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Conserved domains on  [gi|357448657|ref|XP_003594604|]
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plant-specific TFIIB-related protein PTF2 [Medicago truncatula]

Protein Classification

cyclin family protein( domain architecture ID 10036461)

cyclin family protein may associate with and activate its cognate cyclin-dependent kinase (CDK)

CATH:  1.10.472.10
Gene Ontology:  GO:0000079|GO:0019901
PubMed:  30185601
SCOP:  4001102

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 73-153 1.14e-05

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.


:

Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 43.55  E-value: 1.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357448657  73 SARNSIEQFTIKLGLSSK-KIEINTMISDITDGEFGQGDWFQVLIGACCYVVMRRDERALSMNEVANAVGCDVFELGKMV 151
Cdd:cd00043    1 KAVDFIRRLCSKLGLPEEvLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAE 80


                 ..
gi 357448657 152 IR 153
Cdd:cd00043   81 KE 82
SUA7 super family cl34255
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 2-37 7.64e-03

Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription];


The actual alignment was detected with superfamily member COG1405:

Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 38.66  E-value: 7.64e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 357448657   2 STSRRCINCSKTSFTRDDETGGSFCSSCG---AEQHFDQ 37
Cdd:COG1405    9 EETSVCPECGGENLVTDTERGETVCEDCGlvvEEDVIDR 47
 
Name Accession Description Interval E-value
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 73-153 1.14e-05

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 43.55  E-value: 1.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357448657  73 SARNSIEQFTIKLGLSSK-KIEINTMISDITDGEFGQGDWFQVLIGACCYVVMRRDERALSMNEVANAVGCDVFELGKMV 151
Cdd:cd00043    1 KAVDFIRRLCSKLGLPEEvLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAE 80


                 ..
gi 357448657 152 IR 153
Cdd:cd00043   81 KE 82
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 2-37 7.64e-03

Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription];


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 38.66  E-value: 7.64e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 357448657   2 STSRRCINCSKTSFTRDDETGGSFCSSCG---AEQHFDQ 37
Cdd:COG1405    9 EETSVCPECGGENLVTDTERGETVCEDCGlvvEEDVIDR 47
 
Name Accession Description Interval E-value
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 73-153 1.14e-05

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 43.55  E-value: 1.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357448657  73 SARNSIEQFTIKLGLSSK-KIEINTMISDITDGEFGQGDWFQVLIGACCYVVMRRDERALSMNEVANAVGCDVFELGKMV 151
Cdd:cd00043    1 KAVDFIRRLCSKLGLPEEvLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAE 80


                 ..
gi 357448657 152 IR 153
Cdd:cd00043   81 KE 82
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 2-37 7.64e-03

Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription];


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 38.66  E-value: 7.64e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 357448657   2 STSRRCINCSKTSFTRDDETGGSFCSSCG---AEQHFDQ 37
Cdd:COG1405    9 EETSVCPECGGENLVTDTERGETVCEDCGlvvEEDVIDR 47
 
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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