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Conserved domains on  [gi|1127546998|gb|APS24115|]
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pol protein, partial [synthetic HIV-2]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 199-415 3.90e-108

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


The actual alignment was detected with superfamily member cd01645:

Pssm-ID: 477363 [Multi-domain]  Cd Length: 213  Bit Score: 334.64  E-value: 3.90e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  199 GPKLRQWPLTKEKIEALKEICEKMEKEGQLEEAppTNPYNTPTFAIKKKDKnKWRMLIDFRELNKVTQDFTEIQLGIPHP 278
Cdd:cd01645      1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPS--TSPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  279 AGLAKKRRITVLDVGDAYFSIPLHEDFRPYTAFTLPSVNNAEPGKRYIYKVLPQGWKGSPAIFQHTMRQVLEPFRKANKD 358
Cdd:cd01645     78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1127546998  359 VIIIQYMDDILIASDRTDlEHDRVVLQLKELLNGLGFSTPDEKFQKDPPYHWMGYEL 415
Cdd:cd01645    158 IVIYHYMDDILIASDLEG-QLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 499-599 3.22e-57

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: 191.89  E-value: 3.22e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  499 YYQEEKELEATVQKDQDNQWTYKIHQEE-KILKVGKYAKVKNTHTNGIRLLAQVVQKIGKEALVIWGRIPKFHLPVEREI 577
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPfKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|..
gi 1127546998  578 WEQWWDNYWQVTWIPDWDFVST 599
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 ...
 615-737 3.11e-36

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: 133.66  E-value: 3.11e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  615 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKK--LEQTTNQQAELEAFAMAL--TDSGPKVNIIVDSQYVMGIVAS-- 688
Cdd:pfam00075    1 PKAVTVYTDGSCLGNPGPGGAGAVLYRGHENISAplPGRTTNNRAELQAVIEALkaLKSPSKVNIYTDSQYVIGGITQwv 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1127546998  689 -------QPTESESKIV--NQIIEEM---IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGIR 737
Cdd:pfam00075   81 hgwkkngWPTTSEGKPVknKDLWQLLkalCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 93-173 6.10e-21

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: 88.09  E-value: 6.10e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998   93 VTAYIEGQPVEVLLDTGADDSIVAGIELGNN----YSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTG--DTPINI 166
Cdd:cd05482      1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNwpiqPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYvlSLPVNL 80


                   ....*..
gi 1127546998  167 FGRNILT 173
Cdd:cd05482     81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 422-477 7.20e-21

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: 86.99  E-value: 7.20e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1127546998  422 LQKIQLPQKEIWTVNDIQKLVGVLNWAAQLY--PGIKTKHLCRLIRGKMTLTEEVQWT 477
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLT 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 799-885 5.53e-16

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 74.27  E-value: 5.53e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  799 GTWQMDCTHLEGKI------IIVAVHVASGFIEAEVIPQESGRQTALFLLKLASRW---PITHLHTDNGANFTSQEVKMV 869
Cdd:pfam00665    3 QLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrggVPLIIHSDNGSEYTSKAFREF 82

                           90
                   ....*....|....*.
gi 1127546998  870 AWWIGIEQSFGVPYNP 885
Cdd:pfam00665   83 LKDLGIKPSFSRPGNP 98
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 750-785 3.16e-12

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: 61.62  E-value: 3.16e-12
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1127546998  750 EEHEKYHSNVKELSHKFGIPNLVARQIVNSCAQCQQ 785
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
IN_DBD_C super family cl02895
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 965-989 9.54e-06

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: 43.54  E-value: 9.54e-06
                           10        20
                   ....*....|....*....|....*
gi 1127546998  965 VYFREGRDQLWKGPGELLWKGEGAV 989
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAV 25
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 199-415 3.90e-108

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: 334.64  E-value: 3.90e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  199 GPKLRQWPLTKEKIEALKEICEKMEKEGQLEEAppTNPYNTPTFAIKKKDKnKWRMLIDFRELNKVTQDFTEIQLGIPHP 278
Cdd:cd01645      1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPS--TSPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  279 AGLAKKRRITVLDVGDAYFSIPLHEDFRPYTAFTLPSVNNAEPGKRYIYKVLPQGWKGSPAIFQHTMRQVLEPFRKANKD 358
Cdd:cd01645     78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1127546998  359 VIIIQYMDDILIASDRTDlEHDRVVLQLKELLNGLGFSTPDEKFQKDPPYHWMGYEL 415
Cdd:cd01645    158 IVIYHYMDDILIASDLEG-QLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 499-599 3.22e-57

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: 191.89  E-value: 3.22e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  499 YYQEEKELEATVQKDQDNQWTYKIHQEE-KILKVGKYAKVKNTHTNGIRLLAQVVQKIGKEALVIWGRIPKFHLPVEREI 577
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPfKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|..
gi 1127546998  578 WEQWWDNYWQVTWIPDWDFVST 599
Cdd:pfam06815   81 WETWWTEYWQATWIPEWEFVNT 102
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 244-415 1.80e-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: 156.31  E-value: 1.80e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  244 IKKKDKNKWRML----IDFRELNKVTQD-------FTEIQLGIPHPAG-LAKKRRITVLDVGDAYFSIPLHEDFRPYTAF 311
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  312 TLPSVNN----AEPGKRYIYKVLPQGWKGSPAIFQHTMRQVLEPFRKANkDVIIIQYMDDILIASDRTDlEHDRVVLQLK 387
Cdd:pfam00078   81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEE-EHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1127546998  388 ELLNGLGFSTPDEK---FQKDPPYHWMGYEL 415
Cdd:pfam00078  159 EWLKESGLKINPEKtqfFLKSKEVKYLGVTL 189
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 615-737 3.11e-36

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: 133.66  E-value: 3.11e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  615 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKK--LEQTTNQQAELEAFAMAL--TDSGPKVNIIVDSQYVMGIVAS-- 688
Cdd:pfam00075    1 PKAVTVYTDGSCLGNPGPGGAGAVLYRGHENISAplPGRTTNNRAELQAVIEALkaLKSPSKVNIYTDSQYVIGGITQwv 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1127546998  689 -------QPTESESKIV--NQIIEEM---IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGIR 737
Cdd:pfam00075   81 hgwkkngWPTTSEGKPVknKDLWQLLkalCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 93-173 6.10e-21

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: 88.09  E-value: 6.10e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998   93 VTAYIEGQPVEVLLDTGADDSIVAGIELGNN----YSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTG--DTPINI 166
Cdd:cd05482      1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNwpiqPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYvlSLPVNL 80


                   ....*..
gi 1127546998  167 FGRNILT 173
Cdd:cd05482     81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 422-477 7.20e-21

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: 86.99  E-value: 7.20e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1127546998  422 LQKIQLPQKEIWTVNDIQKLVGVLNWAAQLY--PGIKTKHLCRLIRGKMTLTEEVQWT 477
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLT 58
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 87-180 1.21e-17

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: 79.33  E-value: 1.21e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998   87 LWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNY----SPKIVGGIGGFINTKEYKNVEIEVLNKKVRATI---MT 159
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVsplIL 80

                           90       100
                   ....*....|....*....|.
gi 1127546998  160 GDTPINIFGRNILTALGMSLN 180
Cdd:pfam00077   81 PTCPVNIIGRDLLQQLGGRLT 101
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 799-885 5.53e-16

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 74.27  E-value: 5.53e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  799 GTWQMDCTHLEGKI------IIVAVHVASGFIEAEVIPQESGRQTALFLLKLASRW---PITHLHTDNGANFTSQEVKMV 869
Cdd:pfam00665    3 QLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrggVPLIIHSDNGSEYTSKAFREF 82

                           90
                   ....*....|....*.
gi 1127546998  870 AWWIGIEQSFGVPYNP 885
Cdd:pfam00665   83 LKDLGIKPSFSRPGNP 98
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
621-736 1.27e-14

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 71.80  E-value: 1.27e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  621 YTDGSCNRQSKEGKAGYVTdRGKDKVKKL----EQTTNQQAELEAFAMAL---TDSGP-KVNIIVDSQYVM----GIVAS 688
Cdd:COG0328      6 YTDGACRGNPGPGGWGAVI-RYGGEEKELsgglGDTTNNRAELTALIAALealKELGPcEVEIYTDSQYVVnqitGWIHG 84

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1127546998  689 QPTESESKIVN----QIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI 736
Cdd:COG0328     85 WKKNGWKPVKNpdlwQRLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 750-785 3.16e-12

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: 61.62  E-value: 3.16e-12
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1127546998  750 EEHEKYHSNVKELSHKFGIPNLVARQIVNSCAQCQQ 785
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 ...
 621-737 3.63e-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: 61.73  E-value: 3.63e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  621 YTDGSCNRQSkeGKAGY-VTDRGKDKVKKL----EQTTNQQAELEAFAMALT--DSGPKVNIIVDSQYVM-GIvasqpTE 692
Cdd:cd09278      5 YTDGACLGNP--GPGGWaAVIRYGDHEKELsggePGTTNNRMELTAAIEALEalKEPCPVTIYTDSQYVInGI-----TK 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1127546998  693 ------------SESKIV-N----QIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGIR 737
Cdd:cd09278     78 wikgwkkngwktADGKPVkNrdlwQELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAAD 139
transpos_IS481 NF033577
IS481 family transposase; null
 799-940 5.78e-11

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 64.53  E-value: 5.78e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  799 GTWQMDCTHL-----EGKI-IIVAVHVASGFIEAEVIPQESGRQTALFLLKL-ASRW-PITHLHTDNGANFTSqEVKMVA 870
Cdd:NF033577   129 ELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRS-RAHGFE 207

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  871 WWI---GIEQSFGVPYNPQSQGVVEAMNHHLKNQI------SRIREQANTIETIvlmaVHCMNFKRR-GGIGDMTPSERL 940
Cdd:NF033577   208 LALaelGIEHRRTRPYHPQTNGKVERFHRTLKDEFayarpyESLAELQAALDEW----LHHYNHHRPhSALGGKTPAERF 283
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
801-939 1.37e-09

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 60.55  E-value: 1.37e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  801 WQMDCTHL---EGK-----II------IVAVHVASgfieaevipQESGRQTALFLLKLASRWPITH---LHTDNGANFTS 863
Cdd:COG2801    152 WVTDITYIptaEGWlylaaVIdlfsreIVGWSVSD---------SMDAELVVDALEMAIERRGPPKpliLHSDNGSQYTS 222

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  864 QEVKMVAWWIGIEQSFGVPYNPQSQGVVEAMNHHLKNQISRiREQANTIETIVLM---AVHCMNFKRR-GGIGDMTPSER 939
Cdd:COG2801    223 KAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYELLY-RRRFESLEEAREAieeYIEFYNHERPhSSLGYLTPAEY 301
transpos_IS3 NF033516
IS3 family transposase;
853-900 3.12e-07

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 53.72  E-value: 3.12e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1127546998  853 LHTDNGANFTSQEVKMVAWWIGIEQSFGVPYNPQSQGVVEAMNHHLKN 900
Cdd:NF033516   279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKR 326
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 965-989 9.54e-06

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: 43.54  E-value: 9.54e-06
                           10        20
                   ....*....|....*....|....*
gi 1127546998  965 VYFREGRDQLWKGPGELLWKGEGAV 989
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAV 25
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
91-178 2.92e-05

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 45.32  E-value: 2.92e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998   91 PVVTAYIEGQPVEVLLDTGADDSIV-------AGIELGNNYSPKIVGGIGGFINTKEY--KNVEI-EVLNKKVRATIMTG 160
Cdd:COG3577     42 FVVEGTINGQPVRFLVDTGASTVVLsesdarrLGLDPEDLGRPVRVQTANGVVRAARVrlDSVRIgGITLRNVRAVVLPG 121

                           90
                   ....*....|....*...
gi 1127546998  161 DTPINIFgrniltaLGMS 178
Cdd:COG3577    122 GELDDGL-------LGMS 132
rnhA PRK00203
ribonuclease H; Reviewed
 619-740 1.27e-03

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 40.19  E-value: 1.27e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  619 TFYTDGSC--NrqskEGKAGY-VTDRGKDKVKKL----EQTTNQQAELEAFAMAL-TDSGP-KVNIIVDSQYVM-GIvas 688
Cdd:PRK00203     5 EIYTDGAClgN----PGPGGWgAILRYKGHEKELsggeALTTNNRMELMAAIEALeALKEPcEVTLYTDSQYVRqGI--- 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1127546998  689 qpTE------------SESKIV-N----QIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGIRQVL 740
Cdd:PRK00203    78 --TEwihgwkkngwktADKKPVkNvdlwQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEAT 144
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 199-415 3.90e-108

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: 334.64  E-value: 3.90e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  199 GPKLRQWPLTKEKIEALKEICEKMEKEGQLEEAppTNPYNTPTFAIKKKDKnKWRMLIDFRELNKVTQDFTEIQLGIPHP 278
Cdd:cd01645      1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPS--TSPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  279 AGLAKKRRITVLDVGDAYFSIPLHEDFRPYTAFTLPSVNNAEPGKRYIYKVLPQGWKGSPAIFQHTMRQVLEPFRKANKD 358
Cdd:cd01645     78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1127546998  359 VIIIQYMDDILIASDRTDlEHDRVVLQLKELLNGLGFSTPDEKFQKDPPYHWMGYEL 415
Cdd:cd01645    158 IVIYHYMDDILIASDLEG-QLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 499-599 3.22e-57

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: 191.89  E-value: 3.22e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  499 YYQEEKELEATVQKDQDNQWTYKIHQEE-KILKVGKYAKVKNTHTNGIRLLAQVVQKIGKEALVIWGRIPKFHLPVEREI 577
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPfKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|..
gi 1127546998  578 WEQWWDNYWQVTWIPDWDFVST 599
Cdd:pfam06815   81 WETWWTEYWQATWIPEWEFVNT 102
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 244-415 1.80e-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: 156.31  E-value: 1.80e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  244 IKKKDKNKWRML----IDFRELNKVTQD-------FTEIQLGIPHPAG-LAKKRRITVLDVGDAYFSIPLHEDFRPYTAF 311
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  312 TLPSVNN----AEPGKRYIYKVLPQGWKGSPAIFQHTMRQVLEPFRKANkDVIIIQYMDDILIASDRTDlEHDRVVLQLK 387
Cdd:pfam00078   81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEE-EHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1127546998  388 ELLNGLGFSTPDEK---FQKDPPYHWMGYEL 415
Cdd:pfam00078  159 EWLKESGLKINPEKtqfFLKSKEVKYLGVTL 189
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 203-403 8.74e-38

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: 140.56  E-value: 8.74e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  203 RQWPLTKEKIEALKEICEKMEKEGQLeeAPPTNPYNTPTFAIKKKDKNKWRMLIDFRELNKVTqdfTEIQLGIPHPAGL- 281
Cdd:cd03715      5 KQYPLPREAREGITPHIQELLEAGIL--VPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAV---LPIHPAVPNPYTLl 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  282 ----AKKRRITVLDVGDAYFSIPLHEDFRPYTAFTLPsvnnaepGKRYIYKVLPQGWKGSPAIFQHTMRQVLEPFRKANK 357
Cdd:cd03715     80 sllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHE 152

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1127546998  358 DVIIIQYMDDILIASD-RTDLEHD-RVVLQlkeLLNGLGFSTPDEKFQ 403
Cdd:cd03715    153 GTILLQYVDDLLLAADsEEDCLKGtDALLT---HLGELGYKVSPKKAQ 197
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 615-737 3.11e-36

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: 133.66  E-value: 3.11e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  615 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKK--LEQTTNQQAELEAFAMAL--TDSGPKVNIIVDSQYVMGIVAS-- 688
Cdd:pfam00075    1 PKAVTVYTDGSCLGNPGPGGAGAVLYRGHENISAplPGRTTNNRAELQAVIEALkaLKSPSKVNIYTDSQYVIGGITQwv 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1127546998  689 -------QPTESESKIV--NQIIEEM---IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGIR 737
Cdd:pfam00075   81 hgwkkngWPTTSEGKPVknKDLWQLLkalCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 236-385 1.66e-32

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: 124.24  E-value: 1.66e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  236 PYNTPTFAIKKKDkNKWRMLIDFRELNKVT-QDFTEIqlgiPHPAG----LAKKRRITVLDVGDAYFSIPLHEDFRPYTA 310
Cdd:cd01647      9 PYASPVVVVKKKD-GKLRLCVDYRKLNKVTiKDRYPL----PTIDElleeLAGAKVFSKLDLRSGYHQIPLAEESRPKTA 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1127546998  311 FTLPsvnnaepGKRYIYKVLPQGWKGSPAIFQHTMRQVLEPFRkankDVIIIQYMDDILIASDRTD--LEHDRVVLQ 385
Cdd:cd01647     84 FRTP-------FGLYEYTRMPFGLKNAPATFQRLMNKILGDLL----GDFVEVYLDDILVYSKTEEehLEHLREVLE 149
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 93-173 6.10e-21

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: 88.09  E-value: 6.10e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998   93 VTAYIEGQPVEVLLDTGADDSIVAGIELGNN----YSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTG--DTPINI 166
Cdd:cd05482      1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNwpiqPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYvlSLPVNL 80


                   ....*..
gi 1127546998  167 FGRNILT 173
Cdd:cd05482     81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 422-477 7.20e-21

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: 86.99  E-value: 7.20e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1127546998  422 LQKIQLPQKEIWTVNDIQKLVGVLNWAAQLY--PGIKTKHLCRLIRGKMTLTEEVQWT 477
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLT 58
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 87-180 1.21e-17

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: 79.33  E-value: 1.21e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998   87 LWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNY----SPKIVGGIGGFINTKEYKNVEIEVLNKKVRATI---MT 159
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVsplIL 80

                           90       100
                   ....*....|....*....|.
gi 1127546998  160 GDTPINIFGRNILTALGMSLN 180
Cdd:pfam00077   81 PTCPVNIIGRDLLQQLGGRLT 101
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 799-885 5.53e-16

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 74.27  E-value: 5.53e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  799 GTWQMDCTHLEGKI------IIVAVHVASGFIEAEVIPQESGRQTALFLLKLASRW---PITHLHTDNGANFTSQEVKMV 869
Cdd:pfam00665    3 QLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrggVPLIIHSDNGSEYTSKAFREF 82

                           90
                   ....*....|....*.
gi 1127546998  870 AWWIGIEQSFGVPYNP 885
Cdd:pfam00665   83 LKDLGIKPSFSRPGNP 98
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
621-736 1.27e-14

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 71.80  E-value: 1.27e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  621 YTDGSCNRQSKEGKAGYVTdRGKDKVKKL----EQTTNQQAELEAFAMAL---TDSGP-KVNIIVDSQYVM----GIVAS 688
Cdd:COG0328      6 YTDGACRGNPGPGGWGAVI-RYGGEEKELsgglGDTTNNRAELTALIAALealKELGPcEVEIYTDSQYVVnqitGWIHG 84

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1127546998  689 QPTESESKIVN----QIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI 736
Cdd:COG0328     85 WKKNGWKPVKNpdlwQRLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 330-415 2.11e-12

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: 64.29  E-value: 2.11e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  330 LPQGWKGSPAIFQHTMRQVLEPFRKANKDVIIIQYMDDILIASdrtDLEHDRVVLQ-LKELLNGLGFSTPDEK---FQKD 405
Cdd:cd00304     12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIA---KSEQQAVKKReLEEFLARLGLNLSDEKtqfTEKE 88

                           90
                   ....*....|
gi 1127546998  406 PPYHWMGYEL 415
Cdd:cd00304     89 KKFKFLGILV 98
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 290-406 2.33e-12

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: 64.67  E-value: 2.33e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  290 LDVGDAYFSIPLHEDFRPYTAFtlpsvnnAEPGKRYIYKVLPQGWKGSPAIFQHTMRQVLEPFRkaNKDVIIIQYMDDIL 369
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGF-------AWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLR--LLGVRIFSYLDDLL 71

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1127546998  370 I-ASDRTDLEHdrVVLQLKELLNG-LGFSTPDEKFQKDP 406
Cdd:cd03714     72 IiASSIKTSEA--VLRHLRATLLAnLGFTLNLEKSKLGP 108
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 750-785 3.16e-12

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: 61.62  E-value: 3.16e-12
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1127546998  750 EEHEKYHSNVKELSHKFGIPNLVARQIVNSCAQCQQ 785
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 ...
 621-737 3.63e-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: 61.73  E-value: 3.63e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  621 YTDGSCNRQSkeGKAGY-VTDRGKDKVKKL----EQTTNQQAELEAFAMALT--DSGPKVNIIVDSQYVM-GIvasqpTE 692
Cdd:cd09278      5 YTDGACLGNP--GPGGWaAVIRYGDHEKELsggePGTTNNRMELTAAIEALEalKEPCPVTIYTDSQYVInGI-----TK 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1127546998  693 ------------SESKIV-N----QIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGIR 737
Cdd:cd09278     78 wikgwkkngwktADGKPVkNrdlwQELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAAD 139
transpos_IS481 NF033577
IS481 family transposase; null
 799-940 5.78e-11

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 64.53  E-value: 5.78e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  799 GTWQMDCTHL-----EGKI-IIVAVHVASGFIEAEVIPQESGRQTALFLLKL-ASRW-PITHLHTDNGANFTSqEVKMVA 870
Cdd:NF033577   129 ELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRS-RAHGFE 207

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  871 WWI---GIEQSFGVPYNPQSQGVVEAMNHHLKNQI------SRIREQANTIETIvlmaVHCMNFKRR-GGIGDMTPSERL 940
Cdd:NF033577   208 LALaelGIEHRRTRPYHPQTNGKVERFHRTLKDEFayarpyESLAELQAALDEW----LHHYNHHRPhSALGGKTPAERF 283
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 619-737 1.20e-10

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: 60.31  E-value: 1.20e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  619 TFYTDGScnrqSKEGKAGY---VTDRGKDKVKKLE---QTTNQQAELEAFAMAL------TDSGPKVNIIVDSQYVMGIV 686
Cdd:cd09276      1 VIYTDGS----KLEGSVGAgfvIYRGGEVISRSYRlgtHASVFDAELEAILEALelalatARRARKVTIFTDSQSALQAL 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1127546998  687 ASqPTESESKIVNQIIEEMIKKEA-----IYVAWVPAHKGIGGNQEVDHLVSQGIR 737
Cdd:cd09276     77 RN-PRRSSGQVILIRILRLLRLLKakgvkVRLRWVPGHVGIEGNEAADRLAKEAAS 131
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 621-737 8.64e-10

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: 57.96  E-value: 8.64e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  621 YTDGSCNRQSKEG-KAGYVTDRGKD-------KVKKLEQTtNQQAELEAFAMAL----TDSGPKVNIIVDSQYVMGIV-- 686
Cdd:cd09280      3 YTDGSCLNNGKPGaRAGIGVYFGPGdprnvsePLPGRKQT-NNRAELLAVIHALeqapEEGIRKLEIRTDSKYAINCItk 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1127546998  687 ------ASQPTESESKIV-NQ-IIEEMIK-----KEAIYVAWVPAHKGIGGNQEVDHLVSQGIR 737
Cdd:cd09280     82 wipkwkKNGWKTSKGKPVkNQdLIKELDKllrkrGIKVKFEHVKGHSGDPGNEEADRLAREGAD 145
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
801-939 1.37e-09

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 60.55  E-value: 1.37e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  801 WQMDCTHL---EGK-----II------IVAVHVASgfieaevipQESGRQTALFLLKLASRWPITH---LHTDNGANFTS 863
Cdd:COG2801    152 WVTDITYIptaEGWlylaaVIdlfsreIVGWSVSD---------SMDAELVVDALEMAIERRGPPKpliLHSDNGSQYTS 222

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  864 QEVKMVAWWIGIEQSFGVPYNPQSQGVVEAMNHHLKNQISRiREQANTIETIVLM---AVHCMNFKRR-GGIGDMTPSER 939
Cdd:COG2801    223 KAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYELLY-RRRFESLEEAREAieeYIEFYNHERPhSSLGYLTPAEY 301
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 619-734 1.91e-08

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: 53.88  E-value: 1.91e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  619 TFYTDGSCnrqskeGKAGYVTDRGKDKVKK---LEQTTNQQAELEAFAMALTDSGPK-VNIIVDSQYVMGIVASQPT--- 691
Cdd:cd09273      1 TVFTDGSS------FKAGYAIVSGTEIVEAqplPPGTSAQRAELIALIQALELAKGKpVNIYTDSAYAVHALHLLETigi 74

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1127546998  692 ------ESESKIVNQIIEEMI-KKEAIYVAWVPAHKGIG-----GNQEVDHLVSQ 734
Cdd:cd09273     75 ergflkSIKNLSLFLQLLEAVqRPKPVAIIHIRAHSKLPgplaeGNAQADAAAKQ 129
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 93-172 1.20e-07

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: 50.27  E-value: 1.20e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998   93 VTAYIEGQPVEVLLDTGADDSIV-------AGIELGNNYSPKIVGGIGGFINTKEYK--NVEI-EVLNKKVRATIMTGDT 162
Cdd:pfam13975    1 VDVTINGRPVRFLVDTGASVTVIsealaerLGLDRLVDAYPVTVRTANGTVRAARVRldSVKIgGIELRNVPAVVLPGDL 80

                           90
                   ....*....|
gi 1127546998  163 PINIFGRNIL 172
Cdd:pfam13975   81 DDVLLGMDFL 90
transpos_IS3 NF033516
IS3 family transposase;
853-900 3.12e-07

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 53.72  E-value: 3.12e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1127546998  853 LHTDNGANFTSQEVKMVAWWIGIEQSFGVPYNPQSQGVVEAMNHHLKN 900
Cdd:NF033516   279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKR 326
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 621-731 6.64e-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: 49.23  E-value: 6.64e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  621 YTDGSCNRQSKEGKAGYVTDRGKDKV-----KKLEQTTNQQAELEAFAMAL----TDSGPKVNIIVDSQYVMGIVASQPT 691
Cdd:cd06222      2 NVDGSCRGNPGPAGIGGVLRDHEGGWlggfaLKIGAPTALEAELLALLLALelalDLGYLKVIIESDSKYVVDLINSGSF 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1127546998  692 ESES--KIVNQIIEEMIKKEAIYVAWVPAHkgigGNQEVDHL 731
Cdd:cd06222     82 KWSPniLLIEDILLLLSRFWSVKISHVPRE----GNQVADAL 119
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 284-395 1.50e-06

RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.


Pssm-ID: 238822  Cd Length: 213  Bit Score: 50.00  E-value: 1.50e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  284 KRRITVL-DVGDAYFSIPLHEDFRPYTAFTLPSVNNAEPGKRYIYKVLPQGWKGSPAIFQHTMRQVLE--PFRKANKDVI 360
Cdd:cd01644     57 QGKIAVSaDIEKMFHQVKVRPEDRDVLRFLWRKDGDEPKPIEYRMTVVPFGAASAPFLANRALKQHAEdhPHEAAAKIIK 136

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1127546998  361 IIQYMDDILIASDrTDLEHDRVVLQLKELLNGLGF 395
Cdd:cd01644    137 RNFYVDDILVSTD-TLNEAVNVAKRLIALLKKGGF 170
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 93-170 4.58e-06

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: 45.74  E-value: 4.58e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998   93 VTAYIEGQPVEVLLDTGADDSIV-------AGIELGNNYSPKIVGGIGGFINTKEYKNVEIEVLN---KKVRATIM-TGD 161
Cdd:pfam13650    1 VPVTINGKPVRFLVDTGASGTVIspslaerLGLKVRGLAYTVRVSTAGGRVSAARVRLDSLRLGGltlENVPALVLdLGD 80


                   ....*....
gi 1127546998  162 TPINIFGRN 170
Cdd:pfam13650   81 LIDGLLGMD 89
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 965-989 9.54e-06

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: 43.54  E-value: 9.54e-06
                           10        20
                   ....*....|....*....|....*
gi 1127546998  965 VYFREGRDQLWKGPGELLWKGEGAV 989
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAV 25
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
91-178 2.92e-05

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 45.32  E-value: 2.92e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998   91 PVVTAYIEGQPVEVLLDTGADDSIV-------AGIELGNNYSPKIVGGIGGFINTKEY--KNVEI-EVLNKKVRATIMTG 160
Cdd:COG3577     42 FVVEGTINGQPVRFLVDTGASTVVLsesdarrLGLDPEDLGRPVRVQTANGVVRAARVrlDSVRIgGITLRNVRAVVLPG 121

                           90
                   ....*....|....*...
gi 1127546998  161 DTPINIFgrniltaLGMS 178
Cdd:COG3577    122 GELDDGL-------LGMS 132
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 621-737 1.48e-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: 42.46  E-value: 1.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  621 YTDGSCNRQSKEGKAGYVTDRGKDKVKKL-----EQTTNQQAELEAFAMALT---DSGP-KVNIIVDSQyvmgIVASQ-- 689
Cdd:cd09279      4 YFDGASRGNPGPAGAGVVIYSPGGEVLELserlgFPATNNEAEYEALIAGLElalELGAeKLEIYGDSQ----LVVNQln 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1127546998  690 ---PTESES--KIVNQIIEEMIKKEAIYVAWVPAHKgiggNQEVDHLVSQGIR 737
Cdd:cd09279     80 geyKVKNERlkPLLEKVLELLAKFELVELKWIPREQ----NKEADALANQALD 128
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 90-172 1.49e-04

Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. 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 proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133150  Cd Length: 96  Bit Score: 41.85  E-value: 1.49e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998   90 RPVVTAYIEGQPVEVLLDTGADDSIV---AGIELGNNY---SPKIVGGIGGFINTKEYKNVEIEVLN---KKVRATIMTG 160
Cdd:cd05483      2 HFVVPVTINGQPVRFLLDTGASTTVIseeLAERLGLPLtlgGKVTVQTANGRVRAARVRLDSLQIGGitlRNVPAVVLPG 81

                           90
                   ....*....|....
gi 1127546998  161 DT--PINIFGRNIL 172
Cdd:cd05483     82 DAlgVDGLLGMDFL 95
rnhA PRK00203
ribonuclease H; Reviewed
 619-740 1.27e-03

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 40.19  E-value: 1.27e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998  619 TFYTDGSC--NrqskEGKAGY-VTDRGKDKVKKL----EQTTNQQAELEAFAMAL-TDSGP-KVNIIVDSQYVM-GIvas 688
Cdd:PRK00203     5 EIYTDGAClgN----PGPGGWgAILRYKGHEKELsggeALTTNNRMELMAAIEALeALKEPcEVTLYTDSQYVRqGI--- 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1127546998  689 qpTE------------SESKIV-N----QIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGIRQVL 740
Cdd:PRK00203    78 --TEwihgwkkngwktADKKPVkNvdlwQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEAT 144
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 93-173 5.91e-03

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, 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: 133136  Cd Length: 92  Bit Score: 36.93  E-value: 5.91e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1127546998   93 VTAYIEGQPVEVLLDTGADDSIVA-------GIELGNNYSPKIVGGIGG--FINTKEYKNVEIEVLNKKVRATIM---TG 160
Cdd:cd00303      1 LKGKINGVPVRALVDSGASVNFISeslakklGLPPRLLPTPLKVKGANGssVKTLGVILPVTIGIGGKTFTVDFYvldLL 80

                           90
                   ....*....|...
gi 1127546998  161 DTPInIFGRNILT 173
Cdd:cd00303     81 SYDV-ILGRPWLE 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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