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Conserved domains on  [gi|1207189610|ref|XP_002663225|]
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uncharacterized protein K02A2.6-like [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 159-284 2.96e-49

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: 168.83  E-value: 2.96e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 159 RVACDASPYGIGAVLSHKMTDGSERPIAFASRSLTVSERKYAQIDREGLSLVWGVKKFNQYLYGKHFTLITDHQPLVAIF 238
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1207189610 239 SPNKcvpvmAAARLQRWALFLGGHDYSIEFKGTKHHGNADGLSRLP 284
Cdd:cd09274    81 TQKD-----LNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 1-65 1.07e-20

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


The actual alignment was detected with superfamily member cd01647:

Pssm-ID: 477363  Cd Length: 177  Bit Score: 89.96  E-value: 1.07e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1207189610   1 MDQVLQGVAGTQC--YLDDIIVTGHDDKTHLANLNAVLERLAEYGLRANRSKCEFFKDSIEYCGHRI 65
Cdd:cd01647   111 MNKILGDLLGDFVevYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGHIV 177
transpos_IS481 super family cl41329
IS481 family transposase; null
 434-581 2.07e-17

IS481 family transposase; null


The actual alignment was detected with superfamily member NF033577:

Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 83.02  E-value: 2.07e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 434 PTSPWQR---------VHID--YAGPIFDK---MLLVVVDAYSKWPEVFPIKNATSTMTVELLRTLFSRTGLP-EQLVSD 498
Cdd:NF033577  115 KTGKVKRyerahpgelWHIDikKLGRIPDVgrlYLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPiRRVLTD 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 499 NGTQFTS--EEFQSFVKSNGIRHTTSVPYHLATNGLAERFVQSLKQSLkAMGKEKVS---LQEKIANFLLAYRNA-AH-A 571
Cdd:NF033577  195 NGSEFRSraHGFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEF-AYARPYESlaeLQAALDEWLHHYNHHrPHsA 273

                         170
                  ....*....|
gi 1207189610 572 TTGQSPATLF 581
Cdd:NF033577  274 LGGKTPAERF 283
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 367-422 1.42e-13

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: 65.73  E-value: 1.42e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1207189610 367 VPHKLQARVLTALHE--GHLGVVKMKSLARSYVWWPGLDRQIEDLAKACSGCQQIQRQ 422
Cdd:pfam17921   1 VPKSLRKEILKEAHDsgGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 159-284 2.96e-49

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: 168.83  E-value: 2.96e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 159 RVACDASPYGIGAVLSHKMTDGSERPIAFASRSLTVSERKYAQIDREGLSLVWGVKKFNQYLYGKHFTLITDHQPLVAIF 238
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1207189610 239 SPNKcvpvmAAARLQRWALFLGGHDYSIEFKGTKHHGNADGLSRLP 284
Cdd:cd09274    81 TQKD-----LNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 153-259 6.66e-47

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: 161.52  E-value: 6.66e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 153 DPSLPLRVACDASPYGIGAVLSHKMTDGSERPIAFASRSLTVSERKYAQIDREGLSLVWGVKKFNQYLYGKHFTLITDHQ 232
Cdd:pfam17917   1 DPSKPFILETDASDYGIGAVLSQKDEDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHK 80

                          90       100
                  ....*....|....*....|....*..
gi 1207189610 233 PLVAIFSPNKcvpvmAAARLQRWALFL 259
Cdd:pfam17917  81 PLKYLFTPKE-----LNGRLARWALFL 102
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1-65 1.07e-20

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: 89.96  E-value: 1.07e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1207189610   1 MDQVLQGVAGTQC--YLDDIIVTGHDDKTHLANLNAVLERLAEYGLRANRSKCEFFKDSIEYCGHRI 65
Cdd:cd01647   111 MNKILGDLLGDFVevYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGHIV 177
transpos_IS481 NF033577
IS481 family transposase; null
 434-581 2.07e-17

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 83.02  E-value: 2.07e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 434 PTSPWQR---------VHID--YAGPIFDK---MLLVVVDAYSKWPEVFPIKNATSTMTVELLRTLFSRTGLP-EQLVSD 498
Cdd:NF033577  115 KTGKVKRyerahpgelWHIDikKLGRIPDVgrlYLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPiRRVLTD 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 499 NGTQFTS--EEFQSFVKSNGIRHTTSVPYHLATNGLAERFVQSLKQSLkAMGKEKVS---LQEKIANFLLAYRNA-AH-A 571
Cdd:NF033577  195 NGSEFRSraHGFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEF-AYARPYESlaeLQAALDEWLHHYNHHrPHsA 273

                         170
                  ....*....|
gi 1207189610 572 TTGQSPATLF 581
Cdd:NF033577  274 LGGKTPAERF 283
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 437-526 1.06e-16

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: 75.81  E-value: 1.06e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 437 PWQRVHIDY-AGPIFDKM----LLVVVDAYSKWPEVFPIKNATSTMTVE--LLRTLFSRTGLPEQLVSDNGTQFTSEEFQ 509
Cdd:pfam00665   1 PNQLWQGDFtYIRIPGGGgklyLLVIVDDFSREILAWALSSEMDAELVLdaLERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*..
gi 1207189610 510 SFVKSNGIRHTTSVPYH 526
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGN 97
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 367-422 1.42e-13

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: 65.73  E-value: 1.42e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1207189610 367 VPHKLQARVLTALHE--GHLGVVKMKSLARSYVWWPGLDRQIEDLAKACSGCQQIQRQ 422
Cdd:pfam17921   1 VPKSLRKEILKEAHDsgGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
transpos_IS3 NF033516
IS3 family transposase;
419-541 1.80e-13

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 72.60  E-value: 1.80e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 419 IQRQPKA-APLHVW-----EFPTspWQRVHidYagpifdkmLLVVVDAYSKwpEVFPIK---NATSTMTVELLRTLFSRT 489
Cdd:NF033516  206 LNRQFTAtRPNQVWvtditYIRT--AEGWL--Y--------LAVVLDLFSR--EIVGWSvstSMSAELVLDALEMAIEWR 271

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1207189610 490 GLPEQLV--SDNGTQFTSEEFQSFVKSNGIRHTTSVPYHLATNGLAERFVQSLK 541
Cdd:NF033516  272 GKPEGLIlhSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
421-541 1.33e-12

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 69.41  E-value: 1.33e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 421 RQPKAAPLHVWEfPTSPWQRVHID--YaGPIFDKM--LLVVVDAYSK----WpEVFPikNATSTMTVELLRTLFSRTGLP 492
Cdd:COG2801   133 HGGPIAPNLLFT-ATAPNQVWVTDitY-IPTAEGWlyLAAVIDLFSReivgW-SVSD--SMDAELVVDALEMAIERRGPP 207

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1207189610 493 EQLV--SDNGTQFTSEEFQSFVKSNGIRHTTSVPYHLATNGLAERFVQSLK 541
Cdd:COG2801   208 KPLIlhSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLK 258
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-65 3.79e-10

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: 60.01  E-value: 3.79e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207189610   1 MDQVLQGVAG-----TQCYLDDIIVTGHDDKTHLANLNAVLERLAEYGLRANRSKCEFF--KDSIEYCGHRI 65
Cdd:pfam00078 118 MNELLRPLRKragltLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFlkSKEVKYLGVTL 189
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 159-284 2.96e-49

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: 168.83  E-value: 2.96e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 159 RVACDASPYGIGAVLSHKMTDGSERPIAFASRSLTVSERKYAQIDREGLSLVWGVKKFNQYLYGKHFTLITDHQPLVAIF 238
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1207189610 239 SPNKcvpvmAAARLQRWALFLGGHDYSIEFKGTKHHGNADGLSRLP 284
Cdd:cd09274    81 TQKD-----LNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 153-259 6.66e-47

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: 161.52  E-value: 6.66e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 153 DPSLPLRVACDASPYGIGAVLSHKMTDGSERPIAFASRSLTVSERKYAQIDREGLSLVWGVKKFNQYLYGKHFTLITDHQ 232
Cdd:pfam17917   1 DPSKPFILETDASDYGIGAVLSQKDEDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHK 80

                          90       100
                  ....*....|....*....|....*..
gi 1207189610 233 PLVAIFSPNKcvpvmAAARLQRWALFL 259
Cdd:pfam17917  81 PLKYLFTPKE-----LNGRLARWALFL 102
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
128-227 1.42e-45

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 157.66  E-value: 1.42e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 128 WSKDCDKAFKMAKQLITSETVLTHYDPSLPLRVACDASPYGIGAVLSHKMTDGSERPIAFASRSLTVSERKYAQIDREGL 207
Cdd:pfam17919   1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGGERPIAYASRKLSPAERNYSTTEKELL 80

                          90       100
                  ....*....|....*....|
gi 1207189610 208 SLVWGVKKFNQYLYGKHFTL 227
Cdd:pfam17919  81 AIVFALKKFRHYLLGRKFTV 100
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1-65 1.07e-20

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: 89.96  E-value: 1.07e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1207189610   1 MDQVLQGVAGTQC--YLDDIIVTGHDDKTHLANLNAVLERLAEYGLRANRSKCEFFKDSIEYCGHRI 65
Cdd:cd01647   111 MNKILGDLLGDFVevYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGHIV 177
transpos_IS481 NF033577
IS481 family transposase; null
 434-581 2.07e-17

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 83.02  E-value: 2.07e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 434 PTSPWQR---------VHID--YAGPIFDK---MLLVVVDAYSKWPEVFPIKNATSTMTVELLRTLFSRTGLP-EQLVSD 498
Cdd:NF033577  115 KTGKVKRyerahpgelWHIDikKLGRIPDVgrlYLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPiRRVLTD 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 499 NGTQFTS--EEFQSFVKSNGIRHTTSVPYHLATNGLAERFVQSLKQSLkAMGKEKVS---LQEKIANFLLAYRNA-AH-A 571
Cdd:NF033577  195 NGSEFRSraHGFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEF-AYARPYESlaeLQAALDEWLHHYNHHrPHsA 273

                         170
                  ....*....|
gi 1207189610 572 TTGQSPATLF 581
Cdd:NF033577  274 LGGKTPAERF 283
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 437-526 1.06e-16

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: 75.81  E-value: 1.06e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 437 PWQRVHIDY-AGPIFDKM----LLVVVDAYSKWPEVFPIKNATSTMTVE--LLRTLFSRTGLPEQLVSDNGTQFTSEEFQ 509
Cdd:pfam00665   1 PNQLWQGDFtYIRIPGGGgklyLLVIVDDFSREILAWALSSEMDAELVLdaLERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*..
gi 1207189610 510 SFVKSNGIRHTTSVPYH 526
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGN 97
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 367-422 1.42e-13

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: 65.73  E-value: 1.42e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1207189610 367 VPHKLQARVLTALHE--GHLGVVKMKSLARSYVWWPGLDRQIEDLAKACSGCQQIQRQ 422
Cdd:pfam17921   1 VPKSLRKEILKEAHDsgGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
transpos_IS3 NF033516
IS3 family transposase;
419-541 1.80e-13

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 72.60  E-value: 1.80e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 419 IQRQPKA-APLHVW-----EFPTspWQRVHidYagpifdkmLLVVVDAYSKwpEVFPIK---NATSTMTVELLRTLFSRT 489
Cdd:NF033516  206 LNRQFTAtRPNQVWvtditYIRT--AEGWL--Y--------LAVVLDLFSR--EIVGWSvstSMSAELVLDALEMAIEWR 271

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1207189610 490 GLPEQLV--SDNGTQFTSEEFQSFVKSNGIRHTTSVPYHLATNGLAERFVQSLK 541
Cdd:NF033516  272 GKPEGLIlhSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
421-541 1.33e-12

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 69.41  E-value: 1.33e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610 421 RQPKAAPLHVWEfPTSPWQRVHID--YaGPIFDKM--LLVVVDAYSK----WpEVFPikNATSTMTVELLRTLFSRTGLP 492
Cdd:COG2801   133 HGGPIAPNLLFT-ATAPNQVWVTDitY-IPTAEGWlyLAAVIDLFSReivgW-SVSD--SMDAELVVDALEMAIERRGPP 207

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1207189610 493 EQLV--SDNGTQFTSEEFQSFVKSNGIRHTTSVPYHLATNGLAERFVQSLK 541
Cdd:COG2801   208 KPLIlhSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLK 258
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-65 3.79e-10

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: 60.01  E-value: 3.79e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207189610   1 MDQVLQGVAG-----TQCYLDDIIVTGHDDKTHLANLNAVLERLAEYGLRANRSKCEFF--KDSIEYCGHRI 65
Cdd:pfam00078 118 MNELLRPLRKragltLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFlkSKEVKYLGVTL 189
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 13-65 4.01e-04

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


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 40.03  E-value: 4.01e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1207189610  13 CYLDDIIVtGHDDKTHLANLNAVLERLAEYGLRANRSKCEFFKD--SIEYCGHRI 65
Cdd:cd00304    45 RYVDDLVV-IAKSEQQAVKKRELEEFLARLGLNLSDEKTQFTEKekKFKFLGILV 98
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 383-417 5.94e-04

H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters.


Pssm-ID: 430537  Cd Length: 39  Bit Score: 38.08  E-value: 5.94e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1207189610 383 HLGVVKMKSLARSYVWWPGLDRQIEDLAKACSGCQ 417
Cdd:pfam09337   5 HLGINKLTALLARKYHWLGIKETVSEVISSCVACQ 39
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 1-78 3.02e-03

RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.


Pssm-ID: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 38.85  E-value: 3.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207189610   1 MDQVLQGVAGTQcYLDDIIVtGHDDKTHLAN-LNAVLERLAEYGLRANRSKCE-----FFKDSIEYCGHRIDKAGLHKSP 74
Cdd:cd01646    76 LKSKLKGVDYVR-YVDDIRI-FADSKEEAEEiLEELKEFLAELGLSLNLSKTEilplpEGTASKDFLGYRFSPILLIKSS 153


                  ....*
gi 1207189610  75 -DKIN 78
Cdd:cd01646   154 eRKMS 158
Lipoprotein_Ltp pfam07553
Host cell surface-exposed lipoprotein; This is a family of lipoproteins that is involved in ...
 486-509 9.82e-03

Host cell surface-exposed lipoprotein; This is a family of lipoproteins that is involved in superinfection exclusion. Proteins in this family have been shown to act at the stage of DNA release from the phage head into the cell.


Pssm-ID: 462206  Cd Length: 48  Bit Score: 34.86  E-value: 9.82e-03
                          10        20
                  ....*....|....*....|....
gi 1207189610 486 FSRTGLPEQLVSDNGTQFTSEEFQ 509
Cdd:pfam07553  19 MSKDGLYDQLTSEYGEKFTEEQAQ 42
 
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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