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Conserved domains on  [gi|2093551169|ref|XP_043476765|]
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cyclin-K-like [Leptopilina heterotoma]

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 4.53e-79

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: 239.44  E-value: 4.53e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  20 GIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDIIKT 99
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2093551169 100 AKGILSDQKFVTFGEDPKEEVMTLERILLQTIKFD 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 6.80e-73

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: 222.98  E-value: 6.80e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 138 EHPYSYLLKYAKSLKGDKNKLQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKFEVVDWnGRQPKHLRWWD 217
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDW-TSKPPGKRWWE 79

                          90       100
                  ....*....|....*....|..
gi 2093551169 218 MFVEDVTMDLLEDICHQVLDLY 239
Cdd:cd20531    80 QFVEDVSLEVLEDICHQVLDLY 101
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 243-410 1.42e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 44.37  E-value: 1.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 243 NNAKPPDSPPLIASTETVRErlIAPPSIESASSTPNAGITVKPSKTETNSVPTNGCNTTevienskpieVAVHFPSYPTN 322
Cdd:pfam03154 178 SGAASPPSPPPPGTTQAATA--GPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQT----------PTLHPQRLPSP 245

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 323 FASTTNYPPVYPPTNIS---VPPPNVNTlnHIVPTTHNLGT-PSSVrqiptvstptQQPFPPYGYPSNSSFFSGGTPTGP 398
Cdd:pfam03154 246 HPPLQPMTQPPPPSQVSpqpLPQPSLHG--QMPPMPHSLQTgPSHM----------QHPVPPQPFPLTPQSSQSQVPPGP 313

                         170
                  ....*....|....*....
gi 2093551169 399 S------SNQRSYYP-SQS 410
Cdd:pfam03154 314 SpaapgqSQQRIHTPpSQS 332
 
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 4.53e-79

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: 239.44  E-value: 4.53e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  20 GIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDIIKT 99
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2093551169 100 AKGILSDQKFVTFGEDPKEEVMTLERILLQTIKFD 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 6.80e-73

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: 222.98  E-value: 6.80e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 138 EHPYSYLLKYAKSLKGDKNKLQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKFEVVDWnGRQPKHLRWWD 217
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDW-TSKPPGKRWWE 79

                          90       100
                  ....*....|....*....|..
gi 2093551169 218 MFVEDVTMDLLEDICHQVLDLY 239
Cdd:cd20531    80 QFVEDVSLEVLEDICHQVLDLY 101
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 21-197 2.65e-26

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: 107.13  E-value: 2.65e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  21 IDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPkkcKDIikTA 100
Cdd:COG5333    36 LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTP---RDI--SI 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 101 KGILSDQKFVTFGEDPKEEVMTLERILLQTIKFDLQVEHPYSYLLKYAKSLKGDKNKlqKMVQMAWTFVNDSLCTTLCLQ 180
Cdd:COG5333   111 ESFEARDLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKY--KLLQIAWKIINDALRTDLCLL 188

                         170
                  ....*....|....*..
gi 2093551169 181 WEPEIIAVALMYLAGKL 197
Cdd:COG5333   189 YPPHIIALAALLIACEV 205
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 3-135 1.10e-11

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: 61.76  E-value: 1.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169   3 CWYYEKKNLKNTPSVQD-GIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLF 81
Cdd:pfam00134   3 FQYLRELELKYLPKPDYmDQQPDINPKMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLF 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2093551169  82 LAGKVEET-PKKCKDIIktakgILSDQKFvtfgedPKEEVMTLERILLQTIKFDL 135
Cdd:pfam00134  83 IAAKYEEIyPPTVEDLV-----YITDNAY------TREEILRMERLILETLNFDL 126
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 35-129 4.71e-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: 4.71e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169   35 RFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDIIKTAkgilsdqkfvtfGE 114
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT------------GY 68

                           90
                   ....*....|....*
gi 2093551169  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 ...
 52-192 1.60e-09

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: 58.69  E-value: 1.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  52 ATGVVYFHRFYMFHSFKTF-PRFVTAcSCLFLAGKVEE----TPKKCKDIIKTAKGILsdqkfvtfgedpkEEVMTLERI 126
Cdd:TIGR00569  80 GTAIMYFKRFYLNNSVMEYhPKIIML-TCVFLACKVEEfnvsIDQFVGNLKETPLKAL-------------EQVLEYELL 145

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 127 LLQTIKFDLQVEHPY----SYLLKYAKSLKGDKNkLQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMY 192
Cdd:TIGR00569 146 LIQQLNFHLIVHNPYrpleGFLIDIKTRLPGLEN-PEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAIL 214
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 143-197 1.14e-04

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: 40.65  E-value: 1.14e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2093551169  143 YLLKYAKSLKGDknklQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKL 197
Cdd:smart00385   2 FLRRVCKALNLD----PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKT 52
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 243-410 1.42e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 44.37  E-value: 1.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 243 NNAKPPDSPPLIASTETVRErlIAPPSIESASSTPNAGITVKPSKTETNSVPTNGCNTTevienskpieVAVHFPSYPTN 322
Cdd:pfam03154 178 SGAASPPSPPPPGTTQAATA--GPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQT----------PTLHPQRLPSP 245

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 323 FASTTNYPPVYPPTNIS---VPPPNVNTlnHIVPTTHNLGT-PSSVrqiptvstptQQPFPPYGYPSNSSFFSGGTPTGP 398
Cdd:pfam03154 246 HPPLQPMTQPPPPSQVSpqpLPQPSLHG--QMPPMPHSLQTgPSHM----------QHPVPPQPFPLTPQSSQSQVPPGP 313

                         170
                  ....*....|....*....
gi 2093551169 399 S------SNQRSYYP-SQS 410
Cdd:pfam03154 314 SpaapgqSQQRIHTPpSQS 332
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 267-381 8.42e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 38.37  E-value: 8.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 267 PPSiesaSSTPNAGITVKPSKTETNSVPTNGcNTTEVIENSKPIEVAVHFPSYPTNFASTTNYPPVYPPTNISVPPPNVN 346
Cdd:PLN03209  449 PPT----SPSPTAPTGVSPSVSSTSSVPAVP-DTAPATAATDAAAPPPANMRPLSPYAVYDDLKPPTSPSPAAPVGKVAP 523

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2093551169 347 TLNHIVPTTHNLGTPSSVRQIPTVSTPTQQPFPPY 381
Cdd:PLN03209  524 SSTNEVVKVGNSAPPTALADEQHHAQPKPRPLSPY 558
 
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 4.53e-79

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: 239.44  E-value: 4.53e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  20 GIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDIIKT 99
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2093551169 100 AKGILSDQKFVTFGEDPKEEVMTLERILLQTIKFD 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 6.80e-73

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: 222.98  E-value: 6.80e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 138 EHPYSYLLKYAKSLKGDKNKLQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKFEVVDWnGRQPKHLRWWD 217
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDW-TSKPPGKRWWE 79

                          90       100
                  ....*....|....*....|..
gi 2093551169 218 MFVEDVTMDLLEDICHQVLDLY 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 2.09e-39

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: 137.52  E-value: 2.09e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169   4 WYYEKKNLKNTPSVQDGIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLA 83
Cdd:cd20538     2 WYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFLA 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2093551169  84 GKVEETPKKCKDIIKTAKGILSDQKFVTfgeDPKEEV--------MTLERILLQTIKFD 134
Cdd:cd20538    82 AKVEEQPRKLEHVIKVAHACLHRGEPDL---DTKSEAylqqaqelVINENILLQTLGFE 137
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
 4-134 3.18e-30

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: 113.60  E-value: 3.18e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169   4 WYYEKKNLKNTPSVQDGIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLA 83
Cdd:cd20596     4 WFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTALFLA 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2093551169  84 GKVEETPKKCKDIIKTAKGILS------DQKFVTFGEDpKEEVMTLERILLQTIKFD 134
Cdd:cd20596    84 AKVEEQPRKLEHVIKVAHACLNplepqlDTKSDAYLQQ-AQELVILETIMLQTLGFE 139
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 4-134 1.26e-29

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: 111.69  E-value: 1.26e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169   4 WYYEKKNLKNTPSVQDGIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLA 83
Cdd:cd20595     3 WYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALFLA 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2093551169  84 GKVEETPKKCKDIIKTAKGILSDQKFV--TFGE---DPKEEVMTLERILLQTIKFD 134
Cdd:cd20595    83 AKVEEQPKKLEHVIKVAHTCLHPQESLpdTRSEaylQQVQDLVILESIILQTLGFE 138
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 139-241 2.54e-29

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: 109.38  E-value: 2.54e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 139 HPYSYLLKYAKSLKGDKNKlqKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKFEVvdWNGRQPKHLRWWDM 218
Cdd:cd20546     1 HPYQYLIKFAKKLGVSDPK--ELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDL--ELSPNEKLNEWWEL 76

                          90       100
                  ....*....|....*....|...
gi 2093551169 219 FveDVTMDLLEDICHQVLDLYSH 241
Cdd:cd20546    77 F--GVDEEEIADAINEILDLYSS 97
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 21-197 2.65e-26

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: 107.13  E-value: 2.65e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  21 IDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPkkcKDIikTA 100
Cdd:COG5333    36 LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTP---RDI--SI 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 101 KGILSDQKFVTFGEDPKEEVMTLERILLQTIKFDLQVEHPYSYLLKYAKSLKGDKNKlqKMVQMAWTFVNDSLCTTLCLQ 180
Cdd:COG5333   111 ESFEARDLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKY--KLLQIAWKIINDALRTDLCLL 188

                         170
                  ....*....|....*..
gi 2093551169 181 WEPEIIAVALMYLAGKL 197
Cdd:COG5333   189 YPPHIIALAALLIACEV 205
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 139-241 3.20e-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: 95.75  E-value: 3.20e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 139 HPYSYLLKYAKSLKGDKNKlqKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKFEVvdwngrqPKHLRWWDM 218
Cdd:cd20533     1 HPHKFILMYLQVLEGEDNK--KLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAARELGIPL-------PLPPPWWEL 71

                          90       100
                  ....*....|....*....|...
gi 2093551169 219 FveDVTMDLLEDICHQVLDLYSH 241
Cdd:cd20533    72 F--DVSKEDIEEICLTILELYTR 92
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 29-134 1.02e-22

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: 92.02  E-value: 1.02e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  29 YRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDII------KTAKG 102
Cdd:cd20547     1 LRLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILaasynlRHPDK 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2093551169 103 ILSDQKFVtfgEDPKEEVMTLERILLQTIKFD 134
Cdd:cd20547    81 ISVDDQML---EEFRKAILGLERLLLETICFD 109
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 30-134 2.63e-22

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: 91.08  E-value: 2.63e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  30 RKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDIIKTAKGIL-SDQK 108
Cdd:cd20534     2 HFKVLRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRILhPDKP 81

                          90       100
                  ....*....|....*....|....*....
gi 2093551169 109 FVTFGED---PKEEVMTLERILLQTIKFD 134
Cdd:cd20534    82 PLELDDEyweLRDSIVNCELLLLRILKFD 110
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 26-135 1.65e-21

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: 89.02  E-value: 1.65e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  26 ESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDIIKTAKGILS 105
Cdd:cd20545     1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2093551169 106 DQKFVTFGEDPKE------EVMTLERILLQTIKFDL 135
Cdd:cd20545    81 KNPNLVIDEQSKEvwrwrdSILYNEEVLLETLCFDL 116
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 19-134 3.66e-21

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: 88.34  E-value: 3.66e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  19 DGIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDIIK 98
Cdd:cd20587     1 DGIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2093551169  99 TAKGILSD----------QKFVTfgEDPKEEVMTLERILLQTIKFD 134
Cdd:cd20587    81 VSYEIIFKkdpsaaqrikQKEVY--EQQKELVLNGEKLVLSTLGFD 124
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 139-241 1.58e-20

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: 85.77  E-value: 1.58e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 139 HPYSYLLKYAKSLK----GDKNKLQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKFEVVdwNGRQPKHlR 214
Cdd:cd20535     1 LPHKYLLHYLKSLRdwlnPEFWSRSPIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQVYGVKVP--PEEEAEK-P 77

                          90       100
                  ....*....|....*....|....*..
gi 2093551169 215 WWDMFVEDVTMDLLEDICHQVLDLYSH 241
Cdd:cd20535    78 WWQAFCEDLTKETIDEIIEDIINVYDL 104
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 138-239 2.23e-20

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: 85.28  E-value: 2.23e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 138 EHPYSYLLKYAKSLKGDKNKLqkmVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKFEvVDWNGRQPkhlrWWD 217
Cdd:cd20588     1 EHPYKPLVAAIKKFNVAQNAL---AQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVK-LPCDGRKV----WWQ 72

                          90       100
                  ....*....|....*....|..
gi 2093551169 218 MFveDVTMDLLEDICHQVLDLY 239
Cdd:cd20588    73 EF--DVTPRQLEEVSNQMLELY 92
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 16-133 3.20e-19

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: 82.96  E-value: 3.20e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  16 SVQDGIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKD 95
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2093551169  96 IIKTAKGI-------------LSDQKFvtfgEDPKEEVMTLERILLQTIKF 133
Cdd:cd20591    81 VLMVFHRMecrrenlpleplePESKKY----DEMKEDLIRTERHLLKEMGF 127
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 19-133 3.79e-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: 82.61  E-value: 3.79e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  19 DGIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDII- 97
Cdd:cd20532     1 DGIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVIn 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2093551169  98 -----------KTAKGIL---SDQKFVTFgedpKEEVMTLERILLQTIKF 133
Cdd:cd20532    81 vfhrllqrrlgKPAEVLPldiGSAEYEEL----KNDIIKAERRILKELGF 126
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 19-133 2.98e-15

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: 71.70  E-value: 2.98e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  19 DGIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDII- 97
Cdd:cd20589     1 DGLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVIn 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2093551169  98 -----------KTAKGILSDQKFVTFgedpKEEVMTLERILLQTIKF 133
Cdd:cd20589    81 vfhhikqvrgkRTISPLILDQNYINL----KNQVIKAERRVLKELGF 123
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 139-240 3.15e-15

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: 70.73  E-value: 3.15e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 139 HPYSYLLKYAKSLKGDKNklqkMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKLskfevvdwngrQPKHLRWWdm 218
Cdd:cd20514     1 HPYRPLTQYVQDAGLDDE----LLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVL-----------LQKDARQW-- 63

                          90       100
                  ....*....|....*....|...
gi 2093551169 219 FVE-DVTMDLLEDICHQVLDLYS 240
Cdd:cd20514    64 FAElNVDMDKILEITREILSLYE 86
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 11-133 1.33e-14

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: 70.81  E-value: 1.33e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  11 LKNTPSVQDGIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETP 90
Cdd:cd20590    25 LRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVKHSMEHVSMACVHLASKIEEAP 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2093551169  91 KKCKDII------------KTAKGILSDQKFVTFgedpKEEVMTLERILLQTIKF 133
Cdd:cd20590   105 RRIRDVInvfhrlrqlrekKKPVPLILDQEYVNL----KNQIIKAERRVLKELGF 155
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 137-240 3.79e-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: 65.27  E-value: 3.79e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 137 VEHPYSYLLKYAKSLKgdknKLQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKlsKFEVvdwngRQPKHLRWW 216
Cdd:cd20594     2 VEHPHKFILNYLAMLM----APPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAAR--RFQV-----PLPENPPWW 70

                          90       100
                  ....*....|....*....|....
gi 2093551169 217 DMFveDVTMDLLEDICHQVLDLYS 240
Cdd:cd20594    71 KVF--DAEKAEIDVVCKVLADLYR 92
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 138-240 7.88e-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: 65.02  E-value: 7.88e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 138 EHPYSYLLKYAKSLKGDKNklQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKFEVvdwngrqPKHLRWWD 217
Cdd:cd20592     1 KHPHKIIVMYLQVLECERN--QTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPL-------PNRPHWFL 71

                          90       100
                  ....*....|....*....|...
gi 2093551169 218 MFveDVTMDLLEDICHQVLDLYS 240
Cdd:cd20592    72 LF--GATEEEIQEICITTLKLYT 92
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 3-135 1.10e-11

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: 61.76  E-value: 1.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169   3 CWYYEKKNLKNTPSVQD-GIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLF 81
Cdd:pfam00134   3 FQYLRELELKYLPKPDYmDQQPDINPKMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLF 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2093551169  82 LAGKVEET-PKKCKDIIktakgILSDQKFvtfgedPKEEVMTLERILLQTIKFDL 135
Cdd:pfam00134  83 IAAKYEEIyPPTVEDLV-----YITDNAY------TREEILRMERLILETLNFDL 126
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 139-240 1.31e-11

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: 61.52  E-value: 1.31e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 139 HPYSYLLKYAKSLKGDKNklQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKFEVvdwngrqPKHLRWWDM 218
Cdd:cd20593     1 HPHKIIVMYLQVLECERN--RHLVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEIPL-------PNRPHWFLL 71

                          90       100
                  ....*....|....*....|..
gi 2093551169 219 FveDVTMDLLEDICHQVLDLYS 240
Cdd:cd20593    72 F--GATEEEIQEICLKILQLYT 91
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 32-100 3.55e-11

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


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 58.96  E-value: 3.55e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2093551169  32 EGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDIIKTA 100
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVS 69
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 35-129 4.71e-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: 4.71e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169   35 RFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDIIKTAkgilsdqkfvtfGE 114
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT------------GY 68

                           90
                   ....*....|....*
gi 2093551169  115 DPKEEVMTLERILLQ 129
Cdd:smart00385  69 FTEEEILRMERLLLE 83
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 52-128 5.13e-11

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: 59.15  E-value: 5.13e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2093551169  52 ATGVVYFHRFYMFHSFKTF-PRFVtACSCLFLAGKVEETPKKCKDIIKTAKGILSDqKFVTFGEDPKeEVMTLERILL 128
Cdd:cd20513    24 ATAIVYFKRFYARNSFKDIdPRLV-APTCLYLASKVEECPSHARLIVAEAKVLKTK-FSYEFPYRVN-DILECEFYLL 98
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 52-192 1.60e-09

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: 58.69  E-value: 1.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  52 ATGVVYFHRFYMFHSFKTF-PRFVTAcSCLFLAGKVEE----TPKKCKDIIKTAKGILsdqkfvtfgedpkEEVMTLERI 126
Cdd:TIGR00569  80 GTAIMYFKRFYLNNSVMEYhPKIIML-TCVFLACKVEEfnvsIDQFVGNLKETPLKAL-------------EQVLEYELL 145

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 127 LLQTIKFDLQVEHPY----SYLLKYAKSLKGDKNkLQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMY 192
Cdd:TIGR00569 146 LIQQLNFHLIVHNPYrpleGFLIDIKTRLPGLEN-PEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAIL 214
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
 138-238 1.05e-08

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: 52.78  E-value: 1.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 138 EHPYSYLLKYAKSLKGDKNKLQKMVQMAwtfVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKFEV-VDWNGRQpkhlrWW 216
Cdd:cd20598     1 EHPHTDVVKCTQLVRASKDLAQTSYFMA---TNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIpVSTDGKH-----WW 72

                          90       100
                  ....*....|....*....|..
gi 2093551169 217 DMFVEDVTMDLLEDICHQVLDL 238
Cdd:cd20598    73 EYVDPTVTLELLDELTHEFLQI 94
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 8-135 2.01e-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: 52.98  E-value: 2.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169   8 KKNLKNTPSVQDGIDYETESRYRKEGARFIIDTGTKMDLGYNTMATGVVYFHRFYMFHSFKTF-PRFVtACSCLFLAGKV 86
Cdd:cd20524    33 KESLKEEDAEPKFLTPEEELLLVRYYEKKLLEFCRAFKLPDSVLATALTYFKRFYLKNSVMEYhPKEI-MLTCLYLACKV 111

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2093551169  87 EETPKKCKDIIKTAKGilsdqkfvtfGEDPKEEVMTLERILLQTIKFDL 135
Cdd:cd20524   112 EEFNISIDQFVGNIKE----------SEKTAEIILEYELLLLQGLNFHL 150
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 138-238 4.54e-08

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: 50.85  E-value: 4.54e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 138 EHPYSYLLKYAKSLKGDKNKLQKMVQMAwtfVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKFEV-VDWNGRQpkhlrWW 216
Cdd:cd20597     1 DHPHTHVVKCTQLVRASKDLAQTSYFMA---TNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIpVSTDGKH-----WW 72

                          90       100
                  ....*....|....*....|..
gi 2093551169 217 DMFVEDVTMDLLEDICHQVLDL 238
Cdd:cd20597    73 EYVDATVTLELLDELTHEFLQI 94
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 139-236 4.46e-06

second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, cyclin-T1 (CCNT1) and cyclin-T2 (CCNT2), both of which are regulatory subunits of the cyclin-dependent kinase pair (CDK9/cyclin-T) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to productive elongation by phosphorylating the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNA Pol II). Members in this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410242 [Multi-domain]  Cd Length: 92  Bit Score: 44.57  E-value: 4.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 139 HPYSYLLKYAKSLK-GDKNklqkMVQMAWTFVNDSL-CTTLCLQWEPEIIAVALMYLAGKLSKFEVvdwngRQPKHLR-W 215
Cdd:cd20539     1 HPHTHVLKICNLVKaGSKD----LAQTAYFLATNSLhLTTFCLQYKPTVIACVCIHLACKWSNWEI-----PRSSEGKdW 71

                          90       100
                  ....*....|....*....|.
gi 2093551169 216 WDMFVEDVTMDLLEDICHQVL 236
Cdd:cd20539    72 YEYVDPSLTLEELDELTSEFL 92
CYCLIN_AtCycC_rpt2 cd20572
second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 139-239 5.73e-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: 44.77  E-value: 5.73e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 139 HPYSYLLKYAKslkgDKNkLQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKFEVVDWngrqpkhlrwwdm 218
Cdd:cd20572     1 HPYRPLIQLLQ----DAG-LTDMTQFTWSIVNDTYRTDLILIHPPYMIALACIYIASVHKEKDITLW------------- 62

                          90       100
                  ....*....|....*....|..
gi 2093551169 219 FVE-DVTMDLLEDICHQVLDLY 239
Cdd:cd20572    63 FEElRVDMNIIKNIAMEILDFY 84
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
 51-135 5.97e-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: 46.36  E-value: 5.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  51 MATGVVYFHRFYMFHSFKTFPRFVTACSCLFLAGKVEETPKKCKDIiktAKGILSDQKFVTfgedpKEEVmtlerILLQT 130
Cdd:cd20585    99 QATALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEEYHVSAEEL---GKGIQQDHQLIL-----KNEL-----ALLQG 165


                  ....*
gi 2093551169 131 IKFDL 135
Cdd:cd20585   166 LNFDL 170
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 51-109 6.35e-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: 6.35e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169  51 MATGVVYFHRFYMFHSFKTF-PRFVtACSCLFLAGKVEETPKKCKDIIKTAKGILSDQKF 109
Cdd:cd20571    28 VATAITYFRRVYTRKSFTEYdPRLV-APTCLYLASKAEESTVQAKLLVFYMKRLYADEYH 86
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 143-197 1.14e-04

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: 40.65  E-value: 1.14e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2093551169  143 YLLKYAKSLKGDknklQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKL 197
Cdd:smart00385   2 FLRRVCKALNLD----PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKT 52
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 243-410 1.42e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 44.37  E-value: 1.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 243 NNAKPPDSPPLIASTETVRErlIAPPSIESASSTPNAGITVKPSKTETNSVPTNGCNTTevienskpieVAVHFPSYPTN 322
Cdd:pfam03154 178 SGAASPPSPPPPGTTQAATA--GPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQT----------PTLHPQRLPSP 245

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 323 FASTTNYPPVYPPTNIS---VPPPNVNTlnHIVPTTHNLGT-PSSVrqiptvstptQQPFPPYGYPSNSSFFSGGTPTGP 398
Cdd:pfam03154 246 HPPLQPMTQPPPPSQVSpqpLPQPSLHG--QMPPMPHSLQTgPSHM----------QHPVPPQPFPLTPQSSQSQVPPGP 313

                         170
                  ....*....|....*....
gi 2093551169 399 S------SNQRSYYP-SQS 410
Cdd:pfam03154 314 SpaapgqSQQRIHTPpSQS 332
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 139-200 2.64e-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: 39.32  E-value: 2.64e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2093551169 139 HPYSYLLKYAKSLKGDknklQKMVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAGKLSKF 200
Cdd:cd00043     1 KAVDFIRRLCSKLGLP----EEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEEL 58
Enamelin pfam15362
Enamelin; ENAMELIN is involved in the mineralization and structural organization of enamel. It ...
 267-409 1.12e-03

Enamelin; ENAMELIN is involved in the mineralization and structural organization of enamel. It is necessary for the extension of enamel during the secretory stage of dental enamel formation. The proteins are expressed in teeth, particularly in odontoblasts, ameloblasts and cementoblasts.


Pssm-ID: 464672 [Multi-domain]  Cd Length: 907  Bit Score: 41.35  E-value: 1.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 267 PPSIESASSTPNAGITVkpskTETNSVPTN-----GCNTTEVIENSKPIevavhfpsyptnfASTTNYPPVYPPTNisvP 341
Cdd:pfam15362  20 PPKAESPATEPSANSTV----PETNSTQPNpggsqGGNDTSPTGNSAPG-------------PNTGSNPTAQNGVF---P 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 342 PPNVNTLNHIVPTTHNLGTPSSVRQIPTVSTPTQQPFppygyPSNSSFFSGGTPTGPSSNQRSY--YPSQ 409
Cdd:pfam15362  80 PPAVNVSGQGVPRSQIPWGPSQPNIRENYPNPNIRNF-----PSGRQWSPTGTAMGHRQNGPFYrnQQVQ 144
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 267-381 8.42e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 38.37  E-value: 8.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2093551169 267 PPSiesaSSTPNAGITVKPSKTETNSVPTNGcNTTEVIENSKPIEVAVHFPSYPTNFASTTNYPPVYPPTNISVPPPNVN 346
Cdd:PLN03209  449 PPT----SPSPTAPTGVSPSVSSTSSVPAVP-DTAPATAATDAAAPPPANMRPLSPYAVYDDLKPPTSPSPAAPVGKVAP 523

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2093551169 347 TLNHIVPTTHNLGTPSSVRQIPTVSTPTQQPFPPY 381
Cdd:PLN03209  524 SSTNEVVKVGNSAPPTALADEQHHAQPKPRPLSPY 558
 
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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