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Conserved domains on  [gi|766470095|gb|AJR94180|]
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Rnh70p [Saccharomyces cerevisiae YJM1190]

Protein Classification

RNA exonuclease( domain architecture ID 10150223)

RNA exonuclease is a 3'-5' exonuclease that catalyzes the excision of nucleoside monophosphates at the RNA terminus in the 3'-5' direction; belongs to the DnaQ-like (or DEDD) 3'-5' exonuclease superfamily

CATH:  3.30.420.10
EC:  3.1.-.-
Gene Ontology:  GO:0008408|GO:0003676|GO:0006396
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 226-374 3.20e-83

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


:

Pssm-ID: 99848  Cd Length: 150  Bit Score: 255.49  E-value: 3.20e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 226 FALDCEMCLSEQGLVLTRISLVNFDNEVIYEELVKPDVPIVDYLTRYSGITEEKLtVGAKKTLREVQKDLLKIISRSDIL 305
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEML-ENVTTTLEDVQKKLLSLISPDTIL 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 766470095 306 IGHSLQNDLKVMKLKHPLVVDTAIIYHHKAGDPFKPSLKYLSETFLNKSIQN--GEHDSVEDARACLELTK 374
Cdd:cd06145   80 VGHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQgeGGHDSVEDARAALELVK 150
 
Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 226-374 3.20e-83

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


Pssm-ID: 99848  Cd Length: 150  Bit Score: 255.49  E-value: 3.20e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 226 FALDCEMCLSEQGLVLTRISLVNFDNEVIYEELVKPDVPIVDYLTRYSGITEEKLtVGAKKTLREVQKDLLKIISRSDIL 305
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEML-ENVTTTLEDVQKKLLSLISPDTIL 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 766470095 306 IGHSLQNDLKVMKLKHPLVVDTAIIYHHKAGDPFKPSLKYLSETFLNKSIQN--GEHDSVEDARACLELTK 374
Cdd:cd06145   80 VGHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQgeGGHDSVEDARAALELVK 150
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 225-381 9.71e-41

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 145.14  E-value: 9.71e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095   225 IFALDCEM-CLSEQGLVLTRISLVNFDN---EVIYEELVKPDVPIVDYLTRYSGITEEKLTVgaKKTLREVQKDLLKIIS 300
Cdd:smart00479   2 LVVIDCETtGLDPGKDEIIEIAAVDVDGgeiIEVFDTYVKPDRPITDYATEIHGITPEMLDD--APTFEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095   301 RSDILIGHSLQNDLKVMKLKHP----------LVVDTAIIYHHKAGDPFKPSLKYLSETFLNKSIQNgEHDSVEDARACL 370
Cdd:smart00479  80 GRILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQR-AHRALDDARATA 158

                          170
                   ....*....|.
gi 766470095   371 ELTKLKILNGL 381
Cdd:smart00479 159 KLFKKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 227-373 1.20e-11

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 63.14  E-value: 1.20e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095  227 ALDCEM-CLSEQGLVLTRISLVNFDNEVIYEE-----LVKPDVP--IVDYLTRYSGITEEklTVGAKKTLREVQKDLLKI 298
Cdd:pfam00929   2 VIDLETtGLDPEKDEIIEIAAVVIDGGENEIGetfhtYVKPTRLpkLTDECTKFTGITQA--MLDNKPSFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095  299 ISRSDILIGH--------SLQNDLKVMKLKHPL---VVDTAIIYHHKAGDPFKPSLKYLSETFLNKSIQNgEHDSVEDAR 367
Cdd:pfam00929  80 LRKGNLLVAHnasfdvgfLRYDDKRFLKKPMPKlnpVIDTLILDKATYKELPGRSLDALAEKLGLEHIGR-AHRALDDAR 158


                  ....*.
gi 766470095  368 ACLELT 373
Cdd:pfam00929 159 ATAKLF 164
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 244-372 1.58e-11

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 62.89  E-value: 1.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 244 ISLVNFDNEVI---YEELVKPDVPIVDYLTRYSGITEEKLTvgAKKTLREVQKDLLKIIsRSDILIGHSLQNDLKV---- 316
Cdd:COG0847   22 IGAVKVDDGRIvetFHTLVNPERPIPPEATAIHGITDEDVA--DAPPFAEVLPELLEFL-GGAVLVAHNAAFDLGFlnae 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 766470095 317 -----MKLKHPLVVDTAIIYHHKAGDPFKPSLKYLSETFlnkSIQNGE-HDSVEDARACLEL 372
Cdd:COG0847   99 lrragLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERL---GIPFDErHRALADAEATAEL 157
 
Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 226-374 3.20e-83

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


Pssm-ID: 99848  Cd Length: 150  Bit Score: 255.49  E-value: 3.20e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 226 FALDCEMCLSEQGLVLTRISLVNFDNEVIYEELVKPDVPIVDYLTRYSGITEEKLtVGAKKTLREVQKDLLKIISRSDIL 305
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEML-ENVTTTLEDVQKKLLSLISPDTIL 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 766470095 306 IGHSLQNDLKVMKLKHPLVVDTAIIYHHKAGDPFKPSLKYLSETFLNKSIQN--GEHDSVEDARACLELTK 374
Cdd:cd06145   80 VGHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQgeGGHDSVEDARAALELVK 150
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 227-372 3.86e-44

DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.


Pssm-ID: 99847  Cd Length: 152  Bit Score: 153.44  E-value: 3.86e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 227 ALDCEM--CLSEQGL-VLTRISLVNFDNEVIYEELVKPDVPIVDYLTRYSGITEEKLtVGAKkTLREVQKDLLKIIsRSD 303
Cdd:cd06144    2 ALDCEMvgVGPDGSEsALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHL-KDAP-DFEEVQKKVAELL-KGR 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 766470095 304 ILIGHSLQNDLKVMKLKHP--LVVDTA-IIYHHKAGDPFKPSLKYLSETFLNKSIQNGEHDSVEDARACLEL 372
Cdd:cd06144   79 ILVGHALKNDLKVLKLDHPkkLIRDTSkYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRL 150
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 227-372 5.85e-42

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins; This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA.


Pssm-ID: 99840  Cd Length: 161  Bit Score: 147.81  E-value: 5.85e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 227 ALDCEMC-LSEQGLVLTRISLVN-FDNEVIYEELVKPDVPIVDYLTRYSGITEEKLTVGAK--KTLR---EVQKDLLKII 299
Cdd:cd06137    2 ALDCEMVgLADGDSEVVRISAVDvLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKagKTIFgweAARAALWKFI 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 766470095 300 SRSDILIGHSLQNDLKVMKLKHPLVVDTAIIYHHKAGDPFKP---SLKYLSETFLNKSIQNGE--HDSVEDARACLEL 372
Cdd:cd06137   82 DPDTILVGHSLQNDLDALRMIHTRVVDTAILTREAVKGPLAKrqwSLRTLCRDFLGLKIQGGGegHDSLEDALAAREV 159
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 225-381 9.71e-41

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 145.14  E-value: 9.71e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095   225 IFALDCEM-CLSEQGLVLTRISLVNFDN---EVIYEELVKPDVPIVDYLTRYSGITEEKLTVgaKKTLREVQKDLLKIIS 300
Cdd:smart00479   2 LVVIDCETtGLDPGKDEIIEIAAVDVDGgeiIEVFDTYVKPDRPITDYATEIHGITPEMLDD--APTFEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095   301 RSDILIGHSLQNDLKVMKLKHP----------LVVDTAIIYHHKAGDPFKPSLKYLSETFLNKSIQNgEHDSVEDARACL 370
Cdd:smart00479  80 GRILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQR-AHRALDDARATA 158

                          170
                   ....*....|.
gi 766470095   371 ELTKLKILNGL 381
Cdd:smart00479 159 KLFKKLLERLE 169
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 227-374 7.52e-32

DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins; Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral response.


Pssm-ID: 99852  Cd Length: 157  Bit Score: 120.23  E-value: 7.52e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 227 ALDCEM-------CLSEqglvLTRISLVNFDNEVIYEELVKPDVPIVDYLTRYSGITEEKLtVGAKKtLREVQKDLLKII 299
Cdd:cd06149    2 AIDCEMvgtgpggRESE----LARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHL-VNATP-FAVAQKEILKIL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 300 SrSDILIGHSLQNDLKVMKLKHP--LVVDTAII--YHHKAGDPFKP--SLKYLSETFLNKSIQNGE--HDSVEDARACLE 371
Cdd:cd06149   76 K-GKVVVGHAIHNDFKALKYFHPkhMTRDTSTIplLNRKAGFPENCrvSLKVLAKRLLHRDIQVGRqgHSSVEDARATME 154


                 ...
gi 766470095 372 LTK 374
Cdd:cd06149  155 LYK 157
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 241-374 4.84e-22

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.


Pssm-ID: 99846  Cd Length: 174  Bit Score: 93.45  E-value: 4.84e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 241 LTRISLVN---------FDNEVIyeelvKPDVPIVDYLTRYSGITEEKLTVGAKK----TLREVQKDLLKIISRSDILIG 307
Cdd:cd06143   33 LARVSVVRgegelegvpFIDDYI-----STTEPVVDYLTRFSGIKPGDLDPKTSSknltTLKSAYLKLRLLVDLGCIFVG 107

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 766470095 308 HSLQNDLKVMKLKHP--LVVDTAIIYHHkaGDPFKPSLKYLSETFLNKSIQNGEHDSVEDARACLELTK 374
Cdd:cd06143  108 HGLAKDFRVINIQVPkeQVIDTVELFHL--PGQRKLSLRFLAWYLLGEKIQSETHDSIEDARTALKLYR 174
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 227-372 1.60e-12

DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 65.40  E-value: 1.60e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 227 ALDCEM-CLSEQGLVLTRISLVNFDNEVI----YEELVKPDVPIVDYLTRYSGITEEklTVGAKKTLREVQKDLLKIIsR 301
Cdd:cd06127    2 VFDTETtGLDPKKDRIIEIGAVKVDGGIEiverFETLVNPGRPIPPEATAIHGITDE--MLADAPPFEEVLPEFLEFL-G 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 302 SDILIGHSLQNDLKVMK---------LKHPLVVDTAIIYHHKAGDPFKPSLKYLSETFLNKSIQNGeHDSVEDARACLEL 372
Cdd:cd06127   79 GRVLVAHNASFDLRFLNrelrrlggpPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLEGA-HRALADALATAEL 157
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 227-373 1.20e-11

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 63.14  E-value: 1.20e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095  227 ALDCEM-CLSEQGLVLTRISLVNFDNEVIYEE-----LVKPDVP--IVDYLTRYSGITEEklTVGAKKTLREVQKDLLKI 298
Cdd:pfam00929   2 VIDLETtGLDPEKDEIIEIAAVVIDGGENEIGetfhtYVKPTRLpkLTDECTKFTGITQA--MLDNKPSFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095  299 ISRSDILIGH--------SLQNDLKVMKLKHPL---VVDTAIIYHHKAGDPFKPSLKYLSETFLNKSIQNgEHDSVEDAR 367
Cdd:pfam00929  80 LRKGNLLVAHnasfdvgfLRYDDKRFLKKPMPKlnpVIDTLILDKATYKELPGRSLDALAEKLGLEHIGR-AHRALDDAR 158


                  ....*.
gi 766470095  368 ACLELT 373
Cdd:pfam00929 159 ATAKLF 164
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 244-372 1.58e-11

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 62.89  E-value: 1.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 244 ISLVNFDNEVI---YEELVKPDVPIVDYLTRYSGITEEKLTvgAKKTLREVQKDLLKIIsRSDILIGHSLQNDLKV---- 316
Cdd:COG0847   22 IGAVKVDDGRIvetFHTLVNPERPIPPEATAIHGITDEDVA--DAPPFAEVLPELLEFL-GGAVLVAHNAAFDLGFlnae 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 766470095 317 -----MKLKHPLVVDTAIIYHHKAGDPFKPSLKYLSETFlnkSIQNGE-HDSVEDARACLEL 372
Cdd:COG0847   99 lrragLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERL---GIPFDErHRALADAEATAEL 157
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 250-389 1.97e-08

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 53.99  E-value: 1.97e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766470095 250 DNEVI--YEELVKPDVPIVDYLTRYSGITEEKLTvgAKKTLREVQKDLLKIIsRSDILIGHSLQNDLKVMK--------- 318
Cdd:COG2176   37 NGEIVdrFSTLVNPGRPIPPFITELTGITDEMVA--DAPPFEEVLPEFLEFL-GDAVLVAHNASFDLGFLNaalkrlglp 113

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 766470095 319 LKHPlVVDT---AIIYHHKAGdpfKPSLKYLSEtFLNKSIQNgEHDSVEDARACLELtkLKILNGLAFGIGINT 389
Cdd:COG2176  114 FDNP-VLDTlelARRLLPELK---SYKLDTLAE-RLGIPLED-RHRALGDAEATAEL--FLKLLEKLEEKGITT 179
 
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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