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Conserved domains on  [gi|28574303|ref|NP_788082|]
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cyclin K, isoform A [Drosophila melanogaster]

Protein Classification

Graphical summary

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List of domain hits

 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 ...
 20-134 2.47e-81

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: 244.83  E-value: 2.47e-81
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  20 GISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIKT 99
Cdd:cd20530   1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                        90       100       110
                ....*....|....*....|....*....|....*
gi 28574303 100 ARGILTDNYFYSFGDDPKEEVMTLERILLQTIKFD 134
Cdd:cd20530  81 ARSLLNDKQFAQFGDDPKEEVMVLERILLQTIKFD 115
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 138-239 2.47e-68

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: 211.04  E-value: 2.47e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 138 EHPYTFLLKYAKCFKGDQQKLQKMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKLSKFTVQDWeGRQPQQQRWWD 217
Cdd:cd20531   1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDW-TSKPPGKRWWE 79

                        90       100
                ....*....|....*....|..
gi 28574303 218 MFVSDVTMEILEDICHQVLDLY 239
Cdd:cd20531  80 QFVEDVSLEVLEDICHQVLDLY 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 ...
 20-134 2.47e-81

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: 244.83  E-value: 2.47e-81
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  20 GISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIKT 99
Cdd:cd20530   1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                        90       100       110
                ....*....|....*....|....*....|....*
gi 28574303 100 ARGILTDNYFYSFGDDPKEEVMTLERILLQTIKFD 134
Cdd:cd20530  81 ARSLLNDKQFAQFGDDPKEEVMVLERILLQTIKFD 115
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 138-239 2.47e-68

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: 211.04  E-value: 2.47e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 138 EHPYTFLLKYAKCFKGDQQKLQKMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKLSKFTVQDWeGRQPQQQRWWD 217
Cdd:cd20531   1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDW-TSKPPGKRWWE 79

                        90       100
                ....*....|....*....|..
gi 28574303 218 MFVSDVTMEILEDICHQVLDLY 239
Cdd:cd20531  80 QFVEDVSLEVLEDICHQVLDLY 101
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 33-264 1.29e-27

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: 110.59  E-value: 1.29e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  33 GARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIKTARGILTDNYfYSF 112
Cdd:COG5333  48 YLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEP-KSS 126

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 113 gddpKEEVMTLERILLQTIKFDLQVEHPYTFLLKYAKCFKGDQQKlqKMVQMAWNFVNDSLSTVVCLQWEPEIIAVA-LI 191
Cdd:COG5333 127 ----RERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKY--KLLQIAWKIINDALRTDLCLLYPPHIIALAaLL 200

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 192 HLASKLSKFTVQDW--EGRQPQQQRwwdmfVSDVTMEILE------DICHQVLDLYQSTQKEALQPTSPPQKPPSRADSP 263
Cdd:COG5333 201 IACEVLGMPIIKLLdfVSYETKEEV-----IALNYKSIVKnkiktfKAEHLSRDLPFTLQNIAEPQFALDKKPKSEEEAD 275


                .
gi 28574303 264 K 264
Cdd:COG5333 276 K 276
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 3-135 4.47e-13

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: 65.62  E-value: 4.47e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303     3 CWYYDKKELRETPSiLDGISFETE--RRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCL 80
Cdd:pfam00134   3 FQYLRELELKYLPK-PDYMDQQPDinPKMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 28574303    81 FFAGKVEET-PKKCRDIIktargILTDNYFYsfgddpKEEVMTLERILLQTIKFDL 135
Cdd:pfam00134  82 FIAAKYEEIyPPTVEDLV-----YITDNAYT------REEILRMERLILETLNFDL 126
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 35-129 1.30e-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: 63.00  E-value: 1.30e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303     35 RFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIKTArgiltdnyfysfGD 114
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT------------GY 68

                           90
                   ....*....|....*
gi 28574303    115 DPKEEVMTLERILLQ 129
Cdd:smart00385  69 FTEEEILRMERLLLE 83
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 52-197 7.71e-10

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: 59.46  E-value: 7.71e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303    52 ATGVVYFHRFYMFHSFRSF-PRYVTACCcLFFAGKVEE----TPKKCRDIIKTARGILtdnyfysfgddpkEEVMTLERI 126
Cdd:TIGR00569  80 GTAIMYFKRFYLNNSVMEYhPKIIMLTC-VFLACKVEEfnvsIDQFVGNLKETPLKAL-------------EQVLEYELL 145

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28574303   127 LLQTIKFDLQVEHPYT----FLLKYAKCFKGdQQKLQKMVQMAWNFVNDSLSTVVCLQWEPEIIAV-ALIHLASKL 197
Cdd:TIGR00569 146 LIQQLNFHLIVHNPYRplegFLIDIKTRLPG-LENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALaAILHTASRA 220
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 142-197 9.52e-07

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: 46.43  E-value: 9.52e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 28574303    142 TFLLKYAKCFKGDQQklqkMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKL 197
Cdd:smart00385   1 DFLRRVCKALNLDPE----TLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKT 52
 
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 ...
 20-134 2.47e-81

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: 244.83  E-value: 2.47e-81
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  20 GISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIKT 99
Cdd:cd20530   1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                        90       100       110
                ....*....|....*....|....*....|....*
gi 28574303 100 ARGILTDNYFYSFGDDPKEEVMTLERILLQTIKFD 134
Cdd:cd20530  81 ARSLLNDKQFAQFGDDPKEEVMVLERILLQTIKFD 115
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 138-239 2.47e-68

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: 211.04  E-value: 2.47e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 138 EHPYTFLLKYAKCFKGDQQKLQKMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKLSKFTVQDWeGRQPQQQRWWD 217
Cdd:cd20531   1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDW-TSKPPGKRWWE 79

                        90       100
                ....*....|....*....|..
gi 28574303 218 MFVSDVTMEILEDICHQVLDLY 239
Cdd:cd20531  80 QFVEDVSLEVLEDICHQVLDLY 101
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 4-134 3.73e-38

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: 134.06  E-value: 3.73e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303   4 WYYDKKELRETPSILDGISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFA 83
Cdd:cd20538   2 WYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFLA 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 28574303  84 GKVEETPKKCRDIIKTARGILtdnYFYSFGDDPKEEV--------MTLERILLQTIKFD 134
Cdd:cd20538  82 AKVEEQPRKLEHVIKVAHACL---HRGEPDLDTKSEAylqqaqelVINENILLQTLGFE 137
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 33-264 1.29e-27

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: 110.59  E-value: 1.29e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  33 GARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIKTARGILTDNYfYSF 112
Cdd:COG5333  48 YLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEP-KSS 126

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 113 gddpKEEVMTLERILLQTIKFDLQVEHPYTFLLKYAKCFKGDQQKlqKMVQMAWNFVNDSLSTVVCLQWEPEIIAVA-LI 191
Cdd:COG5333 127 ----RERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKY--KLLQIAWKIINDALRTDLCLLYPPHIIALAaLL 200

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 192 HLASKLSKFTVQDW--EGRQPQQQRwwdmfVSDVTMEILE------DICHQVLDLYQSTQKEALQPTSPPQKPPSRADSP 263
Cdd:COG5333 201 IACEVLGMPIIKLLdfVSYETKEEV-----IALNYKSIVKnkiktfKAEHLSRDLPFTLQNIAEPQFALDKKPKSEEEAD 275


                .
gi 28574303 264 K 264
Cdd:COG5333 276 K 276
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
 4-134 1.87e-27

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: 105.90  E-value: 1.87e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303   4 WYYDKKELRETPSILDGISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFA 83
Cdd:cd20596   4 WFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTALFLA 83

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28574303  84 GKVEETPKKCRDIIKTARGIL----------TDNYFYSfgddpKEEVMTLERILLQTIKFD 134
Cdd:cd20596  84 AKVEEQPRKLEHVIKVAHACLnplepqldtkSDAYLQQ-----AQELVILETIMLQTLGFE 139
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 139-241 2.75e-26

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: 101.29  E-value: 2.75e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 139 HPYTFLLKYAKCFKGDQQKlqKMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKLSKftVQDWEGRQPQQQRWWDM 218
Cdd:cd20546   1 HPYQYLIKFAKKLGVSDPK--ELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLG--IDLELSPNEKLNEWWEL 76

                        90       100
                ....*....|....*....|...
gi 28574303 219 FvsDVTMEILEDICHQVLDLYQS 241
Cdd:cd20546  77 F--GVDEEEIADAINEILDLYSS 97
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 30-134 1.94e-25

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: 99.17  E-value: 1.94e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  30 RKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIKTA-------RG 102
Cdd:cd20534   2 HFKVLRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSyrilhpdKP 81

                        90       100       110
                ....*....|....*....|....*....|..
gi 28574303 103 ILTDNYFYsfgDDPKEEVMTLERILLQTIKFD 134
Cdd:cd20534  82 PLELDDEY---WELRDSIVNCELLLLRILKFD 110
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 4-134 3.13e-25

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


Pssm-ID: 410298 [Multi-domain]  Cd Length: 138  Bit Score: 99.74  E-value: 3.13e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303   4 WYYDKKELRETPSILDGISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFA 83
Cdd:cd20595   3 WYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALFLA 82

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28574303  84 GKVEETPKKCRDIIKTARGIL----------TDNYFYSFGDdpkeeVMTLERILLQTIKFD 134
Cdd:cd20595  83 AKVEEQPKKLEHVIKVAHTCLhpqeslpdtrSEAYLQQVQD-----LVILESIILQTLGFE 138
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 139-240 9.89e-24

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: 94.21  E-value: 9.89e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 139 HPYTFLLKYAKCFKGDQQKlqKMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKlskftvqDWEGRQPQQQRWWDM 218
Cdd:cd20533   1 HPHKFILMYLQVLEGEDNK--KLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAAR-------ELGIPLPLPPPWWEL 71

                        90       100
                ....*....|....*....|..
gi 28574303 219 FvsDVTMEILEDICHQVLDLYQ 240
Cdd:cd20533  72 F--DVSKEDIEEICLTILELYT 91
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 26-135 5.62e-22

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: 90.18  E-value: 5.62e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  26 ERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIKTARGILT 105
Cdd:cd20545   1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQ 80

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 28574303 106 DNYFYSFGDDPKE------EVMTLERILLQTIKFDL 135
Cdd:cd20545  81 KNPNLVIDEQSKEvwrwrdSILYNEEVLLETLCFDL 116
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 138-240 7.48e-22

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: 89.13  E-value: 7.48e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 138 EHPYTFLLKYAKCFKGDQQKLqkmVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKLSKFTVQDwEGRQPqqqrWWD 217
Cdd:cd20588   1 EHPYKPLVAAIKKFNVAQNAL---AQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPC-DGRKV----WWQ 72

                        90       100
                ....*....|....*....|...
gi 28574303 218 MFvsDVTMEILEDICHQVLDLYQ 240
Cdd:cd20588  73 EF--DVTPRQLEEVSNQMLELYE 93
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 29-134 8.91e-21

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: 86.63  E-value: 8.91e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  29 YRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIKTA---RGILT 105
Cdd:cd20547   1 LRLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASynlRHPDK 80

                        90       100
                ....*....|....*....|....*....
gi 28574303 106 DNYFYSFGDDPKEEVMTLERILLQTIKFD 134
Cdd:cd20547  81 ISVDDQMLEEFRKAILGLERLLLETICFD 109
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 19-133 4.95e-19

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: 82.22  E-value: 4.95e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  19 DGISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIK 98
Cdd:cd20532   1 DGIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVIN 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 28574303  99 T-----------ARGILTDNYFYSFGDDPKEEVMTLERILLQTIKF 133
Cdd:cd20532  81 VfhrllqrrlgkPAEVLPLDIGSAEYEELKNDIIKAERRILKELGF 126
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 19-134 2.11e-17

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: 77.94  E-value: 2.11e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  19 DGISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIK 98
Cdd:cd20587   1 DGIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIV 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 28574303  99 TARGIL-------------TDNYfysfgDDPKEEVMTLERILLQTIKFD 134
Cdd:cd20587  81 VSYEIIfkkdpsaaqrikqKEVY-----EQQKELVLNGEKLVLSTLGFD 124
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 19-133 6.19e-17

first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; Cyclin-L1-1 (CycL1), also called arginine-rich cyclin 1 (AtRCY1), or protein MODIFIER OF SNC1 12, is the cognate cyclin for cyclin-dependent kinase G1 (CDKG1). It is involved in regulation of DNA methylation and transcriptional silencing. It is required for synapsis and male meiosis, and for the proper splicing of specific resistance (R) genes. L-type cyclins contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410294 [Multi-domain]  Cd Length: 128  Bit Score: 76.41  E-value: 6.19e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  19 DGISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDI-- 96
Cdd:cd20591   4 DGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQVlm 83

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 28574303  97 ----IKTARGILTDNYFYSFG---DDPKEEVMTLERILLQTIKF 133
Cdd:cd20591  84 vfhrMECRRENLPLEPLEPESkkyDEMKEDLIRTERHLLKEMGF 127
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 139-240 1.09e-15

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: 72.29  E-value: 1.09e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 139 HPYTFLLKYAKC----FKGDQQKLQKMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKLSKFTVQDWEGrqpQQQR 214
Cdd:cd20535   1 LPHKYLLHYLKSlrdwLNPEFWSRSPIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQVYGVKVPPEEE---AEKP 77

                        90       100
                ....*....|....*....|....*.
gi 28574303 215 WWDMFVSDVTMEILEDICHQVLDLYQ 240
Cdd:cd20535  78 WWQAFCEDLTKETIDEIIEDIINVYD 103
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 138-239 3.22e-13

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: 65.79  E-value: 3.22e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 138 EHPYTFLLKYAKCFKGDQQklQKMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKLSKFTVqdwegrqPQQQRWWD 217
Cdd:cd20592   1 KHPHKIIVMYLQVLECERN--QTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPL-------PNRPHWFL 71

                        90       100
                ....*....|....*....|..
gi 28574303 218 MFvsDVTMEILEDICHQVLDLY 239
Cdd:cd20592  72 LF--GATEEEIQEICITTLKLY 91
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 137-240 3.96e-13

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: 64.88  E-value: 3.96e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 137 VEHPYTFLLKYAKCFKgdqqKLQKMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKlsKFTVQdwegrQPQQQRWW 216
Cdd:cd20594   2 VEHPHKFILNYLAMLM----APPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAAR--RFQVP-----LPENPPWW 70

                        90       100
                ....*....|....*....|....
gi 28574303 217 DMFvsDVTMEILEDICHQVLDLYQ 240
Cdd:cd20594  71 KVF--DAEKAEIDVVCKVLADLYR 92
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 3-135 4.47e-13

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: 65.62  E-value: 4.47e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303     3 CWYYDKKELRETPSiLDGISFETE--RRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCL 80
Cdd:pfam00134   3 FQYLRELELKYLPK-PDYMDQQPDinPKMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 28574303    81 FFAGKVEET-PKKCRDIIktargILTDNYFYsfgddpKEEVMTLERILLQTIKFDL 135
Cdd:pfam00134  82 FIAAKYEEIyPPTVEDLV-----YITDNAYT------REEILRMERLILETLNFDL 126
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 19-133 6.46e-13

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


Pssm-ID: 410292 [Multi-domain]  Cd Length: 124  Bit Score: 65.15  E-value: 6.46e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  19 DGISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDII- 97
Cdd:cd20589   1 DGLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVIn 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 28574303  98 -----KTARG-------ILTDNYFysfgdDPKEEVMTLERILLQTIKF 133
Cdd:cd20589  81 vfhhiKQVRGkrtisplILDQNYI-----NLKNQVIKAERRVLKELGF 123
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 139-246 8.47e-13

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: 64.60  E-value: 8.47e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 139 HPYTFLLKYAKCFkgDQQKLQKMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKLSKFTVqdwegrqPQQQRWWDM 218
Cdd:cd20593   1 HPHKIIVMYLQVL--ECERNRHLVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEIPL-------PNRPHWFLL 71

                        90       100
                ....*....|....*....|....*...
gi 28574303 219 FvsDVTMEILEDICHQVLDLYqsTQKEA 246
Cdd:cd20593  72 F--GATEEEIQEICLKILQLY--TRKKV 95
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 35-129 1.30e-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: 63.00  E-value: 1.30e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303     35 RFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIKTArgiltdnyfysfGD 114
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT------------GY 68

                           90
                   ....*....|....*
gi 28574303    115 DPKEEVMTLERILLQ 129
Cdd:smart00385  69 FTEEEILRMERLLLE 83
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 11-97 1.43e-12

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: 65.03  E-value: 1.43e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  11 LRETPSILDGISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETP 90
Cdd:cd20590  25 LRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVKHSMEHVSMACVHLASKIEEAP 104


                ....*..
gi 28574303  91 KKCRDII 97
Cdd:cd20590 105 RRIRDVI 111
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 36-128 2.02e-12

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: 63.00  E-value: 2.02e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  36 FIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSF-PRYVtACCCLFFAGKVEETPKKCRDIIKTARGILT-DNYFYSFg 113
Cdd:cd20513   8 FIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIdPRLV-APTCLYLASKVEECPSHARLIVAEAKVLKTkFSYEFPY- 85

                        90
                ....*....|....*
gi 28574303 114 ddPKEEVMTLERILL 128
Cdd:cd20513  86 --RVNDILECEFYLL 98
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 139-239 3.96e-12

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: 61.87  E-value: 3.96e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 139 HPYTFLLKYAKcfkgDQQKLQKMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKLSKFTVQDWegrqpqqqrwwdm 218
Cdd:cd20514   1 HPYRPLTQYVQ----DAGLDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDARQW------------- 63

                        90       100
                ....*....|....*....|..
gi 28574303 219 FVS-DVTMEILEDICHQVLDLY 239
Cdd:cd20514  64 FAElNVDMDKILEITREILSLY 85
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 32-101 7.41e-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: 60.89  E-value: 7.41e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  32 EGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIIKTAR 101
Cdd:cd00043   1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSG 70
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 52-197 7.71e-10

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: 59.46  E-value: 7.71e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303    52 ATGVVYFHRFYMFHSFRSF-PRYVTACCcLFFAGKVEE----TPKKCRDIIKTARGILtdnyfysfgddpkEEVMTLERI 126
Cdd:TIGR00569  80 GTAIMYFKRFYLNNSVMEYhPKIIMLTC-VFLACKVEEfnvsIDQFVGNLKETPLKAL-------------EQVLEYELL 145

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28574303   127 LLQTIKFDLQVEHPYT----FLLKYAKCFKGdQQKLQKMVQMAWNFVNDSLSTVVCLQWEPEIIAV-ALIHLASKL 197
Cdd:TIGR00569 146 LIQQLNFHLIVHNPYRplegFLIDIKTRLPG-LENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALaAILHTASRA 220
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
 138-242 3.10e-09

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: 54.32  E-value: 3.10e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 138 EHPYTFLLKYAKCFKGDQQKLQKMVQMAWNFVNdslSTVVCLQWEPEIIAVALIHLASKLSkftvqDWE-GRQPQQQRWW 216
Cdd:cd20598   1 EHPHTDVVKCTQLVRASKDLAQTSYFMATNSLH---LTTFCLQYKPTVIACVCIHLACKWS-----NWEiPVSTDGKHWW 72

                        90       100
                ....*....|....*....|....*.
gi 28574303 217 DMFVSDVTMEILEDICHQVLDLYQST 242
Cdd:cd20598  73 EYVDPTVTLELLDELTHEFLQILEKT 98
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 138-242 9.86e-09

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: 52.77  E-value: 9.86e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 138 EHPYTFLLKYAKCFKGDQQKLQKMVQMAWNFVNdslSTVVCLQWEPEIIAVALIHLASKLSkftvqDWE-GRQPQQQRWW 216
Cdd:cd20597   1 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLH---LTTFSLQYTPPVVACVCIHLACKWS-----NWEiPVSTDGKHWW 72

                        90       100
                ....*....|....*....|....*.
gi 28574303 217 DMFVSDVTMEILEDICHQVLDLYQST 242
Cdd:cd20597  73 EYVDATVTLELLDELTHEFLQILEKT 98
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 8-135 4.36e-08

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: 51.83  E-value: 4.36e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303   8 KKELRETPSILDGISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVE 87
Cdd:cd20524  33 KESLKEEDAEPKFLTPEEELLLVRYYEKKLLEFCRAFKLPDSVLATALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVE 112

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 28574303  88 ETPkkcRDIIKTARGILTDnyfysfgDDPKEEVMTLERILLQTIKFDL 135
Cdd:cd20524 113 EFN---ISIDQFVGNIKES-------EKTAEIILEYELLLLQGLNFHL 150
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
 21-135 1.48e-07

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: 50.98  E-value: 1.48e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  21 ISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSFPRYVTACCCLFFAGKVEETPKKCRDIiktA 100
Cdd:cd20585  69 LSADEELLMLKYYEQKIQEVCRALRLPNKIQATALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEEYHVSAEEL---G 145

                        90       100       110
                ....*....|....*....|....*....|....*
gi 28574303 101 RGIltdnyfysfgDDPKEEVMTLERILLQTIKFDL 135
Cdd:cd20585 146 KGI----------QQDHQLILKNELALLQGLNFDL 170
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 139-236 4.29e-07

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: 47.65  E-value: 4.29e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 139 HPYTFLLKyakCFKGDQQKLQKMVQMAWNFVNDSLS-TVVCLQWEPEIIAVALIHLASKLSkftvqDWEGRQPQQQR-WW 216
Cdd:cd20539   1 HPHTHVLK---ICNLVKAGSKDLAQTAYFLATNSLHlTTFCLQYKPTVIACVCIHLACKWS-----NWEIPRSSEGKdWY 72

                        90       100
                ....*....|....*....|
gi 28574303 217 DMFVSDVTMEILEDICHQVL 236
Cdd:cd20539  73 EYVDPSLTLEELDELTSEFL 92
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 142-197 9.52e-07

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: 46.43  E-value: 9.52e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 28574303    142 TFLLKYAKCFKGDQQklqkMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKL 197
Cdd:smart00385   1 DFLRRVCKALNLDPE----TLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKT 52
CYCLIN_AtCycC_rpt2 cd20572
second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 139-241 6.84e-06

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: 44.38  E-value: 6.84e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303 139 HPYTFLLKYAKcfkgdQQKLQKMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKLSKFTVQDW--EGRqpqqqrww 216
Cdd:cd20572   1 HPYRPLIQLLQ-----DAGLTDMTQFTWSIVNDTYRTDLILIHPPYMIALACIYIASVHKEKDITLWfeELR-------- 67

                        90       100
                ....*....|....*....|....*
gi 28574303 217 dmfvsdVTMEILEDICHQVLDLYQS 241
Cdd:cd20572  68 ------VDMNIIKNIAMEILDFYDN 86
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 36-124 3.10e-05

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: 42.92  E-value: 3.10e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28574303  36 FIMECGTKMGLGHNTMATGVVYFHRFYMFHSFRSF-PRYVtACCCLFFAGKVEETPKKCRDIIKTARGILTDNYF-YSFG 113
Cdd:cd20571  13 YIKKLAQHIKVRQRVVATAITYFRRVYTRKSFTEYdPRLV-APTCLYLASKAEESTVQAKLLVFYMKRLYADEYHrYEIK 91

                        90
                ....*....|.
gi 28574303 114 DDPKEEVMTLE 124
Cdd:cd20571  92 DILEMEMKLLE 102
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 139-206 3.85e-04

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: 38.93  E-value: 3.85e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28574303 139 HPYTFLLKYAKCFKGDQQklqkMVQMAWNFVNDSLSTVVCLQWEPEIIAVALIHLASKLSKFTVQDWE 206
Cdd:cd00043   1 KAVDFIRRLCSKLGLPEE----VLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKE 64
 
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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