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Conserved domains on  [gi|19115809|ref|NP_594897|]
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retrotransposable element/transposon Tf2-type [Schizosaccharomyces pombe]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_A2_2 super family cl23191
Retrotransposon peptidase; This is a small family of fungal retroviral aspartyl peptidases.
 219-355 3.77e-90

Retrotransposon peptidase; This is a small family of fungal retroviral aspartyl peptidases.


The actual alignment was detected with superfamily member pfam12382:

Pssm-ID: 152817  Cd Length: 137  Bit Score: 287.37  E-value: 3.77e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    219 KNNTTNSRNLRKTNVSRIEYSSNKFLNHTRKRYEMVLQAELPDFKCSIPCLIDTGAQANIITEETVRAHKLPTRPWSKSV 298
Cdd:pfam12382    1 KENDTKDRKLKKTNVSRIEYSSEKFLKHKKKRYEMVLQAELPDFKCSIPCLIDTGAQANIITEETVRAHKLPTRPWLKSV 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 19115809    299 IYGGVYPNKINRKTIKLNISLNGISIKTEFLVVKKFSHPAAISFTTLYDNNIEISSS 355
Cdd:pfam12382   81 IYGGVYPNKINRKTIKLIINLNGISIKTEFLVVKKFSHPAAISFTTLYDNNIEISSS 137
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 439-615 1.49e-73

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: 242.12  E-value: 1.49e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  439 GIIRESKAINACPVMFVPKKEGTLRMVVDYKPLNKYVKPNIYPLPLIEQLLAKIQGSTIFTKLDLKSAYHLIRVRKGDEH 518
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  519 KLAFRCPRGVFEYLVMPYGISIAPAHFQYFINTILGEVKESHVVCYMDNILIHSKSESEHVKHVKDVLQKLKNANLIINQ 598
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 19115809  599 AKCEFHQSQVKFIGYHI 615
Cdd:cd01647  161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 710-833 7.07e-56

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: 189.24  E-value: 7.07e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  710 LETDASDVAVGAVLSQKHDDDKYYPVGYYSAKMSKAQLNYSVSDKEMLAIIKSLKHWRHYLESTiePFKILTDHRNLIgR 789
Cdd:cd09274    2 LETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGR--PFTVYTDHKALK-Y 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 19115809  790 ITNESEPeNKRLARWQLFLQDFNFEINYRPGSANHIADALSRIV 833
Cdd:cd09274   79 LLTQKDL-NGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 907-966 1.76e-15

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


:

Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 71.89  E-value: 1.76e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    907 NDTQLTRTIIKKYHEEGKliHPGIELLTNIILRRFTWKGIRKQIQEYVQNCHTCQINKSR 966
Cdd:pfam17921    1 VPKSLRKEILKEAHDSGG--HLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 983-1079 2.84e-12

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: 64.26  E-value: 2.84e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    983 PWESLSMDFIT-ALPESSGYNALFVVVDRFSKMAILVPCTKSITAEQTARMFDQRVIAYFGNPKEIIADNDHIFTSQTWK 1061
Cdd:pfam00665    1 PNQLWQGDFTYiRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 19115809   1062 DFAHKYNFVMKFSLPYRP 1079
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
 
Name Accession Description Interval E-value
Peptidase_A2_2 pfam12382
Retrotransposon peptidase; This is a small family of fungal retroviral aspartyl peptidases.
 219-355 3.77e-90

Retrotransposon peptidase; This is a small family of fungal retroviral aspartyl peptidases.


Pssm-ID: 152817  Cd Length: 137  Bit Score: 287.37  E-value: 3.77e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    219 KNNTTNSRNLRKTNVSRIEYSSNKFLNHTRKRYEMVLQAELPDFKCSIPCLIDTGAQANIITEETVRAHKLPTRPWSKSV 298
Cdd:pfam12382    1 KENDTKDRKLKKTNVSRIEYSSEKFLKHKKKRYEMVLQAELPDFKCSIPCLIDTGAQANIITEETVRAHKLPTRPWLKSV 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 19115809    299 IYGGVYPNKINRKTIKLNISLNGISIKTEFLVVKKFSHPAAISFTTLYDNNIEISSS 355
Cdd:pfam12382   81 IYGGVYPNKINRKTIKLIINLNGISIKTEFLVVKKFSHPAAISFTTLYDNNIEISSS 137
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 439-615 1.49e-73

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: 242.12  E-value: 1.49e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  439 GIIRESKAINACPVMFVPKKEGTLRMVVDYKPLNKYVKPNIYPLPLIEQLLAKIQGSTIFTKLDLKSAYHLIRVRKGDEH 518
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  519 KLAFRCPRGVFEYLVMPYGISIAPAHFQYFINTILGEVKESHVVCYMDNILIHSKSESEHVKHVKDVLQKLKNANLIINQ 598
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 19115809  599 AKCEFHQSQVKFIGYHI 615
Cdd:cd01647  161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 710-833 7.07e-56

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: 189.24  E-value: 7.07e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  710 LETDASDVAVGAVLSQKHDDDKYYPVGYYSAKMSKAQLNYSVSDKEMLAIIKSLKHWRHYLESTiePFKILTDHRNLIgR 789
Cdd:cd09274    2 LETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGR--PFTVYTDHKALK-Y 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 19115809  790 ITNESEPeNKRLARWQLFLQDFNFEINYRPGSANHIADALSRIV 833
Cdd:cd09274   79 LLTQKDL-NGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
678-779 2.95e-44

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 155.35  E-value: 2.95e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    678 WTPTQTQAIENIKQCLVSPPVLRHFDFSKKILLETDASDVAVGAVLSQKHDDDKYYPVGYYSAKMSKAQLNYSVSDKEML 757
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGGERPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|..
gi 19115809    758 AIIKSLKHWRHYLESTiePFKI 779
Cdd:pfam17919   81 AIVFALKKFRHYLLGR--KFTV 100
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 455-615 7.40e-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: 7.40e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    455 VPKK-EGTLRMV----VDYKPLNKYVKPNI-------YPLPLIEQLLAKIQGSTIFTKLDLKSAYHLIRVRKGDEHKLAF 522
Cdd:pfam00078    1 IPKKgKGKYRPIsllsIDYKALNKIIVKRLkpenldsPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    523 RCP-----------RGVFEYLVMPYGISIAPAHFQYFINTILGEVK---ESHVVCYMDNILIHSKSESEHVKHVKDVLQK 588
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 19115809    589 LKNANLIINQAKCEF--HQSQVKFIGYHI 615
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 907-966 1.76e-15

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 71.89  E-value: 1.76e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    907 NDTQLTRTIIKKYHEEGKliHPGIELLTNIILRRFTWKGIRKQIQEYVQNCHTCQINKSR 966
Cdd:pfam17921    1 VPKSLRKEILKEAHDSGG--HLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 983-1079 2.84e-12

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: 64.26  E-value: 2.84e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    983 PWESLSMDFIT-ALPESSGYNALFVVVDRFSKMAILVPCTKSITAEQTARMFDQRVIAYFGNPKEIIADNDHIFTSQTWK 1061
Cdd:pfam00665    1 PNQLWQGDFTYiRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 19115809   1062 DFAHKYNFVMKFSLPYRP 1079
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 1000-1132 1.30e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 60.68  E-value: 1.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  1000 GYNALFVVVDRFSKMAILVPCTkSITAEQTARMFDqRVIAYFGNP-KEIIADNDHIFTS--QTWKDFAHKYNFVMKFSLP 1076
Cdd:NF033577  145 GRLYLHTAIDDHSRFAYAELYP-DETAETAADFLR-RAFAEHGIPiRRVLTDNGSEFRSraHGFELALAELGIEHRRTRP 222

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19115809  1077 YRPQTDGQTERTNQTvekLLRCVCSTHP-----------NTWVDHislvqqsYNNAI-HSA-TQMTPFE 1132
Cdd:NF033577  223 YHPQTNGKVERFHRT---LKDEFAYARPyeslaelqaalDEWLHH-------YNHHRpHSAlGGKTPAE 281
transpos_IS21 NF033546
IS21 family transposase;
938-1144 4.01e-08

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 56.45  E-value: 4.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809   938 LRRFTWKGIRKQIQEYVQnchtcqinksRNHKPYGPLQPIPPSE-RPWESLSMDFITALPESSGYNA----LFVVVDRFS 1012
Cdd:NF033546   79 LRAEGYPGSYSTVRRYVR----------RWRAEQGPAKVFVRLEhAPGEQAQVDFGEATVVVTGGTGkilhVFVAVLGYS 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  1013 KMAILVpctksITAEQTARM-FD--QRVIAYFGN-PKEIIADN------------DHIFTsQTWKDFAHKYNFVMKFSLP 1076
Cdd:NF033546  149 RYTYVE-----ATPSESQEDlLDghQRAFEFFGGvPREIVYDNlktavdkrdryeEPRLN-PRFAAFAAHYGFEPRPCRP 222

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19115809  1077 YRPQTDGQTERTNQTVEKllRCVCSTHP--------NTWVDHisLVQQSYNNAIHSATQMTPFEIVHRYSPALSPL 1144
Cdd:NF033546  223 YRPQEKGKVERAVGYVRR--WFLRLRGRrfeslaelNAALAE--WLAELANQRPHGTTGGSPAERFEEERPALQPL 294
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 268-338 5.96e-08

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133136  Cd Length: 92  Bit Score: 51.57  E-value: 5.96e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19115809  268 CLIDTGAQANIITEETVRAHKLPTR--PWSKSVIYGGVYPNKINRKTIKLNISLNGISIKTEFLVVKKFSHPA 338
Cdd:cd00303   12 ALVDSGASVNFISESLAKKLGLPPRllPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDV 84
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
1004-1093 3.05e-05

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 48.29  E-value: 3.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809 1004 LFVVVDRFSKMAILVPCTKsitaeQTARMF---DQRVIAYF-GNPKEIIADN-----------DHIFTsQTWKDFAHKYN 1068
Cdd:COG4584  145 VFVAVLGYSRYKYVEAYPS-----QTQEDLleaHVRAFEFFgGVPREIVYDNlktavtkadrgEPVLN-ERFLAFAAHYG 218

                         90       100
                 ....*....|....*....|....*
gi 19115809 1069 FVMKFSLPYRPQTDGQTERTNQTVE 1093
Cdd:COG4584  219 FEPRPCRPRRPKEKGKVENAVGYVR 243
 
Name Accession Description Interval E-value
Peptidase_A2_2 pfam12382
Retrotransposon peptidase; This is a small family of fungal retroviral aspartyl peptidases.
 219-355 3.77e-90

Retrotransposon peptidase; This is a small family of fungal retroviral aspartyl peptidases.


Pssm-ID: 152817  Cd Length: 137  Bit Score: 287.37  E-value: 3.77e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    219 KNNTTNSRNLRKTNVSRIEYSSNKFLNHTRKRYEMVLQAELPDFKCSIPCLIDTGAQANIITEETVRAHKLPTRPWSKSV 298
Cdd:pfam12382    1 KENDTKDRKLKKTNVSRIEYSSEKFLKHKKKRYEMVLQAELPDFKCSIPCLIDTGAQANIITEETVRAHKLPTRPWLKSV 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 19115809    299 IYGGVYPNKINRKTIKLNISLNGISIKTEFLVVKKFSHPAAISFTTLYDNNIEISSS 355
Cdd:pfam12382   81 IYGGVYPNKINRKTIKLIINLNGISIKTEFLVVKKFSHPAAISFTTLYDNNIEISSS 137
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 439-615 1.49e-73

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: 242.12  E-value: 1.49e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  439 GIIRESKAINACPVMFVPKKEGTLRMVVDYKPLNKYVKPNIYPLPLIEQLLAKIQGSTIFTKLDLKSAYHLIRVRKGDEH 518
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  519 KLAFRCPRGVFEYLVMPYGISIAPAHFQYFINTILGEVKESHVVCYMDNILIHSKSESEHVKHVKDVLQKLKNANLIINQ 598
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 19115809  599 AKCEFHQSQVKFIGYHI 615
Cdd:cd01647  161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 710-833 7.07e-56

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: 189.24  E-value: 7.07e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  710 LETDASDVAVGAVLSQKHDDDKYYPVGYYSAKMSKAQLNYSVSDKEMLAIIKSLKHWRHYLESTiePFKILTDHRNLIgR 789
Cdd:cd09274    2 LETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGR--PFTVYTDHKALK-Y 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 19115809  790 ITNESEPeNKRLARWQLFLQDFNFEINYRPGSANHIADALSRIV 833
Cdd:cd09274   79 LLTQKDL-NGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
678-779 2.95e-44

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 155.35  E-value: 2.95e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    678 WTPTQTQAIENIKQCLVSPPVLRHFDFSKKILLETDASDVAVGAVLSQKHDDDKYYPVGYYSAKMSKAQLNYSVSDKEML 757
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGGERPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|..
gi 19115809    758 AIIKSLKHWRHYLESTiePFKI 779
Cdd:pfam17919   81 AIVFALKKFRHYLLGR--KFTV 100
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 703-810 1.63e-42

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: 150.74  E-value: 1.63e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    703 DFSKKILLETDASDVAVGAVLSQKHDDDKYYPVGYYSAKMSKAQLNYSVSDKEMLAIIKSLKHWRHYLESTiePFKILTD 782
Cdd:pfam17917    1 DPSKPFILETDASDYGIGAVLSQKDEDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGR--KFTVYTD 78

                           90       100
                   ....*....|....*....|....*...
gi 19115809    783 HRNLigRITNESEPENKRLARWQLFLQD 810
Cdd:pfam17917   79 HKPL--KYLFTPKELNGRLARWALFLQE 104
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 455-615 7.40e-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: 7.40e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    455 VPKK-EGTLRMV----VDYKPLNKYVKPNI-------YPLPLIEQLLAKIQGSTIFTKLDLKSAYHLIRVRKGDEHKLAF 522
Cdd:pfam00078    1 IPKKgKGKYRPIsllsIDYKALNKIIVKRLkpenldsPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    523 RCP-----------RGVFEYLVMPYGISIAPAHFQYFINTILGEVK---ESHVVCYMDNILIHSKSESEHVKHVKDVLQK 588
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 19115809    589 LKNANLIINQAKCEF--HQSQVKFIGYHI 615
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 415-615 4.57e-22

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: 95.81  E-value: 4.57e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  415 IRNYPLPPGKMQAMNDEINQGLKSGIIRESKAINACPVMFVPKKEGTLRMVVDYKPLNKYVKPnIYPLPLIEQLLAKIQG 494
Cdd:cd01645    4 IKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQD-MGALQPGLPHPAALPK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  495 STIFTKLDLKSAYHLIRVRKGDEHKLAFRCP---------RgvFEYLVMPYGISIAPAHFQYFINTILGEVKESH----V 561
Cdd:cd01645   83 GWPLIVLDLKDCFFSIPLHPDDRERFAFTVPsinnkgpakR--YQWKVLPQGMKNSPTICQSFVAQALEPFRKQYpdivI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 19115809  562 VCYMDNILIHSKSESEHVKHVKDVLQKLKNANLIINQAKCEfHQSQVKFIGYHI 615
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQ-KEPPFQYLGYEL 213
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 415-615 5.07e-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: 90.10  E-value: 5.07e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  415 IRNYPLPPGKMQAMNDEINQGLKSGIIRESKAINACPVMFVPKKEG-TLRMVVDYKPLNKYVKPNIYPLPLIEQLLAKIQ 493
Cdd:cd03715    4 QKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  494 -GSTIFTKLDLKSAYHLIRVRKGDEHKLAFRCPRGVFEYLVMPYGISIAPAHFQYFINTILGEVKESHVVC----YMDNI 568
Cdd:cd03715   84 pKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTillqYVDDL 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 19115809  569 LIHSKSESEHVKHVKDVLQKLKNANLIINQAKCEFHQSQVKFIGYHI 615
Cdd:cd03715  164 LLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 907-966 1.76e-15

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 71.89  E-value: 1.76e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    907 NDTQLTRTIIKKYHEEGKliHPGIELLTNIILRRFTWKGIRKQIQEYVQNCHTCQINKSR 966
Cdd:pfam17921    1 VPKSLRKEILKEAHDSGG--HLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 983-1079 2.84e-12

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: 64.26  E-value: 2.84e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809    983 PWESLSMDFIT-ALPESSGYNALFVVVDRFSKMAILVPCTKSITAEQTARMFDQRVIAYFGNPKEIIADNDHIFTSQTWK 1061
Cdd:pfam00665    1 PNQLWQGDFTYiRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 19115809   1062 DFAHKYNFVMKFSLPYRP 1079
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 1000-1132 1.30e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 60.68  E-value: 1.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  1000 GYNALFVVVDRFSKMAILVPCTkSITAEQTARMFDqRVIAYFGNP-KEIIADNDHIFTS--QTWKDFAHKYNFVMKFSLP 1076
Cdd:NF033577  145 GRLYLHTAIDDHSRFAYAELYP-DETAETAADFLR-RAFAEHGIPiRRVLTDNGSEFRSraHGFELALAELGIEHRRTRP 222

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19115809  1077 YRPQTDGQTERTNQTvekLLRCVCSTHP-----------NTWVDHislvqqsYNNAI-HSA-TQMTPFE 1132
Cdd:NF033577  223 YHPQTNGKVERFHRT---LKDEFAYARPyeslaelqaalDEWLHH-------YNHHRpHSAlGGKTPAE 281
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 710-834 1.67e-09

DIRS1 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. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 56.91  E-value: 1.67e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  710 LETDASDVAVGAVLSQKHDddkyypVGYYSAKmskaQLNYSVSDKEMLAIIKSLKHWRHYLE-STIepfKILTDHRNLIG 788
Cdd:cd09275    2 LFTDASLSGWGAYLLNSRA------HGPWSAD----ERNKHINLLELKAVLLALQHFAAELKnRKI---LIRTDNTTAVA 68

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 19115809  789 RITNE---SEPENKRLAR--WQLFLQdFNFEIN--YRPGSANHIADALSRIVD 834
Cdd:cd09275   69 YINKQggtSSPPLLALARqiLLWCEQ-RNIWLRasHIPGVLNTEADRLSRLGL 120
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 501-612 2.46e-09

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: 2.46e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  501 LDLKSAYHLIRVRKGDEHKLAFrCPRG-VFEYLVMPYGISIAPAHFQYFINTILGEVKE--SHVVCYMDNILI--HSKSE 575
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGF-AWQGeTYQFKALPFGLSLAPRVFTKVVEALLAPLRLlgVRIFSYLDDLLIiaSSIKT 79

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 19115809  576 SEHVKHVKDVLqKLKNANLIINQAKCEFHQSQ-VKFIG 612
Cdd:cd03714   80 SEAVLRHLRAT-LLANLGFTLNLEKSKLGPTQrITFLG 116
transpos_IS21 NF033546
IS21 family transposase;
938-1144 4.01e-08

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 56.45  E-value: 4.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809   938 LRRFTWKGIRKQIQEYVQnchtcqinksRNHKPYGPLQPIPPSE-RPWESLSMDFITALPESSGYNA----LFVVVDRFS 1012
Cdd:NF033546   79 LRAEGYPGSYSTVRRYVR----------RWRAEQGPAKVFVRLEhAPGEQAQVDFGEATVVVTGGTGkilhVFVAVLGYS 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  1013 KMAILVpctksITAEQTARM-FD--QRVIAYFGN-PKEIIADN------------DHIFTsQTWKDFAHKYNFVMKFSLP 1076
Cdd:NF033546  149 RYTYVE-----ATPSESQEDlLDghQRAFEFFGGvPREIVYDNlktavdkrdryeEPRLN-PRFAAFAAHYGFEPRPCRP 222

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19115809  1077 YRPQTDGQTERTNQTVEKllRCVCSTHP--------NTWVDHisLVQQSYNNAIHSATQMTPFEIVHRYSPALSPL 1144
Cdd:NF033546  223 YRPQEKGKVERAVGYVRR--WFLRLRGRrfeslaelNAALAE--WLAELANQRPHGTTGGSPAERFEEERPALQPL 294
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 268-338 5.96e-08

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133136  Cd Length: 92  Bit Score: 51.57  E-value: 5.96e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19115809  268 CLIDTGAQANIITEETVRAHKLPTR--PWSKSVIYGGVYPNKINRKTIKLNISLNGISIKTEFLVVKKFSHPA 338
Cdd:cd00303   12 ALVDSGASVNFISESLAKKLGLPPRllPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDV 84
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
1004-1093 3.05e-05

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 48.29  E-value: 3.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809 1004 LFVVVDRFSKMAILVPCTKsitaeQTARMF---DQRVIAYF-GNPKEIIADN-----------DHIFTsQTWKDFAHKYN 1068
Cdd:COG4584  145 VFVAVLGYSRYKYVEAYPS-----QTQEDLleaHVRAFEFFgGVPREIVYDNlktavtkadrgEPVLN-ERFLAFAAHYG 218

                         90       100
                 ....*....|....*....|....*
gi 19115809 1069 FVMKFSLPYRPQTDGQTERTNQTVE 1093
Cdd:COG4584  219 FEPRPCRPRRPKEKGKVENAVGYVR 243
retropepsin_like_LTR_1 cd05481
Retropepsins_like_LTR; pepsin-like aspartate protease from retrotransposons with long terminal ...
 261-341 1.95e-03

Retropepsins_like_LTR; pepsin-like aspartate protease from retrotransposons with long terminal repeats; Retropepsin of retrotransposons with long terminal repeats are pepsin-like aspartate proteases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133148  Cd Length: 93  Bit Score: 38.78  E-value: 1.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  261 DFKCSIPCLIDTGAQANIITEETVRAHklpTRPWSKSVIYGGVYPNKINRKTI------KLNISLNGISIKTEFLVVKKf 334
Cdd:cd05481    6 NGKQSVKFQLDTGATCNVLPLRWLKSL---TPDKDPELRPSPVRLTAYGGSTIpveggvKLKCRYRNPKYNLTFQVVKE- 81


                 ....*..
gi 19115809  335 SHPAAIS 341
Cdd:cd05481   82 EGPPLLG 88
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 456-594 3.86e-03

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


Pssm-ID: 238822  Cd Length: 213  Bit Score: 40.37  E-value: 3.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  456 PKKEGT-LRMVVDY------KPLNKYVK--PNIYPlPLIEQLLAKIQGSTIFTKlDLKSAYHLIRVRKGDEHKLAF---- 522
Cdd:cd01644   12 PSKTTTkLRVVFDAsaryngVSLNDMLLkgPDLLN-SLFGVLLRFRQGKIAVSA-DIEKMFHQVKVRPEDRDVLRFlwrk 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  523 ----RCPRgVFEYLVMPYGISIAPAHFQYFINTILGEVKESHVV------CYMDNILIHSKSESEHVKHVKDVLQKLKNA 592
Cdd:cd01644   90 dgdePKPI-EYRMTVVPFGAASAPFLANRALKQHAEDHPHEAAAkiikrnFYVDDILVSTDTLNEAVNVAKRLIALLKKG 168


                 ..
gi 19115809  593 NL 594
Cdd:cd01644  169 GF 170
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 755-831 3.99e-03

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 38.83  E-value: 3.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115809  755 EMLAIIKSLKHWRHYlesTIEPFKILTDHRNLIGRITNESE---PENKRLARWQLFLQDF-NFEINYRPGSANHIADALS 830
Cdd:cd06222   44 ELLALLLALELALDL---GYLKVIIESDSKYVVDLINSGSFkwsPNILLIEDILLLLSRFwSVKISHVPREGNQVADALA 120


                 .
gi 19115809  831 R 831
Cdd:cd06222  121 K 121
 
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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