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Conserved domains on  [gi|199562283|ref|NP_001128360|]
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retrotransposon-like protein 1 [Homo sapiens]

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 ...
 607-782 1.07e-39

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: 145.43  E-value: 1.07e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283  607 FYECPSTAPW--EPVGARMQE-RARLQEEYWDLQDMLtnRQDYIQM--IPELFDQLHGAEWFTKLELRGTIVEESVnghR 681
Cdd:cd01647     1 GIIEPSSSPYasPVVVVKKKDgKLRLCVDYRKLNKVT--IKDRYPLptIDELLEELAGAKVFSKLDLRSGYHQIPL---A 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283  682 TEDVWKAAFGLELEEMKS-YQPFALSPDPIIPQNVIHFILKDMLGFFVLSYGQEVLIYSMSQEEHLHHVRQVLVRFRHHN 760
Cdd:cd01647    76 EESRPKTAFRTPFGLYEYtRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAG 155

                         170       180
                  ....*....|....*....|..
gi 199562283  761 VYCSLDKSQFHRQTVEFLGFVV 782
Cdd:cd01647   156 LKLNPEKCEFGVPEVEFLGHIV 177
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
845-942 5.99e-23

RNase H-like domain found in reverse transcriptase;


:

Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 94.49  E-value: 5.99e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   845 WGVEEQEAFECLKRAFRKAPLLHHPKPQNPFYLETGVTGTALHASLIQIDDQTGKRaCCAFYSRNISPIEVEYSQAEMKI 924
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGGER-PIAYASRKLSPAERNYSTTEKEL 79

                           90
                   ....*....|....*...
gi 199562283   925 LPIRAAFMVWCRYLENTE 942
Cdd:pfam17919   80 LAIVFALKKFRHYLLGRK 97
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 413-510 3.34e-19

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: 83.54  E-value: 3.34e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283  413 LMVRVNpyhSVAVQALVDSGADGNFMDEKFAQEHYVELYEKPYPQPVQSVDGSLIgnepVWLYTEPLVCIH-QNHQESIE 491
Cdd:cd00303     1 LKGKIN---GVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSV----KTLGVILPVTIGiGGKTFTVD 73

                          90
                  ....*....|....*....
gi 199562283  492 FDIVPSPNFSVVLGIRWLR 510
Cdd:cd00303    74 FYVLDLLSYDVILGRPWLE 92
Retrotrans_gag super family cl46289
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 200-278 1.27e-12

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


The actual alignment was detected with superfamily member pfam16297:

Pssm-ID: 480629  Cd Length: 112  Bit Score: 65.71  E-value: 1.27e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 199562283   200 LPAPKHFSGDRREFHEFIVLCQLTLQSYPRMFYNDRLRVGYVINHLSGLALEWAKALLQENSPLIGDFPAFLEAMSEVF 278
Cdd:pfam16297   25 IPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQYF 103
Retrotrans_gag super family cl46289
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 240-332 3.44e-11

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


The actual alignment was detected with superfamily member pfam03732:

Pssm-ID: 480629  Cd Length: 97  Bit Score: 60.81  E-value: 3.44e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   240 YVINHLSGLALEWAKALLQENSPLIGDFPAFLEAMSEVFEYRQALRVAEEAMFTIRQGGRSATEYIDEFQSL---VPILG 316
Cdd:pfam03732    2 LAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLarqLPHHG 81

                           90
                   ....*....|....*.
gi 199562283   317 WPDEVLQAHLCQGLNE 332
Cdd:pfam03732   82 RDEEALISAFLRGLRP 97
PHA03169 super family cl27451
hypothetical protein; Provisional
 14-160 9.36e-04

hypothetical protein; Provisional


The actual alignment was detected with superfamily member PHA03169:

Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 43.42  E-value: 9.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   14 EHKNPSSKQMESSEGSSNTTEATSGSGVRGEA--GPASGPAQEKKEPPSGPLQEMEELPTDLLQDMEEPSSGPRKEIEDP 91
Cdd:PHA03169  101 GSPTPSPSGSAEELASGLSPENTSGSSPESPAshSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEP 180

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 199562283   92 PNDLLQDLEESCNGSHQAR--GDPLSGASDRMKEASVNPSGAREEQEA----HTD-LKESGREETPQEQNQTEHST 160
Cdd:PHA03169  181 PTSEPEPDSPGPPQSETPTssPPPQSPPDEPGEPQSPTPQQAPSPNTQqaveHEDePTEPEREGPPFPGHRSHSYT 256
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 607-782 1.07e-39

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: 145.43  E-value: 1.07e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283  607 FYECPSTAPW--EPVGARMQE-RARLQEEYWDLQDMLtnRQDYIQM--IPELFDQLHGAEWFTKLELRGTIVEESVnghR 681
Cdd:cd01647     1 GIIEPSSSPYasPVVVVKKKDgKLRLCVDYRKLNKVT--IKDRYPLptIDELLEELAGAKVFSKLDLRSGYHQIPL---A 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283  682 TEDVWKAAFGLELEEMKS-YQPFALSPDPIIPQNVIHFILKDMLGFFVLSYGQEVLIYSMSQEEHLHHVRQVLVRFRHHN 760
Cdd:cd01647    76 EESRPKTAFRTPFGLYEYtRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAG 155

                         170       180
                  ....*....|....*....|..
gi 199562283  761 VYCSLDKSQFHRQTVEFLGFVV 782
Cdd:cd01647   156 LKLNPEKCEFGVPEVEFLGHIV 177
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
845-942 5.99e-23

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 94.49  E-value: 5.99e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   845 WGVEEQEAFECLKRAFRKAPLLHHPKPQNPFYLETGVTGTALHASLIQIDDQTGKRaCCAFYSRNISPIEVEYSQAEMKI 924
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGGER-PIAYASRKLSPAERNYSTTEKEL 79

                           90
                   ....*....|....*...
gi 199562283   925 LPIRAAFMVWCRYLENTE 942
Cdd:pfam17919   80 LAIVFALKKFRHYLLGRK 97
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 413-510 3.34e-19

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: 83.54  E-value: 3.34e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283  413 LMVRVNpyhSVAVQALVDSGADGNFMDEKFAQEHYVELYEKPYPQPVQSVDGSLIgnepVWLYTEPLVCIH-QNHQESIE 491
Cdd:cd00303     1 LKGKIN---GVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSV----KTLGVILPVTIGiGGKTFTVD 73

                          90
                  ....*....|....*....
gi 199562283  492 FDIVPSPNFSVVLGIRWLR 510
Cdd:cd00303    74 FYVLDLLSYDVILGRPWLE 92
DUF4939 pfam16297
Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around ...
 200-278 1.27e-12

Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown.


Pssm-ID: 465086  Cd Length: 112  Bit Score: 65.71  E-value: 1.27e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 199562283   200 LPAPKHFSGDRREFHEFIVLCQLTLQSYPRMFYNDRLRVGYVINHLSGLALEWAKALLQENSPLIGDFPAFLEAMSEVF 278
Cdd:pfam16297   25 IPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQYF 103
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 240-332 3.44e-11

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 60.81  E-value: 3.44e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   240 YVINHLSGLALEWAKALLQENSPLIGDFPAFLEAMSEVFEYRQALRVAEEAMFTIRQGGRSATEYIDEFQSL---VPILG 316
Cdd:pfam03732    2 LAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLarqLPHHG 81

                           90
                   ....*....|....*.
gi 199562283   317 WPDEVLQAHLCQGLNE 332
Cdd:pfam03732   82 RDEEALISAFLRGLRP 97
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 650-782 5.89e-08

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: 54.23  E-value: 5.89e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   650 IPELFDQLHGAEWFTKLELRG---TIveesvnGHRTEDVWKAAFG-----LELEEMKSYQ-------PFALSPDPIIPQN 714
Cdd:pfam00078   43 FRPGLAKLKKAKWFLKLDLKKafdQV------PLDELDRKLTAFTtppinINWNGELSGGryewkglPQGLVLSPALFQL 116

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 199562283   715 VIHFILKDML---GFFVLSYGQEVLIYSMSQEEHLHHVRQVLVRFRHHNVYCSLDKSQFHRQT--VEFLGFVV 782
Cdd:pfam00078  117 FMNELLRPLRkraGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFLKSkeVKYLGVTL 189
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 413-465 5.47e-04

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.


Pssm-ID: 433378  Cd Length: 90  Bit Score: 40.35  E-value: 5.47e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 199562283   413 LMVRVNpyhSVAVQALVDSGADGNFMDEKFAQEHYVELYEKPYPQPVQSVDGS 465
Cdd:pfam13650    1 VPVTIN---GKPVRFLVDTGASGTVISPSLAERLGLKVRGLAYTVRVSTAGGR 50
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 876-985 5.68e-04

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: 40.94  E-value: 5.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283  876 YLETGVTGTALHASLIQIDDqTGKRACCAFYSRNISPIEVEYSQAEMKILPIRAAFMVWCRYLENTE-------EPIMIL 948
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDD-DGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPftvytdhKALKYL 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 199562283  949 LNTEDLaslnNDRLTvllpgHWVFFFSHFNFDVMELP 985
Cdd:cd09274    80 LTQKDL----NGRLA-----RWLLLLSEFDFEIEYRP 107
PHA03169 PHA03169
hypothetical protein; Provisional
 14-160 9.36e-04

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 43.42  E-value: 9.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   14 EHKNPSSKQMESSEGSSNTTEATSGSGVRGEA--GPASGPAQEKKEPPSGPLQEMEELPTDLLQDMEEPSSGPRKEIEDP 91
Cdd:PHA03169  101 GSPTPSPSGSAEELASGLSPENTSGSSPESPAshSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEP 180

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 199562283   92 PNDLLQDLEESCNGSHQAR--GDPLSGASDRMKEASVNPSGAREEQEA----HTD-LKESGREETPQEQNQTEHST 160
Cdd:PHA03169  181 PTSEPEPDSPGPPQSETPTssPPPQSPPDEPGEPQSPTPQQAPSPNTQqaveHEDePTEPEREGPPFPGHRSHSYT 256
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 607-782 1.07e-39

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: 145.43  E-value: 1.07e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283  607 FYECPSTAPW--EPVGARMQE-RARLQEEYWDLQDMLtnRQDYIQM--IPELFDQLHGAEWFTKLELRGTIVEESVnghR 681
Cdd:cd01647     1 GIIEPSSSPYasPVVVVKKKDgKLRLCVDYRKLNKVT--IKDRYPLptIDELLEELAGAKVFSKLDLRSGYHQIPL---A 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283  682 TEDVWKAAFGLELEEMKS-YQPFALSPDPIIPQNVIHFILKDMLGFFVLSYGQEVLIYSMSQEEHLHHVRQVLVRFRHHN 760
Cdd:cd01647    76 EESRPKTAFRTPFGLYEYtRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAG 155

                         170       180
                  ....*....|....*....|..
gi 199562283  761 VYCSLDKSQFHRQTVEFLGFVV 782
Cdd:cd01647   156 LKLNPEKCEFGVPEVEFLGHIV 177
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
845-942 5.99e-23

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 94.49  E-value: 5.99e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   845 WGVEEQEAFECLKRAFRKAPLLHHPKPQNPFYLETGVTGTALHASLIQIDDQTGKRaCCAFYSRNISPIEVEYSQAEMKI 924
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGGER-PIAYASRKLSPAERNYSTTEKEL 79

                           90
                   ....*....|....*...
gi 199562283   925 LPIRAAFMVWCRYLENTE 942
Cdd:pfam17919   80 LAIVFALKKFRHYLLGRK 97
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 413-510 3.34e-19

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: 83.54  E-value: 3.34e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283  413 LMVRVNpyhSVAVQALVDSGADGNFMDEKFAQEHYVELYEKPYPQPVQSVDGSLIgnepVWLYTEPLVCIH-QNHQESIE 491
Cdd:cd00303     1 LKGKIN---GVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSV----KTLGVILPVTIGiGGKTFTVD 73

                          90
                  ....*....|....*....
gi 199562283  492 FDIVPSPNFSVVLGIRWLR 510
Cdd:cd00303    74 FYVLDLLSYDVILGRPWLE 92
DUF4939 pfam16297
Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around ...
 200-278 1.27e-12

Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown.


Pssm-ID: 465086  Cd Length: 112  Bit Score: 65.71  E-value: 1.27e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 199562283   200 LPAPKHFSGDRREFHEFIVLCQLTLQSYPRMFYNDRLRVGYVINHLSGLALEWAKALLQENSPLIGDFPAFLEAMSEVF 278
Cdd:pfam16297   25 IPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQYF 103
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 240-332 3.44e-11

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 60.81  E-value: 3.44e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   240 YVINHLSGLALEWAKALLQENSPLIGDFPAFLEAMSEVFEYRQALRVAEEAMFTIRQGGRSATEYIDEFQSL---VPILG 316
Cdd:pfam03732    2 LAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLarqLPHHG 81

                           90
                   ....*....|....*.
gi 199562283   317 WPDEVLQAHLCQGLNE 332
Cdd:pfam03732   82 RDEEALISAFLRGLRP 97
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 650-782 5.89e-08

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: 54.23  E-value: 5.89e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   650 IPELFDQLHGAEWFTKLELRG---TIveesvnGHRTEDVWKAAFG-----LELEEMKSYQ-------PFALSPDPIIPQN 714
Cdd:pfam00078   43 FRPGLAKLKKAKWFLKLDLKKafdQV------PLDELDRKLTAFTtppinINWNGELSGGryewkglPQGLVLSPALFQL 116

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 199562283   715 VIHFILKDML---GFFVLSYGQEVLIYSMSQEEHLHHVRQVLVRFRHHNVYCSLDKSQFHRQT--VEFLGFVV 782
Cdd:pfam00078  117 FMNELLRPLRkraGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFLKSkeVKYLGVTL 189
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 413-465 5.47e-04

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.


Pssm-ID: 433378  Cd Length: 90  Bit Score: 40.35  E-value: 5.47e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 199562283   413 LMVRVNpyhSVAVQALVDSGADGNFMDEKFAQEHYVELYEKPYPQPVQSVDGS 465
Cdd:pfam13650    1 VPVTIN---GKPVRFLVDTGASGTVISPSLAERLGLKVRGLAYTVRVSTAGGR 50
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 876-985 5.68e-04

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: 40.94  E-value: 5.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283  876 YLETGVTGTALHASLIQIDDqTGKRACCAFYSRNISPIEVEYSQAEMKILPIRAAFMVWCRYLENTE-------EPIMIL 948
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDD-DGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPftvytdhKALKYL 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 199562283  949 LNTEDLaslnNDRLTvllpgHWVFFFSHFNFDVMELP 985
Cdd:cd09274    80 LTQKDL----NGRLA-----RWLLLLSEFDFEIEYRP 107
PHA03169 PHA03169
hypothetical protein; Provisional
 14-160 9.36e-04

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 43.42  E-value: 9.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   14 EHKNPSSKQMESSEGSSNTTEATSGSGVRGEA--GPASGPAQEKKEPPSGPLQEMEELPTDLLQDMEEPSSGPRKEIEDP 91
Cdd:PHA03169  101 GSPTPSPSGSAEELASGLSPENTSGSSPESPAshSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEP 180

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 199562283   92 PNDLLQDLEESCNGSHQAR--GDPLSGASDRMKEASVNPSGAREEQEA----HTD-LKESGREETPQEQNQTEHST 160
Cdd:PHA03169  181 PTSEPEPDSPGPPQSETPTssPPPQSPPDEPGEPQSPTPQQAPSPNTQqaveHEDePTEPEREGPPFPGHRSHSYT 256
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 415-510 1.04e-03

gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.


Pssm-ID: 464060  Cd Length: 92  Bit Score: 39.48  E-value: 1.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   415 VRVNpyhSVAVQALVDSGADGNFMDEKFAQEHYVELYEKPYPQPVQSVDGSLIGNePVWLYTeplVCIHQNHQESIEFDI 494
Cdd:pfam13975    3 VTIN---GRPVRFLVDTGASVTVISEALAERLGLDRLVDAYPVTVRTANGTVRAA-RVRLDS---VKIGGIELRNVPAVV 75

                           90
                   ....*....|....*.
gi 199562283   495 VPSPNFSVVLGIRWLR 510
Cdd:pfam13975   76 LPGDLDDVLLGMDFLK 91
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 199-353 2.40e-03

Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the Ty3 transposons of yeast as well as other transposable elements.


Pssm-ID: 437091 [Multi-domain]  Cd Length: 197  Bit Score: 40.92  E-value: 2.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199562283   199 QLPAPKHFSGDRREFHEFIvlCQLTLQSYPRMFYNDRLRVGYVINHLSGLALEWAKALLQENSPLIGDFPAFLEAMSEVF 278
Cdd:pfam19259   12 QVILPFRGRKDVLKLKSFI--SEIMLQMSMIFWPNDAERIVFCARHLTGPAAQWFHDFVQEQGILDATFDTFIKAFKQHF 89

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 199562283   279 EYRQALRVAEEAMFTIRQGGRSATEYIDEFQSLVPIL---GWPDEVLQAHLCQGLNEEIRHYLfRVPQPDSLDSLIVL 353
Cdd:pfam19259   90 YGKPDINKLFNDIVNLSEAKLGIERYNSHFNRLWDLLppdFLSEKAAIMFYIRGLKPETYIIV-RLAKPSTLKEAMEI 166
 
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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