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Conserved domains on  [gi|338753414|ref|NP_001229719|]
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transcription factor IIIB 90 kDa subunit isoform 8 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 84-159 2.17e-47

first 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 first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIIB90.


:

Pssm-ID: 410256 [Multi-domain]  Cd Length: 91  Bit Score: 150.76  E-value: 2.17e-47
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 338753414  84 QTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVD 159
Cdd:cd20553    1 ITLQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVN 76
SUA7 super family cl34255
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 4-160 3.89e-17

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: 77.95  E-value: 3.89e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338753414   4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNII----------VSEVQFVESsgggssaVGQFVSL------------- 60
Cdd:COG1405   12 SVCPECGGENLVTDTERGETVCEDCGLVVEEDVIdrgpewrafdSEERDERSR-------TGAPLTLarhdkglsteigw 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338753414  61 ---DGAGKTptLGGG----FHvNLGKE-SRAQT-------LQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRG 125
Cdd:COG1405   85 qdkDAYGKS--LSGRkrrqLA-RLRKWqNRSRVssskernLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRG 161

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 338753414 126 RKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVDS 160
Cdd:COG1405  162 RSIEGVAAAALYAACRQAGVPRTLDEIAEVSRVDR 196
 
Name Accession Description Interval E-value
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 84-159 2.17e-47

first 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 first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIIB90.


Pssm-ID: 410256 [Multi-domain]  Cd Length: 91  Bit Score: 150.76  E-value: 2.17e-47
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 338753414  84 QTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVD 159
Cdd:cd20553    1 ITLQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVN 76
TFIIB pfam00382
Transcription factor TFIIB repeat;
82-158 2.90e-32

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 111.97  E-value: 2.90e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 338753414   82 RAQTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQV 158
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQV 77
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 4-160 3.89e-17

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 77.95  E-value: 3.89e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338753414   4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNII----------VSEVQFVESsgggssaVGQFVSL------------- 60
Cdd:COG1405   12 SVCPECGGENLVTDTERGETVCEDCGLVVEEDVIdrgpewrafdSEERDERSR-------TGAPLTLarhdkglsteigw 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338753414  61 ---DGAGKTptLGGG----FHvNLGKE-SRAQT-------LQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRG 125
Cdd:COG1405   85 qdkDAYGKS--LSGRkrrqLA-RLRKWqNRSRVssskernLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRG 161

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 338753414 126 RKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVDS 160
Cdd:COG1405  162 RSIEGVAAAALYAACRQAGVPRTLDEIAEVSRVDR 196
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 4-45 5.80e-13

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: 60.78  E-value: 5.80e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 338753414    4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNIIVSEVQFVE 45
Cdd:pfam08271   1 YKCPNCGSTNLVEDYERGELVCTDCGLVLEDNSIDEGPEWRE 42
tfb PRK00423
transcription initiation factor IIB; Reviewed
 4-159 9.99e-12

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 62.72  E-value: 9.99e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338753414   4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNIIVSEVQ---FVESSGGGSSAVGQFVSL----------------DGAG 64
Cdd:PRK00423  12 LVCPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEwraFDPEQREKRSRVGAPMTYtihdkglstdidwrnkDSYG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338753414  65 KTPTL------------------GGGFHVNLgkesrAQTLQNGRRhihhLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGR 126
Cdd:PRK00423  92 KSISGknraqlyrlrkwqrrirvSNAAERNL-----AFALSELDR----IASQLGLPRSVREEAAVIYRKAVEKGLIRGR 162

                        170       180       190
                 ....*....|....*....|....*....|...
gi 338753414 127 KMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVD 159
Cdd:PRK00423 163 SIEGVVAAALYAACRRCKVPRTLDEIAEVSRVS 195
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 93-160 1.40e-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: 55.68  E-value: 1.40e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 338753414    93 IHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVDS 160
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFT 70
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 93-168 4.25e-03

Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair];


Pssm-ID: 227640 [Multi-domain]  Cd Length: 297  Bit Score: 37.02  E-value: 4.25e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 338753414  93 IHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTP-HMLLDLSDLLQVDSLRPASFPT 168
Cdd:COG5333   52 IMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPrDISIESFEARDLWSEEPKSSRE 128
 
Name Accession Description Interval E-value
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 84-159 2.17e-47

first 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 first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIIB90.


Pssm-ID: 410256 [Multi-domain]  Cd Length: 91  Bit Score: 150.76  E-value: 2.17e-47
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 338753414  84 QTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVD 159
Cdd:cd20553    1 ITLQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVN 76
TFIIB pfam00382
Transcription factor TFIIB repeat;
82-158 2.90e-32

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 111.97  E-value: 2.90e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 338753414   82 RAQTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQV 158
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQV 77
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 4-160 3.89e-17

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 77.95  E-value: 3.89e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338753414   4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNII----------VSEVQFVESsgggssaVGQFVSL------------- 60
Cdd:COG1405   12 SVCPECGGENLVTDTERGETVCEDCGLVVEEDVIdrgpewrafdSEERDERSR-------TGAPLTLarhdkglsteigw 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338753414  61 ---DGAGKTptLGGG----FHvNLGKE-SRAQT-------LQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRG 125
Cdd:COG1405   85 qdkDAYGKS--LSGRkrrqLA-RLRKWqNRSRVssskernLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRG 161

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 338753414 126 RKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVDS 160
Cdd:COG1405  162 RSIEGVAAAALYAACRQAGVPRTLDEIAEVSRVDR 196
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 93-159 2.12e-13

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: 62.81  E-value: 2.12e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 338753414  93 IHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVD 159
Cdd:cd00043    6 IRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVS 72
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 4-45 5.80e-13

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: 60.78  E-value: 5.80e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 338753414    4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNIIVSEVQFVE 45
Cdd:pfam08271   1 YKCPNCGSTNLVEDYERGELVCTDCGLVLEDNSIDEGPEWRE 42
tfb PRK00423
transcription initiation factor IIB; Reviewed
 4-159 9.99e-12

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 62.72  E-value: 9.99e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338753414   4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNIIVSEVQ---FVESSGGGSSAVGQFVSL----------------DGAG 64
Cdd:PRK00423  12 LVCPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEwraFDPEQREKRSRVGAPMTYtihdkglstdidwrnkDSYG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338753414  65 KTPTL------------------GGGFHVNLgkesrAQTLQNGRRhihhLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGR 126
Cdd:PRK00423  92 KSISGknraqlyrlrkwqrrirvSNAAERNL-----AFALSELDR----IASQLGLPRSVREEAAVIYRKAVEKGLIRGR 162

                        170       180       190
                 ....*....|....*....|....*....|...
gi 338753414 127 KMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVD 159
Cdd:PRK00423 163 SIEGVVAAALYAACRRCKVPRTLDEIAEVSRVS 195
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 86-159 5.29e-11

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: 56.90  E-value: 5.29e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 338753414  86 LQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVD 159
Cdd:cd20549    9 LAQALSELDRMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEATRVS 82
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 93-160 1.40e-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: 55.68  E-value: 1.40e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 338753414    93 IHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVDS 160
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFT 70
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 88-146 1.02e-07

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: 47.97  E-value: 1.02e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 338753414  88 NGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTP 146
Cdd:cd20551    1 AAFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVP 59
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 92-146 2.92e-04

first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or SRB11, is a component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. It mediates stress-induced mitochondrial fission and apoptosis. CCNC contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410217 [Multi-domain]  Cd Length: 101  Bit Score: 38.73  E-value: 2.92e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 338753414  92 HIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTP 146
Cdd:cd20513    8 FIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECP 62
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 86-159 7.08e-04

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: 37.64  E-value: 7.08e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 338753414  86 LQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVS----RHLTRGRKMAHViAACLYLVCRTEGTPHMLLDLSDLLQVD 159
Cdd:cd20555    4 LKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKhpdfRHIRLEKKEVLV-GCCVYIVCRQNNWPVTMGDICSLLQCD 80
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 93-168 4.25e-03

Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair];


Pssm-ID: 227640 [Multi-domain]  Cd Length: 297  Bit Score: 37.02  E-value: 4.25e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 338753414  93 IHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTP-HMLLDLSDLLQVDSLRPASFPT 168
Cdd:COG5333   52 IMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPrDISIESFEARDLWSEEPKSSRE 128
 
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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