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Conserved domains on  [gi|8954034|gb|AAF82208|]
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F10K1.17 [Arabidopsis thaliana]

Protein Classification

single-stranded DNA-binding protein( domain architecture ID 10138990)

single-stranded DNA (ssDNA)-binding protein plays a key role in DNA replication, recombination, and repair

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
hOBFC1_like cd04483
hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein ...
 42-133 1.95e-41

hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. 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 OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.


:

Pssm-ID: 239929  Cd Length: 92  Bit Score: 133.71  E-value: 1.95e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8954034   42 EIVGTIVSRDLTPKFLKFGVDDGTGCVTCVMWLNQLTSSYFSRWDPATILLLASAARKQAAQIRIGAVARVRGRVGSYRG 121
Cdd:cd04483   1 DILGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIRTYRG 80

                        90
                ....*....|..
gi 8954034  122 VMQITANVAVAE 133
Cdd:cd04483  81 EREINASVVYKV 92
 
Name Accession Description Interval E-value
hOBFC1_like cd04483
hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein ...
 42-133 1.95e-41

hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. 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 OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.


Pssm-ID: 239929  Cd Length: 92  Bit Score: 133.71  E-value: 1.95e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8954034   42 EIVGTIVSRDLTPKFLKFGVDDGTGCVTCVMWLNQLTSSYFSRWDPATILLLASAARKQAAQIRIGAVARVRGRVGSYRG 121
Cdd:cd04483   1 DILGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIRTYRG 80

                        90
                ....*....|..
gi 8954034  122 VMQITANVAVAE 133
Cdd:cd04483  81 EREINASVVYKV 92
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 41-128 6.27e-05

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: 39.14  E-value: 6.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8954034     41 VEIVGTIVSRDLTP-KFLKFGVDDGTGCVTCVMWlnqltssyfsrwdpatilllASAARKQAAQIRIGAVARVRGRVGSY 119
Cdd:pfam01336   1 VTVAGRVTSIRRSGgKLLFLTLRDGTGSIQVVVF--------------------KEEAEKLAKKLKEGDVVRVTGKVKKR 60

                          90
                  ....*....|
gi 8954034    120 R-GVMQITAN 128
Cdd:pfam01336  61 KgGELELVVE 70
YhaM COG3481
3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily ...
 55-126 2.15e-04

3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily [Translation, ribosomal structure and biogenesis]; 3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 442704 [Multi-domain]  Cd Length: 316  Bit Score: 40.18  E-value: 2.15e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 8954034   55 KFLKFGVDDGTGCVTCVMWlnqltssyfsrwdpatilllaSAARKQAAQIRIGAVARVRGRVGSYRGVMQIT 126
Cdd:COG3481  35 PYLSLTLQDKTGTIEAKIW---------------------DASEEDIEEFQPGDVVKVRGKVQEYQGRLQLK 85
 
Name Accession Description Interval E-value
hOBFC1_like cd04483
hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein ...
 42-133 1.95e-41

hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. 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 OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.


Pssm-ID: 239929  Cd Length: 92  Bit Score: 133.71  E-value: 1.95e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8954034   42 EIVGTIVSRDLTPKFLKFGVDDGTGCVTCVMWLNQLTSSYFSRWDPATILLLASAARKQAAQIRIGAVARVRGRVGSYRG 121
Cdd:cd04483   1 DILGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIRTYRG 80

                        90
                ....*....|..
gi 8954034  122 VMQITANVAVAE 133
Cdd:cd04483  81 EREINASVVYKV 92
RPA2_DBD_D cd04478
RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding ...
 41-147 4.01e-06

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: 42.97  E-value: 4.01e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8954034   41 VEIVGTIVSRDLTPKFLKFGVDDGTGCVTCVMWLNQltssyfsrwdpatilllASAARKQAAQIRIGAVARVRGRVGSYR 120
Cdd:cd04478   2 VTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDD-----------------DNDDSSEVEPIEEGTYVRVFGNLKSFQ 64

                        90       100
                ....*....|....*....|....*....
gi 8954034  121 GVMQITA-NVAVAErDPNaEI-LHWLECL 147
Cdd:cd04478  65 GKKSIMAfSIRPVT-DFN-EVtYHLLEVI 91
RecG_wedge_OBF cd04488
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal ...
 43-126 1.60e-05

RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched chain substrates.


Pssm-ID: 239934 [Multi-domain]  Cd Length: 75  Bit Score: 41.03  E-value: 1.60e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8954034   43 IVGTIVSRDLTPKF----LKFGVDDGTGCVTCVmWLNqltssyFSRWdpatilllasaarkQAAQIRIGAVARVRGRVGS 118
Cdd:cd04488   2 VEGTVVSVEVVPRRgrrrLKVTLSDGTGTLTLV-FFN------FQPY--------------LKKQLPPGTRVRVSGKVKR 60


                ....*...
gi 8954034  119 YRGVMQIT 126
Cdd:cd04488  61 FRGGLQIV 68
RPA2_OBF_family cd03524
RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold ...
 42-128 1.66e-05

RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-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). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyrococcus abyssi DNA polymerase II (Pol II) small subunit, Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM (a 3'-to-5'exoribonuclease). It also includes the OB folds of breast cancer susceptibility gene 2 protein (BRCA2), Oxytricha nova telomere end binding protein (TEBP), Saccharomyces cerevisiae telomere-binding protein (Cdc13), and human protection of telomeres 1 protein (POT1).


Pssm-ID: 239601 [Multi-domain]  Cd Length: 75  Bit Score: 40.81  E-value: 1.66e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8954034   42 EIVGTIVS---RDLTPKFLKFGVDDGTG-CVTCVMWLNQLTSSYFsrwdpatilllasaarkqaaQIRIGAVARVRGRVG 117
Cdd:cd03524   1 TIVGIVVAveeIRTEGKVLIFTLTDGTGgTIRVTLFGELAEELEN--------------------LLKEGQVVYIKGKVK 60

                        90
                ....*....|.
gi 8954034  118 SYRGVMQITAN 128
Cdd:cd03524  61 KFRGRLQLIVE 71
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 41-128 6.27e-05

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: 39.14  E-value: 6.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8954034     41 VEIVGTIVSRDLTP-KFLKFGVDDGTGCVTCVMWlnqltssyfsrwdpatilllASAARKQAAQIRIGAVARVRGRVGSY 119
Cdd:pfam01336   1 VTVAGRVTSIRRSGgKLLFLTLRDGTGSIQVVVF--------------------KEEAEKLAKKLKEGDVVRVTGKVKKR 60

                          90
                  ....*....|
gi 8954034    120 R-GVMQITAN 128
Cdd:pfam01336  61 KgGELELVVE 70
YhaM_OBF_like cd04492
YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and ...
 54-128 1.96e-04

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: 38.34  E-value: 1.96e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 8954034   54 PKFLKFGVDDGTGCVTCVMWLNQLTssyfsrwdpatilllasaarkQAAQIRIGAVARVRGRVGSYRGVMQITAN 128
Cdd:cd04492  18 KPYLALTLQDKTGEIEAKLWDASEE---------------------DEEKFKPGDIVHVKGRVEEYRGRLQLKIQ 71
YhaM COG3481
3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily ...
 55-126 2.15e-04

3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily [Translation, ribosomal structure and biogenesis]; 3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 442704 [Multi-domain]  Cd Length: 316  Bit Score: 40.18  E-value: 2.15e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 8954034   55 KFLKFGVDDGTGCVTCVMWlnqltssyfsrwdpatilllaSAARKQAAQIRIGAVARVRGRVGSYRGVMQIT 126
Cdd:COG3481  35 PYLSLTLQDKTGTIEAKIW---------------------DASEEDIEEFQPGDVVKVRGKVQEYQGRLQLK 85
RFA2 COG5235
Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA ...
 1-148 1.10e-03

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: 38.03  E-value: 1.10e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8954034    1 MDRSLQSTHAK-LVARDI-QRLTQSPTESNSFSLLGGACVSRVEIVGTIVSRDLTPKFLKFGVDDGTGCVTCVMWLNQlt 78
Cdd:COG5235  27 MDRSEGGYIVNtLRPVTIkQILSCDQDETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVIEDGTGSIEVRFWPGN-- 104

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8954034   79 ssyfsrwdpatilllaSAARKQAAQIRIGAVARVRGRVGSYRGVMQITANVAVAERDPNAEILHWLECLK 148
Cdd:COG5235 105 ----------------SYEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIY 158
 
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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