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Conserved domains on  [gi|1043620572|dbj|BAV25178|]
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pol protein, partial [Simian immunodeficiency virus - agm]

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 ...
 190-406 1.98e-101

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: 316.92  E-value: 1.98e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  190 GPCVKQWPLSREKIKALTDICDSLEKEGKISRIGgeNAYNTPVFCIKKKDqSKWRMLIDFRELNKATQDFFEVQLGIPHP 269
Cdd:cd01645      1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKS-GKWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  270 SGLQKKKQVTVLDIGDAYYSIPLDPEFRKYTAFTIPSINNQGPGQRYQFNCLPQGWKGSPTIFQNTAAKILAQIKEELPG 349
Cdd:cd01645     78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1043620572  350 LEIVQYMDDLWVGSNySEREHDEKVRQLREKLLQWGFETPEKKVQSEPPYEWMGYKL 406
Cdd:cd01645    158 IVIYHYMDDILIASD-LEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 490-589 3.23e-36

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


:

Pssm-ID: 462013  Cd Length: 102  Bit Score: 132.19  E-value: 3.23e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  490 YYDPQKPLRAAVQKLGNGQWGYQIKQEQ-KVLKVGKYEKQKAIHTNELRILAGLVQKIAKESLVIWGTLPKFELPVEREV 568
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPfKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|.
gi 1043620572  569 WEQWWSDYWQVSWIPEWEFVS 589
Cdd:pfam06815   81 WETWWTEYWQATWIPEWEFVN 101
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 606-728 2.30e-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: 128.26  E-value: 2.30e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  606 PKEDVYYVDGACNRQSKEGKAGYITQYGKQ-RVKTLEN-TTNQQAELQAILMALED--SGSKVNIVTDSQYALGILT--- 678
Cdd:pfam00075    1 PKAVTVYTDGSCLGNPGPGGAGAVLYRGHEnISAPLPGrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGITqwv 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1043620572  679 ------AHPTQSDSALV--NQIIEQL---IKKEQVYLQWVPAHKGIGGNEEVDKLVSKGIR 728
Cdd:pfam00075   81 hgwkknGWPTTSEGKPVknKDLWQLLkalCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RVT_thumb super family cl06055
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 413-476 2.65e-19

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


The actual alignment was detected with superfamily member pfam06817:

Pssm-ID: 429135  Cd Length: 66  Bit Score: 82.75  E-value: 2.65e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1043620572  413 LQKLEIEEKDQWTVNDIQKLAGKLNWAAQLY--PGLKTKHICRLIRGKRGLLDPVLWTPEAELELE 476
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 788-876 2.44e-14

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


:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 69.65  E-value: 2.44e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  788 SPGVWQIDCTHIEGHI------IIVAVHVASGFIEAEEIPRETGKATAKFLLK--LLSRWPV-KQIHTDNGPNFVSQEVK 858
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALEraIAFRGGVpLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1043620572  859 AICWWGKIEHTTGVPYNP 876
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 74-168 4.38e-11

Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin 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. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family).


The actual alignment was detected with superfamily member pfam00077:

Pssm-ID: 472175  Cd Length: 101  Bit Score: 60.46  E-value: 4.38e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572   74 LWRRPIKIVRIEGQPIKVLLDTGADDTIIKEQDLALT--GSWRPKIIGGIGGGLQVREYNN--VEVILEDKTLKGAVLLG 149
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNwpKQKATTNIQGIGGGINVRQSDQilILIGEDKFRGTVSPLIL 80

                           90       100
                   ....*....|....*....|
gi 1043620572  150 PT-PINIIGRNFLAQAGVKL 168
Cdd:pfam00077   81 PTcPVNIIGRDLLQQLGGRL 100
IN_DBD_C super family cl02895
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 956-1000 4.99e-10

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: 55.48  E-value: 4.99e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1043620572  956 VYYREGRDPVWKGPAQLIWKGEGAVVIKEADGDLKVIPRRKAKII 1000
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVPQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 741-776 1.20e-09

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: 54.30  E-value: 1.20e-09
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1043620572  741 EEHERYHNNWKEMADTFGIPQVVAKEIVAACPKCQV 776
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 190-406 1.98e-101

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: 316.92  E-value: 1.98e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  190 GPCVKQWPLSREKIKALTDICDSLEKEGKISRIGgeNAYNTPVFCIKKKDqSKWRMLIDFRELNKATQDFFEVQLGIPHP 269
Cdd:cd01645      1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKS-GKWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  270 SGLQKKKQVTVLDIGDAYYSIPLDPEFRKYTAFTIPSINNQGPGQRYQFNCLPQGWKGSPTIFQNTAAKILAQIKEELPG 349
Cdd:cd01645     78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1043620572  350 LEIVQYMDDLWVGSNySEREHDEKVRQLREKLLQWGFETPEKKVQSEPPYEWMGYKL 406
Cdd:cd01645    158 IVIYHYMDDILIASD-LEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 235-406 5.48e-42

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: 152.07  E-value: 5.48e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  235 IKKKDQSKWRML----IDFRELNKATQD-------FFEVQLGIPHPSGLQKKKQ-VTVLDIGDAYYSIPLDPEFRKYTAF 302
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKwFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  303 TIPSINN----QGPGQRYQFNCLPQGWKGSPTIFQNTAAKILAQIKEElPGLEIVQYMDDLWVGSNySEREHDEKVRQLR 378
Cdd:pfam00078   81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1043620572  379 EKLLQWGFETPEKKVQ---SEPPYEWMGYKL 406
Cdd:pfam00078  159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 490-589 3.23e-36

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


Pssm-ID: 462013  Cd Length: 102  Bit Score: 132.19  E-value: 3.23e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  490 YYDPQKPLRAAVQKLGNGQWGYQIKQEQ-KVLKVGKYEKQKAIHTNELRILAGLVQKIAKESLVIWGTLPKFELPVEREV 568
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPfKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|.
gi 1043620572  569 WEQWWSDYWQVSWIPEWEFVS 589
Cdd:pfam06815   81 WETWWTEYWQATWIPEWEFVN 101
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 606-728 2.30e-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: 128.26  E-value: 2.30e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  606 PKEDVYYVDGACNRQSKEGKAGYITQYGKQ-RVKTLEN-TTNQQAELQAILMALED--SGSKVNIVTDSQYALGILT--- 678
Cdd:pfam00075    1 PKAVTVYTDGSCLGNPGPGGAGAVLYRGHEnISAPLPGrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGITqwv 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1043620572  679 ------AHPTQSDSALV--NQIIEQL---IKKEQVYLQWVPAHKGIGGNEEVDKLVSKGIR 728
Cdd:pfam00075   81 hgwkknGWPTTSEGKPVknKDLWQLLkalCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
612-727 2.15e-19

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 85.28  E-value: 2.15e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  612 YVDGACNRQSKEGKAGYITQYGKQRVK---TLENTTNQQAELQAILMALE----DSGSKVNIVTDSQYalgiltahptqs 684
Cdd:COG0328      6 YTDGACRGNPGPGGWGAVIRYGGEEKElsgGLGDTTNNRAELTALIAALEalkeLGPCEVEIYTDSQY------------ 73

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1043620572  685 dsaLVNQI-----------------------IEQLIKKEQVYLQWVPAHKGIGGNEEVDKLVSKGI 727
Cdd:COG0328     74 ---VVNQItgwihgwkkngwkpvknpdlwqrLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 413-476 2.65e-19

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


Pssm-ID: 429135  Cd Length: 66  Bit Score: 82.75  E-value: 2.65e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1043620572  413 LQKLEIEEKDQWTVNDIQKLAGKLNWAAQLY--PGLKTKHICRLIRGKRGLLDPVLWTPEAELELE 476
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 610-728 3.90e-17

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: 79.06  E-value: 3.90e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  610 VYYVDGACNRQSkeGKAGY--ITQYGKQRvKTL----ENTTNQQAELQAILMALE--DSGSKVNIVTDSQYAL-GIltah 680
Cdd:cd09278      3 VIYTDGACLGNP--GPGGWaaVIRYGDHE-KELsggePGTTNNRMELTAAIEALEalKEPCPVTIYTDSQYVInGI---- 75

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1043620572  681 pTQ------------SDSALV-N----QIIEQLIKKEQVYLQWVPAHKGIGGNEEVDKLVSKGIR 728
Cdd:cd09278     76 -TKwikgwkkngwktADGKPVkNrdlwQELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAAD 139
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 788-876 2.44e-14

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


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 69.65  E-value: 2.44e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  788 SPGVWQIDCTHIEGHI------IIVAVHVASGFIEAEEIPRETGKATAKFLLK--LLSRWPV-KQIHTDNGPNFVSQEVK 858
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALEraIAFRGGVpLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1043620572  859 AICWWGKIEHTTGVPYNP 876
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 775-931 5.01e-12

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 67.62  E-value: 5.01e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  775 QVKGEPVHGQVDASPGVWQIDCTHI-----EGHI-IIVAVHVASGFIEAEEIPRETGKATAKFLLKLLSRW--PVKQIHT 846
Cdd:NF033577   114 RKTGKVKRYERAHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHgiPIRRVLT 193

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  847 DNGPNFVS--QEVKAICWWGKIEHTTGVPYNPQSQGSVESMNKQLKEIIGKIR--DDCQYVETAVLMACHIHNFKRK-GG 921
Cdd:NF033577   194 DNGSEFRSraHGFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARpyESLAELQAALDEWLHHYNHHRPhSA 273

                          170
                   ....*....|
gi 1043620572  922 IGGMTSAERL 931
Cdd:NF033577   274 LGGKTPAERF 283
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 74-168 4.38e-11

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: 60.46  E-value: 4.38e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572   74 LWRRPIKIVRIEGQPIKVLLDTGADDTIIKEQDLALT--GSWRPKIIGGIGGGLQVREYNN--VEVILEDKTLKGAVLLG 149
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNwpKQKATTNIQGIGGGINVRQSDQilILIGEDKFRGTVSPLIL 80

                           90       100
                   ....*....|....*....|
gi 1043620572  150 PT-PINIIGRNFLAQAGVKL 168
Cdd:pfam00077   81 PTcPVNIIGRDLLQQLGGRL 100
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 956-1000 4.99e-10

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: 55.48  E-value: 4.99e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1043620572  956 VYYREGRDPVWKGPAQLIWKGEGAVVIKEADGDLKVIPRRKAKII 1000
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVPQDASDPQWVPERLLKRI 45
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 82-162 8.13e-10

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: 56.51  E-value: 8.13e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572   82 VRIEGQPIKVLLDTGADDTIIKEQDLALTGSWRPKIIGGI--GGGLQVREYNNVEVILEDKTLKGAVLLGP--TPINIIG 157
Cdd:cd05482      3 LYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTgiGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNLWG 82


                   ....*
gi 1043620572  158 RNFLA 162
Cdd:cd05482     83 RDILS 87
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 741-776 1.20e-09

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: 54.30  E-value: 1.20e-09
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1043620572  741 EEHERYHNNWKEMADTFGIPQVVAKEIVAACPKCQV 776
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
rnhA PRK00203
ribonuclease H; Reviewed
 612-731 9.29e-09

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 55.22  E-value: 9.29e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  612 YVDGACNRQSKEGKAGYITQYGkQRVKTL----ENTTNQQAELQAILMALE--DSGSKVNIVTDSQYAL-GIltahpTQ- 683
Cdd:PRK00203     7 YTDGACLGNPGPGGWGAILRYK-GHEKELsggeALTTNNRMELMAAIEALEalKEPCEVTLYTDSQYVRqGI-----TEw 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1043620572  684 -----------SDSALV-N----QIIEQLIKKEQVYLQWVPAHKGIGGNEEVDKLVSKGIRQVL 731
Cdd:PRK00203    81 ihgwkkngwktADKKPVkNvdlwQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEAT 144
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
791-938 1.37e-07

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 54.39  E-value: 1.37e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  791 VWQIDCTHI---EGH-----II------IVAVHVASgfieaeeipRETGKATAKFLLKLLSRWPVKQ---IHTDNGPNFV 853
Cdd:COG2801    151 VWVTDITYIptaEGWlylaaVIdlfsreIVGWSVSD---------SMDAELVVDALEMAIERRGPPKpliLHSDNGSQYT 221

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  854 SQEVKAICWWGKIEHTTGVPYNPQSQGSVESMNKQLKE--IIGKIRDDCQYVETAVLMACHIHNFKR-KGGIGGMTSAER 930
Cdd:COG2801    222 SKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpHSSLGYLTPAEY 301


                   ....*...
gi 1043620572  931 LLSILTAQ 938
Cdd:COG2801    302 EKQLAAAA 309
transpos_IS3 NF033516
IS3 family transposase;
791-929 6.69e-04

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 43.32  E-value: 6.69e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  791 VWQIDCTHI---EGH-----II------IVAVHVASgfieaeeipRETGKATAKFLLKLLSRW--PVKQI-HTDNGPNFV 853
Cdd:NF033516   218 VWVTDITYIrtaEGWlylavVLdlfsreIVGWSVST---------SMSAELVLDALEMAIEWRgkPEGLIlHSDNGSQYT 288

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  854 SQEVKAICWWGKIEHTTGVPYNPQSQGSVESMNKQLKeiigkirDDCQY---------VETAVLMACHIHNFKR-KGGIG 923
Cdd:NF033516   289 SKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK-------RECLYrrrfrtleeARQAIEEYIEFYNHERpHSSLG 361


                   ....*.
gi 1043620572  924 GMTSAE 929
Cdd:NF033516   362 YLTPAE 367
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 190-406 1.98e-101

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: 316.92  E-value: 1.98e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  190 GPCVKQWPLSREKIKALTDICDSLEKEGKISRIGgeNAYNTPVFCIKKKDqSKWRMLIDFRELNKATQDFFEVQLGIPHP 269
Cdd:cd01645      1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKS-GKWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  270 SGLQKKKQVTVLDIGDAYYSIPLDPEFRKYTAFTIPSINNQGPGQRYQFNCLPQGWKGSPTIFQNTAAKILAQIKEELPG 349
Cdd:cd01645     78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1043620572  350 LEIVQYMDDLWVGSNySEREHDEKVRQLREKLLQWGFETPEKKVQSEPPYEWMGYKL 406
Cdd:cd01645    158 IVIYHYMDDILIASD-LEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 235-406 5.48e-42

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: 152.07  E-value: 5.48e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  235 IKKKDQSKWRML----IDFRELNKATQD-------FFEVQLGIPHPSGLQKKKQ-VTVLDIGDAYYSIPLDPEFRKYTAF 302
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKwFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  303 TIPSINN----QGPGQRYQFNCLPQGWKGSPTIFQNTAAKILAQIKEElPGLEIVQYMDDLWVGSNySEREHDEKVRQLR 378
Cdd:pfam00078   81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1043620572  379 EKLLQWGFETPEKKVQ---SEPPYEWMGYKL 406
Cdd:pfam00078  159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 490-589 3.23e-36

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


Pssm-ID: 462013  Cd Length: 102  Bit Score: 132.19  E-value: 3.23e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  490 YYDPQKPLRAAVQKLGNGQWGYQIKQEQ-KVLKVGKYEKQKAIHTNELRILAGLVQKIAKESLVIWGTLPKFELPVEREV 568
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPfKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|.
gi 1043620572  569 WEQWWSDYWQVSWIPEWEFVS 589
Cdd:pfam06815   81 WETWWTEYWQATWIPEWEFVN 101
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 191-402 1.03e-35

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: 134.78  E-value: 1.03e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  191 PCVKQWPLSREKIKALTDICDSLEKEGKIsrIGGENAYNTPVFCIKKKDQSKWRMLIDFRELNKATQDffeVQLGIPHP- 269
Cdd:cd03715      2 VNQKQYPLPREAREGITPHIQELLEAGIL--VPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLP---IHPAVPNPy 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  270 ---SGLQKKKQ-VTVLDIGDAYYSIPLDPEFRKYTAFTIPsinnqgpGQRYQFNCLPQGWKGSPTIFQNTAAKILAQIKE 345
Cdd:cd03715     77 tllSLLPPKHQwYTVLDLANAFFSLPLAPDSQPLFAFEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPL 149

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1043620572  346 ELPGLEIVQYMDDLWVGSnyserEHDEKVRQLREKLLQW----GFETPEKKVQSePPYEWM 402
Cdd:cd03715    150 EHEGTILLQYVDDLLLAA-----DSEEDCLKGTDALLTHlgelGYKVSPKKAQI-CRAEVK 204
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 606-728 2.30e-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: 128.26  E-value: 2.30e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  606 PKEDVYYVDGACNRQSKEGKAGYITQYGKQ-RVKTLEN-TTNQQAELQAILMALED--SGSKVNIVTDSQYALGILT--- 678
Cdd:pfam00075    1 PKAVTVYTDGSCLGNPGPGGAGAVLYRGHEnISAPLPGrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGITqwv 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1043620572  679 ------AHPTQSDSALV--NQIIEQL---IKKEQVYLQWVPAHKGIGGNEEVDKLVSKGIR 728
Cdd:pfam00075   81 hgwkknGWPTTSEGKPVknKDLWQLLkalCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 228-419 1.74e-31

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: 121.55  E-value: 1.74e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  228 YNTPVFCIKKKDqSKWRMLIDFRELNKAT-QDFFEvqlgIPHPSG----LQKKKQVTVLDIGDAYYSIPLDPEFRKYTAF 302
Cdd:cd01647     10 YASPVVVVKKKD-GKLRLCVDYRKLNKVTiKDRYP----LPTIDElleeLAGAKVFSKLDLRSGYHQIPLAEESRPKTAF 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  303 TIpsinnqgPGQRYQFNCLPQGWKGSPTIFQNTAAKILaqikEELPGLEIVQYMDDLWVGSNySEREHDEKVRQLREKLL 382
Cdd:cd01647     85 RT-------PFGLYEYTRMPFGLKNAPATFQRLMNKIL----GDLLGDFVEVYLDDILVYSK-TEEEHLEHLREVLERLR 152

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1043620572  383 QWGFetpekkvqseppyewmgyKLWPSKWQLQKLEIE 419
Cdd:cd01647    153 EAGL------------------KLNPEKCEFGVPEVE 171
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
612-727 2.15e-19

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 85.28  E-value: 2.15e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  612 YVDGACNRQSKEGKAGYITQYGKQRVK---TLENTTNQQAELQAILMALE----DSGSKVNIVTDSQYalgiltahptqs 684
Cdd:COG0328      6 YTDGACRGNPGPGGWGAVIRYGGEEKElsgGLGDTTNNRAELTALIAALEalkeLGPCEVEIYTDSQY------------ 73

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1043620572  685 dsaLVNQI-----------------------IEQLIKKEQVYLQWVPAHKGIGGNEEVDKLVSKGI 727
Cdd:COG0328     74 ---VVNQItgwihgwkkngwkpvknpdlwqrLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 413-476 2.65e-19

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


Pssm-ID: 429135  Cd Length: 66  Bit Score: 82.75  E-value: 2.65e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1043620572  413 LQKLEIEEKDQWTVNDIQKLAGKLNWAAQLY--PGLKTKHICRLIRGKRGLLDPVLWTPEAELELE 476
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 610-728 3.90e-17

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: 79.06  E-value: 3.90e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  610 VYYVDGACNRQSkeGKAGY--ITQYGKQRvKTL----ENTTNQQAELQAILMALE--DSGSKVNIVTDSQYAL-GIltah 680
Cdd:cd09278      3 VIYTDGACLGNP--GPGGWaaVIRYGDHE-KELsggePGTTNNRMELTAAIEALEalKEPCPVTIYTDSQYVInGI---- 75

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1043620572  681 pTQ------------SDSALV-N----QIIEQLIKKEQVYLQWVPAHKGIGGNEEVDKLVSKGIR 728
Cdd:cd09278     76 -TKwikgwkkngwktADGKPVkNrdlwQELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAAD 139
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 612-728 3.92e-17

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: 79.15  E-value: 3.92e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  612 YVDGACNRQSKEG-KAGYITQYGK-------QRVkTLENTTNQQAELQAILMALE----DSGSKVNIVTDSQYALGILTA 679
Cdd:cd09280      3 YTDGSCLNNGKPGaRAGIGVYFGPgdprnvsEPL-PGRKQTNNRAELLAVIHALEqapeEGIRKLEIRTDSKYAINCITK 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1043620572  680 HP---------TQSDSALVNQ-IIEQLIKKEQ-----VYLQWVPAHKGIGGNEEVDKLVSKGIR 728
Cdd:cd09280     82 WIpkwkkngwkTSKGKPVKNQdLIKELDKLLRkrgikVKFEHVKGHSGDPGNEEADRLAREGAD 145
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 610-728 4.89e-17

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: 78.41  E-value: 4.89e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  610 VYYVDGacnrqSK-EGKAGY---ITQYGKQ---RVKTLENTTNQQAELQAILMALE------DSGSKVNIVTDSQYALGI 676
Cdd:cd09276      1 VIYTDG-----SKlEGSVGAgfvIYRGGEVisrSYRLGTHASVFDAELEAILEALElalataRRARKVTIFTDSQSALQA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1043620572  677 LTAHPTQSDSALVNQIIEQLIKKE----QVYLQWVPAHKGIGGNEEVDKLVSKGIR 728
Cdd:cd09276     76 LRNPRRSSGQVILIRILRLLRLLKakgvKVRLRWVPGHVGIEGNEAADRLAKEAAS 131
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 788-876 2.44e-14

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


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 69.65  E-value: 2.44e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  788 SPGVWQIDCTHIEGHI------IIVAVHVASGFIEAEEIPRETGKATAKFLLK--LLSRWPV-KQIHTDNGPNFVSQEVK 858
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALEraIAFRGGVpLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1043620572  859 AICWWGKIEHTTGVPYNP 876
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 775-931 5.01e-12

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 67.62  E-value: 5.01e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  775 QVKGEPVHGQVDASPGVWQIDCTHI-----EGHI-IIVAVHVASGFIEAEEIPRETGKATAKFLLKLLSRW--PVKQIHT 846
Cdd:NF033577   114 RKTGKVKRYERAHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHgiPIRRVLT 193

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  847 DNGPNFVS--QEVKAICWWGKIEHTTGVPYNPQSQGSVESMNKQLKEIIGKIR--DDCQYVETAVLMACHIHNFKRK-GG 921
Cdd:NF033577   194 DNGSEFRSraHGFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARpyESLAELQAALDEWLHHYNHHRPhSA 273

                          170
                   ....*....|
gi 1043620572  922 IGGMTSAERL 931
Cdd:NF033577   274 LGGKTPAERF 283
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 612-723 5.70e-12

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: 63.90  E-value: 5.70e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  612 YVDGACnrqSKEGKAGYITQYGKQRVKTLENTTNQQAELQAILMALED-SGSKVNIVTDSQYALGILTAH-------PTQ 683
Cdd:cd09273      3 FTDGSS---FKAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELaKGKPVNIYTDSAYAVHALHLLetigierGFL 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1043620572  684 SDS---ALVNQIIEQLIKKEQVYLQWVPAHKGIG-----GNEEVDKLV 723
Cdd:cd09273     80 KSIknlSLFLQLLEAVQRPKPVAIIHIRAHSKLPgplaeGNAQADAAA 127
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 321-406 4.17e-11

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: 60.44  E-value: 4.17e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  321 LPQGWKGSPTIFQNTAAKILAQIKEELPGLEIVQYMDDLWVGSNYSerEHDEKVRQLREKLLQWGFETPEKKVQ---SEP 397
Cdd:cd00304     12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE--QQAVKKRELEEFLARLGLNLSDEKTQfteKEK 89


                   ....*....
gi 1043620572  398 PYEWMGYKL 406
Cdd:cd00304     90 KFKFLGILV 98
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 74-168 4.38e-11

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: 60.46  E-value: 4.38e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572   74 LWRRPIKIVRIEGQPIKVLLDTGADDTIIKEQDLALT--GSWRPKIIGGIGGGLQVREYNN--VEVILEDKTLKGAVLLG 149
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNwpKQKATTNIQGIGGGINVRQSDQilILIGEDKFRGTVSPLIL 80

                           90       100
                   ....*....|....*....|
gi 1043620572  150 PT-PINIIGRNFLAQAGVKL 168
Cdd:pfam00077   81 PTcPVNIIGRDLLQQLGGRL 100
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 612-722 4.01e-10

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: 58.48  E-value: 4.01e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  612 YVDGACNRQSKEGKAGYITQYGKQRV-----KTLENTTNQQAELQAILMALE----DSGSKVNIVTDSQYALGILTAHPT 682
Cdd:cd06222      2 NVDGSCRGNPGPAGIGGVLRDHEGGWlggfaLKIGAPTALEAELLALLLALElaldLGYLKVIIESDSKYVVDLINSGSF 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1043620572  683 QSDSA--LVNQIIEQLIKKEQVYLQWVPAHkgigGNEEVDKL 722
Cdd:cd06222     82 KWSPNilLIEDILLLLSRFWSVKISHVPRE----GNQVADAL 119
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 956-1000 4.99e-10

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: 55.48  E-value: 4.99e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1043620572  956 VYYREGRDPVWKGPAQLIWKGEGAVVIKEADGDLKVIPRRKAKII 1000
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVPQDASDPQWVPERLLKRI 45
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 82-162 8.13e-10

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: 56.51  E-value: 8.13e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572   82 VRIEGQPIKVLLDTGADDTIIKEQDLALTGSWRPKIIGGI--GGGLQVREYNNVEVILEDKTLKGAVLLGP--TPINIIG 157
Cdd:cd05482      3 LYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTgiGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNLWG 82


                   ....*
gi 1043620572  158 RNFLA 162
Cdd:cd05482     83 RDILS 87
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 281-397 9.95e-10

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.


Pssm-ID: 239684 [Multi-domain]  Cd Length: 119  Bit Score: 57.35  E-value: 9.95e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  281 LDIGDAYYSIPLDPEFRKYTAFtIPSinnqgpGQRYQFNCLPQGWKGSPTIFQNTAAKILAQIKeeLPGLEIVQYMDD-L 359
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVFTKVVEALLAPLR--LLGVRIFSYLDDlL 71

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1043620572  360 WVGSNYSEREHdeKVRQLREKLL-QWGFETPEKKVQSEP 397
Cdd:cd03714     72 IIASSIKTSEA--VLRHLRATLLaNLGFTLNLEKSKLGP 108
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 741-776 1.20e-09

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: 54.30  E-value: 1.20e-09
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1043620572  741 EEHERYHNNWKEMADTFGIPQVVAKEIVAACPKCQV 776
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
rnhA PRK00203
ribonuclease H; Reviewed
 612-731 9.29e-09

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 55.22  E-value: 9.29e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  612 YVDGACNRQSKEGKAGYITQYGkQRVKTL----ENTTNQQAELQAILMALE--DSGSKVNIVTDSQYAL-GIltahpTQ- 683
Cdd:PRK00203     7 YTDGACLGNPGPGGWGAILRYK-GHEKELsggeALTTNNRMELMAAIEALEalKEPCEVTLYTDSQYVRqGI-----TEw 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1043620572  684 -----------SDSALV-N----QIIEQLIKKEQVYLQWVPAHKGIGGNEEVDKLVSKGIRQVL 731
Cdd:PRK00203    81 ihgwkkngwktADKKPVkNvdlwQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEAT 144
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 612-728 1.07e-08

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: 54.40  E-value: 1.07e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  612 YVDGACNRQSKEGKAGYITQYGKQRVKTL-----ENTTNQQAELQAILMALED----SGSKVNIVTDSQyalgiltahpt 682
Cdd:cd09279      4 YFDGASRGNPGPAGAGVVIYSPGGEVLELserlgFPATNNEAEYEALIAGLELalelGAEKLEIYGDSQ----------- 72

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1043620572  683 qsdsALVNQI-----------------IEQLIKK-EQVYLQWVPAHKgiggNEEVDKLVSKGIR 728
Cdd:cd09279     73 ----LVVNQLngeykvknerlkpllekVLELLAKfELVELKWIPREQ----NKEADALANQALD 128
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
791-938 1.37e-07

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 54.39  E-value: 1.37e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  791 VWQIDCTHI---EGH-----II------IVAVHVASgfieaeeipRETGKATAKFLLKLLSRWPVKQ---IHTDNGPNFV 853
Cdd:COG2801    151 VWVTDITYIptaEGWlylaaVIdlfsreIVGWSVSD---------SMDAELVVDALEMAIERRGPPKpliLHSDNGSQYT 221

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  854 SQEVKAICWWGKIEHTTGVPYNPQSQGSVESMNKQLKE--IIGKIRDDCQYVETAVLMACHIHNFKR-KGGIGGMTSAER 930
Cdd:COG2801    222 SKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpHSSLGYLTPAEY 301


                   ....*...
gi 1043620572  931 LLSILTAQ 938
Cdd:COG2801    302 EKQLAAAA 309
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 81-162 1.91e-04

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


Pssm-ID: 133159  Cd Length: 86  Bit Score: 41.16  E-value: 1.91e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572   81 IVRIEGQPIKVLLDTGADDTIIKEqDLALTGSWRPKIIGGI--GGGLQVREYNNVEVI-LEDKTLKGAVLLGPT-PINII 156
Cdd:cd06095      2 TITVEGVPIVFLVDTGATHSVLKS-DLGPKQELSTTSVLIRgvSGQSQQPVTTYRTLVdLGGHTVSHSFLVVPNcPDPLL 80


                   ....*.
gi 1043620572  157 GRNFLA 162
Cdd:cd06095     81 GRDLLS 86
transpos_IS3 NF033516
IS3 family transposase;
791-929 6.69e-04

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 43.32  E-value: 6.69e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  791 VWQIDCTHI---EGH-----II------IVAVHVASgfieaeeipRETGKATAKFLLKLLSRW--PVKQI-HTDNGPNFV 853
Cdd:NF033516   218 VWVTDITYIrtaEGWlylavVLdlfsreIVGWSVST---------SMSAELVLDALEMAIEWRgkPEGLIlHSDNGSQYT 288

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  854 SQEVKAICWWGKIEHTTGVPYNPQSQGSVESMNKQLKeiigkirDDCQY---------VETAVLMACHIHNFKR-KGGIG 923
Cdd:NF033516   289 SKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK-------RECLYrrrfrtleeARQAIEEYIEFYNHERpHSSLG 361


                   ....*.
gi 1043620572  924 GMTSAE 929
Cdd:NF033516   362 YLTPAE 367
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 82-106 8.33e-04

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: 39.48  E-value: 8.33e-04
                           10        20
                   ....*....|....*....|....*
gi 1043620572   82 VRIEGQPIKVLLDTGADDTIIKEQD 106
Cdd:pfam13975    3 VTINGRPVRFLVDTGASVTVISEAL 27
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 610-672 8.63e-04

Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many of which are uncharacterized. 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.


Pssm-ID: 260014 [Multi-domain]  Cd Length: 153  Bit Score: 41.03  E-value: 8.63e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  610 VYYVDGACNRQSKEG-KAGYITQYGK----QRVKTLENT-----TNQQAELQAILMALE----------DSGSKVNIVTD 669
Cdd:cd13934      1 LVYIDGACRNNGRPDaRAGYGVYFGPdssyNVSGRLEDTgghpqTSQRAELRAAIAALRfrswiidpdgEGLKTVVIATD 80


                   ...
gi 1043620572  670 SQY 672
Cdd:cd13934     81 SEY 83
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 82-108 2.58e-03

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: 38.38  E-value: 2.58e-03
                           10        20
                   ....*....|....*....|....*..
gi 1043620572   82 VRIEGQPIKVLLDTGADDTIIKEQDLA 108
Cdd:cd05483      7 VTINGQPVRFLLDTGASTTVISEELAE 33
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 282-387 2.74e-03

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


Pssm-ID: 238822  Cd Length: 213  Bit Score: 40.37  E-value: 2.74e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572  282 DIGDAYYSIPLDPEFRKYTAFTIPSINNQGPGQRYQFNCLPQGWKGSPTIfQNTAAKILAQIKEELPGLEIVQ---YMDD 358
Cdd:cd01644     65 DIEKMFHQVKVRPEDRDVLRFLWRKDGDEPKPIEYRMTVVPFGAASAPFL-ANRALKQHAEDHPHEAAAKIIKrnfYVDD 143

                           90       100
                   ....*....|....*....|....*....
gi 1043620572  359 LWVGSNySEREHDEKVRQLREKLLQWGFE 387
Cdd:cd01644    144 ILVSTD-TLNEAVNVAKRLIALLKKGGFN 171
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 82-160 6.21e-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: 6.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043620572   82 VRIEGQPIKVLLDTGADDTIIKEQD-----LALTGSWRPKIIGGIGGGLQVREYNNVEVILEDKTLKG---AVL-LGPTP 152
Cdd:pfam13650    3 VTINGKPVRFLVDTGASGTVISPSLaerlgLKVRGLAYTVRVSTAGGRVSAARVRLDSLRLGGLTLENvpaLVLdLGDLI 82


                   ....*...
gi 1043620572  153 INIIGRNF 160
Cdd:pfam13650   83 DGLLGMDF 90
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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