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Conserved domains on  [gi|145329613|ref|NP_001077956|]
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Polynucleotidyl transferase, ribonuclease H-like superfamily protein [Arabidopsis thaliana]

Protein Classification

ribonuclease H2 subunit A( domain architecture ID 10163194)

ribonuclease H2 subunit A is the catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_HII_eukaryota_like cd07181
Eukaryotic RNase HII; This family includes eukaryotic type 2 RNase H (RNase HII or H2) which ...
 17-215 2.79e-131

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: 370.70  E-value: 2.79e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  17 MGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEEKREELYESLK-LDKSLGWAVDVIDPRELSAKMLAK- 94
Cdd:cd07181    1 LGIDEAGRGPVLGPMVYGCAYCPLSYEEELKKLGFADSKTLTEEQREELFKKIKeDPDNVGWAVRVLSPEEISAKMLRRs 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  95 ------------------VLDMGVLLTEAYLDTVGDPDKYRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAKVTRDRA 156
Cdd:cd07181   81 kynlneishdaaiglirsVLDKGVNVTEVYVDTVGPPEKYQAKLQKLFPGIKITVSKKADSLYPIVSAASIVAKVTRDRA 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 145329613 157 LKEWLVEETGEDINRNFGSGYPGDPETKAWLVQHKHSVFGFPSLVRFSWGTCTTHLKGE 215
Cdd:cd07181  161 LENWQFEEPGIDIDREFGSGYPSDPKTKAWLKKNVDPVFGFPSLVRFSWSTAKTILEKK 219
 
Name Accession Description Interval E-value
RNase_HII_eukaryota_like cd07181
Eukaryotic RNase HII; This family includes eukaryotic type 2 RNase H (RNase HII or H2) which ...
 17-215 2.79e-131

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: 370.70  E-value: 2.79e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  17 MGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEEKREELYESLK-LDKSLGWAVDVIDPRELSAKMLAK- 94
Cdd:cd07181    1 LGIDEAGRGPVLGPMVYGCAYCPLSYEEELKKLGFADSKTLTEEQREELFKKIKeDPDNVGWAVRVLSPEEISAKMLRRs 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  95 ------------------VLDMGVLLTEAYLDTVGDPDKYRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAKVTRDRA 156
Cdd:cd07181   81 kynlneishdaaiglirsVLDKGVNVTEVYVDTVGPPEKYQAKLQKLFPGIKITVSKKADSLYPIVSAASIVAKVTRDRA 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 145329613 157 LKEWLVEETGEDINRNFGSGYPGDPETKAWLVQHKHSVFGFPSLVRFSWGTCTTHLKGE 215
Cdd:cd07181  161 LENWQFEEPGIDIDREFGSGYPSDPKTKAWLKKNVDPVFGFPSLVRFSWSTAKTILEKK 219
TIGR00729 TIGR00729
ribonuclease H, mammalian HI/archaeal HII subfamily; This enzyme cleaves RNA from DNA-RNA ...
 17-210 1.24e-52

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: 170.34  E-value: 1.24e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613   17 MGIDEAGRGPVLGPMVYgCMYCPISYQSS-LASLHFADSKTLKEEKREELYESLKlDKSLGWAVDVIDPRELSA------ 89
Cdd:TIGR00729   2 AGIDEAGRGPVIGPLVV-GVFAIEEKREEeLRKLGVKDSKKLTPGRREELFSKIR-NKLGRYEVLKITPEEIDRerninl 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613   90 ------KMLAKVLDMGVLLTEAYLDTVGDPDK---YRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAKVTRDRALkEW 160
Cdd:TIGR00729  80 neneieKFSKAAIILIEKPSEVYVDSVDVNPKrfkREIKIKERIEGIKVIAEHKADAKYPVVSAASIIAKVERDREI-ES 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 145329613  161 LVEETGEdinrnFGSGYPGDPETKAWLVQHKHSVFGFPSLVRFSWGTCTT 210
Cdd:TIGR00729 159 LKRKYGD-----FGSGYPSDPRTREWLEEYFKSHGELPDIVRRTWKTVRK 203
RNase_HII pfam01351
Ribonuclease HII;
17-208 8.99e-46

Ribonuclease HII;


Pssm-ID: 396082  Cd Length: 199  Bit Score: 152.54  E-value: 8.99e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613   17 MGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEEKREELYESLK-----LDKSLGWAVDVIDPR------ 85
Cdd:pfam01351   1 IGIDEAGRGPVFGPLVVAAVYVPPERLPELRKLGVKDSKKLSDQKREELAPLIKkrietRYLVAGNIKYMSENEinlnei 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613   86 --ELSAKMLAKVLDMGVLLTEAYLDTVGDPDKYRIKLSERFPsIKFVVSKKADSLFPIVSGASIVAKVTRDRALkEWLVE 163
Cdd:pfam01351  81 kaALHLAMIRLLEKLGVKPDEILVDGFRPPGSLPKKLRDIFG-IKVTAEHKADGKYLAVAAASIIAKVERDEML-ELLKR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 145329613  164 ETGEDInrNFGSGYPGDPETKAWLVQHKHSvfGFPSLVRFSWGTC 208
Cdd:pfam01351 159 FPGYGL--DKGSGYGSDPHTRALLKLGGTP--WLPDFHRLSFKTV 199
rnhB PRK00015
ribonuclease HII; Validated
 18-208 1.28e-34

ribonuclease HII; Validated


Pssm-ID: 234574  Cd Length: 197  Bit Score: 123.73  E-value: 1.28e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  18 GIDEAGRGPVLGPMVYGCMYCPISYqsSLASLhfADSKTLKEEKREELYESLKlDKSLGWAVDVIDPRE------LSAKM 91
Cdd:PRK00015  22 GVDEAGRGPLAGPVVAAAVILDPDR--PIEGL--NDSKKLSEKKREELYEEIK-EKALAYSVGIASPEEidelniLEATL 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  92 LA--KVLDmgVLLTEAYLDTvgdpDKYRIKlSERFPSiKFVVskKADSLFPIVSGASIVAKVTRDRALKEwLVEETGEdI 169
Cdd:PRK00015  97 LAmrRAVE--GLVKPDYVLV----DGNRVP-KLPIPQ-EAIV--KGDAKSPSIAAASILAKVTRDRLMEE-LDKEYPG-Y 164

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 145329613 170 NRNFGSGYPGDPETKAWLvqhKHsvfGFPSLVRFSWGTC 208
Cdd:PRK00015 165 GFAKHKGYGTKEHLEALA---KY---GPTPIHRRSFAPV 197
RnhB COG0164
Ribonuclease HII [Replication, recombination and repair];
18-212 1.20e-33

Ribonuclease HII [Replication, recombination and repair];


Pssm-ID: 439934  Cd Length: 190  Bit Score: 120.94  E-value: 1.20e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  18 GIDEAGRGPVLGPMVYGCMYCPISYqsslASLHFADSKTLKEEKREELYESLKlDKSLGWAVDVIDPRE------LSAKM 91
Cdd:COG0164   10 GVDEAGRGPLAGPVVAAAVILPPDF----PIEGLNDSKKLSPKKREELYEEIK-ERALAWAVGEASPEEidelniLQATL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  92 LAkvldMgvllTEAYLDTVGDPDKYRI---KLSERFPSIKFVVskKADSLFPIVSGASIVAKVTRDRALKEWLVE--ETG 166
Cdd:COG0164   85 LA----M----RRAVEGLSVKPDLVLVdgnRLPGLPIPVEAIV--KGDAKSASIAAASILAKVTRDRLMEELDEEypGYG 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 145329613 167 EDINrnfgSGYPGDpETKAWLVQHkhsvfGFPSLVRFSWGTCTTHL 212
Cdd:COG0164  155 FAKH----KGYPTK-EHREALREY-----GPTPIHRRSFAPVKKLL 190
 
Name Accession Description Interval E-value
RNase_HII_eukaryota_like cd07181
Eukaryotic RNase HII; This family includes eukaryotic type 2 RNase H (RNase HII or H2) which ...
 17-215 2.79e-131

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: 370.70  E-value: 2.79e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  17 MGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEEKREELYESLK-LDKSLGWAVDVIDPRELSAKMLAK- 94
Cdd:cd07181    1 LGIDEAGRGPVLGPMVYGCAYCPLSYEEELKKLGFADSKTLTEEQREELFKKIKeDPDNVGWAVRVLSPEEISAKMLRRs 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  95 ------------------VLDMGVLLTEAYLDTVGDPDKYRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAKVTRDRA 156
Cdd:cd07181   81 kynlneishdaaiglirsVLDKGVNVTEVYVDTVGPPEKYQAKLQKLFPGIKITVSKKADSLYPIVSAASIVAKVTRDRA 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 145329613 157 LKEWLVEETGEDINRNFGSGYPGDPETKAWLVQHKHSVFGFPSLVRFSWGTCTTHLKGE 215
Cdd:cd07181  161 LENWQFEEPGIDIDREFGSGYPSDPKTKAWLKKNVDPVFGFPSLVRFSWSTAKTILEKK 219
TIGR00729 TIGR00729
ribonuclease H, mammalian HI/archaeal HII subfamily; This enzyme cleaves RNA from DNA-RNA ...
 17-210 1.24e-52

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: 170.34  E-value: 1.24e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613   17 MGIDEAGRGPVLGPMVYgCMYCPISYQSS-LASLHFADSKTLKEEKREELYESLKlDKSLGWAVDVIDPRELSA------ 89
Cdd:TIGR00729   2 AGIDEAGRGPVIGPLVV-GVFAIEEKREEeLRKLGVKDSKKLTPGRREELFSKIR-NKLGRYEVLKITPEEIDRerninl 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613   90 ------KMLAKVLDMGVLLTEAYLDTVGDPDK---YRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAKVTRDRALkEW 160
Cdd:TIGR00729  80 neneieKFSKAAIILIEKPSEVYVDSVDVNPKrfkREIKIKERIEGIKVIAEHKADAKYPVVSAASIIAKVERDREI-ES 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 145329613  161 LVEETGEdinrnFGSGYPGDPETKAWLVQHKHSVFGFPSLVRFSWGTCTT 210
Cdd:TIGR00729 159 LKRKYGD-----FGSGYPSDPRTREWLEEYFKSHGELPDIVRRTWKTVRK 203
RNase_HII_archaea_like cd07180
Archaeal Ribonuclease HII; This family includes type 2 RNases H from archaea, some of which ...
 17-208 8.40e-52

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: 168.11  E-value: 8.40e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  17 MGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEEKREELYESLKlDKSLGWAVDVIDPRELSAKML---- 92
Cdd:cd07180    1 IGIDEAGRGPVIGPMVVAGVAIDEEDLKRLKSLGVKDSKKLSPKRREELYEEIL-KSAIDVVVVVVSPEEIDRRREsmnl 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  93 --------AKVLDMGVL-LTEAYLDTVG-DPDKYRIKLSERFPSIKFVVSK-KADSLFPIVSGASIVAKVTRDRALKEwL 161
Cdd:cd07180   80 neleaeafAEIINRLALqPDTVYVDACDvNEERFGRRLRERLNTGVEVVAEhKADAKYPVVSAASIVAKVERDREIEE-L 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 145329613 162 VEETGEdinrnFGSGYPGDPETKAWLVQHKHSVFGFPSLVRFSWGTC 208
Cdd:cd07180  159 KKEYGD-----FGSGYPSDPKTIEFLREYYREHGEPPPIVRKSWKTV 200
RNase_HII cd06266
Ribonuclease H (RNase H) type II family (prokaryotic RNase HII and HIII, and eukaryotic RNase ...
 18-207 7.73e-47

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: 155.05  E-value: 7.73e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  18 GIDEAGRGPVLGPMVYGCMYCPISYQssLASLHFADSKTLKEEKREELYEslKLDKSLGWAVDVIDPRELSAKMLAK--- 94
Cdd:cd06266    2 GVDEAGRGCVAGPVVVAAVYCEKEDR--LRALGVKDSKQLSPAKRERLAD--EIMEKVAVAVGVLSPEEIDLYMAAKnin 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  95 ----------VLDMGVLLTEAYLDTVGDPDKYRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAKVTRDRALKEWLVEE 164
Cdd:cd06266   78 natklaynraLENLSVKPEFVLVDGKGIEPEYLSRELEEILGVRVTCLVKADSKSPLVAAASIIAKVFRDREMEELHRKY 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 145329613 165 TgedinrNFGSGYPGDPETKAWLVQHKHSVFgFPSLVRFSWGT 207
Cdd:cd06266  158 G------LFGSGYYADPETLEELRKNIVLGR-IPPCVRLSFET 193
RNase_HII pfam01351
Ribonuclease HII;
17-208 8.99e-46

Ribonuclease HII;


Pssm-ID: 396082  Cd Length: 199  Bit Score: 152.54  E-value: 8.99e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613   17 MGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEEKREELYESLK-----LDKSLGWAVDVIDPR------ 85
Cdd:pfam01351   1 IGIDEAGRGPVFGPLVVAAVYVPPERLPELRKLGVKDSKKLSDQKREELAPLIKkrietRYLVAGNIKYMSENEinlnei 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613   86 --ELSAKMLAKVLDMGVLLTEAYLDTVGDPDKYRIKLSERFPsIKFVVSKKADSLFPIVSGASIVAKVTRDRALkEWLVE 163
Cdd:pfam01351  81 kaALHLAMIRLLEKLGVKPDEILVDGFRPPGSLPKKLRDIFG-IKVTAEHKADGKYLAVAAASIIAKVERDEML-ELLKR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 145329613  164 ETGEDInrNFGSGYPGDPETKAWLVQHKHSvfGFPSLVRFSWGTC 208
Cdd:pfam01351 159 FPGYGL--DKGSGYGSDPHTRALLKLGGTP--WLPDFHRLSFKTV 199
rnhB PRK00015
ribonuclease HII; Validated
 18-208 1.28e-34

ribonuclease HII; Validated


Pssm-ID: 234574  Cd Length: 197  Bit Score: 123.73  E-value: 1.28e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  18 GIDEAGRGPVLGPMVYGCMYCPISYqsSLASLhfADSKTLKEEKREELYESLKlDKSLGWAVDVIDPRE------LSAKM 91
Cdd:PRK00015  22 GVDEAGRGPLAGPVVAAAVILDPDR--PIEGL--NDSKKLSEKKREELYEEIK-EKALAYSVGIASPEEidelniLEATL 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  92 LA--KVLDmgVLLTEAYLDTvgdpDKYRIKlSERFPSiKFVVskKADSLFPIVSGASIVAKVTRDRALKEwLVEETGEdI 169
Cdd:PRK00015  97 LAmrRAVE--GLVKPDYVLV----DGNRVP-KLPIPQ-EAIV--KGDAKSPSIAAASILAKVTRDRLMEE-LDKEYPG-Y 164

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 145329613 170 NRNFGSGYPGDPETKAWLvqhKHsvfGFPSLVRFSWGTC 208
Cdd:PRK00015 165 GFAKHKGYGTKEHLEALA---KY---GPTPIHRRSFAPV 197
RnhB COG0164
Ribonuclease HII [Replication, recombination and repair];
18-212 1.20e-33

Ribonuclease HII [Replication, recombination and repair];


Pssm-ID: 439934  Cd Length: 190  Bit Score: 120.94  E-value: 1.20e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  18 GIDEAGRGPVLGPMVYGCMYCPISYqsslASLHFADSKTLKEEKREELYESLKlDKSLGWAVDVIDPRE------LSAKM 91
Cdd:COG0164   10 GVDEAGRGPLAGPVVAAAVILPPDF----PIEGLNDSKKLSPKKREELYEEIK-ERALAWAVGEASPEEidelniLQATL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  92 LAkvldMgvllTEAYLDTVGDPDKYRI---KLSERFPSIKFVVskKADSLFPIVSGASIVAKVTRDRALKEWLVE--ETG 166
Cdd:COG0164   85 LA----M----RRAVEGLSVKPDLVLVdgnRLPGLPIPVEAIV--KGDAKSASIAAASILAKVTRDRLMEELDEEypGYG 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 145329613 167 EDINrnfgSGYPGDpETKAWLVQHkhsvfGFPSLVRFSWGTCTTHL 212
Cdd:COG0164  155 FAKH----KGYPTK-EHREALREY-----GPTPIHRRSFAPVKKLL 190
RNase_HII_bacteria_HII_like cd07182
Bacterial Ribonuclease HII-like; This family includes mostly bacterial type 2 RNases H, with ...
 18-160 1.93e-24

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: 96.29  E-value: 1.93e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  18 GIDEAGRGPVLGPMVYGCMYCPISYQSSLaslhFADSKTLKEEKREELYESLKlDKSLGWAVDVIDPRE------LSAKM 91
Cdd:cd07182    2 GVDEAGRGPLAGPVVAAAVILPPDFPIEG----LNDSKKLSEKKREELYEEIK-ENALAYGIGIASVEEidelniLQATL 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 145329613  92 LAkvldmgvlLTEAYLDTVGDPDKYRI---KLSERFPSIKFVVskKADSLFPIVSGASIVAKVTRDRALKEW 160
Cdd:cd07182   77 LA--------MKRAVEGLKVKPDYVLVdgnRLPPLPIPQEAIV--KGDAKSASIAAASILAKVTRDRLMEEL 138
PRK13926 PRK13926
ribonuclease HII; Provisional
 1-159 2.64e-14

ribonuclease HII; Provisional


Pssm-ID: 184400  Cd Length: 207  Bit Score: 69.90  E-value: 2.64e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613   1 MESECLTPEWASQPC--------LMGIDEAGRGPVLGPMVYGCMYCP-ISYQsslaslhFADSKTLKEEKREELYESLKl 71
Cdd:PRK13926   1 MATPPLEPDWAYEREhwrrgylrVAGVDEAGRGAWAGPVVVAAVILPpGEYP-------FRDSKTLSPAAREALAEEVR- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  72 DKSLGWAVDVIDPRE------LSAKMLA--KVLDMGVLLTEAYldtVGDPDKYRIKLSERFPSikfvvskKADSLFPIVS 143
Cdd:PRK13926  73 RVALAWAVGHAEAAEidrlnvLKATHLAaaRALARLAVAPEAL---VTDYLRLPTPLPLLAPP-------KADALSPTVA 142

                        170
                 ....*....|....*.
gi 145329613 144 GASIVAKVTRDRALKE 159
Cdd:PRK13926 143 AASLLAKTERDRLMRE 158
RNase_HII_bacteria_HIII_like cd06590
Bacterial type 2 ribonuclease, HII and HIII-like; This family includes type 2 RNases H from ...
 16-160 7.89e-12

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: 62.92  E-value: 7.89e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  16 LMGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEEKREELYESLKldKSLGWAVDVIDPRE--------- 86
Cdd:cd06590    1 HIGSDEVGKGDYFGPLVVAAVYVDKEDIEFLKELGVKDSKKLTDKKIIKLAPKIK--EKIPYSLLVLDPEKynelyakgk 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  87 --------LSAKMLAKVLDMGVLLTEAYLDTVGDPDKYRIKL-SERFPSIKFVVSKKADSLFPIVSGASIVAkvtRDRAL 157
Cdd:cd06590   79 nlnklkawLHNQAIENLLKKKKKPKFILIDQFASEKVYYNYLkKEKIKKIPLYFETKAESKDLAVAAASILA---RYAFL 155


                 ...
gi 145329613 158 KEW 160
Cdd:cd06590  156 EEM 158
rnhB PRK13925
ribonuclease HII; Provisional
 18-176 1.90e-08

ribonuclease HII; Provisional


Pssm-ID: 184399  Cd Length: 198  Bit Score: 53.09  E-value: 1.90e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  18 GIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEEKREELY---ESLKLDKSLGWA----VDVIDPR---EL 87
Cdd:PRK13925  12 GVDEVGRGALFGPVFAAAVILSEKAEPQLLQAGLTDSKKLSPKRRAQLVpliLTLASDWGIGQAsareIDRLGIRqatEL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  88 SakMLAKVLDMGVLLTEAYLDTVgdpdkyrIKLSERFPSIKFVVskKADSLFPIVSGASIVAKVTRDRALKEWLVEETGE 167
Cdd:PRK13925  92 A--MLRALKKLKSPPSLCLVDGN-------LPLRLWPGPQRTIV--KGDSKSAAIAAASILAKVWRDDLIKRLAKKYPGY 160


                 ....*....
gi 145329613 168 DINRNFGSG 176
Cdd:PRK13925 161 GLEKNKGYG 169
rnhB PRK14550
ribonuclease HII; Provisional
 16-175 3.61e-08

ribonuclease HII; Provisional


Pssm-ID: 173015  Cd Length: 204  Bit Score: 52.64  E-value: 3.61e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  16 LMGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEEKREELYESLKLDKSLGWAVDVIDPRELSAKMLAKV 95
Cdd:PRK14550   2 TLGIDEAGRGCLAGSLFVAGVACNEKTALEFLKMGLKDSKKLSPKKRFFLEDKIKTHGEVGFFVVKKSANEIDSLGLGAC 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613  96 LDMGVlltEAYLDTvGDPDKYRIK--------LSERFPSIKFVVskKADSLFPIVSGASIVAKVTRDRALKEW--LVEET 165
Cdd:PRK14550  82 LKLAI---QEILEN-GCSLANEIKidgntafgLNKRYPNIQTII--KGDETIAQIAMASVLAKAFKDREMLELhaLFKEY 155

                        170
                 ....*....|
gi 145329613 166 GEDINRNFGS 175
Cdd:PRK14550 156 GWDKNCGYGT 165
rnhC TIGR00716
ribonuclease HIII; This enzyme cleaves RNA from DNA-RNA hybrids. Two types of ribonuclease H ...
 17-106 1.53e-06

ribonuclease HIII; This enzyme cleaves RNA from DNA-RNA hybrids. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homolog in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This model describes bacterial RNase III. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129799 [Multi-domain]  Cd Length: 284  Bit Score: 48.40  E-value: 1.53e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329613   17 MGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEEKREELYESLKldKSLGWAVDVIDPRELSaKMLAKVL 96
Cdd:TIGR00716  84 IGCDESGKGDIFGPLVLCCVYIPEENYLKVSSLNPRDSKRLSDKRIERLALNLK--PLVKAYCYELKPEKYN-KLYRKFR 160

                          90
                  ....*....|
gi 145329613   97 DMGVLLTEAY 106
Cdd:TIGR00716 161 NLNKMMAHFH 170
 
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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