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Conserved domains on  [gi|2155267|gb|AAB58786|]
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pol protein, partial [Simian T-lymphotropic virus 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 ...
 120-334 3.59e-64

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: 215.61  E-value: 3.59e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  120 PPQIDQFPFKPERLQALTDLVSKALEASYIEPYSGPGNNPVFPVKKPNGKWRFIHDLRATNAITTTLASPSPGPPDLTSL 199
Cdd:cd01645   1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  200 STALPyVQTIDLADAFFQIPLPKQFQPYFAFTIPQPCNYGPGARYAWTVLPQGFKNSPTLFEQQLAAILSPIRKAFPTST 279
Cdd:cd01645  81 PKGWP-LIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIV 159

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
gi 2155267  280 IIQYMDDILLASPAQGELQQLSKMTLQALVTHGLPVSQAPREQTPGqIRFLGQVI 334
Cdd:cd01645 160 IYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPP-FQYLGYEL 213
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 755-848 1.14e-25

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: 102.01  E-value: 1.14e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267    755 PNHIWQGDVTHYKYKRH--RYCLHVWVDTFSNAVSITCKTKETSSETVSALLH-AITILGK-PLSINTDNGSAFLSQEFQ 830
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSSEMDAELVLDALErAIAFRGGvPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 2155267    831 AFCTSWHIRHSTHVPYNP 848
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 566-687 1.13e-12

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


The actual alignment was detected with superfamily member cd09273:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 131  Bit Score: 65.82  E-value: 1.13e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  566 SSPTGlpkkAAYVLWDQTIlrhdsITLPPHGSNSAQRGELLALLSGLRAAKSWPsLNIFLDSKYLIKYLHSLATG----A 641
Cdd:cd09273   8 SFKAG----YAIVSGTEIV-----EAQPLPPGTSAQRAELIALIQALELAKGKP-VNIYTDSAYAVHALHLLETIgierG 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 2155267  642 FLGTSTHQSLY-AHLPALLHNKVIYLHHIRSHTNLPDPISTLNEYTD 687
Cdd:cd09273  78 FLKSIKNLSLFlQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQAD 124
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 11-81 2.50e-05

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: 43.90  E-value: 2.50e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2155267     11 PLPPSQKVSDTTVLGAGGQTSSQFKLLRSPLCVYLPFR--KAPVTLPSCLLDtdnkwaIIGRDILQQCQSVLY 81
Cdd:pfam00077  35 PTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRgtVSPLILPTCPVN------IIGRDLLQQLGGRLT 101
IN_DBD_C super family cl02895
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 932-970 6.50e-04

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: 38.15  E-value: 6.50e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2155267    932 PGLTNQRWKGPLHLsrkLQER----LLSIDGS-PQWIPWRLLKK 970
Cdd:pfam00552   4 KDLLNGLWKGPDPL---LWWGrgavCVPQDASdPQWVPERLLKR 44
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 120-334 3.59e-64

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: 215.61  E-value: 3.59e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  120 PPQIDQFPFKPERLQALTDLVSKALEASYIEPYSGPGNNPVFPVKKPNGKWRFIHDLRATNAITTTLASPSPGPPDLTSL 199
Cdd:cd01645   1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  200 STALPyVQTIDLADAFFQIPLPKQFQPYFAFTIPQPCNYGPGARYAWTVLPQGFKNSPTLFEQQLAAILSPIRKAFPTST 279
Cdd:cd01645  81 PKGWP-LIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIV 159

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
gi 2155267  280 IIQYMDDILLASPAQGELQQLSKMTLQALVTHGLPVSQAPREQTPGqIRFLGQVI 334
Cdd:cd01645 160 IYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPP-FQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 164-334 1.32e-38

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: 142.44  E-value: 1.32e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267    164 KKPNGKWRFI----HDLRATNAIT-------TTLASPSPGPPDLTSLSTALPYVQTIDLADAFFQIPLPKQFQPYFAFTI 232
Cdd:pfam00078   3 KKGKGKYRPIsllsIDYKALNKIIvkrlkpeNLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267    233 PQPCN----YGPGARYAWTVLPQGFKNSPTLFEQQLAAILSPIRKAFpTSTIIQYMDDILLASPAQGELQQLSKMTLQAL 308
Cdd:pfam00078  83 PPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEEEHQEALEEVLEWL 161

                         170       180
                  ....*....|....*....|....*...
gi 2155267    309 VTHGLPVSQAPREQTPGQ--IRFLGQVI 334
Cdd:pfam00078 162 KESGLKINPEKTQFFLKSkeVKYLGVTL 189
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 755-848 1.14e-25

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: 102.01  E-value: 1.14e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267    755 PNHIWQGDVTHYKYKRH--RYCLHVWVDTFSNAVSITCKTKETSSETVSALLH-AITILGK-PLSINTDNGSAFLSQEFQ 830
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSSEMDAELVLDALErAIAFRGGvPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 2155267    831 AFCTSWHIRHSTHVPYNP 848
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
755-872 3.20e-18

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 86.75  E-value: 3.20e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  755 PNHIWQGDVTHYKYKRHRYCLHVWVDTFSN-AVSITCKTKETSSETVSALLHAITILG--KPLSINTDNGSAFLSQEFQA 831
Cdd:COG2801 148 PNQVWVTDITYIPTAEGWLYLAAVIDLFSReIVGWSVSDSMDAELVVDALEMAIERRGppKPLILHSDNGSQYTSKAYQE 227

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 2155267  832 FCTSWHIRHSTHVPYNPTSSGLVERTNGIVKA-LLNKYLLDS 872
Cdd:COG2801 228 LLKKLGITQSMSRPGNPQDNAFIESFFGTLKYeLLYRRRFES 269
transpos_IS3 NF033516
IS3 family transposase;
755-872 1.40e-14

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 76.45  E-value: 1.40e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267   755 PNHIWQGDVTHYKYKRHRYCLHVWVDTFSN-AVSITCKTKETSSETVSALLHAITILGKP--LSINTDNGSAFLSQEFQA 831
Cdd:NF033516 215 PNQVWVTDITYIRTAEGWLYLAVVLDLFSReIVGWSVSTSMSAELVLDALEMAIEWRGKPegLILHSDNGSQYTSKAYRE 294

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 2155267   832 FCTSWHIRHSTHVPYNPTSSGLVERTNGIVKA-LLNKYLLDS 872
Cdd:NF033516 295 WLKEHGITQSMSRPGNCWDNAVAESFFGTLKReCLYRRRFRT 336
transpos_IS481 NF033577
IS481 family transposase; null
 755-863 8.92e-14

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 73.01  E-value: 8.92e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267   755 PNHIWQGDVTHY---KYKRHRYcLHVWVDTFSNAVSITCKTKETSSETVSALLHAITILGKPL-SINTDNGSAFLS--QE 828
Cdd:NF033577 127 PGELWHIDIKKLgriPDVGRLY-LHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPIrRVLTDNGSEFRSraHG 205

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 2155267   829 FQAFCTSWHIRHSTHVPYNPTSSGLVERTNGIVKA 863
Cdd:NF033577 206 FELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 566-687 1.13e-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: 65.82  E-value: 1.13e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  566 SSPTGlpkkAAYVLWDQTIlrhdsITLPPHGSNSAQRGELLALLSGLRAAKSWPsLNIFLDSKYLIKYLHSLATG----A 641
Cdd:cd09273   8 SFKAG----YAIVSGTEIV-----EAQPLPPGTSAQRAELIALIQALELAKGKP-VNIYTDSAYAVHALHLLETIgierG 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 2155267  642 FLGTSTHQSLY-AHLPALLHNKVIYLHHIRSHTNLPDPISTLNEYTD 687
Cdd:cd09273  78 FLKSIKNLSLFlQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQAD 124
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 566-689 1.37e-11

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: 63.17  E-value: 1.37e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267    566 SSPTGLPKKAAYVLW--DQTIlrhdSITLPPHGSNsaQRGELLALLSGLRAAKSWPSLNIFLDSKYLIK----YLHSLAT 639
Cdd:pfam00075  12 CLGNPGPGGAGAVLYrgHENI----SAPLPGRTTN--NRAELQAVIEALKALKSPSKVNIYTDSQYVIGgitqWVHGWKK 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2155267    640 GAFLGTST-----HQSLYAHLPALLHNKVIYLHHIRSHTNLPDpistlNEYTDSL 689
Cdd:pfam00075  86 NGWPTTSEgkpvkNKDLWQLLKALCKKHQVYWQWVKGHAGNPG-----NEMADRL 135
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
572-689 9.95e-07

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 49.07  E-value: 9.95e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  572 PKKAAY--VLWDQTILRHDSITLPpHGSNsaQRGELLALLSGLRAAKSWP--SLNIFLDSKYLIKYLHSLATG----AFL 643
Cdd:COG0328  15 PGPGGWgaVIRYGGEEKELSGGLG-DTTN--NRAELTALIAALEALKELGpcEVEIYTDSQYVVNQITGWIHGwkknGWK 91

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 2155267  644 GTStHQSLYAHLPALLHNKVIYLHHIRSHTNLPdpistLNEYTDSL 689
Cdd:COG0328  92 PVK-NPDLWQRLDELLARHKVTFEWVKGHAGHP-----GNERADAL 131
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 755-863 7.61e-06

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 48.71  E-value: 7.61e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267   755 PNHIWQGDVTHYKYKRHRYCLHVWVDTFSN-AVSITCKTKETSSETVSALLHAITILGKP--LSINTDNGSAFLSQEFQA 831
Cdd:PHA02517 109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARrIVGWRVSSSMDTDFVLDALEQALWARGRPggLIHHSDKGSQYVSLAYTQ 188

                         90       100       110
                 ....*....|....*....|....*....|..
gi 2155267   832 FCTSWHIRHSTHVPYNPTSSGLVERTNGIVKA 863
Cdd:PHA02517 189 RLKEAGIRASTGSRGDSYDNAPAESINGLYKA 220
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 11-81 2.50e-05

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: 43.90  E-value: 2.50e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2155267     11 PLPPSQKVSDTTVLGAGGQTSSQFKLLRSPLCVYLPFR--KAPVTLPSCLLDtdnkwaIIGRDILQQCQSVLY 81
Cdd:pfam00077  35 PTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRgtVSPLILPTCPVN------IIGRDLLQQLGGRLT 101
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 932-970 6.50e-04

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: 38.15  E-value: 6.50e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2155267    932 PGLTNQRWKGPLHLsrkLQER----LLSIDGS-PQWIPWRLLKK 970
Cdd:pfam00552   4 KDLLNGLWKGPDPL---LWWGrgavCVPQDASdPQWVPERLLKR 44
transpos_IS30 NF033563
IS30 family transposase;
759-869 2.79e-03

IS30 family transposase;


Pssm-ID: 468088 [Multi-domain]  Cd Length: 267  Bit Score: 40.66  E-value: 2.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267   759 WQGDVThyKYKRHRYCLHVWVDTFSNAVsITCKTKETSSETVS-ALLHAITILGKPL--SINTDNGSAF-----LSQEFQ 830
Cdd:NF033563 136 WEGDTI--LGKKHKSALLTLVERKSRFV-ILVKLPDKTAESVNkALIKLLKPLPKHLrkSITADNGKEFarhseIEEALG 212

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 2155267   831 A---FCTswhirhsthvPYNPTSSGLVERTNGivkaLLNKYL 869
Cdd:NF033563 213 IdvyFAD----------PYSPWQRGTNENTNG----LLRQYL 240
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 120-334 3.59e-64

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: 215.61  E-value: 3.59e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  120 PPQIDQFPFKPERLQALTDLVSKALEASYIEPYSGPGNNPVFPVKKPNGKWRFIHDLRATNAITTTLASPSPGPPDLTSL 199
Cdd:cd01645   1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  200 STALPyVQTIDLADAFFQIPLPKQFQPYFAFTIPQPCNYGPGARYAWTVLPQGFKNSPTLFEQQLAAILSPIRKAFPTST 279
Cdd:cd01645  81 PKGWP-LIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIV 159

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
gi 2155267  280 IIQYMDDILLASPAQGELQQLSKMTLQALVTHGLPVSQAPREQTPGqIRFLGQVI 334
Cdd:cd01645 160 IYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPP-FQYLGYEL 213
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 120-334 2.95e-51

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: 179.08  E-value: 2.95e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  120 PPQIDQFPFKPERLQALTDLVSKALEASYIEPYSGPGNNPVFPVKKPNG-KWRFIHDLRATNAITTTLASPSPGPPDLTS 198
Cdd:cd03715   1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  199 -LSTALPYVQTIDLADAFFQIPLPKQFQPYFAFTIPqpcnygpGARYAWTVLPQGFKNSPTLFEQQLAAILSPIRKAFPT 277
Cdd:cd03715  81 lLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEG 153

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 2155267  278 STIIQYMDDILLASPAQGELQQLSKMTLQALVTHGLPVSQAPREQTPGQIRFLGQVI 334
Cdd:cd03715 154 TILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 164-334 1.32e-38

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: 142.44  E-value: 1.32e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267    164 KKPNGKWRFI----HDLRATNAIT-------TTLASPSPGPPDLTSLSTALPYVQTIDLADAFFQIPLPKQFQPYFAFTI 232
Cdd:pfam00078   3 KKGKGKYRPIsllsIDYKALNKIIvkrlkpeNLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267    233 PQPCN----YGPGARYAWTVLPQGFKNSPTLFEQQLAAILSPIRKAFpTSTIIQYMDDILLASPAQGELQQLSKMTLQAL 308
Cdd:pfam00078  83 PPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEEEHQEALEEVLEWL 161

                         170       180
                  ....*....|....*....|....*...
gi 2155267    309 VTHGLPVSQAPREQTPGQ--IRFLGQVI 334
Cdd:pfam00078 162 KESGLKINPEKTQFFLKSkeVKYLGVTL 189
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 148-334 1.73e-30

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: 118.47  E-value: 1.73e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  148 YIEPYSGPGNNPVFPVKKPNGKWRFIHDLRATNAITTTLASPSPGPPDLTSLSTALPYVQTIDLADAFFQIPLPKQFQPY 227
Cdd:cd01647   2 IIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRPK 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  228 FAFTIpqpcnygPGARYAWTVLPQGFKNSPTLFEQQLAAILSPIRKAFptstIIQYMDDILLASPAQGELQQLSKMTLQA 307
Cdd:cd01647  82 TAFRT-------PFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDF----VEVYLDDILVYSKTEEEHLEHLREVLER 150

                       170       180
                ....*....|....*....|....*..
gi 2155267  308 LVTHGLPVSQAPREQTPGQIRFLGQVI 334
Cdd:cd01647 151 LREAGLKLNPEKCEFGVPEVEFLGHIV 177
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 755-848 1.14e-25

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: 102.01  E-value: 1.14e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267    755 PNHIWQGDVTHYKYKRH--RYCLHVWVDTFSNAVSITCKTKETSSETVSALLH-AITILGK-PLSINTDNGSAFLSQEFQ 830
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSSEMDAELVLDALErAIAFRGGvPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 2155267    831 AFCTSWHIRHSTHVPYNP 848
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
755-872 3.20e-18

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 86.75  E-value: 3.20e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  755 PNHIWQGDVTHYKYKRHRYCLHVWVDTFSN-AVSITCKTKETSSETVSALLHAITILG--KPLSINTDNGSAFLSQEFQA 831
Cdd:COG2801 148 PNQVWVTDITYIPTAEGWLYLAAVIDLFSReIVGWSVSDSMDAELVVDALEMAIERRGppKPLILHSDNGSQYTSKAYQE 227

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 2155267  832 FCTSWHIRHSTHVPYNPTSSGLVERTNGIVKA-LLNKYLLDS 872
Cdd:COG2801 228 LLKKLGITQSMSRPGNPQDNAFIESFFGTLKYeLLYRRRFES 269
transpos_IS3 NF033516
IS3 family transposase;
755-872 1.40e-14

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 76.45  E-value: 1.40e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267   755 PNHIWQGDVTHYKYKRHRYCLHVWVDTFSN-AVSITCKTKETSSETVSALLHAITILGKP--LSINTDNGSAFLSQEFQA 831
Cdd:NF033516 215 PNQVWVTDITYIRTAEGWLYLAVVLDLFSReIVGWSVSTSMSAELVLDALEMAIEWRGKPegLILHSDNGSQYTSKAYRE 294

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 2155267   832 FCTSWHIRHSTHVPYNPTSSGLVERTNGIVKA-LLNKYLLDS 872
Cdd:NF033516 295 WLKEHGITQSMSRPGNCWDNAVAESFFGTLKReCLYRRRFRT 336
transpos_IS481 NF033577
IS481 family transposase; null
 755-863 8.92e-14

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 73.01  E-value: 8.92e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267   755 PNHIWQGDVTHY---KYKRHRYcLHVWVDTFSNAVSITCKTKETSSETVSALLHAITILGKPL-SINTDNGSAFLS--QE 828
Cdd:NF033577 127 PGELWHIDIKKLgriPDVGRLY-LHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPIrRVLTDNGSEFRSraHG 205

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 2155267   829 FQAFCTSWHIRHSTHVPYNPTSSGLVERTNGIVKA 863
Cdd:NF033577 206 FELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 209-331 1.06e-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: 65.44  E-value: 1.06e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  209 IDLADAFFQIPLPKQFQPYFAFtIPQpcnygpGARYAWTVLPQGFKNSPTLFEQQLAAILSPIRKAfpTSTIIQYMDDIL 288
Cdd:cd03714   1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVFTKVVEALLAPLRLL--GVRIFSYLDDLL 71

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 2155267  289 LASPAQGE----LQQLSKMTLQALvthGLPVSQAPREQTP-GQIRFLG 331
Cdd:cd03714  72 IIASSIKTseavLRHLRATLLANL---GFTLNLEKSKLGPtQRITFLG 116
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 566-687 1.13e-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: 65.82  E-value: 1.13e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  566 SSPTGlpkkAAYVLWDQTIlrhdsITLPPHGSNSAQRGELLALLSGLRAAKSWPsLNIFLDSKYLIKYLHSLATG----A 641
Cdd:cd09273   8 SFKAG----YAIVSGTEIV-----EAQPLPPGTSAQRAELIALIQALELAKGKP-VNIYTDSAYAVHALHLLETIgierG 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 2155267  642 FLGTSTHQSLY-AHLPALLHNKVIYLHHIRSHTNLPDPISTLNEYTD 687
Cdd:cd09273  78 FLKSIKNLSLFlQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQAD 124
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 566-689 1.37e-11

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: 63.17  E-value: 1.37e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267    566 SSPTGLPKKAAYVLW--DQTIlrhdSITLPPHGSNsaQRGELLALLSGLRAAKSWPSLNIFLDSKYLIK----YLHSLAT 639
Cdd:pfam00075  12 CLGNPGPGGAGAVLYrgHENI----SAPLPGRTTN--NRAELQAVIEALKALKSPSKVNIYTDSQYVIGgitqWVHGWKK 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2155267    640 GAFLGTST-----HQSLYAHLPALLHNKVIYLHHIRSHTNLPDpistlNEYTDSL 689
Cdd:pfam00075  86 NGWPTTSEgkpvkNKDLWQLLKALCKKHQVYWQWVKGHAGNPG-----NEMADRL 135
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
572-689 9.95e-07

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 49.07  E-value: 9.95e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  572 PKKAAY--VLWDQTILRHDSITLPpHGSNsaQRGELLALLSGLRAAKSWP--SLNIFLDSKYLIKYLHSLATG----AFL 643
Cdd:COG0328  15 PGPGGWgaVIRYGGEEKELSGGLG-DTTN--NRAELTALIAALEALKELGpcEVEIYTDSQYVVNQITGWIHGwkknGWK 91

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 2155267  644 GTStHQSLYAHLPALLHNKVIYLHHIRSHTNLPdpistLNEYTDSL 689
Cdd:COG0328  92 PVK-NPDLWQRLDELLARHKVTFEWVKGHAGHP-----GNERADAL 131
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 246-334 3.13e-06

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: 46.58  E-value: 3.13e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  246 WTV-LPQGFKNSPTLFEQQLAAILSPIRKAFPTSTIIQYMDDILLASPAQGELQQLSKMTlQALVTHGLPVSQAPREQTP 324
Cdd:cd00304   8 TSIpLPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSEQQAVKKRELE-EFLARLGLNLSDEKTQFTE 86

                        90
                ....*....|..
gi 2155267  325 --GQIRFLGQVI 334
Cdd:cd00304  87 keKKFKFLGILV 98
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
759-896 5.00e-06

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 49.49  E-value: 5.00e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  759 WQGDVTHYKykRHRYCLHVWVDTFSNAVsITCKTKETSSETVS-ALLHAITILGKPL--SINTDNGSAFLsqEFQAFCTS 835
Cdd:COG2826 175 WEGDLIIGK--RGKSALLTLVERKSRFV-ILLKLPDKTAESVAdALIRLLRKLPAFLrkSITTDNGKEFA--DHKEIEAA 249

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2155267  836 WHIRHS-THvPYNPTSSGLVERTNGivkaLLNKYLLDSPNLP--LDNAISKSLWTLNQ-----LNVMSP 896
Cdd:COG2826 250 LGIKVYfAD-PYSPWQRGTNENTNG----LLRQYFPKGTDFStvTQEELDAIADRLNNrprkcLGYKTP 313
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 755-863 7.61e-06

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 48.71  E-value: 7.61e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267   755 PNHIWQGDVTHYKYKRHRYCLHVWVDTFSN-AVSITCKTKETSSETVSALLHAITILGKP--LSINTDNGSAFLSQEFQA 831
Cdd:PHA02517 109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARrIVGWRVSSSMDTDFVLDALEQALWARGRPggLIHHSDKGSQYVSLAYTQ 188

                         90       100       110
                 ....*....|....*....|....*....|..
gi 2155267   832 FCTSWHIRHSTHVPYNPTSSGLVERTNGIVKA 863
Cdd:PHA02517 189 RLKEAGIRASTGSRGDSYDNAPAESINGLYKA 220
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 11-81 2.50e-05

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: 43.90  E-value: 2.50e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2155267     11 PLPPSQKVSDTTVLGAGGQTSSQFKLLRSPLCVYLPFR--KAPVTLPSCLLDtdnkwaIIGRDILQQCQSVLY 81
Cdd:pfam00077  35 PTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRgtVSPLILPTCPVN------IIGRDLLQQLGGRLT 101
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 575-689 6.91e-05

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: 43.75  E-value: 6.91e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  575 AAYVLWDQTILRHDSITLPPHGSNSAqrGELLALLSGLRAAKSWPS----LNIFLDSKYLIKylhSLATGAFLGTSTHQS 650
Cdd:cd09276  15 AGFVIYRGGEVISRSYRLGTHASVFD--AELEAILEALELALATARrarkVTIFTDSQSALQ---ALRNPRRSSGQVILI 89

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 2155267  651 LYAHLPALLHNK--VIYLHHIRSHTNLPdpistLNEYTDSL 689
Cdd:cd09276  90 RILRLLRLLKAKgvKVRLRWVPGHVGIE-----GNEAADRL 125
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 575-636 1.05e-04

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: 42.69  E-value: 1.05e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2155267  575 AAYVLWDQTILRHDSITLPPHGSnSAQRGELLALLSGLRAAKSWPSLNIFL--DSKYLIKYLHS 636
Cdd:cd06222  16 IGGVLRDHEGGWLGGFALKIGAP-TALEAELLALLLALELALDLGYLKVIIesDSKYVVDLINS 78
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 586-689 2.66e-04

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: 42.17  E-value: 2.66e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267  586 RHDSITLPPHGSNSaQRGELLALLSGLRAAKSWP--SLNIFLDSKYLI----KYLHSLATGAFLGTST----HQSLYAHL 655
Cdd:cd09280  30 RNVSEPLPGRKQTN-NRAELLAVIHALEQAPEEGirKLEIRTDSKYAIncitKWIPKWKKNGWKTSKGkpvkNQDLIKEL 108

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 2155267  656 PALL--HNKVIYLHHIRSHTNLPDpistlNEYTDSL 689
Cdd:cd09280 109 DKLLrkRGIKVKFEHVKGHSGDPG-----NEEADRL 139
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 932-970 6.50e-04

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: 38.15  E-value: 6.50e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2155267    932 PGLTNQRWKGPLHLsrkLQER----LLSIDGS-PQWIPWRLLKK 970
Cdd:pfam00552   4 KDLLNGLWKGPDPL---LWWGrgavCVPQDASdPQWVPERLLKR 44
transpos_IS30 NF033563
IS30 family transposase;
759-869 2.79e-03

IS30 family transposase;


Pssm-ID: 468088 [Multi-domain]  Cd Length: 267  Bit Score: 40.66  E-value: 2.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2155267   759 WQGDVThyKYKRHRYCLHVWVDTFSNAVsITCKTKETSSETVS-ALLHAITILGKPL--SINTDNGSAF-----LSQEFQ 830
Cdd:NF033563 136 WEGDTI--LGKKHKSALLTLVERKSRFV-ILVKLPDKTAESVNkALIKLLKPLPKHLrkSITADNGKEFarhseIEEALG 212

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 2155267   831 A---FCTswhirhsthvPYNPTSSGLVERTNGivkaLLNKYL 869
Cdd:NF033563 213 IdvyFAD----------PYSPWQRGTNENTNG----LLRQYL 240
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 594-632 6.91e-03

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: 37.85  E-value: 6.91e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 2155267  594 PHGSNsaQRGELLALLSGLRAAKSWPSLNIFLDSKYLIK 632
Cdd:cd09278  37 PGTTN--NRMELTAAIEALEALKEPCPVTIYTDSQYVIN 73
 
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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