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Conserved domains on  [gi|701297653|ref|XP_010009123|]
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PREDICTED: DNA polymerase eta, partial [Nestor notabilis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PolY super family cl28996
Y-family of DNA polymerases; Y-family DNA polymerases are a specialized subset of polymerases ...
 11-247 3.01e-104

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.


The actual alignment was detected with superfamily member cd01702:

Pssm-ID: 452909 [Multi-domain]  Cd Length: 359  Bit Score: 316.56  E-value: 3.01e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  11 LTMGAVIVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLGGKLGTAITDT 90
Cdd:cd01702  122 LDLGSRIVEEIRQQVYDELGYTCSAGIAHNKMLAKLASGMNKPNAQTILRNDAVASFLSSLPITSIRGLGGKLGEEIIDL 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  91 LGVEYIGELTQ--YSETELQAHFGDKTGSWLYYLCRGIEEEPVKNRYLPQSIGCSKNFPGKTALATqKEVQHWLLQLALE 168
Cdd:cd01702  202 LGLPTEGDVAGfrSSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFPGKTALST-EDVQHWLLVLASE 280

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653 169 LESRLIKDRRQNHRVAKQLMVVIRMQGD-TRVSRFCALTRYEAQKMCNDAFALIQNCNVAGAHQaAWSPPLISVLLSASK 247
Cdd:cd01702  281 LNSRLEDDRYENNRRPKTLVLSLRQRGDgVRRSRSCALPRYDAQKIVKDAFKLIKAINEEGLGL-AWNYPLTLLSLSFTK 359
zf_UBZ pfam18439
Ubiquitin-Binding Zinc Finger; This is ubiquitin-binding zinc finger (UBZ) domain found in DNA ...
 430-459 1.65e-10

Ubiquitin-Binding Zinc Finger; This is ubiquitin-binding zinc finger (UBZ) domain found in DNA polymerase eta (EC:2.7.7.7). It is important in the recruitment of the polymerase to the stalled replication machinery in translesion synthesis. The UBZ domain adopts a classical C2H2 zinc-finger structure characterized by a beta-beta-alpha fold.


:

Pssm-ID: 465769  Cd Length: 32  Bit Score: 55.98  E-value: 1.65e-10
                          10        20        30
                  ....*....|....*....|....*....|
gi 701297653  430 DQQRCEKCGQLVLVWELPEHMDYHFALELQ 459
Cdd:pfam18439   1 DTYVCPRCGKEIPESELPEHEDWHFAKDLQ 30
 
Name Accession Description Interval E-value
PolY_Pol_eta cd01702
DNA Polymerase eta; Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. ...
 11-247 3.01e-104

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: 316.56  E-value: 3.01e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  11 LTMGAVIVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLGGKLGTAITDT 90
Cdd:cd01702  122 LDLGSRIVEEIRQQVYDELGYTCSAGIAHNKMLAKLASGMNKPNAQTILRNDAVASFLSSLPITSIRGLGGKLGEEIIDL 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  91 LGVEYIGELTQ--YSETELQAHFGDKTGSWLYYLCRGIEEEPVKNRYLPQSIGCSKNFPGKTALATqKEVQHWLLQLALE 168
Cdd:cd01702  202 LGLPTEGDVAGfrSSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFPGKTALST-EDVQHWLLVLASE 280

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653 169 LESRLIKDRRQNHRVAKQLMVVIRMQGD-TRVSRFCALTRYEAQKMCNDAFALIQNCNVAGAHQaAWSPPLISVLLSASK 247
Cdd:cd01702  281 LNSRLEDDRYENNRRPKTLVLSLRQRGDgVRRSRSCALPRYDAQKIVKDAFKLIKAINEEGLGL-AWNYPLTLLSLSFTK 359
DinP COG0389
Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination ...
 17-222 1.64e-35

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


Pssm-ID: 440158 [Multi-domain]  Cd Length: 336  Bit Score: 135.27  E-value: 1.64e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  17 IVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLGGKLGTAITDtLGVEYI 96
Cdd:COG0389  120 IARRIRRRIRRETGLTVSVGIAPNKFLAKIASDLAKPDGLTVIPPGEVAAFLAPLPVEKLWGVGPKTAEKLAR-LGIRTI 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  97 GELTQYSETELQAHFGdKTGSWLYYLCRGIEEEPVKNRYLPQSIGCSKNFPgkTALATQKEVQHWLLQLALELESRLikd 176
Cdd:COG0389  199 GDLAALPRAELRRRFG-KVGERLYRLARGIDPRPVEPRRPRKSIGVERTFG--EDLTDLEELEAALRRLAERLAERL--- 272

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 701297653 177 rRQNHRVAKQLMVVIRMQGDTRVSRFCALTRYeaqkmCNDAFALIQ 222
Cdd:COG0389  273 -RRQGLGARTVTVKLRTSDFRTTTRSRTLPEP-----TDDTAELLR 312
PRK02406 PRK02406
DNA polymerase IV; Validated
 17-192 5.75e-24

DNA polymerase IV; Validated


Pssm-ID: 235035 [Multi-domain]  Cd Length: 343  Bit Score: 102.89  E-value: 5.75e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  17 IVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLG----GKLgtaitDTLG 92
Cdd:PRK02406 114 IAQEIRQDIFEELGLTASAGVAPNKFLAKIASDWNKPNGLFVITPEEVDAFLATLPVEKIPGVGkvtaEKL-----HALG 188

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  93 VEYIGELTQYSETELQAHFGdKTGSWLYYLCRGIEEEPVKNRYLPQSIGCSKNFPgkTALATQKEVQHWLLQLALELESR 172
Cdd:PRK02406 189 IYTCADLQKYDLAELIRHFG-KFGRRLYERARGIDERPVKPDRERKSVGVERTFA--EDLYDLEACLAELPRLAEKLERR 265

                        170       180
                 ....*....|....*....|
gi 701297653 173 LikDRRQNHRVAKQLMVVIR 192
Cdd:PRK02406 266 L--ERAKPDKRIKTVGVKLK 283
zf_UBZ pfam18439
Ubiquitin-Binding Zinc Finger; This is ubiquitin-binding zinc finger (UBZ) domain found in DNA ...
 430-459 1.65e-10

Ubiquitin-Binding Zinc Finger; This is ubiquitin-binding zinc finger (UBZ) domain found in DNA polymerase eta (EC:2.7.7.7). It is important in the recruitment of the polymerase to the stalled replication machinery in translesion synthesis. The UBZ domain adopts a classical C2H2 zinc-finger structure characterized by a beta-beta-alpha fold.


Pssm-ID: 465769  Cd Length: 32  Bit Score: 55.98  E-value: 1.65e-10
                          10        20        30
                  ....*....|....*....|....*....|
gi 701297653  430 DQQRCEKCGQLVLVWELPEHMDYHFALELQ 459
Cdd:pfam18439   1 DTYVCPRCGKEIPESELPEHEDWHFAKDLQ 30
IMS_C pfam11799
impB/mucB/samB family C-terminal domain; These proteins are involved in UV protection (Swiss).
 137-201 2.59e-07

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


Pssm-ID: 463354 [Multi-domain]  Cd Length: 104  Bit Score: 48.71  E-value: 2.59e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 701297653  137 PQSIGCSKNFPgkTALATQKEVQHWLLQLALELESRLikdrRQNHRVAKQLMVVIRMQGDTRVSR 201
Cdd:pfam11799   1 RKSIGAERTFG--RDLTDLEELREALLELAEELAERL----RRQGLVARTVTVKIRYSDFRTITR 59
 
Name Accession Description Interval E-value
PolY_Pol_eta cd01702
DNA Polymerase eta; Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. ...
 11-247 3.01e-104

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: 316.56  E-value: 3.01e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  11 LTMGAVIVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLGGKLGTAITDT 90
Cdd:cd01702  122 LDLGSRIVEEIRQQVYDELGYTCSAGIAHNKMLAKLASGMNKPNAQTILRNDAVASFLSSLPITSIRGLGGKLGEEIIDL 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  91 LGVEYIGELTQ--YSETELQAHFGDKTGSWLYYLCRGIEEEPVKNRYLPQSIGCSKNFPGKTALATqKEVQHWLLQLALE 168
Cdd:cd01702  202 LGLPTEGDVAGfrSSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFPGKTALST-EDVQHWLLVLASE 280

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653 169 LESRLIKDRRQNHRVAKQLMVVIRMQGD-TRVSRFCALTRYEAQKMCNDAFALIQNCNVAGAHQaAWSPPLISVLLSASK 247
Cdd:cd01702  281 LNSRLEDDRYENNRRPKTLVLSLRQRGDgVRRSRSCALPRYDAQKIVKDAFKLIKAINEEGLGL-AWNYPLTLLSLSFTK 359
DinP COG0389
Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination ...
 17-222 1.64e-35

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


Pssm-ID: 440158 [Multi-domain]  Cd Length: 336  Bit Score: 135.27  E-value: 1.64e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  17 IVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLGGKLGTAITDtLGVEYI 96
Cdd:COG0389  120 IARRIRRRIRRETGLTVSVGIAPNKFLAKIASDLAKPDGLTVIPPGEVAAFLAPLPVEKLWGVGPKTAEKLAR-LGIRTI 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  97 GELTQYSETELQAHFGdKTGSWLYYLCRGIEEEPVKNRYLPQSIGCSKNFPgkTALATQKEVQHWLLQLALELESRLikd 176
Cdd:COG0389  199 GDLAALPRAELRRRFG-KVGERLYRLARGIDPRPVEPRRPRKSIGVERTFG--EDLTDLEELEAALRRLAERLAERL--- 272

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 701297653 177 rRQNHRVAKQLMVVIRMQGDTRVSRFCALTRYeaqkmCNDAFALIQ 222
Cdd:COG0389  273 -RRQGLGARTVTVKLRTSDFRTTTRSRTLPEP-----TDDTAELLR 312
PolY_Pol_IV_kappa cd03586
DNA Polymerase IV/Kappa; Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion ...
 17-208 3.47e-33

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: 128.79  E-value: 3.47e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  17 IVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRnlG-GKLGTAITDTLGVEY 95
Cdd:cd03586  117 IAKEIRARIREETGLTASAGIAPNKFLAKIASDLNKPNGLTVIPPEDVEEFLAPLPVRKIP--GvGKVTAEKLKELGIKT 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  96 IGELTQYSETELQAHFGdKTGSWLYYLCRGIEEEPVKNRYLPQSIGCSKNFPgkTALATQKEVQHWLLQLALELESRLIK 175
Cdd:cd03586  195 IGDLAKLDVELLKKLFG-KSGRRLYELARGIDNRPVEPDRERKSIGVERTFS--EDLTDPEELLEELLELAEELAERLRK 271

                        170       180       190
                 ....*....|....*....|....*....|...
gi 701297653 176 DRRQNHRVAkqlmVVIRMQGDTRVSRFCALTRY 208
Cdd:cd03586  272 RGLKGRTVT----VKLKYADFSTRTRSRTLPEP 300
PolY_Rev1 cd01701
DNA polymerase Rev1; Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. ...
 16-189 6.15e-27

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: 112.41  E-value: 6.15e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  16 VIVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLGGKLGTAITDTLGVEY 95
Cdd:cd01701  167 ELAEAIRNEIRETTGCSASVGIGPNILLARLATRKAKPDGQYHLSAEKVEEFLSQLKVGDLPGVGSSLAEKLVKLFGDTC 246

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  96 IG-ELTQYSETELQAHFGDKTGSWLYYLCRGIEEEPVKNRYLPQSIGCSKNFPgkTALATQKEVQHWLLQLALELESRLI 174
Cdd:cd01701  247 GGlELRSKTKEKLQKVLGPKTGEKLYDYCRGIDDRPVTGEKERKSVSAEINYG--IRFTNVDDVEQFLQRLSEELSKRLE 324

                        170
                 ....*....|....*
gi 701297653 175 KDRRQNHRVAKQLMV 189
Cdd:cd01701  325 ESNVTGRQITLKLMK 339
PRK02406 PRK02406
DNA polymerase IV; Validated
 17-192 5.75e-24

DNA polymerase IV; Validated


Pssm-ID: 235035 [Multi-domain]  Cd Length: 343  Bit Score: 102.89  E-value: 5.75e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  17 IVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLG----GKLgtaitDTLG 92
Cdd:PRK02406 114 IAQEIRQDIFEELGLTASAGVAPNKFLAKIASDWNKPNGLFVITPEEVDAFLATLPVEKIPGVGkvtaEKL-----HALG 188

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  93 VEYIGELTQYSETELQAHFGdKTGSWLYYLCRGIEEEPVKNRYLPQSIGCSKNFPgkTALATQKEVQHWLLQLALELESR 172
Cdd:PRK02406 189 IYTCADLQKYDLAELIRHFG-KFGRRLYERARGIDERPVKPDRERKSVGVERTFA--EDLYDLEACLAELPRLAEKLERR 265

                        170       180
                 ....*....|....*....|
gi 701297653 173 LikDRRQNHRVAKQLMVVIR 192
Cdd:PRK02406 266 L--ERAKPDKRIKTVGVKLK 283
PolY cd00424
Y-family of DNA polymerases; Y-family DNA polymerases are a specialized subset of polymerases ...
 7-207 1.51e-21

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: 95.89  E-value: 1.51e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653   7 PDLLLTMGAVIVEEVRVAVEAATG-FRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLGGKLGT 85
Cdd:cd00424  108 SARLLGLGSEVALRIKRHIAEQLGgITASIGIASNKLLAKLAAKYAKPDGLTILDPEDLPGFLSKLPLTDLPGIGAVTAK 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  86 AITDtLGVEYIGELTQYSETELQAHFGDKTGSWLYYLCRGIEEEPVKNRYLPQSIGCSKNFPGKtaLATQKEVQHWLLQL 165
Cdd:cd00424  188 RLEA-VGINPIGDLLAASPDALLALWGGVSGERLWYALRGIDDEPLSPPRPRKSFSHERVLPRD--SRNAEDARPLLRLL 264

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 701297653 166 ALELESRLikdrRQNHRVAKQLMVVIRMQgDTRVSRFCALTR 207
Cdd:cd00424  265 LEKLARRL----RRDGRGATRLRLWLRTV-DGRWSGHADIPS 301
PRK14133 PRK14133
DNA polymerase IV; Provisional
 17-177 7.82e-18

DNA polymerase IV; Provisional


Pssm-ID: 184529 [Multi-domain]  Cd Length: 347  Bit Score: 84.77  E-value: 7.82e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  17 IVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLGGKLGTAITDtLGVEYI 96
Cdd:PRK14133 119 IAKYIKKKVKKETGLTLSVGISYNKFLAKLASDWNKPDGIKIITEDMIPDILKPLPISKVHGIGKKSVEKLNN-IGIYTI 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  97 GELTQYSETELQAHFGdKTGSWLYYLCRGIEEEPVKNRYLPQSIGCSKNFPGKTalATQKEVQHWLLQLALELESRLIKD 176
Cdd:PRK14133 198 EDLLKLSREFLIEYFG-KFGVEIYERIRGIDYREVEVSRERKSIGKETTLKKDT--KDKEELKKYLKDFSNIISEELKKR 274


                 .
gi 701297653 177 R 177
Cdd:PRK14133 275 N 275
PolY_Pol_iota cd01703
DNA Polymerase iota; Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. ...
 5-208 1.59e-15

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: 78.28  E-value: 1.59e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653   5 DCPDLLLTMGAVIVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNL---GG 81
Cdd:cd01703  103 DVTEMRLLVASHIAYEMRERIENELGLTCCAGIASNKLLAKLVGSVNKPNQQTTLLPPSCADLMDFMDLHDLRKIpgiGY 182

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  82 KLGTAITDtLGVEYIGELTQYSETELQAH---------------FGDKTGSWLYYLCRGIEEEPVKN-RYLPQSIGCSKN 145
Cdd:cd01703  183 KTAAKLEA-HGISSVRDLQEFSNRNRQTVgaapsllelllmvkeFGEGIGQRIWKLLFGRDTSPVKPaSDFPQQISIEDS 261

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 701297653 146 FPgKTALATQKEVQHWLLQLALELESRLIKDRRQNH----RVAKQLMVVIRMQGDT-----RVSRFCALTRY 208
Cdd:cd01703  262 YK-KCSLEEIREARNKIEELLASLLERMKQDLQEVKagdgRRPHTLRLTLRRYTSTkkhynRESKQAPIPSH 332
PRK03352 PRK03352
DNA polymerase IV; Validated
 19-192 1.85e-15

DNA polymerase IV; Validated


Pssm-ID: 179564 [Multi-domain]  Cd Length: 346  Bit Score: 77.76  E-value: 1.85e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  19 EEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLGGKLGTAITDtLGVEYIGE 98
Cdd:PRK03352 125 EEIRAAVLERTGLSCSVGIGDNKLRAKIATGFAKPAGVFRLTDANWMAVMGDRPTDALWGVGPKTAKRLAA-LGITTVAD 203

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  99 LTQYSETELQAHFGDKTGSWLYYLCRGIEEEPVKNR-YLPQSIGCSKNFPgkTALATQKEVQHWLLQLALELESRLIKDR 177
Cdd:PRK03352 204 LAAADPAELAATFGPTTGPWLLLLARGGGDTEVSAEpWVPRSRSREVTFP--QDLTDRAEVESAVRELARRVLDEVVAEG 281

                        170
                 ....*....|....*
gi 701297653 178 RQNHRVAkqlmVVIR 192
Cdd:PRK03352 282 RPVTRVA----VKVR 292
PRK03348 PRK03348
DNA polymerase IV; Provisional
 17-201 7.47e-14

DNA polymerase IV; Provisional


Pssm-ID: 235118 [Multi-domain]  Cd Length: 454  Bit Score: 73.43  E-value: 7.47e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  17 IVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLlssrfVPQ-----LFSQLPVsniRNLGGkLGTAITD-- 89
Cdd:PRK03348 126 FAERLRARVREETGLPASVGAGSGKQIAKIASGLAKPDGIRV-----VPPgeereLLAPLPV---RRLWG-IGPVTEEkl 196

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  90 -TLGVEYIGELTQYSETELQAHFGDKTGSWLYYLCRGIEEEPVKNRYLPQSIGCSKNFPgkTALATQKEVQHWLLQLALE 168
Cdd:PRK03348 197 hRLGIETIGDLAALSEAEVANLLGATVGPALHRLARGIDDRPVAERAEAKQISAESTFA--VDLTTRAQLREAIERIAEH 274

                        170       180       190
                 ....*....|....*....|....*....|...
gi 701297653 169 LESRLIKDRRQnhrvAKQLMVVIRMQGDTRVSR 201
Cdd:PRK03348 275 AHRRLLKDGRG----ARTVTVKLRKSDFSTLTR 303
PRK01810 PRK01810
DNA polymerase IV; Validated
 33-192 7.31e-13

DNA polymerase IV; Validated


Pssm-ID: 179337 [Multi-domain]  Cd Length: 407  Bit Score: 70.44  E-value: 7.31e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  33 CSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLGGKlgTAIT-DTLGVEYIGELTQYSETELQAHF 111
Cdd:PRK01810 141 CSIGIAPNKFLAKMASDMKKPLGITVLRKRDVPEMLWPLPVGEMHGIGEK--TAEKlKDIGIQTIGDLAKADEHILRAKL 218

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653 112 GdKTGSWLYYLCRGIEEEPV--KNRYLPQSIGCSKNFPGKTalATQKEVQHWLLQLALELESRLikdrRQNHRVAKQLMV 189
Cdd:PRK01810 219 G-INGVRLQRRANGIDDRPVdpEAIYQFKSVGNSTTLSHDM--DEEKELLDVLRRLSKSVSKRL----QKKTVVSYNVQI 291


                 ...
gi 701297653 190 VIR 192
Cdd:PRK01810 292 MIR 294
PolY_Pol_V_umuC cd01700
umuC subunit of DNA Polymerase V; umuC subunit of Pol V. Pol V is a bacterial translesion ...
 5-192 2.50e-12

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: 67.96  E-value: 2.50e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653   5 DCPDLLLTMGAV-IVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNRQT-----LLSSRFVPQLFSQLPVSNIRN 78
Cdd:cd01700  104 DLTGSLRFGDLEeLARKIRRRILQETGIPVTVGIGPTKTLAKLANDLAKKKNPYggvvdLTDEEVRDKLLKILPVGDVWG 183

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  79 LGGKLGTAITdTLGVEYIGELTQYSETELQAHFGdKTGSWLYYLCRGI-----EEEPVKNrylpQSIGCSKNFPGK-TAL 152
Cdd:cd01700  184 IGRRTAKKLN-AMGIHTAGDLAQADPDLLRKKFG-VVGERLVRELNGIdclplEEYPPPK----KSIGSSRSFGRDvTDL 257

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 701297653 153 ATQKEVqhwLLQLALELESRLikdrRQNHRVAKQLMVVIR 192
Cdd:cd01700  258 DELKQA---LAEYAERAAEKL----RRQKSVARTISVFIG 290
PRK03103 PRK03103
DNA polymerase IV; Reviewed
 17-172 5.45e-11

DNA polymerase IV; Reviewed


Pssm-ID: 235104 [Multi-domain]  Cd Length: 409  Bit Score: 64.64  E-value: 5.45e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  17 IVEEVRVAVEAATGFRCSAGISHNKTLAKLACGL---NKPNRQTLLSSRFVPQLFSQLPVSNIRNLGGKLGTAITDtLGV 93
Cdd:PRK03103 124 IAQKIQQRIMRETGVYARVGIGPNKLLAKMACDNfakKNPDGLFTLDKEDVPADLWPLPVRKLFGVGSRMEKHLRR-MGI 202

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  94 EYIGELTQYSETELQAHFGdKTGSWLYYLCRGIEEEPVKNRYLP--QSIGCSKNFPgkTALATQKEVQHWLLQLALELES 171
Cdd:PRK03103 203 RTIGQLANTPLERLKKRWG-INGEVLWRTANGIDYSPVTPHSLDrqKAIGHQMTLP--RDYRGFEEIKVVLLELCEEVCR 279


                 .
gi 701297653 172 R 172
Cdd:PRK03103 280 R 280
zf_UBZ pfam18439
Ubiquitin-Binding Zinc Finger; This is ubiquitin-binding zinc finger (UBZ) domain found in DNA ...
 430-459 1.65e-10

Ubiquitin-Binding Zinc Finger; This is ubiquitin-binding zinc finger (UBZ) domain found in DNA polymerase eta (EC:2.7.7.7). It is important in the recruitment of the polymerase to the stalled replication machinery in translesion synthesis. The UBZ domain adopts a classical C2H2 zinc-finger structure characterized by a beta-beta-alpha fold.


Pssm-ID: 465769  Cd Length: 32  Bit Score: 55.98  E-value: 1.65e-10
                          10        20        30
                  ....*....|....*....|....*....|
gi 701297653  430 DQQRCEKCGQLVLVWELPEHMDYHFALELQ 459
Cdd:pfam18439   1 DTYVCPRCGKEIPESELPEHEDWHFAKDLQ 30
PRK02794 PRK02794
DNA polymerase IV; Provisional
 24-131 8.36e-09

DNA polymerase IV; Provisional


Pssm-ID: 179473 [Multi-domain]  Cd Length: 419  Bit Score: 57.63  E-value: 8.36e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  24 AVEAATGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLGGKLGTAITDtLGVEYIGELTQYS 103
Cdd:PRK02794 162 RVEREIGITVSVGLSYNKFLAKIASDLDKPRGFSVIGRAEALAFLAPKPVGIIWGVGPATAARLAR-DGIRTIGDLQRAD 240

                         90       100
                 ....*....|....*....|....*...
gi 701297653 104 ETELQAHFGDkTGSWLYYLCRGIEEEPV 131
Cdd:PRK02794 241 EADLMRRFGS-MGLRLWRLARGIDDRKV 267
IMS_C pfam11799
impB/mucB/samB family C-terminal domain; These proteins are involved in UV protection (Swiss).
 137-201 2.59e-07

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


Pssm-ID: 463354 [Multi-domain]  Cd Length: 104  Bit Score: 48.71  E-value: 2.59e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 701297653  137 PQSIGCSKNFPgkTALATQKEVQHWLLQLALELESRLikdrRQNHRVAKQLMVVIRMQGDTRVSR 201
Cdd:pfam11799   1 RKSIGAERTFG--RDLTDLEELREALLELAEELAERL----RRQGLVARTVTVKIRYSDFRTITR 59
PRK01216 PRK01216
DNA polymerase IV; Validated
 29-134 2.67e-07

DNA polymerase IV; Validated


Pssm-ID: 179251 [Multi-domain]  Cd Length: 351  Bit Score: 52.48  E-value: 2.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  29 TGFRCSAGISHNKTLAKLACGLNKPNRQTLLSSRFVPQLFSQLPVSNIRNLgGKLGTAITDTLGVEYIGELTQYSETELQ 108
Cdd:PRK01216 136 EKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRFINELDIADIPGI-GDITAEKLKKLGVNKLVDTLRIEFDELK 214

                         90       100
                 ....*....|....*....|....*.
gi 701297653 109 AHFGDKTGSWLYYLCRGIEEEPVKNR 134
Cdd:PRK01216 215 GIIGEAKAKYLFSLARNEYNEPVRAR 240
PolY_like cd03468
DNA Polymerase Y-family; Y-family DNA polymerases are a specialized subset of polymerases that ...
 14-215 7.11e-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: 51.23  E-value: 7.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  14 GAVIVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKP---NRQTllSSRFVPQLFSQLPVSNIRnlggkLGTAITDT 90
Cdd:cd03468  113 GEDALAASLRAALATLGLSARAGIADTPGAAWLLARAGGGrgvLRRE--ALAAALVLLAPLPVAALR-----LPPETVEL 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  91 L---GVEYIGELTQYSETELQAHFGDKtGSWLYYLCRGIEEEPVKNRYLPqsigcsKNFPGKTALATQKEVQHWLLQLAL 167
Cdd:cd03468  186 LarlGLRTLGDLAALPRAELARRFGLA-LLLRLDQAYGRDPEPLLFSPPP------PAFDFRLELQLEEPIARGLLFPLR 258

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 701297653 168 ELESRLIKDRRQNHRVAKQLMVVIRM--QGDTRVSRFCALTRYEAQKMCN 215
Cdd:cd03468  259 RLLEQLCAFLALRGLGARRLSLTLFRedGRVTRVLVGLARPSRDDLPLLR 308
IMS pfam00817
impB/mucB/samB family; These proteins are involved in UV protection (Swiss).
 17-48 1.48e-05

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


Pssm-ID: 425885 [Multi-domain]  Cd Length: 148  Bit Score: 44.87  E-value: 1.48e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 701297653   17 IVEEVRVAVEAATGFRCSAGISHNKTLAKLAC 48
Cdd:pfam00817 116 LAKRLRREIAEETGLTCSIGIAPNKLLAKLAS 147
PRK03858 PRK03858
DNA polymerase IV; Validated
 17-201 4.81e-05

DNA polymerase IV; Validated


Pssm-ID: 179663 [Multi-domain]  Cd Length: 396  Bit Score: 45.75  E-value: 4.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  17 IVEEVRVAVEAATGFRCSAGISHNKTLAKLACGLNKPNrqTLLssrFVP-----QLFSQLPVsniRNLGGkLGTAITDTL 91
Cdd:PRK03858 119 IAARLRRRVREEVGLPITVGVARTKFLAKVASQVAKPD--GLL---VVPpdrelAFLHPLPV---RRLWG-VGPVTAAKL 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 701297653  92 ---GVEYIGELTQYSETELQAHFGDKTGSWLYYLCRGIEEEPVKNRYLPQSIGcsknfpGKTAL----ATQKEVQHWLLQ 164
Cdd:PRK03858 190 rahGITTVGDVAELPESALVSLLGPAAGRHLHALAHNRDPRRVETGRRRRSVG------AQRALgrgpNSPAEVDAVVVA 263

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 701297653 165 LALELESRLikdrRQNHRVAKQLMVVIRMQGDTRVSR 201
Cdd:PRK03858 264 LVDRVARRM----RAAGRTGRTVVLRLRFDDFTRATR 296
 
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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