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Conserved domains on  [gi|6324017|ref|NP_014087|]
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Rfa2p [Saccharomyces cerevisiae S288C]

Protein Classification

RFA2 family protein( domain architecture ID 11474178)

RFA2 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RFA2 COG5235
Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA ...
 1-273 2.45e-147

Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair];


:

Pssm-ID: 227560 [Multi-domain]  Cd Length: 258  Bit Score: 412.83  E-value: 2.45e-147
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017    1 MATYQPYNEYSSVTGGGFENSESRPGSGESETNTRVNTLTPVTIKQILESKQDIQDGPFVSHNQELHHVCFVGVVRNITD 80
Cdd:COG5235   1 LATLYLLKSLFFITRGQIFGTGSPPPMDRSEGGYIVNTLRPVTIKQILSCDQDETDSTFLVDSAEVTNVQFVGVVRNIKT 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017   81 HTANIFLTIEDGTGQIEVRKWSEDANDLAAGNDDSSGKgygsqvaqqfeiggYVKVFGALKEFGGKKNIQYAVIKPIDSF 160
Cdd:COG5235  81 STTNSMFVIEDGTGSIEVRFWPGNSYEEEQCKDLEEQN--------------YVKVNGSLKTFNGKRSISASHISAIEDS 146

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017  161 NEVLTHHLEVIKCHSIASGMMKQPLESASNNNGQSLFVKDDNDTSSGSSPLQRILEFCKKQCEGKDANSFAVPIPLISQS 240
Cdd:COG5235 147 NEVTYHFLECIYQHLFYTRQLQRPLEEEVKNDGQSLFAKLDNDTSSGSSRLQEDILECYRRNQDENGLHINVVIKMLSQS 226

                       250       260       270
                ....*....|....*....|....*....|...
gi 6324017  241 LNLDETTVRncCTTLTDQGFIYPTFDDNNFFAL 273
Cdd:COG5235 227 YSEDETRVN--IDVLLRDGHIYPTVDGNEFKTT 257
 
Name Accession Description Interval E-value
RFA2 COG5235
Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA ...
 1-273 2.45e-147

Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair];


Pssm-ID: 227560 [Multi-domain]  Cd Length: 258  Bit Score: 412.83  E-value: 2.45e-147
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017    1 MATYQPYNEYSSVTGGGFENSESRPGSGESETNTRVNTLTPVTIKQILESKQDIQDGPFVSHNQELHHVCFVGVVRNITD 80
Cdd:COG5235   1 LATLYLLKSLFFITRGQIFGTGSPPPMDRSEGGYIVNTLRPVTIKQILSCDQDETDSTFLVDSAEVTNVQFVGVVRNIKT 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017   81 HTANIFLTIEDGTGQIEVRKWSEDANDLAAGNDDSSGKgygsqvaqqfeiggYVKVFGALKEFGGKKNIQYAVIKPIDSF 160
Cdd:COG5235  81 STTNSMFVIEDGTGSIEVRFWPGNSYEEEQCKDLEEQN--------------YVKVNGSLKTFNGKRSISASHISAIEDS 146

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017  161 NEVLTHHLEVIKCHSIASGMMKQPLESASNNNGQSLFVKDDNDTSSGSSPLQRILEFCKKQCEGKDANSFAVPIPLISQS 240
Cdd:COG5235 147 NEVTYHFLECIYQHLFYTRQLQRPLEEEVKNDGQSLFAKLDNDTSSGSSRLQEDILECYRRNQDENGLHINVVIKMLSQS 226

                       250       260       270
                ....*....|....*....|....*....|...
gi 6324017  241 LNLDETTVRncCTTLTDQGFIYPTFDDNNFFAL 273
Cdd:COG5235 227 YSEDETRVN--IDVLLRDGHIYPTVDGNEFKTT 257
RPA2_DBD_D cd04478
RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding ...
 68-174 8.36e-39

RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA damage. RPA2 interacts physically with menin; the gene encoding menin is a tumor suppressor gene disrupted in multiple endocrine neoplasia type I. This subfamily also includes RPA2 from Cryptosporidium parvum (CpRPA2). CpRPA2 is an SSB, which can be phosphorylated by DNA-PK in vitro.


Pssm-ID: 239924  Cd Length: 95  Bit Score: 131.18  E-value: 8.36e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017   68 HVCFVGVVRNITDHTANIFLTIEDGTGQIEVRKWSEDANDlaagnddssgkgyGSQVAQQFEIGGYVKVFGALKEFGGKK 147
Cdd:cd04478   1 QVTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDDND-------------DSSEVEPIEEGTYVRVFGNLKSFQGKK 67

                        90       100
                ....*....|....*....|....*..
gi 6324017  148 NIQYAVIKPIDSFNEVLTHHLEVIKCH 174
Cdd:cd04478  68 SIMAFSIRPVTDFNEVTYHLLEVIYVH 94
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 69-147 1.57e-07

OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.


Pssm-ID: 460164 [Multi-domain]  Cd Length: 75  Bit Score: 47.61  E-value: 1.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017     69 VCFVGVVRNITDHTAN-IFLTIEDGTGQIEVRKWSEDANdlaagnddssgkgygsQVAQQFEIGGYVKVFGALKEFGGKK 147
Cdd:pfam01336   1 VTVAGRVTSIRRSGGKlLFLTLRDGTGSIQVVVFKEEAE----------------KLAKKLKEGDVVRVTGKVKKRKGGE 64
 
Name Accession Description Interval E-value
RFA2 COG5235
Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA ...
 1-273 2.45e-147

Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair];


Pssm-ID: 227560 [Multi-domain]  Cd Length: 258  Bit Score: 412.83  E-value: 2.45e-147
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017    1 MATYQPYNEYSSVTGGGFENSESRPGSGESETNTRVNTLTPVTIKQILESKQDIQDGPFVSHNQELHHVCFVGVVRNITD 80
Cdd:COG5235   1 LATLYLLKSLFFITRGQIFGTGSPPPMDRSEGGYIVNTLRPVTIKQILSCDQDETDSTFLVDSAEVTNVQFVGVVRNIKT 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017   81 HTANIFLTIEDGTGQIEVRKWSEDANDLAAGNDDSSGKgygsqvaqqfeiggYVKVFGALKEFGGKKNIQYAVIKPIDSF 160
Cdd:COG5235  81 STTNSMFVIEDGTGSIEVRFWPGNSYEEEQCKDLEEQN--------------YVKVNGSLKTFNGKRSISASHISAIEDS 146

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017  161 NEVLTHHLEVIKCHSIASGMMKQPLESASNNNGQSLFVKDDNDTSSGSSPLQRILEFCKKQCEGKDANSFAVPIPLISQS 240
Cdd:COG5235 147 NEVTYHFLECIYQHLFYTRQLQRPLEEEVKNDGQSLFAKLDNDTSSGSSRLQEDILECYRRNQDENGLHINVVIKMLSQS 226

                       250       260       270
                ....*....|....*....|....*....|...
gi 6324017  241 LNLDETTVRncCTTLTDQGFIYPTFDDNNFFAL 273
Cdd:COG5235 227 YSEDETRVN--IDVLLRDGHIYPTVDGNEFKTT 257
RPA2_DBD_D cd04478
RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding ...
 68-174 8.36e-39

RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA damage. RPA2 interacts physically with menin; the gene encoding menin is a tumor suppressor gene disrupted in multiple endocrine neoplasia type I. This subfamily also includes RPA2 from Cryptosporidium parvum (CpRPA2). CpRPA2 is an SSB, which can be phosphorylated by DNA-PK in vitro.


Pssm-ID: 239924  Cd Length: 95  Bit Score: 131.18  E-value: 8.36e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017   68 HVCFVGVVRNITDHTANIFLTIEDGTGQIEVRKWSEDANDlaagnddssgkgyGSQVAQQFEIGGYVKVFGALKEFGGKK 147
Cdd:cd04478   1 QVTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDDND-------------DSSEVEPIEEGTYVRVFGNLKSFQGKK 67

                        90       100
                ....*....|....*....|....*..
gi 6324017  148 NIQYAVIKPIDSFNEVLTHHLEVIKCH 174
Cdd:cd04478  68 SIMAFSIRPVTDFNEVTYHLLEVIYVH 94
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 69-147 1.57e-07

OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.


Pssm-ID: 460164 [Multi-domain]  Cd Length: 75  Bit Score: 47.61  E-value: 1.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017     69 VCFVGVVRNITDHTAN-IFLTIEDGTGQIEVRKWSEDANdlaagnddssgkgygsQVAQQFEIGGYVKVFGALKEFGGKK 147
Cdd:pfam01336   1 VTVAGRVTSIRRSGGKlLFLTLRDGTGSIQVVVFKEEAE----------------KLAKKLKEGDVVRVTGKVKKRKGGE 64
RPA_C pfam08784
Replication protein A C terminal; This domain corresponds to the C terminal of the single ...
 190-268 6.58e-04

Replication protein A C terminal; This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.


Pssm-ID: 400920  Cd Length: 106  Bit Score: 38.51  E-value: 6.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324017    190 NNNGQSLFvkddNDTSSGSSPLQR-ILEFCKKQCEGKDAnsfaVPIPLISQSLNLDETTVRNCCTTLTDQGFIYPTFDDN 268
Cdd:pfam08784  35 SGGDASVV----NANNGGLTPLQDqVLNLIKQPPNGNEG----VHVDEIAQRLGLPVNDVKQAVDFLSNEGHIYSTIDDD 106
YhaM_OBF_like cd04492
YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and ...
 87-149 1.69e-03

YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.


Pssm-ID: 239938 [Multi-domain]  Cd Length: 83  Bit Score: 36.42  E-value: 1.69e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6324017   87 LTIEDGTGQIEVRKWseDANDlaagnddssgkgygsQVAQQFEIGGYVKVFGALKEFGGKKNI 149
Cdd:cd04492  23 LTLQDKTGEIEAKLW--DASE---------------EDEEKFKPGDIVHVKGRVEEYRGRLQL 68
 
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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