NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2280579211|ref|WP_256430431|]
View 

hypothetical protein [Pseudomonas sp. On1]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 5-36 1.13e-17

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 cd01700:

Pssm-ID: 452909 [Multi-domain]  Cd Length: 344  Bit Score: 72.97  E-value: 1.13e-17
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2280579211   5 ALVDCNSFYCSCERIFRPDLAQKAVVVLSNND 36
Cdd:cd01700     1 ALVDCNSFYASCERVFRPLLLGRPLVVLSNND 32
 
Name Accession Description Interval E-value
PolY_Pol_V_umuC cd01700
umuC subunit of DNA Polymerase V; umuC subunit of Pol V. Pol V is a bacterial translesion ...
 5-36 1.13e-17

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: 72.97  E-value: 1.13e-17
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2280579211   5 ALVDCNSFYCSCERIFRPDLAQKAVVVLSNND 36
Cdd:cd01700     1 ALVDCNSFYASCERVFRPLLLGRPLVVLSNND 32
umuC PRK03609
translesion error-prone DNA polymerase V subunit UmuC;
4-36 7.28e-15

translesion error-prone DNA polymerase V subunit UmuC;


Pssm-ID: 179607 [Multi-domain]  Cd Length: 422  Bit Score: 65.17  E-value: 7.28e-15
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2280579211   4 FALVDCNSFYCSCERIFRPDLAQKAVVVLSNND 36
Cdd:PRK03609    2 FALCDVNSFYASCETVFRPDLRGKPVVVLSNND 34
DinP COG0389
Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination ...
 3-39 1.03e-12

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


Pssm-ID: 440158 [Multi-domain]  Cd Length: 336  Bit Score: 59.00  E-value: 1.03e-12
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2280579211   3 VFALVDCNSFYCSCERIFRPDLAQKAVVVLSNNDlRG 39
Cdd:COG0389     2 RILHVDMDAFYASVEQRDRPELRGKPVAVGGDNN-RG 37
IMS pfam00817
impB/mucB/samB family; These proteins are involved in UV protection (Swiss).
 7-36 9.44e-07

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


Pssm-ID: 425885 [Multi-domain]  Cd Length: 148  Bit Score: 41.79  E-value: 9.44e-07
                          10        20        30
                  ....*....|....*....|....*....|
gi 2280579211   7 VDCNSFYCSCERIFRPDLAQKAVVVLSNND 36
Cdd:pfam00817   1 IDMDAFFASVELLRDPELKGKPVAVGGGNG 30
 
Name Accession Description Interval E-value
PolY_Pol_V_umuC cd01700
umuC subunit of DNA Polymerase V; umuC subunit of Pol V. Pol V is a bacterial translesion ...
 5-36 1.13e-17

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: 72.97  E-value: 1.13e-17
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2280579211   5 ALVDCNSFYCSCERIFRPDLAQKAVVVLSNND 36
Cdd:cd01700     1 ALVDCNSFYASCERVFRPLLLGRPLVVLSNND 32
umuC PRK03609
translesion error-prone DNA polymerase V subunit UmuC;
4-36 7.28e-15

translesion error-prone DNA polymerase V subunit UmuC;


Pssm-ID: 179607 [Multi-domain]  Cd Length: 422  Bit Score: 65.17  E-value: 7.28e-15
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2280579211   4 FALVDCNSFYCSCERIFRPDLAQKAVVVLSNND 36
Cdd:PRK03609    2 FALCDVNSFYASCETVFRPDLRGKPVVVLSNND 34
DinP COG0389
Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination ...
 3-39 1.03e-12

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


Pssm-ID: 440158 [Multi-domain]  Cd Length: 336  Bit Score: 59.00  E-value: 1.03e-12
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2280579211   3 VFALVDCNSFYCSCERIFRPDLAQKAVVVLSNNDlRG 39
Cdd:COG0389     2 RILHVDMDAFYASVEQRDRPELRGKPVAVGGDNN-RG 37
IMS pfam00817
impB/mucB/samB family; These proteins are involved in UV protection (Swiss).
 7-36 9.44e-07

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


Pssm-ID: 425885 [Multi-domain]  Cd Length: 148  Bit Score: 41.79  E-value: 9.44e-07
                          10        20        30
                  ....*....|....*....|....*....|
gi 2280579211   7 VDCNSFYCSCERIFRPDLAQKAVVVLSNND 36
Cdd:pfam00817   1 IDMDAFFASVELLRDPELKGKPVAVGGGNG 30
PRK03103 PRK03103
DNA polymerase IV; Reviewed
 3-40 4.59e-06

DNA polymerase IV; Reviewed


Pssm-ID: 235104 [Multi-domain]  Cd Length: 409  Bit Score: 40.37  E-value: 4.59e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2280579211   3 VFALVDCNSFYCSCERIFRPDLAQKAVVVLSNNDLRGG 40
Cdd:PRK03103    4 VILLVDMQSFYASVEKAANPELKGRPVIVSGDPERRSG 41
PRK01810 PRK01810
DNA polymerase IV; Validated
 7-40 1.15e-05

DNA polymerase IV; Validated


Pssm-ID: 179337 [Multi-domain]  Cd Length: 407  Bit Score: 39.24  E-value: 1.15e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2280579211   7 VDCNSFYCSCERIFRPDLAQKAVVVLSNNDLRGG 40
Cdd:PRK01810   10 VDMNSFFASVEIAYDPSLQGKPLAVAGNEKERKG 43
PolY cd00424
Y-family of DNA polymerases; Y-family DNA polymerases are a specialized subset of polymerases ...
 7-39 3.01e-05

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: 38.11  E-value: 3.01e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2280579211   7 VDCNSFYCSCERIFRPDLAQKAVVVLSNNDLRG 39
Cdd:cd00424     3 IDFDNFFASVEQLARPELKGRPVVVVPFNSDST 35
PolY_Pol_IV_kappa cd03586
DNA Polymerase IV/Kappa; Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion ...
 7-39 1.37e-04

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: 36.35  E-value: 1.37e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2280579211   7 VDCNSFYCSCERIFRPDLAQKAVVVLSNNDlRG 39
Cdd:cd03586     3 IDMDAFYASVEQRDNPELKGKPVAVGGSSD-RG 34
PRK02794 PRK02794
DNA polymerase IV; Provisional
 5-31 3.14e-03

DNA polymerase IV; Provisional


Pssm-ID: 179473 [Multi-domain]  Cd Length: 419  Bit Score: 32.60  E-value: 3.14e-03
                          10        20
                  ....*....|....*....|....*..
gi 2280579211   5 ALVDCNSFYCSCERIFRPDLAQKAVVV 31
Cdd:PRK02794   39 AHIDCDAFYASVEKRDNPELRDKPVII 65
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH