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Conserved domains on  [gi|6319323|ref|NP_009406|]
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truncated gag-pol fusion protein [Saccharomyces cerevisiae S288C]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1047-1183 8.23e-27

Ty1/Copia 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 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 Ty1/Copia family is 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: 260004  Cd Length: 140  Bit Score: 106.78  E-value: 8.23e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323  1047 VAISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQEL---NKKPIIkg 1122
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6319323  1123 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1183
Cdd:cd09272   79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 706-894 5.93e-23

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


The actual alignment was detected with superfamily member pfam07727:

Pssm-ID: 400190  Cd Length: 243  Bit Score: 99.20  E-value: 5.93e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323     706 NTWDTDKyydrkeiDPK--RVINSMFIFNKK----RDGTHKARFVARGDIQHPDTYDTGMQSNTVHHYALMTSLSLALDN 779
Cdd:pfam07727    2 ETWTLVK-------LPKnvKPIGTTWVHTHKindlKEVQYKARLVAQGFRQIAGEDYDKVFSPVIRLSSVRLLLAIAAEY 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323     780 NYYITQLDISSAYLYADIKEELYIRPPPHL---GMNDKLIRLKKSLYGLKQSGANWYETIKSYLIK--------QCGMeE 848
Cdd:pfam07727   75 EWPVHHMDVSSAFLNGDIDEEIYVKQPPGFnidNESGKVWQLNKSLYGLKQAPYMWNTCITKVLMDlnfepdtaESGM-Y 153

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 6319323     849 VRGwscvFKNSQVTICLFVDDMILFSKDLNANKKIITTLKKQYDTK 894
Cdd:pfam07727  154 CRG----FGENKLIVGLYVDDMFITGSDITIINDFKLELAKHFKMK 195
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 105-206 1.08e-11

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: 62.33  E-value: 1.08e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323     105 PFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKLRWVYPLhdRREDSILDVFTTILAFIKNQFQaSVLVIQMDRGSEYTN 184
Cdd:pfam00665    1 PNQLWQGDFT-YIRIPGGGGKLYLLVIVDDFSREILAWAL--SSEMDAELVLDALERAIAFRGG-VPLIIHSDNGSEYTS 76

                           90       100
                   ....*....|....*....|..
gi 6319323     185 RTLHKFLEKNGITPCYTTTADS 206
Cdd:pfam00665   77 KAFREFLKDLGIKPSFSRPGNP 98
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1047-1183 8.23e-27

Ty1/Copia 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 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 Ty1/Copia family is 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: 260004  Cd Length: 140  Bit Score: 106.78  E-value: 8.23e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323  1047 VAISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQEL---NKKPIIkg 1122
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6319323  1123 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1183
Cdd:cd09272   79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 706-894 5.93e-23

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 400190  Cd Length: 243  Bit Score: 99.20  E-value: 5.93e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323     706 NTWDTDKyydrkeiDPK--RVINSMFIFNKK----RDGTHKARFVARGDIQHPDTYDTGMQSNTVHHYALMTSLSLALDN 779
Cdd:pfam07727    2 ETWTLVK-------LPKnvKPIGTTWVHTHKindlKEVQYKARLVAQGFRQIAGEDYDKVFSPVIRLSSVRLLLAIAAEY 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323     780 NYYITQLDISSAYLYADIKEELYIRPPPHL---GMNDKLIRLKKSLYGLKQSGANWYETIKSYLIK--------QCGMeE 848
Cdd:pfam07727   75 EWPVHHMDVSSAFLNGDIDEEIYVKQPPGFnidNESGKVWQLNKSLYGLKQAPYMWNTCITKVLMDlnfepdtaESGM-Y 153

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 6319323     849 VRGwscvFKNSQVTICLFVDDMILFSKDLNANKKIITTLKKQYDTK 894
Cdd:pfam07727  154 CRG----FGENKLIVGLYVDDMFITGSDITIINDFKLELAKHFKMK 195
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 105-206 1.08e-11

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: 62.33  E-value: 1.08e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323     105 PFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKLRWVYPLhdRREDSILDVFTTILAFIKNQFQaSVLVIQMDRGSEYTN 184
Cdd:pfam00665    1 PNQLWQGDFT-YIRIPGGGGKLYLLVIVDDFSREILAWAL--SSEMDAELVLDALERAIAFRGG-VPLIIHSDNGSEYTS 76

                           90       100
                   ....*....|....*....|..
gi 6319323     185 RTLHKFLEKNGITPCYTTTADS 206
Cdd:pfam00665   77 KAFREFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
104-223 5.36e-08

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 55.93  E-value: 5.36e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323   104 EPFQYLHTDIFgpvhnlpksapsYFisftdeTTKLRWVYPLhdrredSILDVFT-TILAF------------------IK 164
Cdd:COG2801  147 APNQVWVTDIT------------YI------PTAEGWLYLA------AVIDLFSrEIVGWsvsdsmdaelvvdalemaIE 202

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 6319323   165 NQFQASVLVIQMDRGSEYTNRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 223
Cdd:COG2801  203 RRGPPKPLILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYEL 261
transpos_IS481 NF033577
IS481 family transposase; null
 93-221 1.00e-07

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 54.90  E-value: 1.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323     93 KGSRLKYQNSYePFQYLHTDIFGpVHNLPKSAPSYFISFTDETTKLRWVYPLHDRREDSILDVFTTILAfiknQFQASVL 172
Cdd:NF033577  116 TGKVKRYERAH-PGELWHIDIKK-LGRIPDVGRLYLHTAIDDHSRFAYAELYPDETAETAADFLRRAFA----EHGIPIR 189

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 6319323    173 VIQMDRGSEYTNRT--LHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLD 221
Cdd:NF033577  190 RVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
transpos_IS3 NF033516
IS3 family transposase;
163-223 1.06e-06

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 52.18  E-value: 1.06e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6319323    163 IKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 223
Cdd:NF033516  268 IEWRGKPEGLILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKREC 328
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 131-223 8.57e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 42.54  E-value: 8.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323    131 FTDETTKLRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 196
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195

                          90       100
                  ....*....|....*....|....*..
gi 6319323    197 TPCYTTTADSRAHGVAERLNRTLLDDC 223
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1047-1183 8.23e-27

Ty1/Copia 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 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 Ty1/Copia family is 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: 260004  Cd Length: 140  Bit Score: 106.78  E-value: 8.23e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323  1047 VAISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQEL---NKKPIIkg 1122
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6319323  1123 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1183
Cdd:cd09272   79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 706-894 5.93e-23

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 400190  Cd Length: 243  Bit Score: 99.20  E-value: 5.93e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323     706 NTWDTDKyydrkeiDPK--RVINSMFIFNKK----RDGTHKARFVARGDIQHPDTYDTGMQSNTVHHYALMTSLSLALDN 779
Cdd:pfam07727    2 ETWTLVK-------LPKnvKPIGTTWVHTHKindlKEVQYKARLVAQGFRQIAGEDYDKVFSPVIRLSSVRLLLAIAAEY 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323     780 NYYITQLDISSAYLYADIKEELYIRPPPHL---GMNDKLIRLKKSLYGLKQSGANWYETIKSYLIK--------QCGMeE 848
Cdd:pfam07727   75 EWPVHHMDVSSAFLNGDIDEEIYVKQPPGFnidNESGKVWQLNKSLYGLKQAPYMWNTCITKVLMDlnfepdtaESGM-Y 153

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 6319323     849 VRGwscvFKNSQVTICLFVDDMILFSKDLNANKKIITTLKKQYDTK 894
Cdd:pfam07727  154 CRG----FGENKLIVGLYVDDMFITGSDITIINDFKLELAKHFKMK 195
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 105-206 1.08e-11

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: 62.33  E-value: 1.08e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323     105 PFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKLRWVYPLhdRREDSILDVFTTILAFIKNQFQaSVLVIQMDRGSEYTN 184
Cdd:pfam00665    1 PNQLWQGDFT-YIRIPGGGGKLYLLVIVDDFSREILAWAL--SSEMDAELVLDALERAIAFRGG-VPLIIHSDNGSEYTS 76

                           90       100
                   ....*....|....*....|..
gi 6319323     185 RTLHKFLEKNGITPCYTTTADS 206
Cdd:pfam00665   77 KAFREFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
104-223 5.36e-08

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 55.93  E-value: 5.36e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323   104 EPFQYLHTDIFgpvhnlpksapsYFisftdeTTKLRWVYPLhdrredSILDVFT-TILAF------------------IK 164
Cdd:COG2801  147 APNQVWVTDIT------------YI------PTAEGWLYLA------AVIDLFSrEIVGWsvsdsmdaelvvdalemaIE 202

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 6319323   165 NQFQASVLVIQMDRGSEYTNRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 223
Cdd:COG2801  203 RRGPPKPLILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYEL 261
transpos_IS481 NF033577
IS481 family transposase; null
 93-221 1.00e-07

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 54.90  E-value: 1.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323     93 KGSRLKYQNSYePFQYLHTDIFGpVHNLPKSAPSYFISFTDETTKLRWVYPLHDRREDSILDVFTTILAfiknQFQASVL 172
Cdd:NF033577  116 TGKVKRYERAH-PGELWHIDIKK-LGRIPDVGRLYLHTAIDDHSRFAYAELYPDETAETAADFLRRAFA----EHGIPIR 189

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 6319323    173 VIQMDRGSEYTNRT--LHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLD 221
Cdd:NF033577  190 RVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
transpos_IS3 NF033516
IS3 family transposase;
163-223 1.06e-06

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 52.18  E-value: 1.06e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6319323    163 IKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 223
Cdd:NF033516  268 IEWRGKPEGLILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKREC 328
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 131-223 8.57e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 42.54  E-value: 8.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319323    131 FTDETTKLRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 196
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195

                          90       100
                  ....*....|....*....|....*..
gi 6319323    197 TPCYTTTADSRAHGVAERLNRTLLDDC 223
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
 
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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