NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|163773539|gb|EDQ87178|]
View 

predicted protein [Monosiga brevicollis MX1]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 270-417 1.33e-76

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: 240.08  E-value: 1.33e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539 270 FAVDCEMVRCGSRYALARISVVDQDEVTVMDEFVVPDEPVTDYVTRFSGITPELLANATSRLADIQHRLAQLLRPHDILV 349
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539 350 GHSLENDLGVLQRSHPHVIDTAVLLAREGR--YKQKLSMLTKKHLRYEIQNAADGHNSVEDALACLRLAK 417
Cdd:cd06145   81 GHSLENDLKALKLIHPRVIDTAILFPHPRGppYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELVK 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 ...
 270-417 1.33e-76

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: 240.08  E-value: 1.33e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539 270 FAVDCEMVRCGSRYALARISVVDQDEVTVMDEFVVPDEPVTDYVTRFSGITPELLANATSRLADIQHRLAQLLRPHDILV 349
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539 350 GHSLENDLGVLQRSHPHVIDTAVLLAREGR--YKQKLSMLTKKHLRYEIQNAADGHNSVEDALACLRLAK 417
Cdd:cd06145   81 GHSLENDLKALKLIHPRVIDTAILFPHPRGppYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELVK 150
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 268-424 2.07e-34

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 128.19  E-value: 2.07e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539   268 RLFAVDCEMVRCGSRYA-LARISVVDQD---EVTVMDEFVVPDEPVTDYVTRFSGITPELLANATSrLADIQHRLAQLLR 343
Cdd:smart00479   1 TLVVIDCETTGLDPGKDeIIEIAAVDVDggeIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPT-FEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539   344 PHDILVGHSLENDLGVLQRSHP----------HVIDTAVLLARE--GRYKQKLSMLTKKHLRYEIQNAadgHNSVEDALA 411
Cdd:smart00479  80 GRILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATnpGLPKYSLKKLAKRLLLEVIQRA---HRALDDARA 156

                          170
                   ....*....|...
gi 163773539   412 CLRLAKHVRQRPE 424
Cdd:smart00479 157 TAKLFKKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 271-415 3.15e-10

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: 59.29  E-value: 3.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539  271 AVDCEMVRCGSRY----ALARISVVDQDEVTV--MDEFVVPDEP--VTDYVTRFSGITPELLANATSrLADIQHRLAQLL 342
Cdd:pfam00929   2 VIDLETTGLDPEKdeiiEIAAVVIDGGENEIGetFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPS-FEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539  343 RPHDILVGHSLENDLGVLQR-----------SHPHVIDT-----AVLLAREGRYKQKLsmltKKHLRYEIQNAAdgHNSV 406
Cdd:pfam00929  81 RKGNLLVAHNASFDVGFLRYddkrflkkpmpKLNPVIDTlildkATYKELPGRSLDAL----AEKLGLEHIGRA--HRAL 154


                  ....*....
gi 163773539  407 EDALACLRL 415
Cdd:pfam00929 155 DDARATAKL 163
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 302-444 1.06e-05

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 47.06  E-value: 1.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539  302 FVVPDEPVTDYVTRFSGITPELLANAtSRLADIQHRLAQLLRpHDILVGHSLENDLGVL-----------QRSHPhVIDT 370
Cdd:TIGR00573  46 YIKPDRPIDPDAIKIHGITDDMLKDK-PDFKEIAEDFADYIR-GAELVIHNASFDVGFLnyefsklykvePKTND-VIDT 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539  371 --AVLLAREGRYKQKLSMLTKKhLRYEIQNAADG-HNSVEDALACLRL-----AKHVRQRPELIEQSNDQHynIIKAVVR 442
Cdd:TIGR00573 123 tdTLQYARPEFPGKRNTLDALC-KRYEITNSHRAlHGALADAFILAKLylvmtGKQTKYGENEGQQSRPYH--AIKSIVK 199


                  ..
gi 163773539  443 RS 444
Cdd:TIGR00573 200 KD 201
 
Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 270-417 1.33e-76

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: 240.08  E-value: 1.33e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539 270 FAVDCEMVRCGSRYALARISVVDQDEVTVMDEFVVPDEPVTDYVTRFSGITPELLANATSRLADIQHRLAQLLRPHDILV 349
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539 350 GHSLENDLGVLQRSHPHVIDTAVLLAREGR--YKQKLSMLTKKHLRYEIQNAADGHNSVEDALACLRLAK 417
Cdd:cd06145   81 GHSLENDLKALKLIHPRVIDTAILFPHPRGppYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELVK 150
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 271-415 6.37e-43

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: 151.13  E-value: 6.37e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539 271 AVDCEMVRCG---SRYALARISVVDQDEVTVMDEFVVPDEPVTDYVTRFSGITPELLANATSrLADIQHRLAQLLRpHDI 347
Cdd:cd06144    2 ALDCEMVGVGpdgSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPD-FEEVQKKVAELLK-GRI 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163773539 348 LVGHSLENDLGVLQRSHP-HVI-DTA--VLLAREGRYK-QKLSMLTKKHLRYEIQNAAdgHNSVEDALACLRL 415
Cdd:cd06144   80 LVGHALKNDLKVLKLDHPkKLIrDTSkyKPLRKTAKGKsPSLKKLAKQLLGLDIQEGE--HSSVEDARAAMRL 150
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 268-424 2.07e-34

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 128.19  E-value: 2.07e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539   268 RLFAVDCEMVRCGSRYA-LARISVVDQD---EVTVMDEFVVPDEPVTDYVTRFSGITPELLANATSrLADIQHRLAQLLR 343
Cdd:smart00479   1 TLVVIDCETTGLDPGKDeIIEIAAVDVDggeIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPT-FEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539   344 PHDILVGHSLENDLGVLQRSHP----------HVIDTAVLLARE--GRYKQKLSMLTKKHLRYEIQNAadgHNSVEDALA 411
Cdd:smart00479  80 GRILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATnpGLPKYSLKKLAKRLLLEVIQRA---HRALDDARA 156

                          170
                   ....*....|...
gi 163773539   412 CLRLAKHVRQRPE 424
Cdd:smart00479 157 TAKLFKKLLERLE 169
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 271-416 7.03e-33

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: 123.54  E-value: 7.03e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539 271 AVDCEMVRCGS-RYALARISVVDQDE-VTVMDEFVVPDEPVTDYVTRFSGITPELLANATSRLADIQHRLA------QLL 342
Cdd:cd06137    2 ALDCEMVGLADgDSEVVRISAVDVLTgEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAaraalwKFI 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163773539 343 RPHDILVGHSLENDLGVLQRSHPHVIDTAVL--LAREGRYKQ---KLSMLTKKHLRYEIQNAADGHNSVEDALACLRLA 416
Cdd:cd06137   82 DPDTILVGHSLQNDLDALRMIHTRVVDTAILtrEAVKGPLAKrqwSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREVV 160
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 271-417 3.83e-29

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: 112.92  E-value: 3.83e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539 271 AVDCEMVRCG---SRYALARISVVDQDEVTVMDEFVVPDEPVTDYVTRFSGITPELLANATSrLADIQHRLAQLLRpHDI 347
Cdd:cd06149    2 AIDCEMVGTGpggRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATP-FAVAQKEILKILK-GKV 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163773539 348 LVGHSLENDLGVLQRSHP-HVI-DTA--VLLAREGRYKQK----LSMLTKKHLRYEIQNAADGHNSVEDALACLRLAK 417
Cdd:cd06149   80 VVGHAIHNDFKALKYFHPkHMTrDTStiPLLNRKAGFPENcrvsLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 281-417 1.42e-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: 94.99  E-value: 1.42e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539 281 SRYALARISVV----DQDEVTVMDEFVVPDEPVTDYVTRFSGITPELLANATSR-----LADIQHRLAQLLRPHDILVGH 351
Cdd:cd06143   29 SQMSLARVSVVrgegELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKTSSknlttLKSAYLKLRLLVDLGCIFVGH 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163773539 352 SLENDLGVLQRSHPH--VIDTAVLLAREGRYKQKLSMLTKKHLRYEIQNaaDGHNSVEDALACLRLAK 417
Cdd:cd06143  109 GLAKDFRVINIQVPKeqVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQS--ETHDSIEDARTALKLYR 174
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 271-415 3.15e-10

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: 59.29  E-value: 3.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539  271 AVDCEMVRCGSRY----ALARISVVDQDEVTV--MDEFVVPDEP--VTDYVTRFSGITPELLANATSrLADIQHRLAQLL 342
Cdd:pfam00929   2 VIDLETTGLDPEKdeiiEIAAVVIDGGENEIGetFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPS-FEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539  343 RPHDILVGHSLENDLGVLQR-----------SHPHVIDT-----AVLLAREGRYKQKLsmltKKHLRYEIQNAAdgHNSV 406
Cdd:pfam00929  81 RKGNLLVAHNASFDVGFLRYddkrflkkpmpKLNPVIDTlildkATYKELPGRSLDAL----AEKLGLEHIGRA--HRAL 154


                  ....*....
gi 163773539  407 EDALACLRL 415
Cdd:pfam00929 155 DDARATAKL 163
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 302-444 1.06e-05

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 47.06  E-value: 1.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539  302 FVVPDEPVTDYVTRFSGITPELLANAtSRLADIQHRLAQLLRpHDILVGHSLENDLGVL-----------QRSHPhVIDT 370
Cdd:TIGR00573  46 YIKPDRPIDPDAIKIHGITDDMLKDK-PDFKEIAEDFADYIR-GAELVIHNASFDVGFLnyefsklykvePKTND-VIDT 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539  371 --AVLLAREGRYKQKLSMLTKKhLRYEIQNAADG-HNSVEDALACLRL-----AKHVRQRPELIEQSNDQHynIIKAVVR 442
Cdd:TIGR00573 123 tdTLQYARPEFPGKRNTLDALC-KRYEITNSHRAlHGALADAFILAKLylvmtGKQTKYGENEGQQSRPYH--AIKSIVK 199


                  ..
gi 163773539  443 RS 444
Cdd:TIGR00573 200 KD 201
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 288-418 2.82e-04

an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains 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. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.


Pssm-ID: 99834 [Multi-domain]  Cd Length: 156  Bit Score: 41.73  E-value: 2.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163773539 288 ISVVDQDEVTvmDEF---VVPDEPVTDYVTRFSGITPELLANAtSRLADIQHRLAQLLRPHdILVGHSLENDLGVLQRS- 363
Cdd:cd06130   21 LVKVRDGQIV--DTFytlIRPPTRFDPFNIAIHGITPEDVADA-PTFPEVWPEIKPFLGGS-LVVAHNASFDRSVLRAAl 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163773539 364 --------HPHVIDTaVLLAR---EGRYKQKLSMLtKKHLRYEIQNaadgHNSVEDALACLRLAKH 418
Cdd:cd06130   97 eayglpppPYQYLCT-VRLARrvwPLLPNHKLNTV-AEHLGIELNH----HDALEDARACAEILLA 156
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH