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Conserved domains on  [gi|1063686772|ref|NP_001321314|]
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cyclin T 1;3 [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CYCLIN_SF super family cl40454
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
1-88 6.31e-54

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.


The actual alignment was detected with superfamily member cd20587:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 124  Bit Score: 169.24  E-value: 6.31e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEIIYEWDPSASIRIHQTECYHEFKEIILSGESL 80
Cdd:cd20587    37 IVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIVVSYEIIFKKDPSAAQRIKQKEVYEQQKELVLNGEKL 116

                  ....*...
gi 1063686772  81 LLSTSAFH 88
Cdd:cd20587   117 VLSTLGFD 124
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
92-181 1.63e-45

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: 146.91  E-value: 1.63e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  92 ELPYKPLAAALNRLN-AWPDLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVG--SRRDWWLEFGVTTKL 168
Cdd:cd20588     1 EHPYKPLVAAIKKFNvAQNALAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPcdGRKVWWQEFDVTPRQ 80
                          90
                  ....*....|...
gi 1063686772 169 LKEVIQEMCTLIE 181
Cdd:cd20588    81 LEEVSNQMLELYE 93
 
Name Accession Description Interval E-value
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
1-88 6.31e-54

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: 169.24  E-value: 6.31e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEIIYEWDPSASIRIHQTECYHEFKEIILSGESL 80
Cdd:cd20587    37 IVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIVVSYEIIFKKDPSAAQRIKQKEVYEQQKELVLNGEKL 116

                  ....*...
gi 1063686772  81 LLSTSAFH 88
Cdd:cd20587   117 VLSTLGFD 124
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
92-181 1.63e-45

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: 146.91  E-value: 1.63e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  92 ELPYKPLAAALNRLN-AWPDLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVG--SRRDWWLEFGVTTKL 168
Cdd:cd20588     1 EHPYKPLVAAIKKFNvAQNALAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPcdGRKVWWQEFDVTPRQ 80
                          90
                  ....*....|...
gi 1063686772 169 LKEVIQEMCTLIE 181
Cdd:cd20588    81 LEEVSNQMLELYE 93
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
1-173 1.02e-14

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: 71.69  E-value: 1.02e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPcqlSSVVVASYEiiyewdpsasIRIHQTECYHEFKEIILSGESL 80
Cdd:COG5333    70 ILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTP---RDISIESFE----------ARDLWSEEPKSSRERILEYEFE 136
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  81 LLSTSAFHLDIELPYKPLAAALN--RLNAWPDLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVgsrrdW 158
Cdd:COG5333   137 LLEALDFDLHVHHPYKYLEGFLKdlQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPI-----I 211
                         170
                  ....*....|....*
gi 1063686772 159 WLEFGVTTKLLKEVI 173
Cdd:COG5333   212 KLLDFVSYETKEEVI 226
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
6-145 5.25e-05

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: 43.28  E-value: 5.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   6 RFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEiiyewDPSASIrihqtecyhefkEIILSGESLLLSTS 85
Cdd:TIGR00569  88 RFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKE-----TPLKAL------------EQVLEYELLLIQQL 150
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063686772  86 AFHLDIELPYKPLAAAL----NRLNAWPD---LATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAA 145
Cdd:TIGR00569 151 NFHLIVHNPYRPLEGFLidikTRLPGLENpeyLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTA 217
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
1-46 5.68e-04

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: 38.65  E-value: 5.68e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACK-AEDEPCQLSSVVVAS 46
Cdd:pfam00134  56 VNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKyEEIYPPTVEDLVYIT 102
 
Name Accession Description Interval E-value
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
1-88 6.31e-54

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: 169.24  E-value: 6.31e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEIIYEWDPSASIRIHQTECYHEFKEIILSGESL 80
Cdd:cd20587    37 IVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIVVSYEIIFKKDPSAAQRIKQKEVYEQQKELVLNGEKL 116

                  ....*...
gi 1063686772  81 LLSTSAFH 88
Cdd:cd20587   117 VLSTLGFD 124
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
92-181 1.63e-45

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: 146.91  E-value: 1.63e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  92 ELPYKPLAAALNRLN-AWPDLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVG--SRRDWWLEFGVTTKL 168
Cdd:cd20588     1 EHPYKPLVAAIKKFNvAQNALAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPcdGRKVWWQEFDVTPRQ 80
                          90
                  ....*....|...
gi 1063686772 169 LKEVIQEMCTLIE 181
Cdd:cd20588    81 LEEVSNQMLELYE 93
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
1-87 8.72e-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: 70.72  E-value: 8.72e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEIIYEwdpsasirIHQTECYHEFKEIILSGESL 80
Cdd:cd20530    36 IVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKTARSLLND--------KQFAQFGDDPKEEVMVLERI 107

                  ....*..
gi 1063686772  81 LLSTSAF 87
Cdd:cd20530   108 LLQTIKF 114
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
92-180 1.09e-15

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: 70.06  E-value: 1.09e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  92 ELPYKPL---AAAL----NRLNAwpdLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKV------GSRRDW 158
Cdd:cd20531     1 EHPYKYLlkyAKQLkgdkNKIQK---LVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLqdwtskPPGKRW 77
                          90       100
                  ....*....|....*....|..
gi 1063686772 159 WLEFGVTTKLlkEVIQEMCTLI 180
Cdd:cd20531    78 WEQFVEDVSL--EVLEDICHQV 97
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
93-179 5.46e-15

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: 68.16  E-value: 5.46e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  93 LPYKPLAAALNRLN--AWPDLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVGSRRD-----WWLEFGVT 165
Cdd:cd20546     1 HPYQYLIKFAKKLGvsDPKELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPNeklneWWELFGVD 80
                          90
                  ....*....|....
gi 1063686772 166 TKLLKEVIQEMCTL 179
Cdd:cd20546    81 EEEIADAINEILDL 94
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
1-173 1.02e-14

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: 71.69  E-value: 1.02e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPcqlSSVVVASYEiiyewdpsasIRIHQTECYHEFKEIILSGESL 80
Cdd:COG5333    70 ILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTP---RDISIESFE----------ARDLWSEEPKSSRERILEYEFE 136
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  81 LLSTSAFHLDIELPYKPLAAALN--RLNAWPDLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVgsrrdW 158
Cdd:COG5333   137 LLEALDFDLHVHHPYKYLEGFLKdlQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPI-----I 211
                         170
                  ....*....|....*
gi 1063686772 159 WLEFGVTTKLLKEVI 173
Cdd:COG5333   212 KLLDFVSYETKEEVI 226
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
93-172 2.09e-14

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: 66.47  E-value: 2.09e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  93 LPYKPLAAALNRLNA--WPDLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVGSRRDWWLEFGVTTKLLK 170
Cdd:cd20533     1 HPHKFILMYLQVLEGedNKKLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAARELGIPLPLPPPWWELFDVSKEDIE 80

                  ..
gi 1063686772 171 EV 172
Cdd:cd20533    81 EI 82
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
94-182 3.20e-14

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: 66.10  E-value: 3.20e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  94 PYKPLAAALNRLNAWPDLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVgsrRDWWLEFGVTTKLLKEVI 173
Cdd:cd20514     2 PYRPLTQYVQDAGLDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDA---RQWFAELNVDMDKILEIT 78

                  ....*....
gi 1063686772 174 QEMCTLIEV 182
Cdd:cd20514    79 REILSLYEL 87
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
1-88 1.10e-12

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: 62.96  E-value: 1.10e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEIIY--EWDPSASIRI-HQTECYHEFKEIILSG 77
Cdd:cd20532    37 QVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVINVFHRLLQrrLGKPAEVLPLdIGSAEYEELKNDIIKA 116
                          90
                  ....*....|.
gi 1063686772  78 ESLLLSTSAFH 88
Cdd:cd20532   117 ERRILKELGFC 127
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
109-178 4.46e-10

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: 55.77  E-value: 4.46e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772 109 PDLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVGSRRDWWLEFGVTtkllKEVIQEMCT 178
Cdd:cd20592    20 QTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPNRPHWFLLFGAT----EEEIQEICI 85
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
1-87 6.71e-10

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: 55.45  E-value: 6.71e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEIIYEWDPSASIRihqTECYHEFKEIILSGESL 80
Cdd:cd20595    54 IVYMHRFYMIQSFTQFHRNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTR---SEAYLQQVQDLVILESI 130

                  ....*..
gi 1063686772  81 LLSTSAF 87
Cdd:cd20595   131 ILQTLGF 137
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
1-87 2.28e-09

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: 53.93  E-value: 2.28e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEIIYEWDPSASIRihqTECYHEFKEIILSGESL 80
Cdd:cd20538    53 IVYMHRFYMFHSFTKFHRNSIAAAALFLAAKVEEQPRKLEHVIKVAHACLHRGEPDLDTK---SEAYLQQAQELVINENI 129

                  ....*..
gi 1063686772  81 LLSTSAF 87
Cdd:cd20538   130 LLQTLGF 136
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
91-179 5.11e-09

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: 52.17  E-value: 5.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  91 IELPYKPLAAALNRLNAWPDLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVGSRRDWWLEFGVTTKLLK 170
Cdd:cd20594     2 VEHPHKFILNYLAMLMAPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKVFDAEKAEID 81

                  ....*....
gi 1063686772 171 EVIQEMCTL 179
Cdd:cd20594    82 VVCKVLADL 90
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
2-88 8.23e-09

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: 51.79  E-value: 8.23e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   2 VMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEIIyewDPSASIRIHQTEcYHEFKEIILSGESLL 81
Cdd:cd20534    28 VLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRIL---HPDKPPLELDDE-YWELRDSIVNCELLL 103

                  ....*..
gi 1063686772  82 LSTSAFH 88
Cdd:cd20534   104 LRILKFD 110
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
111-180 8.96e-09

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: 52.28  E-value: 8.96e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772 111 LATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVGSRRDWWLEFGVTtkllKEVIQEMCTLI 180
Cdd:cd20593    21 LVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEIPLPNRPHWFLLFGAT----EEEIQEICLKI 86
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
1-87 1.05e-08

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: 51.58  E-value: 1.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEIIYEWDPSASirihqTECYHEFKEIILSGESL 80
Cdd:cd20547    27 MLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNLRHPDKISVD-----DQMLEEFRKAILGLERL 101

                  ....*..
gi 1063686772  81 LLSTSAF 87
Cdd:cd20547   102 LLETICF 108
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
5-89 3.02e-08

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: 50.50  E-value: 3.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   5 HRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEIIYEwdPSASIRIHQTECYHEFKEIILSGESLLLST 84
Cdd:cd20545    34 HRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQK--NPNLVIDEQSKEVWRWRDSILYNEEVLLET 111

                  ....*
gi 1063686772  85 SAFHL 89
Cdd:cd20545   112 LCFDL 116
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
111-181 5.21e-08

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: 49.56  E-value: 5.21e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063686772 111 LATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKV----GSRRDWWLEF--GVTTKLLKEVIQEMCTLIE 181
Cdd:cd20535    27 IAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQVYGVKVppeeEAEKPWWQAFceDLTKETIDEIIEDIINVYD 103
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
1-87 3.39e-07

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: 48.12  E-value: 3.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEIIYEWDPSASIRihqTECYHEFKEIILSGESL 80
Cdd:cd20596    55 IVYMHRFYMHHSFTKFHRNIISPTALFLAAKVEEQPRKLEHVIKVAHACLNPLEPQLDTK---SDAYLQQAQELVILETI 131

                  ....*..
gi 1063686772  81 LLSTSAF 87
Cdd:cd20596   132 MLQTLGF 138
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
6-145 5.25e-05

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: 43.28  E-value: 5.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   6 RFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEiiyewDPSASIrihqtecyhefkEIILSGESLLLSTS 85
Cdd:TIGR00569  88 RFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKE-----TPLKAL------------EQVLEYELLLIQQL 150
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063686772  86 AFHLDIELPYKPLAAAL----NRLNAWPD---LATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAA 145
Cdd:TIGR00569 151 NFHLIVHNPYRPLEGFLidikTRLPGLENpeyLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTA 217
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
92-181 6.27e-05

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


Pssm-ID: 410301 [Multi-domain]  Cd Length: 114  Bit Score: 41.22  E-value: 6.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  92 ELPYKPLAAALNRLNAWPDLATAAWNFVHDWIR-TTLCLQYKPHVIATATVHLAATFQNAKVGSRRD---WW--LEFGVT 165
Cdd:cd20598     1 EHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHlTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDgkhWWeyVDPTVT 80
                          90
                  ....*....|....*.
gi 1063686772 166 TKLLKEVIQEMCTLIE 181
Cdd:cd20598    81 LELLDELTHEFLQILE 96
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
2-87 1.71e-04

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: 40.20  E-value: 1.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772   2 VMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVASYEIIYEWD--PSASIRIHQTEcYHEFKEIILSGES 79
Cdd:cd20591    41 VLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQVLMVFHRMECRREnlPLEPLEPESKK-YDEMKEDLIRTER 119

                  ....*...
gi 1063686772  80 LLLSTSAF 87
Cdd:cd20591   120 HLLKEMGF 127
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
1-46 2.40e-04

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: 38.55  E-value: 2.40e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACKAEDEPCQLSSVVVAS 46
Cdd:cd00043    24 IELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVS 69
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
125-175 5.22e-04

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: 38.02  E-value: 5.22e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1063686772 125 TTLCLQYKPHVIATATVHLAATFQNAK---VGSRRDWW--LEFGVTTKLLKEVIQE 175
Cdd:cd20539    35 TTFCLQYKPTVIACVCIHLACKWSNWEiprSSEGKDWYeyVDPSLTLEELDELTSE 90
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
1-46 5.68e-04

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: 38.65  E-value: 5.68e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063686772   1 MVMCHRFYMRQSHAKNDWQTIATSSLFLACK-AEDEPCQLSSVVVAS 46
Cdd:pfam00134  56 VNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKyEEIYPPTVEDLVYIT 102
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
94-181 1.18e-03

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


Pssm-ID: 410300 [Multi-domain]  Cd Length: 109  Bit Score: 37.37  E-value: 1.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  94 PYKPLAAALNRLNAWPDLATAAWNFVHDWIR-TTLCLQYKPHVIATATVHLAATFQNAKVGSRRD---WW--LEFGVTTK 167
Cdd:cd20597     3 PHTHVVKCTQLVRASKDLAQTSYFMATNSLHlTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDgkhWWeyVDATVTLE 82
                          90
                  ....*....|....
gi 1063686772 168 LLKEVIQEMCTLIE 181
Cdd:cd20597    83 LLDELTHEFLQILE 96
CYCLIN_AtCycC_rpt2 cd20572
second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
94-176 3.67e-03

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: 35.91  E-value: 3.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  94 PYKPLAAALNRLNAwPDLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVgsrRDWWLEFGVTTKLLKEVI 173
Cdd:cd20572     2 PYRPLIQLLQDAGL-TDMTQFTWSIVNDTYRTDLILIHPPYMIALACIYIASVHKEKDI---TLWFEELRVDMNIIKNIA 77

                  ...
gi 1063686772 174 QEM 176
Cdd:cd20572    78 MEI 80
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
94-175 9.05e-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: 34.31  E-value: 9.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063686772  94 PYKPLAAALNRLNAWPDLATAAWNFVHDWIRTTLCLQYKPHVIATATVHLAATFQNAKVgSRRDWWLEFGVTTKLLKEVI 173
Cdd:cd00043     2 AVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPR-TLKEIAKVSGVSEKELRKAE 80

                  ..
gi 1063686772 174 QE 175
Cdd:cd00043    81 KE 82
 
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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