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Conserved domains on  [gi|1585729908|ref|XP_028061023|]
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cyclin-L1-1-like isoform X7 [Camellia sinensis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 21-148 3.08e-85

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: 252.45  E-value: 3.08e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  21 SRKDGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQ 100
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1585729908 101 VLIVFHRMECRRENLPIEHLDTFPKKYAELKMDLNRTERHLLKEMGFI 148
Cdd:cd20591    81 VLMVFHRMECRRENLPLEPLEPESKKYDEMKEDLIRTERHLLKEMGFI 128
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 150-250 1.27e-68

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: 209.33  E-value: 1.27e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 150 HVEHPHKFISNYLAALETPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSGI 229
Cdd:cd20594     1 HVEHPHKFILNYLAMLMAPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKVFDAEKAEI 80

                          90       100
                  ....*....|....*....|.
gi 1585729908 230 DEVCRVLAHLYSLPKAKYIPV 250
Cdd:cd20594    81 DVVCKVLADLYRQPKARYIEV 101
 
Name Accession Description Interval E-value
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 21-148 3.08e-85

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: 252.45  E-value: 3.08e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  21 SRKDGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQ 100
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1585729908 101 VLIVFHRMECRRENLPIEHLDTFPKKYAELKMDLNRTERHLLKEMGFI 148
Cdd:cd20591    81 VLMVFHRMECRRENLPLEPLEPESKKYDEMKEDLIRTERHLLKEMGFI 128
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 150-250 1.27e-68

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: 209.33  E-value: 1.27e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 150 HVEHPHKFISNYLAALETPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSGI 229
Cdd:cd20594     1 HVEHPHKFILNYLAMLMAPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKVFDAEKAEI 80

                          90       100
                  ....*....|....*....|.
gi 1585729908 230 DEVCRVLAHLYSLPKAKYIPV 250
Cdd:cd20594    81 DVVCKVLADLYRQPKARYIEV 101
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 31-230 3.76e-25

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: 102.50  E-value: 3.76e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  31 ETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRkarqvlivFHRMEC 110
Cdd:COG5333    41 ELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPR--------DISIES 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 111 RRENlpiehlDTFPKKYAELKMDLNRTERHLLKEMGFICHVEHPHKFISNYLAALET--PPELRQEAWNLANDSLRTTLC 188
Cdd:COG5333   113 FEAR------DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEkdKYKLLQIAWKIINDALRTDLC 186

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1585729908 189 VRFKSEVVACGVVYAAARRFQVPLPENppWWKAFDADKSGID 230
Cdd:COG5333   187 LLYPPHIIALAALLIACEVLGMPIIKL--LDFVSYETKEEVI 226
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 40-106 1.84e-08

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: 50.67  E-value: 1.84e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1585729908   40 DLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQVLIVFH 106
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTG 67
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 10-147 4.87e-08

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: 50.98  E-value: 4.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  10 YLTDEQLQNSPSRkDGIDEATETTL--RIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWL 87
Cdd:pfam00134   5 YLRELELKYLPKP-DYMDQQPDINPkmRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFI 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1585729908  88 ASKLEE-SPRKArqvlivfhrmecrrENLPIEHLDTFPKKyaelkmDLNRTERHLLKEMGF 147
Cdd:pfam00134  84 AAKYEEiYPPTV--------------EDLVYITDNAYTRE------EILRMERLILETLNF 124
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 156-213 1.78e-06

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: 45.28  E-value: 1.78e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1585729908  156 KFISNYLAALETPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLP 213
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPW 58
 
Name Accession Description Interval E-value
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 21-148 3.08e-85

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: 252.45  E-value: 3.08e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  21 SRKDGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQ 100
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1585729908 101 VLIVFHRMECRRENLPIEHLDTFPKKYAELKMDLNRTERHLLKEMGFI 148
Cdd:cd20591    81 VLMVFHRMECRRENLPLEPLEPESKKYDEMKEDLIRTERHLLKEMGFI 128
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 150-250 1.27e-68

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: 209.33  E-value: 1.27e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 150 HVEHPHKFISNYLAALETPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSGI 229
Cdd:cd20594     1 HVEHPHKFILNYLAMLMAPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKVFDAEKAEI 80

                          90       100
                  ....*....|....*....|.
gi 1585729908 230 DEVCRVLAHLYSLPKAKYIPV 250
Cdd:cd20594    81 DVVCKVLADLYRQPKARYIEV 101
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 24-148 1.85e-67

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: 207.03  E-value: 1.85e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  24 DGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQVLI 103
Cdd:cd20532     1 DGIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVIN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1585729908 104 VFHRMECRRENLPIEH--LDTFPKKYAELKMDLNRTERHLLKEMGFI 148
Cdd:cd20532    81 VFHRLLQRRLGKPAEVlpLDIGSAEYEELKNDIIKAERRILKELGFC 127
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 153-241 2.83e-42

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: 141.20  E-value: 2.83e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 153 HPHKFISNYLAALET--PPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSGID 230
Cdd:cd20533     1 HPHKFILMYLQVLEGedNKKLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAARELGIPLPLPPPWWELFDVSKEDIE 80

                          90
                  ....*....|.
gi 1585729908 231 EVCRVLAHLYS 241
Cdd:cd20533    81 EICLTILELYT 91
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 11-147 4.48e-42

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: 143.22  E-value: 4.48e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  11 LTDEQLQNSPSRKDGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASK 90
Cdd:cd20590    20 LPEERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVKHSMEHVSMACVHLASK 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1585729908  91 LEESPRKARQVLIVFHRM-ECRRENLPIEHLdtFPKKYAELKMDLNRTERHLLKEMGF 147
Cdd:cd20590   100 IEEAPRRIRDVINVFHRLrQLREKKKPVPLI--LDQEYVNLKNQIIKAERRVLKELGF 155
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 24-147 1.02e-41

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: 141.04  E-value: 1.02e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  24 DGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQVLI 103
Cdd:cd20589     1 DGLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVIN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1585729908 104 VFHRMECRRENLPIEHLdTFPKKYAELKMDLNRTERHLLKEMGF 147
Cdd:cd20589    81 VFHHIKQVRGKRTISPL-ILDQNYINLKNQVIKAERRVLKELGF 123
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 9-147 5.12e-29

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: 108.25  E-value: 5.12e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908   9 FYLTDEQLQNSPSRKDGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLA 88
Cdd:cd20538     2 WYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFLA 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1585729908  89 SKLEESPRKARQVLIVFHrmECRRENLPieHLDTFPKKYAELKMDLNRTERHLLKEMGF 147
Cdd:cd20538    82 AKVEEQPRKLEHVIKVAH--ACLHRGEP--DLDTKSEAYLQQAQELVINENILLQTLGF 136
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 25-147 2.12e-26

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: 100.77  E-value: 2.12e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  25 GIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQVLIV 104
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1585729908 105 FHRMecrrenLPIEHLDTFPKKYAELKMDLnrtERHLLKEMGF 147
Cdd:cd20530    81 ARSL------LNDKQFAQFGDDPKEEVMVL---ERILLQTIKF 114
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 152-247 2.02e-25

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: 98.53  E-value: 2.02e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 152 EHPHKFISNYLAALETP--PELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSGI 229
Cdd:cd20592     1 KHPHKIIVMYLQVLECErnQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPNRPHWFLLFGATEEEI 80

                          90
                  ....*....|....*...
gi 1585729908 230 DEVCRVLAHLYSLPKAKY 247
Cdd:cd20592    81 QEICITTLKLYTRKKPNY 98
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 9-147 2.13e-25

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: 98.97  E-value: 2.13e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908   9 FYLTDEQLQNSPSRKDGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLA 88
Cdd:cd20595     3 WYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALFLA 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1585729908  89 SKLEESPRKARQVLIVFHRMECRRENLPiehlDTFPKKYAELKMDLNRTERHLLKEMGF 147
Cdd:cd20595    83 AKVEEQPKKLEHVIKVAHTCLHPQESLP----DTRSEAYLQQVQDLVILESIILQTLGF 137
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 31-230 3.76e-25

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: 102.50  E-value: 3.76e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  31 ETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRkarqvlivFHRMEC 110
Cdd:COG5333    41 ELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPR--------DISIES 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 111 RRENlpiehlDTFPKKYAELKMDLNRTERHLLKEMGFICHVEHPHKFISNYLAALET--PPELRQEAWNLANDSLRTTLC 188
Cdd:COG5333   113 FEAR------DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEkdKYKLLQIAWKIINDALRTDLC 186

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1585729908 189 VRFKSEVVACGVVYAAARRFQVPLPENppWWKAFDADKSGID 230
Cdd:COG5333   187 LLYPPHIIALAALLIACEVLGMPIIKL--LDFVSYETKEEVI 226
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 153-245 4.47e-23

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: 92.34  E-value: 4.47e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 153 HPHKFISNYLAALETP--PELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSGID 230
Cdd:cd20593     1 HPHKIIVMYLQVLECErnRHLVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEIPLPNRPHWFLLFGATEEEIQ 80

                          90
                  ....*....|....*
gi 1585729908 231 EVCRVLAHLYSLPKA 245
Cdd:cd20593    81 EICLKILQLYTRKKV 95
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
 9-147 7.02e-23

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: 92.42  E-value: 7.02e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908   9 FYLTDEQLQNSPSRKDGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLA 88
Cdd:cd20596     4 WFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTALFLA 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  89 SKLEESPRKARQVLIVFHrmECRRenlPIE-HLDTFPKKYAELKMDLNRTERHLLKEMGF 147
Cdd:cd20596    84 AKVEEQPRKLEHVIKVAH--ACLN---PLEpQLDTKSDAYLQQAQELVILETIMLQTLGF 138
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 39-147 2.48e-20

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: 84.53  E-value: 2.48e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  39 CDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQVLIVFHRMeCRRENLPIE 118
Cdd:cd20534     6 LRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRI-LHPDKPPLE 84

                          90       100
                  ....*....|....*....|....*....
gi 1585729908 119 HLDtfpkKYAELKMDLNRTERHLLKEMGF 147
Cdd:cd20534    85 LDD----EYWELRDSIVNCELLLLRILKF 109
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 24-147 2.81e-19

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: 82.18  E-value: 2.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  24 DGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQVLI 103
Cdd:cd20587     1 DGIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1585729908 104 VFHRMECRREnlPIEHLDTFPKK-YAELKMDLNRTERHLLKEMGF 147
Cdd:cd20587    81 VSYEIIFKKD--PSAAQRIKQKEvYEQQKELVLNGEKLVLSTLGF 123
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 35-147 1.44e-17

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: 77.08  E-value: 1.44e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  35 RIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQVLIVFHRMECRREN 114
Cdd:cd20545     5 RSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQKNPN 84

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1585729908 115 LPIehlDTFPKKYAELKMDLNRTERHLLKEMGF 147
Cdd:cd20545    85 LVI---DEQSKEVWRWRDSILYNEEVLLETLCF 114
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 152-240 1.74e-17

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: 76.61  E-value: 1.74e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 152 EHPHKFISNYLAAL----ETPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAAR--RFQVPLPENPP----WWKA 221
Cdd:cd20531     1 EHPYKYLLKYAKQLkgdkNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKlsKFDLQDWTSKPpgkrWWEQ 80

                          90       100
                  ....*....|....*....|.
gi 1585729908 222 FDADKSG--IDEVCRVLAHLY 240
Cdd:cd20531    81 FVEDVSLevLEDICHQVLDLY 101
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 153-241 4.67e-17

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: 75.10  E-value: 4.67e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 153 HPHKFISNYLAALETP--PELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENP-----PWWKAFDAD 225
Cdd:cd20546     1 HPYQYLIKFAKKLGVSdpKELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPneklnEWWELFGVD 80

                          90
                  ....*....|....*.
gi 1585729908 226 KSGIDEVCRVLAHLYS 241
Cdd:cd20546    81 EEEIADAINEILDLYS 96
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 34-145 5.67e-17

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: 74.94  E-value: 5.67e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  34 LRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARqvLIVFHRMECRre 113
Cdd:cd20513     1 LHIFFANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPSHAR--LIVAEAKVLK-- 76

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1585729908 114 nlpiehldtfPKKYAELKMDLNR---TERHLLKEM 145
Cdd:cd20513    77 ----------TKFSYEFPYRVNDileCEFYLLEAL 101
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 152-240 5.00e-15

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: 69.48  E-value: 5.00e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 152 EHPHKFISNYLAALE-TPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPEN--PPWWKAFDADKSG 228
Cdd:cd20588     1 EHPYKPLVAAIKKFNvAQNALAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPCDgrKVWWQEFDVTPRQ 80

                          90
                  ....*....|..
gi 1585729908 229 IDEVCRVLAHLY 240
Cdd:cd20588    81 LEEVSNQMLELY 92
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 153-242 3.99e-14

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: 67.28  E-value: 3.99e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 153 HPHKFISNYLAALE--TPPE------LRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENP----PWWK 220
Cdd:cd20535     1 LPHKYLLHYLKSLRdwLNPEfwsrspIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQVYGVKVPPEEeaekPWWQ 80

                          90       100
                  ....*....|....*....|....
gi 1585729908 221 AF--DADKSGIDEVCRVLAHLYSL 242
Cdd:cd20535    81 AFceDLTKETIDEIIEDIINVYDL 104
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 37-106 3.61e-11

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: 58.58  E-value: 3.61e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  37 YGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQVLIVFH 106
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSG 70
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 34-108 4.77e-09

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: 53.50  E-value: 4.77e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1585729908  34 LRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQVLIVFHRM 108
Cdd:cd20547     1 LRLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNL 75
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 40-106 1.84e-08

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: 50.67  E-value: 1.84e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1585729908   40 DLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARQVLIVFH 106
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTG 67
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 153-238 2.27e-08

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: 50.74  E-value: 2.27e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 153 HPHKFISNYLAALE-TPPELRQEAWNLANDSLR-TTLCVRFKSEVVACGVVYAAAR--RFQVPLP-ENPPWWKAFdaDKS 227
Cdd:cd20539     1 HPHTHVLKICNLVKaGSKDLAQTAYFLATNSLHlTTFCLQYKPTVIACVCIHLACKwsNWEIPRSsEGKDWYEYV--DPS 78

                          90
                  ....*....|.
gi 1585729908 228 GIDEVCRVLAH 238
Cdd:cd20539    79 LTLEELDELTS 89
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 10-147 4.87e-08

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: 50.98  E-value: 4.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  10 YLTDEQLQNSPSRkDGIDEATETTL--RIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWL 87
Cdd:pfam00134   5 YLRELELKYLPKP-DYMDQQPDINPkmRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFI 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1585729908  88 ASKLEE-SPRKArqvlivfhrmecrrENLPIEHLDTFPKKyaelkmDLNRTERHLLKEMGF 147
Cdd:pfam00134  84 AAKYEEiYPPTV--------------EDLVYITDNAYTRE------EILRMERLILETLNF 124
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 34-106 7.96e-08

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: 49.85  E-value: 7.96e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1585729908  34 LRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEESPRKARqvLIVFH 106
Cdd:cd20571     6 IKIHMSNYIKKLAQHIKVRQRVVATAITYFRRVYTRKSFTEYDPRLVAPTCLYLASKAEESTVQAK--LLVFY 76
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 153-244 8.27e-07

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: 46.46  E-value: 8.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908 153 HPHKFISNYLAALETPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPEnppWWKAFDADKSGIDEV 232
Cdd:cd20514     1 HPYRPLTQYVQDAGLDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDARQ---WFAELNVDMDKILEI 77

                          90
                  ....*....|..
gi 1585729908 233 CRVLAHLYSLPK 244
Cdd:cd20514    78 TREILSLYELWK 89
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 14-100 8.83e-07

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: 47.98  E-value: 8.83e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585729908  14 EQLQNSPSRKDGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEE 93
Cdd:cd20524    34 ESLKEEDAEPKFLTPEEELLLVRYYEKKLLEFCRAFKLPDSVLATALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVEE 113


                  ....*..
gi 1585729908  94 SPRKARQ 100
Cdd:cd20524   114 FNISIDQ 120
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 153-231 1.45e-06

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: 45.48  E-value: 1.45e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1585729908 153 HPHKFISNYLAALETPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFqvplpENPPWWKAFdADKSGIDE 231
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLE-----ELPRTLKEI-AKVSGVSE 73
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 156-213 1.78e-06

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: 45.28  E-value: 1.78e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1585729908  156 KFISNYLAALETPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLP 213
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPW 58
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
 26-94 9.97e-06

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: 45.20  E-value: 9.97e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1585729908  26 IDEatETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKKSFARFNVKRVAASCVWLASKLEES 94
Cdd:cd20585    71 ADE--ELLMLKYYEQKIQEVCRALRLPNKIQATALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEEY 137
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
 152-223 9.68e-04

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: 38.52  E-value: 9.68e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1585729908 152 EHPHKFISNYLAALETPPELRQEAWNLANDSLR-TTLCVRFKSEVVACGVVYAAAR--RFQVPLP-ENPPWWKAFD 223
Cdd:cd20598     1 EHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHlTTFCLQYKPTVIACVCIHLACKwsNWEIPVStDGKHWWEYVD 76
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 152-224 3.34e-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: 36.60  E-value: 3.34e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1585729908 152 EHPHKFISNYLAALETPPELRQEAWNLANDSLR-TTLCVRFKSEVVACGVVYAAAR--RFQVPLP-ENPPWWKAFDA 224
Cdd:cd20597     1 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHlTTFSLQYTPPVVACVCIHLACKwsNWEIPVStDGKHWWEYVDA 77
 
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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