NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1720399878|ref|XP_030107720|]
View 

agouti-signaling protein isoform X1 [Mus musculus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 1-150 3.22e-80

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 cd01645:

Pssm-ID: 477363 [Multi-domain]  Cd Length: 213  Bit Score: 256.83  E-value: 3.22e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878   1 MVPMGALQPGIPSPVAIPRGYVKLMIDLKDCFFSIPLHPKDCKRFAFTLPMINCIGPSPRFQWKVLPQGMANSPTLCQRY 80
Cdd:cd01645    64 TQDMGALQPGLPHPAALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSF 143

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878  81 VAQVIDPFRMSYPDLYVVHYMDDILVAGPDQDQLYSASQELINALQNQGLQVSPEKVQIHPPHLFLGFEL 150
Cdd:cd01645   144 VAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 369-490 4.90e-35

Bel/Pao 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 eukaryote. 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. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


:

Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 129.77  E-value: 4.90e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 369 LVFTDGSSS--GMAAFYINGKVSRFM-TDFSSAQLVKLAAIVKVFEQLPKTSFNLYTDSAYVAASVPLLETVPYIRP--- 442
Cdd:cd09273     1 TVFTDGSSFkaGYAIVSGTEIVEAQPlPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGIERGflk 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1720399878 443 STNASPMFAKLQsLILARNFPFFIGHIRAHSGLPGPLSEGNDIVDQAT 490
Cdd:cd09273    81 SIKNLSLFLQLL-EAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAA 127
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 158-222 1.83e-31

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


:

Pssm-ID: 429135  Cd Length: 66  Bit Score: 117.04  E-value: 1.83e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720399878 158 QKVQVRQDSLQTLNDFQRLLGDINWLRPYLKLTTGELKPLFDILRGDPDPSSPRMLTQEARRSLA 222
Cdd:pfam06817   2 QKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
transpos_IS481 super family cl41329
IS481 family transposase; null
 558-666 1.03e-22

IS481 family transposase; null


The actual alignment was detected with superfamily member NF033577:

Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 98.82  E-value: 1.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 558 PGELWQMDVTHYTPFKKLK--YIHVSVDTSSGFICASL---QTGEATKHVISHVLsclAAVPQP--KILkTDNGPGYTS- 629
Cdd:NF033577  127 PGELWHIDIKKLGRIPDVGrlYLHTAIDDHSRFAYAELypdETAETAADFLRRAF---AEHGIPirRVL-TDNGSEFRSr 202

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1720399878 630 -ASFKQFCAQMGIKHITGIPYNPQGQGIVERTHQTLKN 666
Cdd:NF033577  203 aHGFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 725-768 2.85e-13

Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


:

Pssm-ID: 425747  Cd Length: 45  Bit Score: 64.73  E-value: 2.85e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1720399878 725 MWRDPLSNKWQGPDPVLIWGKGHACIYDSkAQNARWLPERLIKP 768
Cdd:pfam00552   2 KWKDLLNGLWKGPDPLLWWGRGAVCVPQD-ASDPQWVPERLLKR 44
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 507-540 3.21e-13

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


:

Pssm-ID: 426567  Cd Length: 36  Bit Score: 64.32  E-value: 3.21e-13
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1720399878 507 QAHDLHHLNAHTLRLKFSITREQARQIVRQCKGC 540
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTC 34
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 1-150 3.22e-80

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: 256.83  E-value: 3.22e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878   1 MVPMGALQPGIPSPVAIPRGYVKLMIDLKDCFFSIPLHPKDCKRFAFTLPMINCIGPSPRFQWKVLPQGMANSPTLCQRY 80
Cdd:cd01645    64 TQDMGALQPGLPHPAALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSF 143

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878  81 VAQVIDPFRMSYPDLYVVHYMDDILVAGPDQDQLYSASQELINALQNQGLQVSPEKVQIHPPHLFLGFEL 150
Cdd:cd01645   144 VAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 2-150 7.57e-36

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: 133.97  E-value: 7.57e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878   2 VPMGALQPGIPSPVAIPRGYVKLM-IDLKDCFFSIPLHPKDCKRFAFTLPMIN----CIGPSPRFQWKVLPQGMANSPTL 76
Cdd:pfam00078  34 NLDSPPQPGFRPGLAKLKKAKWFLkLDLKKAFDQVPLDELDRKLTAFTTPPINinwnGELSGGRYEWKGLPQGLVLSPAL 113

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399878  77 CQRYVAQVIDPFRmSYPDLYVVHYMDDILVAGPDQDQLYSASQELINALQNQGLQVSPEKVQIHPPHL---FLGFEL 150
Cdd:pfam00078 114 FQLFMNELLRPLR-KRAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFLKSKevkYLGVTL 189
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 369-490 4.90e-35

Bel/Pao 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 eukaryote. 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. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 129.77  E-value: 4.90e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 369 LVFTDGSSS--GMAAFYINGKVSRFM-TDFSSAQLVKLAAIVKVFEQLPKTSFNLYTDSAYVAASVPLLETVPYIRP--- 442
Cdd:cd09273     1 TVFTDGSSFkaGYAIVSGTEIVEAQPlPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGIERGflk 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1720399878 443 STNASPMFAKLQsLILARNFPFFIGHIRAHSGLPGPLSEGNDIVDQAT 490
Cdd:cd09273    81 SIKNLSLFLQLL-EAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAA 127
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 158-222 1.83e-31

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


Pssm-ID: 429135  Cd Length: 66  Bit Score: 117.04  E-value: 1.83e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720399878 158 QKVQVRQDSLQTLNDFQRLLGDINWLRPYLKLTTGELKPLFDILRGDPDPSSPRMLTQEARRSLA 222
Cdd:pfam06817   2 QKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
transpos_IS481 NF033577
IS481 family transposase; null
 558-666 1.03e-22

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 98.82  E-value: 1.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 558 PGELWQMDVTHYTPFKKLK--YIHVSVDTSSGFICASL---QTGEATKHVISHVLsclAAVPQP--KILkTDNGPGYTS- 629
Cdd:NF033577  127 PGELWHIDIKKLGRIPDVGrlYLHTAIDDHSRFAYAELypdETAETAADFLRRAF---AEHGIPirRVL-TDNGSEFRSr 202

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1720399878 630 -ASFKQFCAQMGIKHITGIPYNPQGQGIVERTHQTLKN 666
Cdd:NF033577  203 aHGFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 558-651 4.55e-22

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: 91.22  E-value: 4.55e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 558 PGELWQMDVTHY---TPFKKLkYIHVSVDTSSGFICASLQTGEATKHVISHVLSCLAAV--PQPKILKTDNGPGYTSASF 632
Cdd:pfam00665   1 PNQLWQGDFTYIripGGGGKL-YLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrgGVPLIIHSDNGSEYTSKAF 79

                          90
                  ....*....|....*....
gi 1720399878 633 KQFCAQMGIKHITGIPYNP 651
Cdd:pfam00665  80 REFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
525-669 9.32e-15

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 75.96  E-value: 9.32e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 525 ITREQARQIVRQCKGCLTLLPEPHVGVNPRGLI----PGELWQMDVTH-YTPFKKLkYIHVSVDTSSGFICA-SLQTGEA 598
Cdd:COG2801   111 LMRELGLQARRRRKKKYTTYSGHGGPIAPNLLFtataPNQVWVTDITYiPTAEGWL-YLAAVIDLFSREIVGwSVSDSMD 189

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720399878 599 TKHVISHVLSCLAA--VPQPKILKTDNGPGYTSASFKQFCAQMGIKHITGIPYNPQGQGIVERTHQTLKNMLF 669
Cdd:COG2801   190 AELVVDALEMAIERrgPPKPLILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYELL 262
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 725-768 2.85e-13

Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


Pssm-ID: 425747  Cd Length: 45  Bit Score: 64.73  E-value: 2.85e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1720399878 725 MWRDPLSNKWQGPDPVLIWGKGHACIYDSkAQNARWLPERLIKP 768
Cdd:pfam00552   2 KWKDLLNGLWKGPDPLLWWGRGAVCVPQD-ASDPQWVPERLLKR 44
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 507-540 3.21e-13

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


Pssm-ID: 426567  Cd Length: 36  Bit Score: 64.32  E-value: 3.21e-13
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1720399878 507 QAHDLHHLNAHTLRLKFSITREQARQIVRQCKGC 540
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTC 34
transpos_IS3 NF033516
IS3 family transposase;
558-666 4.60e-11

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 65.28  E-value: 4.60e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 558 PGELWQMDVTH-YTPFKKLkYIHVSVDTSSGFICA-SLQTGEATKHVISHVLSCLAA--VPQPKILKTDNGPGYTSASFK 633
Cdd:NF033516  215 PNQVWVTDITYiRTAEGWL-YLAVVLDLFSREIVGwSVSTSMSAELVLDALEMAIEWrgKPEGLILHSDNGSQYTSKAYR 293

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1720399878 634 QFCAQMGIKHITGIPYNPQGQGIVERTHQTLKN 666
Cdd:NF033516  294 EWLKEHGITQSMSRPGNCWDNAVAESFFGTLKR 326
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 365-490 6.55e-11

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 60.85  E-value: 6.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 365 PGAMLVFTDGSSS-----GMAAFYING---KVSRFMTDFSSAQLVKLAAIVKVFEQLPK-TSFNLYTDSAYV--AASVPL 433
Cdd:pfam00075   1 PKAVTVYTDGSCLgnpgpGGAGAVLYRgheNISAPLPGRTTNNRAELQAVIEALKALKSpSKVNIYTDSQYVigGITQWV 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720399878 434 LETVPYIRPSTNAS-PMFAKL---QSLILARNFPFFIGHIRAHSGLPgplseGNDIVDQAT 490
Cdd:pfam00075  81 HGWKKNGWPTTSEGkPVKNKDlwqLLKALCKKHQVYWQWVKGHAGNP-----GNEMADRLA 136
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 558-694 2.62e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 43.70  E-value: 2.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 558 PGELWQMDVTHYTPFKKLKYIHVSVDTSSGFICA-SLQTGEATKHVISHVLSCLAAVPQPK--ILKTDNGPGYTSASFKQ 634
Cdd:PHA02517  109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVGwRVSSSMDTDFVLDALEQALWARGRPGglIHHSDKGSQYVSLAYTQ 188

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 635 FCAQMGIKHITGIPYNPQGQGIVERTHQTLKNmlfklqsgrEILYPQSGNSKMLLNHALF 694
Cdd:PHA02517  189 RLKEAGIRASTGSRGDSYDNAPAESINGLYKA---------EVIHRVSWKNREEVELATL 239
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 558-664 1.79e-03

ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes several apparently unrelated families of transposases. Members of this family resemble the transposases of ISNCY family elements such as IS1202, ISTde1, ISKpn21, and ISCARN1.


Pssm-ID: 468103 [Multi-domain]  Cd Length: 367  Bit Score: 41.31  E-value: 1.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 558 PGELWQMDVTHYTPFKKLK---YIHVSVDTSSG-----FICASlqtgEATkhvishvLSCLAAVPQ-------PKILKTD 622
Cdd:NF033594  126 FGELIQIDGSPHDWFEGRGpkcTLLVAIDDATGrlmglRFVES----EST-------FGYFEVTRQylekhgkPVAFYSD 194

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1720399878 623 NGPGYTSAS---------FKQF---CAQMGIKHITGipYNPQGQGIVERTHQTL 664
Cdd:NF033594  195 KHSVFRVNEeelagkgdgLTQFgraLKELGIEIICA--NSPQAKGRVERANQTL 246
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 1-150 3.22e-80

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: 256.83  E-value: 3.22e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878   1 MVPMGALQPGIPSPVAIPRGYVKLMIDLKDCFFSIPLHPKDCKRFAFTLPMINCIGPSPRFQWKVLPQGMANSPTLCQRY 80
Cdd:cd01645    64 TQDMGALQPGLPHPAALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSF 143

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878  81 VAQVIDPFRMSYPDLYVVHYMDDILVAGPDQDQLYSASQELINALQNQGLQVSPEKVQIHPPHLFLGFEL 150
Cdd:cd01645   144 VAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 2-150 7.57e-36

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: 133.97  E-value: 7.57e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878   2 VPMGALQPGIPSPVAIPRGYVKLM-IDLKDCFFSIPLHPKDCKRFAFTLPMIN----CIGPSPRFQWKVLPQGMANSPTL 76
Cdd:pfam00078  34 NLDSPPQPGFRPGLAKLKKAKWFLkLDLKKAFDQVPLDELDRKLTAFTTPPINinwnGELSGGRYEWKGLPQGLVLSPAL 113

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720399878  77 CQRYVAQVIDPFRmSYPDLYVVHYMDDILVAGPDQDQLYSASQELINALQNQGLQVSPEKVQIHPPHL---FLGFEL 150
Cdd:pfam00078 114 FQLFMNELLRPLR-KRAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFLKSKevkYLGVTL 189
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 369-490 4.90e-35

Bel/Pao 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 eukaryote. 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. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 129.77  E-value: 4.90e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 369 LVFTDGSSS--GMAAFYINGKVSRFM-TDFSSAQLVKLAAIVKVFEQLPKTSFNLYTDSAYVAASVPLLETVPYIRP--- 442
Cdd:cd09273     1 TVFTDGSSFkaGYAIVSGTEIVEAQPlPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGIERGflk 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1720399878 443 STNASPMFAKLQsLILARNFPFFIGHIRAHSGLPGPLSEGNDIVDQAT 490
Cdd:cd09273    81 SIKNLSLFLQLL-EAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAA 127
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 158-222 1.83e-31

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


Pssm-ID: 429135  Cd Length: 66  Bit Score: 117.04  E-value: 1.83e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720399878 158 QKVQVRQDSLQTLNDFQRLLGDINWLRPYLKLTTGELKPLFDILRGDPDPSSPRMLTQEARRSLA 222
Cdd:pfam06817   2 QKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 26-148 6.69e-24

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: 100.50  E-value: 6.69e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878  26 IDLKDCFFSIPLHPKDCKRFAFTLPmincigpSPRFQWKVLPQGMANSPTLCQRYVAQVIDPFRMSYPDLYVVHYMDDIL 105
Cdd:cd03715    92 LDLANAFFSLPLAPDSQPLFAFEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVDDLL 164

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1720399878 106 VAGPDQDQLYSASQELINALQNQGLQVSPEKVQIHPPHL-FLGF 148
Cdd:cd03715   165 LAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVkFLGV 208
transpos_IS481 NF033577
IS481 family transposase; null
 558-666 1.03e-22

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 98.82  E-value: 1.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 558 PGELWQMDVTHYTPFKKLK--YIHVSVDTSSGFICASL---QTGEATKHVISHVLsclAAVPQP--KILkTDNGPGYTS- 629
Cdd:NF033577  127 PGELWHIDIKKLGRIPDVGrlYLHTAIDDHSRFAYAELypdETAETAADFLRRAF---AEHGIPirRVL-TDNGSEFRSr 202

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1720399878 630 -ASFKQFCAQMGIKHITGIPYNPQGQGIVERTHQTLKN 666
Cdd:NF033577  203 aHGFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 558-651 4.55e-22

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: 91.22  E-value: 4.55e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 558 PGELWQMDVTHY---TPFKKLkYIHVSVDTSSGFICASLQTGEATKHVISHVLSCLAAV--PQPKILKTDNGPGYTSASF 632
Cdd:pfam00665   1 PNQLWQGDFTYIripGGGGKL-YLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrgGVPLIIHSDNGSEYTSKAF 79

                          90
                  ....*....|....*....
gi 1720399878 633 KQFCAQMGIKHITGIPYNP 651
Cdd:pfam00665  80 REFLKDLGIKPSFSRPGNP 98
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 25-148 1.12e-18

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: 84.18  E-value: 1.12e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878  25 MIDLKDCFFSIPLHPKDCKRFAFTLPMinciGpspRFQWKVLPQGMANSPTLCQRYVAQVIDPFRmsypDLYVVHYMDDI 104
Cdd:cd01647    62 KLDLRSGYHQIPLAEESRPKTAFRTPF----G---LYEYTRMPFGLKNAPATFQRLMNKILGDLL----GDFVEVYLDDI 130

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1720399878 105 LVAGPDQDQLYSASQELINALQNQGLQVSPEKVQIHPPHL-FLGF 148
Cdd:cd01647   131 LVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVeFLGH 175
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
525-669 9.32e-15

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 75.96  E-value: 9.32e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 525 ITREQARQIVRQCKGCLTLLPEPHVGVNPRGLI----PGELWQMDVTH-YTPFKKLkYIHVSVDTSSGFICA-SLQTGEA 598
Cdd:COG2801   111 LMRELGLQARRRRKKKYTTYSGHGGPIAPNLLFtataPNQVWVTDITYiPTAEGWL-YLAAVIDLFSREIVGwSVSDSMD 189

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720399878 599 TKHVISHVLSCLAA--VPQPKILKTDNGPGYTSASFKQFCAQMGIKHITGIPYNPQGQGIVERTHQTLKNMLF 669
Cdd:COG2801   190 AELVVDALEMAIERrgPPKPLILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYELL 262
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 26-150 2.52e-13

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: 66.61  E-value: 2.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878  26 IDLKDCFFSIPLhpkdckrfaftlpmincigpsprfqwkvlPQGMANSPTLCQRYVAQVIDPFRMSYPDLYVVHYMDDIL 105
Cdd:cd00304     1 FDVKSFFTSIPL-----------------------------PQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLV 51

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1720399878 106 VAGPDQDQLYSAsQELINALQNQGLQVSPEKVQIHPPHL---FLGFEL 150
Cdd:cd00304    52 VIAKSEQQAVKK-RELEEFLARLGLNLSDEKTQFTEKEKkfkFLGILV 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 725-768 2.85e-13

Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


Pssm-ID: 425747  Cd Length: 45  Bit Score: 64.73  E-value: 2.85e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1720399878 725 MWRDPLSNKWQGPDPVLIWGKGHACIYDSkAQNARWLPERLIKP 768
Cdd:pfam00552   2 KWKDLLNGLWKGPDPLLWWGRGAVCVPQD-ASDPQWVPERLLKR 44
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 507-540 3.21e-13

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


Pssm-ID: 426567  Cd Length: 36  Bit Score: 64.32  E-value: 3.21e-13
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1720399878 507 QAHDLHHLNAHTLRLKFSITREQARQIVRQCKGC 540
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTC 34
transpos_IS3 NF033516
IS3 family transposase;
558-666 4.60e-11

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 65.28  E-value: 4.60e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 558 PGELWQMDVTH-YTPFKKLkYIHVSVDTSSGFICA-SLQTGEATKHVISHVLSCLAA--VPQPKILKTDNGPGYTSASFK 633
Cdd:NF033516  215 PNQVWVTDITYiRTAEGWL-YLAVVLDLFSREIVGwSVSTSMSAELVLDALEMAIEWrgKPEGLILHSDNGSQYTSKAYR 293

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1720399878 634 QFCAQMGIKHITGIPYNPQGQGIVERTHQTLKN 666
Cdd:NF033516  294 EWLKEHGITQSMSRPGNCWDNAVAESFFGTLKR 326
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 365-490 6.55e-11

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 60.85  E-value: 6.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 365 PGAMLVFTDGSSS-----GMAAFYING---KVSRFMTDFSSAQLVKLAAIVKVFEQLPK-TSFNLYTDSAYV--AASVPL 433
Cdd:pfam00075   1 PKAVTVYTDGSCLgnpgpGGAGAVLYRgheNISAPLPGRTTNNRAELQAVIEALKALKSpSKVNIYTDSQYVigGITQWV 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720399878 434 LETVPYIRPSTNAS-PMFAKL---QSLILARNFPFFIGHIRAHSGLPgplseGNDIVDQAT 490
Cdd:pfam00075  81 HGWKKNGWPTTSEGkPVKNKDlwqLLKALCKKHQVYWQWVKGHAGNP-----GNEMADRLA 136
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 26-150 1.75e-10

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: 58.89  E-value: 1.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878  26 IDLKDCFFSIPLHPKDCK--RFAFTlpmincigpSPRFQWKVLPQGMANSPTLCQRYVAQVIDPFRMSypDLYVVHYMDD 103
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDllGFAWQ---------GETYQFKALPFGLSLAPRVFTKVVEALLAPLRLL--GVRIFSYLDD 69

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1720399878 104 ILVAGPDQDQL-YSASQELINALQNQGLQVSPEKVQIHPP--HLFLGFEL 150
Cdd:cd03714    70 LLIIASSIKTSeAVLRHLRATLLANLGFTLNLEKSKLGPTqrITFLGLEL 119
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 27-153 6.42e-08

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: 52.72  E-value: 6.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878  27 DLKDCFFSIPLH--PKDCKRFAFTLPM-----------INCIGPSPRFQWKVLPQGMANSptlcqRYVAQVIdpfrMSYP 93
Cdd:cd01646     2 DISNFYDSIYTHslPWALHGKIKAKQLlkllrllgnllDLLLLSSQYGQTNGLPIGPLTS-----RFLANIY----LNDV 72

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720399878  94 DLYVVH---------YMDDILVAGPDQDQLYSASQELINALQNQGLQVSPEKVQIHP-PHL-----FLGFELFPN 153
Cdd:cd01646    73 DHELKSklkgvdyvrYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILPlPEGtaskdFLGYRFSPI 147
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 27-150 6.79e-06

RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).


Pssm-ID: 238828 [Multi-domain]  Cd Length: 226  Bit Score: 47.97  E-value: 6.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878  27 DLKDCFFSIP--------LHPKDCKRFAFTLPMINCIGPSPRFQWKVL----PQGMANSPTLC-----------QRYVAQ 83
Cdd:cd01651    76 DIKGFFDNIDhdlllkilKRRIGDKRVLRLIRKWLKAGVLEDGKLVETekgtPQGGVISPLLAniylheldkfvEEKLKE 155

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720399878  84 VIDPFRMSYPDLYVVHYMDDILVAGPDQDQLYSASQELINALQNQGLQVSPEKVQIHppHL------FLGFEL 150
Cdd:cd01651   156 YYDTSDPKFRRLRYVRYADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRIT--HFksegfdFLGFTF 226
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 558-694 2.62e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 43.70  E-value: 2.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 558 PGELWQMDVTHYTPFKKLKYIHVSVDTSSGFICA-SLQTGEATKHVISHVLSCLAAVPQPK--ILKTDNGPGYTSASFKQ 634
Cdd:PHA02517  109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVGwRVSSSMDTDFVLDALEQALWARGRPGglIHHSDKGSQYVSLAYTQ 188

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 635 FCAQMGIKHITGIPYNPQGQGIVERTHQTLKNmlfklqsgrEILYPQSGNSKMLLNHALF 694
Cdd:PHA02517  189 RLKEAGIRASTGSRGDSYDNAPAESINGLYKA---------EVIHRVSWKNREEVELATL 239
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 558-664 1.79e-03

ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes several apparently unrelated families of transposases. Members of this family resemble the transposases of ISNCY family elements such as IS1202, ISTde1, ISKpn21, and ISCARN1.


Pssm-ID: 468103 [Multi-domain]  Cd Length: 367  Bit Score: 41.31  E-value: 1.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878 558 PGELWQMDVTHYTPFKKLK---YIHVSVDTSSG-----FICASlqtgEATkhvishvLSCLAAVPQ-------PKILKTD 622
Cdd:NF033594  126 FGELIQIDGSPHDWFEGRGpkcTLLVAIDDATGrlmglRFVES----EST-------FGYFEVTRQylekhgkPVAFYSD 194

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1720399878 623 NGPGYTSAS---------FKQF---CAQMGIKHITGipYNPQGQGIVERTHQTL 664
Cdd:NF033594  195 KHSVFRVNEeelagkgdgLTQFgraLKELGIEIICA--NSPQAKGRVERANQTL 246
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 19-122 3.16e-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: 39.98  E-value: 3.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720399878  19 RGYVKLMIDLKDCFFSIPLHPKDCK--RFAFtLPMINCIGPSPrFQWKVLPQGMANSPTLCQRYVAQVIDpfrmSYPDLY 96
Cdd:cd01644    57 QGKIAVSADIEKMFHQVKVRPEDRDvlRFLW-RKDGDEPKPIE-YRMTVVPFGAASAPFLANRALKQHAE----DHPHEA 130

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1720399878  97 VV------HYMDDILVAGPDQDQLYSASQELI 122
Cdd:cd01644   131 AAkiikrnFYVDDILVSTDTLNEAVNVAKRLI 162
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH