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Conserved domains on  [gi|922567036|ref|XP_013611824|]
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PREDICTED: telomere repeat-binding protein 1 isoform X1 [Brassica oleracea var. oleracea]

Protein Classification

telomere repeat binding protein( domain architecture ID 13217419)

telomere repeat binding 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 ...
 469-519 5.61e-17

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: 74.91  E-value: 5.61e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 922567036 469 RPFSVTEVEALVQAVEKLGTGRWRDVKHsAFEDADHRTYVDLKDKWKTLVH 519
Cdd:cd11660    1 RKWTDEEDEALVEGVEKYGVGNWAKILK-DYFFVNNRTSVDLKDKWRNLKK 50
Ubl1_cv_Nsp3_N-like super family cl28922
first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV ...
 298-367 1.70e-04

first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV non-structural protein 3 (Nsp3) and related proteins; This ubiquitin-like (Ubl) domain (Ubl1) is found at the N-terminus of coronavirus Nsp3, a large multi-functional multi-domain protein which is an essential component of the replication/transcription complex (RTC). The functions of Ubl1 in CoVs are related to single-stranded RNA (ssRNA) binding and to interacting with the nucleocapsid (N) protein. SARS-CoV Ubl1 has been shown to bind ssRNA having AUA patterns, and since the 5'-UTR of the SARS-CoV genome has a number of AUA repeats, it may bind there. In mouse hepatitis virus (MHV), this Ubl1 domain binds the cognate N protein. Adjacent to Ubl1 is a Glu-rich acidic region (also referred to as hypervariable region, HVR); Ubl1 together with HVR has been called Nsp3a. Currently, the function of HVR in CoVs is unknown. This model corresponds to one of two Ubl domains in Nsp3; the other is located N-terminal to the papain-like protease (PLpro) and is not represented by this model.


The actual alignment was detected with superfamily member cd17057:

Pssm-ID: 475130  Cd Length: 74  Bit Score: 40.28  E-value: 1.70e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922567036 298 VRLRIKSFRVPELFVEIPETATVGSLKRMVMeavSTLLSDGHRVGLMVQGKKVRDDNKTLHQTGIsQDNT 367
Cdd:cd17057    2 ITIRLKFLNETERVVYARPEDTVGDFKRRHF---PDELAQGKRVRLIYQGQLLRDDSRTLSSYGI-QDGS 67
 
Name Accession Description Interval E-value
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 469-519 5.61e-17

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: 74.91  E-value: 5.61e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 922567036 469 RPFSVTEVEALVQAVEKLGTGRWRDVKHsAFEDADHRTYVDLKDKWKTLVH 519
Cdd:cd11660    1 RKWTDEEDEALVEGVEKYGVGNWAKILK-DYFFVNNRTSVDLKDKWRNLKK 50
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
468-520 3.34e-06

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 44.14  E-value: 3.34e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 922567036   468 RRPFSVTEVEALVQAVEKLGTGRWRDVKhsafEDADHRTYVDLKDKWKTLVHT 520
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGKNNWEKIA----KELPGRTAEQCRERWRNLLKP 49
Ubl_TMUB1_like cd17057
ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing ...
 298-367 1.70e-04

ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing proteins TMUB1, TMUB2, and similar proteins; TMUB1, also termed dendritic cell-derived ubiquitin-like protein (DULP), or hepatocyte odd protein shuttling protein, or ubiquitin-like protein SB144, or HOPS, is highly expressed in the nervous system. It is involved in the termination of liver regeneration and plays a negative role in interleukin-6-induced hepatocyte proliferation. The overexpression of Tmub1 has been shown to play a role in the inhibition of cell proliferation. TMUB1 has been implicated in the regulation of locomotor activity and wakefulness in mice, perhaps acting through its interaction with CAMLG. It also facilitates the recycling of AMPA receptors into synaptic membrane in cultured primary neurons. TMUB1 contains transmembrane domains and a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. TMUB2 is an uncharacterized transmembrane domain and Ubl domain-containing protein that shows high sequence similarity to TMUB1.


Pssm-ID: 340577  Cd Length: 74  Bit Score: 40.28  E-value: 1.70e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922567036 298 VRLRIKSFRVPELFVEIPETATVGSLKRMVMeavSTLLSDGHRVGLMVQGKKVRDDNKTLHQTGIsQDNT 367
Cdd:cd17057    2 ITIRLKFLNETERVVYARPEDTVGDFKRRHF---PDELAQGKRVRLIYQGQLLRDDSRTLSSYGI-QDGS 67
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 468-517 3.86e-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: 3.86e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 922567036  468 RRPFSVTEVEALVQAVEKLGtGRWRDVkhsafedADH---RTYVDLKDKWKTL 517
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKI-------AKLlpgRTDNQCKNRWQNY 45
Ubiquitin_4 pfam18036
Ubiquitin-like domain; This domain has a ubiquitin-like fold. It is found in a diverse range ...
 299-375 5.16e-03

Ubiquitin-like domain; This domain has a ubiquitin-like fold. It is found in a diverse range of proteins including the 25KDa U11/U12 component.


Pssm-ID: 465624  Cd Length: 89  Bit Score: 36.47  E-value: 5.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922567036  299 RLRIKSFRVPELFVEIPETATVGSLKRMVMEAVSTLLSDGHRVG------------LMVQGKKVRDDNKTLHQTGISQDn 366
Cdd:pfam18036   2 TVTVCKLDGESLPVVVPQNATVLDLKKAIERQFTLKLKREGGQRhiswkyvwktycLSFKGQKLLDDDAKLRDYGIRNG- 80


                  ....*....
gi 922567036  367 thlDSLDFS 375
Cdd:pfam18036  81 ---DELHFV 86
 
Name Accession Description Interval E-value
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 469-519 5.61e-17

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: 74.91  E-value: 5.61e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 922567036 469 RPFSVTEVEALVQAVEKLGTGRWRDVKHsAFEDADHRTYVDLKDKWKTLVH 519
Cdd:cd11660    1 RKWTDEEDEALVEGVEKYGVGNWAKILK-DYFFVNNRTSVDLKDKWRNLKK 50
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
468-520 3.34e-06

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 44.14  E-value: 3.34e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 922567036   468 RRPFSVTEVEALVQAVEKLGTGRWRDVKhsafEDADHRTYVDLKDKWKTLVHT 520
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGKNNWEKIA----KELPGRTAEQCRERWRNLLKP 49
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 470-518 2.33e-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: 41.79  E-value: 2.33e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 922567036 470 PFSVTEVEALVQAVEKLGTGRWRDVKHSAFedadHRTYVDLKDKWKTLV 518
Cdd:cd00167    1 PWTEEEDELLLEAVKKYGKNNWEKIAKELP----GRTPKQCRERWRNLL 45
Ubl_TMUB1_like cd17057
ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing ...
 298-367 1.70e-04

ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing proteins TMUB1, TMUB2, and similar proteins; TMUB1, also termed dendritic cell-derived ubiquitin-like protein (DULP), or hepatocyte odd protein shuttling protein, or ubiquitin-like protein SB144, or HOPS, is highly expressed in the nervous system. It is involved in the termination of liver regeneration and plays a negative role in interleukin-6-induced hepatocyte proliferation. The overexpression of Tmub1 has been shown to play a role in the inhibition of cell proliferation. TMUB1 has been implicated in the regulation of locomotor activity and wakefulness in mice, perhaps acting through its interaction with CAMLG. It also facilitates the recycling of AMPA receptors into synaptic membrane in cultured primary neurons. TMUB1 contains transmembrane domains and a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. TMUB2 is an uncharacterized transmembrane domain and Ubl domain-containing protein that shows high sequence similarity to TMUB1.


Pssm-ID: 340577  Cd Length: 74  Bit Score: 40.28  E-value: 1.70e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922567036 298 VRLRIKSFRVPELFVEIPETATVGSLKRMVMeavSTLLSDGHRVGLMVQGKKVRDDNKTLHQTGIsQDNT 367
Cdd:cd17057    2 ITIRLKFLNETERVVYARPEDTVGDFKRRHF---PDELAQGKRVRLIYQGQLLRDDSRTLSSYGI-QDGS 67
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 300-367 1.67e-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: 37.19  E-value: 1.67e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 922567036 300 LRIKSFRVPELFVEIPETATVGSLKRMVMEAVSTLLSDgHRvgLMVQGKKVRDDnKTLHQTGISQDNT 367
Cdd:cd17039    1 ITVKTLDGKTYTVEVDPDDTVADLKEKIEEKTGIPVEQ-QR--LIYNGKELKDD-KTLSDYGIKDGST 64
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 468-517 3.86e-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: 3.86e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 922567036  468 RRPFSVTEVEALVQAVEKLGtGRWRDVkhsafedADH---RTYVDLKDKWKTL 517
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKI-------AKLlpgRTDNQCKNRWQNY 45
Ubl_SNRNP25 cd17058
ubiquitin-like (Ubl) domain found in small nuclear ribonucleoprotein U11/U12 subunit 25 ...
 299-364 4.88e-03

ubiquitin-like (Ubl) domain found in small nuclear ribonucleoprotein U11/U12 subunit 25 (SNRNP25) and similar proteins; SNRNP25, also termed U11/U12 small nuclear ribonucleoprotein 25 kDa protein, U11/U12 snRNP 25 kDa protein (U11/U12-25K), or minus-99 protein, is a component of the U11/U12 snRNPs that are part of the U12-type spliceosome. It contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340578  Cd Length: 89  Bit Score: 36.34  E-value: 4.88e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 922567036 299 RLRIKSFRVPELFVEIPETATVGSLKRMVMEAVSTLLSDGHRVG------------LMVQGKKVRDDNKTLHQTGISQ 364
Cdd:cd17058    3 TLSVLRLDGESLPVVVPQNATVLDLKKAIERYFTLKLKREGGTKkiswkyvwktycLCFDGQKLTDDKAKLKDYGIRN 80
Ubiquitin_4 pfam18036
Ubiquitin-like domain; This domain has a ubiquitin-like fold. It is found in a diverse range ...
 299-375 5.16e-03

Ubiquitin-like domain; This domain has a ubiquitin-like fold. It is found in a diverse range of proteins including the 25KDa U11/U12 component.


Pssm-ID: 465624  Cd Length: 89  Bit Score: 36.47  E-value: 5.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922567036  299 RLRIKSFRVPELFVEIPETATVGSLKRMVMEAVSTLLSDGHRVG------------LMVQGKKVRDDNKTLHQTGISQDn 366
Cdd:pfam18036   2 TVTVCKLDGESLPVVVPQNATVLDLKKAIERQFTLKLKREGGQRhiswkyvwktycLSFKGQKLLDDDAKLRDYGIRNG- 80


                  ....*....
gi 922567036  367 thlDSLDFS 375
Cdd:pfam18036  81 ---DELHFV 86
 
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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