NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1907109799|ref|XP_036015000|]
View 

cyclin-T1 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 10-147 2.55e-104

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: 298.12  E-value: 2.55e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  10 KRWYFTREQLENSPSRRFGVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALF 89
Cdd:cd20595     1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907109799  90 LAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 147
Cdd:cd20595    81 LAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 138
CYCLIN_SF super family cl40454
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 151-235 7.55e-57

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 cd20597:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 109  Bit Score: 176.81  E-value: 7.55e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799 151 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVT 230
Cdd:cd20597     1 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVT 80


                  ....*
gi 1907109799 231 LELLD 235
Cdd:cd20597    81 LELLD 85
 
Name Accession Description Interval E-value
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 10-147 2.55e-104

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: 298.12  E-value: 2.55e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  10 KRWYFTREQLENSPSRRFGVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALF 89
Cdd:cd20595     1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907109799  90 LAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 147
Cdd:cd20595    81 LAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 138
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 151-235 7.55e-57

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: 176.81  E-value: 7.55e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799 151 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVT 230
Cdd:cd20597     1 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVT 80


                  ....*
gi 1907109799 231 LELLD 235
Cdd:cd20597    81 LELLD 85
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 32-217 1.60e-20

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: 87.87  E-value: 1.60e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  32 DKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPkkleHVIKVAHTC 111
Cdd:COG5333    39 EKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTP----RDISIESFE 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799 112 LHPQESLPDTRSEAYLQQvqdlviLESIILQTLGFELTIDHPHT---HVVKCTQLVrASKDLAQTSYFMATNSLHlTTFS 188
Cdd:COG5333   115 ARDLWSEEPKSSRERILE------YEFELLEALDFDLHVHHPYKyleGFLKDLQEK-DKYKLLQIAWKIINDALR-TDLC 186

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1907109799 189 LQYTPPVVACVCIHLACK------WSNWEIPVSTD 217
Cdd:COG5333   187 LLYPPHIIALAALLIACEvlgmpiIKLLDFVSYET 221
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 12-149 4.69e-17

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: 74.86  E-value: 4.69e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  12 WYFTREQLENSPSRR-FGVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFL 90
Cdd:pfam00134   4 QYLRELELKYLPKPDyMDQQPDINPKMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFI 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  91 AAKVEE-QPKKLEHVIKVAhtclhpqeslpDtrsEAYlqQVQDLVILESIILQTLGFELT 149
Cdd:pfam00134  84 AAKYEEiYPPTVEDLVYIT-----------D---NAY--TREEILRMERLILETLNFDLS 127
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 43-111 1.40e-13

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: 64.15  E-value: 1.40e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907109799   43 NLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKKLEHVIKVAHTC 111
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYF 69
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 1-197 2.23e-07

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: 50.60  E-value: 2.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799   1 MEGERKNNNKRWYFTREQLENSPSRRFGVDSDKELSYRQQAANLLQDMGQRLNVSQLT--INTAIVYMHRFYMIQSFTQF 78
Cdd:TIGR00569  19 QEKRADANAKFREAHEEEEKVLEAKPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTsvVGTAIMYFKRFYLNNSVMEY 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  79 HRYSMAPAALFLAAKVEeqpkklEHVIKVAHTClhpqESLPDTRSEAyLQQVQDlviLESIILQTLGFELTIDHPHTHV- 157
Cdd:TIGR00569  99 HPKIIMLTCVFLACKVE------EFNVSIDQFV----GNLKETPLKA-LEQVLE---YELLLIQQLNFHLIVHNPYRPLe 164

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1907109799 158 -----VKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVA 197
Cdd:TIGR00569 165 gflidIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIA 209
 
Name Accession Description Interval E-value
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 10-147 2.55e-104

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: 298.12  E-value: 2.55e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  10 KRWYFTREQLENSPSRRFGVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALF 89
Cdd:cd20595     1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907109799  90 LAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 147
Cdd:cd20595    81 LAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 138
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 11-147 3.12e-99

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: 285.05  E-value: 3.12e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  11 RWYFTREQLENSPSRRFGVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFL 90
Cdd:cd20538     1 RWYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907109799  91 AAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 147
Cdd:cd20538    81 AAKVEEQPRKLEHVIKVAHACLHRGEPDLDTKSEAYLQQAQELVINENILLQTLGFE 137
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
 11-147 6.44e-89

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: 259.21  E-value: 6.44e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  11 RWYFTREQLENSPSRRFGVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFL 90
Cdd:cd20596     3 RWFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTALFL 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907109799  91 AAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 147
Cdd:cd20596    83 AAKVEEQPRKLEHVIKVAHACLNPLEPQLDTKSDAYLQQAQELVILETIMLQTLGFE 139
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 151-235 7.55e-57

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: 176.81  E-value: 7.55e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799 151 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVT 230
Cdd:cd20597     1 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVT 80


                  ....*
gi 1907109799 231 LELLD 235
Cdd:cd20597    81 LELLD 85
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
 151-235 1.50e-51

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: 163.33  E-value: 1.50e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799 151 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVT 230
Cdd:cd20598     1 EHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVT 80


                  ....*
gi 1907109799 231 LELLD 235
Cdd:cd20598    81 LELLD 85
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 152-235 5.62e-51

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: 161.29  E-value: 5.62e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799 152 HPHTHVVKCTQLVRA-SKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVT 230
Cdd:cd20539     1 HPHTHVLKICNLVKAgSKDLAQTAYFLATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPRSSEGKDWYEYVDPSLT 80


                  ....*
gi 1907109799 231 LELLD 235
Cdd:cd20539    81 LEELD 85
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 28-147 2.51e-42

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: 139.68  E-value: 2.51e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  28 GVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKKLEHVIKV 107
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1907109799 108 AHTCLHPQESlpdtrSEAYLQQVQDLVILESIILQTLGFE 147
Cdd:cd20530    81 ARSLLNDKQF-----AQFGDDPKEEVMVLERILLQTIKFD 115
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 28-147 9.64e-29

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: 105.29  E-value: 9.64e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  28 GVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKKLEHVIKV 107
Cdd:cd20587     2 GIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIVV 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1907109799 108 AHTCLH---PQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 147
Cdd:cd20587    82 SYEIIFkkdPSAAQRIKQKEVYEQQKELVLNGEKLVLSTLGFD 124
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 28-146 3.39e-25

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: 96.09  E-value: 3.39e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  28 GVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKKLEHVIKV 107
Cdd:cd20532     2 GIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVINV 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1907109799 108 AHTCLHPQESLP------DTRSEAYLQQVQDLVILESIILQTLGF 146
Cdd:cd20532    82 FHRLLQRRLGKPaevlplDIGSAEYEELKNDIIKAERRILKELGF 126
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 38-147 9.56e-21

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: 84.14  E-value: 9.56e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  38 RQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPqES 117
Cdd:cd20534     2 HFKVLRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRILHP-DK 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1907109799 118 LPDTRSEAYLQQVQDLVILESIILQTLGFE 147
Cdd:cd20534    81 PPLELDDEYWELRDSIVNCELLLLRILKFD 110
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 32-217 1.60e-20

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: 87.87  E-value: 1.60e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  32 DKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPkkleHVIKVAHTC 111
Cdd:COG5333    39 EKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTP----RDISIESFE 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799 112 LHPQESLPDTRSEAYLQQvqdlviLESIILQTLGFELTIDHPHT---HVVKCTQLVrASKDLAQTSYFMATNSLHlTTFS 188
Cdd:COG5333   115 ARDLWSEEPKSSRERILE------YEFELLEALDFDLHVHHPYKyleGFLKDLQEK-DKYKLLQIAWKIINDALR-TDLC 186

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1907109799 189 LQYTPPVVACVCIHLACK------WSNWEIPVSTD 217
Cdd:COG5333   187 LLYPPHIIALAALLIACEvlgmpiIKLLDFVSYET 221
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 34-148 2.68e-20

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: 82.86  E-value: 2.68e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  34 ELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKKLEHVIKVAHTCLH 113
Cdd:cd20545     1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1907109799 114 PQESLPDTRSEAYLQQVQDLVIL-ESIILQTLGFEL 148
Cdd:cd20545    81 KNPNLVIDEQSKEVWRWRDSILYnEEVLLETLCFDL 116
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 24-146 1.46e-18

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: 78.72  E-value: 1.46e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  24 SRRFGVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKKLEH 103
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1907109799 104 VIKVAHTCLHPQESLP----DTRSEAYLQQVQDLVILESIILQTLGF 146
Cdd:cd20591    81 VLMVFHRMECRRENLPleplEPESKKYDEMKEDLIRTERHLLKEMGF 127
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 12-149 4.69e-17

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: 74.86  E-value: 4.69e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  12 WYFTREQLENSPSRR-FGVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFL 90
Cdd:pfam00134   4 QYLRELELKYLPKPDyMDQQPDINPKMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFI 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  91 AAKVEE-QPKKLEHVIKVAhtclhpqeslpDtrsEAYlqQVQDLVILESIILQTLGFELT 149
Cdd:pfam00134  84 AAKYEEiYPPTVEDLVYIT-----------D---NAY--TREEILRMERLILETLNFDLS 127
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 42-144 6.69e-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: 73.40  E-value: 6.69e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  42 ANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKklehVIKVAHTClhpQESLPDT 121
Cdd:cd20513     6 ANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPS----HARLIVAE---AKVLKTK 78

                          90       100
                  ....*....|....*....|...
gi 1907109799 122 RSEAYLQQVQDLVILESIILQTL 144
Cdd:cd20513    79 FSYEFPYRVNDILECEFYLLEAL 101
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 37-146 7.72e-16

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: 71.22  E-value: 7.72e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  37 YRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQE 116
Cdd:cd20547     1 LRLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNLRHPDK 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1907109799 117 SLPDTRseaYLQQVQDLVI-LESIILQTLGF 146
Cdd:cd20547    81 ISVDDQ---MLEEFRKAILgLERLLLETICF 108
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 17-146 3.63e-14

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: 67.72  E-value: 3.63e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  17 EQLENSPSRRFGVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEE 96
Cdd:cd20590    23 ERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVKHSMEHVSMACVHLASKIEE 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907109799  97 QPKKLEHVIKVAHTCLH---PQESLPDTRSEAYLQQVQDLVILESIILQTLGF 146
Cdd:cd20590   103 APRRIRDVINVFHRLRQlreKKKPVPLILDQEYVNLKNQIIKAERRVLKELGF 155
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 43-111 1.40e-13

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: 64.15  E-value: 1.40e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907109799   43 NLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKKLEHVIKVAHTC 111
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYF 69
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 40-111 1.92e-13

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 63.97  E-value: 1.92e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907109799  40 QAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKKLEHVIKVAHTC 111
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVS 72
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 151-241 1.16e-11

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: 59.66  E-value: 1.16e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799 151 DHPHTHVVKCTQLVRASKD----LAQTSYFMATNSLHlTTFSLQYTPPVVACVCIHLACKWSNWEIP---VSTDGKHWWE 223
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNkiqkLVQMAWTFVNDSLC-TTLCLQWEPEIIAVALMYLAAKLSKFDLQdwtSKPPGKRWWE 79

                          90
                  ....*....|....*...
gi 1907109799 224 YVDATVTLELLDGVpgCH 241
Cdd:cd20531    80 QFVEDVSLEVLEDI--CH 95
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 152-235 1.91e-10

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: 56.22  E-value: 1.91e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799 152 HPHTHVVK-CTQL-VRASKDLAQTSYFMATNSLHlTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKH--WWEYVDA 227
Cdd:cd20546     1 HPYQYLIKfAKKLgVSDPKELAQLAWAFLNDSYR-TPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPNEKLneWWELFGV 79

                          90
                  ....*....|....
gi 1907109799 228 T------VTLELLD 235
Cdd:cd20546    80 DeeeiadAINEILD 93
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 152-228 1.25e-09

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: 53.76  E-value: 1.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799 152 HPHTHVVKCTQLVRA--SKDLAQTSY-FMatNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPvstDGKHWWEYVDAT 228
Cdd:cd20533     1 HPHKFILMYLQVLEGedNKKLAQTAWnYM--NDSLRTDLCVRYPPEVIACACIYLAARELGIPLP---LPPPWWELFDVS 75
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 28-146 8.27e-09

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: 52.44  E-value: 8.27e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  28 GVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKKLEHVIKV 107
Cdd:cd20589     2 GLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVINV 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1907109799 108 AH---TCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGF 146
Cdd:cd20589    82 FHhikQVRGKRTISPLILDQNYINLKNQVIKAERRVLKELGF 123
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 40-96 1.26e-07

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: 48.70  E-value: 1.26e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907109799  40 QAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEE 96
Cdd:cd20571     9 HMSNYIKKLAQHIKVRQRVVATAITYFRRVYTRKSFTEYDPRLVAPTCLYLASKAEE 65
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 1-197 2.23e-07

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: 50.60  E-value: 2.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799   1 MEGERKNNNKRWYFTREQLENSPSRRFGVDSDKELSYRQQAANLLQDMGQRLNVSQLT--INTAIVYMHRFYMIQSFTQF 78
Cdd:TIGR00569  19 QEKRADANAKFREAHEEEEKVLEAKPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTsvVGTAIMYFKRFYLNNSVMEY 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  79 HRYSMAPAALFLAAKVEeqpkklEHVIKVAHTClhpqESLPDTRSEAyLQQVQDlviLESIILQTLGFELTIDHPHTHV- 157
Cdd:TIGR00569  99 HPKIIMLTCVFLACKVE------EFNVSIDQFV----GNLKETPLKA-LEQVLE---YELLLIQQLNFHLIVHNPYRPLe 164

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1907109799 158 -----VKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVA 197
Cdd:TIGR00569 165 gflidIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIA 209
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 10-148 2.30e-06

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: 46.05  E-value: 2.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  10 KRWYFT-REQL-------------------ENSPSRRFGVDSDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRF 69
Cdd:cd20524     7 KHWIFSsEEELaelraeanekareklkeslKEEDAEPKFLTPEEELLLVRYYEKKLLEFCRAFKLPDSVLATALTYFKRF 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907109799  70 YMIQSFTQFHRYSMAPAALFLAAKVEeqpkklEHVIKVAHTClhpqESLPdtRSEAYLQQVQDlviLESIILQTLGFEL 148
Cdd:cd20524    87 YLKNSVMEYHPKEIMLTCLYLACKVE------EFNISIDQFV----GNIK--ESEKTAEIILE---YELLLLQGLNFHL 150
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 152-228 2.04e-05

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: 43.03  E-value: 2.04e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907109799 152 HPHTHVVKCTQLVRASKD--LAQTSYFMATNSLHLTTFsLQYTPPVVACVCIHLACKwsNWEIPVStDGKHWWEYVDAT 228
Cdd:cd20593     1 HPHKIIVMYLQVLECERNrhLVQTSWNYMNDSLRTDVF-VRFNPETIACACIYLAAR--TLEIPLP-NRPHWFLLFGAT 75
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 152-228 7.10e-05

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: 40.59  E-value: 7.10e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907109799 152 HPHTHVVKC-TQLVRASKDLAQTSYFMATNSLHlTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDgKHWWEYVDAT 228
Cdd:cd20588     2 HPYKPLVAAiKKFNVAQNALAQAAWNFVNDGLR-TSLCLQFKPHHIAAGAIFLAAKFLKVKLPCDGR-KVWWQEFDVT 77
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 150-227 2.09e-04

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: 39.46  E-value: 2.09e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907109799 150 IDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHlTTFSLQYTPPVVACVCIHLACKWSNWEIPvstDGKHWWEYVDA 227
Cdd:cd20594     2 VEHPHKFILNYLAMLMAPPELRQEAWNLANDSLR-TTLCVRFKSEVVACGVVYAAARRFQVPLP---ENPPWWKVFDA 75
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 152-228 2.79e-04

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: 39.60  E-value: 2.79e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907109799 152 HPHTHVVKCTQLVRASKD--LAQTSYFMATNSLHLTTFsLQYTPPVVACVCIHLACKwsNWEIPVSTDgKHWWEYVDAT 228
Cdd:cd20592     2 HPHKIIVMYLQVLECERNqtLVQTAWNYMNDSLRTNVF-VRFQPETIACACIYLAAR--ALQIPLPNR-PHWFLLFGAT 76
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
 32-148 9.07e-03

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: 35.96  E-value: 9.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907109799  32 DKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRYSMAPAALFLAAKVEEQPKKLEHVIKVahtc 111
Cdd:cd20585    72 DEELLMLKYYEQKIQEVCRALRLPNKIQATALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEEYHVSAEELGKG---- 147

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1907109799 112 lhpqeslpdtrseayLQQVQDLVI-LESIILQTLGFEL 148
Cdd:cd20585   148 ---------------IQQDHQLILkNELALLQGLNFDL 170
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH