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Conserved domains on  [gi|485099481|gb|AGK81956|]
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pol protein, partial [Human immunodeficiency virus 1]

Protein Classification

pol protein( domain architecture ID 15830062)

HIV-1 pol protein containing the retroviral aspartyl protease, reverse transcriptase (RT), RT thumb, RT connection, RNase H, and integrase domains

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 169-385 4.62e-118

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: 360.06  E-value: 4.62e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 169 GPKVKQWPLTEEKIKALTEICDEMEKEGKITKIGpeNPYNTPIFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 248
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 249 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPD 328
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 485099481 329 IVIYQYMDDLYVGSDLEiGQHRAKIEELREHLLKWGFTTPDKKHQKEPPFLWMGYEL 385
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 469-570 1.33e-36

Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains.


:

Pssm-ID: 462013  Cd Length: 102  Bit Score: 133.34  E-value: 1.33e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  469 YYDPSKDLIAEIQKQGHDQWTYQIYQEPFKNLKTGKYAKMRAAHTNDVKQLTEAVQKIAMESIVIWGKTPKFRLPIQKET 548
Cdd:pfam06815   1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                          90       100
                  ....*....|....*....|..
gi 485099481  549 WETWWTDYWQATWIPEWEFVNT 570
Cdd:pfam06815  81 WETWWTEYWQATWIPEWEFVNT 102
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 588-708 2.69e-33

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: 125.18  E-value: 2.69e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  588 AETFYVDGAANRETKIGKAGYITDRGRKKIVSLTE--TTNQKTELQAICIALQD--SGSEVNIVTDSQYALGII------ 657
Cdd:pfam00075   3 AVTVYTDGSCLGNPGPGGAGAVLYRGHENISAPLPgrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGItqwvhg 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 485099481  658 ---QAQPDKSES-ELVN----QIIEHLIKKERVYLTWVPAHKGIGGNEQVDKLVSSGIR 708
Cdd:pfam00075  83 wkkNGWPTTSEGkPVKNkdlwQLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 57-150 1.14e-32

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


:

Pssm-ID: 425454  Cd Length: 101  Bit Score: 122.09  E-value: 1.14e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481   57 LWQRPLVSIKVGGQIKEALLDTGADDTVLEEINLPGKW----KPKMIGGIGGFIKVRQYDQISIEICGKKAIGTV--LVG 130
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 485099481  131 PT-PVNIIGRNLMTQLGCTLN 150
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
RVT_thumb super family cl06055
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 392-447 3.31e-19

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


The actual alignment was detected with superfamily member pfam06817:

Pssm-ID: 429135  Cd Length: 66  Bit Score: 82.37  E-value: 3.31e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 485099481  392 VQPIQLPEKDSWTVNDIQKLVGKLNWASQIY--PGIKVRQLCKLLRGAKALTDIVPLT 447
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLT 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 768-856 1.40e-14

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: 70.42  E-value: 1.40e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  768 SPGIWQLDCTHLEGKI------ILVAVHVASGYMEAEVIPAETGQETAYFLLKLA---GRWPVKVIHTDNGSNFTSAAVK 838
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 485099481  839 AACWWAGVKQEFGIPYNP 856
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 936-979 9.68e-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: 63.19  E-value: 9.68e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 485099481  936 VYYRDSRDPIWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 979
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 721-756 1.04e-11

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: 60.08  E-value: 1.04e-11
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 485099481  721 EEHERYHSNWRAMASDFNLPPIVAKEIVASCNQCQQ 756
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
Tra5 super family cl34487
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
823-906 2.82e-10

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


The actual alignment was detected with superfamily member COG2801:

Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 62.86  E-value: 2.82e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 823 VIHTDNGSNFTSAAVKAACWWAGVKQEFGIPYNPQSQGVVESMNKELKT--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 899
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 485099481 900 GGIGGYS 906
Cdd:COG2801  291 SSLGYLT 297
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 169-385 4.62e-118

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: 360.06  E-value: 4.62e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 169 GPKVKQWPLTEEKIKALTEICDEMEKEGKITKIGpeNPYNTPIFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 248
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 249 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPD 328
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 485099481 329 IVIYQYMDDLYVGSDLEiGQHRAKIEELREHLLKWGFTTPDKKHQKEPPFLWMGYEL 385
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 214-385 3.37e-45

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: 161.32  E-value: 3.37e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  214 IKKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLDEDFRKYTAF 281
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  282 TIPSINN----ETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQnPDIVIYQYMDDLYVGSDlEIGQHRAKIEELR 357
Cdd:pfam00078  81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 485099481  358 EHLLKWGFTTPDKKHQ---KEPPFLWMGYEL 385
Cdd:pfam00078 159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 469-570 1.33e-36

Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains.


Pssm-ID: 462013  Cd Length: 102  Bit Score: 133.34  E-value: 1.33e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  469 YYDPSKDLIAEIQKQGHDQWTYQIYQEPFKNLKTGKYAKMRAAHTNDVKQLTEAVQKIAMESIVIWGKTPKFRLPIQKET 548
Cdd:pfam06815   1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                          90       100
                  ....*....|....*....|..
gi 485099481  549 WETWWTDYWQATWIPEWEFVNT 570
Cdd:pfam06815  81 WETWWTEYWQATWIPEWEFVNT 102
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 588-708 2.69e-33

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: 125.18  E-value: 2.69e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  588 AETFYVDGAANRETKIGKAGYITDRGRKKIVSLTE--TTNQKTELQAICIALQD--SGSEVNIVTDSQYALGII------ 657
Cdd:pfam00075   3 AVTVYTDGSCLGNPGPGGAGAVLYRGHENISAPLPgrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGItqwvhg 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 485099481  658 ---QAQPDKSES-ELVN----QIIEHLIKKERVYLTWVPAHKGIGGNEQVDKLVSSGIR 708
Cdd:pfam00075  83 wkkNGWPTTSEGkPVKNkdlwQLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 57-150 1.14e-32

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 122.09  E-value: 1.14e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481   57 LWQRPLVSIKVGGQIKEALLDTGADDTVLEEINLPGKW----KPKMIGGIGGFIKVRQYDQISIEICGKKAIGTV--LVG 130
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 485099481  131 PT-PVNIIGRNLMTQLGCTLN 150
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 63-143 7.21e-24

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133149  Cd Length: 87  Bit Score: 96.18  E-value: 7.21e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  63 VSIKVGGQIKEALLDTGADDTVLEEINLPGKW----KPKMIGGIGGFIKVRQYDQISIEICGKKAIGTVLVGP--TPVNI 136
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                 ....*..
gi 485099481 137 IGRNLMT 143
Cdd:cd05482   81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 392-447 3.31e-19

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: 82.37  E-value: 3.31e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 485099481  392 VQPIQLPEKDSWTVNDIQKLVGKLNWASQIY--PGIKVRQLCKLLRGAKALTDIVPLT 447
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLT 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 768-856 1.40e-14

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: 70.42  E-value: 1.40e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  768 SPGIWQLDCTHLEGKI------ILVAVHVASGYMEAEVIPAETGQETAYFLLKLA---GRWPVKVIHTDNGSNFTSAAVK 838
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 485099481  839 AACWWAGVKQEFGIPYNP 856
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
592-707 2.10e-14

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 71.03  E-value: 2.10e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 592 YVDGAANRETkiGKAGY---ITDRGRKKIVS--LTETTNQKTELQAICIALQ----DSGSEVNIVTDSQYALGIIQAQPD 662
Cdd:COG0328    6 YTDGACRGNP--GPGGWgavIRYGGEEKELSggLGDTTNNRAELTALIAALEalkeLGPCEVEIYTDSQYVVNQITGWIH 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 485099481 663 KSES---------ELVNQIIEhLIKKERVYLTWVPAHKGIGGNEQVDKLVSSGI 707
Cdd:COG0328   84 GWKKngwkpvknpDLWQRLDE-LLARHKVTFEWVKGHAGHPGNERADALANKAL 136
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 936-979 9.68e-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: 63.19  E-value: 9.68e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 485099481  936 VYYRDSRDPIWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 979
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 592-702 1.24e-12

Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and 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 (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos.


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 66.05  E-value: 1.24e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 592 YVDGAA-NRETKIGKAGY------ITDRGRKKIVSLTETTNQKTELQAICIALQ----DSGSEVNIVTDSQYALGII--- 657
Cdd:cd09280    3 YTDGSClNNGKPGARAGIgvyfgpGDPRNVSEPLPGRKQTNNRAELLAVIHALEqapeEGIRKLEIRTDSKYAINCItkw 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 485099481 658 ----QAQPDKSES-------ELVNQIIEHLIKKE-RVYLTWVPAHKGIGGNEQVDKL 702
Cdd:cd09280   83 ipkwKKNGWKTSKgkpvknqDLIKELDKLLRKRGiKVKFEHVKGHSGDPGNEEADRL 139
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 721-756 1.04e-11

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: 60.08  E-value: 1.04e-11
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 485099481  721 EEHERYHSNWRAMASDFNLPPIVAKEIVASCNQCQQ 756
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
823-906 2.82e-10

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 62.86  E-value: 2.82e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 823 VIHTDNGSNFTSAAVKAACWWAGVKQEFGIPYNPQSQGVVESMNKELKT--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 899
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 485099481 900 GGIGGYS 906
Cdd:COG2801  291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
823-871 4.63e-09

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 59.50  E-value: 4.63e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 485099481 823 VIHTDNGSNFTSAAVKAACWWAGVKQEFGIPYNPQSQGVVESMNKELKT 871
Cdd:NF033516 278 ILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKR 326
transpos_IS481 NF033577
IS481 family transposase; null
 766-911 8.87e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 57.99  E-value: 8.87e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 766 DCSPGIWQLDCTHL-----EGKI-ILVAVHVASGYMEAEVIPAETGQETAYFLLKLAGRWPVKV--IHTDNGSNFTSAA- 836
Cdd:NF033577 125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPIrrVLTDNGSEFRSRAh 204

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 837 -VKAACWWAGVKQEFGIPYNPQSQGVVESMNKELKTIIGQVR--DQAEHLKTAvqMAVFIH--NFKRK-GGIGGYSAGER 910
Cdd:NF033577 205 gFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARpyESLAELQAA--LDEWLHhyNHHRPhSALGGKTPAER 282


                 .
gi 485099481 911 I 911
Cdd:NF033577 283 F 283
PRK08719 PRK08719
ribonuclease H; Reviewed
 590-709 3.80e-04

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 41.77  E-value: 3.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 590 TFYVDGAA-NRETK-----IGKAGYITDRGRKKIVSLT---ETTNQKTELQAICIALQDSGSEVNIVTDSQYALGIIQAQ 660
Cdd:PRK08719   6 SIYIDGAApNNQHGcvrggIGLVVYDEAGEIVDEQSITvnrYTDNAELELLALIEALEYARDGDVIYSDSDYCVRGFNEW 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 485099481 661 PD--------KSESELVN-----QIIEHLIKKERVYLTWVPAHKGIGGNEQVDKLVSSGIRK 709
Cdd:PRK08719  86 LDtwkqkgwrKSDKKPVAnrdlwQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQAAAEL 147
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 169-385 4.62e-118

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: 360.06  E-value: 4.62e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 169 GPKVKQWPLTEEKIKALTEICDEMEKEGKITKIGpeNPYNTPIFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 248
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 249 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPD 328
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 485099481 329 IVIYQYMDDLYVGSDLEiGQHRAKIEELREHLLKWGFTTPDKKHQKEPPFLWMGYEL 385
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 214-385 3.37e-45

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: 161.32  E-value: 3.37e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  214 IKKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLDEDFRKYTAF 281
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  282 TIPSINN----ETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQnPDIVIYQYMDDLYVGSDlEIGQHRAKIEELR 357
Cdd:pfam00078  81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 485099481  358 EHLLKWGFTTPDKKHQ---KEPPFLWMGYEL 385
Cdd:pfam00078 159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 469-570 1.33e-36

Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains.


Pssm-ID: 462013  Cd Length: 102  Bit Score: 133.34  E-value: 1.33e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  469 YYDPSKDLIAEIQKQGHDQWTYQIYQEPFKNLKTGKYAKMRAAHTNDVKQLTEAVQKIAMESIVIWGKTPKFRLPIQKET 548
Cdd:pfam06815   1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                          90       100
                  ....*....|....*....|..
gi 485099481  549 WETWWTDYWQATWIPEWEFVNT 570
Cdd:pfam06815  81 WETWWTEYWQATWIPEWEFVNT 102
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 588-708 2.69e-33

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: 125.18  E-value: 2.69e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  588 AETFYVDGAANRETKIGKAGYITDRGRKKIVSLTE--TTNQKTELQAICIALQD--SGSEVNIVTDSQYALGII------ 657
Cdd:pfam00075   3 AVTVYTDGSCLGNPGPGGAGAVLYRGHENISAPLPgrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGItqwvhg 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 485099481  658 ---QAQPDKSES-ELVN----QIIEHLIKKERVYLTWVPAHKGIGGNEQVDKLVSSGIR 708
Cdd:pfam00075  83 wkkNGWPTTSEGkPVKNkdlwQLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 170-373 3.28e-33

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: 127.46  E-value: 3.28e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 170 PKVKQWPLTEEKIKALTEICDEMEKEGKItkIGPENPYNTPIFAIKKKDSTKWRKLVDFRELNKRTQDfweVQLGIPHPA 249
Cdd:cd03715    2 VNQKQYPLPREAREGITPHIQELLEAGIL--VPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLP---IHPAVPNPY 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 250 GL-----KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPsinnetpGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRK 324
Cdd:cd03715   77 TLlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPL 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 485099481 325 QNPDIVIYQYMDDLYVGSDLEIGQHRAKIEELReHLLKWGFTTPDKKHQ 373
Cdd:cd03715  150 EHEGTILLQYVDDLLLAADSEEDCLKGTDALLT-HLGELGYKVSPKKAQ 197
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 57-150 1.14e-32

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 122.09  E-value: 1.14e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481   57 LWQRPLVSIKVGGQIKEALLDTGADDTVLEEINLPGKW----KPKMIGGIGGFIKVRQYDQISIEICGKKAIGTV--LVG 130
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 485099481  131 PT-PVNIIGRNLMTQLGCTLN 150
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 206-362 1.97e-27

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: 109.61  E-value: 1.97e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 206 PYNTPIFAIKKKDStKWRKLVDFRELNKRT-QDFWEvqlgIPHPAG----LKKKKSVTVLDVGDAYFSVPLDEDFRKYTA 280
Cdd:cd01647    9 PYASPVVVVKKKDG-KLRLCVDYRKLNKVTiKDRYP----LPTIDElleeLAGAKVFSKLDLRSGYHQIPLAEESRPKTA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 281 FTipsinneTPGIRYQYNVLPQGWKGSPAIFQSSMTKIlepFRKQNPDIVIyQYMDDLYVGSDlEIGQHRAKIEE----L 356
Cdd:cd01647   84 FR-------TPFGLYEYTRMPFGLKNAPATFQRLMNKI---LGDLLGDFVE-VYLDDILVYSK-TEEEHLEHLREvlerL 151


                 ....*.
gi 485099481 357 REHLLK 362
Cdd:cd01647  152 REAGLK 157
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 63-143 7.21e-24

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133149  Cd Length: 87  Bit Score: 96.18  E-value: 7.21e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  63 VSIKVGGQIKEALLDTGADDTVLEEINLPGKW----KPKMIGGIGGFIKVRQYDQISIEICGKKAIGTVLVGP--TPVNI 136
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                 ....*..
gi 485099481 137 IGRNLMT 143
Cdd:cd05482   81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 392-447 3.31e-19

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: 82.37  E-value: 3.31e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 485099481  392 VQPIQLPEKDSWTVNDIQKLVGKLNWASQIY--PGIKVRQLCKLLRGAKALTDIVPLT 447
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLT 58
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 300-385 6.36e-19

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: 82.78  E-value: 6.36e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 300 LPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEigQHRAKIEELREHLLKWGFTTPDKKHQ---KEP 376
Cdd:cd00304   12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE--QQAVKKRELEEFLARLGLNLSDEKTQfteKEK 89


                 ....*....
gi 485099481 377 PFLWMGYEL 385
Cdd:cd00304   90 KFKFLGILV 98
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 768-856 1.40e-14

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: 70.42  E-value: 1.40e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  768 SPGIWQLDCTHLEGKI------ILVAVHVASGYMEAEVIPAETGQETAYFLLKLA---GRWPVKVIHTDNGSNFTSAAVK 838
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 485099481  839 AACWWAGVKQEFGIPYNP 856
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
592-707 2.10e-14

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 71.03  E-value: 2.10e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 592 YVDGAANRETkiGKAGY---ITDRGRKKIVS--LTETTNQKTELQAICIALQ----DSGSEVNIVTDSQYALGIIQAQPD 662
Cdd:COG0328    6 YTDGACRGNP--GPGGWgavIRYGGEEKELSggLGDTTNNRAELTALIAALEalkeLGPCEVEIYTDSQYVVNQITGWIH 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 485099481 663 KSES---------ELVNQIIEhLIKKERVYLTWVPAHKGIGGNEQVDKLVSSGI 707
Cdd:COG0328   84 GWKKngwkpvknpDLWQRLDE-LLARHKVTFEWVKGHAGHPGNERADALANKAL 136
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 936-979 9.68e-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: 63.19  E-value: 9.68e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 485099481  936 VYYRDSRDPIWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 979
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 592-702 1.24e-12

Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and 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 (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos.


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 66.05  E-value: 1.24e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 592 YVDGAA-NRETKIGKAGY------ITDRGRKKIVSLTETTNQKTELQAICIALQ----DSGSEVNIVTDSQYALGII--- 657
Cdd:cd09280    3 YTDGSClNNGKPGARAGIgvyfgpGDPRNVSEPLPGRKQTNNRAELLAVIHALEqapeEGIRKLEIRTDSKYAINCItkw 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 485099481 658 ----QAQPDKSES-------ELVNQIIEHLIKKE-RVYLTWVPAHKGIGGNEQVDKL 702
Cdd:cd09280   83 ipkwKKNGWKTSKgkpvknqDLIKELDKLLRKRGiKVKFEHVKGHSGDPGNEEADRL 139
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 721-756 1.04e-11

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: 60.08  E-value: 1.04e-11
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 485099481  721 EEHERYHSNWRAMASDFNLPPIVAKEIVASCNQCQQ 756
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 592-708 2.90e-11

RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and 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 (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 62.12  E-value: 2.90e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 592 YVDGAANRETkiGKAGY---ITDRGRKKIVSLTE--TTNQKTELQAICIALQ--DSGSEVNIVTDSQYAL-GIIQAQPD- 662
Cdd:cd09278    5 YTDGACLGNP--GPGGWaavIRYGDHEKELSGGEpgTTNNRMELTAAIEALEalKEPCPVTIYTDSQYVInGITKWIKGw 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 485099481 663 ------KSESELV-N----QIIEHLIKKERVYLTWVPAHKGIGGNEQVDKLVSSGIR 708
Cdd:cd09278   83 kkngwkTADGKPVkNrdlwQELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAAD 139
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 590-702 5.41e-11

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, 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. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 61.08  E-value: 5.41e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 590 TFYVDGAANrETKIGKA-----GYITDRGRKKIVSLTETTNqkTELQAICIALQ------DSGSEVNIVTDSQYALGIIQ 658
Cdd:cd09276    1 VIYTDGSKL-EGSVGAGfviyrGGEVISRSYRLGTHASVFD--AELEAILEALElalataRRARKVTIFTDSQSALQALR 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 485099481 659 AqPDKSESELVNQIIEHLIKKER-----VYLTWVPAHKGIGGNEQVDKL 702
Cdd:cd09276   78 N-PRRSSGQVILIRILRLLRLLKakgvkVRLRWVPGHVGIEGNEAADRL 125
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
823-906 2.82e-10

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 62.86  E-value: 2.82e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 823 VIHTDNGSNFTSAAVKAACWWAGVKQEFGIPYNPQSQGVVESMNKELKT--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 899
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 485099481 900 GGIGGYS 906
Cdd:COG2801  291 SSLGYLT 297
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 590-703 2.29e-09

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: 56.58  E-value: 2.29e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 590 TFYVDGAAnreTKIGKAGYITDRGRKKIVSLTETTNQKTELQAICIALQD-SGSEVNIVTDSQYALGIIQA--------- 659
Cdd:cd09273    1 TVFTDGSS---FKAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELaKGKPVNIYTDSAYAVHALHLletigierg 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 485099481 660 -QPDKSESELVNQIIEHLIKKERVYLTWVPAHKGIG-----GNEQVDKLV 703
Cdd:cd09273   78 fLKSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPgplaeGNAQADAAA 127
transpos_IS3 NF033516
IS3 family transposase;
823-871 4.63e-09

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 59.50  E-value: 4.63e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 485099481 823 VIHTDNGSNFTSAAVKAACWWAGVKQEFGIPYNPQSQGVVESMNKELKT 871
Cdd:NF033516 278 ILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKR 326
transpos_IS481 NF033577
IS481 family transposase; null
 766-911 8.87e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 57.99  E-value: 8.87e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 766 DCSPGIWQLDCTHL-----EGKI-ILVAVHVASGYMEAEVIPAETGQETAYFLLKLAGRWPVKV--IHTDNGSNFTSAA- 836
Cdd:NF033577 125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPIrrVLTDNGSEFRSRAh 204

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 837 -VKAACWWAGVKQEFGIPYNPQSQGVVESMNKELKTIIGQVR--DQAEHLKTAvqMAVFIH--NFKRK-GGIGGYSAGER 910
Cdd:NF033577 205 gFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARpyESLAELQAA--LDEWLHhyNHHRPhSALGGKTPAER 282


                 .
gi 485099481 911 I 911
Cdd:NF033577 283 F 283
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 592-702 8.27e-08

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: 51.55  E-value: 8.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 592 YVDGAANRETKIGKAGY-ITDRGRKKIVSLTE----TTNQKTELQAICIALQ----DSGSEVNIVTDSQYALGIIQAQPD 662
Cdd:cd06222    2 NVDGSCRGNPGPAGIGGvLRDHEGGWLGGFALkigaPTALEAELLALLLALElaldLGYLKVIIESDSKYVVDLINSGSF 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 485099481 663 KSES--ELVNQIIEHLIKKERVYLTWVPAHkgigGNEQVDKL 702
Cdd:cd06222   82 KWSPniLLIEDILLLLSRFWSVKISHVPRE----GNQVADAL 119
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 260-376 3.86e-07

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: 49.65  E-value: 3.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 260 LDVGDAYFSVPLDEDFRKYTAFtIPSinnetpGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNpdIVIYQYMDD-L 338
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLG--VRIFSYLDDlL 71

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 485099481 339 YVGSDLEIGQHRAKieELREHLL-KWGFTTPDKKHQKEP 376
Cdd:cd03714   72 IIASSIKTSEAVLR--HLRATLLaNLGFTLNLEKSKLGP 108
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 592-708 3.13e-04

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and 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 (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 41.69  E-value: 3.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 592 YVDGAANRETKIGKAGY-ITDRGRKKI---VSLTE-TTNQKTELQAICIALQD----SGSEVNIVTDSQyaLGIIQAQPD 662
Cdd:cd09279    4 YFDGASRGNPGPAGAGVvIYSPGGEVLelsERLGFpATNNEAEYEALIAGLELalelGAEKLEIYGDSQ--LVVNQLNGE 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 485099481 663 ---KSES--ELVNQIIEHLIKKERVYLTWVPAHKgiggNEQVDKLVSSGIR 708
Cdd:cd09279   82 ykvKNERlkPLLEKVLELLAKFELVELKWIPREQ----NKEADALANQALD 128
PRK08719 PRK08719
ribonuclease H; Reviewed
 590-709 3.80e-04

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 41.77  E-value: 3.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481 590 TFYVDGAA-NRETK-----IGKAGYITDRGRKKIVSLT---ETTNQKTELQAICIALQDSGSEVNIVTDSQYALGIIQAQ 660
Cdd:PRK08719   6 SIYIDGAApNNQHGcvrggIGLVVYDEAGEIVDEQSITvnrYTDNAELELLALIEALEYARDGDVIYSDSDYCVRGFNEW 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 485099481 661 PD--------KSESELVN-----QIIEHLIKKERVYLTWVPAHKGIGGNEQVDKLVSSGIRK 709
Cdd:PRK08719  86 LDtwkqkgwrKSDKKPVAnrdlwQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQAAAEL 147
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 63-143 4.17e-04

Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133159  Cd Length: 86  Bit Score: 40.01  E-value: 4.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481  63 VSIKVGGQIKEALLDTGADDTVLEEiNLPGKWKPKM----IGGIGGFIK--VRQYDQiSIEICGKKAIGTVLVGPT-PVN 135
Cdd:cd06095    1 VTITVEGVPIVFLVDTGATHSVLKS-DLGPKQELSTtsvlIRGVSGQSQqpVTTYRT-LVDLGGHTVSHSFLVVPNcPDP 78


                 ....*...
gi 485099481 136 IIGRNLMT 143
Cdd:cd06095   79 LLGRDLLS 86
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 63-141 4.77e-03

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


Pssm-ID: 433378  Cd Length: 90  Bit Score: 37.26  E-value: 4.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485099481   63 VSIKVGGQIKEALLDTGADDTVL-----EEINLPGKWK--PKMIGGIGGFIKVR--QYDQISIeicGKKAIG--TVLV-- 129
Cdd:pfam13650   1 VPVTINGKPVRFLVDTGASGTVIspslaERLGLKVRGLayTVRVSTAGGRVSAArvRLDSLRL---GGLTLEnvPALVld 77

                          90
                  ....*....|...
gi 485099481  130 -GPTPVNIIGRNL 141
Cdd:pfam13650  78 lGDLIDGLLGMDF 90
 
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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