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Conserved domains on  [gi|1998862056|gb|KAG4222987|]
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hypothetical protein PC116_g28540 [Phytophthora cactorum]

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) ...
 556-695 2.03e-85

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: 265.49  E-value: 2.03e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056 556 QGYSDADWAGDIESRRSTSGYAFMMNGGCISWRSKKQRTVALSSTEAEYMALSEATQEAVWLKVFLCELGeMANDEAVKI 635
Cdd:cd09272     1 EGYSDADWAGDPDDRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELG-IPLDGPTTI 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056 636 YEDNQGSIALAKNPEFHKRTKHIDIRYHFVREKVEDGQVVLQYVSTTDMLADIMTKPIPA 695
Cdd:cd09272    80 YCDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPR 139
transpos_IS481 super family cl41329
IS481 family transposase; null
 36-146 3.12e-18

IS481 family transposase; null


The actual alignment was detected with superfamily member NF033577:

Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 85.72  E-value: 3.12e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056  36 EVIHSDVCGpMQTSTFSGKRYFVTFTDDKSHFCVVYLLrnKSEVADKFAEFVAMAETQTGKRVKTLRSDNGGEYTSGAM- 114
Cdd:NF033577  129 ELWHIDIKK-LGRIPDVGRLYLHTAIDDHSRFAYAELY--PDETAETAADFLRRAFAEHGIPIRRVLTDNGSEFRSRAHg 205

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1998862056 115 -AKFCKDRGIEQKFTPPYTPQLNGVAERMNRTL 146
Cdd:NF033577  206 fELALAELGIEHRRTRPYHPQTNGKVERFHRTL 238
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 397-429 5.87e-06

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: 48.36  E-value: 5.87e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1998862056 397 NETWILVPLPKGRKAIGNRWVFRVKENQAGEIE 429
Cdd:pfam07727   1 NETWTLVKLPKNVKPIGTTWVHTHKINDLKEVQ 33
 
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) ...
 556-695 2.03e-85

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: 265.49  E-value: 2.03e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056 556 QGYSDADWAGDIESRRSTSGYAFMMNGGCISWRSKKQRTVALSSTEAEYMALSEATQEAVWLKVFLCELGeMANDEAVKI 635
Cdd:cd09272     1 EGYSDADWAGDPDDRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELG-IPLDGPTTI 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056 636 YEDNQGSIALAKNPEFHKRTKHIDIRYHFVREKVEDGQVVLQYVSTTDMLADIMTKPIPA 695
Cdd:cd09272    80 YCDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPR 139
transpos_IS481 NF033577
IS481 family transposase; null
 36-146 3.12e-18

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 85.72  E-value: 3.12e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056  36 EVIHSDVCGpMQTSTFSGKRYFVTFTDDKSHFCVVYLLrnKSEVADKFAEFVAMAETQTGKRVKTLRSDNGGEYTSGAM- 114
Cdd:NF033577  129 ELWHIDIKK-LGRIPDVGRLYLHTAIDDHSRFAYAELY--PDETAETAADFLRRAFAEHGIPIRRVLTDNGSEFRSRAHg 205

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1998862056 115 -AKFCKDRGIEQKFTPPYTPQLNGVAERMNRTL 146
Cdd:NF033577  206 fELALAELGIEHRRTRPYHPQTNGKVERFHRTL 238
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 36-133 2.98e-15

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: 71.96  E-value: 2.98e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056  36 EVIHSDVCgPMQTSTFSGKRYFVTFTDDKSHFCVVYLLRNKSEVADKFAEFVAMAETQtGKRVKTLRSDNGGEYTSGAMA 115
Cdd:pfam00665   3 QLWQGDFT-YIRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFR-GGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 1998862056 116 KFCKDRGIEQKFTPPYTP 133
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
31-146 2.37e-14

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 74.42  E-value: 2.37e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056  31 AKQVLEVIHSDVcgpMQTSTFSGKRYFVTFTDDKSHFCVVYLLRNkSEVADKFAEFVAMAETQTGKRVK-TLRSDNGGEY 109
Cdd:COG2801   145 ATAPNQVWVTDI---TYIPTAEGWLYLAAVIDLFSREIVGWSVSD-SMDAELVVDALEMAIERRGPPKPlILHSDNGSQY 220

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1998862056 110 TSGAMAKFCKDRGIEQKFTPPYTPQLNGVAERMNRTL 146
Cdd:COG2801   221 TSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTL 257
transpos_IS3 NF033516
IS3 family transposase;
49-149 1.40e-10

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 63.74  E-value: 1.40e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056  49 STFSGKRYFVTFTDDKSHFCVVYllrnksEVADKF-AEFVA----MAETQTGK-RVKTLRSDNGGEYTSGAMAKFCKDRG 122
Cdd:NF033516  227 RTAEGWLYLAVVLDLFSREIVGW------SVSTSMsAELVLdaleMAIEWRGKpEGLILHSDNGSQYTSKAYREWLKEHG 300

                          90       100
                  ....*....|....*....|....*...
gi 1998862056 123 IEQKFTPPYTPQLNGVAERMNRTL-VEC 149
Cdd:NF033516  301 ITQSMSRPGNCWDNAVAESFFGTLkREC 328
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 397-429 5.87e-06

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: 48.36  E-value: 5.87e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1998862056 397 NETWILVPLPKGRKAIGNRWVFRVKENQAGEIE 429
Cdd:pfam07727   1 NETWTLVKLPKNVKPIGTTWVHTHKINDLKEVQ 33
 
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) ...
 556-695 2.03e-85

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: 265.49  E-value: 2.03e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056 556 QGYSDADWAGDIESRRSTSGYAFMMNGGCISWRSKKQRTVALSSTEAEYMALSEATQEAVWLKVFLCELGeMANDEAVKI 635
Cdd:cd09272     1 EGYSDADWAGDPDDRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELG-IPLDGPTTI 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056 636 YEDNQGSIALAKNPEFHKRTKHIDIRYHFVREKVEDGQVVLQYVSTTDMLADIMTKPIPA 695
Cdd:cd09272    80 YCDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPR 139
transpos_IS481 NF033577
IS481 family transposase; null
 36-146 3.12e-18

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 85.72  E-value: 3.12e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056  36 EVIHSDVCGpMQTSTFSGKRYFVTFTDDKSHFCVVYLLrnKSEVADKFAEFVAMAETQTGKRVKTLRSDNGGEYTSGAM- 114
Cdd:NF033577  129 ELWHIDIKK-LGRIPDVGRLYLHTAIDDHSRFAYAELY--PDETAETAADFLRRAFAEHGIPIRRVLTDNGSEFRSRAHg 205

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1998862056 115 -AKFCKDRGIEQKFTPPYTPQLNGVAERMNRTL 146
Cdd:NF033577  206 fELALAELGIEHRRTRPYHPQTNGKVERFHRTL 238
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 36-133 2.98e-15

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: 71.96  E-value: 2.98e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056  36 EVIHSDVCgPMQTSTFSGKRYFVTFTDDKSHFCVVYLLRNKSEVADKFAEFVAMAETQtGKRVKTLRSDNGGEYTSGAMA 115
Cdd:pfam00665   3 QLWQGDFT-YIRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFR-GGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 1998862056 116 KFCKDRGIEQKFTPPYTP 133
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
31-146 2.37e-14

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 74.42  E-value: 2.37e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056  31 AKQVLEVIHSDVcgpMQTSTFSGKRYFVTFTDDKSHFCVVYLLRNkSEVADKFAEFVAMAETQTGKRVK-TLRSDNGGEY 109
Cdd:COG2801   145 ATAPNQVWVTDI---TYIPTAEGWLYLAAVIDLFSREIVGWSVSD-SMDAELVVDALEMAIERRGPPKPlILHSDNGSQY 220

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1998862056 110 TSGAMAKFCKDRGIEQKFTPPYTPQLNGVAERMNRTL 146
Cdd:COG2801   221 TSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTL 257
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
53-146 3.90e-12

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 67.98  E-value: 3.90e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056  53 GKRYFVTFTDDKSHFCVVYLLRNKS--EVADKFAEFVAMAETQtgkRVKTLRSDNGGEYTsgAMAKFCKDRGIEQKFTPP 130
Cdd:COG2826   185 GKSALLTLVERKSRFVILLKLPDKTaeSVADALIRLLRKLPAF---LRKSITTDNGKEFA--DHKEIEAALGIKVYFADP 259

                          90
                  ....*....|....*.
gi 1998862056 131 YTPQLNGVAERMNRTL 146
Cdd:COG2826   260 YSPWQRGTNENTNGLL 275
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 558-691 6.82e-12

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


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 63.10  E-value: 6.82e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056 558 YSDADWAGDieSRRSTSGYAFMM-NGGCISWRSKKQRtvALSSTEAEYMALSEATQEAVWLkvflcelgemaNDEAVKIY 636
Cdd:cd06222     2 NVDGSCRGN--PGPAGIGGVLRDhEGGWLGGFALKIG--APTALEAELLALLLALELALDL-----------GYLKVIIE 66

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1998862056 637 EDNQGSIALAKNPEFHKRtKHIDIRYHFVREKVEDGQVVLQYVS-TTDMLADIMTK 691
Cdd:cd06222    67 SDSKYVVDLINSGSFKWS-PNILLIEDILLLLSRFWSVKISHVPrEGNQVADALAK 121
transpos_IS3 NF033516
IS3 family transposase;
49-149 1.40e-10

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 63.74  E-value: 1.40e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998862056  49 STFSGKRYFVTFTDDKSHFCVVYllrnksEVADKF-AEFVA----MAETQTGK-RVKTLRSDNGGEYTSGAMAKFCKDRG 122
Cdd:NF033516  227 RTAEGWLYLAVVLDLFSREIVGW------SVSTSMsAELVLdaleMAIEWRGKpEGLILHSDNGSQYTSKAYREWLKEHG 300

                          90       100
                  ....*....|....*....|....*...
gi 1998862056 123 IEQKFTPPYTPQLNGVAERMNRTL-VEC 149
Cdd:NF033516  301 ITQSMSRPGNCWDNAVAESFFGTLkREC 328
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 397-429 5.87e-06

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: 48.36  E-value: 5.87e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1998862056 397 NETWILVPLPKGRKAIGNRWVFRVKENQAGEIE 429
Cdd:pfam07727   1 NETWTLVKLPKNVKPIGTTWVHTHKINDLKEVQ 33
rve_3 pfam13683
Integrase core domain;
121-146 3.13e-05

Integrase core domain;


Pssm-ID: 433402 [Multi-domain]  Cd Length: 67  Bit Score: 42.20  E-value: 3.13e-05
                          10        20
                  ....*....|....*....|....*.
gi 1998862056 121 RGIEQKFTPPYTPQLNGVAERMNRTL 146
Cdd:pfam13683   1 LGIEISYIAPGKPMQNGLVESFNGTL 26
 
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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