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Conserved domains on  [gi|1780603391|emb|VYS47028|]
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unnamed protein product [Arabidopsis thaliana]

Protein Classification

single stranded DNA-binding domain-containing protein( domain architecture ID 489)

single stranded DNA-binding domain-containing protein may bind preferentially to single-stranded DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPA_2b-aaRSs_OBF_like super family cl09930
Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with ...
 15-123 1.04e-17

Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism. This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B, of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases.


The actual alignment was detected with superfamily member PRK06461:

Pssm-ID: 471953 [Multi-domain]  Cd Length: 129  Bit Score: 73.53  E-value: 1.04e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780603391  15 TKVDQLRPGTSGHNVNVKIVST---KMVLQKGradGPQarqlRISECIVGDETGVIVFTARNDQVDLMKEGSTVTLRNAK 91
Cdd:PRK06461    5 TKIKDLKPGMERVNVTVRVLEVgepKVIQTKG---GPR----TISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAW 77

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1780603391  92 IDMYKGSMRLAVDKWGRVEVTE----PASFKVKEDT 123
Cdd:PRK06461   78 TTLYRGKVQLNVGKYGSISESDdeevPEAEEIPEET 113
 
Name Accession Description Interval E-value
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 15-123 1.04e-17

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 73.53  E-value: 1.04e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780603391  15 TKVDQLRPGTSGHNVNVKIVST---KMVLQKGradGPQarqlRISECIVGDETGVIVFTARNDQVDLMKEGSTVTLRNAK 91
Cdd:PRK06461    5 TKIKDLKPGMERVNVTVRVLEVgepKVIQTKG---GPR----TISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAW 77

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1780603391  92 IDMYKGSMRLAVDKWGRVEVTE----PASFKVKEDT 123
Cdd:PRK06461   78 TTLYRGKVQLNVGKYGSISESDdeevPEAEEIPEET 113
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 28-111 6.30e-15

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 64.95  E-value: 6.30e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780603391  28 NVNVKIVSTKMVLQKGRADGPQarqlRISECIVGDETGVIVFTARNDQV-DLMKEGSTVTLRNAKIDMYKGSMRLAVDKW 106
Cdd:cd04491     1 SVEGKVLSISEPREFTRDGSEG----KVQSGLVGDETGTIRFTLWDEKAaDDLEPGDVVRIENAYVREFNGRLELSVGKN 76


                  ....*
gi 1780603391 107 GRVEV 111
Cdd:cd04491    77 SEIEK 81
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
15-129 8.61e-11

ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 57.76  E-value: 8.61e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780603391  15 TKVDQLRPGTSGHNVNVKIVSTKMVLQKGRADGpqaRQLRISECIVGDETGVIVFTARNDQVDL-MKEGSTVTLRNAKID 93
Cdd:COG1599    22 VKISDLSPGDRDVNVEGRVLEIGEERTFDRKDG---SEGRVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIENAYVR 98

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1780603391  94 MYKGSMRLAVDKWGRVEVTEpASFKVKEDTNMSLIE 129
Cdd:COG1599    99 EFNGGPELNLGERTTIEKLD-EDVEVIPDEERTPIG 133
 
Name Accession Description Interval E-value
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 15-123 1.04e-17

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 73.53  E-value: 1.04e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780603391  15 TKVDQLRPGTSGHNVNVKIVST---KMVLQKGradGPQarqlRISECIVGDETGVIVFTARNDQVDLMKEGSTVTLRNAK 91
Cdd:PRK06461    5 TKIKDLKPGMERVNVTVRVLEVgepKVIQTKG---GPR----TISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAW 77

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1780603391  92 IDMYKGSMRLAVDKWGRVEVTE----PASFKVKEDT 123
Cdd:PRK06461   78 TTLYRGKVQLNVGKYGSISESDdeevPEAEEIPEET 113
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 28-111 6.30e-15

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 64.95  E-value: 6.30e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780603391  28 NVNVKIVSTKMVLQKGRADGPQarqlRISECIVGDETGVIVFTARNDQV-DLMKEGSTVTLRNAKIDMYKGSMRLAVDKW 106
Cdd:cd04491     1 SVEGKVLSISEPREFTRDGSEG----KVQSGLVGDETGTIRFTLWDEKAaDDLEPGDVVRIENAYVREFNGRLELSVGKN 76


                  ....*
gi 1780603391 107 GRVEV 111
Cdd:cd04491    77 SEIEK 81
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
15-129 8.61e-11

ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 57.76  E-value: 8.61e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780603391  15 TKVDQLRPGTSGHNVNVKIVSTKMVLQKGRADGpqaRQLRISECIVGDETGVIVFTARNDQVDL-MKEGSTVTLRNAKID 93
Cdd:COG1599    22 VKISDLSPGDRDVNVEGRVLEIGEERTFDRKDG---SEGRVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIENAYVR 98

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1780603391  94 MYKGSMRLAVDKWGRVEVTEpASFKVKEDTNMSLIE 129
Cdd:COG1599    99 EFNGGPELNLGERTTIEKLD-EDVEVIPDEERTPIG 133
PRK06386 PRK06386
replication factor A; Reviewed
 59-135 1.92e-05

replication factor A; Reviewed


Pssm-ID: 235790 [Multi-domain]  Cd Length: 358  Bit Score: 42.58  E-value: 1.92e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1780603391  59 IVGDETGVIVFTARNDQvDLMKEGSTVTLRNAKIDMYKGSMRLAVDkwGRVEVTepasfkVKEDTNMSLIE-YELVNV 135
Cdd:PRK06386   42 IIGDETGTVPFTAWEFP-DAVKSGDVIEIKYCYSKEYNGKIRIYFD--SRSEVM------LKPDENIEVKRtYKLVKI 110
PRK07218 PRK07218
Single-stranded DNA binding protein;
20-114 1.76e-04

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 39.99  E-value: 1.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780603391  20 LRPGTSGHNVNVKI--VSTKMVLQKGRadgpqarQLRISECIVGDETGVIVFTARnDQVDLMKEGSTVTLRNAKIDMYKG 97
Cdd:PRK07218  168 LGPGDRGVNVEARVleLEHREIDGRDG-------ETTILSGVLADETGRLPFTDW-DPLPEIEIGASIRIEDAYVREFRG 239

                          90
                  ....*....|....*..
gi 1780603391  98 SMRLAVDKWGRVEVTEP 114
Cdd:PRK07218  240 VPSVNVSEFTTVEALDR 256
PRK15491 PRK15491
replication factor A; Provisional
 15-130 8.49e-04

replication factor A; Provisional


Pssm-ID: 185388 [Multi-domain]  Cd Length: 374  Bit Score: 37.94  E-value: 8.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780603391  15 TKVDQLRPGTSGHNVNVKIVSTKMVLQKGRADGPQARqlrISECIVGDETGVIVFTARNDQVDLMKEGSTVTLRNAKI-- 92
Cdd:PRK15491   58 TKIADINESSSNVNFTAKVVSIFEPKEFNRNDGTTGR---VGNIIVADETGSIRLTLWDDLADLIKTGDIEVGKSLNIsg 134

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1780603391  93 ---DMYKGsMRLAVDKWGRVEVTEPasfKVKEDTNMSLIEY 130
Cdd:PRK15491  135 yakEGYSG-IEVNIGRYGGISESDE---NVKASINSQKISD 171
PRK14699 PRK14699
replication factor A; Provisional
 16-95 1.30e-03

replication factor A; Provisional


Pssm-ID: 173162 [Multi-domain]  Cd Length: 484  Bit Score: 37.67  E-value: 1.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780603391  16 KVDQLRPGTSGHNVNVKIVSTKMVLQKGRADGPQARqlrISECIVGDETGVIVFTARNDQVDLMKEGSTVTLRNAKIDMY 95
Cdd:PRK14699   59 KIENITPESGPVNFIARVVSVFDTKEFTRNDGTIGR---VGNLIVGDETGKIKLTLWDNMADLIKAGKIKAGQTLQISGY 135
PRK07211 PRK07211
single-stranded DNA binding protein;
15-110 2.26e-03

single-stranded DNA binding protein;


Pssm-ID: 180887 [Multi-domain]  Cd Length: 485  Bit Score: 36.66  E-value: 2.26e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780603391  15 TKVDQLRPGTSGHNVNVKIVSTKMVLQKGRADGPQARqlrISECIVGDETGVIVFTARNDQVDLMKE---GSTVTLRNAK 91
Cdd:PRK07211  162 YTVEDLSLGLSDVTLVGVVLDTDSVRTFDRDDGSEGR---VSNLTVGDETGRVRVTLWDDRADLAEEldaGESVEIVDGY 238

                          90
                  ....*....|....*....
gi 1780603391  92 IDMYKGSMRLAVDKWGRVE 110
Cdd:PRK07211  239 VRERDGSLELHVGDRGAVE 257
PRK07218 PRK07218
Single-stranded DNA binding protein;
12-124 3.06e-03

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 36.14  E-value: 3.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780603391  12 PAFTKVDQLRPGTSGHNVNVKI--VSTKMVlqkgRADGpqaRQLRISECIVGDETGVIVFTARNDqVDLMKeGSTVTLRN 89
Cdd:PRK07218   56 PSSKDIKELSTDDKNVTVTGRVltIGERSI----RYQG---DDHVIYEGILADETGTISYTAWKD-FGLSP-GDTVTIGN 126

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1780603391  90 AKIDMYKGSMRLAVDKWGRVEVTEPASFKVKEDTN 124
Cdd:PRK07218  127 AGVREWDGRPELNIGESTTVSLLDDSSLPPYSIGG 161
PRK07217 PRK07217
replication factor A; Reviewed
 59-105 3.24e-03

replication factor A; Reviewed


Pssm-ID: 235970 [Multi-domain]  Cd Length: 311  Bit Score: 36.15  E-value: 3.24e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1780603391  59 IVGDETGVIVFT--ARNDQVDLmKEGSTVTLRNAKIDMYKGSMRLAVDK 105
Cdd:PRK07217  107 LLGDETGTIKFTkwAKSDLPEL-EEGKSYLLKNVVTDEYQGRFSVKLNR 154
 
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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