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Conserved domains on  [gi|1845974322|ref|NP_001370392|]
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Cyclin-T1.1 [Caenorhabditis elegans]

Protein Classification

cyclin family protein( domain architecture ID 15751087)

cyclin family protein may associate with and activate its cognate cyclin-dependent kinase (CDK); similar to Caenorhabditis elegans cyclin-T1.1 and cyclin-T1.2

CATH:  1.10.472.10
Gene Ontology:  GO:0000079|GO:0019901
PubMed:  30185601
SCOP:  4001102

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CYCLIN_SF super family cl40454
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 19-160 5.33e-35

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 cd20538:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 137  Bit Score: 127.12  E-value: 5.33e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  19 KWLFTKEEMKKTASIQEGMSREEELASRQMAAAFIQEMIDGLNNvkdpkmkighTGLCV--AHTHMHRFYYLHSFKKYDY 96
Cdd:cd20538     1 RWYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQV----------SQLCIntAIVYMHRFYMFHSFTKFHR 70

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1845974322  97 RDVGAACVFLAGKSQECPRKLSHVISV---WRERKDRKQLTTETARNEAAQIIVLLESMILQTIAFD 160
Cdd:cd20538    71 NSIAAAALFLAAKVEEQPRKLEHVIKVahaCLHRGEPDLDTKSEAYLQQAQELVINENILLQTLGFE 137
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 165-263 5.88e-31

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: 114.68  E-value: 5.88e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322 165 LPHIYVLDIMKKVDKKehYRPLTSCAYYFATDVIAVTDWSLRYSAASMSIVIIHLMAAYANVRIERlfadfINEDSPWYA 244
Cdd:cd20539     1 HPHTHVLKICNLVKAG--SKDLAQTAYFLATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPR-----SSEGKDWYE 73

                          90
                  ....*....|....*....
gi 1845974322 245 KFDETMTNEKLREMEVDFL 263
Cdd:cd20539    74 YVDPSLTLEELDELTSEFL 92
 
Name Accession Description Interval E-value
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 19-160 5.33e-35

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: 127.12  E-value: 5.33e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  19 KWLFTKEEMKKTASIQEGMSREEELASRQMAAAFIQEMIDGLNNvkdpkmkighTGLCV--AHTHMHRFYYLHSFKKYDY 96
Cdd:cd20538     1 RWYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQV----------SQLCIntAIVYMHRFYMFHSFTKFHR 70

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1845974322  97 RDVGAACVFLAGKSQECPRKLSHVISV---WRERKDRKQLTTETARNEAAQIIVLLESMILQTIAFD 160
Cdd:cd20538    71 NSIAAAALFLAAKVEEQPRKLEHVIKVahaCLHRGEPDLDTKSEAYLQQAQELVINENILLQTLGFE 137
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 165-263 5.88e-31

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: 114.68  E-value: 5.88e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322 165 LPHIYVLDIMKKVDKKehYRPLTSCAYYFATDVIAVTDWSLRYSAASMSIVIIHLMAAYANVRIERlfadfINEDSPWYA 244
Cdd:cd20539     1 HPHTHVLKICNLVKAG--SKDLAQTAYFLATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPR-----SSEGKDWYE 73

                          90
                  ....*....|....*....
gi 1845974322 245 KFDETMTNEKLREMEVDFL 263
Cdd:cd20539    74 YVDPSLTLEELDELTSEFL 92
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 67-196 9.29e-09

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: 56.66  E-value: 9.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  67 KMKIGHTGLCVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQECPRklsHVISVWRERKDRKQLTTETARNEAAQIi 146
Cdd:COG5333    58 RLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPR---DISIESFEARDLWSEEPKSSRERILEY- 133

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1845974322 147 vllESMILQTIAFDLNVHLPH---IYVLDIMKKVDKKEhyrpLTSCAYYFATD 196
Cdd:COG5333   134 ---EFELLEALDFDLHVHHPYkylEGFLKDLQEKDKYK----LLQIAWKIIND 179
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 75-162 9.14e-06

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: 44.81  E-value: 9.14e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  75 LCVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQE-CPRKLSHVISVWRERKDRKQlttetarneaaqiIVLLESMI 153
Cdd:pfam00134  52 LYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYEEiYPPTVEDLVYITDNAYTREE-------------ILRMERLI 118


                  ....*....
gi 1845974322 154 LQTIAFDLN 162
Cdd:pfam00134 119 LETLNFDLS 127
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 76-201 4.17e-04

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: 42.13  E-value: 4.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  76 CVAHTHMH---RFYYLHSFKKYDYRDVGAACVFLAGKSQEcprklsHVISVWRERKDRKQlttetARNEAAQIIVLLESM 152
Cdd:TIGR00569  77 SVVGTAIMyfkRFYLNNSVMEYHPKIIMLTCVFLACKVEE------FNVSIDQFVGNLKE-----TPLKALEQVLEYELL 145

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1845974322 153 ILQTIAFDLNVHLP----HIYVLDI---MKKVDKKEHYRP----------LTSCAYYFATDVIAVT 201
Cdd:TIGR00569 146 LIQQLNFHLIVHNPyrplEGFLIDIktrLPGLENPEYLRKhadkflnrtlLTDAYLLYTPSQIALA 211
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 75-123 1.18e-03

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: 37.96  E-value: 1.18e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1845974322   75 LCVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQECPRKLSHVISV 123
Cdd:smart00385  17 LNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHY 65
 
Name Accession Description Interval E-value
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 19-160 5.33e-35

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: 127.12  E-value: 5.33e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  19 KWLFTKEEMKKTASIQEGMSREEELASRQMAAAFIQEMIDGLNNvkdpkmkighTGLCV--AHTHMHRFYYLHSFKKYDY 96
Cdd:cd20538     1 RWYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQV----------SQLCIntAIVYMHRFYMFHSFTKFHR 70

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1845974322  97 RDVGAACVFLAGKSQECPRKLSHVISV---WRERKDRKQLTTETARNEAAQIIVLLESMILQTIAFD 160
Cdd:cd20538    71 NSIAAAALFLAAKVEEQPRKLEHVIKVahaCLHRGEPDLDTKSEAYLQQAQELVINENILLQTLGFE 137
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 165-263 5.88e-31

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: 114.68  E-value: 5.88e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322 165 LPHIYVLDIMKKVDKKehYRPLTSCAYYFATDVIAVTDWSLRYSAASMSIVIIHLMAAYANVRIERlfadfINEDSPWYA 244
Cdd:cd20539     1 HPHTHVLKICNLVKAG--SKDLAQTAYFLATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPR-----SSEGKDWYE 73

                          90
                  ....*....|....*....
gi 1845974322 245 KFDETMTNEKLREMEVDFL 263
Cdd:cd20539    74 YVDPSLTLEELDELTSEFL 92
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
 18-160 1.46e-25

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: 101.66  E-value: 1.46e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  18 TKWLFTKEEMKKTASIQEGMSREEELASRQMAAAFIQEMIDGLNnvkdpkmkIGHTGLCVAHTHMHRFYYLHSFKKYDYR 97
Cdd:cd20596     2 SRWFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLN--------VSQLTINTAIVYMHRFYMHHSFTKFHRN 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1845974322  98 DVGAACVFLAGKSQECPRKLSHVISVWRE--RKDRKQLTTET-ARNEAAQIIVLLESMILQTIAFD 160
Cdd:cd20596    74 IISPTALFLAAKVEEQPRKLEHVIKVAHAclNPLEPQLDTKSdAYLQQAQELVILETIMLQTLGFE 139
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 19-160 2.34e-25

first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor essential for HIV-1 replication in CD4 T cells and macrophages. It is a regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin-T1) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to productive elongation by phosphorylating the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNA Pol II). CCNT1 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410298 [Multi-domain]  Cd Length: 138  Bit Score: 100.90  E-value: 2.34e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  19 KWLFTKEEMKKTASIQEGMSREEELASRQMAAAFIQEMIDGLNnvkdpkmkIGHTGLCVAHTHMHRFYYLHSFKKYDYRD 98
Cdd:cd20595     2 RWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLN--------VSQLTINTAIVYMHRFYMIQSFTQFHRNS 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1845974322  99 VGAACVFLAGKSQECPRKLSHVISVWRERKDRKQLTTETaRNEA----AQIIVLLESMILQTIAFD 160
Cdd:cd20595    74 VAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDT-RSEAylqqVQDLVILESIILQTLGFE 138
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 36-160 6.00e-22

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: 90.76  E-value: 6.00e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  36 GMSREEELASRQMAAAFIQEMidGLnnvkdpKMKIGHTGLCVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQECPR 115
Cdd:cd20530     1 GIDPETEARYRREGARFIQDV--GT------KLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPK 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1845974322 116 KLSHVISVWRERKDRKQLTT--ETARNEaaqiIVLLESMILQTIAFD 160
Cdd:cd20530    73 KCKDIIKTARSLLNDKQFAQfgDDPKEE----VMVLERILLQTIKFD 115
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 67-161 1.72e-14

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: 69.76  E-value: 1.72e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  67 KMKIGHTGLCVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQECPRKLSHVISVWrERKDRKQLTTETARNEAA--- 143
Cdd:cd20545    18 RLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIAC-AKVAQKNPNLVIDEQSKEvwr 96

                          90       100
                  ....*....|....*....|
gi 1845974322 144 --QIIVLLESMILQTIAFDL 161
Cdd:cd20545    97 wrDSILYNEEVLLETLCFDL 116
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 78-125 3.69e-13

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: 66.04  E-value: 3.69e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1845974322  78 AHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQECPRKLSHVISVWR 125
Cdd:cd20532    36 AQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVINVFH 83
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 35-160 1.07e-10

first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; CycTs associate with their partner cyclin-dependent kinases (CDKs) to trigger their kinase activity. CycTs show high sequence similarity with metazoan cyclin-K (CCNK). CycTs contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410290 [Multi-domain]  Cd Length: 124  Bit Score: 59.07  E-value: 1.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  35 EGMSREEELASRQMAAAFIQEMIDGLNNvkdPKMKIGhtglcVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQECP 114
Cdd:cd20587     1 DGIDLKKETYLRKSYCTFLQDLGMRLKV---PQVTIA-----TAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETP 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1845974322 115 RKLSHVISVWRERKDRKQLTTETAR------NEAAQIIVLLESMILQTIAFD 160
Cdd:cd20587    73 RPLKDVIVVSYEIIFKKDPSAAQRIkqkevyEQQKELVLNGEKLVLSTLGFD 124
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 67-196 9.29e-09

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: 56.66  E-value: 9.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  67 KMKIGHTGLCVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQECPRklsHVISVWRERKDRKQLTTETARNEAAQIi 146
Cdd:COG5333    58 RLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPR---DISIESFEARDLWSEEPKSSRERILEY- 133

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1845974322 147 vllESMILQTIAFDLNVHLPH---IYVLDIMKKVDKKEhyrpLTSCAYYFATD 196
Cdd:COG5333   134 ---EFELLEALDFDLHVHHPYkylEGFLKDLQEKDKYK----LLQIAWKIIND 179
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 76-160 3.52e-08

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


Pssm-ID: 410237 [Multi-domain]  Cd Length: 110  Bit Score: 51.40  E-value: 3.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  76 CVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQECPRKLSHVISVWRE--RKDRKQLTTETARNEAAQIIVLLESMI 153
Cdd:cd20534    24 ATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRilHPDKPPLELDDEYWELRDSIVNCELLL 103


                  ....*..
gi 1845974322 154 LQTIAFD 160
Cdd:cd20534   104 LRILKFD 110
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 83-160 5.92e-08

first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar proteins; CTK2, also called CTD kinase subunit beta, CTDK-I subunit beta, or CTD kinase 38 kDa subunit, is the cyclin subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. CTK2 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410250 [Multi-domain]  Cd Length: 110  Bit Score: 50.81  E-value: 5.92e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1845974322  83 HRFYYLHSFKKYDYRDVGAACVFLAGKSQECPRKLSHVISVWRERKDRKQLTTETARNEAAQIIVL-LESMILQTIAFD 160
Cdd:cd20547    31 QRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNLRHPDKISVDDQMLEEFRKAILgLERLLLETICFD 109
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 21-159 6.33e-08

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: 51.93  E-value: 6.33e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  21 LFTKEEMKKTASIQEGMSREEELASRQMAAAFIQEMidGLnnvkdpKMKIGHTGLCVAHTHMHRFYYLHSFKKYDYRDVG 100
Cdd:cd20590    19 LLPEERLRFTPSMSSGLDVDTETDLRVVGCELIQAA--GI------LLRLPQVAMATGQVLFQRFFYTKSFVKHSMEHVS 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1845974322 101 AACVFLAGKSQECPRKLSHVISVW---RERKDRKQLTTETARNEAAQI---IVLLESMILQTIAF 159
Cdd:cd20590    91 MACVHLASKIEEAPRRIRDVINVFhrlRQLREKKKPVPLILDQEYVNLknqIIKAERRVLKELGF 155
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 83-136 3.32e-07

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: 49.06  E-value: 3.32e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1845974322  83 HRFYYLHSFKKYDYRDVGAACVFLAGKSQECPRKLSHVISVW-RERKDRKQLTTE 136
Cdd:cd20591    44 QRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQVLMVFhRMECRRENLPLE 98
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 67-123 1.19e-06

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


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 46.25  E-value: 1.19e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1845974322  67 KMKIGHTGLCVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQECPRKLSHVISV 123
Cdd:cd00043    12 KLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKV 68
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 68-131 2.16e-06

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


Pssm-ID: 410292 [Multi-domain]  Cd Length: 124  Bit Score: 46.66  E-value: 2.16e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1845974322  68 MKIGHTGLCVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQECPRKLSHVISVWRERKDRK 131
Cdd:cd20589    26 LRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVINVFHHIKQVR 89
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 75-162 9.14e-06

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: 44.81  E-value: 9.14e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  75 LCVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQE-CPRKLSHVISVWRERKDRKQlttetarneaaqiIVLLESMI 153
Cdd:pfam00134  52 LYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYEEiYPPTVEDLVYITDNAYTREE-------------ILRMERLI 118


                  ....*....
gi 1845974322 154 LQTIAFDLN 162
Cdd:pfam00134 119 LETLNFDLS 127
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 78-114 2.45e-05

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: 42.97  E-value: 2.45e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1845974322  78 AHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQECP 114
Cdd:cd20513    26 AIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECP 62
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
 29-161 1.47e-04

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: 42.51  E-value: 1.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  29 KTASIQEGMSREEELASRQMAAAFIQEmidglnnvKDPKMKIGHTGLCVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAG 108
Cdd:cd20585    61 KAAKLPEPLSADEELLMLKYYEQKIQE--------VCRALRLPNKIQATALLYFKRFYLQWSVMEHDPKRIMLTCIYLAC 132

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1845974322 109 KSQEcprklSHVISvwrerkdrkqltTETAR--NEAAQIIVLLESMILQTIAFDL 161
Cdd:cd20585   133 KVEE-----YHVSA------------EELGKgiQQDHQLILKNELALLQGLNFDL 170
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 76-201 4.17e-04

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: 42.13  E-value: 4.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  76 CVAHTHMH---RFYYLHSFKKYDYRDVGAACVFLAGKSQEcprklsHVISVWRERKDRKQlttetARNEAAQIIVLLESM 152
Cdd:TIGR00569  77 SVVGTAIMyfkRFYLNNSVMEYHPKIIMLTCVFLACKVEE------FNVSIDQFVGNLKE-----TPLKALEQVLEYELL 145

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1845974322 153 ILQTIAFDLNVHLP----HIYVLDI---MKKVDKKEHYRP----------LTSCAYYFATDVIAVT 201
Cdd:TIGR00569 146 LIQQLNFHLIVHNPyrplEGFLIDIktrLPGLENPEYLRKhadkflnrtlLTDAYLLYTPSQIALA 211
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 166-263 9.80e-04

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: 38.91  E-value: 9.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322 166 PHIYVLDIMKKVDKKehyRPLTSCAYYFATDVIAVTDWSLRYSAASMSIVIIHLMAAYANVRIErlfadFINEDSPWYAK 245
Cdd:cd20597     3 PHTHVVKCTQLVRAS---KDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIP-----VSTDGKHWWEY 74

                          90
                  ....*....|....*...
gi 1845974322 246 FDETMTNEKLREMEVDFL 263
Cdd:cd20597    75 VDATVTLELLDELTHEFL 92
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 75-123 1.18e-03

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: 37.96  E-value: 1.18e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1845974322   75 LCVAHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQECPRKLSHVISV 123
Cdd:smart00385  17 LNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHY 65
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 78-161 3.83e-03

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: 37.96  E-value: 3.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845974322  78 AHTHMHRFYYLHSFKKYDYRDVGAACVFLAGKSQEcprklsHVISVwrerkdrKQLTTETARNE-AAQIIVLLESMILQT 156
Cdd:cd20524    79 ALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVEE------FNISI-------DQFVGNIKESEkTAEIILEYELLLLQG 145


                  ....*
gi 1845974322 157 IAFDL 161
Cdd:cd20524   146 LNFHL 150
 
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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