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Conserved domains on  [gi|9945320|ref|NP_064703|]
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cyclin-L1 isoform 1 [Homo sapiens]

Protein Classification

cyclin family protein( domain architecture ID 1750054)

cyclin family protein may associate with and activate its cognate cyclin-dependent kinase (CDK)

CATH:  1.10.472.10
Gene Ontology:  GO:0000079|GO:0019901|GO:0007049
PubMed:  14744433|30185601|15269391|15840440
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 ...
 40-195 1.98e-90

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 cd20590:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 156  Bit Score: 273.81  E-value: 1.98e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   40 ILIGDRLYSEVSLTIDHSLIPEERLSPTPSMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKS 119
Cdd:cd20590   1 VLIGDRLYSGVLITLENCLLPEERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKS 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9945320  120 FVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQLRGKRTPSPLILDQNYINTKNQVIKAERRVLKELGFC 195
Cdd:cd20590  81 FVKHSMEHVSMACVHLASKIEEAPRRIRDVINVFHRLRQLREKKKPVPLILDQEYVNLKNQIIKAERRVLKELGFC 156
CYCLIN_SF super family cl40454
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 199-321 4.36e-85

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 cd20592:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 123  Bit Score: 258.77  E-value: 4.36e-85
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320  199 KHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEI 278
Cdd:cd20592   1 KHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPNRPHWFLLFGATEEEI 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 9945320  279 QEICIETLRLYTRKKPNYELLEKEVEKRKVALQEAKLKAKGLN 321
Cdd:cd20592  81 QEICITTLKLYTRKKPNYEFLEKEVEKRKVALQEAKLKAKGLN 123
 
Name Accession Description Interval E-value
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 40-195 1.98e-90

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: 273.81  E-value: 1.98e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   40 ILIGDRLYSEVSLTIDHSLIPEERLSPTPSMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKS 119
Cdd:cd20590   1 VLIGDRLYSGVLITLENCLLPEERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKS 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9945320  120 FVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQLRGKRTPSPLILDQNYINTKNQVIKAERRVLKELGFC 195
Cdd:cd20590  81 FVKHSMEHVSMACVHLASKIEEAPRRIRDVINVFHRLRQLREKKKPVPLILDQEYVNLKNQIIKAERRVLKELGFC 156
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 199-321 4.36e-85

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: 258.77  E-value: 4.36e-85
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320  199 KHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEI 278
Cdd:cd20592   1 KHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPNRPHWFLLFGATEEEI 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 9945320  279 QEICIETLRLYTRKKPNYELLEKEVEKRKVALQEAKLKAKGLN 321
Cdd:cd20592  81 QEICITTLKLYTRKKPNYEFLEKEVEKRKVALQEAKLKAKGLN 123
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 74-274 6.30e-30

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: 119.07  E-value: 6.30e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   74 LDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRdvinvf 153
Cdd:COG5333  36 LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDIS------ 109

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320  154 hhLRQLRgKRTPSPLILDqnyiNTKNQVIKAERRVLKELGFCVHVKHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLR 233
Cdd:COG5333 110 --IESFE-ARDLWSEEPK----SSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALR 182

                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 9945320  234 TNVFVRFQPETIACACIYLAARAlqIPLPTRPHWFLLFGTT 274
Cdd:COG5333 183 TDLCLLYPPHIIALAALLIACEV--LGMPIIKLLDFVSYET 221
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 205-274 3.29e-10

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: 56.45  E-value: 3.29e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320     205 IVMYLQVLECerNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTT 274
Cdd:smart00385   3 LRRVCKALNL--DPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFT 70
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 90-190 4.56e-08

domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 50.28  E-value: 4.56e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320      90 IQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHhlrqlrgkrtpspli 169
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTG--------------- 67

                           90       100
                   ....*....|....*....|.
gi 9945320     170 ldqnyINTKNQVIKAERRVLK 190
Cdd:smart00385  68 -----YFTEEEILRMERLLLE 83
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 61-196 1.34e-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: 47.51  E-value: 1.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320     61 EERLSPTPSMQDGLDLPSETDLRILgCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIE 140
Cdd:pfam00134  10 ELKYLPKPDYMDQQPDINPKMRAIL-IDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYE 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320    141 EaprrirdvinvfhhlrqlrgkrTPSPLILDQNYIN----TKNQVIKAERRVLKELGFCV 196
Cdd:pfam00134  89 E----------------------IYPPTVEDLVYITdnayTREEILRMERLILETLNFDL 126
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 99-264 9.81e-06

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: 47.52  E-value: 9.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320     99 LPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEaprrirdvinVFHHLRQLRGKRTPSPLildqnyiNTK 178
Cdd:TIGR00569  74 MPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE----------FNVSIDQFVGNLKETPL-------KAL 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320    179 NQVIKAERRVLKELGFCVHVKHPHKIIVMYLqvLEC-------ERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIY 251
Cdd:TIGR00569 137 EQVLEYELLLIQQLNFHLIVHNPYRPLEGFL--IDIktrlpglENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAIL 214

                         170
                  ....*....|...
gi 9945320    252 LAARALQIPLPTR 264
Cdd:TIGR00569 215 HTASRAGLNMESY 227
 
Name Accession Description Interval E-value
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 40-195 1.98e-90

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: 273.81  E-value: 1.98e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   40 ILIGDRLYSEVSLTIDHSLIPEERLSPTPSMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKS 119
Cdd:cd20590   1 VLIGDRLYSGVLITLENCLLPEERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKS 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9945320  120 FVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQLRGKRTPSPLILDQNYINTKNQVIKAERRVLKELGFC 195
Cdd:cd20590  81 FVKHSMEHVSMACVHLASKIEEAPRRIRDVINVFHRLRQLREKKKPVPLILDQEYVNLKNQIIKAERRVLKELGFC 156
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 72-195 1.12e-86

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: 262.76  E-value: 1.12e-86
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   72 DGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVIN 151
Cdd:cd20589   1 DGLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVIN 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 9945320  152 VFHHLRQLRGKRTPSPLILDQNYINTKNQVIKAERRVLKELGFC 195
Cdd:cd20589  81 VFHHIKQVRGKRTISPLILDQNYINLKNQVIKAERRVLKELGFC 124
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 199-321 4.36e-85

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: 258.77  E-value: 4.36e-85
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320  199 KHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEI 278
Cdd:cd20592   1 KHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPNRPHWFLLFGATEEEI 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 9945320  279 QEICIETLRLYTRKKPNYELLEKEVEKRKVALQEAKLKAKGLN 321
Cdd:cd20592  81 QEICITTLKLYTRKKPNYEFLEKEVEKRKVALQEAKLKAKGLN 123
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 72-195 8.69e-72

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: 224.36  E-value: 8.69e-72
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   72 DGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVIN 151
Cdd:cd20532   1 DGIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVIN 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 9945320  152 VFHHLRQLRGKRTPSPLILD---QNYINTKNQVIKAERRVLKELGFC 195
Cdd:cd20532  81 VFHRLLQRRLGKPAEVLPLDigsAEYEELKNDIIKAERRILKELGFC 127
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 200-322 6.67e-71

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: 222.15  E-value: 6.67e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320  200 HPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEIQ 279
Cdd:cd20593   1 HPHKIIVMYLQVLECERNRHLVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEIPLPNRPHWFLLFGATEEEIQ 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 9945320  280 EICIETLRLYTRKKPNYELLEKEVEKRKVALQEAKLKAKGLNP 322
Cdd:cd20593  81 EICLKILQLYTRKKVDLEHLESKVEKRKLAIEEAKAKAKGLLP 123
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 200-291 9.63e-50

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: 165.85  E-value: 9.63e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320  200 HPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEIQ 279
Cdd:cd20533   1 HPHKFILMYLQVLEGEDNKKLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAARELGIPLPLPPPWWELFDVSKEDIE 80

                        90
                ....*....|..
gi 9945320  280 EICIETLRLYTR 291
Cdd:cd20533  81 EICLTILELYTR 92
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 69-194 4.69e-41

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: 143.82  E-value: 4.69e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   69 SMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRD 148
Cdd:cd20591   1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 9945320  149 VINVFHHLRQLRGKRTPSPLILD-QNYINTKNQVIKAERRVLKELGF 194
Cdd:cd20591  81 VLMVFHRMECRRENLPLEPLEPEsKKYDEMKEDLIRTERHLLKEMGF 127
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 74-274 6.30e-30

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: 119.07  E-value: 6.30e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   74 LDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRdvinvf 153
Cdd:COG5333  36 LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDIS------ 109

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320  154 hhLRQLRgKRTPSPLILDqnyiNTKNQVIKAERRVLKELGFCVHVKHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLR 233
Cdd:COG5333 110 --IESFE-ARDLWSEEPK----SSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALR 182

                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 9945320  234 TNVFVRFQPETIACACIYLAARAlqIPLPTRPHWFLLFGTT 274
Cdd:COG5333 183 TDLCLLYPPHIIALAALLIACEV--LGMPIIKLLDFVSYET 221
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 73-194 1.74e-25

first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase II-associated C-type cyclin possessing both carboxy-terminal domain kinase and Cdk-activating kinase activity. It is a regulatory subunit of cyclin-dependent kinases that mediates the activation of these target kinases. It plays a role in transcriptional regulation by controlling the phosphorylation of the C-terminal domain (CTD) of the large subunit of RNA polymerase II (POLR2A). CCNK contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410233 [Multi-domain]  Cd Length: 115  Bit Score: 100.77  E-value: 1.74e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   73 GLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINV 152
Cdd:cd20530   1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 9945320  153 FHHLRqlrgkrtpSPLILDQNYINTKNQVIKAERRVLKELGF 194
Cdd:cd20530  81 ARSLL--------NDKQFAQFGDDPKEEVMVLERILLQTIKF 114
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 83-194 1.12e-23

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: 95.70  E-value: 1.12e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   83 RILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQlrgk 162
Cdd:cd20534   2 HFKVLRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRILH---- 77

                        90       100       110
                ....*....|....*....|....*....|..
gi 9945320  163 RTPSPLILDQNYINTKNQVIKAERRVLKELGF 194
Cdd:cd20534  78 PDKPPLELDDEYWELRDSIVNCELLLLRILKF 109
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 197-271 2.94e-22

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: 91.46  E-value: 2.94e-22
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9945320  197 HVKHPHKIIVMYLQVLECErnQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLF 271
Cdd:cd20594   1 HVEHPHKFILNYLAMLMAP--PELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKVF 73
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 72-194 3.29e-19

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


Pssm-ID: 410290 [Multi-domain]  Cd Length: 124  Bit Score: 83.34  E-value: 3.29e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   72 DGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVIN 151
Cdd:cd20587   1 DGIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIV 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 9945320  152 VFHhlrQLRGKRTPSPLILDQN---YINTKNQVIKAERRVLKELGF 194
Cdd:cd20587  81 VSY---EIIFKKDPSAAQRIKQkevYEQQKELVLNGEKLVLSTLGF 123
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 79-194 2.66e-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: 80.55  E-value: 2.66e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   79 ETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQ 158
Cdd:cd20545   1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQ 80

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 9945320  159 lrgkRTPSPLILDQN--YINTKNQVIKAERRVLKELGF 194
Cdd:cd20545  81 ----KNPNLVIDEQSkeVWRWRDSILYNEEVLLETLCF 114
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 200-291 5.77e-18

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: 78.95  E-value: 5.77e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320  200 HPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPH-----WFLLFGTT 274
Cdd:cd20546   1 HPYQYLIKFAKKLGVSDPKELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPNeklneWWELFGVD 80

                        90
                ....*....|....*..
gi 9945320  275 EEEIQEICIETLRLYTR 291
Cdd:cd20546  81 EEEIADAINEILDLYSS 97
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 62-194 1.33e-16

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: 76.66  E-value: 1.33e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   62 ERLSPTPSMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEE 141
Cdd:cd20538   7 EQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFLAAKVEE 86

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 9945320  142 APRRIRDVINVFHHLRQlrgKRTPSPLILDQNYINTKNQVIKAERRVLKELGF 194
Cdd:cd20538  87 QPRKLEHVIKVAHACLH---RGEPDLDTKSEAYLQQAQELVINENILLQTLGF 136
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 62-194 5.15e-16

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: 74.71  E-value: 5.15e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   62 ERLSPTPSMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEE 141
Cdd:cd20595   8 EQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALFLAAKVEE 87

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 9945320  142 APRRIRDVINVFHHLRQlrgKRTPSPLILDQNYINTKNQVIKAERRVLKELGF 194
Cdd:cd20595  88 QPKKLEHVIKVAHTCLH---PQESLPDTRSEAYLQQVQDLVILESIILQTLGF 137
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 200-262 1.11e-13

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: 66.98  E-value: 1.11e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9945320  200 HPHKIIVMYLQVLECERN--QTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLP 262
Cdd:cd20531   2 HPYKYLLKYAKQLKGDKNkiQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQ 66
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
 62-194 1.87e-13

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: 67.76  E-value: 1.87e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   62 ERLSPTPSMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEE 141
Cdd:cd20596   9 EQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTALFLAAKVEE 88

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 9945320  142 APRRIRDVINVFHHLRQlrgkrtPSPLILDQN---YINTKNQVIKAERRVLKELGF 194
Cdd:cd20596  89 QPRKLEHVIKVAHACLN------PLEPQLDTKsdaYLQQAQELVILETIMLQTLGF 138
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 200-289 4.04e-13

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: 65.25  E-value: 4.04e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320  200 HPHKIIVMYLQVLECERNQtLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPT--RPHWFLLFGTTEEE 277
Cdd:cd20588   2 HPYKPLVAAIKKFNVAQNA-LAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPCdgRKVWWQEFDVTPRQ 80

                        90
                ....*....|..
gi 9945320  278 IQEICIETLRLY 289
Cdd:cd20588  81 LEEVSNQMLELY 92
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 82-194 1.69e-11

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: 61.21  E-value: 1.69e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   82 LRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQlrg 161
Cdd:cd20547   1 LRLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNLRH--- 77

                        90       100       110
                ....*....|....*....|....*....|....
gi 9945320  162 krtPSPLILDQNYI-NTKNQVIKAERRVLKELGF 194
Cdd:cd20547  78 ---PDKISVDDQMLeEFRKAILGLERLLLETICF 108
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 86-158 8.13e-11

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


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 58.19  E-value: 8.13e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 9945320   86 GCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQ 158
Cdd:cd00043   2 AVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEK 74
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 205-274 3.29e-10

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: 56.45  E-value: 3.29e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320     205 IVMYLQVLECerNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTT 274
Cdd:smart00385   3 LRRVCKALNL--DPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFT 70
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 82-151 3.89e-10

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: 56.83  E-value: 3.89e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320   82 LRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVIN 151
Cdd:cd20513   1 LHIFFANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPSHARLIVA 70
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 200-266 1.19e-09

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: 55.73  E-value: 1.19e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 9945320  200 HPHKIIVMYLQVL------ECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPH 266
Cdd:cd20535   1 LPHKYLLHYLKSLrdwlnpEFWSRSPIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQVYGVKVPPEEE 73
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 200-268 1.81e-09

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: 54.55  E-value: 1.81e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 9945320  200 HPHKIIVMYLQvlECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLptrPHWF 268
Cdd:cd20514   1 HPYRPLTQYVQ--DAGLDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDA---RQWF 64
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 90-190 4.56e-08

domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 50.28  E-value: 4.56e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320      90 IQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHhlrqlrgkrtpspli 169
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTG--------------- 67

                           90       100
                   ....*....|....*....|.
gi 9945320     170 ldqnyINTKNQVIKAERRVLK 190
Cdd:smart00385  68 -----YFTEEEILRMERLLLE 83
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 200-264 8.86e-08

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: 49.72  E-value: 8.86e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9945320  200 HPHKIIVMYLQVLECerNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTR 264
Cdd:cd00043   1 KAVDFIRRLCSKLGL--PEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLK 63
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 61-196 1.34e-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: 47.51  E-value: 1.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320     61 EERLSPTPSMQDGLDLPSETDLRILgCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIE 140
Cdd:pfam00134  10 ELKYLPKPDYMDQQPDINPKMRAIL-IDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYE 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320    141 EaprrirdvinvfhhlrqlrgkrTPSPLILDQNYIN----TKNQVIKAERRVLKELGFCV 196
Cdd:pfam00134  89 E----------------------IYPPTVEDLVYITdnayTREEILRMERLILETLNFDL 126
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 99-264 9.81e-06

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: 47.52  E-value: 9.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320     99 LPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEaprrirdvinVFHHLRQLRGKRTPSPLildqnyiNTK 178
Cdd:TIGR00569  74 MPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE----------FNVSIDQFVGNLKETPL-------KAL 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320    179 NQVIKAERRVLKELGFCVHVKHPHKIIVMYLqvLEC-------ERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIY 251
Cdd:TIGR00569 137 EQVLEYELLLIQQLNFHLIVHNPYRPLEGFL--IDIktrlpglENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAIL 214

                         170
                  ....*....|...
gi 9945320    252 LAARALQIPLPTR 264
Cdd:TIGR00569 215 HTASRAGLNMESY 227
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 200-268 1.45e-05

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: 43.42  E-value: 1.45e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9945320  200 HPHKIIVMYLQVLEcERNQTLVQTAwNYM--NDSLRTNVFVRFQPETIACACIYLAAR--ALQIPLPTR-PHWF 268
Cdd:cd20539   1 HPHTHVLKICNLVK-AGSKDLAQTA-YFLatNSLHLTTFCLQYKPTVIACVCIHLACKwsNWEIPRSSEgKDWY 72
CYCLIN_AtCycC_rpt2 cd20572
second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 200-254 3.15e-04

second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; CycCs are the cognate cyclin partners of cyclin-dependent kinase CDK8. They may be involved in cell cycle control. CycCs contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410275 [Multi-domain]  Cd Length: 102  Bit Score: 40.14  E-value: 3.15e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 9945320  200 HPHKIIVMYLQvlecERNQT-LVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAA 254
Cdd:cd20572   1 HPYRPLIQLLQ----DAGLTdMTQFTWSIVNDTYRTDLILIHPPYMIALACIYIAS 52
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 97-172 9.83e-04

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: 39.89  E-value: 9.83e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9945320   97 LRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDvinvFhhLRQLRGKRTPSPLILDQ 172
Cdd:cd20524  69 FKLPDSVLATALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVEEFNISIDQ----F--VGNIKESEKTAEIILEY 138
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
 199-268 1.20e-03

second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to production elongation by phosphorylating the CTD (carboxy-terminal domain) of the large subunit of RNA polymerase II (RNAP II). CCNT2 contains two cyclin boxs. The model responds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410301 [Multi-domain]  Cd Length: 114  Bit Score: 38.91  E-value: 1.20e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9945320  199 KHPHKIIVMYLQVLECERNqtLVQTAWNYMNDSLRTNVF-VRFQPETIACACIYLAAR--ALQIPLPTR-PHWF 268
Cdd:cd20598   1 EHPHTDVVKCTQLVRASKD--LAQTSYFMATNSLHLTTFcLQYKPTVIACVCIHLACKwsNWEIPVSTDgKHWW 72
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
 90-141 1.51e-03

first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH associates with and activates the cyclin-dependent kinases, CDK-2 and CDK-3. CycH contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410288  Cd Length: 170  Bit Score: 39.43  E-value: 1.51e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 9945320   90 IQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEE 141
Cdd:cd20585  85 IQEVCRALRLPNKIQATALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEE 136
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 200-268 1.71e-03

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


Pssm-ID: 410300 [Multi-domain]  Cd Length: 109  Bit Score: 38.14  E-value: 1.71e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 9945320  200 HPHKIIVMYLQVLECERNqtLVQTAWNYMNDSLRTNVF-VRFQPETIACACIYLAAR--ALQIPLPTR-PHWF 268
Cdd:cd20597   2 HPHTHVVKCTQLVRASKD--LAQTSYFMATNSLHLTTFsLQYTPPVVACVCIHLACKwsNWEIPVSTDgKHWW 72
CYCLIN_CNTD1 cd20541
cyclin box found in Cyclin N-terminal domain-containing protein 1 (CNTD1) and similar proteins; ...
 121-196 3.71e-03

cyclin box found in Cyclin N-terminal domain-containing protein 1 (CNTD1) and similar proteins; CNTD1 is a cyclin-related protein critical for meiotic crossover maturation and deselection of excess precrossover sites. CNTD1 contains one cyclin box. The cyclin box is a protein binding domain.


Pssm-ID: 410244  Cd Length: 127  Bit Score: 37.57  E-value: 3.71e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9945320  121 VKHSFEIVAMACINLASKIEEAPRRI--RDVINvfhhlrQLRgkrtpsplilDQNYINTKNQVIKAERRVLKELGFCV 196
Cdd:cd20541  66 LSKQLPLRLVSCVQLASKLSSHYKIVsaNKAKN------FLQ----------SLGHPYTKSSILKSELRVLKTLNFRV 127
CYCLIN_CCNB1-like_rpt1 cd20507
first cyclin box found in cyclin-B1 (CCNB1)-like family; The CCNB1-like family includes two ...
 113-194 4.39e-03

first cyclin box found in cyclin-B1 (CCNB1)-like family; The CCNB1-like family includes two B-type cyclins, CCNB1 and CCNB2, both of which are essential for the control of the cell cycle at the G2/M (mitosis) transition. Members in this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410211 [Multi-domain]  Cd Length: 130  Bit Score: 37.51  E-value: 4.39e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9945320  113 RFFYSKSFVKHSFEIVAMACINLASKIEE--APrRIRDVInvfhhlrqlrgkrtpspLILDQNYinTKNQVIKAERRVLK 190
Cdd:cd20507  67 RYLSKKQVPRKKLQLVGVTALLIASKYEEiyPP-EIKDFV-----------------YITDNAY--TREEILQMERDILK 126


                ....
gi 9945320  191 ELGF 194
Cdd:cd20507 127 TLDF 130
 
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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