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Conserved domains on  [gi|1376140826|ref|XP_024504512|]
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Cyclin-K [Strongyloides ratti]

Protein Classification

cyclin family protein( domain architecture ID 1750054)

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

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 ...
22-135 6.65e-35

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


The actual alignment was detected with superfamily member cd20530:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 115  Bit Score: 120.80  E-value: 6.65e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  22 GWSSAAEKKKRVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIIS 101
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLP-YDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIK 79
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1376140826 102 AAREIYSNALPYNGVSI--ESVIEFERILLRTMKFD 135
Cdd:cd20530    80 TARSLLNDKQFAQFGDDpkEEVMVLERILLQTIKFD 115
CYCLIN_SF super family cl40454
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
139-239 1.74e-26

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 cd20531:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 101  Bit Score: 98.95  E-value: 1.74e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826 139 EAPYDPLLEYCKLLKIPKKQQNSVAQTGWGFLNDCTYTHLPLLWEAEIIAIGAIHLSLQMNNIENVDYEGRTNDEPWWSK 218
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDWTSKPPGKRWWEQ 80
                          90       100
                  ....*....|....*....|.
gi 1376140826 219 VVGNFTLRSLEGICHKFLDHY 239
Cdd:cd20531    81 FVEDVSLEVLEDICHQVLDLY 101
 
Name Accession Description Interval E-value
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
22-135 6.65e-35

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: 120.80  E-value: 6.65e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  22 GWSSAAEKKKRVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIIS 101
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLP-YDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIK 79
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1376140826 102 AAREIYSNALPYNGVSI--ESVIEFERILLRTMKFD 135
Cdd:cd20530    80 TARSLLNDKQFAQFGDDpkEEVMVLERILLQTIKFD 115
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
139-239 1.74e-26

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: 98.95  E-value: 1.74e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826 139 EAPYDPLLEYCKLLKIPKKQQNSVAQTGWGFLNDCTYTHLPLLWEAEIIAIGAIHLSLQMNNIENVDYEGRTNDEPWWSK 218
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDWTSKPPGKRWWEQ 80
                          90       100
                  ....*....|....*....|.
gi 1376140826 219 VVGNFTLRSLEGICHKFLDHY 239
Cdd:cd20531    81 FVEDVSLEVLEDICHQVLDLY 101
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
28-213 7.70e-24

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: 97.11  E-value: 7.70e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  28 EKKKRVDAIDVIRKVGIQLNISLHgTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIISAAREIY 107
Cdd:COG5333    41 ELNLVIYYLKLIMDLCTRLNLPQT-VLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLW 119
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826 108 SNaLPYNgvSIESVIEFERILLRTMKFDLTVEAPYDPLLEYCKLLKIpkKQQNSVAQTGWGFLNDCTYTHLPLLWEAEII 187
Cdd:COG5333   120 SE-EPKS--SRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQE--KDKYKLLQIAWKIINDALRTDLCLLYPPHII 194
                         170       180
                  ....*....|....*....|....*....
gi 1376140826 188 AIGAIHLS---LQMNNIENVDYEGRTNDE 213
Cdd:COG5333   195 ALAALLIAcevLGMPIIKLLDFVSYETKE 223
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
32-137 8.80e-14

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: 66.00  E-value: 8.80e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  32 RVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEET-PKKIKDIISAAREIYsna 110
Cdd:pfam00134  31 RAILIDWLVEVHEKFKLL-PETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYEEIyPPTVEDLVYITDNAY--- 106
                          90       100
                  ....*....|....*....|....*..
gi 1376140826 111 lpyngvSIESVIEFERILLRTMKFDLT 137
Cdd:pfam00134 107 ------TREEILRMERLILETLNFDLS 127
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
56-192 5.69e-12

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: 64.08  E-value: 5.69e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  56 TASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIISAAREIYSNALpyngvsiESVIEFERILLRTMKFD 135
Cdd:TIGR00569  81 TAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKETPLKAL-------EQVLEYELLLIQQLNFH 153
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826 136 LTVEAPYDPL---LEYCKLLKIPKKQQNSVAQTGWGFLNDCTYTHLPLLWEAEIIAIGAI 192
Cdd:TIGR00569 154 LIVHNPYRPLegfLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAI 213
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
37-130 2.41e-11

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: 58.37  E-value: 2.41e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826   37 DVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIISAAReiysnalpynGV 116
Cdd:smart00385   1 DFLRRVCKALNLD-PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTG----------YF 69
                           90
                   ....*....|....
gi 1376140826  117 SIESVIEFERILLR 130
Cdd:smart00385  70 TEEEILRMERLLLE 83
 
Name Accession Description Interval E-value
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
22-135 6.65e-35

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: 120.80  E-value: 6.65e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  22 GWSSAAEKKKRVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIIS 101
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLP-YDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIK 79
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1376140826 102 AAREIYSNALPYNGVSI--ESVIEFERILLRTMKFD 135
Cdd:cd20530    80 TARSLLNDKQFAQFGDDpkEEVMVLERILLQTIKFD 115
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
139-239 1.74e-26

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: 98.95  E-value: 1.74e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826 139 EAPYDPLLEYCKLLKIPKKQQNSVAQTGWGFLNDCTYTHLPLLWEAEIIAIGAIHLSLQMNNIENVDYEGRTNDEPWWSK 218
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDWTSKPPGKRWWEQ 80
                          90       100
                  ....*....|....*....|.
gi 1376140826 219 VVGNFTLRSLEGICHKFLDHY 239
Cdd:cd20531    81 FVEDVSLEVLEDICHQVLDLY 101
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
6-135 2.92e-26

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: 99.39  E-value: 2.92e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826   6 WIFNEEDMNNTPSQKKGWSSAAEKKKRVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFL 85
Cdd:cd20538     2 WYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVS-QLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFL 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1376140826  86 AGKVEETPKKIKDIISAAREIYSNALPYNGVSIES-------VIEFERILLRTMKFD 135
Cdd:cd20538    81 AAKVEEQPRKLEHVIKVAHACLHRGEPDLDTKSEAylqqaqeLVINENILLQTLGFE 137
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
28-213 7.70e-24

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: 97.11  E-value: 7.70e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  28 EKKKRVDAIDVIRKVGIQLNISLHgTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIISAAREIY 107
Cdd:COG5333    41 ELNLVIYYLKLIMDLCTRLNLPQT-VLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLW 119
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826 108 SNaLPYNgvSIESVIEFERILLRTMKFDLTVEAPYDPLLEYCKLLKIpkKQQNSVAQTGWGFLNDCTYTHLPLLWEAEII 187
Cdd:COG5333   120 SE-EPKS--SRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQE--KDKYKLLQIAWKIINDALRTDLCLLYPPHII 194
                         170       180
                  ....*....|....*....|....*....
gi 1376140826 188 AIGAIHLS---LQMNNIENVDYEGRTNDE 213
Cdd:COG5333   195 ALAALLIAcevLGMPIIKLLDFVSYETKE 223
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
3-135 2.17e-23

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: 92.03  E-value: 2.17e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826   3 TNNWIFNEEDMNNTPSQKKGWSSAAEKKKRVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGC 82
Cdd:cd20596     1 SSRWFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVS-QLTINTAIVYMHRFYMHHSFTKFHRNIISPTA 79
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1376140826  83 LFLAGKVEETPKKIKDIISAAREIYSNALP--------YNGVSIESVIeFERILLRTMKFD 135
Cdd:cd20596    80 LFLAAKVEEQPRKLEHVIKVAHACLNPLEPqldtksdaYLQQAQELVI-LETIMLQTLGFE 139
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
4-135 2.85e-21

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: 86.26  E-value: 2.85e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826   4 NNWIFNEEDMNNTPSQKKGWSSAAEKKKRVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCL 83
Cdd:cd20595     1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVS-QLTINTAIVYMHRFYMIQSFTQFHRNSVAPAAL 79
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1376140826  84 FLAGKVEETPKKIKDIISAAREIYSNALPYNGVSIESVIE-------FERILLRTMKFD 135
Cdd:cd20595    80 FLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQqvqdlviLESIILQTLGFE 138
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
28-136 5.59e-20

first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar proteins; Cyclin pch1 is essential for progression through the whole cell cycle. It is a homolog of cyclin T; it forms a heterodimer with its partner kinase, cyclin-dependent kinase 9 (CDK9), that can phosphorylate both the pol II C-terminal domain (CTD) and the CTD of transcription elongation factor Spt5. Yeast Cdk9/Pch1, with mRNA capping enzyme Pct1, may also form an elongation checkpoint for mRNA quality control. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410248 [Multi-domain]  Cd Length: 116  Bit Score: 82.47  E-value: 5.59e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  28 EKKKRVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIISA-AREI 106
Cdd:cd20545     1 EQEDRSKGVNFIIRVGSRLKLP-QTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIAcAKVA 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1376140826 107 YSNALPyngVSIESVIEFER----------ILLRTMKFDL 136
Cdd:cd20545    80 QKNPNL---VIDEQSKEVWRwrdsilyneeVLLETLCFDL 116
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
34-135 6.03e-18

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: 76.83  E-value: 6.03e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  34 DAIDVIRKVGIQLNISLHgTLYTASVYLQRFYMFHSFDEYN-YMVtALGCLFLAGKVEETPKKIKDIISAAREIYSNALP 112
Cdd:cd20534     4 KVLRFIREAGLKLELSSV-TIATACVLYHRFYRELSLEDYDpYLV-AMACLYLAGKAEEQPRRLRDIINVSYRILHPDKP 81
                          90       100
                  ....*....|....*....|....*....
gi 1376140826 113 YNGVSI------ESVIEFERILLRTMKFD 135
Cdd:cd20534    82 PLELDDeywelrDSIVNCELLLLRILKFD 110
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
22-134 3.53e-16

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: 72.59  E-value: 3.53e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  22 GWSSAAEKKKRVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIIS 101
Cdd:cd20532     2 GIDEETEIDLRIYGCELIQDAGILLKLP-QVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVIN 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1376140826 102 AAREIY---------SNALPYNGVSIES----VIEFERILLRTMKF 134
Cdd:cd20532    81 VFHRLLqrrlgkpaeVLPLDIGSAEYEElkndIIKAERRILKELGF 126
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
141-241 5.83e-16

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: 71.24  E-value: 5.83e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826 141 PYDPLLEYCKLLKIPkkQQNSVAQTGWGFLNDCTYTHLPLLWEAEIIAIGAIHLSLQMNNIENVDYEgRTNDEPWWSKVv 220
Cdd:cd20546     2 PYQYLIKFAKKLGVS--DPKELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDLELSP-NEKLNEWWELF- 77
                          90       100
                  ....*....|....*....|.
gi 1376140826 221 gNFTLRSLEGICHKFLDHYSE 241
Cdd:cd20546    78 -GVDEEEIADAINEILDLYSS 97
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
53-135 2.31e-15

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: 69.68  E-value: 2.31e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  53 TLYTASVYLQRFYMFHSF-DEYNYMVtALGCLFLAGKVEETPKKIKDIISAA-REIYSNALPYNGVSIES----VIEFER 126
Cdd:cd20547    22 TLGTAMLLYQRFHLFNPFtDSSNYEV-ALACLFLASKIEDTQKKSKDILAASyNLRHPDKISVDDQMLEEfrkaILGLER 100

                  ....*....
gi 1376140826 127 ILLRTMKFD 135
Cdd:cd20547   101 LLLETICFD 109
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
32-137 8.80e-14

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: 66.00  E-value: 8.80e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  32 RVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEET-PKKIKDIISAAREIYsna 110
Cdd:pfam00134  31 RAILIDWLVEVHEKFKLL-PETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYEEIyPPTVEDLVYITDNAY--- 106
                          90       100
                  ....*....|....*....|....*..
gi 1376140826 111 lpyngvSIESVIEFERILLRTMKFDLT 137
Cdd:pfam00134 107 ------TREEILRMERLILETLNFDLS 127
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
36-132 9.69e-14

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: 65.31  E-value: 9.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  36 IDVIRKVGIQLNISLHgTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIISAAREIYSNALPYNG 115
Cdd:cd20513     6 ANFIQALGERLKLRQR-VIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPSHARLIVAEAKVLKTKFSYEFP 84
                          90
                  ....*....|....*..
gi 1376140826 116 VSIESVIEFERILLRTM 132
Cdd:cd20513    85 YRVNDILECEFYLLEAL 101
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
39-135 2.81e-13

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: 64.85  E-value: 2.81e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  39 IRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIISAAREIYSNALPYNGVSI 118
Cdd:cd20587    19 LQDLGMRLKVP-QVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIVVSYEIIFKKDPSAAQRI 97
                          90       100
                  ....*....|....*....|....*..
gi 1376140826 119 ----------ESVIEFERILLRTMKFD 135
Cdd:cd20587    98 kqkevyeqqkELVLNGEKLVLSTLGFD 124
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
18-134 3.74e-12

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: 61.78  E-value: 3.74e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  18 SQKKGWSSAAEKKKRVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIK 97
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLP-QAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIR 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1376140826  98 DIISAAREI--YSNALPYNGVSIES---------VIEFERILLRTMKF 134
Cdd:cd20591    80 QVLMVFHRMecRRENLPLEPLEPESkkydemkedLIRTERHLLKEMGF 127
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
56-192 5.69e-12

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: 64.08  E-value: 5.69e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  56 TASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIISAAREIYSNALpyngvsiESVIEFERILLRTMKFD 135
Cdd:TIGR00569  81 TAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKETPLKAL-------EQVLEYELLLIQQLNFH 153
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826 136 LTVEAPYDPL---LEYCKLLKIPKKQQNSVAQTGWGFLNDCTYTHLPLLWEAEIIAIGAI 192
Cdd:TIGR00569 154 LIVHNPYRPLegfLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAI 213
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
34-127 6.12e-12

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: 59.73  E-value: 6.12e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  34 DAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIISAAreiysnalpy 113
Cdd:cd00043     1 KAVDFIRRLCSKLGLP-EEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVS---------- 69
                          90
                  ....*....|....
gi 1376140826 114 nGVSIESVIEFERI 127
Cdd:cd00043    70 -GVSEKELRKAEKE 82
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
139-239 1.51e-11

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: 59.08  E-value: 1.51e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826 139 EAPYDPLLEYCKLLKipkKQQNSVAQTGWGFLNDCTYTHLPLLWEAEIIAIGAIHLSLQMNNIEnvdyEGRTNDEPWWSK 218
Cdd:cd20588     1 EHPYKPLVAAIKKFN---VAQNALAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVK----LPCDGRKVWWQE 73
                          90       100
                  ....*....|....*....|.
gi 1376140826 219 VvgNFTLRSLEGICHKFLDHY 239
Cdd:cd20588    74 F--DVTPRQLEEVSNQMLELY 92
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
37-130 2.41e-11

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: 58.37  E-value: 2.41e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826   37 DVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIISAAReiysnalpynGV 116
Cdd:smart00385   1 DFLRRVCKALNLD-PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTG----------YF 69
                           90
                   ....*....|....
gi 1376140826  117 SIESVIEFERILLR 130
Cdd:smart00385  70 TEEEILRMERLLLE 83
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
5-101 8.69e-11

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: 58.86  E-value: 8.69e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826   5 NWIFNEEDMNNTPSQKKGWSSAAEKKKRVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLF 84
Cdd:cd20590    17 NCLLPEERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLP-QVAMATGQVLFQRFFYTKSFVKHSMEHVSMACVH 95
                          90
                  ....*....|....*..
gi 1376140826  85 LAGKVEETPKKIKDIIS 101
Cdd:cd20590    96 LASKIEEAPRRIRDVIN 112
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
27-134 1.57e-10

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: 57.06  E-value: 1.57e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  27 AEKKKRVDAIDVIRKVGIQLNISlHGTLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIIS----- 101
Cdd:cd20589     7 TETDLRILGCELIQTAGILLRLP-QVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVINvfhhi 85
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1376140826 102 ----AAREIYSNALPYNGVSIES-VIEFERILLRTMKF 134
Cdd:cd20589    86 kqvrGKRTISPLILDQNYINLKNqVIKAERRVLKELGF 123
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
54-136 8.72e-10

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: 55.68  E-value: 8.72e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  54 LYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIIsaareiysNALPYNGVSIESVIEFERILLRTMK 133
Cdd:cd20524    76 LATALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVEEFNISIDQFV--------GNIKESEKTAEIILEYELLLLQGLN 147

                  ...
gi 1376140826 134 FDL 136
Cdd:cd20524   148 FHL 150
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
141-240 1.77e-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: 53.80  E-value: 1.77e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826 141 PYDPLLEYCKLLK--IPKKQQNS--VAQTGWGFLNDCTYTHLPLLWEAEIIAIGAIHLSLQMNNIENVDYEGRTNdePWW 216
Cdd:cd20535     2 PHKYLLHYLKSLRdwLNPEFWSRspIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQVYGVKVPPEEEAEK--PWW 79
                          90       100
                  ....*....|....*....|....
gi 1376140826 217 SKVVGNFTLRSLEGICHKFLDHYS 240
Cdd:cd20535    80 QAFCEDLTKETIDEIIEDIINVYD 103
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
141-240 1.50e-06

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: 45.29  E-value: 1.50e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826 141 PYDPLLEYCKLLKIPKKQQnsVAQTGWGFLNDCTYTHLPLLWEAEIIAIGAIHLSLQMNNIEnvdyegRTNDEPWWSkvV 220
Cdd:cd20533     2 PHKFILMYLQVLEGEDNKK--LAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAARELGIP------LPLPPPWWE--L 71
                          90       100
                  ....*....|....*....|
gi 1376140826 221 GNFTLRSLEGICHKFLDHYS 240
Cdd:cd20533    72 FDVSKEDIEEICLTILELYT 91
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
56-134 2.91e-06

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


Pssm-ID: 410274 [Multi-domain]  Cd Length: 107  Bit Score: 44.85  E-value: 2.91e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1376140826  56 TASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIISAAREIYSNAlpYNGVSIESVIEFERILLRTMKF 134
Cdd:cd20571    30 TAITYFRRVYTRKSFTEYDPRLVAPTCLYLASKAEESTVQAKLLVFYMKRLYADE--YHRYEIKDILEMEMKLLEALDY 106
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
56-136 3.69e-06

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: 45.97  E-value: 3.69e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  56 TASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEETPKKIKDIisaAREIysnalpynGVSIESVIEFERILLRTMKFD 135
Cdd:cd20585   101 TALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEEYHVSAEEL---GKGI--------QQDHQLILKNELALLQGLNFD 169

                  .
gi 1376140826 136 L 136
Cdd:cd20585   170 L 170
CYCLIN_AtCycD-like_rpt1 cd20543
first cyclin box found in plant cyclin-delta family; This subfamily is composed of plant delta ...
32-92 4.22e-05

first cyclin box found in plant cyclin-delta family; This subfamily is composed of plant delta family cyclins, including a group of G1/S-specific D-type cyclins from Arabidopsis thaliana which may activate the cell cycle in the root apical meristem (RAM) and promote embryonic root (radicle) protrusion. 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: 410246  Cd Length: 99  Bit Score: 41.53  E-value: 4.22e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1376140826  32 RVDAIDVIRKVGIQLNISlHGTLYTASVYLQRF---YMFHSFDEYNYMVTALGCLFLAGKVEET 92
Cdd:cd20543     2 RNEAIDWILKVRSRYGFG-PLTAYLAVNYLDRFlssYDLPKDKPWMLQLLAVACLSLAAKMEET 64
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
141-195 4.35e-05

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: 41.07  E-value: 4.35e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1376140826 141 PYDPLLEYCKLLKipkkQQNSVAQTGWGFLNDCTYTHLPLLWEAEIIAIGAIHLS 195
Cdd:cd20514     2 PYRPLTQYVQDAG----LDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMA 52
CYCLIN_CNTD2 cd20542
cyclin box found in Cyclin N-terminal domain-containing protein 2 (CNTD2) and similar proteins; ...
53-136 4.87e-05

cyclin box found in Cyclin N-terminal domain-containing protein 2 (CNTD2) and similar proteins; CNTD2 is an atypical cyclin upregulated in human cancer tissues. It promotes cell proliferation and migration, as well as increases tumor growth in vivo. It can function as a prognostic factor and drug target. CNTD2 contains one cyclin box. The cyclin box is a protein binding domain.


Pssm-ID: 410245 [Multi-domain]  Cd Length: 96  Bit Score: 41.15  E-value: 4.87e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826  53 TLYTASVYLQRFYMFHSFDEYNYMVTALGCLFLAGKVEET-PKKIKDIISAAREIYSNAlpyngvsieSVIEFERILLRT 131
Cdd:cd20542    21 TLHLAVALLDRYLSRQKISLSLLQLLGITCLFIACKFEERfPPEVATLCYLTDDSYSKK---------QVLRMERRVLRR 91

                  ....*
gi 1376140826 132 MKFDL 136
Cdd:cd20542    92 LRFDL 96
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
141-242 6.33e-04

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


Pssm-ID: 410295 [Multi-domain]  Cd Length: 123  Bit Score: 38.82  E-value: 6.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376140826 141 PYDPLLEYCKLLKIPKKQqnSVAQTGWGFLNDCTYTHLPLLWEAEIIAIGAIHLSLQMNNIEnvdyegrTNDEPWWSKVV 220
Cdd:cd20592     3 PHKIIVMYLQVLECERNQ--TLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIP-------LPNRPHWFLLF 73
                          90       100
                  ....*....|....*....|..
gi 1376140826 221 GNfTLRSLEGICHKFLDHYSEQ 242
Cdd:cd20592    74 GA-TEEEIQEICITTLKLYTRK 94
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
138-216 1.25e-03

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: 37.15  E-value: 1.25e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1376140826 138 VEAPYDPLLEYCKLLKIPKKQQnsvaQTGWGFLNDCTYTHLPLLWEAEIIAIGAIHLSLQMNNIEnvdyegRTNDEPWW 216
Cdd:cd20594     2 VEHPHKFILNYLAMLMAPPELR----QEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVP------LPENPPWW 70
 
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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