDHMVSDRGRQFISGAWKAFAEQMGV 630
Cdd:pfam00665  13 RIPGGGGKLY--LLVIVDDFSREILAWALSSEMDAELVlDALER--AIAFRGGvPLIIHSDNGSEYTSKAFREFLKDLGI 88

                          90
                  ....*....|
gi 2274520711 631 KHSLSMAYHP 640
Cdd:pfam00665  89 KPSFSRPGNP 98
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 150-264 1.40e-06

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: 47.72  E-value: 1.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 150 LDLRAAYNLIQIAKgDEWK-TAFGTQLGLYEYLVMPFGLANAPAHFQSFINDIFRDI--IGVYVVVYLDDFLIFSDTeEV 226
Cdd:cd03714     1 VDLKDAYFHIPILP-RSRDlLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLrlLGVRIFSYLDDLLIIASS-IK 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2274520711 227 HVKHVTEVL--TRLRSNRLFAKLSKCE-FHTKTVEFLGYII 264
Cdd:cd03714    79 TSEAVLRHLraTLLANLGFTLNLEKSKlGPTQRITFLGLEL 119
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
610-691 7.25e-05

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 45.53  E-value: 7.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 610 SDRGRQFISGAWKAFAEQMGVKHSLSMAYHPQTDGQTERVNQVIEQ---YLRMYCNYEQddwANlLDTAAFV--YNNT-V 683
Cdd:COG2801   214 SDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYellYRRRFESLEE---AR-EAIEEYIefYNHErP 289


                  ....*....
gi 2274520711 684 HNSIG-VSP 691
Cdd:COG2801   290 HSSLGyLTP 298
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
565-682 2.31e-03

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 41.02  E-value: 2.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 565 ILVIVNRLTKFAILA--PTHKTVTAKQTavllyghMVRLF-GYPDHMV----SDRGRQFisGAWKAFAEQMGVKHSLSMA 637
Cdd:COG2826   189 LLTLVERKSRFVILLklPDKTAESVADA-------LIRLLrKLPAFLRksitTDNGKEF--ADHKEIEAALGIKVYFADP 259

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2274520711 638 YHPQTDGQTERVNQVIEQYLRMYCNYEQDDwANLLDTAAFVYNNT 682
Cdd:COG2826   260 YSPWQRGTNENTNGLLRQYFPKGTDFSTVT-QEELDAIADRLNNR 303
transpos_IS30 NF033563
IS30 family transposase;
560-657 6.94e-03

IS30 family transposase;


Pssm-ID: 468088 [Multi-domain]  Cd Length: 267  Bit Score: 39.12  E-value: 6.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2274520711 560 KTYDSILVIVNRLTKFAILA--PTHKTVTAKQTAVLLyghmvrLFGYPDHMV----SDRGRQFisGAWKAFAEQMGVK-- 631
Cdd:NF033563  145 KHKSALLTLVERKSRFVILVklPDKTAESVNKALIKL------LKPLPKHLRksitADNGKEF--ARHSEIEEALGIDvy 216

                          90       100
                  ....*....|....*....|....*...
gi 2274520711 632 --HslsmAYHPQTDGQTERVNQVIEQYL 657
Cdd:NF033563  217 faD----PYSPWQRGTNENTNGLLRQYL 240
 
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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