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Conserved domains on  [gi|17557646|ref|NP_504838|]
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Exonuclease domain-containing protein [Caenorhabditis elegans]

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 ...
 222-372 5.16e-75

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: 235.46  E-value: 5.16e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646 222 FSVDCEMCETDvANRELTRISIVDEFENTILDTLVKPEGRITDYVTRWSGITPDMMEGVTTTLGDVQKAIQSLLPPDAIL 301
Cdd:cd06145   1 FALDCEMCYTT-DGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTIL 79

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17557646 302 VGHSLEHDLQAMKMTHPFCLDVGHVLNYTNSNTeFRNSLKNLTELFLGAQIQ-SEFGHCSYEDAWAAMRLAQ 372
Cdd:cd06145  80 VGHSLENDLKALKLIHPRVIDTAILFPHPRGPP-YKPSLKNLAKKYLGRDIQqGEGGHDSVEDARAALELVK 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 ...
 222-372 5.16e-75

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: 235.46  E-value: 5.16e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646 222 FSVDCEMCETDvANRELTRISIVDEFENTILDTLVKPEGRITDYVTRWSGITPDMMEGVTTTLGDVQKAIQSLLPPDAIL 301
Cdd:cd06145   1 FALDCEMCYTT-DGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTIL 79

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17557646 302 VGHSLEHDLQAMKMTHPFCLDVGHVLNYTNSNTeFRNSLKNLTELFLGAQIQ-SEFGHCSYEDAWAAMRLAQ 372
Cdd:cd06145  80 VGHSLENDLKALKLIHPRVIDTAILFPHPRGPP-YKPSLKNLAKKYLGRDIQqGEGGHDSVEDARAALELVK 150
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 221-379 1.26e-36

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 134.35  E-value: 1.26e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646    221 MFSVDCEMCETDVANRELTRISIVDEF---ENTILDTLVKPEGRITDYVTRWSGITPDMMEGvTTTLGDVQKAIQSLLPP 297
Cdd:smart00479   2 LVVIDCETTGLDPGKDEIIEIAAVDVDggeIIEVFDTYVKPDRPITDYATEIHGITPEMLDD-APTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646    298 DAILVGHSLEHDLQAMKMTHP----------FCLDVGHVLNYTNSNTeFRNSLKNLTELFLGAQIQSEfgHCSYEDAWAA 367
Cdd:smart00479  81 RILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATNPGL-PKYSLKKLAKRLLLEVIQRA--HRALDDARAT 157

                          170
                   ....*....|..
gi 17557646    368 MRLAQLKLEKGL 379
Cdd:smart00479 158 AKLFKKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 224-370 1.94e-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: 59.67  E-value: 1.94e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646   224 VDCEMCETDVAN---RELTRISIVDEFENTI--LDTLVKPE--GRITDYVTRWSGITPDMMEGVTTTLgDVQKAIQSLLP 296
Cdd:pfam00929   3 IDLETTGLDPEKdeiIEIAAVVIDGGENEIGetFHTYVKPTrlPKLTDECTKFTGITQAMLDNKPSFE-EVLEEFLEFLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646   297 PDAILVGHS----LEHDLQAMKM--------THPFcLDVGHVLNYTNSNtEFRNSLKNLTELFLGAQIQSEfgHCSYEDA 364
Cdd:pfam00929  82 KGNLLVAHNasfdVGFLRYDDKRflkkpmpkLNPV-IDTLILDKATYKE-LPGRSLDALAEKLGLEHIGRA--HRALDDA 157


                  ....*.
gi 17557646   365 WAAMRL 370
Cdd:pfam00929 158 RATAKL 163
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 243-310 1.71e-06

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 48.60  E-value: 1.71e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17557646 243 IVDEFEntildTLVKPEGRITDYVTRWSGITPDMMEGvTTTLGDVQKAIQSLLpPDAILVGHSLEHDL 310
Cdd:COG2176  40 IVDRFS-----TLVNPGRPIPPFITELTGITDEMVAD-APPFEEVLPEFLEFL-GDAVLVAHNASFDL 100
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 224-313 4.99e-03

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 39.04  E-value: 4.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646  224 VDCEMCETDVANRELTRISIVDEFENTILD---TLVKPEGRITDYVTRWSGITPDMMEGvTTTLGDVQKAIQSLLPPDAI 300
Cdd:PRK06310  12 LDCETTGLDVKKDRIIEFAAIRFTFDEVIDsveFLINPERVVSAESQRIHHISDAMLRD-KPKIAEVFPQIKGFFKEGDY 90

                         90
                 ....*....|...
gi 17557646  301 LVGHSLEHDLQAM 313
Cdd:PRK06310  91 IVGHSVGFDLQVL 103
 
Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 222-372 5.16e-75

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: 235.46  E-value: 5.16e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646 222 FSVDCEMCETDvANRELTRISIVDEFENTILDTLVKPEGRITDYVTRWSGITPDMMEGVTTTLGDVQKAIQSLLPPDAIL 301
Cdd:cd06145   1 FALDCEMCYTT-DGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTIL 79

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17557646 302 VGHSLEHDLQAMKMTHPFCLDVGHVLNYTNSNTeFRNSLKNLTELFLGAQIQ-SEFGHCSYEDAWAAMRLAQ 372
Cdd:cd06145  80 VGHSLENDLKALKLIHPRVIDTAILFPHPRGPP-YKPSLKNLAKKYLGRDIQqGEGGHDSVEDARAALELVK 150
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 223-370 5.47e-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: 5.47e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646 223 SVDCEM--CETDVANRELTRISIVDEFENTILDTLVKPEGRITDYVTRWSGITPDMMEGvTTTLGDVQKAIQSLLpPDAI 300
Cdd:cd06144   2 ALDCEMvgVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKD-APDFEEVQKKVAELL-KGRI 79

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17557646 301 LVGHSLEHDLQAMKMTHPFCL--DVGHVLNYTNSNTEFRNSLKNLTELFLGAQIQSEfGHCSYEDAWAAMRL 370
Cdd:cd06144  80 LVGHALKNDLKVLKLDHPKKLirDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEG-EHSSVEDARAAMRL 150
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 221-379 1.26e-36

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 134.35  E-value: 1.26e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646    221 MFSVDCEMCETDVANRELTRISIVDEF---ENTILDTLVKPEGRITDYVTRWSGITPDMMEGvTTTLGDVQKAIQSLLPP 297
Cdd:smart00479   2 LVVIDCETTGLDPGKDEIIEIAAVDVDggeIIEVFDTYVKPDRPITDYATEIHGITPEMLDD-APTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646    298 DAILVGHSLEHDLQAMKMTHP----------FCLDVGHVLNYTNSNTeFRNSLKNLTELFLGAQIQSEfgHCSYEDAWAA 367
Cdd:smart00479  81 RILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATNPGL-PKYSLKKLAKRLLLEVIQRA--HRALDDARAT 157

                          170
                   ....*....|..
gi 17557646    368 MRLAQLKLEKGL 379
Cdd:smart00479 158 AKLFKKLLERLE 169
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 223-372 1.14e-31

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: 120.08  E-value: 1.14e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646 223 SVDCEMCETDVANRELTRISIVDEFENTIL-DTLVKPEGRITDYVTRWSGITPDMMEGV----TTTLGD--VQKAIQSLL 295
Cdd:cd06137   2 ALDCEMVGLADGDSEVVRISAVDVLTGEVLiDSLVRPSVRVTDWRTRFSGVTPADLEEAakagKTIFGWeaARAALWKFI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646 296 PPDAILVGHSLEHDLQAMKMTHPFCLDVGHV--LNYTNSNTEFRNSLKNLTELFLGAQIQ-SEFGHCSYEDAWAAMRLAQ 372
Cdd:cd06137  82 DPDTILVGHSLQNDLDALRMIHTRVVDTAILtrEAVKGPLAKRQWSLRTLCRDFLGLKIQgGGEGHDSLEDALAAREVVL 161
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 223-372 6.25e-25

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: 100.97  E-value: 6.25e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646 223 SVDCEMCETDVANR--ELTRISIVDEFENTILDTLVKPEGRITDYVTRWSGITPDMMEGvTTTLGDVQKAIQSLLpPDAI 300
Cdd:cd06149   2 AIDCEMVGTGPGGResELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVN-ATPFAVAQKEILKIL-KGKV 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646 301 LVGHSLEHDLQAMKMTHPfcldvGHVLNYTNS----------NTEFRNSLKNLTELFLGAQIQ-SEFGHCSYEDAWAAMR 369
Cdd:cd06149  80 VVGHAIHNDFKALKYFHP-----KHMTRDTSTipllnrkagfPENCRVSLKVLAKRLLHRDIQvGRQGHSSVEDARATME 154


                ...
gi 17557646 370 LAQ 372
Cdd:cd06149 155 LYK 157
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 234-370 1.17e-11

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: 63.40  E-value: 1.17e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646 234 ANRELTRISIV----DEFENTILDTLVKPEGRITDYVTRWSGITPDMMEGVT-----TTLGDVQKAIQSLLPPDAILVGH 304
Cdd:cd06143  29 SQMSLARVSVVrgegELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKTssknlTTLKSAYLKLRLLVDLGCIFVGH 108

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17557646 305 SLEHDLQAMKMTHP-FCldVGHVLNYTNSNTEFRNSLKNLTELFLGAQIQSEfGHCSYEDAWAAMRL 370
Cdd:cd06143 109 GLAKDFRVINIQVPkEQ--VIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSE-THDSIEDARTALKL 172
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 224-370 1.94e-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: 59.67  E-value: 1.94e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646   224 VDCEMCETDVAN---RELTRISIVDEFENTI--LDTLVKPE--GRITDYVTRWSGITPDMMEGVTTTLgDVQKAIQSLLP 296
Cdd:pfam00929   3 IDLETTGLDPEKdeiIEIAAVVIDGGENEIGetFHTYVKPTrlPKLTDECTKFTGITQAMLDNKPSFE-EVLEEFLEFLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646   297 PDAILVGHS----LEHDLQAMKM--------THPFcLDVGHVLNYTNSNtEFRNSLKNLTELFLGAQIQSEfgHCSYEDA 364
Cdd:pfam00929  82 KGNLLVAHNasfdVGFLRYDDKRflkkpmpkLNPV-IDTLILDKATYKE-LPGRSLDALAEKLGLEHIGRA--HRALDDA 157


                  ....*.
gi 17557646   365 WAAMRL 370
Cdd:pfam00929 158 RATAKL 163
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 224-310 1.32e-06

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: 48.45  E-value: 1.32e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646 224 VDCEMCETDVANRELTRISIVDeFENTI-----LDTLVKPEGRITDYVTRWSGITPDMMEGVtTTLGDVQKAIQSLLpPD 298
Cdd:cd06127   3 FDTETTGLDPKKDRIIEIGAVK-VDGGIeiverFETLVNPGRPIPPEATAIHGITDEMLADA-PPFEEVLPEFLEFL-GG 79

                        90
                ....*....|..
gi 17557646 299 AILVGHSLEHDL 310
Cdd:cd06127  80 RVLVAHNASFDL 91
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 243-310 1.71e-06

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 48.60  E-value: 1.71e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17557646 243 IVDEFEntildTLVKPEGRITDYVTRWSGITPDMMEGvTTTLGDVQKAIQSLLpPDAILVGHSLEHDL 310
Cdd:COG2176  40 IVDRFS-----TLVNPGRPIPPFITELTGITDEMVAD-APPFEEVLPEFLEFL-GDAVLVAHNASFDL 100
STKc_Trio_C cd14113
C-terminal kinase domain of the Large Serine/Threonine Kinase and Rho Guanine Nucleotide ...
 241-306 6.58e-04

C-terminal kinase domain of the Large Serine/Threonine Kinase and Rho Guanine Nucleotide Exchange Factor, Triple functional domain protein; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Triple functional domain protein (Trio), also called PTPRF-interacting protein, is a large multidomain protein containing a series of spectrin-like repeats, two each of RhoGEF and SH3 domains, an immunoglobulin-like (Ig) domain and a C-terminal kinase. Trio plays important roles in neuronal cell migration and axon guidance. It was originally identified as an interacting partner of the of the receptor-like tyrosine phosphatase (RPTP) LAR (leukocyte-antigen-related protein), a family of receptors that function in the signaling to the actin cytoskeleton during development. Trio functions as a GEF for Rac1, RhoG, and RhoA, and is involved in the regulation of lamellipodia formation, mediating Rac1-dependent cell spreading and migration. The Trio subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.


Pssm-ID: 271015 [Multi-domain]  Cd Length: 263  Bit Score: 41.88  E-value: 6.58e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17557646 241 ISIVDEFE---NTILDTLVKPEGRITDYVTRWSGITPdmmEGVTTTLGDVQKAIQSL---------LPPDAILVGHSL 306
Cdd:cd14113  66 VGLLDTFEtptSYILVLEMADQGRLLDYVVRWGNLTE---EKIRFYLREILEALQYLhncriahldLKPENILVDQSL 140
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 229-314 1.24e-03

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 39.78  E-value: 1.24e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646 229 CET---DVANRELTRISIVDEFENTILD---TLVKPEGRITDYVTRWSGITPDMMEGvTTTLGDVQKAIQSLLpPDAILV 302
Cdd:COG0847   7 TETtglDPAKDRIIEIGAVKVDDGRIVEtfhTLVNPERPIPPEATAIHGITDEDVAD-APPFAEVLPELLEFL-GGAVLV 84

                        90
                ....*....|..
gi 17557646 303 GHSLEHDLQAMK 314
Cdd:COG0847  85 AHNAAFDLGFLN 96
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 224-313 4.99e-03

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 39.04  E-value: 4.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17557646  224 VDCEMCETDVANRELTRISIVDEFENTILD---TLVKPEGRITDYVTRWSGITPDMMEGvTTTLGDVQKAIQSLLPPDAI 300
Cdd:PRK06310  12 LDCETTGLDVKKDRIIEFAAIRFTFDEVIDsveFLINPERVVSAESQRIHHISDAMLRD-KPKIAEVFPQIKGFFKEGDY 90

                         90
                 ....*....|...
gi 17557646  301 LVGHSLEHDLQAM 313
Cdd:PRK06310  91 IVGHSVGFDLQVL 103
polC PRK00448
DNA polymerase III PolC; Validated
 243-304 7.71e-03

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 39.44  E-value: 7.71e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17557646   243 IVDEFEntildTLVKPEGRITDYVTRWSGITPDMMEGvtttlgdvQKAIQSLLPP------DAILVGH 304
Cdd:PRK00448  451 IIDKFE-----FFIKPGHPLSAFTTELTGITDDMVKD--------APSIEEVLPKfkefcgDSILVAH 505
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 243-314 8.99e-03

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: 37.11  E-value: 8.99e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17557646 243 IVDEFEntildTLVKPEGRITDYVTRWSGITPDMMEGVtTTLGDVQKAIQSLLPPDaILVGHSLEHDLQAMK 314
Cdd:cd06130  29 IVDTFY-----TLIRPPTRFDPFNIAIHGITPEDVADA-PTFPEVWPEIKPFLGGS-LVVAHNASFDRSVLR 93
 
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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