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Conserved domains on  [gi|83033558|gb|ABB97232|]
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DinB, partial [Bacillus cereus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK01810 super family cl32019
DNA polymerase IV; Validated
 1-133 3.24e-93

DNA polymerase IV; Validated


The actual alignment was detected with superfamily member PRK01810:

Pssm-ID: 179337 [Multi-domain]  Cd Length: 407  Bit Score: 274.60  E-value: 3.24e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYALGSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTASD 80
Cdd:PRK01810  78 PNFDRYREASRQMFQILSEFTPLVQPVSIDEGYLDITDCYALGSPLEIAKMIQQRLLTELQLPCSIGIAPNKFLAKMASD 157

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 83033558   81 MKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAKGD 133
Cdd:PRK01810 158 MKKPLGITVLRKRDVPEMLWPLPVGEMHGIGEKTAEKLKDIGIQTIGDLAKAD 210
 
Name Accession Description Interval E-value
PRK01810 PRK01810
DNA polymerase IV; Validated
 1-133 3.24e-93

DNA polymerase IV; Validated


Pssm-ID: 179337 [Multi-domain]  Cd Length: 407  Bit Score: 274.60  E-value: 3.24e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYALGSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTASD 80
Cdd:PRK01810  78 PNFDRYREASRQMFQILSEFTPLVQPVSIDEGYLDITDCYALGSPLEIAKMIQQRLLTELQLPCSIGIAPNKFLAKMASD 157

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 83033558   81 MKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAKGD 133
Cdd:PRK01810 158 MKKPLGITVLRKRDVPEMLWPLPVGEMHGIGEKTAEKLKDIGIQTIGDLAKAD 210
PolY_Pol_IV_kappa cd03586
DNA Polymerase IV/Kappa; Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion ...
 1-133 2.86e-64

DNA Polymerase IV/Kappa; Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a higher error rate than other Y-family polymerases.


Pssm-ID: 176459 [Multi-domain]  Cd Length: 334  Bit Score: 198.51  E-value: 2.86e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558   1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYAL-GSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTAS 79
Cdd:cd03586  69 PRFDKYREVSRQIMEILREYTPLVEPLSIDEAYLDVTDYVRLfGSATEIAKEIRARIREETGLTASAGIAPNKFLAKIAS 148

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 83033558  80 DMKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAKGD 133
Cdd:cd03586 149 DLNKPNGLTVIPPEDVEEFLAPLPVRKIPGVGKVTAEKLKELGIKTIGDLAKLD 202
DinP COG0389
Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination ...
 1-131 1.36e-58

Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination and repair];


Pssm-ID: 440158 [Multi-domain]  Cd Length: 336  Bit Score: 184.19  E-value: 1.36e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558   1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYAL-GSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTAS 79
Cdd:COG0389  72 PDFELYRDVSRRVMAILERYTPLVEPLSIDEAFLDVTGSARLfGSAEAIARRIRRRIRRETGLTVSVGIAPNKFLAKIAS 151

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 83033558  80 DMKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAK 131
Cdd:COG0389 152 DLAKPDGLTVIPPGEVAAFLAPLPVEKLWGVGPKTAEKLARLGIRTIGDLAA 203
IMS pfam00817
impB/mucB/samB family; These proteins are involved in UV protection (Swiss).
 1-80 7.43e-28

impB/mucB/samB family; These proteins are involved in UV protection (Swiss).


Pssm-ID: 425885 [Multi-domain]  Cd Length: 148  Bit Score: 99.96  E-value: 7.43e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558     1 PNFTLYREASFQMFQILSRF-TEKIQPVSIDEGYLDITDCYAL-GSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTA 78
Cdd:pfam00817  67 PDLELYRRASRKIFEILRRFsTPKVEQASIDEAFLDLTGLEKLfGAEEALAKRLRREIAEETGLTCSIGIAPNKLLAKLA 146


                  ..
gi 83033558    79 SD 80
Cdd:pfam00817 147 SD 148
TIGR03491 TIGR03491
RecB family nuclease, putative, TM0106 family; Members of this uncharacterized protein family ...
 103-133 4.82e-03

RecB family nuclease, putative, TM0106 family; Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.


Pssm-ID: 274603 [Multi-domain]  Cd Length: 457  Bit Score: 35.77  E-value: 4.82e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 83033558   103 SVAEMHGIGEKTAEKLKDIHIHTIEQLAKGD 133
Cdd:TIGR03491 208 HLSLVPGIGPSRYRLLQELGIHTLEDLAAAD 238
 
Name Accession Description Interval E-value
PRK01810 PRK01810
DNA polymerase IV; Validated
 1-133 3.24e-93

DNA polymerase IV; Validated


Pssm-ID: 179337 [Multi-domain]  Cd Length: 407  Bit Score: 274.60  E-value: 3.24e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYALGSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTASD 80
Cdd:PRK01810  78 PNFDRYREASRQMFQILSEFTPLVQPVSIDEGYLDITDCYALGSPLEIAKMIQQRLLTELQLPCSIGIAPNKFLAKMASD 157

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 83033558   81 MKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAKGD 133
Cdd:PRK01810 158 MKKPLGITVLRKRDVPEMLWPLPVGEMHGIGEKTAEKLKDIGIQTIGDLAKAD 210
PolY_Pol_IV_kappa cd03586
DNA Polymerase IV/Kappa; Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion ...
 1-133 2.86e-64

DNA Polymerase IV/Kappa; Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a higher error rate than other Y-family polymerases.


Pssm-ID: 176459 [Multi-domain]  Cd Length: 334  Bit Score: 198.51  E-value: 2.86e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558   1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYAL-GSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTAS 79
Cdd:cd03586  69 PRFDKYREVSRQIMEILREYTPLVEPLSIDEAYLDVTDYVRLfGSATEIAKEIRARIREETGLTASAGIAPNKFLAKIAS 148

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 83033558  80 DMKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAKGD 133
Cdd:cd03586 149 DLNKPNGLTVIPPEDVEEFLAPLPVRKIPGVGKVTAEKLKELGIKTIGDLAKLD 202
DinP COG0389
Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination ...
 1-131 1.36e-58

Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination and repair];


Pssm-ID: 440158 [Multi-domain]  Cd Length: 336  Bit Score: 184.19  E-value: 1.36e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558   1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYAL-GSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTAS 79
Cdd:COG0389  72 PDFELYRDVSRRVMAILERYTPLVEPLSIDEAFLDVTGSARLfGSAEAIARRIRRRIRRETGLTVSVGIAPNKFLAKIAS 151

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 83033558  80 DMKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAK 131
Cdd:COG0389 152 DLAKPDGLTVIPPGEVAAFLAPLPVEKLWGVGPKTAEKLARLGIRTIGDLAA 203
PRK02406 PRK02406
DNA polymerase IV; Validated
 1-131 2.15e-46

DNA polymerase IV; Validated


Pssm-ID: 235035 [Multi-domain]  Cd Length: 343  Bit Score: 152.97  E-value: 2.15e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDC-YALGSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTAS 79
Cdd:PRK02406  66 GRFDVYKEVSRQIREIFRRYTDLIEPLSLDEAYLDVTDNkLCIGSATLIAQEIRQDIFEELGLTASAGVAPNKFLAKIAS 145

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 83033558   80 DMKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAK 131
Cdd:PRK02406 146 DWNKPNGLFVITPEEVDAFLATLPVEKIPGVGKVTAEKLHALGIYTCADLQK 197
PRK03103 PRK03103
DNA polymerase IV; Reviewed
 1-130 4.88e-38

DNA polymerase IV; Reviewed


Pssm-ID: 235104 [Multi-domain]  Cd Length: 409  Bit Score: 132.43  E-value: 4.88e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYAL-GSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTAS 79
Cdd:PRK03103  76 PRMQRYIDVSLQITRILEDFTDLVEPFSIDEQFLDVTGSQKLfGSPLEIAQKIQQRIMRETGVYARVGIGPNKLLAKMAC 155

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 83033558   80 DM---KKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLA 130
Cdd:PRK03103 156 DNfakKNPDGLFTLDKEDVPADLWPLPVRKLFGVGSRMEKHLRRMGIRTIGQLA 209
PRK14133 PRK14133
DNA polymerase IV; Provisional
 6-131 7.09e-38

DNA polymerase IV; Provisional


Pssm-ID: 184529 [Multi-domain]  Cd Length: 347  Bit Score: 130.99  E-value: 7.09e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    6 YREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYAlgSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTASDMKKPL 85
Cdd:PRK14133  79 YKEVSKNIFKILYEVTPIVEPVSIDEAYLDITNIKE--EPIKIAKYIKKKVKKETGLTLSVGISYNKFLAKLASDWNKPD 156

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 83033558   86 GITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAK 131
Cdd:PRK14133 157 GIKIITEDMIPDILKPLPISKVHGIGKKSVEKLNNIGIYTIEDLLK 202
PolY_Pol_V_umuC cd01700
umuC subunit of DNA Polymerase V; umuC subunit of Pol V. Pol V is a bacterial translesion ...
 1-130 2.33e-36

umuC subunit of DNA Polymerase V; umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.


Pssm-ID: 176454 [Multi-domain]  Cd Length: 344  Bit Score: 126.89  E-value: 2.33e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558   1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYALGSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTASD 80
Cdd:cd01700  70 SNYALYGDMSRRIMSILERFSPDVEVYSIDESFLDLTGSLRFGDLEELARKIRRRILQETGIPVTVGIGPTKTLAKLAND 149

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 83033558  81 M--KKP--LGITVLRKRDIPEIIWPRS-VAEMHGIGEKTAEKLKDIHIHTIEQLA 130
Cdd:cd01700 150 LakKKNpyGGVVDLTDEEVRDKLLKILpVGDVWGIGRRTAKKLNAMGIHTAGDLA 204
PolY cd00424
Y-family of DNA polymerases; Y-family DNA polymerases are a specialized subset of polymerases ...
 1-131 1.01e-29

Y-family of DNA polymerases; Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.


Pssm-ID: 176453 [Multi-domain]  Cd Length: 343  Bit Score: 109.37  E-value: 1.01e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558   1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDC-YALGSPPEIAKMIQQALLTEL-QLPCSIGIAPNLFLAKTA 78
Cdd:cd00424  70 ARLDLYRRLSERLLSELEEVAPLVEVASIDELFLDLTGSaRLLGLGSEVALRIKRHIAEQLgGITASIGIASNKLLAKLA 149

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 83033558  79 SDMKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAK 131
Cdd:cd00424 150 AKYAKPDGLTILDPEDLPGFLSKLPLTDLPGIGAVTAKRLEAVGINPIGDLLA 202
PRK02794 PRK02794
DNA polymerase IV; Provisional
 1-133 1.74e-28

DNA polymerase IV; Provisional


Pssm-ID: 179473 [Multi-domain]  Cd Length: 419  Bit Score: 107.33  E-value: 1.74e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYAL-GSPPeiAKM---IQQALLTELQLPCSIGIAPNLFLAK 76
Cdd:PRK02794 106 PDMEKYVRVGREVRAMMQALTPLVEPLSIDEAFLDLSGTERLhGAPP--AVVlarFARRVEREIGITVSVGLSYNKFLAK 183

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 83033558   77 TASDMKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAKGD 133
Cdd:PRK02794 184 IASDLDKPRGFSVIGRAEALAFLAPKPVGIIWGVGPATAARLARDGIRTIGDLQRAD 240
IMS pfam00817
impB/mucB/samB family; These proteins are involved in UV protection (Swiss).
 1-80 7.43e-28

impB/mucB/samB family; These proteins are involved in UV protection (Swiss).


Pssm-ID: 425885 [Multi-domain]  Cd Length: 148  Bit Score: 99.96  E-value: 7.43e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558     1 PNFTLYREASFQMFQILSRF-TEKIQPVSIDEGYLDITDCYAL-GSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTA 78
Cdd:pfam00817  67 PDLELYRRASRKIFEILRRFsTPKVEQASIDEAFLDLTGLEKLfGAEEALAKRLRREIAEETGLTCSIGIAPNKLLAKLA 146


                  ..
gi 83033558    79 SD 80
Cdd:pfam00817 147 SD 148
PRK03348 PRK03348
DNA polymerase IV; Provisional
 1-130 5.34e-25

DNA polymerase IV; Provisional


Pssm-ID: 235118 [Multi-domain]  Cd Length: 454  Bit Score: 98.08  E-value: 5.34e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYALgSPPEI---AKMIQQALLTELQLPCSIGIAPNLFLAKT 77
Cdd:PRK03348  77 PRFVVYRAASRRVFDTLRELSPVVEQLSFDEAFVEPAELAGA-SAEEVeafAERLRARVREETGLPASVGAGSGKQIAKI 155

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 83033558   78 ASDMKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLA 130
Cdd:PRK03348 156 ASGLAKPDGIRVVPPGEERELLAPLPVRRLWGIGPVTEEKLHRLGIETIGDLA 208
PRK03858 PRK03858
DNA polymerase IV; Validated
 1-130 1.42e-24

DNA polymerase IV; Validated


Pssm-ID: 179663 [Multi-domain]  Cd Length: 396  Bit Score: 96.59  E-value: 1.42e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYAL-GSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTAS 79
Cdd:PRK03858  71 PRMSAYSRASKAVFEVFRDTTPLVEGLSIDEAFLDVGGLRRIsGTPVQIAARLRRRVREEVGLPITVGVARTKFLAKVAS 150

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 83033558   80 DMKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLA 130
Cdd:PRK03858 151 QVAKPDGLLVVPPDRELAFLHPLPVRRLWGVGPVTAAKLRAHGITTVGDVA 201
PolY_Rev1 cd01701
DNA polymerase Rev1; Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. ...
 2-119 2.56e-23

DNA polymerase Rev1; Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.


Pssm-ID: 176455 [Multi-domain]  Cd Length: 404  Bit Score: 93.15  E-value: 2.56e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558   2 NFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYALGS--PPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTAS 79
Cdd:cd01701 120 DFEAYEEVSLTFYEILASYTDNIEAVSCDEALIDITSLLEETYelPEELAEAIRNEIRETTGCSASVGIGPNILLARLAT 199

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 83033558  80 DMKKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLK 119
Cdd:cd01701 200 RKAKPDGQYHLSAEKVEEFLSQLKVGDLPGVGSSLAEKLV 239
PRK03352 PRK03352
DNA polymerase IV; Validated
 6-133 3.63e-22

DNA polymerase IV; Validated


Pssm-ID: 179564 [Multi-domain]  Cd Length: 346  Bit Score: 89.31  E-value: 3.63e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    6 YREASFQMFQILSRFTEKIQPVSIDEGYLDITdcyaLGSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTASDMKKPL 85
Cdd:PRK03352  85 YDAASEEVMATLRDLGVPVEVWGWDEAFLGVD----TDDPEALAEEIRAAVLERTGLSCSVGIGDNKLRAKIATGFAKPA 160

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 83033558   86 GITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAKGD 133
Cdd:PRK03352 161 GVFRLTDANWMAVMGDRPTDALWGVGPKTAKRLAALGITTVADLAAAD 208
PRK01216 PRK01216
DNA polymerase IV; Validated
 5-123 2.38e-21

DNA polymerase IV; Validated


Pssm-ID: 179251 [Multi-domain]  Cd Length: 351  Bit Score: 87.15  E-value: 2.38e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    5 LYREASFQMFQILSRFTEKIQPVSIDEGYLDITD-CYALGSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTASDMKK 83
Cdd:PRK01216  80 VYQQVSNRIMKLLREYSEKIEIASIDEAYLDISDkVKNYQDAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAK 159

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 83033558   84 PLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHI 123
Cdd:PRK01216 160 PNGIKVIDDEEVKRFINELDIADIPGIGDITAEKLKKLGV 199
PolY_Pol_eta cd01702
DNA Polymerase eta; Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. ...
 2-122 5.30e-20

DNA Polymerase eta; Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.


Pssm-ID: 176456 [Multi-domain]  Cd Length: 359  Bit Score: 83.52  E-value: 5.30e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558   2 NFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDitdcyaLGSppEIAKMIQQALLTELQLPCSIGIAPNLFLAKTASDM 81
Cdd:cd01702  90 SLDPYRRASRKILNILKRFGDVVEKASIDEAYLD------LGS--RIVEEIRQQVYDELGYTCSAGIAHNKMLAKLASGM 161

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 83033558  82 KKPLGITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIH 122
Cdd:cd01702 162 NKPNAQTILRNDAVASFLSSLPITSIRGLGGKLGEEIIDLL 202
PolY_Pol_iota cd01703
DNA Polymerase iota; Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. ...
 4-130 6.27e-16

DNA Polymerase iota; Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.


Pssm-ID: 176457 [Multi-domain]  Cd Length: 379  Bit Score: 72.50  E-value: 6.27e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558   4 TLYREASFQMFQILSRFT--EKIQPVSIDEGYLDITDC-YALGSppEIAKMIQQALLTELQLPCSIGIAPNLFLAKTASD 80
Cdd:cd01703  70 TPFRDMSKKVYRLLRSYSwnDRVERLGFDENFMDVTEMrLLVAS--HIAYEMRERIENELGLTCCAGIASNKLLAKLVGS 147

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 83033558  81 MKKPLGITVL---RKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLA 130
Cdd:cd01703 148 VNKPNQQTTLlppSCADLMDFMDLHDLRKIPGIGYKTAAKLEAHGISSVRDLQ 200
umuC PRK03609
translesion error-prone DNA polymerase V subunit UmuC;
2-133 4.95e-09

translesion error-prone DNA polymerase V subunit UmuC;


Pssm-ID: 179607 [Multi-domain]  Cd Length: 422  Bit Score: 52.85  E-value: 4.95e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    2 NFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITDCYALGSPPEIAKMIQQALLTELQLPCSIGIAPNLFLAKTASDM 81
Cdd:PRK03609  73 NYELYADMSNRVMSTLEELSPRVEIYSIDEAFCDLTGVRNCRDLTDFGREIRATVLQRTHLTVGVGIAQTKTLAKLANHA 152

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 83033558   82 KKPL-----GITVLRKRD-IPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAKGD 133
Cdd:PRK03609 153 AKKWqrqtgGVVDLSNLErQRKLLSLQPVEEVWGVGRRISKKLNAMGIKTALDLADTN 210
PolY_like cd03468
DNA Polymerase Y-family; Y-family DNA polymerases are a specialized subset of polymerases that ...
 6-130 6.19e-07

DNA Polymerase Y-family; Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.


Pssm-ID: 176458 [Multi-domain]  Cd Length: 335  Bit Score: 46.99  E-value: 6.19e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558   6 YREASFQMFQILS----RFTEKIQPVSIDEGYLDITDCYALgSPPEIAKMIQQ-ALLTELQLPCSIGIAPNLFLAKTASD 80
Cdd:cd03468  70 DPEADARALQELAlwllRFTPLVALDGPDGLLLDVTGCLHL-FGGEDALAASLrAALATLGLSARAGIADTPGAAWLLAR 148

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 83033558  81 MKKPLGI---TVLRKRdipEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLA 130
Cdd:cd03468 149 AGGGRGVlrrEALAAA---LVLLAPLPVAALRLPPETVELLARLGLRTLGDLA 198
IMS_HHH pfam11798
IMS family HHH motif; These proteins are involved in UV protection, eg.
 94-123 8.24e-07

IMS family HHH motif; These proteins are involved in UV protection, eg.


Pssm-ID: 432081 [Multi-domain]  Cd Length: 32  Bit Score: 42.77  E-value: 8.24e-07
                          10        20        30
                  ....*....|....*....|....*....|
gi 83033558    94 DIPEIIWPRSVAEMHGIGEKTAEKLKDIHI 123
Cdd:pfam11798   3 DVPEFLWPLPISKIPGIGKKLAEKLKALGI 32
PTZ00205 PTZ00205
DNA polymerase kappa; Provisional
 1-129 3.09e-05

DNA polymerase kappa; Provisional


Pssm-ID: 140232 [Multi-domain]  Cd Length: 571  Bit Score: 41.93  E-value: 3.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83033558    1 PNFTLYREASFQMFQILSRFTEKIQPVSIDEGYLDITdCY-----ALGSPPEIAKMIQQALLTELQLPCSIGIAPNLFLA 75
Cdd:PTZ00205 201 PDFDAYNEESNTVRRIVAEYDPNYISFGLDELTLEVS-AYierfeGTKTAEDVASELRVRVFGETKLTASAGIGPTAALA 279

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 83033558   76 KTASDMKKPLG---ITVLRKRDIPEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQL 129
Cdd:PTZ00205 280 KIASNINKPNGqhdLNLHTRGDVMTYVRDLGLRSVPGVGKVTEALLKGLGITTLSDI 336
TIGR03491 TIGR03491
RecB family nuclease, putative, TM0106 family; Members of this uncharacterized protein family ...
 103-133 4.82e-03

RecB family nuclease, putative, TM0106 family; Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.


Pssm-ID: 274603 [Multi-domain]  Cd Length: 457  Bit Score: 35.77  E-value: 4.82e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 83033558   103 SVAEMHGIGEKTAEKLKDIHIHTIEQLAKGD 133
Cdd:TIGR03491 208 HLSLVPGIGPSRYRLLQELGIHTLEDLAAAD 238
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 103-130 6.43e-03

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 35.51  E-value: 6.43e-03
                         10        20
                 ....*....|....*....|....*...
gi 83033558  103 SVAEMHGIGEKTAEKLKDIHIHTIEQLA 130
Cdd:PRK10917  10 PLTSLKGVGPKTAEKLAKLGIHTVQDLL 37
PRK07220 PRK07220
DNA topoisomerase I; Validated
 96-133 9.73e-03

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 34.73  E-value: 9.73e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 83033558   96 PEIIWPRSVAEMHGIGEKTAEKLKDIHIHTIEQLAKGD 133
Cdd:PRK07220 680 PKKEKPKSIKDIKGIGKKTAEKLEEAGITTVEALAEAD 717
 
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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