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Conserved domains on  [gi|1002302556|ref|XP_015614656|]
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uncharacterized protein [Oryza sativa Japonica Group]

Protein Classification

transcription initiation factor IIE subunit beta family protein( domain architecture ID 5050)

transcription initiation factor IIE (TFIIE) subunit beta binds to the region where the promoter starts to open upon transcription initiation by RNA polymerase II and plays a role in double-stranded DNA binding of TFIIE .

Gene Ontology:  GO:0006367|GO:0005673|GO:0003677
PubMed:  26483468|10716934|9348072

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TFIIE_beta_winged_helix super family cl02153
TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with ...
 27-270 1.34e-20

TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity; Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional domains, an N-terminal serine-rich region, a central core domain exhibiting a winged-helix structure capable of binding double-stranded DNA, a leucine repeat, a sigma3 region, and a C-terminal domain containing two basic regions. The assembly of transcription preinitiation complex (PIC) includes the general transcription factors and RNA polymerase II (pol II) initiated by the binding of the TBP subunit of TFIID to the TATA box, followed by either the sequential assembly of other general transcription factors and pol II or a preassembled pol II holoenzyme pathway. TFIIE interacts directly with TFIIF, TFIIB, pol II, and promoter DNA. TFIIE recruits TFIIH and regulates its activities. TFIIE and TFIIH are also important for the transition from initiation to elongation.


The actual alignment was detected with superfamily member COG5174:

Pssm-ID: 470477 [Multi-domain]  Cd Length: 285  Bit Score: 88.90  E-value: 1.34e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302556  27 STSKPKHRAQPVNAPSAPARPLQPIKFSN----------------------------DTERLQHINSVRKSPIGAQIKLV 78
Cdd:COG5174     9 NAFKSKVKSAPVIAPAQKKRMASPCHFEVglnsndghsstawskgssptkkariprmDRDRIQSIDRGVQRHTNSYLHAA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302556  79 IELLYKTRQAFTAEQINETTYVDIHGNKSVFDSLRNNPKVHYDGRRFSYKSKHDLKGKDQLLVLVR--KYPEGLAVVEVK 156
Cdd:COG5174    89 IEYLKQHDRPLSFEEIKDYLSIDLHNNYVLLLKKKRRIRIDATHSTFMFKPLYSIRSVEDLLKVLRsqGTEEGLSMKKLM 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302556 157 DAYPTVMEDLQALKAAGEVWLL-SNMDSQEDIVYPNDPKAKIKVDDDLKQLFREMELPRdMVDIEKELQKNGIKPMT--- 232
Cdd:COG5174   169 DGWPNVVPFVEELEKSNEILILrTDKDGSPVVVWNNTQNLECPVDPEFKSLWNQVRIPT-YHDLIRELNTAGLKPTSvdp 247

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1002302556 233 NTAKRRaaaqingvqpkAKPKKKQREITRRTKLTNAHL 270
Cdd:COG5174   248 NTKKRP-----------TIKIKKKKRSRRKGKITNTHV 274
 
Name Accession Description Interval E-value
TFA2 COG5174
Transcription initiation factor IIE, beta subunit [Transcription];
27-270 1.34e-20

Transcription initiation factor IIE, beta subunit [Transcription];


Pssm-ID: 227501 [Multi-domain]  Cd Length: 285  Bit Score: 88.90  E-value: 1.34e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302556  27 STSKPKHRAQPVNAPSAPARPLQPIKFSN----------------------------DTERLQHINSVRKSPIGAQIKLV 78
Cdd:COG5174     9 NAFKSKVKSAPVIAPAQKKRMASPCHFEVglnsndghsstawskgssptkkariprmDRDRIQSIDRGVQRHTNSYLHAA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302556  79 IELLYKTRQAFTAEQINETTYVDIHGNKSVFDSLRNNPKVHYDGRRFSYKSKHDLKGKDQLLVLVR--KYPEGLAVVEVK 156
Cdd:COG5174    89 IEYLKQHDRPLSFEEIKDYLSIDLHNNYVLLLKKKRRIRIDATHSTFMFKPLYSIRSVEDLLKVLRsqGTEEGLSMKKLM 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302556 157 DAYPTVMEDLQALKAAGEVWLL-SNMDSQEDIVYPNDPKAKIKVDDDLKQLFREMELPRdMVDIEKELQKNGIKPMT--- 232
Cdd:COG5174   169 DGWPNVVPFVEELEKSNEILILrTDKDGSPVVVWNNTQNLECPVDPEFKSLWNQVRIPT-YHDLIRELNTAGLKPTSvdp 247

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1002302556 233 NTAKRRaaaqingvqpkAKPKKKQREITRRTKLTNAHL 270
Cdd:COG5174   248 NTKKRP-----------TIKIKKKKRSRRKGKITNTHV 274
TFA2_Winged_2 pfam18121
TFA2 Winged helix domain 2; This is the second winged helix domain can be found in TFA2 ...
 134-191 2.38e-14

TFA2 Winged helix domain 2; This is the second winged helix domain can be found in TFA2 proteins present in Saccharomyces cerevisiae. In form 2, the domain interacts directly with Rad3, a DNA helicase.


Pssm-ID: 465658  Cd Length: 61  Bit Score: 65.98  E-value: 2.38e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002302556 134 KGKDQLLVLVRKY--PEGLAVVEVKDAYPTVMEDLQALKAAGEVWLLSNM-DSQEDIVYPN 191
Cdd:pfam18121   1 RNKEDLLALLQKQstAGGIPVKDLKDSWPDVEEAIEELEAEGKILVLRTKkDGKPRIVFYN 61
 
Name Accession Description Interval E-value
TFA2 COG5174
Transcription initiation factor IIE, beta subunit [Transcription];
27-270 1.34e-20

Transcription initiation factor IIE, beta subunit [Transcription];


Pssm-ID: 227501 [Multi-domain]  Cd Length: 285  Bit Score: 88.90  E-value: 1.34e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302556  27 STSKPKHRAQPVNAPSAPARPLQPIKFSN----------------------------DTERLQHINSVRKSPIGAQIKLV 78
Cdd:COG5174     9 NAFKSKVKSAPVIAPAQKKRMASPCHFEVglnsndghsstawskgssptkkariprmDRDRIQSIDRGVQRHTNSYLHAA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302556  79 IELLYKTRQAFTAEQINETTYVDIHGNKSVFDSLRNNPKVHYDGRRFSYKSKHDLKGKDQLLVLVR--KYPEGLAVVEVK 156
Cdd:COG5174    89 IEYLKQHDRPLSFEEIKDYLSIDLHNNYVLLLKKKRRIRIDATHSTFMFKPLYSIRSVEDLLKVLRsqGTEEGLSMKKLM 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302556 157 DAYPTVMEDLQALKAAGEVWLL-SNMDSQEDIVYPNDPKAKIKVDDDLKQLFREMELPRdMVDIEKELQKNGIKPMT--- 232
Cdd:COG5174   169 DGWPNVVPFVEELEKSNEILILrTDKDGSPVVVWNNTQNLECPVDPEFKSLWNQVRIPT-YHDLIRELNTAGLKPTSvdp 247

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1002302556 233 NTAKRRaaaqingvqpkAKPKKKQREITRRTKLTNAHL 270
Cdd:COG5174   248 NTKKRP-----------TIKIKKKKRSRRKGKITNTHV 274
TFA2_Winged_2 pfam18121
TFA2 Winged helix domain 2; This is the second winged helix domain can be found in TFA2 ...
 134-191 2.38e-14

TFA2 Winged helix domain 2; This is the second winged helix domain can be found in TFA2 proteins present in Saccharomyces cerevisiae. In form 2, the domain interacts directly with Rad3, a DNA helicase.


Pssm-ID: 465658  Cd Length: 61  Bit Score: 65.98  E-value: 2.38e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002302556 134 KGKDQLLVLVRKY--PEGLAVVEVKDAYPTVMEDLQALKAAGEVWLLSNM-DSQEDIVYPN 191
Cdd:pfam18121   1 RNKEDLLALLQKQstAGGIPVKDLKDSWPDVEEAIEELEAEGKILVLRTKkDGKPRIVFYN 61
TFIIE_beta pfam02186
TFIIE beta subunit core domain; General transcription factor TFIIE consists of two subunits, ...
 71-132 5.18e-07

TFIIE beta subunit core domain; General transcription factor TFIIE consists of two subunits, TFIIE alpha pfam02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The structure of the DNA binding core region has been solved and has a winged helix fold.


Pssm-ID: 460479  Cd Length: 66  Bit Score: 45.99  E-value: 5.18e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002302556  71 IGAQIKLVIELLYKTRQAFTAEQINETTYVDI-HGNKSVFDSLRNNPKVHYDGR--RFSYKSKHD 132
Cdd:pfam02186   1 LFTQLHKAVEYLKKQDGPLTLEEILDYLSLDLgDKNWLLLEALKNNPKIEYDPKtgTFSYKPLYN 65
 
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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