NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2462611183|ref|XP_054212666|]
View 

cyclin-C isoform X1 [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 154-245 2.21e-57

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.


:

Pssm-ID: 410218 [Multi-domain]  Cd Length: 92  Bit Score: 178.58  E-value: 2.21e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 154 HPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSVDMEKILEIIRV 233
Cdd:cd20514     1 HPYRPLTQYVQDAGLDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDARQWFAELNVDMDKILEITRE 80

                          90
                  ....*....|..
gi 2462611183 234 ILKLYEQWKNFD 245
Cdd:cd20514    81 ILSLYELWKTFD 92
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 40-146 6.12e-53

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: 167.77  E-value: 6.12e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  40 LQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFgvVSNTRLIAAATSVLKTR 119
Cdd:cd20513     1 LHIFFANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEEC--PSHARLIVAEAKVLKTK 78

                          90       100
                  ....*....|....*....|....*..
gi 2462611183 120 FSYafpkEFPYRMNHILECEFYLLELM 146
Cdd:cd20513    79 FSY----EFPYRVNDILECEFYLLEAL 101
 
Name Accession Description Interval E-value
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 154-245 2.21e-57

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.


Pssm-ID: 410218 [Multi-domain]  Cd Length: 92  Bit Score: 178.58  E-value: 2.21e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 154 HPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSVDMEKILEIIRV 233
Cdd:cd20514     1 HPYRPLTQYVQDAGLDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDARQWFAELNVDMDKILEITRE 80

                          90
                  ....*....|..
gi 2462611183 234 ILKLYEQWKNFD 245
Cdd:cd20514    81 ILSLYELWKTFD 92
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 40-146 6.12e-53

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: 167.77  E-value: 6.12e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  40 LQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFgvVSNTRLIAAATSVLKTR 119
Cdd:cd20513     1 LHIFFANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEEC--PSHARLIVAEAKVLKTK 78

                          90       100
                  ....*....|....*....|....*..
gi 2462611183 120 FSYafpkEFPYRMNHILECEFYLLELM 146
Cdd:cd20513    79 FSY----EFPYRVNDILECEFYLLEAL 101
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 1-212 9.48e-39

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: 137.56  E-value: 9.48e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183   1 MAGNFWQSSHYLQWILdKQDLLKERQKdlkFLSEEEYwKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKS 80
Cdd:COG5333    10 VSSRPLLSFDSSQNAI-ELDLLVLEPE---LTLEKEL-NLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  81 IDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATsvLKTRFSYAFPKEfpyrmnhILECEFYLLELMDCCLIVYHPYRPLL 160
Cdd:COG5333    85 ISLYSVVTTCVYLACKVEDTPRDISIESFEARD--LWSEEPKSSRER-------ILEYEFELLEALDFDLHVHHPYKYLE 155

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462611183 161 QYVQDmGQEDM---LLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKD 212
Cdd:COG5333   156 GFLKD-LQEKDkykLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMP 209
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 8-257 1.15e-24

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]


Pssm-ID: 129660 [Multi-domain]  Cd Length: 305  Bit Score: 100.29  E-value: 1.15e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183   8 SSHYLQWILDKQDLLKERQKDLK-------------------FLSEEEYWKLQIFFTNVIQALGEHLK--LRQQVIATAT 66
Cdd:TIGR00569   4 SSQKRHWTFTSEEQLQEKRADANakfreaheeeekvleakpiFLTPEEELDLVKYYEKRLLDFCSAFKptMPTSVVGTAI 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  67 VYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNtrliaaatsvlktRFSYAFPKEFPYRMNHILECEFYLLELM 146
Cdd:TIGR00569  84 MYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSID-------------QFVGNLKETPLKALEQVLEYELLLIQQL 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 147 DCCLIVYHPYRPLLQYVQD-------MGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIAL-ACLHVACVVQQKDARQWFA 218
Cdd:TIGR00569 151 NFHLIVHNPYRPLEGFLIDiktrlpgLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALaAILHTASRAGLNMESYLTE 230

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 2462611183 219 ELSV-----DMEKILEI---IRVILKLYEQwknfDERKEMATILSKM 257
Cdd:TIGR00569 231 QLSVpgnreELPQLIDImreLRILVKKYEE----PRSEKVAALKKKL 273
Cyclin_C_2 pfam16899
Cyclin C-terminal domain; Cyclins contain two domains of similar all-alpha fold, this family ...
 154-242 6.63e-11

Cyclin C-terminal domain; Cyclins contain two domains of similar all-alpha fold, this family corresponds with the C-terminal domain of some cyclins including cyclin C and cyclin H.


Pssm-ID: 465303  Cd Length: 98  Bit Score: 57.93  E-value: 6.63e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 154 HPYRPLLQYVQDMGQE--------DMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACvvqQKDARQWFAE---LSV 222
Cdd:pfam16899   1 HPFRPLEGFLLDLKTRpplledriESLYKRAREILKSALLTDAYFLYTPSQIALAALLLAD---SPLAEFYLTEkfgLPE 77

                          90       100
                  ....*....|....*....|.
gi 2462611183 223 DMEKILE-IIRVILKLYEQWK 242
Cdd:pfam16899  78 DRETKLEkLLDTIESCRNLLK 98
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 48-144 1.14e-07

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: 48.36  E-value: 1.14e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183   48 IQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVvsNTRLIAAATSVlktrfsyafpke 127
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPP--WTKELVHYTGY------------ 68

                           90
                   ....*....|....*..
gi 2462611183  128 fpYRMNHILECEFYLLE 144
Cdd:smart00385  69 --FTEEEILRMERLLLE 83
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 51-99 9.97e-07

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.


Pssm-ID: 459686 [Multi-domain]  Cd Length: 127  Bit Score: 46.74  E-value: 9.97e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2462611183  51 LGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEE 99
Cdd:pfam00134  41 VHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYEE 89
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 161-236 1.87e-05

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: 42.19  E-value: 1.87e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  161 QYVQDMGQEDML----LPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDArqWFAELSV-----DMEKILEII 231
Cdd:smart00385   1 DFLRRVCKALNLdpetLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPP--WTKELVHytgyfTEEEILRME 78


                   ....*
gi 2462611183  232 RVILK 236
Cdd:smart00385  79 RLLLE 83
 
Name Accession Description Interval E-value
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 154-245 2.21e-57

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.


Pssm-ID: 410218 [Multi-domain]  Cd Length: 92  Bit Score: 178.58  E-value: 2.21e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 154 HPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSVDMEKILEIIRV 233
Cdd:cd20514     1 HPYRPLTQYVQDAGLDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDARQWFAELNVDMDKILEITRE 80

                          90
                  ....*....|..
gi 2462611183 234 ILKLYEQWKNFD 245
Cdd:cd20514    81 ILSLYELWKTFD 92
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 40-146 6.12e-53

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: 167.77  E-value: 6.12e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  40 LQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFgvVSNTRLIAAATSVLKTR 119
Cdd:cd20513     1 LHIFFANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEEC--PSHARLIVAEAKVLKTK 78

                          90       100
                  ....*....|....*....|....*..
gi 2462611183 120 FSYafpkEFPYRMNHILECEFYLLELM 146
Cdd:cd20513    79 FSY----EFPYRVNDILECEFYLLEAL 101
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 1-212 9.48e-39

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: 137.56  E-value: 9.48e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183   1 MAGNFWQSSHYLQWILdKQDLLKERQKdlkFLSEEEYwKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKS 80
Cdd:COG5333    10 VSSRPLLSFDSSQNAI-ELDLLVLEPE---LTLEKEL-NLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  81 IDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATsvLKTRFSYAFPKEfpyrmnhILECEFYLLELMDCCLIVYHPYRPLL 160
Cdd:COG5333    85 ISLYSVVTTCVYLACKVEDTPRDISIESFEARD--LWSEEPKSSRER-------ILEYEFELLEALDFDLHVHHPYKYLE 155

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462611183 161 QYVQDmGQEDM---LLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKD 212
Cdd:COG5333   156 GFLKD-LQEKDkykLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMP 209
CYCLIN_AtCycC_rpt2 cd20572
second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 154-248 6.50e-34

second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; CycCs are the cognate cyclin partners of cyclin-dependent kinase CDK8. They may be involved in cell cycle control. CycCs contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410275 [Multi-domain]  Cd Length: 102  Bit Score: 119.11  E-value: 6.50e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 154 HPYRPLLQYVQDMGQEDMLlPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSVDMEKILEIIRV 233
Cdd:cd20572     1 HPYRPLIQLLQDAGLTDMT-QFTWSIVNDTYRTDLILIHPPYMIALACIYIASVHKEKDITLWFEELRVDMNIIKNIAME 79

                          90
                  ....*....|....*
gi 2462611183 234 ILKLYEQWKNFDERK 248
Cdd:cd20572    80 ILDFYDNYRLIPEER 94
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 8-257 1.15e-24

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]


Pssm-ID: 129660 [Multi-domain]  Cd Length: 305  Bit Score: 100.29  E-value: 1.15e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183   8 SSHYLQWILDKQDLLKERQKDLK-------------------FLSEEEYWKLQIFFTNVIQALGEHLK--LRQQVIATAT 66
Cdd:TIGR00569   4 SSQKRHWTFTSEEQLQEKRADANakfreaheeeekvleakpiFLTPEEELDLVKYYEKRLLDFCSAFKptMPTSVVGTAI 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  67 VYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNtrliaaatsvlktRFSYAFPKEFPYRMNHILECEFYLLELM 146
Cdd:TIGR00569  84 MYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSID-------------QFVGNLKETPLKALEQVLEYELLLIQQL 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 147 DCCLIVYHPYRPLLQYVQD-------MGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIAL-ACLHVACVVQQKDARQWFA 218
Cdd:TIGR00569 151 NFHLIVHNPYRPLEGFLIDiktrlpgLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALaAILHTASRAGLNMESYLTE 230

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 2462611183 219 ELSV-----DMEKILEI---IRVILKLYEQwknfDERKEMATILSKM 257
Cdd:TIGR00569 231 QLSVpgnreELPQLIDImreLRILVKKYEE----PRSEKVAALKKKL 273
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 154-240 9.76e-20

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.


Pssm-ID: 410249 [Multi-domain]  Cd Length: 97  Bit Score: 81.64  E-value: 9.76e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 154 HPYRPLLQYVQDMGQEDM--LLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDA--------RQWFAELSVD 223
Cdd:cd20546     1 HPYQYLIKFAKKLGVSDPkeLAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDLelspneklNEWWELFGVD 80

                          90
                  ....*....|....*..
gi 2462611183 224 MEKILEIIRVILKLYEQ 240
Cdd:cd20546    81 EEEIADAINEILDLYSS 97
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 7-100 3.91e-19

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.


Pssm-ID: 410228  Cd Length: 150  Bit Score: 81.87  E-value: 3.91e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183   7 QSSHYLQWILDKQDLLKERQKDL-------------------KFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATV 67
Cdd:cd20524     2 TSTQRKHWIFSSEEELAELRAEAnekareklkeslkeedaepKFLTPEEELLLVRYYEKKLLEFCRAFKLPDSVLATALT 81

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2462611183  68 YFKRFYARYSLKSIDPVLMAPTCVFLASKVEEF 100
Cdd:cd20524    82 YFKRFYLKNSVMEYHPKEIMLTCLYLACKVEEF 114
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 35-147 5.85e-18

first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; Plant CycCs are the cognate cyclin partners of cyclin-dependent kinase CDK8. They may be involved in cell cycle control. CycCs contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410274 [Multi-domain]  Cd Length: 107  Bit Score: 77.20  E-value: 5.85e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  35 EEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEfgvvsntRLIAAATS 114
Cdd:cd20571     1 EDVKLIKIHMSNYIKKLAQHIKVRQRVVATAITYFRRVYTRKSFTEYDPRLVAPTCLYLASKAEE-------STVQAKLL 73

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2462611183 115 VLKTRFSYAfPKEFPYRMNHILECEFYLLELMD 147
Cdd:cd20571    74 VFYMKRLYA-DEYHRYEIKDILEMEMKLLEALD 105
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 48-100 3.50e-16

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.


Pssm-ID: 410233 [Multi-domain]  Cd Length: 115  Bit Score: 72.65  E-value: 3.50e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462611183  48 IQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEF 100
Cdd:cd20530    18 IQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEET 70
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 154-238 8.57e-16

second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 and CCNL2. CCNL1 is involved in regulation of RNA polymerase II (pol II) transcription. It functions in association with cyclin-dependent kinases (CDKs). CCNL2 is a novel RNA polymerase II-associated cyclin involved in pre-mRNA splicing. It may induce cell death, possibly by acting on the transcription and RNA processing of apoptosis-related factors. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410236 [Multi-domain]  Cd Length: 92  Bit Score: 71.09  E-value: 8.57e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 154 HPYRPLLQYVQDMGQED--MLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVA---CVVQQKDARQWFAELSVDMEKIL 228
Cdd:cd20533     1 HPHKFILMYLQVLEGEDnkKLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAareLGIPLPLPPPWWELFDVSKEDIE 80

                          90
                  ....*....|
gi 2462611183 229 EIIRVILKLY 238
Cdd:cd20533    81 EICLTILELY 90
CYCLIN_CCNH_rpt2 cd20525
second cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 153-257 6.85e-14

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


Pssm-ID: 410229  Cd Length: 126  Bit Score: 66.93  E-value: 6.85e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 153 YHPYRPL------LQYVQDMGQEDMLLPL---AWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAEL--- 220
Cdd:cd20525     1 HHPYRPLegflldLKTRLPDLKAENLEKLykeAREFLNRSLLTDAPLLYPPSQIALAALLLAASEAGIDVEEYLSEKlpg 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2462611183 221 ---SVDMEKILEIIRVILKLYEQWKNFDERKEMATILSKM 257
Cdd:cd20525    81 seeSEELEKLLEIIREIKKLVKKYEGPPDKEEVKALDKKL 120
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 46-144 2.09e-12

first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) 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. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410248 [Multi-domain]  Cd Length: 116  Bit Score: 62.44  E-value: 2.09e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  46 NVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTR--FSYA 123
Cdd:cd20545    10 NFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQKNPnlVIDE 89

                          90       100
                  ....*....|....*....|.
gi 2462611183 124 FPKEFPYRMNHILECEFYLLE 144
Cdd:cd20545    90 QSKEVWRWRDSILYNEEVLLE 110
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 45-99 1.36e-11

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.


Pssm-ID: 410241 [Multi-domain]  Cd Length: 137  Bit Score: 60.87  E-value: 1.36e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462611183  45 TNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEE 99
Cdd:cd20538    32 ANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFLAAKVEE 86
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
 4-102 2.06e-11

first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH associates with and activates the cyclin-dependent kinases, CDK-2 and CDK-3. CycH contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410288  Cd Length: 170  Bit Score: 61.00  E-value: 2.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183   4 NFWQSSHYLQWILDKQDLLKERQ----------------------------------------KDLKFLSEEEYWKLQIF 43
Cdd:cd20585     1 DFATSTHRQRWIFTPQDLTEKREaanqravdalqqcgatrveaqaagslgggaevggsngkaaKLPEPLSADEELLMLKY 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462611183  44 FTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGV 102
Cdd:cd20585    81 YEQKIQEVCRALRLPNKIQATALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEEYHV 139
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 31-99 5.36e-11

first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 and CCNL2. CCNL1 is involved in the regulation of RNA polymerase II (pol II) transcription. It functions in association with cyclin-dependent kinases (CDKs). CCNL2 is a novel RNA polymerase II-associated cyclin involved in pre-mRNA splicing. It may induce cell death, possibly by acting on the transcription and RNA processing of apoptosis-related factors. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410235 [Multi-domain]  Cd Length: 127  Bit Score: 58.72  E-value: 5.36e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462611183  31 FLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEE 99
Cdd:cd20532     2 GIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEE 70
Cyclin_C_2 pfam16899
Cyclin C-terminal domain; Cyclins contain two domains of similar all-alpha fold, this family ...
 154-242 6.63e-11

Cyclin C-terminal domain; Cyclins contain two domains of similar all-alpha fold, this family corresponds with the C-terminal domain of some cyclins including cyclin C and cyclin H.


Pssm-ID: 465303  Cd Length: 98  Bit Score: 57.93  E-value: 6.63e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 154 HPYRPLLQYVQDMGQE--------DMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACvvqQKDARQWFAE---LSV 222
Cdd:pfam16899   1 HPFRPLEGFLLDLKTRpplledriESLYKRAREILKSALLTDAYFLYTPSQIALAALLLAD---SPLAEFYLTEkfgLPE 77

                          90       100
                  ....*....|....*....|.
gi 2462611183 223 DMEKILE-IIRVILKLYEQWK 242
Cdd:pfam16899  78 DRETKLEkLLDTIESCRNLLK 98
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 48-99 9.53e-11

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.


Pssm-ID: 410237 [Multi-domain]  Cd Length: 110  Bit Score: 57.57  E-value: 9.53e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2462611183  48 IQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEE 99
Cdd:cd20534     9 IREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEE 60
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 153-239 9.56e-11

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


Pssm-ID: 410291 [Multi-domain]  Cd Length: 93  Bit Score: 57.16  E-value: 9.56e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 153 YHPYRPLLQYVQD-MGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQ----QKDARQ-WFAELSVDMEK 226
Cdd:cd20588     1 EHPYKPLVAAIKKfNVAQNALAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLkvklPCDGRKvWWQEFDVTPRQ 80

                          90
                  ....*....|...
gi 2462611183 227 ILEIIRVILKLYE 239
Cdd:cd20588    81 LEEVSNQMLELYE 93
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 154-240 2.21e-10

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.


Pssm-ID: 410238 [Multi-domain]  Cd Length: 104  Bit Score: 56.50  E-value: 2.21e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 154 HPYRPLLQYVQ------DMGQED--MLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVA---CVVQQK----DARQWFA 218
Cdd:cd20535     1 LPHKYLLHYLKslrdwlNPEFWSrsPIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLAlqvYGVKVPpeeeAEKPWWQ 80

                          90       100
                  ....*....|....*....|....
gi 2462611183 219 ELS--VDMEKILEIIRVILKLYEQ 240
Cdd:cd20535    81 AFCedLTKETIDEIIEDIINVYDL 104
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 153-238 4.07e-10

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.


Pssm-ID: 410234 [Multi-domain]  Cd Length: 101  Bit Score: 55.81  E-value: 4.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 153 YHPYRPLLQYVQ----DMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKD---------ARQWFAE 219
Cdd:cd20531     1 EHPYKYLLKYAKqlkgDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDlqdwtskppGKRWWEQ 80

                          90       100
                  ....*....|....*....|.
gi 2462611183 220 LSVD--MEKILEIIRVILKLY 238
Cdd:cd20531    81 FVEDvsLEVLEDICHQVLDLY 101
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 32-99 4.62e-10

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.


Pssm-ID: 410290 [Multi-domain]  Cd Length: 124  Bit Score: 56.37  E-value: 4.62e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462611183  32 LSEEEYwkLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEE 99
Cdd:cd20587     5 LKKETY--LRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEE 70
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
 46-99 5.94e-10

first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit 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 production elongation by phosphorylating the CTD (carboxy-terminal domain) of the large subunit of RNA polymerase II (RNAP II). CCNT2 contains two cyclin boxs. The model responds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410299 [Multi-domain]  Cd Length: 139  Bit Score: 56.21  E-value: 5.94e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2462611183  46 NVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEE 99
Cdd:cd20596    35 NLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTALFLAAKVEE 88
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 40-99 7.23e-10

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.


Pssm-ID: 410294 [Multi-domain]  Cd Length: 128  Bit Score: 56.00  E-value: 7.23e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  40 LQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEE 99
Cdd:cd20591    14 LRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEE 73
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 154-242 6.36e-08

second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin involved in the regulation of RNA polymerase II (pol II) transcription. It functions in association with cyclin-dependent kinases (CDKs). CCNL1 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410295 [Multi-domain]  Cd Length: 123  Bit Score: 50.38  E-value: 6.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 154 HPYRPLLQYVQDMGQE--DMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQ---KDARQWFAELSVDMEKIL 228
Cdd:cd20592     2 HPHKIIVMYLQVLECErnQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQiplPNRPHWFLLFGATEEEIQ 81

                          90
                  ....*....|....
gi 2462611183 229 EIIRVILKLYEQWK 242
Cdd:cd20592    82 EICITTLKLYTRKK 95
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 48-102 1.12e-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: 48.56  E-value: 1.12e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462611183  48 IQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGV 102
Cdd:cd00043     6 IRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPR 60
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 48-144 1.14e-07

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: 48.36  E-value: 1.14e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183   48 IQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVvsNTRLIAAATSVlktrfsyafpke 127
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPP--WTKELVHYTGY------------ 68

                           90
                   ....*....|....*..
gi 2462611183  128 fpYRMNHILECEFYLLE 144
Cdd:smart00385  69 --FTEEEILRMERLLLE 83
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 46-99 1.51e-07

first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor essential for HIV-1 replication in CD4 T cells and macrophages. It is a regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin-T1) 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). CCNT1 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410298 [Multi-domain]  Cd Length: 138  Bit Score: 49.67  E-value: 1.51e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2462611183  46 NVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEE 99
Cdd:cd20595    34 NLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALFLAAKVEE 87
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 154-242 2.27e-07

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


Pssm-ID: 410296 [Multi-domain]  Cd Length: 123  Bit Score: 48.81  E-value: 2.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 154 HPYRPLLQYVQDMGQE--DMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQ---KDARQWFAELSVDMEKIL 228
Cdd:cd20593     1 HPHKIIVMYLQVLECErnRHLVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEiplPNRPHWFLLFGATEEEIQ 80

                          90
                  ....*....|....
gi 2462611183 229 EIIRVILKLYEQWK 242
Cdd:cd20593    81 EICLKILQLYTRKK 94
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 51-99 9.97e-07

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.


Pssm-ID: 459686 [Multi-domain]  Cd Length: 127  Bit Score: 46.74  E-value: 9.97e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2462611183  51 LGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEE 99
Cdd:pfam00134  41 VHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYEE 89
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 32-99 1.49e-06

first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin involved in the regulation of RNA polymerase II (pol II) transcription. It functions in association with cyclin-dependent kinases (CDKs). CCNL1 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410292 [Multi-domain]  Cd Length: 124  Bit Score: 46.28  E-value: 1.49e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  32 LSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSL--KSIDPVLMAptCVFLASKVEE 99
Cdd:cd20589     3 LDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFvkHSMEIVAMA--CINLASKIEE 70
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 152-242 3.96e-06

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


Pssm-ID: 410297 [Multi-domain]  Cd Length: 101  Bit Score: 44.47  E-value: 3.96e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 152 VYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVAC---VVQQKDARQWFAELSVDMEKIL 228
Cdd:cd20594     2 VEHPHKFILNYLAMLMAPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAArrfQVPLPENPPWWKVFDAEKAEID 81

                          90
                  ....*....|....
gi 2462611183 229 EIIRVILKLYEQWK 242
Cdd:cd20594    82 VVCKVLADLYRQPK 95
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 48-145 1.30e-05

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.


Pssm-ID: 410250 [Multi-domain]  Cd Length: 110  Bit Score: 43.49  E-value: 1.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  48 IQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEfgVVSNTRLIAAATSVL----KTRFSYA 123
Cdd:cd20547     9 ISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIED--TQKKSKDILAASYNLrhpdKISVDDQ 86

                          90       100
                  ....*....|....*....|..
gi 2462611183 124 FPKEFPYRMNHIlecEFYLLEL 145
Cdd:cd20547    87 MLEEFRKAILGL---ERLLLET 105
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 161-236 1.87e-05

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: 42.19  E-value: 1.87e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  161 QYVQDMGQEDML----LPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDArqWFAELSV-----DMEKILEII 231
Cdd:smart00385   1 DFLRRVCKALNLdpetLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPP--WTKELVHytgyfTEEEILRME 78


                   ....*
gi 2462611183  232 RVILK 236
Cdd:smart00385  79 RLLLE 83
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 40-99 4.51e-05

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.


Pssm-ID: 410293 [Multi-domain]  Cd Length: 156  Bit Score: 42.69  E-value: 4.51e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462611183  40 LQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSL--KSIDPVLMAptCVFLASKVEE 99
Cdd:cd20590    43 LRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFvkHSMEHVSMA--CVHLASKIEE 102
CYCLIN_AcCycH_rpt2 cd20586
second cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; ...
 153-219 1.20e-04

second cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH associates with and activates the cyclin-dependent kinases, CDK-2 and CDK-3. CycH contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410289 [Multi-domain]  Cd Length: 132  Bit Score: 41.26  E-value: 1.20e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462611183 153 YHPYRPLLQYVQDM------------GQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAE 219
Cdd:cd20586     1 YAPYRALEGFVQDLeeflaagsgpdsQGLQELRKAALAAVDKLMLTDAPLLYPPGQLALAALRSANKAKGGVDFDRYLE 79
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 154-232 1.93e-03

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: 36.62  E-value: 1.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183 154 HPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQ-WFAELS-VDMEKILEII 231
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLkEIAKVSgVSEKELRKAE 80


                  .
gi 2462611183 232 R 232
Cdd:cd00043    81 K 81
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 48-124 6.87e-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: 34.87  E-value: 6.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462611183  48 IQALGEHLKLRQQVIATATVYFKRFYARYSLK--SIDPVLMAptCVFLASKVEEfgvVSNT-RLIAAATSVLKTRFSYAF 124
Cdd:cd20551     6 IGEMADRMNLPRTIKDRAKELFKQVHDQKSLKgrSNDAIAAA--CLYIACRQEG---VPRTfKEICAVSNVSKKEIGRCF 80
CYCLIN_AtCycD-like_rpt1 cd20543
first cyclin box found in plant cyclin-delta family; This subfamily is composed of plant delta ...
 46-99 8.75e-03

first cyclin box found in plant cyclin-delta family; This subfamily is composed of plant delta family cyclins, including a group of G1/S-specific D-type cyclins from Arabidopsis thaliana which may activate the cell cycle in the root apical meristem (RAM) and promote embryonic root (radicle) protrusion. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410246  Cd Length: 99  Bit Score: 34.99  E-value: 8.75e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462611183  46 NVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDP---VLMAPTCVFLASKVEE 99
Cdd:cd20543     7 DWILKVRSRYGFGPLTAYLAVNYLDRFLSSYDLPKDKPwmlQLLAVACLSLAAKMEE 63
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 186-232 9.96e-03

second 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 in this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410242 [Multi-domain]  Cd Length: 92  Bit Score: 34.56  E-value: 9.96e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462611183 186 TDLCLLYPPFMIALACLHVAC------VVQQKDARQWFAelSVDMEKILEIIR 232
Cdd:cd20539    35 TTFCLQYKPTVIACVCIHLACkwsnweIPRSSEGKDWYE--YVDPSLTLEELD 85
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH