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Conserved domains on  [gi|1063699735|ref|NP_001325364|]
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myb domain protein 88 [Arabidopsis thaliana]

Protein Classification

SANT/Myb-like DNA-binding domain-containing protein( domain architecture ID 999994)

SANT (SWI3, ADA2, N-CoR and TFIIIB)/Myb-like DNA-binding domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03091 super family cl33633
hypothetical protein; Provisional
 19-132 2.30e-18

hypothetical protein; Provisional


The actual alignment was detected with superfamily member PLN03091:

Pssm-ID: 215570 [Multi-domain]  Cd Length: 459  Bit Score: 85.41  E-value: 2.30e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699735  19 HSDDSKKKERHIVtWSPEEDDILRKQISLQGTENWAIIASKFN-DKSTRQCRRRWYTYLNSDFKRGGWSPEEDTLLCEAQ 97
Cdd:PLN03091    4 HSCCYKQKLRKGL-WSPEEDEKLLRHITKYGHGCWSSVPKQAGlQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELH 82

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1063699735  98 RLFGNRWTEIAKVVSGRTDNAVKNRFTTLCKKRAK 132
Cdd:PLN03091   83 AVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLR 117
 
Name Accession Description Interval E-value
PLN03091 PLN03091
hypothetical protein; Provisional
 19-132 2.30e-18

hypothetical protein; Provisional


Pssm-ID: 215570 [Multi-domain]  Cd Length: 459  Bit Score: 85.41  E-value: 2.30e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699735  19 HSDDSKKKERHIVtWSPEEDDILRKQISLQGTENWAIIASKFN-DKSTRQCRRRWYTYLNSDFKRGGWSPEEDTLLCEAQ 97
Cdd:PLN03091    4 HSCCYKQKLRKGL-WSPEEDEKLLRHITKYGHGCWSSVPKQAGlQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELH 82

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1063699735  98 RLFGNRWTEIAKVVSGRTDNAVKNRFTTLCKKRAK 132
Cdd:PLN03091   83 AVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLR 117
REB1 COG5147
Myb superfamily proteins, including transcription factors and mRNA splicing factors ...
 24-141 1.11e-16

Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning];


Pssm-ID: 227476 [Multi-domain]  Cd Length: 512  Bit Score: 80.60  E-value: 1.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699735  24 KKKERHIVTWSPEEDDILRKQISLQGTENWAIIASKFNDKSTRQCRRRWYTYLNSDFKRGGWSPEEDTLLCEAQRLFGNR 103
Cdd:COG5147    14 MQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQ 93

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1063699735 104 WTEIAKVVSGRTDNAVKNRFTTLCKKRAKHEAMAKENR 141
Cdd:COG5147    94 WSTIADYKDRRTAQQCVERYVNTLEDLSSTHDSKLQRR 131
Myb_DNA-bind_6 pfam13921
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 33-93 4.43e-13

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 372817 [Multi-domain]  Cd Length: 60  Bit Score: 63.10  E-value: 4.43e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063699735  33 WSPEEDDILRKQISLQGtENWAIIASKFNDKSTRQCRRRWYTYLNSDFKRGGWSPEEDTLL 93
Cdd:pfam13921   1 WTEEEDEKLLKLVEKYG-NDWKQIAKELGRRTPKQCFDRWRRKLNPKISRGPWSKEEDQRL 60
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 32-76 1.78e-10

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


Pssm-ID: 238096 [Multi-domain]  Cd Length: 45  Bit Score: 55.27  E-value: 1.78e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063699735  32 TWSPEEDDILRKQISLQGTENWAIIASKFNDKSTRQCRRRWYTYL 76
Cdd:cd00167     1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
32-78 5.09e-10

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 54.15  E-value: 5.09e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1063699735   32 TWSPEEDDILRKQISLQGTENWAIIASKFNDKSTRQCRRRWYTYLNS 78
Cdd:smart00717   3 EWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWRNLLKP 49
 
Name Accession Description Interval E-value
PLN03091 PLN03091
hypothetical protein; Provisional
 19-132 2.30e-18

hypothetical protein; Provisional


Pssm-ID: 215570 [Multi-domain]  Cd Length: 459  Bit Score: 85.41  E-value: 2.30e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699735  19 HSDDSKKKERHIVtWSPEEDDILRKQISLQGTENWAIIASKFN-DKSTRQCRRRWYTYLNSDFKRGGWSPEEDTLLCEAQ 97
Cdd:PLN03091    4 HSCCYKQKLRKGL-WSPEEDEKLLRHITKYGHGCWSSVPKQAGlQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELH 82

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1063699735  98 RLFGNRWTEIAKVVSGRTDNAVKNRFTTLCKKRAK 132
Cdd:PLN03091   83 AVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLR 117
REB1 COG5147
Myb superfamily proteins, including transcription factors and mRNA splicing factors ...
 24-141 1.11e-16

Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning];


Pssm-ID: 227476 [Multi-domain]  Cd Length: 512  Bit Score: 80.60  E-value: 1.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699735  24 KKKERHIVTWSPEEDDILRKQISLQGTENWAIIASKFNDKSTRQCRRRWYTYLNSDFKRGGWSPEEDTLLCEAQRLFGNR 103
Cdd:COG5147    14 MQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQ 93

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1063699735 104 WTEIAKVVSGRTDNAVKNRFTTLCKKRAKHEAMAKENR 141
Cdd:COG5147    94 WSTIADYKDRRTAQQCVERYVNTLEDLSSTHDSKLQRR 131
PLN03212 PLN03212
Transcription repressor MYB5; Provisional
 33-130 1.41e-16

Transcription repressor MYB5; Provisional


Pssm-ID: 178751 [Multi-domain]  Cd Length: 249  Bit Score: 77.81  E-value: 1.41e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699735  33 WSPEEDDILRKQISLQGTENWAIIASKFND-KSTRQCRRRWYTYLNSDFKRGGWSPEEDTLLCEAQRLFGNRWTEIAKVV 111
Cdd:PLN03212   28 WTVEEDEILVSFIKKEGEGRWRSLPKRAGLlRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNRWSLIAGRI 107

                          90
                  ....*....|....*....
gi 1063699735 112 SGRTDNAVKNRFTTLCKKR 130
Cdd:PLN03212  108 PGRTDNEIKNYWNTHLRKK 126
Myb_DNA-bind_6 pfam13921
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 33-93 4.43e-13

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 372817 [Multi-domain]  Cd Length: 60  Bit Score: 63.10  E-value: 4.43e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063699735  33 WSPEEDDILRKQISLQGtENWAIIASKFNDKSTRQCRRRWYTYLNSDFKRGGWSPEEDTLL 93
Cdd:pfam13921   1 WTEEEDEKLLKLVEKYG-NDWKQIAKELGRRTPKQCFDRWRRKLNPKISRGPWSKEEDQRL 60
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 82-126 1.28e-11

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 58.67  E-value: 1.28e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063699735  82 RGGWSPEEDTLLCEAQRLFGNRWTEIAKVVSGRTDNAVKNRFTTL 126
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLGNRWKKIAKLLPGRTDNQCKNRWQNY 45
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 32-76 1.78e-10

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


Pssm-ID: 238096 [Multi-domain]  Cd Length: 45  Bit Score: 55.27  E-value: 1.78e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063699735  32 TWSPEEDDILRKQISLQGTENWAIIASKFNDKSTRQCRRRWYTYL 76
Cdd:cd00167     1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
32-78 5.09e-10

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 54.15  E-value: 5.09e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1063699735   32 TWSPEEDDILRKQISLQGTENWAIIASKFNDKSTRQCRRRWYTYLNS 78
Cdd:smart00717   3 EWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWRNLLKP 49
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 33-76 7.74e-10

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 53.66  E-value: 7.74e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1063699735  33 WSPEEDDILRKQISLQGTeNWAIIASKFNDKSTRQCRRRWYTYL 76
Cdd:pfam00249   4 WTPEEDELLLEAVEKLGN-RWKKIAKLLPGRTDNQCKNRWQNYL 46
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 85-126 2.09e-09

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


Pssm-ID: 238096 [Multi-domain]  Cd Length: 45  Bit Score: 52.58  E-value: 2.09e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1063699735  85 WSPEEDTLLCEAQRLFG-NRWTEIAKVVSGRTDNAVKNRFTTL 126
Cdd:cd00167     2 WTEEEDELLLEAVKKYGkNNWEKIAKELPGRTPKQCRERWRNL 44
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
82-129 6.45e-09

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 51.07  E-value: 6.45e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1063699735   82 RGGWSPEEDTLLCEAQRLFG-NRWTEIAKVVSGRTDNAVKNRFTTLCKK 129
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGkNNWEKIAKELPGRTAEQCRERWRNLLKP 49
Myb_DNA-bind_6 pfam13921
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 85-139 3.05e-05

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 372817 [Multi-domain]  Cd Length: 60  Bit Score: 41.14  E-value: 3.05e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063699735  85 WSPEEDTLLCEAQRLFGNRWTEIAKVVSGRTDNAVKNRFTTLCKKRAKHEAMAKE 139
Cdd:pfam13921   1 WTEEEDEKLLKLVEKYGNDWKQIAKELGRRTPKQCFDRWRRKLNPKISRGPWSKE 55
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 33-74 1.26e-03

Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1.


Pssm-ID: 212558 [Multi-domain]  Cd Length: 50  Bit Score: 36.39  E-value: 1.26e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063699735  33 WSPEEDDILRKQISLQGTENWAIIASKFNDKSTR---QCRRRWYT 74
Cdd:cd11660     3 WTDEEDEALVEGVEKYGVGNWAKILKDYFFVNNRtsvDLKDKWRN 47
SANT_CDC5_II cd11659
SANT/myb-like DNA-binding domain of Cell Division Cycle 5-Like Protein repeat II; In humans, ...
 81-126 2.44e-03

SANT/myb-like DNA-binding domain of Cell Division Cycle 5-Like Protein repeat II; In humans, cell division cycle 5-like protein (CDC5) functions in pre-mRNA splicing in cell cycle control. The DNA-binding, myb-like domain of CDC5 is a member of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of DNA-binding Myb domains and is found in a diverse set of proteins.


Pssm-ID: 212557 [Multi-domain]  Cd Length: 53  Bit Score: 35.75  E-value: 2.44e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1063699735  81 KRGGWSPEEDTLLCEAQRLFGNRWTEIAKVVsGRTDNAVKNRFTTL 126
Cdd:cd11659     4 KKTEWTREEDEKLLHLAKLLPTQWRTIAPIV-GRTAQQCLERYNKL 48
 
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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