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Conserved domains on  [gi|941020168|gb|JAK59900|]
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Transcription initiation factor IIB, partial [Daphnia magna]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 138-236 4.56e-66

second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; TFIIB, also called B-related factor 2 (BRF-2) or S300-II, is a general transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). It is involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA. TFIIB contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


:

Pssm-ID: 410255 [Multi-domain]  Cd Length: 97  Bit Score: 199.81  E-value: 4.56e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168 138 TTADFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVAAAAIYMASQASDEksKKTQKEIGDIAGVADVTIRQ 217
Cdd:cd20552    1 STEDFMSRFCSNLGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEE--KKTQKEIGDVAGVAEVTIRQ 78

                         90
                 ....*....|....*....
gi 941020168 218 SYKLMYPRAAELFPEDFRF 236
Cdd:cd20552   79 SYKLLYPRAEKLFPPDFKF 97
SUA7 super family cl34255
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 1-220 1.82e-51

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: 169.62  E-value: 1.82e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168   1 GDQICSECGLVVGDRVIDVGSEWRTFSNEKANaDPSRVGGAENALLNGTDLSTMIGpgtgTASFDEHGVA---------- 70
Cdd:COG1405   29 GETVCEDCGLVVEEDVIDRGPEWRAFDSEERD-ERSRTGAPLTLARHDKGLSTEIG----WQDKDAYGKSlsgrkrrqla 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168  71 ---KYQNR-RTMSSSDRALVNAFKEISNMADRINLPRTIVDRANNLFKQVHDgKNL------------------------ 122
Cdd:COG1405  104 rlrKWQNRsRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVE-KGLlrgrsiegvaaaalyaacrqagvp 182

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168 123 --------------KEL------ILKALETSVDIITTADFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVA 182
Cdd:COG1405  183 rtldeiaevsrvdrKEIarayrlLNRELGLKVPPIDPIEYIPRIASELGLSEEVERRAREILEKAKEKGLTSGKNPAGLA 262

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 941020168 183 AAAIYMASQASDEksKKTQKEIGDIAGVADVTIRQSYK 220
Cdd:COG1405  263 AAALYLAALLLGE--KVTQKEVAEVAGVTEVTIRNRYK 298
 
Name Accession Description Interval E-value
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 138-236 4.56e-66

second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; TFIIB, also called B-related factor 2 (BRF-2) or S300-II, is a general transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). It is involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA. TFIIB contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410255 [Multi-domain]  Cd Length: 97  Bit Score: 199.81  E-value: 4.56e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168 138 TTADFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVAAAAIYMASQASDEksKKTQKEIGDIAGVADVTIRQ 217
Cdd:cd20552    1 STEDFMSRFCSNLGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEE--KKTQKEIGDVAGVAEVTIRQ 78

                         90
                 ....*....|....*....
gi 941020168 218 SYKLMYPRAAELFPEDFRF 236
Cdd:cd20552   79 SYKLLYPRAEKLFPPDFKF 97
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 1-220 1.82e-51

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 169.62  E-value: 1.82e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168   1 GDQICSECGLVVGDRVIDVGSEWRTFSNEKANaDPSRVGGAENALLNGTDLSTMIGpgtgTASFDEHGVA---------- 70
Cdd:COG1405   29 GETVCEDCGLVVEEDVIDRGPEWRAFDSEERD-ERSRTGAPLTLARHDKGLSTEIG----WQDKDAYGKSlsgrkrrqla 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168  71 ---KYQNR-RTMSSSDRALVNAFKEISNMADRINLPRTIVDRANNLFKQVHDgKNL------------------------ 122
Cdd:COG1405  104 rlrKWQNRsRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVE-KGLlrgrsiegvaaaalyaacrqagvp 182

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168 123 --------------KEL------ILKALETSVDIITTADFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVA 182
Cdd:COG1405  183 rtldeiaevsrvdrKEIarayrlLNRELGLKVPPIDPIEYIPRIASELGLSEEVERRAREILEKAKEKGLTSGKNPAGLA 262

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 941020168 183 AAAIYMASQASDEksKKTQKEIGDIAGVADVTIRQSYK 220
Cdd:COG1405  263 AAALYLAALLLGE--KVTQKEVAEVAGVTEVTIRNRYK 298
tfb PRK00423
transcription initiation factor IIB; Reviewed
 1-220 1.65e-45

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 154.40  E-value: 1.65e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168   1 GDQICSECGLVVGDRVIDVGSEWRTFSNEKaNADPSRVGGAENALLNGTDLSTMIGPGTGtasfDEHG------------ 68
Cdd:PRK00423  29 GEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNK----DSYGksisgknraqly 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168  69 -VAKYQNR-RTMSSSDRALVNAFKEISNMADRINLPRTIVDRANNLFKQVHDgKNL------------------------ 122
Cdd:PRK00423 104 rLRKWQRRiRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVE-KGLirgrsiegvvaaalyaacrrckvp 182

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168 123 --------------KE------LILKALETSVDIITTADFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVA 182
Cdd:PRK00423 183 rtldeiaevsrvsrKEigrcyrFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLA 262

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 941020168 183 AAAIYMASQASDEksKKTQKEIGDIAGVADVTIRQSYK 220
Cdd:PRK00423 263 AAAIYIASLLLGE--RRTQREVAEVAGVTEVTVRNRYK 298
TFIIB pfam00382
Transcription factor TFIIB repeat;
132-224 1.14e-30

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 109.27  E-value: 1.14e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168  132 TSVDIITTADFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVAAAAIYMASQASDEksKKTQKEIGDIAGVA 211
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGT--KRTLKEISSVLQVT 78

                          90
                  ....*....|...
gi 941020168  212 DVTIRQSYKLMYP 224
Cdd:pfam00382  79 EYTIGKTFKELKK 91
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 87-123 3.96e-17

first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; TFIIB, also called B-related factor 2 (BRF-2) or S300-II, is a general transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). It is involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA. TFIIB contains two cyclin boxes. This model corresponds to the first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410254 [Multi-domain]  Cd Length: 88  Bit Score: 73.77  E-value: 3.96e-17
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 941020168  87 NAFKEISNMADRINLPRTIVDRANNLFKQVHDGKNLK 123
Cdd:cd20551    1 AAFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLK 37
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 141-223 1.48e-10

domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 56.06  E-value: 1.48e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168   141 DFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVAAAAIYMASQAsdEKSKKTQKEIGDIAGVADV-TIRQSY 219
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKT--EETPPWTKELVHYTGYFTEeEILRME 78


                   ....
gi 941020168   220 KLMY 223
Cdd:smart00385  79 RLLL 82
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 1-26 8.33e-08

TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.


Pssm-ID: 400527 [Multi-domain]  Cd Length: 43  Bit Score: 47.30  E-value: 8.33e-08
                          10        20
                  ....*....|....*....|....*.
gi 941020168    1 GDQICSECGLVVGDRVIDVGSEWRTF 26
Cdd:pfam08271  18 GELVCTDCGLVLEDNSIDEGPEWREF 43
 
Name Accession Description Interval E-value
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 138-236 4.56e-66

second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; TFIIB, also called B-related factor 2 (BRF-2) or S300-II, is a general transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). It is involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA. TFIIB contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410255 [Multi-domain]  Cd Length: 97  Bit Score: 199.81  E-value: 4.56e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168 138 TTADFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVAAAAIYMASQASDEksKKTQKEIGDIAGVADVTIRQ 217
Cdd:cd20552    1 STEDFMSRFCSNLGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEE--KKTQKEIGDVAGVAEVTIRQ 78

                         90
                 ....*....|....*....
gi 941020168 218 SYKLMYPRAAELFPEDFRF 236
Cdd:cd20552   79 SYKLLYPRAEKLFPPDFKF 97
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 1-220 1.82e-51

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 169.62  E-value: 1.82e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168   1 GDQICSECGLVVGDRVIDVGSEWRTFSNEKANaDPSRVGGAENALLNGTDLSTMIGpgtgTASFDEHGVA---------- 70
Cdd:COG1405   29 GETVCEDCGLVVEEDVIDRGPEWRAFDSEERD-ERSRTGAPLTLARHDKGLSTEIG----WQDKDAYGKSlsgrkrrqla 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168  71 ---KYQNR-RTMSSSDRALVNAFKEISNMADRINLPRTIVDRANNLFKQVHDgKNL------------------------ 122
Cdd:COG1405  104 rlrKWQNRsRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVE-KGLlrgrsiegvaaaalyaacrqagvp 182

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168 123 --------------KEL------ILKALETSVDIITTADFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVA 182
Cdd:COG1405  183 rtldeiaevsrvdrKEIarayrlLNRELGLKVPPIDPIEYIPRIASELGLSEEVERRAREILEKAKEKGLTSGKNPAGLA 262

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 941020168 183 AAAIYMASQASDEksKKTQKEIGDIAGVADVTIRQSYK 220
Cdd:COG1405  263 AAALYLAALLLGE--KVTQKEVAEVAGVTEVTIRNRYK 298
tfb PRK00423
transcription initiation factor IIB; Reviewed
 1-220 1.65e-45

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 154.40  E-value: 1.65e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168   1 GDQICSECGLVVGDRVIDVGSEWRTFSNEKaNADPSRVGGAENALLNGTDLSTMIGPGTGtasfDEHG------------ 68
Cdd:PRK00423  29 GEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNK----DSYGksisgknraqly 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168  69 -VAKYQNR-RTMSSSDRALVNAFKEISNMADRINLPRTIVDRANNLFKQVHDgKNL------------------------ 122
Cdd:PRK00423 104 rLRKWQRRiRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVE-KGLirgrsiegvvaaalyaacrrckvp 182

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168 123 --------------KE------LILKALETSVDIITTADFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVA 182
Cdd:PRK00423 183 rtldeiaevsrvsrKEigrcyrFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLA 262

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 941020168 183 AAAIYMASQASDEksKKTQKEIGDIAGVADVTIRQSYK 220
Cdd:PRK00423 263 AAAIYIASLLLGE--RRTQREVAEVAGVTEVTVRNRYK 298
TFIIB pfam00382
Transcription factor TFIIB repeat;
132-224 1.14e-30

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 109.27  E-value: 1.14e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168  132 TSVDIITTADFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVAAAAIYMASQASDEksKKTQKEIGDIAGVA 211
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGT--KRTLKEISSVLQVT 78

                          90
                  ....*....|...
gi 941020168  212 DVTIRQSYKLMYP 224
Cdd:pfam00382  79 EYTIGKTFKELKK 91
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 140-220 1.57e-28

second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar proteins; Archaeal TFIIB stabilizes TATA-binding protein (TBP) binding to an archaeal box-A promoter. It is also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB). TFIIB contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410253 [Multi-domain]  Cd Length: 87  Bit Score: 103.44  E-value: 1.57e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168 140 ADFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVAAAAIYMASQASDEksKKTQKEIGDIAGVADVTIRQSY 219
Cdd:cd20550    3 ADYVPRFASKLGLSGEVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGE--RRTQKEIAEVAGVTEVTIRNRY 80


                 .
gi 941020168 220 K 220
Cdd:cd20550   81 K 81
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 87-123 3.96e-17

first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; TFIIB, also called B-related factor 2 (BRF-2) or S300-II, is a general transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). It is involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA. TFIIB contains two cyclin boxes. This model corresponds to the first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410254 [Multi-domain]  Cd Length: 88  Bit Score: 73.77  E-value: 3.96e-17
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 941020168  87 NAFKEISNMADRINLPRTIVDRANNLFKQVHDGKNLK 123
Cdd:cd20551    1 AAFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLK 37
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 138-221 4.49e-16

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: 70.90  E-value: 4.49e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168 138 TTADFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVAAAAIYMASQAsdEKSKKTQKEIGDIAGVADVTIRQ 217
Cdd:cd00043    1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKL--EELPRTLKEIAKVSGVSEKELRK 78


                 ....
gi 941020168 218 SYKL 221
Cdd:cd00043   79 AEKE 82
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 141-223 1.48e-10

domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 56.06  E-value: 1.48e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168   141 DFMSRFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVAAAAIYMASQAsdEKSKKTQKEIGDIAGVADV-TIRQSY 219
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKT--EETPPWTKELVHYTGYFTEeEILRME 78


                   ....
gi 941020168   220 KLMY 223
Cdd:smart00385  79 RLLL 82
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 145-205 1.61e-08

first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar proteins; Archaeal TFIIB stabilizes TATA-binding protein (TBP) binding to an archaeal box-A promoter. It is also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB). TFIIB contains two cyclin boxes. This model corresponds to the first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410252 [Multi-domain]  Cd Length: 99  Bit Score: 50.74  E-value: 1.61e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168 145 RFCSNLGLPTMVQRAASHIARKAVELDIVPGRSPISVAAAAIYMASQAS------DEKSKKTQ---KEIG 205
Cdd:cd20549   18 RMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICnvprtlDEIAEATRvsrKEIA 87
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 1-26 8.33e-08

TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.


Pssm-ID: 400527 [Multi-domain]  Cd Length: 43  Bit Score: 47.30  E-value: 8.33e-08
                          10        20
                  ....*....|....*....|....*.
gi 941020168    1 GDQICSECGLVVGDRVIDVGSEWRTF 26
Cdd:pfam08271  18 GELVCTDCGLVLEDNSIDEGPEWREF 43
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 142-217 2.37e-04

second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar proteins; TFIIIB90, also called B-related factor 1 (BRF-1), or TATA box-binding protein-associated factor, RNA polymerase III, subunit 2 (TAF3B2), is a general activator of RNA polymerase which utilizes different TFIIIB complexes at structurally distinct promoters. TFIIIB90 contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIIB90.


Pssm-ID: 410257 [Multi-domain]  Cd Length: 92  Bit Score: 39.03  E-value: 2.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168 142 FMSRFCSNLGLPtmvqRAASHIARKAVEL------D-IVPGRSPISVAAAAIYMASQASDEKskKTQKEIGDIAGVADVT 214
Cdd:cd20554    8 YIHRFASKLEFG----DKTHEVANTALRLvqrmkrDwIHTGRRPSGICGAALLIAARMHGFK--RTVEEIVRVVRVCEST 81


                 ...
gi 941020168 215 IRQ 217
Cdd:cd20554   82 LRK 84
NptA COG1283
Na+/phosphate symporter [Inorganic ion transport and metabolism];
51-170 4.22e-03

Na+/phosphate symporter [Inorganic ion transport and metabolism];


Pssm-ID: 440894 [Multi-domain]  Cd Length: 540  Bit Score: 37.85  E-value: 4.22e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941020168  51 LSTMIGPGTGTAsfDEHGVAKYQNRRTMSSSDRALVNAFKEISNMADRInlpRTIVDRANNLFKQvHDGKNLKEliLKAL 130
Cdd:COG1283  303 LLERLIPDKEEE--EEPARPKYLDPSLLETPSLALAQARREVLRMGDLV---EEMLRRALELLRE-GDEKLAEE--IRKL 374

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 941020168 131 ETSVDIITTA--DFMSRfCSNLGLPTMVQRAASHIARKAVEL 170
Cdd:COG1283  375 EDAVDRLEREikLYLAK-LSRESLSEEESRRLAELLHIANDL 415
 
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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