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Conserved domains on  [gi|150406858|gb|EDN02399|]
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predicted protein [Histoplasma mississippiense (nom. inval.)]

Protein Classification

RNA-directed DNA polymerase( domain architecture ID 13284307)

RNA-directed DNA polymerase catalyzes DNA replication from an RNA template; contains an exonuclease-endonuclease phosphatase (EEP) domain and may be a fragment of a retrovirus-related Pol polyprotein;

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 1446-1573 6.53e-46

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: 161.62  E-value: 6.53e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1446 AVYTDGSDIHGKVGAAALAPS--IHTQELAYLGkeTSTTVYAAELLGIHMGLNLILASGR--RRAAIFTDNQAALKALQN 1521
Cdd:cd09276     1 VIYTDGSKLEGSVGAGFVIYRggEVISRSYRLG--THASVFDAELEAILEALELALATARraRKVTIFTDSQSALQALRN 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 150406858 1522 PRRSSGQSILRRIMDTLERVNSQGLQVEFYWIPAHQGIEGNELADKLAKEAT 1573
Cdd:cd09276    79 PRRSSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVGIEGNEAADRLAKEAA 130
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 971-1233 8.98e-44

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.


:

Pssm-ID: 238827 [Multi-domain]  Cd Length: 220  Bit Score: 158.99  E-value: 8.98e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  971 AKTVVLPKPNKKdlSEVKSYRPIALLNTLGKALESILATRISQAVEEHQLlpRTHVGGRKGMSTEHALHGLMELIYQSWD 1050
Cdd:cd01650     2 ARIILIPKKGKP--SDPKNYRPISLLSVLYKLLEKILANRLRPVLEENIL--PNQFGFRPGRSTTDAILLLREVIEKAKE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1051 NDQVASLLLLDVTGAFDHVSHPRLLHNLrkrrmdekivgwvasflqsrtttiqlreytteplhvetGIPQGSPISPVLYL 1130
Cdd:cd01650    78 KKKSLVLVFLDFEKAFDSVDHEFLLKAL--------------------------------------GVRQGDPLSPLLFN 119

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1131 FYNADILEDAPLRVTGAAAGGWI------DDIYFFTSScttdeNCRKLARMHGRAEAWSATHGSKFDLKKYQFIHLTRNP 1204
Cdd:cd01650   120 LALDDLLRLLNKEEEIKLGGPGIthlayaDDIVLFSEG-----KSRKLQELLQRLQEWSKESGLKINPSKSKVMLIGNKK 194

                         250       260
                  ....*....|....*....|....*....
gi 150406858 1205 RRHDVqraLTISDLTIAPTKEVRYLGVML 1233
Cdd:cd01650   195 KRLKD---ITLNGTPIEAVETFKYLGVTI 220
Exo_endo_phos_2 pfam14529
Endonuclease-reverse transcriptase; This domain represents the endonuclease region of ...
 584-704 8.80e-27

Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.


:

Pssm-ID: 434019 [Multi-domain]  Cd Length: 118  Bit Score: 106.68  E-value: 8.80e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858   584 IHIHNLYNPETSTGNSTIPLLRRTITEANSEKQIVVGDFNLHHPLWGGTgSDRDAEAEELVTLMADQQLELLIPQGTV-T 662
Cdd:pfam14529    1 ILIISVYCPPSDQLRNLLDTLEDILRSLDRPPIIIGGDFNAHHPLWGSN-STDVSRGEELIEFLNEHGLNLLNLPKSGpT 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 150406858   663 YDEHNRQTTIDLALGTPWIHERKAycgLREDLDHQSDHQPIA 704
Cdd:pfam14529   80 FISSNGDSTIDLTLTSDPLAVRVL---SDLGPDSGSDHRPIA 118
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 294-344 3.16e-03

universal minicircle sequence binding protein (UMSBP); Provisional


The actual alignment was detected with superfamily member PTZ00368:

Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.79  E-value: 3.16e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 150406858  294 CYKCQKYGHIGTQC------NANETCGYCAEP-HNTRDCRKKEEDPNSTPKCALCKGP 344
Cdd:PTZ00368   55 CYNCGKTGHLSRECpeappgSGPRSCYNCGQTgHISRECPNRAKGGAARRACYNCGGE 112
 
Name Accession Description Interval E-value
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 1446-1573 6.53e-46

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: 161.62  E-value: 6.53e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1446 AVYTDGSDIHGKVGAAALAPS--IHTQELAYLGkeTSTTVYAAELLGIHMGLNLILASGR--RRAAIFTDNQAALKALQN 1521
Cdd:cd09276     1 VIYTDGSKLEGSVGAGFVIYRggEVISRSYRLG--THASVFDAELEAILEALELALATARraRKVTIFTDSQSALQALRN 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 150406858 1522 PRRSSGQSILRRIMDTLERVNSQGLQVEFYWIPAHQGIEGNELADKLAKEAT 1573
Cdd:cd09276    79 PRRSSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVGIEGNEAADRLAKEAA 130
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 971-1233 8.98e-44

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.


Pssm-ID: 238827 [Multi-domain]  Cd Length: 220  Bit Score: 158.99  E-value: 8.98e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  971 AKTVVLPKPNKKdlSEVKSYRPIALLNTLGKALESILATRISQAVEEHQLlpRTHVGGRKGMSTEHALHGLMELIYQSWD 1050
Cdd:cd01650     2 ARIILIPKKGKP--SDPKNYRPISLLSVLYKLLEKILANRLRPVLEENIL--PNQFGFRPGRSTTDAILLLREVIEKAKE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1051 NDQVASLLLLDVTGAFDHVSHPRLLHNLrkrrmdekivgwvasflqsrtttiqlreytteplhvetGIPQGSPISPVLYL 1130
Cdd:cd01650    78 KKKSLVLVFLDFEKAFDSVDHEFLLKAL--------------------------------------GVRQGDPLSPLLFN 119

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1131 FYNADILEDAPLRVTGAAAGGWI------DDIYFFTSScttdeNCRKLARMHGRAEAWSATHGSKFDLKKYQFIHLTRNP 1204
Cdd:cd01650   120 LALDDLLRLLNKEEEIKLGGPGIthlayaDDIVLFSEG-----KSRKLQELLQRLQEWSKESGLKINPSKSKVMLIGNKK 194

                         250       260
                  ....*....|....*....|....*....
gi 150406858 1205 RRHDVqraLTISDLTIAPTKEVRYLGVML 1233
Cdd:cd01650   195 KRLKD---ITLNGTPIEAVETFKYLGVTI 220
Exo_endo_phos_2 pfam14529
Endonuclease-reverse transcriptase; This domain represents the endonuclease region of ...
 584-704 8.80e-27

Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.


Pssm-ID: 434019 [Multi-domain]  Cd Length: 118  Bit Score: 106.68  E-value: 8.80e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858   584 IHIHNLYNPETSTGNSTIPLLRRTITEANSEKQIVVGDFNLHHPLWGGTgSDRDAEAEELVTLMADQQLELLIPQGTV-T 662
Cdd:pfam14529    1 ILIISVYCPPSDQLRNLLDTLEDILRSLDRPPIIIGGDFNAHHPLWGSN-STDVSRGEELIEFLNEHGLNLLNLPKSGpT 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 150406858   663 YDEHNRQTTIDLALGTPWIHERKAycgLREDLDHQSDHQPIA 704
Cdd:pfam14529   80 FISSNGDSTIDLTLTSDPLAVRVL---SDLGPDSGSDHRPIA 118
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 976-1233 4.30e-18

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: 83.89  E-value: 4.30e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858   976 LPKPNKKdlsevkSYRPIALLNTLGKALESILATRISQAVEEHQLLPRThvggRKGMstehalhglmeliyqsWDNDQVA 1055
Cdd:pfam00078    1 IPKKGKG------KYRPISLLSIDYKALNKIIVKRLKPENLDSPPQPGF----RPGL----------------AKLKKAK 54

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  1056 SLLLLDVTGAFDHVSHPRLLHNLRKRRMDEKIVGWVASFLQSRTTTiqlreytteplhveTGIPQGSPISPVLYLFYNAD 1135
Cdd:pfam00078   55 WFLKLDLKKAFDQVPLDELDRKLTAFTTPPININWNGELSGGRYEW--------------KGLPQGLVLSPALFQLFMNE 120

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  1136 ILEDAPLRvTGAAAGGWIDDIYFFTSS-CTTDENCRKLarmhgraEAWSATHGSKFDLKKYQFIHltrnprrhdvqralt 1214
Cdd:pfam00078  121 LLRPLRKR-AGLTLVRYADDILIFSKSeEEHQEALEEV-------LEWLKESGLKINPEKTQFFL--------------- 177

                          250
                   ....*....|....*....
gi 150406858  1215 isdltiaPTKEVRYLGVML 1233
Cdd:pfam00078  178 -------KSKEVKYLGVTL 189
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1447-1572 3.62e-14

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 71.03  E-value: 3.62e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1447 VYTDGSdIHGKVGAAALAPSI----HTQELAylGKETSTTVYAAELLGIHMGLNLILASGRRRAAIFTDNQAALKALQNP 1522
Cdd:COG0328     5 IYTDGA-CRGNPGPGGWGAVIryggEEKELS--GGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITGW 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 150406858 1523 RRSSGQSILRRIM--DTLERVN--SQGLQVEFYWIPAHQGIEGNELADKLAKEA 1572
Cdd:COG0328    82 IHGWKKNGWKPVKnpDLWQRLDelLARHKVTFEWVKGHAGHPGNERADALANKA 135
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 511-707 1.51e-13

Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197311 [Multi-domain]  Cd Length: 205  Bit Score: 71.17  E-value: 1.51e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  511 DVIAIQEPWRNNFTNTthyprpqsfdlVYLDDPGTRTCMFINRRIPRGRWTATTPSPDFCTVSIQCteapedtIHIHNLY 590
Cdd:cd09077    28 DIALIQEPYLVPVNNP-----------NWVTDESGRAAIVVSDRLPRKPIQRLSLGLGIVAARVGG-------ITVVSCY 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  591 NPETSTGNSTIPLLRRTITEA--NSEKQIVVGDFNLHHPLWGgtGSDRDAEAEELVTLMAdqQLELLI-PQGTV-TYDEH 666
Cdd:cd09077    90 APPSESLEEFEEYLENLVRIVrgLSRPVIIGGDFNAWSPAWG--SKRTDRRGRLLEDWIA--NLGLVLlNDGNSpTFVRP 165

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 150406858  667 NRQTTIDLALGTP-WIHERKAYCgLREDLdHQSDHQPIAVTI 707
Cdd:cd09077   166 RGTSIIDVTFCSPsLARRISNWR-VLEDE-TLSDHRYIRFTI 205
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
925-1130 2.02e-12

Retron-type reverse transcriptase [Mobilome: prophages, transposons];


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 71.26  E-value: 2.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  925 AAKKAPGQDGIPahiLQQLLPYLTPHLLQIYNASLDLQYCPahfRQAKTVVLPKPNKKdlsevksYRPiallntLG--KA 1002
Cdd:COG3344    40 ANKGAAGIDGVT---VEDFEEYLEENLYDLRERLRSGSYRP---QPVRRVEIPKPDGG-------VRP------LGipTV 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1003 LESILATRISQAVE---EHQLLPRTHvGGRKGMSTEHALHGLMELIYqsWDNDQVASLlllDVTGAFDHVSHPRLLHNLR 1079
Cdd:COG3344   101 RDRVVQQAVKQVLEpifEPDFSDSSY-GFRPGRSAHDALKKAREYIN--EGYRWVVDA---DIKKFFDNVDHDLLMKRLR 174

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 150406858 1080 KRRMDEKIVGWVASFLQSrttTIQLREYTTEPlhvETGIPQGSPISPVL---YL 1130
Cdd:COG3344   175 RRIKDKRVLRLIRRWLKA---GVMEDGVVEER---EEGTPQGGPLSPLLaniYL 222
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1442-1572 6.27e-12

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: 64.71  E-value: 6.27e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  1442 DPPLAVYTDGSDIH--GKVGAAALAPSIHTQELAYLGKETSTTVyaAELLGIHMGLNlILASGRRrAAIFTDNQAALKAL 1519
Cdd:pfam00075    1 PKAVTVYTDGSCLGnpGPGGAGAVLYRGHENISAPLPGRTTNNR--AELQAVIEALK-ALKSPSK-VNIYTDSQYVIGGI 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150406858  1520 --------QNPRR--SSGQSILRRimDTLERVNS--QGLQVEFYWIPAHQGIEGNELADKLAKEA 1572
Cdd:pfam00075   77 tqwvhgwkKNGWPttSEGKPVKNK--DLWQLLKAlcKKHQVYWQWVKGHAGNPGNEMADRLAKQG 139
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 925-1130 7.84e-09

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]


Pssm-ID: 275209 [Multi-domain]  Cd Length: 354  Bit Score: 59.39  E-value: 7.84e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858   925 AAKKAPGQDGIpahILQQLLPYLTPHLLQIYNASLDLQYCPahfrQA-KTVVLPKPNKKdlsevksYRPI---------- 993
Cdd:TIGR04416   13 ANKGAAGVDGV---TIEDFEEYLEENLYKLWNRLKSGSYRP----QPvRRVEIPKPNGK-------QRPLgiptvrdrvv 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858   994 --ALLNtlgkALESILatrisqaveEHQLLPRTHvGGRKGMSTEHALHGLMELI--YQSWdndqvasLLLLDVTGAFDHV 1069
Cdd:TIGR04416   79 qqAVKQ----VLEPIF---------EPDFSENSY-GFRPGRSAHDAIAKARKRLnrGYRW-------VVDADIKGFFDNI 137

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 150406858  1070 SHPRLLHNLRKRRMDEKIVGWVASFLQSRTTTIQLREYTTEplhvetGIPQGSPISPVL---YL 1130
Cdd:TIGR04416  138 NHDLLMKAVARRISDKRVLRLIRRWLKAGVMEDGEVQETEE------GTPQGGVISPLLaniYL 195
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 294-344 3.16e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.79  E-value: 3.16e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 150406858  294 CYKCQKYGHIGTQC------NANETCGYCAEP-HNTRDCRKKEEDPNSTPKCALCKGP 344
Cdd:PTZ00368   55 CYNCGKTGHLSRECpeappgSGPRSCYNCGQTgHISRECPNRAKGGAARRACYNCGGE 112
rnhA PRK00203
ribonuclease H; Reviewed
 1543-1572 3.54e-03

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 39.81  E-value: 3.54e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 150406858 1543 SQGLQVEFYWIPAHQGIEGNELADKLAKEA 1572
Cdd:PRK00203  110 LKRHQIKWHWVKGHAGHPENERCDELARAG 139
 
Name Accession Description Interval E-value
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 1446-1573 6.53e-46

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: 161.62  E-value: 6.53e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1446 AVYTDGSDIHGKVGAAALAPS--IHTQELAYLGkeTSTTVYAAELLGIHMGLNLILASGR--RRAAIFTDNQAALKALQN 1521
Cdd:cd09276     1 VIYTDGSKLEGSVGAGFVIYRggEVISRSYRLG--THASVFDAELEAILEALELALATARraRKVTIFTDSQSALQALRN 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 150406858 1522 PRRSSGQSILRRIMDTLERVNSQGLQVEFYWIPAHQGIEGNELADKLAKEAT 1573
Cdd:cd09276    79 PRRSSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVGIEGNEAADRLAKEAA 130
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 971-1233 8.98e-44

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.


Pssm-ID: 238827 [Multi-domain]  Cd Length: 220  Bit Score: 158.99  E-value: 8.98e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  971 AKTVVLPKPNKKdlSEVKSYRPIALLNTLGKALESILATRISQAVEEHQLlpRTHVGGRKGMSTEHALHGLMELIYQSWD 1050
Cdd:cd01650     2 ARIILIPKKGKP--SDPKNYRPISLLSVLYKLLEKILANRLRPVLEENIL--PNQFGFRPGRSTTDAILLLREVIEKAKE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1051 NDQVASLLLLDVTGAFDHVSHPRLLHNLrkrrmdekivgwvasflqsrtttiqlreytteplhvetGIPQGSPISPVLYL 1130
Cdd:cd01650    78 KKKSLVLVFLDFEKAFDSVDHEFLLKAL--------------------------------------GVRQGDPLSPLLFN 119

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1131 FYNADILEDAPLRVTGAAAGGWI------DDIYFFTSScttdeNCRKLARMHGRAEAWSATHGSKFDLKKYQFIHLTRNP 1204
Cdd:cd01650   120 LALDDLLRLLNKEEEIKLGGPGIthlayaDDIVLFSEG-----KSRKLQELLQRLQEWSKESGLKINPSKSKVMLIGNKK 194

                         250       260
                  ....*....|....*....|....*....
gi 150406858 1205 RRHDVqraLTISDLTIAPTKEVRYLGVML 1233
Cdd:cd01650   195 KRLKD---ITLNGTPIEAVETFKYLGVTI 220
Exo_endo_phos_2 pfam14529
Endonuclease-reverse transcriptase; This domain represents the endonuclease region of ...
 584-704 8.80e-27

Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.


Pssm-ID: 434019 [Multi-domain]  Cd Length: 118  Bit Score: 106.68  E-value: 8.80e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858   584 IHIHNLYNPETSTGNSTIPLLRRTITEANSEKQIVVGDFNLHHPLWGGTgSDRDAEAEELVTLMADQQLELLIPQGTV-T 662
Cdd:pfam14529    1 ILIISVYCPPSDQLRNLLDTLEDILRSLDRPPIIIGGDFNAHHPLWGSN-STDVSRGEELIEFLNEHGLNLLNLPKSGpT 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 150406858   663 YDEHNRQTTIDLALGTPWIHERKAycgLREDLDHQSDHQPIA 704
Cdd:pfam14529   80 FISSNGDSTIDLTLTSDPLAVRVL---SDLGPDSGSDHRPIA 118
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 976-1233 4.30e-18

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: 83.89  E-value: 4.30e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858   976 LPKPNKKdlsevkSYRPIALLNTLGKALESILATRISQAVEEHQLLPRThvggRKGMstehalhglmeliyqsWDNDQVA 1055
Cdd:pfam00078    1 IPKKGKG------KYRPISLLSIDYKALNKIIVKRLKPENLDSPPQPGF----RPGL----------------AKLKKAK 54

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  1056 SLLLLDVTGAFDHVSHPRLLHNLRKRRMDEKIVGWVASFLQSRTTTiqlreytteplhveTGIPQGSPISPVLYLFYNAD 1135
Cdd:pfam00078   55 WFLKLDLKKAFDQVPLDELDRKLTAFTTPPININWNGELSGGRYEW--------------KGLPQGLVLSPALFQLFMNE 120

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  1136 ILEDAPLRvTGAAAGGWIDDIYFFTSS-CTTDENCRKLarmhgraEAWSATHGSKFDLKKYQFIHltrnprrhdvqralt 1214
Cdd:pfam00078  121 LLRPLRKR-AGLTLVRYADDILIFSKSeEEHQEALEEV-------LEWLKESGLKINPEKTQFFL--------------- 177

                          250
                   ....*....|....*....
gi 150406858  1215 isdltiaPTKEVRYLGVML 1233
Cdd:pfam00078  178 -------KSKEVKYLGVTL 189
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 1447-1573 8.50e-15

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: 73.37  E-value: 8.50e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1447 VYTDGSDIH-GKVGAAA-----------------LAPSIHTQElaylgketsttvyAAELLGIHMGLNLILASGRRRAAI 1508
Cdd:cd09280     2 VYTDGSCLNnGKPGARAgigvyfgpgdprnvsepLPGRKQTNN-------------RAELLAVIHALEQAPEEGIRKLEI 68

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 150406858 1509 FTDNQAALKAL---------QNPRRSSGQSILRR--IMDTLERVNSQGLQVEFYWIPAHQGIEGNELADKLAKEAT 1573
Cdd:cd09280    69 RTDSKYAINCItkwipkwkkNGWKTSKGKPVKNQdlIKELDKLLRKRGIKVKFEHVKGHSGDPGNEEADRLAREGA 144
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1447-1572 3.62e-14

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 71.03  E-value: 3.62e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1447 VYTDGSdIHGKVGAAALAPSI----HTQELAylGKETSTTVYAAELLGIHMGLNLILASGRRRAAIFTDNQAALKALQNP 1522
Cdd:COG0328     5 IYTDGA-CRGNPGPGGWGAVIryggEEKELS--GGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITGW 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 150406858 1523 RRSSGQSILRRIM--DTLERVN--SQGLQVEFYWIPAHQGIEGNELADKLAKEA 1572
Cdd:COG0328    82 IHGWKKNGWKPVKnpDLWQRLDelLARHKVTFEWVKGHAGHPGNERADALANKA 135
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 511-707 1.51e-13

Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197311 [Multi-domain]  Cd Length: 205  Bit Score: 71.17  E-value: 1.51e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  511 DVIAIQEPWRNNFTNTthyprpqsfdlVYLDDPGTRTCMFINRRIPRGRWTATTPSPDFCTVSIQCteapedtIHIHNLY 590
Cdd:cd09077    28 DIALIQEPYLVPVNNP-----------NWVTDESGRAAIVVSDRLPRKPIQRLSLGLGIVAARVGG-------ITVVSCY 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  591 NPETSTGNSTIPLLRRTITEA--NSEKQIVVGDFNLHHPLWGgtGSDRDAEAEELVTLMAdqQLELLI-PQGTV-TYDEH 666
Cdd:cd09077    90 APPSESLEEFEEYLENLVRIVrgLSRPVIIGGDFNAWSPAWG--SKRTDRRGRLLEDWIA--NLGLVLlNDGNSpTFVRP 165

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 150406858  667 NRQTTIDLALGTP-WIHERKAYCgLREDLdHQSDHQPIAVTI 707
Cdd:cd09077   166 RGTSIIDVTFCSPsLARRISNWR-VLEDE-TLSDHRYIRFTI 205
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
925-1130 2.02e-12

Retron-type reverse transcriptase [Mobilome: prophages, transposons];


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 71.26  E-value: 2.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  925 AAKKAPGQDGIPahiLQQLLPYLTPHLLQIYNASLDLQYCPahfRQAKTVVLPKPNKKdlsevksYRPiallntLG--KA 1002
Cdd:COG3344    40 ANKGAAGIDGVT---VEDFEEYLEENLYDLRERLRSGSYRP---QPVRRVEIPKPDGG-------VRP------LGipTV 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1003 LESILATRISQAVE---EHQLLPRTHvGGRKGMSTEHALHGLMELIYqsWDNDQVASLlllDVTGAFDHVSHPRLLHNLR 1079
Cdd:COG3344   101 RDRVVQQAVKQVLEpifEPDFSDSSY-GFRPGRSAHDALKKAREYIN--EGYRWVVDA---DIKKFFDNVDHDLLMKRLR 174

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 150406858 1080 KRRMDEKIVGWVASFLQSrttTIQLREYTTEPlhvETGIPQGSPISPVL---YL 1130
Cdd:COG3344   175 RRIKDKRVLRLIRRWLKA---GVMEDGVVEER---EEGTPQGGPLSPLLaniYL 222
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1442-1572 6.27e-12

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: 64.71  E-value: 6.27e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  1442 DPPLAVYTDGSDIH--GKVGAAALAPSIHTQELAYLGKETSTTVyaAELLGIHMGLNlILASGRRrAAIFTDNQAALKAL 1519
Cdd:pfam00075    1 PKAVTVYTDGSCLGnpGPGGAGAVLYRGHENISAPLPGRTTNNR--AELQAVIEALK-ALKSPSK-VNIYTDSQYVIGGI 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150406858  1520 --------QNPRR--SSGQSILRRimDTLERVNS--QGLQVEFYWIPAHQGIEGNELADKLAKEA 1572
Cdd:pfam00075   77 tqwvhgwkKNGWPttSEGKPVKNK--DLWQLLKAlcKKHQVYWQWVKGHAGNPGNEMADRLAKQG 139
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 1447-1572 1.65e-11

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


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 63.66  E-value: 1.65e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1447 VYTDGSdIHGKVG----AAALAPSIHTQELAylGKETSTTVYAAELLGIHMGLNLILASgrRRAAIFTDNQAALKALQ-- 1520
Cdd:cd09278     4 IYTDGA-CLGNPGpggwAAVIRYGDHEKELS--GGEPGTTNNRMELTAAIEALEALKEP--CPVTIYTDSQYVINGITkw 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150406858 1521 -------NPRRSSGQSILRRimDTLERVNS--QGLQVEFYWIPAHQGIEGNELADKLAKEA 1572
Cdd:cd09278    79 ikgwkknGWKTADGKPVKNR--DLWQELDAllAGHKVTWEWVKGHAGHPGNERADRLANKA 137
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 972-1132 8.00e-11

RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).


Pssm-ID: 238828 [Multi-domain]  Cd Length: 226  Bit Score: 63.76  E-value: 8.00e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  972 KTVVLPKPNKKDlsevksyRPIALLN----TLGKALESILatrisQAVEEHQLLPRTHvGGRKGMSTEHALHGLMELIYQ 1047
Cdd:cd01651     1 RRVYIPKPNGKK-------RPLGIPTvrdrIVQEALKLVL-----EPIYEPRFSDCSY-GFRPGRSAHDALKAIRRNVKG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1048 S--WdndqvasLLLLDVTGAFDHVSHPRLLHNLRKRRMDEKIVGWVASFLQSRTTTIQLREYTTEplhvetGIPQGSPIS 1125
Cdd:cd01651    68 GytW-------VIEGDIKGFFDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVLEDGKLVETEK------GTPQGGVIS 134

                         170
                  ....*....|
gi 150406858 1126 PVL---YLFY 1132
Cdd:cd01651   135 PLLaniYLHE 144
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1447-1570 2.61e-09

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: 56.55  E-value: 2.61e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1447 VYTDGSdIHGKVGAAALAPSIHTQELAYLG----KETSTTVYAAELLGIHMGLNLILASGRRRAAIFTDNQAALKALQNP 1522
Cdd:cd06222     1 INVDGS-CRGNPGPAGIGGVLRDHEGGWLGgfalKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSG 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 150406858 1523 --RRSSGQSILRRIMDTLervnSQGLQVEFYWIPAhqgiEGNELADKLAK 1570
Cdd:cd06222    80 sfKWSPNILLIEDILLLL----SRFWSVKISHVPR----EGNQVADALAK 121
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 925-1130 7.84e-09

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]


Pssm-ID: 275209 [Multi-domain]  Cd Length: 354  Bit Score: 59.39  E-value: 7.84e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858   925 AAKKAPGQDGIpahILQQLLPYLTPHLLQIYNASLDLQYCPahfrQA-KTVVLPKPNKKdlsevksYRPI---------- 993
Cdd:TIGR04416   13 ANKGAAGVDGV---TIEDFEEYLEENLYKLWNRLKSGSYRP----QPvRRVEIPKPNGK-------QRPLgiptvrdrvv 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858   994 --ALLNtlgkALESILatrisqaveEHQLLPRTHvGGRKGMSTEHALHGLMELI--YQSWdndqvasLLLLDVTGAFDHV 1069
Cdd:TIGR04416   79 qqAVKQ----VLEPIF---------EPDFSENSY-GFRPGRSAHDAIAKARKRLnrGYRW-------VVDADIKGFFDNI 137

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 150406858  1070 SHPRLLHNLRKRRMDEKIVGWVASFLQSRTTTIQLREYTTEplhvetGIPQGSPISPVL---YL 1130
Cdd:TIGR04416  138 NHDLLMKAVARRISDKRVLRLIRRWLKAGVMEDGEVQETEE------GTPQGGVISPLLaniYL 195
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 1447-1572 1.59e-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: 54.79  E-value: 1.59e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1447 VYTDGS--DIHGKVGAAAL--APSIHTQELA-YLGKETSTTVyaAELLGIHMGLNLILASGRRRAAIFTDNQAALKALQ- 1520
Cdd:cd09279     3 LYFDGAsrGNPGPAGAGVViySPGGEVLELSeRLGFPATNNE--AEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNg 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 150406858 1521 -----NPRrssgqsiLRRIMDTLERVNSQGLQVEFYWIPAHQgiegNELADKLAKEA 1572
Cdd:cd09279    81 eykvkNER-------LKPLLEKVLELLAKFELVELKWIPREQ----NKEADALANQA 126
RNase_HI_bacteria_like cd09277
Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H ...
 1543-1573 2.38e-07

Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; 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 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. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids.


Pssm-ID: 260009 [Multi-domain]  Cd Length: 133  Bit Score: 51.33  E-value: 2.38e-07
                          10        20        30
                  ....*....|....*....|....*....|.
gi 150406858 1543 SQGLQVEFYWIPAHQGIEGNELADKLAKEAT 1573
Cdd:cd09277   103 KKKIKIEFVKVKAHSGDKYNELADKLAKKAL 133
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 1531-1573 4.21e-05

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: 45.65  E-value: 4.21e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 150406858 1531 LRRIMDTLERVNSQGLQVEFYWIPAHQgiegNELADKLAKEAT 1573
Cdd:cd13934   114 FELLLDEIEDLEEGGVEVQFWHVPREL----NKEADRLAKAAA 152
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 1479-1572 4.79e-05

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 44.56  E-value: 4.79e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858  1479 TSTTVYAAELLGIHMGLNLILASGRRRAAIFTDNQAALKALQN--PRRSSGQSILRRIMDTLERVNSqglqVEFYWIPAh 1556
Cdd:pfam13456   36 PGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGrsPKQSKLANLLDEIRKLLKRFES----VSFEHIPR- 110

                           90
                   ....*....|....*.
gi 150406858  1557 qgiEGNELADKLAKEA 1572
Cdd:pfam13456  111 ---EQNRVADTLAKMA 123
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1447-1572 1.31e-03

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: 40.78  E-value: 1.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150406858 1447 VYTDGSDihGKVGAAAL-APSIHTQelAYLGKETSTTVyaAELLGIHMGLNLilASGRRrAAIFTDNQAALKALQN---- 1521
Cdd:cd09273     2 VFTDGSS--FKAGYAIVsGTEIVEA--QPLPPGTSAQR--AELIALIQALEL--AKGKP-VNIYTDSAYAVHALHLleti 72

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150406858 1522 -PRRSSGQSI--LRRIMDTLERVNsqgLQVEFY--WIPAHQG-----IEGNELADKLAKEA 1572
Cdd:cd09273    73 gIERGFLKSIknLSLFLQLLEAVQ---RPKPVAiiHIRAHSKlpgplAEGNAQADAAAKQA 130
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 294-344 3.16e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.79  E-value: 3.16e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 150406858  294 CYKCQKYGHIGTQC------NANETCGYCAEP-HNTRDCRKKEEDPNSTPKCALCKGP 344
Cdd:PTZ00368   55 CYNCGKTGHLSRECpeappgSGPRSCYNCGQTgHISRECPNRAKGGAARRACYNCGGE 112
rnhA PRK00203
ribonuclease H; Reviewed
 1543-1572 3.54e-03

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 39.81  E-value: 3.54e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 150406858 1543 SQGLQVEFYWIPAHQGIEGNELADKLAKEA 1572
Cdd:PRK00203  110 LKRHQIKWHWVKGHAGHPENERCDELARAG 139
 
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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