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Conserved domains on  [gi|375298703|ref|NP_001243540|]
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cyclin-T1 [Danio rerio]

Protein Classification

cyclin-T1( domain architecture ID 15334822)

cyclin-T1 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)

Graphical summary

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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 ...
 13-150 2.67e-100

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: 302.74  E-value: 2.67e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  13 NKWYFTREQIENSPSRRAGLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALF 92
Cdd:cd20595    1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 375298703  93 LAAKVEEQPRKLEHVIKVTHACLNPQDPSPDTRSDTYLQQAQDLVILESIILQTLGFE 150
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 ...
 154-262 8.79e-74

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: 233.05  E-value: 8.79e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 154 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYSPPIVACVCIHLACKWSNWEIPVSTDGKHWWQYVDPTVT 233
Cdd:cd20597    1 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVT 80

                         90       100
                 ....*....|....*....|....*....
gi 375298703 234 LELLDELTHEFLQILEKTPSRLKRTRNWK 262
Cdd:cd20597   81 LELLDELTHEFLQILEKTPNRLKRIWNWR 109
 
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 ...
 13-150 2.67e-100

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: 302.74  E-value: 2.67e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  13 NKWYFTREQIENSPSRRAGLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALF 92
Cdd:cd20595    1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 375298703  93 LAAKVEEQPRKLEHVIKVTHACLNPQDPSPDTRSDTYLQQAQDLVILESIILQTLGFE 150
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 ...
 154-262 8.79e-74

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: 233.05  E-value: 8.79e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 154 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYSPPIVACVCIHLACKWSNWEIPVSTDGKHWWQYVDPTVT 233
Cdd:cd20597    1 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVT 80

                         90       100
                 ....*....|....*....|....*....
gi 375298703 234 LELLDELTHEFLQILEKTPSRLKRTRNWK 262
Cdd:cd20597   81 LELLDELTHEFLQILEKTPNRLKRIWNWR 109
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 22-220 1.07e-19

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: 90.18  E-value: 1.07e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  22 IENSPS-RRAGLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQ 100
Cdd:COG5333   25 IELDLLvLEPELTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDT 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 101 PRKlehvIKVTHACLNPQDPSPDTRSDTYLQQaqdlviLESIILQTLGFEITIDHPHT---HVVKCTQLVrASKDLAQTS 177
Cdd:COG5333  105 PRD----ISIESFEARDLWSEEPKSSRERILE------YEFELLEALDFDLHVHHPYKyleGFLKDLQEK-DKYKLLQIA 173

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 375298703 178 YFMATNSLHlTTFCLQYSPPIVACVCIHLACK------WSNWEIPVSTD 220
Cdd:COG5333  174 WKIINDALR-TDLCLLYPPHIIALAALLIACEvlgmpiIKLLDFVSYET 221
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 15-152 2.83e-18

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: 81.41  E-value: 2.83e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703   15 WYFTREQIENSPSRRaGLD--PDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALF 92
Cdd:pfam00134   4 QYLRELELKYLPKPD-YMDqqPDINPKMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLF 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 375298703   93 LAAKVEE-QPRKLEHVIKVThaclnpqDpspdtrsDTYlqQAQDLVILESIILQTLGFEIT 152
Cdd:pfam00134  83 IAAKYEEiYPPTVEDLVYIT-------D-------NAY--TREEILRMERLILETLNFDLS 127
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 46-114 4.00e-15

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: 70.70  E-value: 4.00e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 375298703    46 NLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQPRKLEHVIKVTHAC 114
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYF 69
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 19-200 4.44e-08

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: 55.23  E-value: 4.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703   19 REQIENSPSRRAGLDPDKELLYRQQAANLLQDMGQRLNVSQLT--INTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAK 96
Cdd:TIGR00569  34 EEEEKVLEAKPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTsvVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACK 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703   97 VEeqprklEHVIKVTHACLNPQDpSPDTRSDTYLQqaqdlviLESIILQTLGFEITIDHPHTHV------VKCTQLVRAS 170
Cdd:TIGR00569 114 VE------EFNVSIDQFVGNLKE-TPLKALEQVLE-------YELLLIQQLNFHLIVHNPYRPLegflidIKTRLPGLEN 179

                         170       180       190
                  ....*....|....*....|....*....|
gi 375298703  171 KDLAQTSYFMATNSLHLTTFCLQYSPPIVA 200
Cdd:TIGR00569 180 PEYLRKHADKFLNRTLLTDAYLLYTPSQIA 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 ...
 13-150 2.67e-100

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: 302.74  E-value: 2.67e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  13 NKWYFTREQIENSPSRRAGLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALF 92
Cdd:cd20595    1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 375298703  93 LAAKVEEQPRKLEHVIKVTHACLNPQDPSPDTRSDTYLQQAQDLVILESIILQTLGFE 150
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, ...
 14-150 9.00e-93

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: 283.13  E-value: 9.00e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  14 KWYFTREQIENSPSRRAGLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFL 93
Cdd:cd20538    1 RWYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFL 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 375298703  94 AAKVEEQPRKLEHVIKVTHACLNPQDPSPDTRSDTYLQQAQDLVILESIILQTLGFE 150
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 ...
 13-150 5.72e-87

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: 268.45  E-value: 5.72e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  13 NKWYFTREQIENSPSRRAGLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALF 92
Cdd:cd20596    2 SRWFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTALF 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 375298703  93 LAAKVEEQPRKLEHVIKVTHACLNPQDPSPDTRSDTYLQQAQDLVILESIILQTLGFE 150
Cdd:cd20596   82 LAAKVEEQPRKLEHVIKVAHACLNPLEPQLDTKSDAYLQQAQELVILETIMLQTLGFE 139
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 154-262 8.79e-74

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: 233.05  E-value: 8.79e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 154 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYSPPIVACVCIHLACKWSNWEIPVSTDGKHWWQYVDPTVT 233
Cdd:cd20597    1 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVT 80

                         90       100
                 ....*....|....*....|....*....
gi 375298703 234 LELLDELTHEFLQILEKTPSRLKRTRNWK 262
Cdd:cd20597   81 LELLDELTHEFLQILEKTPNRLKRIWNWR 109
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
 154-263 6.57e-69

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: 220.34  E-value: 6.57e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 154 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYSPPIVACVCIHLACKWSNWEIPVSTDGKHWWQYVDPTVT 233
Cdd:cd20598    1 EHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVT 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 375298703 234 LELLDELTHEFLQILEKTPSRLKRTRNWKA 263
Cdd:cd20598   81 LELLDELTHEFLQILEKTPSRLKRIRNWRA 110
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 155-245 1.61e-55

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: 183.63  E-value: 1.61e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 155 HPHTHVVKCTQLVRA-SKDLAQTSYFMATNSLHLTTFCLQYSPPIVACVCIHLACKWSNWEIPVSTDGKHWWQYVDPTVT 233
Cdd:cd20539    1 HPHTHVLKICNLVKAgSKDLAQTAYFLATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPRSSEGKDWYEYVDPSLT 80

                         90
                 ....*....|..
gi 375298703 234 LELLDELTHEFL 245
Cdd:cd20539   81 LEELDELTSEFL 92
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 31-150 4.38e-39

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: 4.38e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  31 GLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQPRKLEHVIKV 110
Cdd:cd20530    1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 375298703 111 THACLNPQDPSpdtrsdTYLQQAQDLVI-LESIILQTLGFE 150
Cdd:cd20530   81 ARSLLNDKQFA------QFGDDPKEEVMvLERILLQTIKFD 115
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 31-150 3.93e-30

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: 114.92  E-value: 3.93e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  31 GLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQPRKLEHVIKV 110
Cdd:cd20587    2 GIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIVV 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 375298703 111 THACLNPQDPSPDTR---SDTYLQQAQDLVILESIILQTLGFE 150
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 ...
 31-149 7.32e-27

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: 105.72  E-value: 7.32e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  31 GLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQPRKLEHVIKV 110
Cdd:cd20532    2 GIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVINV 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 375298703 111 THACLN------PQDPSPDTRSDTYLQQAQDLVILESIILQTLGF 149
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 ...
 41-150 2.14e-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: 86.84  E-value: 2.14e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  41 RQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQPRKLEHVIKVTHACLNPQDP 120
Cdd:cd20534    2 HFKVLRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRILHPDKP 81

                         90       100       110
                 ....*....|....*....|....*....|
gi 375298703 121 sPDTRSDTYLQQAQDLVILESIILQTLGFE 150
Cdd:cd20534   82 -PLELDDEYWELRDSIVNCELLLLRILKFD 110
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 22-220 1.07e-19

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: 90.18  E-value: 1.07e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  22 IENSPS-RRAGLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQ 100
Cdd:COG5333   25 IELDLLvLEPELTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDT 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 101 PRKlehvIKVTHACLNPQDPSPDTRSDTYLQQaqdlviLESIILQTLGFEITIDHPHT---HVVKCTQLVrASKDLAQTS 177
Cdd:COG5333  105 PRD----ISIESFEARDLWSEEPKSSRERILE------YEFELLEALDFDLHVHHPYKyleGFLKDLQEK-DKYKLLQIA 173

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 375298703 178 YFMATNSLHlTTFCLQYSPPIVACVCIHLACK------WSNWEIPVSTD 220
Cdd:COG5333  174 WKIINDALR-TDLCLLYPPHIIALAALLIACEvlgmpiIKLLDFVSYET 221
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 37-151 1.15e-18

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: 82.09  E-value: 1.15e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  37 ELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQPRKLEHVIKVThACLN 116
Cdd:cd20545    1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIAC-AKVA 79

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 375298703 117 PQDPSP--DTRSDTYLQQaQDLVIL-ESIILQTLGFEI 151
Cdd:cd20545   80 QKNPNLviDEQSKEVWRW-RDSILYnEEVLLETLCFDL 116
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 15-152 2.83e-18

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: 81.41  E-value: 2.83e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703   15 WYFTREQIENSPSRRaGLD--PDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALF 92
Cdd:pfam00134   4 QYLRELELKYLPKPD-YMDqqPDINPKMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLF 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 375298703   93 LAAKVEE-QPRKLEHVIKVThaclnpqDpspdtrsDTYlqQAQDLVILESIILQTLGFEIT 152
Cdd:pfam00134  83 IAAKYEEiYPPTVEDLVYIT-------D-------NAY--TREEILRMERLILETLNFDLS 127
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 27-149 1.73e-17

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: 79.11  E-value: 1.73e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  27 SRRAGLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQPRKLEH 106
Cdd:cd20591    1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 375298703 107 VIKVTHACLNPQDPSP----DTRSDTYLQQAQDLVILESIILQTLGF 149
Cdd:cd20591   81 VLMVFHRMECRRENLPleplEPESKKYDEMKEDLIRTERHLLKEMGF 127
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 45-116 1.66e-15

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: 72.63  E-value: 1.66e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 375298703  45 ANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQPRklehVIKVTHACLN 116
Cdd:cd20513    6 ANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPS----HARLIVAEAK 73
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 46-114 4.00e-15

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: 70.70  E-value: 4.00e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 375298703    46 NLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQPRKLEHVIKVTHAC 114
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYF 69
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 43-112 1.29e-14

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: 69.36  E-value: 1.29e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  43 QAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQPRKLEHVIKVTH 112
Cdd:cd00043    1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSG 70
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 154-249 1.44e-14

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: 69.67  E-value: 1.44e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 154 DHPHTHVVKCTQLVRASKD----LAQTSYFMATNSLHlTTFCLQYSPPIVACVCIHLACKWSNWEIP---VSTDGKHWWQ 226
Cdd:cd20531    1 EHPYKYLLKYAKQLKGDKNkiqkLVQMAWTFVNDSLC-TTLCLQWEPEIIAVALMYLAAKLSKFDLQdwtSKPPGKRWWE 79

                         90       100
                 ....*....|....*....|...
gi 375298703 227 YVDPTVTLELLDELTHeflQILE 249
Cdd:cd20531   80 QFVEDVSLEVLEDICH---QVLD 99
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 20-149 1.76e-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: 71.58  E-value: 1.76e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  20 EQIENSPSRRAGLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEE 99
Cdd:cd20590   23 ERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVKHSMEHVSMACVHLASKIEE 102

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 375298703 100 QPRKLEHVIKVTH---ACLNPQDPSPDTRSDTYLQQAQDLVILESIILQTLGF 149
Cdd:cd20590  103 APRRIRDVINVFHrlrQLREKKKPVPLILDQEYVNLKNQIIKAERRVLKELGF 155
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 40-149 4.26e-13

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: 65.83  E-value: 4.26e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  40 YRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQPRKLEHVIKVTHACLNPQD 119
Cdd:cd20547    1 LRLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNLRHPDK 80

                         90       100       110
                 ....*....|....*....|....*....|.
gi 375298703 120 PSPDtrsDTYLQQAQDLVI-LESIILQTLGF 149
Cdd:cd20547   81 ISVD---DQMLEEFRKAILgLERLLLETICF 108
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 31-149 1.11e-12

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: 65.15  E-value: 1.11e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  31 GLDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEEQPRKLEHVIKV 110
Cdd:cd20589    2 GLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVINV 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 375298703 111 TH---ACLNPQDPSPDTRSDTYLQQAQDLVILESIILQTLGF 149
Cdd:cd20589   82 FHhikQVRGKRTISPLILDQNYINLKNQVIKAERRVLKELGF 123
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 155-246 2.58e-12

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: 63.15  E-value: 2.58e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 155 HPHTHVVK-CTQL-VRASKDLAQTSYFMATNSLHlTTFCLQYSPPIVACVCIHLACKWSNWEIPVSTDGKH--WWQYVDp 230
Cdd:cd20546    1 HPYQYLIKfAKKLgVSDPKELAQLAWAFLNDSYR-TPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPNEKLneWWELFG- 78

                         90
                 ....*....|....*.
gi 375298703 231 tVTLELLDELTHEFLQ 246
Cdd:cd20546   79 -VDEEEIADAINEILD 93
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 155-249 2.69e-10

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: 57.23  E-value: 2.69e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 155 HPHTHVVKCTQLVRA--SKDLAQTSY-FMatNSLHLTTFCLQYSPPIVACVCIHLACKWSNWEIPvstDGKHWWQYVDpt 231
Cdd:cd20533    1 HPHKFILMYLQVLEGedNKKLAQTAWnYM--NDSLRTDLCVRYPPEVIACACIYLAARELGIPLP---LPPPWWELFD-- 73

                         90
                 ....*....|....*...
gi 375298703 232 VTLELLDELThefLQILE 249
Cdd:cd20533   74 VSKEDIEEIC---LTILE 88
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 4-105 7.40e-09

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: 54.91  E-value: 7.40e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703   4 SFPSPSQ-------NNNKwyfTREQIENSPSRRAG----LDPDKELLYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRF 72
Cdd:cd20524   10 IFSSEEElaelraeANEK---AREKLKESLKEEDAepkfLTPEEELLLVRYYEKKLLEFCRAFKLPDSVLATALTYFKRF 86

                         90       100       110
                 ....*....|....*....|....*....|...
gi 375298703  73 YMVQSFTRFHRNVIAPAALFLAAKVEEQPRKLE 105
Cdd:cd20524   87 YLKNSVMEYHPKEIMLTCLYLACKVEEFNISID 119
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 155-249 1.16e-08

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: 52.92  E-value: 1.16e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 155 HPHTHVVKC-TQLVRASKDLAQTSYFMATNSLHlTTFCLQYSPPIVACVCIHLACKWSNWEIPVSTDgKHWWQYVDptVT 233
Cdd:cd20588    2 HPYKPLVAAiKKFNVAQNALAQAAWNFVNDGLR-TSLCLQFKPHHIAAGAIFLAAKFLKVKLPCDGR-KVWWQEFD--VT 77

                         90
                 ....*....|....*.
gi 375298703 234 LELLDELTHEFLQILE 249
Cdd:cd20588   78 PRQLEEVSNQMLELYE 93
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 39-99 2.08e-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: 52.55  E-value: 2.08e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 375298703  39 LYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAKVEE 99
Cdd:cd20571    5 LIKIHMSNYIKKLAQHIKVRQRVVATAITYFRRVYTRKSFTEYDPRLVAPTCLYLASKAEE 65
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 155-247 4.21e-08

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


Pssm-ID: 410238 [Multi-domain]  Cd Length: 104  Bit Score: 51.49  E-value: 4.21e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 155 HPHTHVVKCTQLVR--------ASKDLAQTSYFMATNSLHlTTFCLQYSPPIVACVCIHLACKWSNWEIPVSTDG-KHWW 225
Cdd:cd20535    1 LPHKYLLHYLKSLRdwlnpefwSRSPIAKTAWSLLRDFYH-SPLCLQFKPQHIALAVIYLALQVYGVKVPPEEEAeKPWW 79

                         90       100
                 ....*....|....*....|..
gi 375298703 226 QYVDPTVTLELLDELTHEFLQI 247
Cdd:cd20535   80 QAFCEDLTKETIDEIIEDIINV 101
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 19-200 4.44e-08

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: 55.23  E-value: 4.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703   19 REQIENSPSRRAGLDPDKELLYRQQAANLLQDMGQRLNVSQLT--INTAIVYMHRFYMVQSFTRFHRNVIAPAALFLAAK 96
Cdd:TIGR00569  34 EEEEKVLEAKPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTsvVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACK 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703   97 VEeqprklEHVIKVTHACLNPQDpSPDTRSDTYLQqaqdlviLESIILQTLGFEITIDHPHTHV------VKCTQLVRAS 170
Cdd:TIGR00569 114 VE------EFNVSIDQFVGNLKE-TPLKALEQVLE-------YELLLIQQLNFHLIVHNPYRPLegflidIKTRLPGLEN 179

                         170       180       190
                  ....*....|....*....|....*....|
gi 375298703  171 KDLAQTSYFMATNSLHLTTFCLQYSPPIVA 200
Cdd:TIGR00569 180 PEYLRKHADKFLNRTLLTDAYLLYTPSQIA 209
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 155-225 3.10e-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: 43.80  E-value: 3.10e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 375298703 155 HPHTHVVKCTQLVRASKD--LAQTSYFMATNSLHLTTFcLQYSPPIVACVCIHLACKwsNWEIPVStDGKHWW 225
Cdd:cd20593    1 HPHKIIVMYLQVLECERNrhLVQTSWNYMNDSLRTDVF-VRFNPETIACACIYLAAR--TLEIPLP-NRPHWF 69
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 153-229 1.13e-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: 41.77  E-value: 1.13e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 375298703 153 IDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHlTTFCLQYSPPIVACVCIHLACKWSNWEIPvstDGKHWWQYVD 229
Cdd:cd20594    2 VEHPHKFILNYLAMLMAPPELRQEAWNLANDSLR-TTLCVRFKSEVVACGVVYAAARRFQVPLP---ENPPWWKVFD 74
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 155-240 2.47e-04

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: 40.30  E-value: 2.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703 155 HPHTHVVKCTQLVRASKDLAQTSYFMATNSLHlTTFCLQYSPPIVACVCIHLACkwsnweIPVSTDGKHWWQ--YVDPTV 232
Cdd:cd20514    1 HPYRPLTQYVQDAGLDDELLPLAWRIVNDSYR-TDVCLLYPPYLIALACLHMAC------VLLQKDARQWFAelNVDMDK 73


                 ....*...
gi 375298703 233 TLELLDEL 240
Cdd:cd20514   74 ILEITREI 81
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 155-225 5.23e-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: 40.37  E-value: 5.23e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 375298703 155 HPHTHVVKCTQLVRASKD--LAQTSYFMATNSLHLTTFcLQYSPPIVACVCIHLACKwsNWEIPVSTDgKHWW 225
Cdd:cd20592    2 HPHKIIVMYLQVLECERNqtLVQTAWNYMNDSLRTNVF-VRFQPETIACACIYLAAR--ALQIPLPNR-PHWF 70
CYCLIN_CCNE_rpt1 cd20519
first cyclin box found in G1/S-specific cyclin-E (CCNE) family; The CCNE family includes two ...
 67-149 7.70e-03

first cyclin box found in G1/S-specific cyclin-E (CCNE) family; The CCNE family includes two E-type cyclins, CCNE1 and CCNE2. CCNE1 is essential for the control of the cell cycle at the G1/S (start) transition. It interacts with CDK2 protein kinase to form a serine/threonine kinase holoenzyme complex. CCNE2 is essential for the control of the cell cycle at the late G1 and early S phase. It interacts with the CDK2 (in vivo) and CDK3 (in vitro) protein kinases to form a serine/threonine kinase holoenzyme complexes. 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: 410223  Cd Length: 131  Bit Score: 37.29  E-value: 7.70e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375298703  67 VY-MHR--FYMVQSFT-RF---HRNV-------IAPAALFLAAKVEE-QPRKLEHVIKVTH-AClnpqdpspdtrsdtyl 130
Cdd:cd20519   50 VYrLHRetFYLAVDFVdRYlstQTNVpktqlqlIGITCLFIAAKLEEiYPPKLSEFAYVTDgAC---------------- 113

                         90
                 ....*....|....*....
gi 375298703 131 qQAQDLVILESIILQTLGF 149
Cdd:cd20519  114 -TEDEILTMELIILKALNW 131
 
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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