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Conserved domains on  [gi|79314485|ref|NP_001030821|]
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TRF-like 1 [Arabidopsis thaliana]

Protein Classification

Ubl_ubiquitin_like and SANT_TRF domain-containing protein( domain architecture ID 13017888)

Ubl_ubiquitin_like and SANT_TRF domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 454-504 2.30e-16

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: 72.99  E-value: 2.30e-16
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 79314485 454 RPFSVTEVEALVQAVEKLGTGRWRDVKvRAFEDADHRTYVDLKDKWKTLVH 504
Cdd:cd11660   1 RKWTDEEDEALVEGVEKYGVGNWAKIL-KDYFFVNNRTSVDLKDKWRNLKK 50
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 287-353 5.47e-03

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.


:

Pssm-ID: 340559 [Multi-domain]  Cd Length: 68  Bit Score: 35.65  E-value: 5.47e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 79314485 287 LRIKSFRVPELFVEIPETATVGSLKRMVmEAVTTILGDGLRvgLMVQGKKVRDDgKTLLQTGISEEN 353
Cdd:cd17039   1 ITVKTLDGKTYTVEVDPDDTVADLKEKI-EEKTGIPVEQQR--LIYNGKELKDD-KTLSDYGIKDGS 63
 
Name Accession Description Interval E-value
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 454-504 2.30e-16

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: 72.99  E-value: 2.30e-16
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 79314485 454 RPFSVTEVEALVQAVEKLGTGRWRDVKvRAFEDADHRTYVDLKDKWKTLVH 504
Cdd:cd11660   1 RKWTDEEDEALVEGVEKYGVGNWAKIL-KDYFFVNNRTSVDLKDKWRNLKK 50
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
453-505 2.47e-06

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 44.52  E-value: 2.47e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 79314485    453 RRPFSVTEVEALVQAVEKLGTGRWRDVKvrafEDADHRTYVDLKDKWKTLVHT 505
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGKNNWEKIA----KELPGRTAEQCRERWRNLLKP 49
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 453-502 3.41e-03

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: 35.56  E-value: 3.41e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 79314485   453 RRPFSVTEVEALVQAVEKLGtGRWRDVkvrafedADH---RTYVDLKDKWKTL 502
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKI-------AKLlpgRTDNQCKNRWQNY 45
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 287-353 5.47e-03

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340559 [Multi-domain]  Cd Length: 68  Bit Score: 35.65  E-value: 5.47e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 79314485 287 LRIKSFRVPELFVEIPETATVGSLKRMVmEAVTTILGDGLRvgLMVQGKKVRDDgKTLLQTGISEEN 353
Cdd:cd17039   1 ITVKTLDGKTYTVEVDPDDTVADLKEKI-EEKTGIPVEQQR--LIYNGKELKDD-KTLSDYGIKDGS 63
 
Name Accession Description Interval E-value
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 454-504 2.30e-16

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: 72.99  E-value: 2.30e-16
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 79314485 454 RPFSVTEVEALVQAVEKLGTGRWRDVKvRAFEDADHRTYVDLKDKWKTLVH 504
Cdd:cd11660   1 RKWTDEEDEALVEGVEKYGVGNWAKIL-KDYFFVNNRTSVDLKDKWRNLKK 50
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
453-505 2.47e-06

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 44.52  E-value: 2.47e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 79314485    453 RRPFSVTEVEALVQAVEKLGTGRWRDVKvrafEDADHRTYVDLKDKWKTLVHT 505
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGKNNWEKIA----KELPGRTAEQCRERWRNLLKP 49
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 455-503 3.23e-05

'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: 41.41  E-value: 3.23e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 79314485 455 PFSVTEVEALVQAVEKLGTGRWRDVkvrafedADH---RTYVDLKDKWKTLV 503
Cdd:cd00167   1 PWTEEEDELLLEAVKKYGKNNWEKI-------AKElpgRTPKQCRERWRNLL 45
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 453-502 3.41e-03

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: 35.56  E-value: 3.41e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 79314485   453 RRPFSVTEVEALVQAVEKLGtGRWRDVkvrafedADH---RTYVDLKDKWKTL 502
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKI-------AKLlpgRTDNQCKNRWQNY 45
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 287-353 5.47e-03

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340559 [Multi-domain]  Cd Length: 68  Bit Score: 35.65  E-value: 5.47e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 79314485 287 LRIKSFRVPELFVEIPETATVGSLKRMVmEAVTTILGDGLRvgLMVQGKKVRDDgKTLLQTGISEEN 353
Cdd:cd17039   1 ITVKTLDGKTYTVEVDPDDTVADLKEKI-EEKTGIPVEQQR--LIYNGKELKDD-KTLSDYGIKDGS 63
 
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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