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];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112745   1 MAANYWASSQLTQLFLSTDLESLEPT----CLSKDTIYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEkGFSLE 76
Cdd:COG5333  10 VSSRPLLSFDSSQNAIELDLLVLEPEltleKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVE-EISLY 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112745  77 ALVATCIYLSCKVEECPVHIRTICNEANDLWSLKVKLSRSNISEIEFEIISVLDAFLIVHHPYTSLEQAFHDGIINQ--K 154
Cdd:COG5333  89 SVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDkyK 168

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19112745 155 QLEFAWSIVNDSYASSLCLMAHPHQLAYAALLISCCNDENTIPKLLDLIKSTDAFKVILCV---QRIISIYYFEDIE 228
Cdd:COG5333 169 LLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPIIKLLDFVSYETKEEVIALNyksIVKNKIKTFKAEH 245

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];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112745   1 MAANYWASSQLTQLFLSTDLESLEPT----CLSKDTIYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEkGFSLE 76
Cdd:COG5333  10 VSSRPLLSFDSSQNAIELDLLVLEPEltleKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVE-EISLY 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112745  77 ALVATCIYLSCKVEECPVHIRTICNEANDLWSLKVKLSRSNISEIEFEIISVLDAFLIVHHPYTSLEQAFHDGIINQ--K 154
Cdd:COG5333  89 SVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDkyK 168

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19112745 155 QLEFAWSIVNDSYASSLCLMAHPHQLAYAALLISCCNDENTIPKLLDLIKSTDAFKVILCV---QRIISIYYFEDIE 228
Cdd:COG5333 169 LLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPIIKLLDFVSYETKEEVIALNyksIVKNKIKTFKAEH 245

cyclin ccl1; All proteins in this family for which functions are known are cyclins that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, StanfordUniversity). [DNA metabolism, DNA replication, recombination, and repair]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112745    34 YQWKVVQTFGDRLR--LRQRVLATAIVLLRRYMLKkNEEKGFSLEALVATCIYLSCKVEECPVHIRTICNeandlwslKV 111
Cdd:TIGR00569  58 YYEKRLLDFCSAFKptMPTSVVGTAIMYFKRFYLN-NSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVG--------NL 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112745   112 KLSRSNISEI----EFEIISVLDAFLIVHHPYTSLEQAFHD------GIINQKQLE-FAWSIVNDSYASSLCLMAHPHQL 180
Cdd:TIGR00569 129 KETPLKALEQvleyELLLIQQLNFHLIVHNPYRPLEGFLIDiktrlpGLENPEYLRkHADKFLNRTLLTDAYLLYTPSQI 208

                  ....*...
gi 19112745   181 AYAALLIS 188
Cdd:TIGR00569 209 ALAAILHT 216

Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112745    45 RLRLRQRVLATAIVLLRRYMLKKNEEKgFSLEALVATCIYLSCKVEE-CPVHIRTICNEANDLWslkvklSRSNISEIEF 123
Cdd:pfam00134  44 KFKLLPETLYLAVNYLDRFLSKKSVPK-NKLQLVGVTCLFIAAKYEEiYPPTVEDLVYITDNAY------TREEILRMER 116

                  ....*..
gi 19112745   124 EIISVLD 130
Cdd:pfam00134 117 LILETLN 123

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];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112745   1 MAANYWASSQLTQLFLSTDLESLEPT----CLSKDTIYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEkGFSLE 76
Cdd:COG5333  10 VSSRPLLSFDSSQNAIELDLLVLEPEltleKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVE-EISLY 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112745  77 ALVATCIYLSCKVEECPVHIRTICNEANDLWSLKVKLSRSNISEIEFEIISVLDAFLIVHHPYTSLEQAFHDGIINQ--K 154
Cdd:COG5333  89 SVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDkyK 168

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19112745 155 QLEFAWSIVNDSYASSLCLMAHPHQLAYAALLISCCNDENTIPKLLDLIKSTDAFKVILCV---QRIISIYYFEDIE 228
Cdd:COG5333 169 LLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPIIKLLDFVSYETKEEVIALNyksIVKNKIKTFKAEH 245

second 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 second one. The cyclin box is a protein binding domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 19112745 137 HPYTSLEQAFHDGIINQKQLEFAWSIVNDSYASSLCLMAHPHQLAYAALLISC 189
Cdd:cd20514   1 HPYRPLTQYVQDAGLDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMAC 53

first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called MO15-associated protein, p34, or p37, is normally associated with the cyclin-dependent kinase cdk7, the catalytic subunit of the CDK-activating kinase (CAK) enzymatic complex. CCNH contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112745  37 KVVQTFGDRLRLRQRVLATAIVLLRRYMLKKN--EekgFSLEALVATCIYLSCKVEECPVHIRTICNeandlwslKVKLS 114
Cdd:cd20524  60 KKLLEFCRAFKLPDSVLATALTYFKRFYLKNSvmE---YHPKEIMLTCLYLACKVEEFNISIDQFVG--------NIKES 128

                        90
                ....*....|....*....
gi 19112745 115 RSNISEI---EFEIISVLD 130
Cdd:cd20524 129 EKTAEIIleyELLLLQGLN 147

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19112745  39 VQTFGDRLRLRQRVLATAIVLLRRYmLKKNEEKGFSLEALVATCIYLSCKVEECPVHIRTICNEAN 104
Cdd:cd00043   6 IRRLCSKLGLPEEVLELAIELLDRF-LSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSG 70

second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2), and similar proteins; Cyclin pch1 is essential for progression through the whole cell cycle. It is a homolog of cyclin T; it forms a heterodimer with its partner kinase, cyclin-dependent kinase 9 (CDK9), that can phosphorylate both the pol II C-terminal domain (CTD) and the CTD of transcription elongation factor Spt5. Yeast Cdk9/Pch1, with mRNA capping enzyme Pct1, may also form an elongation checkpoint for mRNA quality control. CTK2, also called CTD kinase subunit beta, CTDK-I subunit beta, or CTD kinase 38 kDa subunit, is the cyclin subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. This group also includes yeast RNA polymerase II holoenzyme cyclin-like subunit, a component of the SRB8-11 complex, a regulatory module of the Mediator complex which is involved in regulation of basal and activated RNA polymerase II-dependent transcription. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19112745 137 HPYTSLEQA--FHDGIINQKQLEFAWSIVNDSYASSLCLMAHPHQLAYAALLISCC 190
Cdd:cd20546   1 HPYQYLIKFakKLGVSDPKELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAK 56

first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ancient conserved domain proteins (ACDPs), are evolutionarily conserved Mg2+ transporters. CCNM, also called cyclin-Q (CCNQ), or CDK10-activating cyclin, or cyclin-related protein FAM58A, associates with CDK10 to promote its kinase activity. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19112745  43 GDRLRLRQRVLATAIVLLRRYMLKKNEEKgFSLEALVATCIYLSCKVEECPVHIRTICN 101
Cdd:cd20534  13 GLKLELSSVTIATACVLYHRFYRELSLED-YDPYLVAMACLYLAGKAEEQPRRLRDIIN 70

first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA polymerase II-associated cyclin that is involved in pre-mRNA splicing. It may induce cell death, possibly by acting on the transcription and RNA processing of apoptosis-related factors. CCNL2 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19112745  37 KVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKgFSLEALVATCIYLSCKVEECPVHIRTICNEANDLWSLKVK 112
Cdd:cd20590  49 ELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVK-HSMEHVSMACVHLASKIEEAPRRIRDVINVFHRLRQLREK 123

first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase II-associated C-type cyclin possessing both carboxy-terminal domain kinase and Cdk-activating kinase activity. It is a regulatory subunit of cyclin-dependent kinases that mediates the activation of these target kinases. It plays a role in transcriptional regulation by controlling the phosphorylation of the C-terminal domain (CTD) of the large subunit of RNA polymerase II (POLR2A). CCNK contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19112745  37 KVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEeKGFSLEALVATCIYLSCKVEECPVHIRTICNEA 103
Cdd:cd20530  16 RFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSF-KDFDRYVTAACCLFLAGKVEETPKKCKDIIKTA 81

first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; Cyclin-L1-1 (CycL1), also called arginine-rich cyclin 1 (AtRCY1), or protein MODIFIER OF SNC1 12, is the cognate cyclin for cyclin-dependent kinase G1 (CDKG1). It is involved in regulation of DNA methylation and transcriptional silencing. It is required for synapsis and male meiosis, and for the proper splicing of specific resistance (R) genes. L-type cyclins contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19112745  33 IYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKgFSLEALVATCIYLSCKVEECPVHIRTICN 101
Cdd:cd20591  16 IFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFAR-FNVKRVAASCVWLAAKLEESPRKIRQVLM 83

first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; CycTs associate with their partner cyclin-dependent kinases (CDKs) to trigger their kinase activity. CycTs show high sequence similarity with metazoan cyclin-K (CCNK). CycTs contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19112745  28 LSKDTIYQWK---VVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKgfSLEALVAT-CIYLSCKVEECPVHIRTI 99
Cdd:cd20587   5 LKKETYLRKSyctFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAK--NDRQTIATvCMFLAGKVEETPRPLKDV 78

first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, cyclin-T1 (CCNT1) and cyclin-T2 (CCNT2), both of which are regulatory subunits of the cyclin-dependent kinase pair (CDK9/cyclin-T) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to productive elongation by phosphorylating the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNA Pol II). Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19112745  39 VQTFGDRLRLRQRVLATAIVLLRR-YMLkkNEEKGFSLEALVATCIYLSCKVEECP 93
Cdd:cd20538  35 IQEMGQRLQVSQLCINTAIVYMHRfYMF--HSFTKFHRNSIAAAALFLAAKVEEQP 88

first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar proteins; CTK2, also called CTD kinase subunit beta, CTDK-I subunit beta, or CTD kinase 38 kDa subunit, is the cyclin subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. CTK2 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19112745  46 LRLRQRVLATAIVLLRRYMLKkNEEKGFSLEALVATCIYLSCKVEECPVHIRTICNEANDL 106
Cdd:cd20547  16 LKFPRRTLGTAMLLYQRFHLF-NPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNL 75

second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase II-associated C-type cyclin possessing both carboxy-terminal domain kinase and Cdk-activating kinase activity. It is a regulatory subunit of cyclin-dependent kinases that mediates the activation of these target kinases. It plays a role in transcriptional regulation by controlling the phosphorylation of the C-terminal domain (CTD) of the large subunit of RNA polymerase II (POLR2A). CCNK contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 19112745 137 HPYTSL----EQAFHDGIINQKQLEFAWSIVNDSYASSLCLMAHPHQLAYAAL 185
Cdd:cd20531   2 HPYKYLlkyaKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALM 54

transcription initiation factor IIB; Reviewed

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 19112745   43 GDRLRLRQRVLATAIVLLRRyMLKKNEEKGFSLEALVATCIYLSCKVEECPvhiRTI 99
Cdd:PRK00423 133 ASQLGLPRSVREEAAVIYRK-AVEKGLIRGRSIEGVVAAALYAACRRCKVP---RTL 185

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19112745  43 GDRLRLRQRVLATAIVLLRRyMLKKNEEKGFSLEALVATCIYLSCKVEECPVHIRTI 99
Cdd:cd20549  20 ASKLGLPRSVREEAAVIYRK-AVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEI 75

second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ancient conserved domain proteins (ACDPs), are evolutionarily conserved Mg2+ transporters. CCNM, also called cyclin-Q (CCNQ), or CDK10-activating cyclin, or cyclin-related protein FAM58A, associates with CDK10 to promote its kinase activity. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19112745 137 HPY-----TSLEQAFHDGIINQKQL-EFAWSIVNDSYASSLCLMAHPHQLAYAA--LLISCCN 191
Cdd:cd20535   3 HKYllhylKSLRDWLNPEFWSRSPIaKTAWSLLRDFYHSPLCLQFKPQHIALAViyLALQVYG 65