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Conserved domains on  [gi|1780584262|emb|VYS68815|]
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unnamed protein product [Arabidopsis thaliana]

Protein Classification

SANT/Myb-like DNA-binding domain-containing protein( domain architecture ID 1000535)

SANT (SWI3, ADA2, N-CoR and TFIIIB)/Myb-like DNA-binding domain-containing protein may be involved in the regulation of gene expression

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03212 super family cl31985
Transcription repressor MYB5; Provisional
 13-116 2.44e-53

Transcription repressor MYB5; Provisional


The actual alignment was detected with superfamily member PLN03212:

Pssm-ID: 178751 [Multi-domain]  Cd Length: 249  Bit Score: 171.80  E-value: 2.44e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780584262  13 KKGLWTVEEDKILMDYVRTHGQGHWNRIAKKTGLKRCGKSCRLRWMNYLSPNVNRGNFTDQEEDLIIRLHKLLGNRWSLI 92
Cdd:PLN03212   24 KRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNRWSLI 103

                          90       100
                  ....*....|....*....|....
gi 1780584262  93 AKRVPGRTDNQVKNYWNTHLSKKL 116
Cdd:PLN03212  104 AGRIPGRTDNEIKNYWNTHLRKKL 127
 
Name Accession Description Interval E-value
PLN03212 PLN03212
Transcription repressor MYB5; Provisional
 13-116 2.44e-53

Transcription repressor MYB5; Provisional


Pssm-ID: 178751 [Multi-domain]  Cd Length: 249  Bit Score: 171.80  E-value: 2.44e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780584262  13 KKGLWTVEEDKILMDYVRTHGQGHWNRIAKKTGLKRCGKSCRLRWMNYLSPNVNRGNFTDQEEDLIIRLHKLLGNRWSLI 92
Cdd:PLN03212   24 KRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNRWSLI 103

                          90       100
                  ....*....|....*....|....
gi 1780584262  93 AKRVPGRTDNQVKNYWNTHLSKKL 116
Cdd:PLN03212  104 AGRIPGRTDNEIKNYWNTHLRKKL 127
REB1 COG5147
Myb superfamily proteins, including transcription factors and mRNA splicing factors ...
 13-109 8.12e-20

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: 87.15  E-value: 8.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780584262  13 KKGLWTVEEDKILMDYVRTHGQGHWNRIAKKTGlKRCGKSCRLRWMNYLSPNVNRGNFTDQEEDLIIRLHKLLGNRWSLI 92
Cdd:COG5147    19 KGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQWSTI 97

                          90
                  ....*....|....*..
gi 1780584262  93 AKRVPGRTDNQVKNYWN 109
Cdd:COG5147    98 ADYKDRRTAQQCVERYV 114
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 67-112 4.57e-18

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: 74.46  E-value: 4.57e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1780584262  67 RGNFTDQEEDLIIRLHKLLGNRWSLIAKRVPGRTDNQVKNYWNTHL 112
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLGNRWKKIAKLLPGRTDNQCKNRWQNYL 46
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
67-114 1.13e-13

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 63.01  E-value: 1.13e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1780584262   67 RGNFTDQEEDLIIRLHKLLG-NRWSLIAKRVPGRTDNQVKNYWNTHLSK 114
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGkNNWEKIAKELPGRTAEQCRERWRNLLKP 49
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 69-112 2.01e-13

'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: 62.21  E-value: 2.01e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1780584262  69 NFTDQEEDLIIRLHKLLG-NRWSLIAKRVPGRTDNQVKNYWNTHL 112
Cdd:cd00167     1 PWTEEEDELLLEAVKKYGkNNWEKIAKELPGRTPKQCRERWRNLL 45
 
Name Accession Description Interval E-value
PLN03212 PLN03212
Transcription repressor MYB5; Provisional
 13-116 2.44e-53

Transcription repressor MYB5; Provisional


Pssm-ID: 178751 [Multi-domain]  Cd Length: 249  Bit Score: 171.80  E-value: 2.44e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780584262  13 KKGLWTVEEDKILMDYVRTHGQGHWNRIAKKTGLKRCGKSCRLRWMNYLSPNVNRGNFTDQEEDLIIRLHKLLGNRWSLI 92
Cdd:PLN03212   24 KRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNRWSLI 103

                          90       100
                  ....*....|....*....|....
gi 1780584262  93 AKRVPGRTDNQVKNYWNTHLSKKL 116
Cdd:PLN03212  104 AGRIPGRTDNEIKNYWNTHLRKKL 127
PLN03091 PLN03091
hypothetical protein; Provisional
 13-187 3.52e-50

hypothetical protein; Provisional


Pssm-ID: 215570 [Multi-domain]  Cd Length: 459  Bit Score: 169.00  E-value: 3.52e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780584262  13 KKGLWTVEEDKILMDYVRTHGQGHWNRIAKKTGLKRCGKSCRLRWMNYLSPNVNRGNFTDQEEDLIIRLHKLLGNRWSLI 92
Cdd:PLN03091   13 RKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNRWSQI 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780584262  93 AKRVPGRTDNQVKNYWNTHLSKKL---GL--GDHSTAVKAACGVESPPSmalittTSSSHQEISGGKNSTLrfdTLVDES 167
Cdd:PLN03091   93 AAQLPGRTDNEIKNLWNSCLKKKLrqrGIdpNTHKPLSEVENGEDKNPP------TDDKSDKASSVVSNEL---NLLKAD 163

                         170       180
                  ....*....|....*....|
gi 1780584262 168 KLKPKSKLVHATPTDVEVAA 187
Cdd:PLN03091  164 NSKPLAALQEKRSSSISPAG 183
REB1 COG5147
Myb superfamily proteins, including transcription factors and mRNA splicing factors ...
 13-109 8.12e-20

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: 87.15  E-value: 8.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780584262  13 KKGLWTVEEDKILMDYVRTHGQGHWNRIAKKTGlKRCGKSCRLRWMNYLSPNVNRGNFTDQEEDLIIRLHKLLGNRWSLI 92
Cdd:COG5147    19 KGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQWSTI 97

                          90
                  ....*....|....*..
gi 1780584262  93 AKRVPGRTDNQVKNYWN 109
Cdd:COG5147    98 ADYKDRRTAQQCVERYV 114
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 67-112 4.57e-18

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: 74.46  E-value: 4.57e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1780584262  67 RGNFTDQEEDLIIRLHKLLGNRWSLIAKRVPGRTDNQVKNYWNTHL 112
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLGNRWKKIAKLLPGRTDNQCKNRWQNYL 46
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 14-61 8.95e-14

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: 63.29  E-value: 8.95e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1780584262  14 KGLWTVEEDKILMDYVRTHGqGHWNRIAKKTGlKRCGKSCRLRWMNYL 61
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKIAKLLP-GRTDNQCKNRWQNYL 46
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
67-114 1.13e-13

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 63.01  E-value: 1.13e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1780584262   67 RGNFTDQEEDLIIRLHKLLG-NRWSLIAKRVPGRTDNQVKNYWNTHLSK 114
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGkNNWEKIAKELPGRTAEQCRERWRNLLKP 49
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 69-112 2.01e-13

'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: 62.21  E-value: 2.01e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1780584262  69 NFTDQEEDLIIRLHKLLG-NRWSLIAKRVPGRTDNQVKNYWNTHL 112
Cdd:cd00167     1 PWTEEEDELLLEAVKKYGkNNWEKIAKELPGRTPKQCRERWRNLL 45
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
14-63 4.66e-12

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 58.77  E-value: 4.66e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1780584262   14 KGLWTVEEDKILMDYVRTHGQGHWNRIAKKTGlKRCGKSCRLRWMNYLSP 63
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELP-GRTAEQCRERWRNLLKP 49
Myb_DNA-bind_6 pfam13921
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 17-75 5.91e-12

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: 58.86  E-value: 5.91e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1780584262  17 WTVEEDKILMDYVRTHGQGhWNRIAKKTGlKRCGKSCRLRWMNYLSPNVNRGNFTDQEE 75
Cdd:pfam13921   1 WTEEEDEKLLKLVEKYGND-WKQIAKELG-RRTPKQCFDRWRRKLNPKISRGPWSKEED 57
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 17-61 6.29e-12

'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: 58.36  E-value: 6.29e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1780584262  17 WTVEEDKILMDYVRTHGQGHWNRIAKKTGlKRCGKSCRLRWMNYL 61
Cdd:cd00167     2 WTEEEDELLLEAVKKYGKNNWEKIAKELP-GRTPKQCRERWRNLL 45
Myb_DNA-bind_6 pfam13921
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 70-116 2.74e-08

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: 48.85  E-value: 2.74e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1780584262  70 FTDQEEDLIIRLHKLLGNRWSLIAKRVPGRTDNQVKNYWNTHLSKKL 116
Cdd:pfam13921   1 WTEEEDEKLLKLVEKYGNDWKQIAKELGRRTPKQCFDRWRRKLNPKI 47
SANT_CDC5_II cd11659
SANT/myb-like DNA-binding domain of Cell Division Cycle 5-Like Protein repeat II; In humans, ...
 63-103 3.42e-06

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: 43.07  E-value: 3.42e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1780584262  63 PNVNRGNFTDQEEDLIIRLHKLLGNRWSLIAKRVpGRTDNQ 103
Cdd:cd11659     1 PSIKKTEWTREEDEKLLHLAKLLPTQWRTIAPIV-GRTAQQ 40
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 17-43 4.65e-04

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: 36.78  E-value: 4.65e-04
                          10        20
                  ....*....|....*....|....*..
gi 1780584262  17 WTVEEDKILMDYVRTHGQGHWNRIAKK 43
Cdd:cd11660     3 WTDEEDEALVEGVEKYGVGNWAKILKD 29
 
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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