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Conserved domains on  [gi|923400948|gb|KOR33197|]
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hypothetical protein TI05_02565 [Achromatium sp. WMS3]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 261-502 5.91e-130

DNA polymerase III subunit epsilon; Provisional


:

Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 377.28  E-value: 5.91e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 261 TKKLRQIVLDTETTGLTP-DEHRIIEIGAIELIDRRFTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADL 339
Cdd:PRK05711   1 TAIMRQIVLDTETTGLNQrEGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 340 IAYLQGAELIIHNAPFDTGFLDAEFARLanKQHIAtvKVNKICTVTDTLIMARQAYPGKSNNLDALCKRYNIDQSHRTVH 419
Cdd:PRK05711  81 LDFIRGAELIIHNAPFDIGFMDYEFALL--GRDIP--KTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLH 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 420 GALLDAKLLATVYLAMTGGQATLSLaADLNDNIQIDKPNKIPQANAKRLPLQIIRATLEELELHQTRLEQINqKSNGQCL 499
Cdd:PRK05711 157 GALLDAEILAEVYLAMTGGQTSLGF-AMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLD-KKGGSCL 234


                 ...
gi 923400948 500 WLK 502
Cdd:PRK05711 235 WRK 237
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 5-141 2.89e-83

RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


:

Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 253.94  E-value: 2.89e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   5 IEMYTDGACKSNPGPGGWGVLIHAAKKKQELCGGEINTTNNRMELTAVIKGVESLPQNSQVRIITDSQYVKDGMTKWIKK 84
Cdd:cd09278    2 IVIYTDGACLGNPGPGGWAAVIRYGDHEKELSGGEPGTTNNRMELTAAIEALEALKEPCPVTIYTDSQYVINGITKWIKG 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 923400948  85 WRNNGWVTSNKQPVKNRDLWEQLDTVLQRlHKIEWVWVKGHAGTPGNERADQLANQG 141
Cdd:cd09278   82 WKKNGWKTADGKPVKNRDLWQELDALLAG-HKVTWEWVKGHAGHPGNERADRLANKA 137
 
Name Accession Description Interval E-value
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 261-502 5.91e-130

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 377.28  E-value: 5.91e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 261 TKKLRQIVLDTETTGLTP-DEHRIIEIGAIELIDRRFTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADL 339
Cdd:PRK05711   1 TAIMRQIVLDTETTGLNQrEGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 340 IAYLQGAELIIHNAPFDTGFLDAEFARLanKQHIAtvKVNKICTVTDTLIMARQAYPGKSNNLDALCKRYNIDQSHRTVH 419
Cdd:PRK05711  81 LDFIRGAELIIHNAPFDIGFMDYEFALL--GRDIP--KTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLH 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 420 GALLDAKLLATVYLAMTGGQATLSLaADLNDNIQIDKPNKIPQANAKRLPLQIIRATLEELELHQTRLEQINqKSNGQCL 499
Cdd:PRK05711 157 GALLDAEILAEVYLAMTGGQTSLGF-AMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLD-KKGGSCL 234


                 ...
gi 923400948 500 WLK 502
Cdd:PRK05711 235 WRK 237
dnaQ_proteo TIGR01406
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ...
 265-494 8.00e-101

DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130473 [Multi-domain]  Cd Length: 225  Bit Score: 302.39  E-value: 8.00e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  265 RQIVLDTETTGLTPDE-HRIIEIGAIELIDRRFTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAYL 343
Cdd:TIGR01406   1 RQIILDTETTGLDPKGgHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  344 QGAELIIHNAPFDTGFLDAEFARLANKQHiatvKVNKICTVTDTLIMARQAYPGKSNNLDALCKRYNIDQSHRTVHGALL 423
Cdd:TIGR01406  81 GGSELVIHNAAFDVGFLNYELERLGPTIK----KIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALL 156

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 923400948  424 DAKLLATVYLAMTGGQATLSLAADLNDNIqIDKPNKIPqANAKRLPLQIIRATLEELELHQTRLEQINQKS 494
Cdd:TIGR01406 157 DAHLLAEVYLALTGGQESLLELAESNSGE-AAKPSKSA-EMKLGATLRVLAPREAELQAHEAYLDKLLKKS 225
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 266-436 1.13e-98

DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme 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: 99835 [Multi-domain]  Cd Length: 167  Bit Score: 294.44  E-value: 1.13e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 266 QIVLDTETTGLTPDE-HRIIEIGAIELIDRRFTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAYLQ 344
Cdd:cd06131    1 QIVLDTETTGLDPREgHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 345 GAELIIHNAPFDTGFLDAEFARLANKQhiatvKVNKICTVTDTLIMARQAYPGKSNNLDALCKRYNIDQSHRTVHGALLD 424
Cdd:cd06131   81 GAELVIHNASFDVGFLNAELSLLGLGK-----KIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLD 155

                        170
                 ....*....|..
gi 923400948 425 AKLLATVYLAMT 436
Cdd:cd06131  156 AELLAEVYLELT 167
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 5-141 2.89e-83

RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 253.94  E-value: 2.89e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   5 IEMYTDGACKSNPGPGGWGVLIHAAKKKQELCGGEINTTNNRMELTAVIKGVESLPQNSQVRIITDSQYVKDGMTKWIKK 84
Cdd:cd09278    2 IVIYTDGACLGNPGPGGWAAVIRYGDHEKELSGGEPGTTNNRMELTAAIEALEALKEPCPVTIYTDSQYVINGITKWIKG 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 923400948  85 WRNNGWVTSNKQPVKNRDLWEQLDTVLQRlHKIEWVWVKGHAGTPGNERADQLANQG 141
Cdd:cd09278   82 WKKNGWKTADGKPVKNRDLWQELDALLAG-HKVTWEWVKGHAGHPGNERADRLANKA 137
rnhA PRK00203
ribonuclease H; Reviewed
 5-142 9.53e-79

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 242.81  E-value: 9.53e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   5 IEMYTDGACKSNPGPGGWGVLIHAAKKKQELCGGEINTTNNRMELTAVIKGVESLPQNSQVRIITDSQYVKDGMTKWIKK 84
Cdd:PRK00203   4 VEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKEPCEVTLYTDSQYVRQGITEWIHG 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 923400948  85 WRNNGWVTSNKQPVKNRDLWEQLDTVLQRlHKIEWVWVKGHAGTPGNERADQLANQGV 142
Cdd:PRK00203  84 WKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGA 140
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 265-437 4.49e-69

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 218.12  E-value: 4.49e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 265 RQIVLDTETTGLTPDEHRIIEIGAIELIDRRFTNNnFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAYLQ 344
Cdd:COG0847    1 RFVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVET-FHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 345 GAELIIHNAPFDTGFLDAEFARLANKqhiatvkvNKICTVTDTLIMARQAYPG-KSNNLDALCKRYNIDQSHRtvHGALL 423
Cdd:COG0847   80 GAVLVAHNAAFDLGFLNAELRRAGLP--------LPPFPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRALA 149

                        170
                 ....*....|....
gi 923400948 424 DAKLLATVYLAMTG 437
Cdd:COG0847  150 DAEATAELFLALLR 163
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
5-142 2.98e-68

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 215.09  E-value: 2.98e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   5 IEMYTDGACKSNPGPGGWGVLIHAAKKKQELCGGEINTTNNRMELTAVIKGVESLPQN--SQVRIITDSQYVKDGMTKWI 82
Cdd:COG0328    3 IEIYTDGACRGNPGPGGWGAVIRYGGEEKELSGGLGDTTNNRAELTALIAALEALKELgpCEVEIYTDSQYVVNQITGWI 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  83 KKWRNNGWvtsnkQPVKNRDLWEQLDTVLQRlHKIEWVWVKGHAGTPGNERADQLANQGV 142
Cdd:COG0328   83 HGWKKNGW-----KPVKNPDLWQRLDELLAR-HKVTFEWVKGHAGHPGNERADALANKAL 136
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 5-142 1.04e-49

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 167.17  E-value: 1.04e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948    5 IEMYTDGACKSNPGPGGWGVLI---HAAKKKQElcggEINTTNNRMELTAVIKGVESLPQNSQVRIITDSQYVKDGMTKW 81
Cdd:pfam00075   4 VTVYTDGSCLGNPGPGGAGAVLyrgHENISAPL----PGRTTNNRAELQAVIEALKALKSPSKVNIYTDSQYVIGGITQW 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 923400948   82 IKKWRNNGW-VTSNKQPVKNRDLWEQLDTVLQRlHKIEWVWVKGHAGTPGNERADQLANQGV 142
Cdd:pfam00075  80 VHGWKKNGWpTTSEGKPVKNKDLWQLLKALCKK-HQVYWQWVKGHAGNPGNEMADRLAKQGA 140
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 265-437 2.01e-46

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 159.39  E-value: 2.01e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   265 RQIVLDTETTGLTPDEHRIIEIGAIELIDRRfTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAYLQ 344
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   345 GAELIIHN-APFDTGFLDAEFARLANKQHIAtvkvnkiCTVTDTLIMARQAYPG-KSNNLDALCKRYNIDQSHRTvHGAL 422
Cdd:smart00479  80 GRILVAGNsAHFDLRFLKLEHPRLGIKQPPK-------LPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQRA-HRAL 151

                          170
                   ....*....|....*
gi 923400948   423 LDAKLLATVYLAMTG 437
Cdd:smart00479 152 DDARATAKLFKKLLE 166
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 267-432 2.35e-38

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: 137.48  E-value: 2.35e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  267 IVLDTETTGLTPDEHRIIEIGAIELI-DRRFTNNNFHQYLQPDR--EIEPGATKVHGIVNAFLEDKPRFADIAADLIAYL 343
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDgGENEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  344 Q-GAELIIHNAPFDTGFLDAEFARLANKQhiatvkVNKICTVTDTLIMARQAYPG-KSNNLDALCKRYNIDQShRTVHGA 421
Cdd:pfam00929  81 RkGNLLVAHNASFDVGFLRYDDKRFLKKP------MPKLNPVIDTLILDKATYKElPGRSLDALAEKLGLEHI-GRAHRA 153

                         170
                  ....*....|.
gi 923400948  422 LLDAKLLATVY 432
Cdd:pfam00929 154 LDDARATAKLF 164
 
Name Accession Description Interval E-value
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 261-502 5.91e-130

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 377.28  E-value: 5.91e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 261 TKKLRQIVLDTETTGLTP-DEHRIIEIGAIELIDRRFTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADL 339
Cdd:PRK05711   1 TAIMRQIVLDTETTGLNQrEGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 340 IAYLQGAELIIHNAPFDTGFLDAEFARLanKQHIAtvKVNKICTVTDTLIMARQAYPGKSNNLDALCKRYNIDQSHRTVH 419
Cdd:PRK05711  81 LDFIRGAELIIHNAPFDIGFMDYEFALL--GRDIP--KTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLH 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 420 GALLDAKLLATVYLAMTGGQATLSLaADLNDNIQIDKPNKIPQANAKRLPLQIIRATLEELELHQTRLEQINqKSNGQCL 499
Cdd:PRK05711 157 GALLDAEILAEVYLAMTGGQTSLGF-AMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLD-KKGGSCL 234


                 ...
gi 923400948 500 WLK 502
Cdd:PRK05711 235 WRK 237
dnaQ_proteo TIGR01406
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ...
 265-494 8.00e-101

DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130473 [Multi-domain]  Cd Length: 225  Bit Score: 302.39  E-value: 8.00e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  265 RQIVLDTETTGLTPDE-HRIIEIGAIELIDRRFTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAYL 343
Cdd:TIGR01406   1 RQIILDTETTGLDPKGgHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  344 QGAELIIHNAPFDTGFLDAEFARLANKQHiatvKVNKICTVTDTLIMARQAYPGKSNNLDALCKRYNIDQSHRTVHGALL 423
Cdd:TIGR01406  81 GGSELVIHNAAFDVGFLNYELERLGPTIK----KIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALL 156

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 923400948  424 DAKLLATVYLAMTGGQATLSLAADLNDNIqIDKPNKIPqANAKRLPLQIIRATLEELELHQTRLEQINQKS 494
Cdd:TIGR01406 157 DAHLLAEVYLALTGGQESLLELAESNSGE-AAKPSKSA-EMKLGATLRVLAPREAELQAHEAYLDKLLKKS 225
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 266-436 1.13e-98

DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme 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: 99835 [Multi-domain]  Cd Length: 167  Bit Score: 294.44  E-value: 1.13e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 266 QIVLDTETTGLTPDE-HRIIEIGAIELIDRRFTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAYLQ 344
Cdd:cd06131    1 QIVLDTETTGLDPREgHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 345 GAELIIHNAPFDTGFLDAEFARLANKQhiatvKVNKICTVTDTLIMARQAYPGKSNNLDALCKRYNIDQSHRTVHGALLD 424
Cdd:cd06131   81 GAELVIHNASFDVGFLNAELSLLGLGK-----KIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLD 155

                        170
                 ....*....|..
gi 923400948 425 AKLLATVYLAMT 436
Cdd:cd06131  156 AELLAEVYLELT 167
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 5-141 2.89e-83

RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 253.94  E-value: 2.89e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   5 IEMYTDGACKSNPGPGGWGVLIHAAKKKQELCGGEINTTNNRMELTAVIKGVESLPQNSQVRIITDSQYVKDGMTKWIKK 84
Cdd:cd09278    2 IVIYTDGACLGNPGPGGWAAVIRYGDHEKELSGGEPGTTNNRMELTAAIEALEALKEPCPVTIYTDSQYVINGITKWIKG 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 923400948  85 WRNNGWVTSNKQPVKNRDLWEQLDTVLQRlHKIEWVWVKGHAGTPGNERADQLANQG 141
Cdd:cd09278   82 WKKNGWKTADGKPVKNRDLWQELDALLAG-HKVTWEWVKGHAGHPGNERADRLANKA 137
rnhA PRK00203
ribonuclease H; Reviewed
 5-142 9.53e-79

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 242.81  E-value: 9.53e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   5 IEMYTDGACKSNPGPGGWGVLIHAAKKKQELCGGEINTTNNRMELTAVIKGVESLPQNSQVRIITDSQYVKDGMTKWIKK 84
Cdd:PRK00203   4 VEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKEPCEVTLYTDSQYVRQGITEWIHG 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 923400948  85 WRNNGWVTSNKQPVKNRDLWEQLDTVLQRlHKIEWVWVKGHAGTPGNERADQLANQGV 142
Cdd:PRK00203  84 WKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGA 140
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 265-483 4.11e-69

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: 220.40  E-value: 4.11e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  265 RQIVLDTETTGLTP-----DEHRIIEIGAIELIDRRFTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADL 339
Cdd:TIGR00573   2 RQLVLDTETTGDNEttglyAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  340 IAYLQGAELIIHNAPFDTGFLDAEFARLANKQhiatVKVNKICTVTDTLIMARQAYPGKSNNLDALCKRYNIDQSHRTVH 419
Cdd:TIGR00573  82 ADYIRGAELVIHNASFDVGFLNYEFSKLYKVE----PKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALH 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 923400948  420 GALLDAKLLATVYLAMTGGQATlslaadLNDNIQIDKPNKIPQANAKRLP--LQIIRATLEELELH 483
Cdd:TIGR00573 158 GALADAFILAKLYLVMTGKQTK------YGENEGQQSRPYHAIKSIVKKDmlLKLIKAVSTELQAH 217
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 265-437 4.49e-69

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 218.12  E-value: 4.49e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 265 RQIVLDTETTGLTPDEHRIIEIGAIELIDRRFTNNnFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAYLQ 344
Cdd:COG0847    1 RFVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVET-FHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 345 GAELIIHNAPFDTGFLDAEFARLANKqhiatvkvNKICTVTDTLIMARQAYPG-KSNNLDALCKRYNIDQSHRtvHGALL 423
Cdd:COG0847   80 GAVLVAHNAAFDLGFLNAELRRAGLP--------LPPFPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRALA 149

                        170
                 ....*....|....
gi 923400948 424 DAKLLATVYLAMTG 437
Cdd:COG0847  150 DAEATAELFLALLR 163
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
5-142 2.98e-68

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 215.09  E-value: 2.98e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   5 IEMYTDGACKSNPGPGGWGVLIHAAKKKQELCGGEINTTNNRMELTAVIKGVESLPQN--SQVRIITDSQYVKDGMTKWI 82
Cdd:COG0328    3 IEIYTDGACRGNPGPGGWGAVIRYGGEEKELSGGLGDTTNNRAELTALIAALEALKELgpCEVEIYTDSQYVVNQITGWI 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  83 KKWRNNGWvtsnkQPVKNRDLWEQLDTVLQRlHKIEWVWVKGHAGTPGNERADQLANQGV 142
Cdd:COG0328   83 HGWKKNGW-----KPVKNPDLWQRLDELLAR-HKVTFEWVKGHAGHPGNERADALANKAL 136
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 5-142 1.04e-49

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 167.17  E-value: 1.04e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948    5 IEMYTDGACKSNPGPGGWGVLI---HAAKKKQElcggEINTTNNRMELTAVIKGVESLPQNSQVRIITDSQYVKDGMTKW 81
Cdd:pfam00075   4 VTVYTDGSCLGNPGPGGAGAVLyrgHENISAPL----PGRTTNNRAELQAVIEALKALKSPSKVNIYTDSQYVIGGITQW 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 923400948   82 IKKWRNNGW-VTSNKQPVKNRDLWEQLDTVLQRlHKIEWVWVKGHAGTPGNERADQLANQGV 142
Cdd:pfam00075  80 VHGWKKNGWpTTSEGKPVKNKDLWQLLKALCKK-HQVYWQWVKGHAGNPGNEMADRLAKQGA 140
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 267-435 1.36e-46

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 160.31  E-value: 1.36e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 267 IVLDTETTGLTPDEHRIIEIGAI-----ELIDRrftnnnFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIA 341
Cdd:COG2176   11 VVFDLETTGLSPKKDEIIEIGAVkvengEIVDR------FSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 342 YLQGAELIIHNAPFDTGFLDAEFARLANKQHIATVkvnkictvtDTLIMARQAYPG-KSNNLDALCKRYNIDQSHRtvHG 420
Cdd:COG2176   85 FLGDAVLVAHNASFDLGFLNAALKRLGLPFDNPVL---------DTLELARRLLPElKSYKLDTLAERLGIPLEDR--HR 153

                        170
                 ....*....|....*
gi 923400948 421 ALLDAKLLATVYLAM 435
Cdd:COG2176  154 ALGDAEATAELFLKL 168
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 265-437 2.01e-46

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 159.39  E-value: 2.01e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   265 RQIVLDTETTGLTPDEHRIIEIGAIELIDRRfTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAYLQ 344
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   345 GAELIIHN-APFDTGFLDAEFARLANKQHIAtvkvnkiCTVTDTLIMARQAYPG-KSNNLDALCKRYNIDQSHRTvHGAL 422
Cdd:smart00479  80 GRILVAGNsAHFDLRFLKLEHPRLGIKQPPK-------LPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQRA-HRAL 151

                          170
                   ....*....|....*
gi 923400948   423 LDAKLLATVYLAMTG 437
Cdd:smart00479 152 DDARATAKLFKKLLE 166
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 7-141 5.25e-46

Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos.


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 157.34  E-value: 5.25e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   7 MYTDGACKSNPGPG---GWGVLI--HAAKKKQELCGGEiNTTNNRMELTAVIKGVESLPQNS--QVRIITDSQYVKDGMT 79
Cdd:cd09280    2 VYTDGSCLNNGKPGaraGIGVYFgpGDPRNVSEPLPGR-KQTNNRAELLAVIHALEQAPEEGirKLEIRTDSKYAINCIT 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 923400948  80 KWIKKWRNNGWVTSNKQPVKNRDLWEQLDTVLQRLH-KIEWVWVKGHAGTPGNERADQLANQG 141
Cdd:cd09280   81 KWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRKRGiKVKFEHVKGHSGDPGNEEADRLAREG 143
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 267-433 2.68e-45

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: 155.92  E-value: 2.68e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 267 IVLDTETTGLTPDEHRIIEIGAIELIDRRFTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAYLQGA 346
Cdd:cd06127    1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 347 ELIIHNAPFDTGFLDAEFARLANKQHiatvKVNKICTVTdtliMARQAYPGKSNNL--DALCKRYNIDQSHRtvHGALLD 424
Cdd:cd06127   81 VLVAHNASFDLRFLNRELRRLGGPPL----PNPWIDTLR----LARRLLPGLRSHRlgLLLAERYGIPLEGA--HRALAD 150


                 ....*....
gi 923400948 425 AKLLATVYL 433
Cdd:cd06127  151 ALATAELLL 159
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 267-432 2.35e-38

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: 137.48  E-value: 2.35e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  267 IVLDTETTGLTPDEHRIIEIGAIELI-DRRFTNNNFHQYLQPDR--EIEPGATKVHGIVNAFLEDKPRFADIAADLIAYL 343
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDgGENEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  344 Q-GAELIIHNAPFDTGFLDAEFARLANKQhiatvkVNKICTVTDTLIMARQAYPG-KSNNLDALCKRYNIDQShRTVHGA 421
Cdd:pfam00929  81 RkGNLLVAHNASFDVGFLRYDDKRFLKKP------MPKLNPVIDTLILDKATYKElPGRSLDALAEKLGLEHI-GRAHRA 153

                         170
                  ....*....|.
gi 923400948  422 LLDAKLLATVY 432
Cdd:pfam00929 154 LDDARATAKLF 164
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 7-142 2.49e-30

Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many of which are uncharacterized. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication.


Pssm-ID: 260014 [Multi-domain]  Cd Length: 153  Bit Score: 115.37  E-value: 2.49e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   7 MYTDGACKSNPGPG---GWGVLIHAAKKKQElCG-----GEINTTNNRMELTAVIKGVE-----SLPQN---SQVRIITD 70
Cdd:cd13934    2 VYIDGACRNNGRPDaraGYGVYFGPDSSYNV-SGrledtGGHPQTSQRAELRAAIAALRfrswiIDPDGeglKTVVIATD 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 923400948  71 SQYVKDGMTKWIKKWRNNGWVTSNKQPVKNRDLWEQLDTVLQRL--HKIE-WVWvkgHAGTPGNERADQLANQGV 142
Cdd:cd13934   81 SEYVVKGATEWIPKWKRNGWRTSKGKPVKNRDLFELLLDEIEDLeeGGVEvQFW---HVPRELNKEADRLAKAAA 152
PRK06063 PRK06063
DEDDh family exonuclease;
268-449 7.33e-25

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 104.78  E-value: 7.33e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 268 VLDTETTGLTPDEHRIIEIGAIELIDRRFTNNNFHQYLQPdrEIEPGATKVHGIVNAFLEDKPRFADIAADLIAYLQGAE 347
Cdd:PRK06063  19 VVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNP--GVDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRGRT 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 348 LIIHNAPFDTGFLDAEFARLANKQHIATVkvnkICTVTdtliMARQAYPGKSN-NLDALCKRYNIDQsHRTvHGALLDAK 426
Cdd:PRK06063  97 LVAHNVAFDYSFLAAEAERAGAELPVDQV----MCTVE----LARRLGLGLPNlRLETLAAHWGVPQ-QRP-HDALDDAR 166

                        170       180
                 ....*....|....*....|...
gi 923400948 427 LLATVYlamtggQATLSLAADLN 449
Cdd:PRK06063 167 VLAGIL------RPSLERARERD 183
polC PRK00448
DNA polymerase III PolC; Validated
 254-435 3.35e-24

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 106.85  E-value: 3.35e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  254 YSNKKSSTKKLRQIVLDTETTGLTPDEHRIIEIGAI-----ELIDRrftnnnFHQYLQPDREIEPGATKVHGIVNAFLED 328
Cdd:PRK00448  409 YNEVDRDLKDATYVVFDVETTGLSAVYDEIIEIGAVkikngEIIDK------FEFFIKPGHPLSAFTTELTGITDDMVKD 482

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  329 KPRFADIAADLIAYLQGAELIIHNAPFDTGFLDAEFARLaNKQHIAtvkvnkiCTVTDTLIMARQAYPG-KSNNLDALCK 407
Cdd:PRK00448  483 APSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKL-GLEKIK-------NPVIDTLELSRFLYPElKSHRLNTLAK 554

                         170       180       190
                  ....*....|....*....|....*....|
gi 923400948  408 RYNI--DQSHRtvhgALLDAKLLATVYLAM 435
Cdd:PRK00448  555 KFGVelEHHHR----ADYDAEATAYLLIKF 580
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 262-435 9.26e-23

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 102.34  E-value: 9.26e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 262 KKLRQIVLDTETTGLTP-DEHRIIEIGAI-----ELIDRrftnnnFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADI 335
Cdd:PRK08074   1 MSKRFVVVDLETTGNSPkKGDKIIQIAAVvvedgEILER------FSSFVNPERPIPPFITELTGISEEMVKQAPLFEDV 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 336 AADLIAYLQGAELIIHNAPFDTGFLDAEFaRLANKQHIAtvkvnkiCTVTDTLIMARQAYPG-KSNNLDALCKRYNI--D 412
Cdd:PRK08074  75 APEIVELLEGAYFVAHNVHFDLNFLNEEL-ERAGYTEIH-------CPKLDTVELARILLPTaESYKLRDLSEELGLehD 146

                        170       180
                 ....*....|....*....|...
gi 923400948 413 QSHRtvhgALLDAKLLATVYLAM 435
Cdd:PRK08074 147 QPHR----ADSDAEVTAELFLQL 165
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
268-431 2.08e-22

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 100.38  E-value: 2.08e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 268 VLDTETTGLTPDEHRIIEIGAI-----ELIDRrftnnnFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAY 342
Cdd:PRK07883  19 VVDLETTGGSPAGDAITEIGAVkvrggEVLGE------FATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEF 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 343 LQGAELIIHNAPFDTGFLDAEFARLankqHIATVKVnkicTVTDTLIMARQAYPG---KSNNLDALCKRYNIDQ--SHRt 417
Cdd:PRK07883  93 ARGAVLVAHNAPFDIGFLRAAAARC----GYPWPGP----PVLCTVRLARRVLPRdeaPNVRLSTLARLFGATTtpTHR- 163

                        170
                 ....*....|....
gi 923400948 418 vhgALLDAKllATV 431
Cdd:PRK07883 164 ---ALDDAR--ATV 172
PRK06548 PRK06548
ribonuclease H; Provisional
 9-141 7.32e-21

ribonuclease H; Provisional


Pssm-ID: 75628 [Multi-domain]  Cd Length: 161  Bit Score: 89.49  E-value: 7.32e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   9 TDGACKSNPGPGGWGVLIHAAKKKQelcGGEINTTNNRMELTAVIKG-VESLPQNSQVRIITDSQYVKDGMTKWIKKWRN 87
Cdd:PRK06548  10 TDGSSLANPGPSGWAWYVDENTWDS---GGWDIATNNIAELTAVRELlIATRHTDRPILILSDSKYVINSLTKWVYSWKM 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 923400948  88 NGWVTSNKQPVKNRDLWEQLDTVLQRlHKIEWVWVKGHAGTPGNERADQLANQG 141
Cdd:PRK06548  87 RKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQA 139
PRK08719 PRK08719
ribonuclease H; Reviewed
 1-140 7.83e-21

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 88.76  E-value: 7.83e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   1 MNAWIEMYTDGACKSNPG---PGGWGVLIH-AAKKKQELCGGEIN--TTNNRMELTAVIKGVEsLPQNSQVrIITDSQYV 74
Cdd:PRK08719   1 MRASYSIYIDGAAPNNQHgcvRGGIGLVVYdEAGEIVDEQSITVNryTDNAELELLALIEALE-YARDGDV-IYSDSDYC 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 923400948  75 KDGMTKWIKKWRNNGWVTSNKQPVKNRDLWEQLDTvLQRLHKIEWVWVKGHAGTPGNERADQLANQ 140
Cdd:PRK08719  79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDE-LRARKYVEVEKVTAHSGIEGNEAADMLAQA 143
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 8-139 1.56e-20

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 86.98  E-value: 1.56e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   8 YTDGACKSNPGPGGWGVLIHAAKKKQeLCGGEINT---TNNRMELTAVIKGVESLPQ--NSQVRIITDSQYVKDGMTKWI 82
Cdd:cd06222    2 NVDGSCRGNPGPAGIGGVLRDHEGGW-LGGFALKIgapTALEAELLALLLALELALDlgYLKVIIESDSKYVVDLINSGS 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 923400948  83 KKWRNNGwvtsnkqpvknrDLWEQLDTVLQRLHKIEWVWVKGhagtPGNERADQLAN 139
Cdd:cd06222   81 FKWSPNI------------LLIEDILLLLSRFWSVKISHVPR----EGNQVADALAK 121
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 267-434 5.78e-18

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: 81.02  E-value: 5.78e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 267 IVLDTETTglTPDEHRIIEIGAI-----ELIDRrftnnnFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIA 341
Cdd:cd06130    2 VAIDFETA--NADRASACSIGLVkvrdgQIVDT------FYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKP 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 342 YLQGAELIIHNAPFDTGFLDAEFARLAnkqhIATVKVNKICTVTdtliMARQAYPGKSN-NLDALCKRYNIDQSHrtvHG 420
Cdd:cd06130   74 FLGGSLVVAHNASFDRSVLRAALEAYG----LPPPPYQYLCTVR----LARRVWPLLPNhKLNTVAEHLGIELNH---HD 142

                        170
                 ....*....|....
gi 923400948 421 ALLDAKLLATVYLA 434
Cdd:cd06130  143 ALEDARACAEILLA 156
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 262-443 6.21e-18

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 83.34  E-value: 6.21e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 262 KKLRQIVLDTETTGLTPDEHRIIEIGAIelidrRFTNNN----FHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAA 337
Cdd:PRK06310   5 KDTEFVCLDCETTGLDVKKDRIIEFAAI-----RFTFDEvidsVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 338 DLIAYLQGAELII-HNAPFDTGFLDAEFARlankqhIATVKVNKICTVTDTLIMARQAYPGKSNNLDALCKRYNIDqsHR 416
Cdd:PRK06310  80 QIKGFFKEGDYIVgHSVGFDLQVLSQESER------IGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVP--YD 151

                        170       180
                 ....*....|....*....|....*..
gi 923400948 417 TVHGALLDAKLLATVYLAMTGGQATLS 443
Cdd:PRK06310 152 GNHRAMKDVEINIKVFKHLCKRFRTLE 178
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 5-141 1.31e-17

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 79.05  E-value: 1.31e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   5 IEMYTDGACKSNPGPGGWGVLIHAAKKKQELCGGEI--NTTNNRMELTAVIKGVESL--PQNSQVRIITDSQYVKDGMTk 80
Cdd:cd09279    1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVLELSERLgfPATNNEAEYEALIAGLELAleLGAEKLEIYGDSQLVVNQLN- 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 923400948  81 wiKKWRnngwvtsnkqpVKN---RDLWEQLDTVLQRLHKIEWVWVKGHAgtpgNERADQLANQG 141
Cdd:cd09279   80 --GEYK-----------VKNerlKPLLEKVLELLAKFELVELKWIPREQ----NKEADALANQA 126
PRK07740 PRK07740
hypothetical protein; Provisional
 262-432 2.30e-17

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 81.64  E-value: 2.30e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 262 KKLRQIVLDTETTGLTPDE-HRIIEIGAIELIDRRFTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLI 340
Cdd:PRK07740  57 TDLPFVVFDLETTGFSPQQgDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFY 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 341 AYLQGAELIIHNAPFDTGFLDAEFARlankqhiaTVKVNKICTVTDT-LIMARQAYPGKSNNLDALCKRYNIDQSHRtvH 419
Cdd:PRK07740 137 AFIGAGVLVAHHAGHDKAFLRHALWR--------TYRQPFTHRLIDTmFLTKLLAHERDFPTLDDALAYYGIPIPRR--H 206

                        170
                 ....*....|...
gi 923400948 420 GALLDAKLLATVY 432
Cdd:PRK07740 207 HALGDALMTAKLW 219
PRK06807 PRK06807
3'-5' exonuclease;
267-433 1.55e-16

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 80.24  E-value: 1.55e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 267 IVLDTETTGLTPDEHRIIEIGAI-----ELIDRrftnnnFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIA 341
Cdd:PRK06807  11 VVIDFETTGFNPYNDKIIQVAAVkyrnhELVDQ------FVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 342 YLQGAELIIHNAPFDTGFLDAEFARLaNKQHIATVkvnkictVTDTLIMARQAYPGKSNNLDALCKRY-NIDQSHrtvHG 420
Cdd:PRK06807  85 FLHTNVIVAHNASFDMRFLKSNVNML-GLPEPKNK-------VIDTVFLAKKYMKHAPNHKLETLKRMlGIRLSS---HN 153

                        170
                 ....*....|...
gi 923400948 421 ALLDAKLLATVYL 433
Cdd:PRK06807 154 AFDDCITCAAVYQ 166
PRK09145 PRK09145
3'-5' exonuclease;
267-440 4.14e-16

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 76.86  E-value: 4.14e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 267 IVLDTETTGLTPDEHRIIEIGAIELIDRR-FTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAYLQG 345
Cdd:PRK09145  32 VALDCETTGLDPRRAEIVSIAAVKIRGNRiLTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIGN 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 346 AELIIHNAPFDTGFLDaefarLANKQHIATVKVNKICTVT----DTLImaRQAYPGKSN-NLDALCKRYNIDQSHRtvHG 420
Cdd:PRK09145 112 RPLVGYYLEFDVAMLN-----RYVRPLLGIPLPNPLIEVSalyyDKKE--RHLPDAYIDlRFDAILKHLDLPVLGR--HD 182

                        170       180
                 ....*....|....*....|
gi 923400948 421 ALLDAKLLATVYLAMTGGQA 440
Cdd:PRK09145 183 ALNDAIMAALIFLRLRKGDA 202
PRK09182 PRK09182
DNA polymerase III subunit epsilon; Validated
 261-370 1.17e-14

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236397 [Multi-domain]  Cd Length: 294  Bit Score: 74.63  E-value: 1.17e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 261 TKKLRQIVLDTETTGLTPDEHRIIEIGAIELidrRFTNNN--------FHQYLQPDREIEPGATKVHGIVNAFLEDKPrf 332
Cdd:PRK09182  34 EFVRLGVILDTETTGLDPRKDEIIEIGMVAF---EYDDDGrigdvldtFGGLQQPSRPIPPEITRLTGITDEMVAGQT-- 108

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 923400948 333 ADIAAdLIAYLQGAELII-HNAPFDTGFLDAEFARLANK 370
Cdd:PRK09182 109 IDPAA-VDALIAPADLIIaHNAGFDRPFLERFSPVFATK 146
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 267-434 4.77e-14

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 71.55  E-value: 4.77e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 267 IVLDTETTGLTPDEHRIIEiGAIELIDRRFTNNNFHQYL-QPDREIEPGATKVHGIVNAFLEDKPR-FADIAADLIAYLQ 344
Cdd:PRK07942   9 AAFDLETTGVDPETARIVT-AALVVVDADGEVVESREWLaDPGVEIPEEASAVHGITTEYARAHGRpAAEVLAEIADALR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 345 -----GAELIIHNAPFDTGFLDAEFARLANKQHIATVkvnkictVTDTLIMARQA--Y-PGKsNNLDALCKRYNIDQShr 416
Cdd:PRK07942  88 eawarGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGP-------VIDPYVIDKAVdrYrKGK-RTLTALCEHYGVRLD-- 157

                        170
                 ....*....|....*...
gi 923400948 417 TVHGALLDAklLATVYLA 434
Cdd:PRK07942 158 NAHEATADA--LAAARVA 173
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 268-428 7.40e-14

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 70.90  E-value: 7.40e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 268 VLDTETTGLtpdEHRIIEIGAIELIDRRFTNNNFHqYLQPDREIEPGATKVHGIVNAFLEDKPRFADIaadlIAYLQGAE 347
Cdd:PRK07983   4 VIDTETCGL---QGGIVEIASVDVIDGKIVNPMSH-LVRPDRPISPQAMAIHRITEAMVADKPWIEDV----IPHYYGSE 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 348 L-IIHNAPFDTGFL---DAEFarlankqhiatvkvnkICTVTdtliMARQAYPGKSNNLDALCKRYNIDQS-------HR 416
Cdd:PRK07983  76 WyVAHNASFDRRVLpemPGEW----------------ICTMK----LARRLWPGIKYSNMALYKSRKLNVQtppglhhHR 135

                        170
                 ....*....|..
gi 923400948 417 TVHGALLDAKLL 428
Cdd:PRK07983 136 ALYDCYITAALL 147
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 265-437 8.09e-14

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 70.99  E-value: 8.09e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 265 RQIVLDTETTGLTPDEHRIIEIGAIELIdrrfTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAYLQ 344
Cdd:PRK06309   3 ALIFYDTETTGTQIDKDRIIEIAAYNGV----TSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 345 G-AELIIHNA-PFDTGFLDAEFARlankqHIATVKVNKictVTDTLIMARQAYPG-KSNNLDALCKRYNI--DQSHRtvh 419
Cdd:PRK06309  79 TdNILVAHNNdAFDFPLLRKECRR-----HGLEPPTLR---TIDSLKWAQKYRPDlPKHNLQYLRQVYGFeeNQAHR--- 147

                        170
                 ....*....|....*...
gi 923400948 420 gALLDAKLLATVYLAMTG 437
Cdd:PRK06309 148 -ALDDVITLHRVFSALVG 164
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 8-142 2.24e-12

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 64.16  E-value: 2.24e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   8 YTDGAckSNPGPGGWGVLIHAAKKKQELCGG-EINTTNNRMELTAVIKGVESL----PQNSQVRIITDSQYVKDGMTKWi 82
Cdd:cd09276    3 YTDGS--KLEGSVGAGFVIYRGGEVISRSYRlGTHASVFDAELEAILEALELAlataRRARKVTIFTDSQSALQALRNP- 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  83 kkwrnngwvTSNKQPVKNRDLWEQLDTVLQRLHKIEWVWVKGHAGTPGNERADQLANQGV 142
Cdd:cd09276   80 ---------RRSSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVGIEGNEAADRLAKEAA 130
PRK08517 PRK08517
3'-5' exonuclease;
255-428 7.39e-12

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 65.43  E-value: 7.39e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 255 SNKKSSTKKLRQIVLDTETTGLTPDEHRIIEIGAI-----ELIDRrftnnnFHQYLQPDrEIEPGATKVHGIVNAFLEDK 329
Cdd:PRK08517  59 KTRFTPIKDQVFCFVDIETNGSKPKKHQIIEIGAVkvkngEIIDR------FESFVKAK-EVPEYITELTGITYEDLENA 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 330 PRFADIAADLIAYLQGAELIIHNAPFDTGFLDAEFAR-----LANKqhiatvkvnKICTVTdtliMARQAYPGKSNNLDA 404
Cdd:PRK08517 132 PSLKEVLEEFRLFLGDSVFVAHNVNFDYNFISRSLEEiglgpLLNR---------KLCTID----LAKRTIESPRYGLSF 198

                        170       180
                 ....*....|....*....|....*.
gi 923400948 405 LCKRYNID--QSHRTVHGALLDAKLL 428
Cdd:PRK08517 199 LKELLGIEieVHHRAYADALAAYEIF 224
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 269-362 2.34e-10

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 60.71  E-value: 2.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 269 LDTETTGLTPDEHRIIEIGAIEL-IDRRFTNNNFHQYLQPDREIEPGATKVHGIVNAFLEDKPRFADIAADLIAYLQGAE 347
Cdd:PRK09146  52 LDFETTGLDAEQDAIVSIGLVPFtLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEALAGKV 131

                         90
                 ....*....|....*
gi 923400948 348 LIIHNAPFDTGFLDA 362
Cdd:PRK09146 132 VVVHYRRIERDFLDQ 146
PRK05601 PRK05601
DNA polymerase III subunit epsilon; Validated
 241-369 2.76e-09

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235529 [Multi-domain]  Cd Length: 377  Bit Score: 59.07  E-value: 2.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 241 NVKKTTSKNTKRSYSNKKSSTKKLRQIVLDTETTGLTPDEHRIIEIGAIELIDRRFTNNNFHQYLQPdrEIEPGATKVHG 320
Cdd:PRK05601  23 STTSPSEDHAARQEAARQEAIEAAPFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNP--GEDPGPFHLHG 100

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 923400948 321 IVNAFLEDKPRFADIAADLIAYLQGAELIIHNAPFDTGFLDAEFARLAN 369
Cdd:PRK05601 101 LSAEEFAQGKRFSQILKPLDRLIDGRTLILHNAPRTWGFIVSEAKRAMN 149
RNase_HI_bacteria_like cd09277
Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H ...
 5-142 2.87e-08

Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids.


Pssm-ID: 260009 [Multi-domain]  Cd Length: 133  Bit Score: 52.49  E-value: 2.87e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   5 IEMYTDGACKSNPGPGGWGVLIHAAKKKQELCGGEINTTNNRM-----ELTAVIKGVESLPQN--SQVRIITDSQyvkdG 77
Cdd:cd09277    1 VIAYVDGSYNKETKKYGYGVVIIKNGKEEEFSGSGNDPEYASMrnvagEIKGAMKAIKYAIENgiKKITIYYDYE----G 76

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 923400948  78 mtkwIKKWRNNGWVTSNKQPVKNRDLWEQLdtvlQRLHKIEWVWVKGHAGTPGNERADQLANQGV 142
Cdd:cd09277   77 ----IEKWATGEWKANKELTKEYKEFMQKY----KKKIKIEFVKVKAHSGDKYNELADKLAKKAL 133
TREX1_2 cd06136
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ...
 267-370 3.03e-08

DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins; Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TREX2 that point to different biological roles for these proteins. The main difference is the presence of about 70 amino acids at the C-terminus of TREX1. In addition, TREX1 has a nonrepetitive proline-rich region that is not present in the TREX2 protein. Furthermore, TREX2 contains a conserved DNA binding loop positioned adjacent to the active site that has a sequence distinct from the corresponding loop in TREX1. Truncations in the C-terminus of human TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy (RVCL), a neurovascular syndrome featuring a progressive loss of visual acuity combined with a variable neurological picture.


Pssm-ID: 99839 [Multi-domain]  Cd Length: 177  Bit Score: 53.49  E-value: 3.03e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 267 IVLDTETTGLTP-DEHRIIEIGAIElIDRRFTNNNFHQYL-------------QPDREIEPGATKVHGIVNAFLEDKPRF 332
Cdd:cd06136    2 VFLDLETTGLPKhNRPEITELCLVA-VHRDHLLNTSRDKPalprvldklslcfNPGRAISPGASEITGLSNDLLEHKAPF 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 923400948 333 ADIAADLI-AYLQGAE----LIIHNA-PFDTGFLDAEFARLANK 370
Cdd:cd06136   81 DSDTANLIkLFLRRQPkpicLVAHNGnRFDFPILRSELERLGTK 124
rnhA PRK13907
ribonuclease H; Provisional
 5-142 6.45e-08

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 51.21  E-value: 6.45e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   5 IEMYTDGACKSNPGPGGWGVLIHAAKKKQELCGGEINTTNNRMELTAVIKGVESLPQN--SQVRIITDSQYVKDGMtkwi 82
Cdd:PRK13907   2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHnyNIVSFRTDSQLVERAV---- 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  83 kkwrnngwvtsNKQPVKNRDLWEQLDTVLQRLHKIEWVWVKgHAGTPGNERADQLANQGV 142
Cdd:PRK13907  78 -----------EKEYAKNKMFAPLLEEALQYIKSFDLFFIK-WIPSSQNKVADELARKAI 125
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
 267-429 8.92e-07

DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. 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. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.


Pssm-ID: 99837 [Multi-domain]  Cd Length: 189  Bit Score: 49.21  E-value: 8.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 267 IVLDTETTGLTPDEHRIIEIGAIEL-IDRR---FTNNNFHQYLQP--DREIEPGATKVHGIV--NAFledkpRFADIAAD 338
Cdd:cd06134    8 VVVDVETGGFNPQTDALLEIAAVTLeMDEQgnlYPDETFHFHILPfeGANLDPAALEFNGIDpfHPF-----RFAVDEKE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 339 LIAYL-------------QGAELIIHNAPFDTGFLDAEFARlankqhiATVKVNKI--CTVTDTLIMARQAYpGKSnNLD 403
Cdd:cd06134   83 ALKEIfkpirkalkaqgcTRAILVGHNAHFDLGFLNAAVAR-------CKIKRNPFhpFSTFDTATLAGLAY-GQT-VLA 153

                        170       180
                 ....*....|....*....|....*.
gi 923400948 404 ALCKRYNIDQSHRTVHGALLDAKLLA 429
Cdd:cd06134  154 KACQAAGIEFDNKEAHSALYDTQKTA 179
YprB COG3359
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ...
 267-373 5.78e-05

Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];


Pssm-ID: 442587 [Multi-domain]  Cd Length: 198  Bit Score: 44.17  E-value: 5.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 267 IVLDTETTGLTPDEHRIIEIGAIELIDRRFTnnnFHQYLQPDREIEPgatkvhgivnAFLEdkprfadiaaDLIAYLQGA 346
Cdd:COG3359   18 LFFDIETTGLSGGGTVIFLIGLADGEGDGFV---VRQYFGEDPGEEA----------ALLE----------AFLEWLADY 74

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 923400948 347 ELIIH-N-APFDTGFLDAEFA------RLANKQHI 373
Cdd:COG3359   75 KLLVTyNgKSFDLPFLKTRFTlhrlppPLPEFPHL 109
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 318-434 8.62e-05

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 44.39  E-value: 8.62e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 318 VHGIVNAFLEDKPRFADIAADLIAYLQGAELIIHNAPFDTGFLDAEfARLANkqhIATVKVNKICTVTdtliMARQAYPG 397
Cdd:PRK06195  53 IHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKT-LELYN---IPMPSFEYICTMK----LAKNFYSN 124

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 923400948 398 KSN-NLDALCKRYNIDQSHrtvHGALLDAKLLATVYLA 434
Cdd:PRK06195 125 IDNaRLNTVNNFLGYEFKH---HDALADAMACSNILLN 159
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 267-344 2.08e-04

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These 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. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.


Pssm-ID: 99836 [Multi-domain]  Cd Length: 176  Bit Score: 42.21  E-value: 2.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 267 IVLDTETT-----GLTPDEHRIIEIGAIeLIDRRFTNN--NFHQYLQPdrEIEPGA----TKVHGIVNAFLEDKPRFADI 335
Cdd:cd06133    2 LVIDFEATcwegnSKPDYPNEIIEIGAV-LVDVKTKEIidTFSSYVKP--VINPKLsdfcTELTGITQEDVDNAPSFPEV 78


                 ....*....
gi 923400948 336 AADLIAYLQ 344
Cdd:cd06133   79 LKEFLEWLG 87
Orn cd06135
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease ...
 269-289 4.30e-04

DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. 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. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.


Pssm-ID: 99838 [Multi-domain]  Cd Length: 173  Bit Score: 40.99  E-value: 4.30e-04
                         10        20
                 ....*....|....*....|.
gi 923400948 269 LDTETTGLTPDEHRIIEIGAI 289
Cdd:cd06135    4 IDLEMTGLDPEKDRILEIACI 24
UvrD_C pfam13361
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 265-330 8.27e-04

UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.


Pssm-ID: 433145 [Multi-domain]  Cd Length: 377  Bit Score: 41.62  E-value: 8.27e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 923400948  265 RQIVLDTETTGLTPDEHRIIEIGAIELIDRRFTNNNFHQYLQPDREIePGATKVHGIVNAFLEDKP 330
Cdd:pfam13361 187 NIVVFDVETTGLDTTEDEIIQIAAIKLNKKGVVIESFERFLRLKKPV-GDSLQVHGFSDEFLQENG 251
PRK05359 PRK05359
oligoribonuclease; Provisional
 267-289 8.86e-04

oligoribonuclease; Provisional


Pssm-ID: 235429  Cd Length: 181  Bit Score: 40.14  E-value: 8.86e-04
                         10        20
                 ....*....|....*....|...
gi 923400948 267 IVLDTETTGLTPDEHRIIEIGAI 289
Cdd:PRK05359   6 IWIDLEMTGLDPERDRIIEIATI 28
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 265-350 1.80e-03

3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 39.46  E-value: 1.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 265 RQIVLDTETT---GLTPDEHR--IIEIGAIELIDRRFTNNNFHQYLQPDR--EIEPGATKVHGIVNAFLEDKPRFADIAA 337
Cdd:COG5018    3 KYLVIDLEATcwdGKPPPGFPmeIIEIGAVKVDENGEIIDEFSSFVKPVRrpKLSPFCTELTGITQEDVDSAPSFAEAIE 82

                         90
                 ....*....|...
gi 923400948 338 DLIAYLQGAELII 350
Cdd:COG5018   83 DFKKWIGSEDYIL 95
Orn COG1949
Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];
269-289 2.31e-03

Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];


Pssm-ID: 441552  Cd Length: 177  Bit Score: 38.94  E-value: 2.31e-03
                         10        20
                 ....*....|....*....|.
gi 923400948 269 LDTETTGLTPDEHRIIEIGAI 289
Cdd:COG1949    7 IDLEMTGLDPETDRIIEIATI 27
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 8-140 2.90e-03

Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 38.09  E-value: 2.90e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948   8 YTDGACKSNpgpggwGVLIHAAKKKQELCGGEINTTNNRMELTAVIKGVEsLPQNSQVRIITDSQYV----KDGMTKWIK 83
Cdd:cd09273    3 FTDGSSFKA------GYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALE-LAKGKPVNIYTDSAYAvhalHLLETIGIE 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 923400948  84 KwrnngwvtSNKQPVKNRDLWEQLDTVLQRLHKIEWVWVKGHAGTP-----GNERADQLANQ 140
Cdd:cd09273   76 R--------GFLKSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPgplaeGNAQADAAAKQ 129
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 259-433 3.98e-03

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 40.06  E-value: 3.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 259 SSTKKLRQIVLDTETTGLTPDEhRIIEIGAI-----ELIDRRFTNNNFHQYLqpDREIepgatkVH--GIVNAFLEDKPR 331
Cdd:PRK07246   2 TQKKLRKYAVVDLEATGAGPNA-SIIQVGIViieggEIIDSYTTDVNPHEPL--DEHI------KHltGITDQQLAQAPD 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 332 FADIAADLIAYLQGAELIIHNAPFDTGFLdAEfARLANKQHIATVKVnkictvtDTLIMARQAYPG-KSNNLDALCKRYN 410
Cdd:PRK07246  73 FSQVARHIYDLIEDCIFVAHNVKFDANLL-AE-ALFLEGYELRTPRV-------DTVELAQVFFPTlEKYSLSHLSRELN 143

                        170       180
                 ....*....|....*....|...
gi 923400948 411 IDQSHrtVHGALLDAKLLATVYL 433
Cdd:PRK07246 144 IDLAD--AHTAIADARATAELFL 164
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 267-416 5.67e-03

3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyzes the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homolog of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.


Pssm-ID: 396266 [Multi-domain]  Cd Length: 173  Bit Score: 37.67  E-value: 5.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948  267 IVLDTETTGLTPDEHRIIEIgaieLIDRRFTNNNFHQ--YLQPDREIEPgatkvhgiVNAFLEDKPRfadiaadliaylq 344
Cdd:pfam01612  23 VAVDTETTSLDTYSYYLRGA----LIQIGTGEGAYIIdpLALGDDVLSA--------LKRLLEDPNI------------- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 923400948  345 gaELIIHNAPFDTGFLDAEFArlankqhiatvkvNKICTVTDTLIMARQAYPGKSNNLDALCKRY---NIDQSHR 416
Cdd:pfam01612  78 --TKVGHNAKFDLEVLARDFG-------------IKLRNLFDTMLAAYLLGYDRSHSLADLAEKYlgvELDKEEQ 137
ExoI_N cd06138
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ...
 270-321 7.69e-03

N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI 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. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.


Pssm-ID: 99841 [Multi-domain]  Cd Length: 183  Bit Score: 37.63  E-value: 7.69e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 923400948 270 DTETTGLTPDEHRIIEIGAIElidrrfTNNNFHQ--------YLQPDREIEPGATKVHGI 321
Cdd:cd06138    4 DYETFGLNPSFDQILQFAAIR------TDENFNEiepfnifcRLPPDVLPSPEALIVTGI 57
 
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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