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Conserved domains on  [gi|612672004|gb|EZS88086|]
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ribonuclease HII [Staphylococcus aureus VET0159R]

Protein Classification

ribonuclease HII( domain architecture ID 10000679)

ribonuclease HII is a type 2 RNase H; RNase H endonucleolytically hydrolyzes RNA/DNA hybrids in DNA replication and repair

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RnhB COG0164
Ribonuclease HII [Replication, recombination and repair];
68-255 2.12e-99

Ribonuclease HII [Replication, recombination and repair];


:

Pssm-ID: 439934  Cd Length: 190  Bit Score: 287.73  E-value: 2.12e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  68 EHPNAIICGIDEVGRGPLAGPVVACATILNSNHNYLGLDDSKKVPVTKRLELNEALKNEVTAFAYGIATAEEIDEFNIYK 147
Cdd:COG0164    2 RRGFRLVAGVDEAGRGPLAGPVVAAAVILPPDFPIEGLNDSKKLSPKKREELYEEIKERALAWAVGEASPEEIDELNILQ 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 148 ATQIAMQRAIDGLSVQPTHLLIDAMTLDN-ALPQVSLIKGDARSVSIAAASIMAKVFRDDYMTQLSKNYPEYGFEKNAGY 226
Cdd:COG0164   82 ATLLAMRRAVEGLSVKPDLVLVDGNRLPGlPIPVEAIVKGDAKSASIAAASILAKVTRDRLMEELDEEYPGYGFAKHKGY 161
                        170       180
                 ....*....|....*....|....*....
gi 612672004 227 GTKQHLLAIDDIGIMKEHRKSFEPIKSLL 255
Cdd:COG0164  162 PTKEHREALREYGPTPIHRRSFAPVKKLL 190
 
Name Accession Description Interval E-value
RnhB COG0164
Ribonuclease HII [Replication, recombination and repair];
68-255 2.12e-99

Ribonuclease HII [Replication, recombination and repair];


Pssm-ID: 439934  Cd Length: 190  Bit Score: 287.73  E-value: 2.12e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  68 EHPNAIICGIDEVGRGPLAGPVVACATILNSNHNYLGLDDSKKVPVTKRLELNEALKNEVTAFAYGIATAEEIDEFNIYK 147
Cdd:COG0164    2 RRGFRLVAGVDEAGRGPLAGPVVAAAVILPPDFPIEGLNDSKKLSPKKREELYEEIKERALAWAVGEASPEEIDELNILQ 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 148 ATQIAMQRAIDGLSVQPTHLLIDAMTLDN-ALPQVSLIKGDARSVSIAAASIMAKVFRDDYMTQLSKNYPEYGFEKNAGY 226
Cdd:COG0164   82 ATLLAMRRAVEGLSVKPDLVLVDGNRLPGlPIPVEAIVKGDAKSASIAAASILAKVTRDRLMEELDEEYPGYGFAKHKGY 161
                        170       180
                 ....*....|....*....|....*....
gi 612672004 227 GTKQHLLAIDDIGIMKEHRKSFEPIKSLL 255
Cdd:COG0164  162 PTKEHREALREYGPTPIHRRSFAPVKKLL 190
RNase_HII_bacteria_HII_like cd07182
Bacterial Ribonuclease HII-like; This family includes mostly bacterial type 2 RNases H, with ...
75-250 4.79e-97

Bacterial Ribonuclease HII-like; This family includes mostly bacterial type 2 RNases H, with some eukaryotic members. Bacterial RNase HII has a role in primer removal based on its involvement in ribonucleotide-specific catalytic activity in the presence of RNA/DNA hybrid substrates. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII; double deletion of these leads to cellular lethality. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype. In Leishmania mitochondria, of the four distinct RNase H genes (H1, HIIA, HIIB, HIIC), HIIC is essential for the survival of the parasite and thus can be a potential target for anti-leishmanial chemotherapy. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair.


Pssm-ID: 260003  Cd Length: 177  Bit Score: 281.57  E-value: 4.79e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  75 CGIDEVGRGPLAGPVVACATILNSNHNYLGLDDSKKVPVTKRLELNEALKNEVTAFAYGIATAEEIDEFNIYKATQIAMQ 154
Cdd:cd07182    1 AGVDEAGRGPLAGPVVAAAVILPPDFPIEGLNDSKKLSEKKREELYEEIKENALAYGIGIASVEEIDELNILQATLLAMK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 155 RAIDGLSVQPTHLLIDAMTLDN-ALPQVSLIKGDARSVSIAAASIMAKVFRDDYMTQLSKNYPEYGFEKNAGYGTKQHLL 233
Cdd:cd07182   81 RAVEGLKVKPDYVLVDGNRLPPlPIPQEAIVKGDAKSASIAAASILAKVTRDRLMEELDKEYPEYGFAKHKGYGTKEHLE 160
                        170
                 ....*....|....*..
gi 612672004 234 AIDDIGIMKEHRKSFEP 250
Cdd:cd07182  161 ALKKYGPSPIHRKSFAP 177
rnhB PRK00015
ribonuclease HII; Validated
57-251 7.09e-94

ribonuclease HII; Validated


Pssm-ID: 234574  Cd Length: 197  Bit Score: 274.34  E-value: 7.09e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  57 EMTYFENEILKEHPnAIICGIDEVGRGPLAGPVVACATILNSNHNYLGLDDSKKVPVTKRLELNEALKNEVTAFAYGIAT 136
Cdd:PRK00015   4 PMLSFERALLKQGL-GLIAGVDEAGRGPLAGPVVAAAVILDPDRPIEGLNDSKKLSEKKREELYEEIKEKALAYSVGIAS 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 137 AEEIDEFNIYKATQIAMQRAIDGLsVQPTHLLIDAMTLDN-ALPQVSLIKGDARSVSIAAASIMAKVFRDDYMTQLSKNY 215
Cdd:PRK00015  83 PEEIDELNILEATLLAMRRAVEGL-VKPDYVLVDGNRVPKlPIPQEAIVKGDAKSPSIAAASILAKVTRDRLMEELDKEY 161
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 612672004 216 PEYGFEKNAGYGTKQHLLAIDDIGIMKEHRKSFEPI 251
Cdd:PRK00015 162 PGYGFAKHKGYGTKEHLEALAKYGPTPIHRRSFAPV 197
RNase_HII pfam01351
Ribonuclease HII;
75-248 5.56e-37

Ribonuclease HII;


Pssm-ID: 396082  Cd Length: 199  Bit Score: 129.04  E-value: 5.56e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004   75 CGIDEVGRGPLAGPVVACATILN-SNHNYL---GLDDSKKVPVTKRLELNEALKNEVT---AFAYGI--ATAEEIDEFNI 145
Cdd:pfam01351   1 IGIDEAGRGPVFGPLVVAAVYVPpERLPELrklGVKDSKKLSDQKREELAPLIKKRIEtryLVAGNIkyMSENEINLNEI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  146 YKATQIAMQRAIDGLSVQPTHLLIDAMTLDNALPQ----------VSLIKGDARSVSIAAASIMAKVFRDDyMTQLSKNY 215
Cdd:pfam01351  81 KAALHLAMIRLLEKLGVKPDEILVDGFRPPGSLPKklrdifgikvTAEHKADGKYLAVAAASIIAKVERDE-MLELLKRF 159
                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 612672004  216 PEYGFEKNAGYGTKQHLLAIDDIGIMKE----HRKSF 248
Cdd:pfam01351 160 PGYGLDKGSGYGSDPHTRALLKLGGTPWlpdfHRLSF 196
TIGR00729 TIGR00729
ribonuclease H, mammalian HI/archaeal HII subfamily; This enzyme cleaves RNA from DNA-RNA ...
74-226 3.96e-20

ribonuclease H, mammalian HI/archaeal HII subfamily; This enzyme cleaves RNA from DNA-RNA hybrids. Archaeal members of this subfamily of RNase H are designated RNase HII and one has been shown to be active as a monomer. A member from Homo sapiens was characterized as RNase HI, large subunit. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129812  Cd Length: 206  Bit Score: 85.21  E-value: 3.96e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004   74 ICGIDEVGRGPLAGPVVACA--------TILNSnhnyLGLDDSKKVPVTKRLELNEALKNEVTAFAYGIATAEEIDEFNI 145
Cdd:TIGR00729   1 VAGIDEAGRGPVIGPLVVGVfaieekreEELRK----LGVKDSKKLTPGRREELFSKIRNKLGRYEVLKITPEEIDRERN 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  146 YKATQIAMQ---RAIDGLSVQPTHLLIDAMTLDNAL-----------PQVSLI---KGDARSVSIAAASIMAKVFRDDYM 208
Cdd:TIGR00729  77 INLNENEIEkfsKAAIILIEKPSEVYVDSVDVNPKRfkreikikeriEGIKVIaehKADAKYPVVSAASIIAKVERDREI 156
                         170
                  ....*....|....*...
gi 612672004  209 TQLSKNYPEYGfeknAGY 226
Cdd:TIGR00729 157 ESLKRKYGDFG----SGY 170
 
Name Accession Description Interval E-value
RnhB COG0164
Ribonuclease HII [Replication, recombination and repair];
68-255 2.12e-99

Ribonuclease HII [Replication, recombination and repair];


Pssm-ID: 439934  Cd Length: 190  Bit Score: 287.73  E-value: 2.12e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  68 EHPNAIICGIDEVGRGPLAGPVVACATILNSNHNYLGLDDSKKVPVTKRLELNEALKNEVTAFAYGIATAEEIDEFNIYK 147
Cdd:COG0164    2 RRGFRLVAGVDEAGRGPLAGPVVAAAVILPPDFPIEGLNDSKKLSPKKREELYEEIKERALAWAVGEASPEEIDELNILQ 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 148 ATQIAMQRAIDGLSVQPTHLLIDAMTLDN-ALPQVSLIKGDARSVSIAAASIMAKVFRDDYMTQLSKNYPEYGFEKNAGY 226
Cdd:COG0164   82 ATLLAMRRAVEGLSVKPDLVLVDGNRLPGlPIPVEAIVKGDAKSASIAAASILAKVTRDRLMEELDEEYPGYGFAKHKGY 161
                        170       180
                 ....*....|....*....|....*....
gi 612672004 227 GTKQHLLAIDDIGIMKEHRKSFEPIKSLL 255
Cdd:COG0164  162 PTKEHREALREYGPTPIHRRSFAPVKKLL 190
RNase_HII_bacteria_HII_like cd07182
Bacterial Ribonuclease HII-like; This family includes mostly bacterial type 2 RNases H, with ...
75-250 4.79e-97

Bacterial Ribonuclease HII-like; This family includes mostly bacterial type 2 RNases H, with some eukaryotic members. Bacterial RNase HII has a role in primer removal based on its involvement in ribonucleotide-specific catalytic activity in the presence of RNA/DNA hybrid substrates. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII; double deletion of these leads to cellular lethality. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype. In Leishmania mitochondria, of the four distinct RNase H genes (H1, HIIA, HIIB, HIIC), HIIC is essential for the survival of the parasite and thus can be a potential target for anti-leishmanial chemotherapy. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair.


Pssm-ID: 260003  Cd Length: 177  Bit Score: 281.57  E-value: 4.79e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  75 CGIDEVGRGPLAGPVVACATILNSNHNYLGLDDSKKVPVTKRLELNEALKNEVTAFAYGIATAEEIDEFNIYKATQIAMQ 154
Cdd:cd07182    1 AGVDEAGRGPLAGPVVAAAVILPPDFPIEGLNDSKKLSEKKREELYEEIKENALAYGIGIASVEEIDELNILQATLLAMK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 155 RAIDGLSVQPTHLLIDAMTLDN-ALPQVSLIKGDARSVSIAAASIMAKVFRDDYMTQLSKNYPEYGFEKNAGYGTKQHLL 233
Cdd:cd07182   81 RAVEGLKVKPDYVLVDGNRLPPlPIPQEAIVKGDAKSASIAAASILAKVTRDRLMEELDKEYPEYGFAKHKGYGTKEHLE 160
                        170
                 ....*....|....*..
gi 612672004 234 AIDDIGIMKEHRKSFEP 250
Cdd:cd07182  161 ALKKYGPSPIHRKSFAP 177
rnhB PRK00015
ribonuclease HII; Validated
57-251 7.09e-94

ribonuclease HII; Validated


Pssm-ID: 234574  Cd Length: 197  Bit Score: 274.34  E-value: 7.09e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  57 EMTYFENEILKEHPnAIICGIDEVGRGPLAGPVVACATILNSNHNYLGLDDSKKVPVTKRLELNEALKNEVTAFAYGIAT 136
Cdd:PRK00015   4 PMLSFERALLKQGL-GLIAGVDEAGRGPLAGPVVAAAVILDPDRPIEGLNDSKKLSEKKREELYEEIKEKALAYSVGIAS 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 137 AEEIDEFNIYKATQIAMQRAIDGLsVQPTHLLIDAMTLDN-ALPQVSLIKGDARSVSIAAASIMAKVFRDDYMTQLSKNY 215
Cdd:PRK00015  83 PEEIDELNILEATLLAMRRAVEGL-VKPDYVLVDGNRVPKlPIPQEAIVKGDAKSPSIAAASILAKVTRDRLMEELDKEY 161
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 612672004 216 PEYGFEKNAGYGTKQHLLAIDDIGIMKEHRKSFEPI 251
Cdd:PRK00015 162 PGYGFAKHKGYGTKEHLEALAKYGPTPIHRRSFAPV 197
rnhB PRK13925
ribonuclease HII; Provisional
74-250 9.33e-62

ribonuclease HII; Provisional


Pssm-ID: 184399  Cd Length: 198  Bit Score: 192.53  E-value: 9.33e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  74 ICGIDEVGRGPLAGPVVACATILnSNHNY-----LGLDDSKKVPVTKRLELNEALKNEVTAFAYGIATAEEIDEFNIYKA 148
Cdd:PRK13925  10 IAGVDEVGRGALFGPVFAAAVIL-SEKAEpqllqAGLTDSKKLSPKRRAQLVPLILTLASDWGIGQASAREIDRLGIRQA 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 149 TQIAMQRAIDGLSVQPTHLLIDAMTL--DNALPQVSLIKGDARSVSIAAASIMAKVFRDDYMTQLSKNYPEYGFEKNAGY 226
Cdd:PRK13925  89 TELAMLRALKKLKSPPSLCLVDGNLPlrLWPGPQRTIVKGDSKSAAIAAASILAKVWRDDLIKRLAKKYPGYGLEKNKGY 168
                        170       180
                 ....*....|....*....|....
gi 612672004 227 GTKQHLLAIDDIGIMKEHRKSFEP 250
Cdd:PRK13925 169 GTAQHRQALLKLGPTPLHRKSFLP 192
PRK13926 PRK13926
ribonuclease HII; Provisional
74-255 9.68e-50

ribonuclease HII; Provisional


Pssm-ID: 184400  Cd Length: 207  Bit Score: 162.34  E-value: 9.68e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  74 ICGIDEVGRGPLAGPVVACATIL-NSNHNYlglDDSKKVPVTKRLELNEALKNEVTAFAYGIATAEEIDEFNIYKATQIA 152
Cdd:PRK13926  24 VAGVDEAGRGAWAGPVVVAAVILpPGEYPF---RDSKTLSPAAREALAEEVRRVALAWAVGHAEAAEIDRLNVLKATHLA 100
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 153 MQRAIDGLSVQPTHLLIDAMTLDNALPQVSLIKGDARSVSIAAASIMAKVFRDDYMTQLSKNYPEYGFEKNAGYGTKQHL 232
Cdd:PRK13926 101 AARALARLAVAPEALVTDYLRLPTPLPLLAPPKADALSPTVAAASLLAKTERDRLMRELDARYPGYGFARHKGYGTPAHR 180
                        170       180
                 ....*....|....*....|...
gi 612672004 233 LAIDDIGIMKEHRKSFEPIKSLL 255
Cdd:PRK13926 181 EALAALGPSPVHRRSFAPVRRLL 203
RNase_HII pfam01351
Ribonuclease HII;
75-248 5.56e-37

Ribonuclease HII;


Pssm-ID: 396082  Cd Length: 199  Bit Score: 129.04  E-value: 5.56e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004   75 CGIDEVGRGPLAGPVVACATILN-SNHNYL---GLDDSKKVPVTKRLELNEALKNEVT---AFAYGI--ATAEEIDEFNI 145
Cdd:pfam01351   1 IGIDEAGRGPVFGPLVVAAVYVPpERLPELrklGVKDSKKLSDQKREELAPLIKKRIEtryLVAGNIkyMSENEINLNEI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  146 YKATQIAMQRAIDGLSVQPTHLLIDAMTLDNALPQ----------VSLIKGDARSVSIAAASIMAKVFRDDyMTQLSKNY 215
Cdd:pfam01351  81 KAALHLAMIRLLEKLGVKPDEILVDGFRPPGSLPKklrdifgikvTAEHKADGKYLAVAAASIIAKVERDE-MLELLKRF 159
                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 612672004  216 PEYGFEKNAGYGTKQHLLAIDDIGIMKE----HRKSF 248
Cdd:pfam01351 160 PGYGLDKGSGYGSDPHTRALLKLGGTPWlpdfHRLSF 196
rnhB PRK14550
ribonuclease HII; Provisional
73-248 2.27e-29

ribonuclease HII; Provisional


Pssm-ID: 173015  Cd Length: 204  Bit Score: 109.65  E-value: 2.27e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  73 IICGIDEVGRGPLAGPV----VACATILNSNHNYLGLDDSKKVPVTKRLELNEALKN--EVTAFAYGiATAEEIDEFNIY 146
Cdd:PRK14550   1 MTLGIDEAGRGCLAGSLfvagVACNEKTALEFLKMGLKDSKKLSPKKRFFLEDKIKThgEVGFFVVK-KSANEIDSLGLG 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 147 KATQIAMQRAIDGLSVQPTHLLIDAMT---LDNALPQV-SLIKGDARSVSIAAASIMAKVFRDDYMTQLSKNYPEYGFEK 222
Cdd:PRK14550  80 ACLKLAIQEILENGCSLANEIKIDGNTafgLNKRYPNIqTIIKGDETIAQIAMASVLAKAFKDREMLELHALFKEYGWDK 159
                        170       180
                 ....*....|....*....|....*.
gi 612672004 223 NAGYGTKQHLLAIDDIGIMKEHRKSF 248
Cdd:PRK14550 160 NCGYGTKQHIEAIIKLGATPFHRHSF 185
RNase_HII cd06266
Ribonuclease H (RNase H) type II family (prokaryotic RNase HII and HIII, and eukaryotic RNase ...
76-250 4.15e-27

Ribonuclease H (RNase H) type II family (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII); This family contains ribonucleases HII (RNases H2) which include bacterial RNase HII and HIII, and eukaryotic and archaeal RNase H2/HII. RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thereby preventing genomic instability and the accumulation of aberrant nucleic acid which can induce Aicardi-Goutieres syndrome, a severe autoimmune disorder in humans. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, but no prokaryotic genome contains the combination of only RNase HI and HIII. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli.


Pssm-ID: 259999  Cd Length: 193  Bit Score: 103.44  E-value: 4.15e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  76 GIDEVGRGPLAGPVVACATILNSNHNY--LGLDDSKKVPVTKRLELNEALKnEVTAFAYGIATAEEIDE----FNIYKAT 149
Cdd:cd06266    2 GVDEAGRGCVAGPVVVAAVYCEKEDRLraLGVKDSKQLSPAKRERLADEIM-EKVAVAVGVLSPEEIDLymaaKNINNAT 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 150 QIAMQRAIDGLSVQPTHLLIDAMTLDNA-----------LPQVSLIKGDARSVSIAAASIMAKVFRDDYMTQLSKNYPEY 218
Cdd:cd06266   81 KLAYNRALENLSVKPEFVLVDGKGIEPEylsreleeilgVRVTCLVKADSKSPLVAAASIIAKVFRDREMEELHRKYGLF 160
                        170       180       190
                 ....*....|....*....|....*....|...
gi 612672004 219 GFEKNAGYGTKQHLLA-IDDIGIMKEHRKSFEP 250
Cdd:cd06266  161 GSGYYADPETLEELRKnIVLGRIPPCVRLSFET 193
RNase_HII_archaea_like cd07180
Archaeal Ribonuclease HII; This family includes type 2 RNases H from archaea, some of which ...
75-219 2.12e-24

Archaeal Ribonuclease HII; This family includes type 2 RNases H from archaea, some of which show broad divalent cation specificity. It is proposed that three of the four acidic residues at the active site are involved in metal binding and the fourth one is involved in the catalytic process in archaea. Most archaeal genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair.


Pssm-ID: 260001  Cd Length: 204  Bit Score: 96.46  E-value: 2.12e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  75 CGIDEVGRGPLAGP-VVACATILNSNHNYL---GLDDSKKVPVTKRLELNEALKNEVTAFAYGIATAEEIDE----FNIY 146
Cdd:cd07180    1 IGIDEAGRGPVIGPmVVAGVAIDEEDLKRLkslGVKDSKKLSPKRREELYEEILKSAIDVVVVVVSPEEIDRrresMNLN 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 147 KATQIAMQRAIDGLSVQPTHLLIDA-------------MTLDNALPQVSLIKGDARSVSIAAASIMAKVFRDDYMTQLSK 213
Cdd:cd07180   81 ELEAEAFAEIINRLALQPDTVYVDAcdvneerfgrrlrERLNTGVEVVAEHKADAKYPVVSAASIVAKVERDREIEELKK 160

                 ....*.
gi 612672004 214 NYPEYG 219
Cdd:cd07180  161 EYGDFG 166
TIGR00729 TIGR00729
ribonuclease H, mammalian HI/archaeal HII subfamily; This enzyme cleaves RNA from DNA-RNA ...
74-226 3.96e-20

ribonuclease H, mammalian HI/archaeal HII subfamily; This enzyme cleaves RNA from DNA-RNA hybrids. Archaeal members of this subfamily of RNase H are designated RNase HII and one has been shown to be active as a monomer. A member from Homo sapiens was characterized as RNase HI, large subunit. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129812  Cd Length: 206  Bit Score: 85.21  E-value: 3.96e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004   74 ICGIDEVGRGPLAGPVVACA--------TILNSnhnyLGLDDSKKVPVTKRLELNEALKNEVTAFAYGIATAEEIDEFNI 145
Cdd:TIGR00729   1 VAGIDEAGRGPVIGPLVVGVfaieekreEELRK----LGVKDSKKLTPGRREELFSKIRNKLGRYEVLKITPEEIDRERN 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  146 YKATQIAMQ---RAIDGLSVQPTHLLIDAMTLDNAL-----------PQVSLI---KGDARSVSIAAASIMAKVFRDDYM 208
Cdd:TIGR00729  77 INLNENEIEkfsKAAIILIEKPSEVYVDSVDVNPKRfkreikikeriEGIKVIaehKADAKYPVVSAASIIAKVERDREI 156
                         170
                  ....*....|....*...
gi 612672004  209 TQLSKNYPEYGfeknAGY 226
Cdd:TIGR00729 157 ESLKRKYGDFG----SGY 170
RNase_HII_eukaryota_like cd07181
Eukaryotic RNase HII; This family includes eukaryotic type 2 RNase H (RNase HII or H2) which ...
76-255 7.33e-16

Eukaryotic RNase HII; This family includes eukaryotic type 2 RNase H (RNase HII or H2) which is active during replication and is believed to play a role in the removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII (RNASEH2A) is functional when it forms a heterotrimeric complex with two other accessory proteins (RNASEH2B and RNASEH2C). It is speculated that these accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause the severe genetic neurological disorder Aicardi-Goutieres syndrome. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms.


Pssm-ID: 260002  Cd Length: 221  Bit Score: 74.09  E-value: 7.33e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  76 GIDEVGRGPLAGPVV-ACATILNSNHN---YLGLDDSKKVPVTKRLELNEALKN--EVTAFAYGIATAEEIDE----FNI 145
Cdd:cd07181    2 GIDEAGRGPVLGPMVyGCAYCPLSYEEelkKLGFADSKTLTEEQREELFKKIKEdpDNVGWAVRVLSPEEISAkmlrRSK 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 146 YKATQIAM-------QRAIDgLSVQPTHLLIDA--------MTLDNALPQVSLI---KGDARSVSIAAASIMAKVFRDDY 207
Cdd:cd07181   82 YNLNEISHdaaigliRSVLD-KGVNVTEVYVDTvgppekyqAKLQKLFPGIKITvskKADSLYPIVSAASIVAKVTRDRA 160
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 612672004 208 MTQLskNYPEYGFEKNAGYG--------TKQHLLAIDD--IGIMKEHRKSFEPIKSLL 255
Cdd:cd07181  161 LENW--QFEEPGIDIDREFGsgypsdpkTKAWLKKNVDpvFGFPSLVRFSWSTAKTIL 216
RNase_HII_bacteria_HIII_like cd06590
Bacterial type 2 ribonuclease, HII and HIII-like; This family includes type 2 RNases H from ...
74-229 1.43e-09

Bacterial type 2 ribonuclease, HII and HIII-like; This family includes type 2 RNases H from several bacteria, such as Bacillus subtilis, which have two different RNases, HII and HIII. RNases HIII are distinguished by having a large (70-90 residues) N-terminal extension of unknown function. In addition, the active site of RNase HIII differs from that of other RNases H; replacing the fourth residue (aspartate) of the acidic "DEDD" motif with a glutamate. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes; however, no prokaryotic genomes contain the combination of both RNase HI and HIII. This mutual exclusive gene inheritance might be the result of functional redundancy of RNase HI and HIII in prokaryotes. Ribonuclease (RNase) H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair.


Pssm-ID: 260000  Cd Length: 207  Bit Score: 56.37  E-value: 1.43e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004  74 ICGIDEVGRGPLAGPVVACATILNSNH----NYLGLDDSKKVPVTKRLELNEALKNEVTafaYGIAT------AEEIDEF 143
Cdd:cd06590    1 HIGSDEVGKGDYFGPLVVAAVYVDKEDieflKELGVKDSKKLTDKKIIKLAPKIKEKIP---YSLLVldpekyNELYAKG 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612672004 144 ---NIYKAtqIAMQRAIDGL---SVQPTHLLIDAMT----LDNAL-----PQVSLI---KGDARSVSIAAASIMAKVFRD 205
Cdd:cd06590   78 knlNKLKA--WLHNQAIENLlkkKKKPKFILIDQFAsekvYYNYLkkekiKKIPLYfetKAESKDLAVAAASILARYAFL 155
                        170       180
                 ....*....|....*....|....
gi 612672004 206 DYMTQLSKnypEYGFEKNAGYGTK 229
Cdd:cd06590  156 EEMDKLSK---EYGMKLPKGASAK 176
 
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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