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Conserved domains on  [gi|406855992|gb|AFS63997|]
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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 ...
 173-389 3.23e-114

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: 350.43  E-value: 3.23e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  173 GPKVKQWPLTEEKIKALTEICKEMEDEGKISKIGpeNPYNTPVFAIRKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 252
Cdd:cd01645     1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  253 AGLKKKKSVTVLDVGDAYFSVPLDESFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRIKNPE 332
Cdd:cd01645    78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 406855992  333 IAIYQYMDDLYVGSDLEiGQHRTKIEELRAHLLNWGFTTPDKKHQKEPPFLWMGYEL 389
Cdd:cd01645   158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 473-574 8.64e-37

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: 133.73  E-value: 8.64e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   473 YYDPSKDLVAEVQKQGQDQWTYQIYQEPFKNLKTGKYARKRSAHTNDVRQLTEVVQKIATESIVIWGKTPKFKLPIQRET 552
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|..
gi 406855992   553 WETWWMEYWQATWIPEWEFVNT 574
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 ...
 592-712 1.66e-34

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: 128.65  E-value: 1.66e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   592 AETFYVDGAASRETKLGKAGYVTDRGRQ-KVVSLTE-TTNQKTELHAIHLALQD--SGSEVNIVTDSQYALGII------ 661
Cdd:pfam00075    3 AVTVYTDGSCLGNPGPGGAGAVLYRGHEnISAPLPGrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGItqwvhg 82

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 406855992   662 ---QAQPDRSES-EVVN----QIIEELIKKEKVYLSWVPAHKGIGGNEQVDKLVSSGIR 712
Cdd:pfam00075   83 wkkNGWPTTSEGkPVKNkdlwQLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 61-154 2.73e-34

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: 126.71  E-value: 2.73e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992    61 LWQRPLVTVKIGGQLKEALLDTGADDTVLEDINLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKKAIGTV--LVG 134
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                           90       100
                   ....*....|....*....|.
gi 406855992   135 PT-PVNIIGRNMLTQIGCTLN 154
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 ...
 396-451 4.03e-18

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: 79.29  E-value: 4.03e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 406855992   396 VQPIELPEKDSWTVNDIQKLVGKLNWASQIYA--GIKVKQLCKLLRGAKALTDIVPLT 451
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGitTYDLKPLFSLLRGDSDLTSPRTLT 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 772-860 3.85e-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: 3.85e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   772 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFVLKLA---GRWPVKVIHTDNGSNFTSAAVK 842
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 406855992   843 AACWWANVQQEFGIPYNP 860
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C super family cl02895
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 940-983 1.15e-12

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.


The actual alignment was detected with superfamily member pfam00552:

Pssm-ID: 425747  Cd Length: 45  Bit Score: 63.19  E-value: 1.15e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 406855992   940 VYYRDSRDPIWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 983
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 725-759 1.42e-10

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: 57.00  E-value: 1.42e-10
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 406855992   725 EEHERYHSNWRTMASEFNLPPIVAKEIVANCDKCQ 759
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
Tra5 super family cl34487
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
827-910 1.73e-09

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: 60.17  E-value: 1.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  827 VIHTDNGSNFTSAAVKAACWWANVQQEFGIPYNPQSQGVVESMNKELKK--IIGQIREQAEHLKTAVQMAVFIHNFKR-K 903
Cdd:COG2801   211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                  ....*..
gi 406855992  904 GGIGGYS 910
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 ...
 173-389 3.23e-114

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: 350.43  E-value: 3.23e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  173 GPKVKQWPLTEEKIKALTEICKEMEDEGKISKIGpeNPYNTPVFAIRKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 252
Cdd:cd01645     1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  253 AGLKKKKSVTVLDVGDAYFSVPLDESFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRIKNPE 332
Cdd:cd01645    78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 406855992  333 IAIYQYMDDLYVGSDLEiGQHRTKIEELRAHLLNWGFTTPDKKHQKEPPFLWMGYEL 389
Cdd:cd01645   158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 218-389 5.75e-43

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: 154.77  E-value: 5.75e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   218 IRKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLDESFRKYTAF 285
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   286 TIPSINN----ETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRiKNPEIAIYQYMDDLYVGSDlEIGQHRTKIEELR 361
Cdd:pfam00078   81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLR-KRAGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 406855992   362 AHLLNWGFTTPDKKHQ---KEPPFLWMGYEL 389
Cdd:pfam00078  159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 473-574 8.64e-37

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: 133.73  E-value: 8.64e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   473 YYDPSKDLVAEVQKQGQDQWTYQIYQEPFKNLKTGKYARKRSAHTNDVRQLTEVVQKIATESIVIWGKTPKFKLPIQRET 552
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|..
gi 406855992   553 WETWWMEYWQATWIPEWEFVNT 574
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 ...
 592-712 1.66e-34

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: 128.65  E-value: 1.66e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   592 AETFYVDGAASRETKLGKAGYVTDRGRQ-KVVSLTE-TTNQKTELHAIHLALQD--SGSEVNIVTDSQYALGII------ 661
Cdd:pfam00075    3 AVTVYTDGSCLGNPGPGGAGAVLYRGHEnISAPLPGrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGItqwvhg 82

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 406855992   662 ---QAQPDRSES-EVVN----QIIEELIKKEKVYLSWVPAHKGIGGNEQVDKLVSSGIR 712
Cdd:pfam00075   83 wkkNGWPTTSEGkPVKNkdlwQLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 61-154 2.73e-34

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: 126.71  E-value: 2.73e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992    61 LWQRPLVTVKIGGQLKEALLDTGADDTVLEDINLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKKAIGTV--LVG 134
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                           90       100
                   ....*....|....*....|.
gi 406855992   135 PT-PVNIIGRNMLTQIGCTLN 154
Cdd:pfam00077   81 PTcPVNIIGRDLLQQLGGRLT 101
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 67-147 4.41e-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: 96.95  E-value: 4.41e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   67 VTVKIGGQLKEALLDTGADDTVLEDINLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKKAIGTVLVGP--TPVNI 140
Cdd:cd05482     1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                  ....*..
gi 406855992  141 IGRNMLT 147
Cdd:cd05482    81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 396-451 4.03e-18

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: 79.29  E-value: 4.03e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 406855992   396 VQPIELPEKDSWTVNDIQKLVGKLNWASQIYA--GIKVKQLCKLLRGAKALTDIVPLT 451
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGitTYDLKPLFSLLRGDSDLTSPRTLT 58
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
596-711 6.29e-16

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 75.27  E-value: 6.29e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  596 YVDGAASRETklGKAGY---VTDRGRQKVVS--LTETTNQKTELHAIHLALQ----DSGSEVNIVTDSQYAL----GIIQ 662
Cdd:COG0328     6 YTDGACRGNP--GPGGWgavIRYGGEEKELSggLGDTTNNRAELTALIAALEalkeLGPCEVEIYTDSQYVVnqitGWIH 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 406855992  663 AQPDRSESEVVN----QIIEELIKKEKVYLSWVPAHKGIGGNEQVDKLVSSGI 711
Cdd:COG0328    84 GWKKNGWKPVKNpdlwQRLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 772-860 3.85e-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: 3.85e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   772 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFVLKLA---GRWPVKVIHTDNGSNFTSAAVK 842
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 406855992   843 AACWWANVQQEFGIPYNP 860
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 594-706 4.50e-13

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: 67.24  E-value: 4.50e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  594 TFYVDGAASrETKLGkAGYVTDRGRQKVVSLTETTNQKT----ELHAIHLALQ------DSGSEVNIVTDSQYALGIIQA 663
Cdd:cd09276     1 VIYTDGSKL-EGSVG-AGFVIYRGGEVISRSYRLGTHASvfdaELEAILEALElalataRRARKVTIFTDSQSALQALRN 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 406855992  664 qPDRSESEVVNQIIEELIKKE-----KVYLSWVPAHKGIGGNEQVDKL 706
Cdd:cd09276    79 -PRRSSGQVILIRILRLLRLLkakgvKVRLRWVPGHVGIEGNEAADRL 125
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 940-983 1.15e-12

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: 1.15e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 406855992   940 VYYRDSRDPIWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 983
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 725-759 1.42e-10

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: 57.00  E-value: 1.42e-10
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 406855992   725 EEHERYHSNWRTMASEFNLPPIVAKEIVANCDKCQ 759
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
827-910 1.73e-09

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 60.17  E-value: 1.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  827 VIHTDNGSNFTSAAVKAACWWANVQQEFGIPYNPQSQGVVESMNKELKK--IIGQIREQAEHLKTAVQMAVFIHNFKR-K 903
Cdd:COG2801   211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                  ....*..
gi 406855992  904 GGIGGYS 910
Cdd:COG2801   291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
827-874 4.12e-08

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 56.42  E-value: 4.12e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 406855992  827 VIHTDNGSNFTSAAVKAACWWANVQQEFGIPYNPQSQGVVESMNKELK 874
Cdd:NF033516  278 ILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
transpos_IS481 NF033577
IS481 family transposase; null
 770-915 7.52e-08

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 54.90  E-value: 7.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  770 DCSPGIWQLDCTHL-----EGKV-ILVAVHVASGYIEAEVIPAETGQETAYFVLKLAGRWPVKV--IHTDNGSNFTSAA- 840
Cdd:NF033577  125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPIrrVLTDNGSEFRSRAh 204

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  841 -VKAACwwanvqQEFGI------PYNPQSQGVVESMNKELK------KIIGQIREQAEHLktavqmAVFIH--NFKRK-G 904
Cdd:NF033577  205 gFELAL------AELGIehrrtrPYHPQTNGKVERFHRTLKdefayaRPYESLAELQAAL------DEWLHhyNHHRPhS 272

                         170
                  ....*....|.
gi 406855992  905 GIGGYSAGERI 915
Cdd:NF033577  273 ALGGKTPAERF 283
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
49-89 7.57e-03

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 38.01  E-value: 7.57e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 406855992   49 QGSVSFSFPQITLWQRP----LVTVKIGGQLKEALLDTGADDTVL 89
Cdd:COG3577    22 QAPVSTGGGEVVLKRDRdghfVVEGTINGQPVRFLVDTGASTVVL 66
PRK08719 PRK08719
ribonuclease H; Reviewed
 594-713 9.10e-03

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 37.92  E-value: 9.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  594 TFYVDGAA----SRETKLGKAGYVTDRGRQKV--VSLT---ETTNQKTELHAIHLALQDSGSEVNIVTDSQYALGIIQAQ 664
Cdd:PRK08719    6 SIYIDGAApnnqHGCVRGGIGLVVYDEAGEIVdeQSITvnrYTDNAELELLALIEALEYARDGDVIYSDSDYCVRGFNEW 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 406855992  665 PD---------RSESEVVN----QIIEELIKKEKVYLSWVPAHKGIGGNEQVDKLVSSGIRK 713
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 ...
 173-389 3.23e-114

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: 350.43  E-value: 3.23e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  173 GPKVKQWPLTEEKIKALTEICKEMEDEGKISKIGpeNPYNTPVFAIRKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 252
Cdd:cd01645     1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  253 AGLKKKKSVTVLDVGDAYFSVPLDESFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRIKNPE 332
Cdd:cd01645    78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 406855992  333 IAIYQYMDDLYVGSDLEiGQHRTKIEELRAHLLNWGFTTPDKKHQKEPPFLWMGYEL 389
Cdd:cd01645   158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 218-389 5.75e-43

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: 154.77  E-value: 5.75e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   218 IRKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLDESFRKYTAF 285
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   286 TIPSINN----ETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRiKNPEIAIYQYMDDLYVGSDlEIGQHRTKIEELR 361
Cdd:pfam00078   81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLR-KRAGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 406855992   362 AHLLNWGFTTPDKKHQ---KEPPFLWMGYEL 389
Cdd:pfam00078  159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 473-574 8.64e-37

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: 133.73  E-value: 8.64e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   473 YYDPSKDLVAEVQKQGQDQWTYQIYQEPFKNLKTGKYARKRSAHTNDVRQLTEVVQKIATESIVIWGKTPKFKLPIQRET 552
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|..
gi 406855992   553 WETWWMEYWQATWIPEWEFVNT 574
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 ...
 592-712 1.66e-34

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: 128.65  E-value: 1.66e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   592 AETFYVDGAASRETKLGKAGYVTDRGRQ-KVVSLTE-TTNQKTELHAIHLALQD--SGSEVNIVTDSQYALGII------ 661
Cdd:pfam00075    3 AVTVYTDGSCLGNPGPGGAGAVLYRGHEnISAPLPGrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGItqwvhg 82

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 406855992   662 ---QAQPDRSES-EVVN----QIIEELIKKEKVYLSWVPAHKGIGGNEQVDKLVSSGIR 712
Cdd:pfam00075   83 wkkNGWPTTSEGkPVKNkdlwQLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 61-154 2.73e-34

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: 126.71  E-value: 2.73e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992    61 LWQRPLVTVKIGGQLKEALLDTGADDTVLEDINLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKKAIGTV--LVG 134
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                           90       100
                   ....*....|....*....|.
gi 406855992   135 PT-PVNIIGRNMLTQIGCTLN 154
Cdd:pfam00077   81 PTcPVNIIGRDLLQQLGGRLT 101
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 174-377 4.49e-32

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: 124.38  E-value: 4.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  174 PKVKQWPLTEEKIKALTEICKEMEDEGKIskIGPENPYNTPVFAIRKKDSTKWRKLVDFRELNKRTQDfweVQLGIPHPA 253
Cdd:cd03715     2 VNQKQYPLPREAREGITPHIQELLEAGIL--VPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLP---IHPAVPNPY 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  254 GL-----KKKKSVTVLDVGDAYFSVPLDESFRKYTAFTIPsinnetpGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRI 328
Cdd:cd03715    77 TLlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPL 149

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 406855992  329 KNPEIAIYQYMDDLYVGSDLEIGQHRTKIEELRaHLLNWGFTTPDKKHQ 377
Cdd:cd03715   150 EHEGTILLQYVDDLLLAADSEEDCLKGTDALLT-HLGELGYKVSPKKAQ 197
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 210-364 1.91e-26

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: 106.91  E-value: 1.91e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  210 PYNTPVFAIRKKDStKWRKLVDFRELNKRT-QDFWEvqlgIPHPAG----LKKKKSVTVLDVGDAYFSVPLDESFRKYTA 284
Cdd:cd01647     9 PYASPVVVVKKKDG-KLRLCVDYRKLNKVTiKDRYP----LPTIDElleeLAGAKVFSKLDLRSGYHQIPLAEESRPKTA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  285 FTipsinneTPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRIKNPEIaiyqYMDDLYVGSDleigqhrtKIEELRAHL 364
Cdd:cd01647    84 FR-------TPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEV----YLDDILVYSK--------TEEEHLEHL 144
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 67-147 4.41e-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: 96.95  E-value: 4.41e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   67 VTVKIGGQLKEALLDTGADDTVLEDINLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKKAIGTVLVGP--TPVNI 140
Cdd:cd05482     1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                  ....*..
gi 406855992  141 IGRNMLT 147
Cdd:cd05482    81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 396-451 4.03e-18

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: 79.29  E-value: 4.03e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 406855992   396 VQPIELPEKDSWTVNDIQKLVGKLNWASQIYA--GIKVKQLCKLLRGAKALTDIVPLT 451
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGitTYDLKPLFSLLRGDSDLTSPRTLT 58
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 304-389 1.44e-16

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: 75.85  E-value: 1.44e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  304 LPQGWKGSPAIFQSSMTKILEPFRIKNPEIAIYQYMDDLYVGSDLEigQHRTKIEELRAHLLNWGFTTPDKKHQ---KEP 380
Cdd:cd00304    12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE--QQAVKKRELEEFLARLGLNLSDEKTQfteKEK 89


                  ....*....
gi 406855992  381 PFLWMGYEL 389
Cdd:cd00304    90 KFKFLGILV 98
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
596-711 6.29e-16

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 75.27  E-value: 6.29e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  596 YVDGAASRETklGKAGY---VTDRGRQKVVS--LTETTNQKTELHAIHLALQ----DSGSEVNIVTDSQYAL----GIIQ 662
Cdd:COG0328     6 YTDGACRGNP--GPGGWgavIRYGGEEKELSggLGDTTNNRAELTALIAALEalkeLGPCEVEIYTDSQYVVnqitGWIH 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 406855992  663 AQPDRSESEVVN----QIIEELIKKEKVYLSWVPAHKGIGGNEQVDKLVSSGI 711
Cdd:COG0328    84 GWKKNGWKPVKNpdlwQRLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 772-860 3.85e-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: 3.85e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   772 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFVLKLA---GRWPVKVIHTDNGSNFTSAAVK 842
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 406855992   843 AACWWANVQQEFGIPYNP 860
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 594-706 4.50e-13

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: 67.24  E-value: 4.50e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  594 TFYVDGAASrETKLGkAGYVTDRGRQKVVSLTETTNQKT----ELHAIHLALQ------DSGSEVNIVTDSQYALGIIQA 663
Cdd:cd09276     1 VIYTDGSKL-EGSVG-AGFVIYRGGEVISRSYRLGTHASvfdaELEAILEALElalataRRARKVTIFTDSQSALQALRN 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 406855992  664 qPDRSESEVVNQIIEELIKKE-----KVYLSWVPAHKGIGGNEQVDKL 706
Cdd:cd09276    79 -PRRSSGQVILIRILRLLRLLkakgvKVRLRWVPGHVGIEGNEAADRL 125
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 596-706 7.58e-13

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: 66.82  E-value: 7.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  596 YVDGAASRETKLG-KAGYV------TDRGRQKVVSLTETTNQKTELHAIHLALQ----DSGSEVNIVTDSQYALGII--- 661
Cdd:cd09280     3 YTDGSCLNNGKPGaRAGIGvyfgpgDPRNVSEPLPGRKQTNNRAELLAVIHALEqapeEGIRKLEIRTDSKYAINCItkw 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 406855992  662 ----QAQPDRSES--EVVNQ-IIEELIK-----KEKVYLSWVPAHKGIGGNEQVDKL 706
Cdd:cd09280    83 ipkwKKNGWKTSKgkPVKNQdLIKELDKllrkrGIKVKFEHVKGHSGDPGNEEADRL 139
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 940-983 1.15e-12

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: 1.15e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 406855992   940 VYYRDSRDPIWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 983
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 725-759 1.42e-10

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: 57.00  E-value: 1.42e-10
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 406855992   725 EEHERYHSNWRTMASEFNLPPIVAKEIVANCDKCQ 759
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
827-910 1.73e-09

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 60.17  E-value: 1.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  827 VIHTDNGSNFTSAAVKAACWWANVQQEFGIPYNPQSQGVVESMNKELKK--IIGQIREQAEHLKTAVQMAVFIHNFKR-K 903
Cdd:COG2801   211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                  ....*..
gi 406855992  904 GGIGGYS 910
Cdd:COG2801   291 SSLGYLT 297
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 596-712 2.50e-09

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: 56.72  E-value: 2.50e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  596 YVDGAASRETklGKAGY---VTDRGRQKVVSLTE--TTNQKTELHAIHLALQ--DSGSEVNIVTDSQYAL-GIIQAQP-- 665
Cdd:cd09278     5 YTDGACLGNP--GPGGWaavIRYGDHEKELSGGEpgTTNNRMELTAAIEALEalKEPCPVTIYTDSQYVInGITKWIKgw 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 406855992  666 ------DRSESEVVN----QIIEELIKKEKVYLSWVPAHKGIGGNEQVDKLVSSGIR 712
Cdd:cd09278    83 kkngwkTADGKPVKNrdlwQELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAAD 139
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 594-707 5.88e-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: 55.42  E-value: 5.88e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  594 TFYVDGAAsreTKLGKAGYVTDRGRQKVVSLTETTNQKTELHAIHLALQD-SGSEVNIVTDSQYALGIIQAQ-------P 665
Cdd:cd09273     1 TVFTDGSS---FKAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELaKGKPVNIYTDSAYAVHALHLLetigierG 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 406855992  666 DRSESEVVN---QIIEELIKKEKVYLSWVPAHKGIG-----GNEQVDKLV 707
Cdd:cd09273    78 FLKSIKNLSlflQLLEAVQRPKPVAIIHIRAHSKLPgplaeGNAQADAAA 127
transpos_IS3 NF033516
IS3 family transposase;
827-874 4.12e-08

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 56.42  E-value: 4.12e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 406855992  827 VIHTDNGSNFTSAAVKAACWWANVQQEFGIPYNPQSQGVVESMNKELK 874
Cdd:NF033516  278 ILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
transpos_IS481 NF033577
IS481 family transposase; null
 770-915 7.52e-08

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 54.90  E-value: 7.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  770 DCSPGIWQLDCTHL-----EGKV-ILVAVHVASGYIEAEVIPAETGQETAYFVLKLAGRWPVKV--IHTDNGSNFTSAA- 840
Cdd:NF033577  125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPIrrVLTDNGSEFRSRAh 204

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  841 -VKAACwwanvqQEFGI------PYNPQSQGVVESMNKELK------KIIGQIREQAEHLktavqmAVFIH--NFKRK-G 904
Cdd:NF033577  205 gFELAL------AELGIehrrtrPYHPQTNGKVERFHRTLKdefayaRPYESLAELQAAL------DEWLHhyNHHRPhS 272

                         170
                  ....*....|.
gi 406855992  905 GIGGYSAGERI 915
Cdd:NF033577  273 ALGGKTPAERF 283
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 596-706 1.10e-07

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: 1.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  596 YVDGAASRETKLGKAGYVTDRGRQKVVSLT-----ETTNQKTELHAIHLALQ----DSGSEVNIVTDSQYALGIIQAQPD 666
Cdd:cd06222     2 NVDGSCRGNPGPAGIGGVLRDHEGGWLGGFalkigAPTALEAELLALLLALElaldLGYLKVIIESDSKYVVDLINSGSF 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 406855992  667 RSES--EVVNQIIEELIKKEKVYLSWVPAHkgigGNEQVDKL 706
Cdd:cd06222    82 KWSPniLLIEDILLLLSRFWSVKISHVPRE----GNQVADAL 119
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 264-380 3.29e-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: 50.03  E-value: 3.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  264 LDVGDAYFSVPLDESFRKYTAFtIPSinnetpGIRYQYNVLPQGWKGSPAIFqssmTKILEP--FRIKNPEIAIYQYMDD 341
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVF----TKVVEAllAPLRLLGVRIFSYLDD 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 406855992  342 -LYVGSDLEIGQHRtkIEELRAHLL-NWGFTTPDKKHQKEP 380
Cdd:cd03714    70 lLIIASSIKTSEAV--LRHLRATLLaNLGFTLNLEKSKLGP 108
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 596-712 1.26e-03

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: 39.76  E-value: 1.26e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  596 YVDGAASRETKLGKAGYV----TDRGRQKVVSLTE-TTNQKTELHAIHLALQD----SGSEVNIVTDSQyaLgiiqaqpd 666
Cdd:cd09279     4 YFDGASRGNPGPAGAGVViyspGGEVLELSERLGFpATNNEAEYEALIAGLELalelGAEKLEIYGDSQ--L-------- 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 406855992  667 rseseVVNQI-----------------IEELIKK-EKVYLSWVPAHKgiggNEQVDKLVSSGIR 712
Cdd:cd09279    74 -----VVNQLngeykvknerlkpllekVLELLAKfELVELKWIPREQ----NKEADALANQALD 128
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 67-147 2.51e-03

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: 38.08  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992   67 VTVKIGGQLKEALLDTGADDTVL-EDINLPGKWKPK--MIGGIGGFIK--VRQYDQiLIEICGKKAIGTVLVGPT-PVNI 140
Cdd:cd06095     1 VTITVEGVPIVFLVDTGATHSVLkSDLGPKQELSTTsvLIRGVSGQSQqpVTTYRT-LVDLGGHTVSHSFLVVPNcPDPL 79


                  ....*..
gi 406855992  141 IGRNMLT 147
Cdd:cd06095    80 LGRDLLS 86
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 67-113 5.71e-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: 36.88  E-value: 5.71e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 406855992    67 VTVKIGGQLKEALLDTGADDTVL-----EDINLPGKWK--PKMIGGIGGFIKVR 113
Cdd:pfam13650    1 VPVTINGKPVRFLVDTGASGTVIspslaERLGLKVRGLayTVRVSTAGGRVSAA 54
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
49-89 7.57e-03

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 38.01  E-value: 7.57e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 406855992   49 QGSVSFSFPQITLWQRP----LVTVKIGGQLKEALLDTGADDTVL 89
Cdd:COG3577    22 QAPVSTGGGEVVLKRDRdghfVVEGTINGQPVRFLVDTGASTVVL 66
PRK08719 PRK08719
ribonuclease H; Reviewed
 594-713 9.10e-03

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 37.92  E-value: 9.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992  594 TFYVDGAA----SRETKLGKAGYVTDRGRQKV--VSLT---ETTNQKTELHAIHLALQDSGSEVNIVTDSQYALGIIQAQ 664
Cdd:PRK08719    6 SIYIDGAApnnqHGCVRGGIGLVVYDEAGEIVdeQSITvnrYTDNAELELLALIEALEYARDGDVIYSDSDYCVRGFNEW 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 406855992  665 PD---------RSESEVVN----QIIEELIKKEKVYLSWVPAHKGIGGNEQVDKLVSSGIRK 713
Cdd:PRK08719   86 LDtwkqkgwrkSDKKPVANrdlwQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQAAAEL 147
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 67-148 9.42e-03

gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.


Pssm-ID: 464060  Cd Length: 92  Bit Score: 36.40  E-value: 9.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 406855992    67 VTVKIGGQLKEALLDTGADDTVL-----EDINLP--GKWKPKMIGGIGGFIKVRQYDQILIEICGKKA---IGTVLVGPT 136
Cdd:pfam13975    1 VDVTINGRPVRFLVDTGASVTVIsealaERLGLDrlVDAYPVTVRTANGTVRAARVRLDSVKIGGIELrnvPAVVLPGDL 80

                           90
                   ....*....|..
gi 406855992   137 PVNIIGRNMLTQ 148
Cdd:pfam13975   81 DDVLLGMDFLKR 92
 
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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