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Conserved domains on  [gi|466002240|gb|EMP41735|]
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Transcription factor IIIB 50 kDa subunit, partial [Chelonia mydas]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 1324-1420 9.36e-48

cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called transcription factor IIIB 50 kDa subunit (TFIIIB50), or BRFU, is a general activator of RNA polymerase (Pol) III transcription and is required for Pol III transcription of genes with promoter elements upstream of the initiation sites. It recruits Pol III to type III gene-external promoters, including the U6 spliceosomal RNA and selenocysteine tRNA genes. BRF-2 contains one cyclin box. The cyclin box fold is generally a protein binding domain, but binds DNA in BRF-2.


:

Pssm-ID: 410258 [Multi-domain]  Cd Length: 97  Bit Score: 165.53  E-value: 9.36e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1324 SRCKQRGIKRVQDLCKVLYLPAVFEETALSYFQRAIEHPSFHLVSLEKKEILVGCCVFVTCRQRNWPLTMGTICSLLYAD 1403
Cdd:cd20555     1 SRGLKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKHPDFRHIRLEKKEVLVGCCVYIVCRQNNWPVTMGDICSLLQCD 80

                          90
                  ....*....|....*..
gi 466002240 1404 KELFASVYLCVLKELEL 1420
Cdd:cd20555    81 VSDFSSVYKELLKELNI 97
SUA7 super family cl34255
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 1260-1491 1.20e-15

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: 79.87  E-value: 1.20e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1260 SGQRKCPDCGSCEIVEDAHyaQNQLVCAACGFVLTEGLLTT-----TFQDEEHLQE------VTYSR------------- 1315
Cdd:COG1405     9 EETSVCPECGGENLVTDTE--RGETVCEDCGLVVEEDVIDRgpewrAFDSEERDERsrtgapLTLARhdkglsteigwqd 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1316 --------STGQNEQLSRC-KQRGIKRVQD---------------LCKVLYLPAVFEETALSYFQRAIEHpsfHLV---S 1368
Cdd:COG1405    87 kdaygkslSGRKRRQLARLrKWQNRSRVSSskernlvqalseidrLASALGLPDSVRETAAVIYRKAVEK---GLLrgrS 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1369 LEKkeiLVGCCVFVTCRQRNWPLTMGTICSLLYADKELFASVYLCVLKELELDVPALSLTDLVkthlnsfklfqssasip 1448
Cdd:COG1405   164 IEG---VAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYI----------------- 223

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 466002240 1449 AKFAED---KEKMVARTIQIVELASETWLVTGRHPVPIVTAAAYLA 1491
Cdd:COG1405   224 PRIASElglSEEVERRAREILEKAKEKGLTSGKNPAGLAAAALYLA 269
C2 super family cl14603
C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed ...
 1-23 6.38e-07

C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions.


The actual alignment was detected with superfamily member cd08682:

Pssm-ID: 472691 [Multi-domain]  Cd Length: 126  Bit Score: 50.14  E-value: 6.38e-07
                          10        20
                  ....*....|....*....|...
gi 466002240    1 WYTLHSKPGKKEKERGEIEVDIQ 23
Cdd:cd08682   104 WFKLESKPGKDDKERGEIEVDIQ 126
 
Name Accession Description Interval E-value
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 1324-1420 9.36e-48

cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called transcription factor IIIB 50 kDa subunit (TFIIIB50), or BRFU, is a general activator of RNA polymerase (Pol) III transcription and is required for Pol III transcription of genes with promoter elements upstream of the initiation sites. It recruits Pol III to type III gene-external promoters, including the U6 spliceosomal RNA and selenocysteine tRNA genes. BRF-2 contains one cyclin box. The cyclin box fold is generally a protein binding domain, but binds DNA in BRF-2.


Pssm-ID: 410258 [Multi-domain]  Cd Length: 97  Bit Score: 165.53  E-value: 9.36e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1324 SRCKQRGIKRVQDLCKVLYLPAVFEETALSYFQRAIEHPSFHLVSLEKKEILVGCCVFVTCRQRNWPLTMGTICSLLYAD 1403
Cdd:cd20555     1 SRGLKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKHPDFRHIRLEKKEVLVGCCVYIVCRQNNWPVTMGDICSLLQCD 80

                          90
                  ....*....|....*..
gi 466002240 1404 KELFASVYLCVLKELEL 1420
Cdd:cd20555    81 VSDFSSVYKELLKELNI 97
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 1260-1491 1.20e-15

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 79.87  E-value: 1.20e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1260 SGQRKCPDCGSCEIVEDAHyaQNQLVCAACGFVLTEGLLTT-----TFQDEEHLQE------VTYSR------------- 1315
Cdd:COG1405     9 EETSVCPECGGENLVTDTE--RGETVCEDCGLVVEEDVIDRgpewrAFDSEERDERsrtgapLTLARhdkglsteigwqd 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1316 --------STGQNEQLSRC-KQRGIKRVQD---------------LCKVLYLPAVFEETALSYFQRAIEHpsfHLV---S 1368
Cdd:COG1405    87 kdaygkslSGRKRRQLARLrKWQNRSRVSSskernlvqalseidrLASALGLPDSVRETAAVIYRKAVEK---GLLrgrS 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1369 LEKkeiLVGCCVFVTCRQRNWPLTMGTICSLLYADKELFASVYLCVLKELELDVPALSLTDLVkthlnsfklfqssasip 1448
Cdd:COG1405   164 IEG---VAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYI----------------- 223

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 466002240 1449 AKFAED---KEKMVARTIQIVELASETWLVTGRHPVPIVTAAAYLA 1491
Cdd:COG1405   224 PRIASElglSEEVERRAREILEKAKEKGLTSGKNPAGLAAAALYLA 269
tfb PRK00423
transcription initiation factor IIB; Reviewed
 1258-1491 3.90e-14

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 75.43  E-value: 3.90e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1258 KMSGQRKCPDCGSCEIVEDahYAQNQLVCAACGFVLTE------------------------GLLTTTFQDEEHLQEVTY 1313
Cdd:PRK00423    7 EEEEKLVCPECGSDKLIYD--YERGEIVCADCGLVIEEniidqgpewrafdpeqrekrsrvgAPMTYTIHDKGLSTDIDW 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1314 SR--STGQN------EQLSRCK--QRGIkRVQD---------------LCKVLYLPAVFEETALSYFQRAIEHpsfHLVS 1368
Cdd:PRK00423   85 RNkdSYGKSisgknrAQLYRLRkwQRRI-RVSNaaernlafalseldrIASQLGLPRSVREEAAVIYRKAVEK---GLIR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1369 LEKKEILVGCCVFVTCRQRNWPLTMGTICSLLYADKELFASVYLCVLKELELDVPALSLTDLVKTHLNSFKLfqssasip 1448
Cdd:PRK00423  161 GRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGL-------- 232

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 466002240 1449 akfaedKEKMVARTIQIVELASETWLVTGRHPVPIVTAAAYLA 1491
Cdd:PRK00423  233 ------SGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIA 269
C2_Rab11-FIP_classI cd08682
C2 domain found in Rab11-family interacting proteins (FIP) class I; Rab GTPases recruit ...
 1-23 6.38e-07

C2 domain found in Rab11-family interacting proteins (FIP) class I; Rab GTPases recruit various effector proteins to organelles and vesicles. Rab11-family interacting proteins (FIPs) are involved in mediating the role of Rab11. FIPs can be divided into three classes: class I FIPs (Rip11a, Rip11b, RCP, and FIP2) which contain a C2 domain after N-terminus of the protein, class II FIPs (FIP3 and FIP4) which contain two EF-hands and a proline rich region, and class III FIPs (FIP1) which exhibits no homology to known protein domains. All FIP proteins contain a highly conserved, 20-amino acid motif at the C-terminus of the protein, known as Rab11/25 binding domain (RBD). Class I FIPs are thought to bind to endocytic membranes via their C2 domain, which interacts directly with phospholipids. Class II FIPs do not have any membrane binding domains leaving much to speculate about the mechanism involving FIP3 and FIP4 interactions with endocytic membranes. The members in this CD are class I FIPs. The exact function of the Rab11 and FIP interaction is unknown, but there is speculation that it involves the role of forming a targeting complex that recruits a group of proteins involved in membrane transport to organelles. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions.


Pssm-ID: 176064 [Multi-domain]  Cd Length: 126  Bit Score: 50.14  E-value: 6.38e-07
                          10        20
                  ....*....|....*....|...
gi 466002240    1 WYTLHSKPGKKEKERGEIEVDIQ 23
Cdd:cd08682   104 WFKLESKPGKDDKERGEIEVDIQ 126
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 1263-1295 3.71e-05

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: 42.29  E-value: 3.71e-05
                           10        20        30
                   ....*....|....*....|....*....|...
gi 466002240  1263 RKCPDCGSCEIVEDahYAQNQLVCAACGFVLTE 1295
Cdd:pfam08271    1 YKCPNCGSTNLVED--YERGELVCTDCGLVLED 31
 
Name Accession Description Interval E-value
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 1324-1420 9.36e-48

cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called transcription factor IIIB 50 kDa subunit (TFIIIB50), or BRFU, is a general activator of RNA polymerase (Pol) III transcription and is required for Pol III transcription of genes with promoter elements upstream of the initiation sites. It recruits Pol III to type III gene-external promoters, including the U6 spliceosomal RNA and selenocysteine tRNA genes. BRF-2 contains one cyclin box. The cyclin box fold is generally a protein binding domain, but binds DNA in BRF-2.


Pssm-ID: 410258 [Multi-domain]  Cd Length: 97  Bit Score: 165.53  E-value: 9.36e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1324 SRCKQRGIKRVQDLCKVLYLPAVFEETALSYFQRAIEHPSFHLVSLEKKEILVGCCVFVTCRQRNWPLTMGTICSLLYAD 1403
Cdd:cd20555     1 SRGLKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKHPDFRHIRLEKKEVLVGCCVYIVCRQNNWPVTMGDICSLLQCD 80

                          90
                  ....*....|....*..
gi 466002240 1404 KELFASVYLCVLKELEL 1420
Cdd:cd20555    81 VSDFSSVYKELLKELNI 97
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 1260-1491 1.20e-15

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 79.87  E-value: 1.20e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1260 SGQRKCPDCGSCEIVEDAHyaQNQLVCAACGFVLTEGLLTT-----TFQDEEHLQE------VTYSR------------- 1315
Cdd:COG1405     9 EETSVCPECGGENLVTDTE--RGETVCEDCGLVVEEDVIDRgpewrAFDSEERDERsrtgapLTLARhdkglsteigwqd 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1316 --------STGQNEQLSRC-KQRGIKRVQD---------------LCKVLYLPAVFEETALSYFQRAIEHpsfHLV---S 1368
Cdd:COG1405    87 kdaygkslSGRKRRQLARLrKWQNRSRVSSskernlvqalseidrLASALGLPDSVRETAAVIYRKAVEK---GLLrgrS 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1369 LEKkeiLVGCCVFVTCRQRNWPLTMGTICSLLYADKELFASVYLCVLKELELDVPALSLTDLVkthlnsfklfqssasip 1448
Cdd:COG1405   164 IEG---VAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYI----------------- 223

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 466002240 1449 AKFAED---KEKMVARTIQIVELASETWLVTGRHPVPIVTAAAYLA 1491
Cdd:COG1405   224 PRIASElglSEEVERRAREILEKAKEKGLTSGKNPAGLAAAALYLA 269
tfb PRK00423
transcription initiation factor IIB; Reviewed
 1258-1491 3.90e-14

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 75.43  E-value: 3.90e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1258 KMSGQRKCPDCGSCEIVEDahYAQNQLVCAACGFVLTE------------------------GLLTTTFQDEEHLQEVTY 1313
Cdd:PRK00423    7 EEEEKLVCPECGSDKLIYD--YERGEIVCADCGLVIEEniidqgpewrafdpeqrekrsrvgAPMTYTIHDKGLSTDIDW 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1314 SR--STGQN------EQLSRCK--QRGIkRVQD---------------LCKVLYLPAVFEETALSYFQRAIEHpsfHLVS 1368
Cdd:PRK00423   85 RNkdSYGKSisgknrAQLYRLRkwQRRI-RVSNaaernlafalseldrIASQLGLPRSVREEAAVIYRKAVEK---GLIR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1369 LEKKEILVGCCVFVTCRQRNWPLTMGTICSLLYADKELFASVYLCVLKELELDVPALSLTDLVKTHLNSFKLfqssasip 1448
Cdd:PRK00423  161 GRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGL-------- 232

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 466002240 1449 akfaedKEKMVARTIQIVELASETWLVTGRHPVPIVTAAAYLA 1491
Cdd:PRK00423  233 ------SGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIA 269
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 1329-1412 2.09e-07

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: 50.10  E-value: 2.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1329 RGIKRVQDLCKVLYLPAVFEETALSYFQRAIEHPSFHLVSLEkkeILVGCCVFVTCRQRNWPLTMGTICSLLYADKELFA 1408
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPE---LIAAACLYLACKLEELPRTLKEIAKVSGVSEKELR 77


                  ....
gi 466002240 1409 SVYL 1412
Cdd:cd00043    78 KAEK 81
C2_Rab11-FIP_classI cd08682
C2 domain found in Rab11-family interacting proteins (FIP) class I; Rab GTPases recruit ...
 1-23 6.38e-07

C2 domain found in Rab11-family interacting proteins (FIP) class I; Rab GTPases recruit various effector proteins to organelles and vesicles. Rab11-family interacting proteins (FIPs) are involved in mediating the role of Rab11. FIPs can be divided into three classes: class I FIPs (Rip11a, Rip11b, RCP, and FIP2) which contain a C2 domain after N-terminus of the protein, class II FIPs (FIP3 and FIP4) which contain two EF-hands and a proline rich region, and class III FIPs (FIP1) which exhibits no homology to known protein domains. All FIP proteins contain a highly conserved, 20-amino acid motif at the C-terminus of the protein, known as Rab11/25 binding domain (RBD). Class I FIPs are thought to bind to endocytic membranes via their C2 domain, which interacts directly with phospholipids. Class II FIPs do not have any membrane binding domains leaving much to speculate about the mechanism involving FIP3 and FIP4 interactions with endocytic membranes. The members in this CD are class I FIPs. The exact function of the Rab11 and FIP interaction is unknown, but there is speculation that it involves the role of forming a targeting complex that recruits a group of proteins involved in membrane transport to organelles. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions.


Pssm-ID: 176064 [Multi-domain]  Cd Length: 126  Bit Score: 50.14  E-value: 6.38e-07
                          10        20
                  ....*....|....*....|...
gi 466002240    1 WYTLHSKPGKKEKERGEIEVDIQ 23
Cdd:cd08682   104 WFKLESKPGKDDKERGEIEVDIQ 126
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 1263-1295 3.71e-05

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: 42.29  E-value: 3.71e-05
                           10        20        30
                   ....*....|....*....|....*....|...
gi 466002240  1263 RKCPDCGSCEIVEDahYAQNQLVCAACGFVLTE 1295
Cdd:pfam08271    1 YKCPNCGSTNLVED--YERGELVCTDCGLVLED 31
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 1329-1419 1.63e-03

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: 39.11  E-value: 1.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 466002240 1329 RGIKRVQDLCKVLYLPAVFEETALSYFQRAIEHPSfhlvsLEKKEI--LVGCCVFVTCRQRNWPLTMGTICSLLYADKEL 1406
Cdd:cd20551     1 AAFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKS-----LKGRSNdaIAAACLYIACRQEGVPRTFKEICAVSNVSKKE 75

                          90
                  ....*....|...
gi 466002240 1407 FASVYLCVLKELE 1419
Cdd:cd20551    76 IGRCFKLILKALE 88
 
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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