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Conserved domains on  [gi|1123947473|ref|XP_019587516|]
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PREDICTED: cyclin-L1 isoform X1 [Rhinolophus sinicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 199-321 1.26e-94

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: 283.43  E-value: 1.26e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 199 KHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEI 278
Cdd:cd20592     1 KHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPNRPHWFLLFGATEEEI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1123947473 279 QDICIETLRLYTRKKPNYELLEKEVEKRKVALQEAKLKAKGLN 321
Cdd:cd20592    81 QEICITTLKLYTRKKPNYEFLEKEVEKRKVALQEAKLKAKGLN 123
CYCLIN_SF super family cl40454
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 40-195 6.77e-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: 272.26  E-value: 6.77e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  40 ILIGDRLYSEVSLTIDHSLIPEERLSPTPSMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKS 119
Cdd:cd20590     1 VLIGDRLYSGVLITLENCLLPEERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1123947473 120 FVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQLRGKRTPSPLVLDQNYINTKNQVIKAERRVLKELGFC 195
Cdd:cd20590    81 FVKHSMEHVSMACVHLASKIEEAPRRIRDVINVFHRLRQLREKKKPVPLILDQEYVNLKNQIIKAERRVLKELGFC 156
 
Name Accession Description Interval E-value
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 199-321 1.26e-94

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: 283.43  E-value: 1.26e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 199 KHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEI 278
Cdd:cd20592     1 KHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPNRPHWFLLFGATEEEI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1123947473 279 QDICIETLRLYTRKKPNYELLEKEVEKRKVALQEAKLKAKGLN 321
Cdd:cd20592    81 QEICITTLKLYTRKKPNYEFLEKEVEKRKVALQEAKLKAKGLN 123
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 40-195 6.77e-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: 272.26  E-value: 6.77e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  40 ILIGDRLYSEVSLTIDHSLIPEERLSPTPSMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKS 119
Cdd:cd20590     1 VLIGDRLYSGVLITLENCLLPEERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1123947473 120 FVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQLRGKRTPSPLVLDQNYINTKNQVIKAERRVLKELGFC 195
Cdd:cd20590    81 FVKHSMEHVSMACVHLASKIEEAPRRIRDVINVFHRLRQLREKKKPVPLILDQEYVNLKNQIIKAERRVLKELGFC 156
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 74-278 1.93e-31

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: 123.30  E-value: 1.93e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  74 LDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRdvinvf 153
Cdd:COG5333    36 LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDIS------ 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 154 hhLRQLRgKRTPSPLVLDqnyiNTKNQVIKAERRVLKELGFCVHVKHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLR 233
Cdd:COG5333   110 --IESFE-ARDLWSEEPK----SSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALR 182

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1123947473 234 TNVFVRFQPETIACACIYLAARAlqIPLPTRPHWFLLFGTTEEEI 278
Cdd:COG5333   183 TDLCLLYPPHIIALAALLIACEV--LGMPIIKLLDFVSYETKEEV 225
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 205-281 1.05e-12

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: 63.77  E-value: 1.05e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1123947473  205 IVMYLQVLECerNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEIQDI 281
Cdd:smart00385   3 LRRVCKALNL--DPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFTEEEILRM 77
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 90-154 4.74e-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: 4.74e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1123947473   90 IQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINVFH 154
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTG 67
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 61-196 1.70e-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: 47.13  E-value: 1.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  61 EERLSPTPSMQDGLDLPSETDLRILgCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIE 140
Cdd:pfam00134  10 ELKYLPKPDYMDQQPDINPKMRAIL-IDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYE 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 141 EaprrirdvinvfhhlrqlrgkrTPSPLVLDQNYIN----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 ...
 99-322 2.76e-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: 49.45  E-value: 2.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  99 LPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEaprrirdvinVFHHLRQLRGKRTPSPLvldqnyiNTK 178
Cdd:TIGR00569  74 MPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE----------FNVSIDQFVGNLKETPL-------KAL 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 179 NQVIKAERRVLKELGFCVHVKHPHKIIVMYLqvLEC-------ERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIY 251
Cdd:TIGR00569 137 EQVLEYELLLIQQLNFHLIVHNPYRPLEGFL--IDIktrlpglENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAIL 214

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1123947473 252 LAARALQIPLPTRPHWFLLFGTTEEEIQDICIETLRLYTRKKPNYELLEKEVEKRKVALQEAKLKAKGLNP 322
Cdd:TIGR00569 215 HTASRAGLNMESYLTEQLSVPGNREELPQLIDIMRELRILVKKYEEPRSEKVAALKKKLDECHSIEENLSS 285
 
Name Accession Description Interval E-value
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 199-321 1.26e-94

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: 283.43  E-value: 1.26e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 199 KHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEI 278
Cdd:cd20592     1 KHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPNRPHWFLLFGATEEEI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1123947473 279 QDICIETLRLYTRKKPNYELLEKEVEKRKVALQEAKLKAKGLN 321
Cdd:cd20592    81 QEICITTLKLYTRKKPNYEFLEKEVEKRKVALQEAKLKAKGLN 123
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 40-195 6.77e-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: 272.26  E-value: 6.77e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  40 ILIGDRLYSEVSLTIDHSLIPEERLSPTPSMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKS 119
Cdd:cd20590     1 VLIGDRLYSGVLITLENCLLPEERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1123947473 120 FVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQLRGKRTPSPLVLDQNYINTKNQVIKAERRVLKELGFC 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 2.51e-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: 261.99  E-value: 2.51e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  72 DGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVIN 151
Cdd:cd20589     1 DGLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVIN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1123947473 152 VFHHLRQLRGKRTPSPLVLDQNYINTKNQVIKAERRVLKELGFC 195
Cdd:cd20589    81 VFHHIKQVRGKRTISPLILDQNYINLKNQVIKAERRVLKELGFC 124
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 200-322 5.35e-79

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: 242.95  E-value: 5.35e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 200 HPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEIQ 279
Cdd:cd20593     1 HPHKIIVMYLQVLECERNRHLVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEIPLPNRPHWFLLFGATEEEIQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1123947473 280 DICIETLRLYTRKKPNYELLEKEVEKRKVALQEAKLKAKGLNP 322
Cdd:cd20593    81 EICLKILQLYTRKKVDLEHLESKVEKRKLAIEEAKAKAKGLLP 123
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 72-195 1.57e-71

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: 223.98  E-value: 1.57e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  72 DGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVIN 151
Cdd:cd20532     1 DGIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVIN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1123947473 152 VFHHLRQLRGKRTPSPLVLD---QNYINTKNQVIKAERRVLKELGFC 195
Cdd:cd20532    81 VFHRLLQRRLGKPAEVLPLDigsAEYEELKNDIIKAERRILKELGFC 127
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 200-291 5.53e-58

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: 187.42  E-value: 5.53e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 200 HPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEIQ 279
Cdd:cd20533     1 HPHKFILMYLQVLEGEDNKKLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAARELGIPLPLPPPWWELFDVSKEDIE 80

                          90
                  ....*....|..
gi 1123947473 280 DICIETLRLYTR 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 1.70e-40

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: 142.67  E-value: 1.70e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  69 SMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRD 148
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1123947473 149 VINVFHHLRQLRGKRTPSPLVLD-QNYINTKNQVIKAERRVLKELGF 194
Cdd:cd20591    81 VLMVFHRMECRRENLPLEPLEPEsKKYDEMKEDLIRTERHLLKEMGF 127
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 74-278 1.93e-31

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: 123.30  E-value: 1.93e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  74 LDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRdvinvf 153
Cdd:COG5333    36 LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDIS------ 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 154 hhLRQLRgKRTPSPLVLDqnyiNTKNQVIKAERRVLKELGFCVHVKHPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLR 233
Cdd:COG5333   110 --IESFE-ARDLWSEEPK----SSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALR 182

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1123947473 234 TNVFVRFQPETIACACIYLAARAlqIPLPTRPHWFLLFGTTEEEI 278
Cdd:COG5333   183 TDLCLLYPPHIIALAALLIACEV--LGMPIIKLLDFVSYETKEEV 225
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 197-296 1.12e-26

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: 103.79  E-value: 1.12e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 197 HVKHPHKIIVMYLQVLECErnQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEE 276
Cdd:cd20594     1 HVEHPHKFILNYLAMLMAP--PELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKVFDAEKA 78

                          90       100
                  ....*....|....*....|
gi 1123947473 277 EIQDICIETLRLYTRKKPNY 296
Cdd:cd20594    79 EIDVVCKVLADLYRQPKARY 98
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 73-194 2.23e-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: 2.23e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  73 GLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINV 152
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1123947473 153 FHHLRqlrgkrtpSPLVLDQNYINTKNQVIKAERRVLKELGF 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 4.77e-24

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: 96.86  E-value: 4.77e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  83 RILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQlrgk 162
Cdd:cd20534     2 HFKVLRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRILH---- 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1123947473 163 RTPSPLVLDQNYINTKNQVIKAERRVLKELGF 194
Cdd:cd20534    78 PDKPPLELDDEYWELRDSIVNCELLLLRILKF 109
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 200-291 8.08e-24

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: 95.51  E-value: 8.08e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 200 HPHKIIVMYLQVLECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPH-----WFLLFGTT 274
Cdd:cd20546     1 HPYQYLIKFAKKLGVSDPKELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPNeklneWWELFGVD 80

                          90
                  ....*....|....*..
gi 1123947473 275 EEEIQDICIETLRLYTR 291
Cdd:cd20546    81 EEEIADAINEILDLYSS 97
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 72-194 7.52e-19

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


Pssm-ID: 410290 [Multi-domain]  Cd Length: 124  Bit Score: 82.57  E-value: 7.52e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  72 DGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVIN 151
Cdd:cd20587     1 DGIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1123947473 152 VFHhlrQLRGKRTPSPLVLDQN---YINTKNQVIKAERRVLKELGF 194
Cdd:cd20587    81 VSY---EIIFKKDPSAAQRIKQkevYEQQKELVLNGEKLVLSTLGF 123
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 200-289 3.56e-18

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: 79.69  E-value: 3.56e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 200 HPHKIIVMYLQVLECERN--QTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPH------WFLLF 271
Cdd:cd20531     2 HPYKYLLKYAKQLKGDKNkiQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDWTSkppgkrWWEQF 81

                          90       100
                  ....*....|....*....|
gi 1123947473 272 --GTTEEEIQDICIETLRLY 289
Cdd:cd20531    82 veDVSLEVLEDICHQVLDLY 101
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 79-194 3.96e-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: 80.16  E-value: 3.96e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  79 ETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQ 158
Cdd:cd20545     1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1123947473 159 lrgkRTPSPLVLDQN--YINTKNQVIKAERRVLKELGF 194
Cdd:cd20545    81 ----KNPNLVIDEQSkeVWRWRDSILYNEEVLLETLCF 114
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 62-194 9.08e-17

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: 77.05  E-value: 9.08e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  62 ERLSPTPSMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEE 141
Cdd:cd20538     7 EQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFLAAKVEE 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1123947473 142 APRRIRDVINVFHHLRQlrgKRTPSPLVLDQNYINTKNQVIKAERRVLKELGF 194
Cdd:cd20538    87 QPRKLEHVIKVAHACLH---RGEPDLDTKSEAYLQQAQELVINENILLQTLGF 136
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 200-289 1.51e-16

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: 74.88  E-value: 1.51e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 200 HPHKIIVMYLQVLECERNQtLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPT--RPHWFLLFGTTEEE 277
Cdd:cd20588     2 HPYKPLVAAIKKFNVAQNA-LAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPCdgRKVWWQEFDVTPRQ 80

                          90
                  ....*....|..
gi 1123947473 278 IQDICIETLRLY 289
Cdd:cd20588    81 LEEVSNQMLELY 92
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 62-194 8.21e-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: 74.32  E-value: 8.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  62 ERLSPTPSMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEE 141
Cdd:cd20595     8 EQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALFLAAKVEE 87

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1123947473 142 APRRIRDVINVFHHLRQlrgKRTPSPLVLDQNYINTKNQVIKAERRVLKELGF 194
Cdd:cd20595    88 QPKKLEHVIKVAHTCLH---PQESLPDTRSEAYLQQVQDLVILESIILQTLGF 137
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 200-290 1.71e-13

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: 66.51  E-value: 1.71e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 200 HPHKIIVMYLQVL------ECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPH----WFL 269
Cdd:cd20535     1 LPHKYLLHYLKSLrdwlnpEFWSRSPIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQVYGVKVPPEEEaekpWWQ 80

                          90       100
                  ....*....|....*....|...
gi 1123947473 270 LF--GTTEEEIQDICIETLRLYT 290
Cdd:cd20535    81 AFceDLTKETIDEIIEDIINVYD 103
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
 62-194 2.21e-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: 67.38  E-value: 2.21e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  62 ERLSPTPSMQDGLDLPSETDLRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEE 141
Cdd:cd20596     9 EQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTALFLAAKVEE 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1123947473 142 APRRIRDVINVFHHLRQlrgkrtPSPLVLDQN---YINTKNQVIKAERRVLKELGF 194
Cdd:cd20596    89 QPRKLEHVIKVAHACLN------PLEPQLDTKsdaYLQQAQELVILETIMLQTLGF 138
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 205-281 1.05e-12

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: 63.77  E-value: 1.05e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1123947473  205 IVMYLQVLECerNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEIQDI 281
Cdd:smart00385   3 LRRVCKALNL--DPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFTEEEILRM 77
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 82-194 8.08e-12

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: 61.98  E-value: 8.08e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  82 LRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQlrg 161
Cdd:cd20547     1 LRLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNLRH--- 77

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1123947473 162 krtPSPLVLDQNYI-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 9.14e-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: 9.14e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1123947473  86 GCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINVFHHLRQ 158
Cdd:cd00043     2 AVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEK 74
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 200-294 1.41e-10

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: 58.01  E-value: 1.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 200 HPHKIIVMYLQvlECERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLptrPHWFLLFGTTEEEIQ 279
Cdd:cd20514     1 HPYRPLTQYVQ--DAGLDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDA---RQWFAELNVDMDKIL 75

                          90
                  ....*....|....*
gi 1123947473 280 DICIETLRLYTRKKP 294
Cdd:cd20514    76 EITREILSLYELWKT 90
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 82-151 4.42e-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: 4.42e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  82 LRILGCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVIN 151
Cdd:cd20513     1 LHIFFANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPSHARLIVA 70
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 200-284 7.33e-09

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: 52.80  E-value: 7.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 200 HPHKIIVMYLQVLECerNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTRpHWFLLFGTTEEEIQ 279
Cdd:cd00043     1 KAVDFIRRLCSKLGL--PEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLK-EIAKVSGVSEKELR 77


                  ....*
gi 1123947473 280 DICIE 284
Cdd:cd00043    78 KAEKE 82
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 90-154 4.74e-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: 4.74e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1123947473   90 IQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRIRDVINVFH 154
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTG 67
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 61-196 1.70e-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: 47.13  E-value: 1.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  61 EERLSPTPSMQDGLDLPSETDLRILgCELIQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIE 140
Cdd:pfam00134  10 ELKYLPKPDYMDQQPDINPKMRAIL-IDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYE 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 141 EaprrirdvinvfhhlrqlrgkrTPSPLVLDQNYIN----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 ...
 99-322 2.76e-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: 49.45  E-value: 2.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473  99 LPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEaprrirdvinVFHHLRQLRGKRTPSPLvldqnyiNTK 178
Cdd:TIGR00569  74 MPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE----------FNVSIDQFVGNLKETPL-------KAL 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 179 NQVIKAERRVLKELGFCVHVKHPHKIIVMYLqvLEC-------ERNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIY 251
Cdd:TIGR00569 137 EQVLEYELLLIQQLNFHLIVHNPYRPLEGFL--IDIktrlpglENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAIL 214

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1123947473 252 LAARALQIPLPTRPHWFLLFGTTEEEIQDICIETLRLYTRKKPNYELLEKEVEKRKVALQEAKLKAKGLNP 322
Cdd:TIGR00569 215 HTASRAGLNMESYLTEQLSVPGNREELPQLIDIMRELRILVKKYEEPRSEKVAALKKKLDECHSIEENLSS 285
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 200-286 8.66e-06

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: 44.19  E-value: 8.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 200 HPHKIIVMYLQVLEcERNQTLVQTAwNYM--NDSLRTNVFVRFQPETIACACIYLAAR--ALQIPLPTR-PHWFLLFGT- 273
Cdd:cd20539     1 HPHTHVLKICNLVK-AGSKDLAQTA-YFLatNSLHLTTFCLQYKPTVIACVCIHLACKwsNWEIPRSSEgKDWYEYVDPs 78

                          90
                  ....*....|....
gi 1123947473 274 -TEEEIQDICIETL 286
Cdd:cd20539    79 lTLEELDELTSEFL 92
CYCLIN_AtCycC_rpt2 cd20572
second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 200-302 6.76e-05

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: 42.07  E-value: 6.76e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1123947473 200 HPHKIIVMYLQvlecERNQT-LVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPTrphWFLLFGTTEEEI 278
Cdd:cd20572     1 HPYRPLIQLLQ----DAGLTdMTQFTWSIVNDTYRTDLILIHPPYMIALACIYIASVHKEKDITL---WFEELRVDMNII 73

                          90       100
                  ....*....|....*....|....
gi 1123947473 279 QDICIETLRLYTrkkpNYELLEKE 302
Cdd:cd20572    74 KNIAMEILDFYD----NYRLIPEE 93
CYCLIN_CCNO-like_rpt2 cd20537
second cyclin box found in cyclin-O (CCNO) and similar proteins; This subfamily is composed of ...
 237-289 9.68e-05

second cyclin box found in cyclin-O (CCNO) and similar proteins; This subfamily is composed of CCNO and similar proteins including Schizosaccharomyces pombe meiosis-specific cyclin rem1, Drosophila melanogaster G2/mitotic-specific cyclin-A (CCNA), and Candida albicans G1/S-specific cyclin CCN1, among others. Rem1 is required for pre-meiotic DNA synthesis and S phase progression. CCNA is essential for the control of the cell cycle at the G2/M (mitosis) transition. CCN1 is essential for the control of the cell cycle at the G1/S (start) transition and for maintenance of filamentous growth. CCNO is specifically required for generation of multiciliated cells, possibly by promoting a cell cycle state compatible with centriole amplification and maturation. It is involved in the activation of cyclin-dependent kinase 2. Members of this subfamily contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410240 [Multi-domain]  Cd Length: 91  Bit Score: 41.14  E-value: 9.68e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1123947473 237 FVRFQPETIACACIYLAARALQIPLPTRPHWFLLFGTTEEEIQDICIETLRLY 289
Cdd:cd20537    37 FLKYRPSLIAAAALYLARKILGEPPPSPQLLQLVTGYSENDLQECAKELLELL 89
CYCLIN_CCNJ-like_rpt2 cd20529
second cyclin box found in cyclin-J (CCNJ) family; The CCNJ family includes two cyclins, CCNJ ...
 230-286 3.28e-04

second cyclin box found in cyclin-J (CCNJ) family; The CCNJ family includes two cyclins, CCNJ and CCNJ-like. CCNJ may regulate the cell cycle or 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: 410232 [Multi-domain]  Cd Length: 101  Bit Score: 40.04  E-value: 3.28e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1123947473 230 DSLRTNVFVRFQPETIACACIYLAARALQIpLPTRPHWF-LLFGTTEEEIQDiCIETL 286
Cdd:cd20529    46 LSLQDYAFLNYKPSLLAAACIAAARKALGL-SPTWPEELeKLTGYSEDELEP-CVELL 101
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
 199-268 1.10e-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: 1.10e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1123947473 199 KHPHKIIVMYLQVLECERNqtLVQTAWNYMNDSLRTNVF-VRFQPETIACACIYLAAR--ALQIPLPTR-PHWF 268
Cdd:cd20598     1 EHPHTDVVKCTQLVRASKD--LAQTSYFMATNSLHLTTFcLQYKPTVIACVCIHLACKwsNWEIPVSTDgKHWW 72
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 200-268 1.54e-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: 38.52  E-value: 1.54e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1123947473 200 HPHKIIVMYLQVLECERNqtLVQTAWNYMNDSLRTNVF-VRFQPETIACACIYLAAR--ALQIPLPTR-PHWF 268
Cdd:cd20597     2 HPHTHVVKCTQLVRASKD--LAQTSYFMATNSLHLTTFsLQYTPPVVACVCIHLACKwsNWEIPVSTDgKHWW 72
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 97-146 1.56e-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: 39.12  E-value: 1.56e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1123947473  97 LRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEEAPRRI 146
Cdd:cd20524    69 FKLPDSVLATALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVEEFNISI 118
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
 90-141 1.64e-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: 1.64e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1123947473  90 IQAAGILLRLPQVAMATGQVLFHRFFYSKSFVKHSFEIVAMACINLASKIEE 141
Cdd:cd20585    85 IQEVCRALRLPNKIQATALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEE 136
CYCLIN_CNTD1 cd20541
cyclin box found in Cyclin N-terminal domain-containing protein 1 (CNTD1) and similar proteins; ...
 121-196 3.74e-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: 3.74e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1123947473 121 VKHSFEIVAMACINLASKIEEAPRRI--RDVINvfhhlrQLRgkrtpsplvlDQNYINTKNQVIKAERRVLKELGFCV 196
Cdd:cd20541    66 LSKQLPLRLVSCVQLASKLSSHYKIVsaNKAKN------FLQ----------SLGHPYTKSSILKSELRVLKTLNFRV 127
 
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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