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Conserved domains on  [gi|1002986200|ref|WP_061430727|]
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hypothetical protein [Microcystis aeruginosa]

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 ...
 55-125 3.32e-05

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 cd04489:

Pssm-ID: 471953 [Multi-domain]  Cd Length: 78  Bit Score: 40.97  E-value: 3.32e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002986200  55 VYLRGTVSNYAPFLAGGAYL-LQDGSGKI----WIRTNSN--KLPRQGEEIVIKGKIDFEAiPQGS-QtvneLYVVELE 125
Cdd:cd04489     2 VWVEGEISNLKRPSSGHLYFtLKDEDASIrcvmWRSNARRlgFPLEEGMEVLVRGKVSFYE-PRGGyQ----LIVEEIE 75
Retinal super family cl37892
Retinal protein; This family of proteins is found in the photoreceptor cells of the retina. ...
 134-199 1.55e-03

Retinal protein; This family of proteins is found in the photoreceptor cells of the retina. Mutations of the gene encoding this protein have been associated with retinal disorders such as retinitis pigmentosa and late-onset progressive retinal atrophy. The function of this family of proteins is unknown, but it is likely to be important in the development and function of the retina.


The actual alignment was detected with superfamily member pfam15449:

Pssm-ID: 464722 [Multi-domain]  Cd Length: 1293  Bit Score: 39.37  E-value: 1.55e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002986200  134 SLPT--PSPSPEIKPSPTSEVKPPENNSPPVSTKPLENPRQVTIPSAaetkPPETPVVTPVKPNPPVQ 199
Cdd:pfam15449 1046 SLPTvqRSPSPPLSPRAPSPPRSPRVLSPPTSKKRTSPPPQHKLPSP----PPESPPAQHKLSSPPTQ 1109
 
Name Accession Description Interval E-value
ExoVII_LU_OBF cd04489
ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of ...
 55-125 3.32e-05

ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.


Pssm-ID: 239935 [Multi-domain]  Cd Length: 78  Bit Score: 40.97  E-value: 3.32e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002986200  55 VYLRGTVSNYAPFLAGGAYL-LQDGSGKI----WIRTNSN--KLPRQGEEIVIKGKIDFEAiPQGS-QtvneLYVVELE 125
Cdd:cd04489     2 VWVEGEISNLKRPSSGHLYFtLKDEDASIrcvmWRSNARRlgFPLEEGMEVLVRGKVSFYE-PRGGyQ----LIVEEIE 75
tRNA_anti_2 pfam13742
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 55-125 3.92e-04

OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids.


Pssm-ID: 463974 [Multi-domain]  Cd Length: 95  Bit Score: 38.59  E-value: 3.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002986200  55 VYLRGTVSNYAPFLAGGAYL-LQDGSGKI----WiRTNSNKL---PRQGEEIVIKGKIDFEAiPQGS-QtvneLYVVELE 125
Cdd:pfam13742  22 VWVEGEISNLKRRSSGHLYFtLKDEKAQIrcvmF-RSRARRLkftPEDGMKVLVRGRVSVYE-PRGSyQ----LIVEDIE 95
Retinal pfam15449
Retinal protein; This family of proteins is found in the photoreceptor cells of the retina. ...
 134-199 1.55e-03

Retinal protein; This family of proteins is found in the photoreceptor cells of the retina. Mutations of the gene encoding this protein have been associated with retinal disorders such as retinitis pigmentosa and late-onset progressive retinal atrophy. The function of this family of proteins is unknown, but it is likely to be important in the development and function of the retina.


Pssm-ID: 464722 [Multi-domain]  Cd Length: 1293  Bit Score: 39.37  E-value: 1.55e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002986200  134 SLPT--PSPSPEIKPSPTSEVKPPENNSPPVSTKPLENPRQVTIPSAaetkPPETPVVTPVKPNPPVQ 199
Cdd:pfam15449 1046 SLPTvqRSPSPPLSPRAPSPPRSPRVLSPPTSKKRTSPPPQHKLPSP----PPESPPAQHKLSSPPTQ 1109
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 128-204 1.97e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 39.02  E-value: 1.97e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002986200 128 DAVAVNSLPTPSPSPEIKP-SPTSEVKPPENNSPPVSTKPLENPRQVTIPSAAETKP-PETPVVTPVKPNPPVQPVAEA 204
Cdd:PRK14950  381 PTPAPSTRPKAAAAANIPPkEPVRETATPPPVPPRPVAPPVPHTPESAPKLTRAAIPvDEKPKYTPPAPPKEEEKALIA 459
 
Name Accession Description Interval E-value
ExoVII_LU_OBF cd04489
ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of ...
 55-125 3.32e-05

ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.


Pssm-ID: 239935 [Multi-domain]  Cd Length: 78  Bit Score: 40.97  E-value: 3.32e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002986200  55 VYLRGTVSNYAPFLAGGAYL-LQDGSGKI----WIRTNSN--KLPRQGEEIVIKGKIDFEAiPQGS-QtvneLYVVELE 125
Cdd:cd04489     2 VWVEGEISNLKRPSSGHLYFtLKDEDASIrcvmWRSNARRlgFPLEEGMEVLVRGKVSFYE-PRGGyQ----LIVEEIE 75
tRNA_anti_2 pfam13742
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 55-125 3.92e-04

OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids.


Pssm-ID: 463974 [Multi-domain]  Cd Length: 95  Bit Score: 38.59  E-value: 3.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002986200  55 VYLRGTVSNYAPFLAGGAYL-LQDGSGKI----WiRTNSNKL---PRQGEEIVIKGKIDFEAiPQGS-QtvneLYVVELE 125
Cdd:pfam13742  22 VWVEGEISNLKRRSSGHLYFtLKDEKAQIrcvmF-RSRARRLkftPEDGMKVLVRGRVSVYE-PRGSyQ----LIVEDIE 95
Retinal pfam15449
Retinal protein; This family of proteins is found in the photoreceptor cells of the retina. ...
 134-199 1.55e-03

Retinal protein; This family of proteins is found in the photoreceptor cells of the retina. Mutations of the gene encoding this protein have been associated with retinal disorders such as retinitis pigmentosa and late-onset progressive retinal atrophy. The function of this family of proteins is unknown, but it is likely to be important in the development and function of the retina.


Pssm-ID: 464722 [Multi-domain]  Cd Length: 1293  Bit Score: 39.37  E-value: 1.55e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002986200  134 SLPT--PSPSPEIKPSPTSEVKPPENNSPPVSTKPLENPRQVTIPSAaetkPPETPVVTPVKPNPPVQ 199
Cdd:pfam15449 1046 SLPTvqRSPSPPLSPRAPSPPRSPRVLSPPTSKKRTSPPPQHKLPSP----PPESPPAQHKLSSPPTQ 1109
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 128-204 1.97e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 39.02  E-value: 1.97e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002986200 128 DAVAVNSLPTPSPSPEIKP-SPTSEVKPPENNSPPVSTKPLENPRQVTIPSAAETKP-PETPVVTPVKPNPPVQPVAEA 204
Cdd:PRK14950  381 PTPAPSTRPKAAAAANIPPkEPVRETATPPPVPPRPVAPPVPHTPESAPKLTRAAIPvDEKPKYTPPAPPKEEEKALIA 459
PHA03247 PHA03247
large tegument protein UL36; Provisional
 132-203 2.11e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.15  E-value: 2.11e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002986200  132 VNSLPTPSPSPEIKPSPTSEVKPPENNSPPVSTKPLENPrqvTIPSAAETKPPETPvvtPVKPNPPVQPVAE 203
Cdd:PHA03247  2883 VRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQP---QPPPPPQPQPPPPP---PPRPQPPLAPTTD 2948
PRK14948 PRK14948
DNA polymerase III subunit gamma/tau;
136-204 2.58e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237862 [Multi-domain]  Cd Length: 620  Bit Score: 38.41  E-value: 2.58e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002986200 136 PTPSPSPEIKPSPTSEVKPPENNSPPVSTKPLENPrqvTIPSAAETKPPETPVVTPVKPNPPVQPVAEA 204
Cdd:PRK14948  367 EIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAA---TTPSPPPAKASPPIPVPAEPTEPSPTPPANA 432
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 134-204 3.79e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 38.25  E-value: 3.79e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002986200 134 SLPTPSPS-----PEIKPSPTSEVKPPENNSPPVSTKPLENPRQVTIPSAAETKPPETPV-VTPVKPNPPVQPVAEA 204
Cdd:PRK14950  379 VRPTPAPStrpkaAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTPESAPKLTRAAIPVdEKPKYTPPAPPKEEEK 455
PRK14948 PRK14948
DNA polymerase III subunit gamma/tau;
110-184 4.35e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237862 [Multi-domain]  Cd Length: 620  Bit Score: 38.02  E-value: 4.35e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002986200 110 PQGSQTVNELYVVELEQMDAVAVNSLPTPSPSPEIKPSPTSEVKPPENNSPPVSTKPLENPRQVTIPSAAETKPP 184
Cdd:PRK14948  363 AFISEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAEPTEPSPTPPANAANAPP 437
PRK14954 PRK14954
DNA polymerase III subunits gamma and tau; Provisional
 118-204 8.84e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184918 [Multi-domain]  Cd Length: 620  Bit Score: 36.84  E-value: 8.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002986200 118 ELYVVELEQMDAVAVNSLPTPSPSPEIKpSPTSEVKPPENNSPPVSTKPlENP--RQVTIPSAAETKPPETpvVTPVKPN 195
Cdd:PRK14954  364 ELALLRLIELVRNDGGVAPSPAGSPDVK-KKAPEPDLPQPDRHPGPAKP-EAPgaRPAELPSPASAPTPEQ--QPPVARS 439


                  ....*....
gi 1002986200 196 PPVQPVAEA 204
Cdd:PRK14954  440 APLPPSPQA 448
 
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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