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Conserved domains on  [gi|1334650867|ref|XP_023587430|]
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cyclin-K [Trichechus manatus latirostris]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
76-176 1.56e-71

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: 1.56e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  76 EHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQ 155
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDWTSKPPGKRWWEQ 80
                          90       100
                  ....*....|....*....|.
gi 1334650867 156 FVQDVPVDVLEDICHQILDLY 176
Cdd:cd20531    81 FVEDVSLEVLEDICHQVLDLY 101
CYCLIN_SF super family cl40454
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
1-72 1.39e-46

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


The actual alignment was detected with superfamily member cd20530:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 115  Bit Score: 158.17  E-value: 1.39e-46
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1334650867   1 MFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFD 72
Cdd:cd20530    44 MFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKTARSLLNDKQFAQFGDDPKEEVMVLERILLQTIKFD 115
 
Name Accession Description Interval E-value
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
76-176 1.56e-71

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: 1.56e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  76 EHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQ 155
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDWTSKPPGKRWWEQ 80
                          90       100
                  ....*....|....*....|.
gi 1334650867 156 FVQDVPVDVLEDICHQILDLY 176
Cdd:cd20531    81 FVEDVSLEVLEDICHQVLDLY 101
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
1-72 1.39e-46

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: 158.17  E-value: 1.39e-46
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1334650867   1 MFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFD 72
Cdd:cd20530    44 MFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKTARSLLNDKQFAQFGDDPKEEVMVLERILLQTIKFD 115
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
2-135 1.11e-17

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: 83.63  E-value: 1.11e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867   2 FHSFKQFPRYVTGACCLFLAGKVEETPKKckdiIKTARSLLNDVQFGQFGDDPkEEVMVLERILLQTIKFDLQVEHPYQF 81
Cdd:COG5333    79 KNSVEEISLYSVVTTCVYLACKVEDTPRD----ISIESFEARDLWSEEPKSSR-ERILEYEFELLEALDFDLHVHHPYKY 153
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1334650867  82 LLKYAKQLKGDKNKiqKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRL 135
Cdd:COG5333   154 LEGFLKDLQEKDKY--KLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEV 205
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
1-67 2.55e-06

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: 45.28  E-value: 2.55e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1334650867    1 MFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTArsllndvqfgqfGDDPKEEVMVLERILLQ 67
Cdd:smart00385  29 SDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT------------GYFTEEEILRMERLLLE 83
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
80-174 2.76e-06

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: 45.28  E-value: 2.76e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867   80 QFLLKYAKQLKGDknkiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCkfEIQEWTSKpmyrrwWEQFVQD 159
Cdd:smart00385   1 DFLRRVCKALNLD----PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTE--ETPPWTKE------LVHYTGY 68
                           90
                   ....*....|....*
gi 1334650867  160 VPVDVLEDICHQILD 174
Cdd:smart00385  69 FTEEEILRMERLLLE 83
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
2-142 8.46e-06

cyclin ccl1; All proteins in this family for which functions are known are cyclins that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, StanfordUniversity). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129660 [Multi-domain]  Cd Length: 305  Bit Score: 47.91  E-value: 8.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867   2 FHSFKQF----------PRYVTgACCLFLAGKVEE----TPKKCKDIIKTARSLLndvqfgqfgddpkEEVMVLERILLQ 67
Cdd:TIGR00569  83 IMYFKRFylnnsvmeyhPKIIM-LTCVFLACKVEEfnvsIDQFVGNLKETPLKAL-------------EQVLEYELLLIQ 148
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  68 TIKFDLQVEHPYQ----FLLKYAKQLKGDKNKiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAV-AVMYLAGRLC-KFEIQ 141
Cdd:TIGR00569 149 QLNFHLIVHNPYRplegFLIDIKTRLPGLENP-EYLRKHADKFLNRTLLTDAYLLYTPSQIALaAILHTASRAGlNMESY 227

                  .
gi 1334650867 142 E 142
Cdd:TIGR00569 228 L 228
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
2-73 2.06e-03

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: 38.27  E-value: 2.06e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1334650867   2 FHSFKQFPRY---VTGACCLFLAGKVEET-PKKCKDIIktarsLLNDVQFgqfgddPKEEVMVLERILLQTIKFDL 73
Cdd:pfam00134  62 FLSKKSVPKNklqLVGVTCLFIAAKYEEIyPPTVEDLV-----YITDNAY------TREEILRMERLILETLNFDL 126
 
Name Accession Description Interval E-value
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
76-176 1.56e-71

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: 1.56e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  76 EHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQ 155
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDWTSKPPGKRWWEQ 80
                          90       100
                  ....*....|....*....|.
gi 1334650867 156 FVQDVPVDVLEDICHQILDLY 176
Cdd:cd20531    81 FVEDVSLEVLEDICHQVLDLY 101
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
1-72 1.39e-46

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: 158.17  E-value: 1.39e-46
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1334650867   1 MFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFD 72
Cdd:cd20530    44 MFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKTARSLLNDKQFAQFGDDPKEEVMVLERILLQTIKFD 115
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
77-178 1.51e-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: 111.69  E-value: 1.51e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  77 HPYQFLLKYAKQLKGDKNKiqKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMyRRWWEQF 156
Cdd:cd20546     1 HPYQYLIKFAKKLGVSDPK--ELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPNEKL-NEWWELF 77
                          90       100
                  ....*....|....*....|..
gi 1334650867 157 vqDVPVDVLEDICHQILDLYSQ 178
Cdd:cd20546    78 --GVDEEEIADAINEILDLYSS 97
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
77-177 6.52e-25

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: 98.44  E-value: 6.52e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  77 HPYQFLLKYAKQLKGDKNKiqKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEwtSKPmyrrWWEQF 156
Cdd:cd20533     1 HPHKFILMYLQVLEGEDNK--KLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAARELGIPLPL--PPP----WWELF 72
                          90       100
                  ....*....|....*....|.
gi 1334650867 157 vqDVPVDVLEDICHQILDLYS 177
Cdd:cd20533    73 --DVSKEDIEEICLTILELYT 91
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
76-176 2.89e-19

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: 82.58  E-value: 2.89e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  76 EHPYQFLLKYAKQLKGDKNKiqkLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQewtsKPMYRRWWEQ 155
Cdd:cd20588     1 EHPYKPLVAAIKKFNVAQNA---LAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLP----CDGRKVWWQE 73
                          90       100
                  ....*....|....*....|.
gi 1334650867 156 FvqDVPVDVLEDICHQILDLY 176
Cdd:cd20588    74 F--DVTPRQLEEVSNQMLELY 92
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
77-178 3.16e-19

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: 82.69  E-value: 3.16e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  77 HPYQFLLKYAKQLK----GDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMyrRW 152
Cdd:cd20535     1 LPHKYLLHYLKSLRdwlnPEFWSRSPIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQVYGVKVPPEEEAEK--PW 78
                          90       100
                  ....*....|....*....|....*.
gi 1334650867 153 WEQFVQDVPVDVLEDICHQILDLYSQ 178
Cdd:cd20535    79 WQAFCEDLTKETIDEIIEDIINVYDL 104
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
2-135 1.11e-17

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: 83.63  E-value: 1.11e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867   2 FHSFKQFPRYVTGACCLFLAGKVEETPKKckdiIKTARSLLNDVQFGQFGDDPkEEVMVLERILLQTIKFDLQVEHPYQF 81
Cdd:COG5333    79 KNSVEEISLYSVVTTCVYLACKVEDTPRD----ISIESFEARDLWSEEPKSSR-ERILEYEFELLEALDFDLHVHHPYKY 153
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1334650867  82 LLKYAKQLKGDKNKiqKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRL 135
Cdd:COG5333   154 LEGFLKDLQEKDKY--KLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEV 205
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
1-72 3.33e-17

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


Pssm-ID: 410241 [Multi-domain]  Cd Length: 137  Bit Score: 78.20  E-value: 3.33e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867   1 MFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDvqfGQFGDDPKEEV--------MVLERILLQTIKFD 72
Cdd:cd20538    61 MFHSFTKFHRNSIAAAALFLAAKVEEQPRKLEHVIKVAHACLHR---GEPDLDTKSEAylqqaqelVINENILLQTLGFE 137
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
75-182 4.36e-15

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: 71.05  E-value: 4.36e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  75 VEHPYQFLLKYAKQLKgdknKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRlcKFEIqewtSKPMYRRWWE 154
Cdd:cd20594     2 VEHPHKFILNYLAMLM----APPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAAR--RFQV----PLPENPPWWK 71
                          90       100
                  ....*....|....*....|....*...
gi 1334650867 155 QFvqDVPVDVLEDICHQILDLYSQGKQQ 182
Cdd:cd20594    72 VF--DAEKAEIDVVCKVLADLYRQPKAR 97
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
77-182 1.30e-14

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: 69.19  E-value: 1.30e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  77 HPYQFLLKYAKQLKGDKNkiqkLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKpmyrrwweqf 156
Cdd:cd20514     1 HPYRPLTQYVQDAGLDDE----LLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDARQWFAE---------- 66
                          90       100
                  ....*....|....*....|....*.
gi 1334650867 157 vQDVPVDVLEDICHQILDLYSQGKQQ 182
Cdd:cd20514    67 -LNVDMDKILEITREILSLYELWKTF 91
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
76-186 2.86e-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: 66.56  E-value: 2.86e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  76 EHPYQFLLKYAKQLKGDKNkiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIqewTSKPmyrRWWEQ 155
Cdd:cd20592     1 KHPHKIIVMYLQVLECERN--QTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPL---PNRP---HWFLL 72
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1334650867 156 FvqDVPVDVLEDICHQILDLYSQGKqqmPHH 186
Cdd:cd20592    73 F--GATEEEIQEICITTLKLYTRKK---PNY 98
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
77-185 6.59e-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: 65.37  E-value: 6.59e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  77 HPYQFLLKYAKQLKGDKNkiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIqewtskPMYRRWWEQF 156
Cdd:cd20593     1 HPHKIIVMYLQVLECERN--RHLVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEIPL------PNRPHWFLLF 72
                          90       100
                  ....*....|....*....|....*....
gi 1334650867 157 vqDVPVDVLEDICHQILDLYSQGKQQMPH 185
Cdd:cd20593    73 --GATEEEIQEICLKILQLYTRKKVDLEH 99
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
1-72 1.10e-11

first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar proteins; CTK2, also called CTD kinase subunit beta, CTDK-I subunit beta, or CTD kinase 38 kDa subunit, is the cyclin subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. CTK2 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410250 [Multi-domain]  Cd Length: 110  Bit Score: 61.59  E-value: 1.10e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1334650867   1 MFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFG---QFGDDPKEEVMVLERILLQTIKFD 72
Cdd:cd20547    35 LFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNLRHPDKISvddQMLEEFRKAILGLERLLLETICFD 109
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
1-72 8.79e-11

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: 60.06  E-value: 8.79e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1334650867   1 MFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDV--QFGQFGD---DPKEEVMVLERILLQTIKFD 72
Cdd:cd20596    63 MHHSFTKFHRNIISPTALFLAAKVEEQPRKLEHVIKVAHACLNPLepQLDTKSDaylQQAQELVILETIMLQTLGFE 139
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
2-72 1.96e-10

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: 57.95  E-value: 1.96e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1334650867   2 FHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLN-DVQFGQFGDD---PKEEVMVLERILLQTIKFD 72
Cdd:cd20534    36 ELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRILHpDKPPLELDDEyweLRDSIVNCELLLLRILKFD 110
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
1-72 7.36e-10

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: 57.37  E-value: 7.36e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1334650867   1 MFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLN------DVQFGQFGDDpKEEVMVLERILLQTIKFD 72
Cdd:cd20595    62 MIQSFTQFHRNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHpqeslpDTRSEAYLQQ-VQDLVILESIILQTLGFE 138
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
1-73 8.14e-08

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: 50.89  E-value: 8.14e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1334650867   1 MFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDII----KTARSLLNDVQFGQFGDDPKEEVMVL--ERILLQTIKFDL 73
Cdd:cd20545    38 MRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIViacaKVAQKNPNLVIDEQSKEVWRWRDSILynEEVLLETLCFDL 116
CYCLIN_AtCycC_rpt2 cd20572
second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
77-176 1.77e-07

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: 49.39  E-value: 1.77e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  77 HPYQFLLkyakQLKGDKNkIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIqewtskpmyRRWWEQF 156
Cdd:cd20572     1 HPYRPLI----QLLQDAG-LTDMTQFTWSIVNDTYRTDLILIHPPYMIALACIYIASVHKEKDI---------TLWFEEL 66
                          90       100
                  ....*....|....*....|
gi 1334650867 157 VQDvpVDVLEDICHQILDLY 176
Cdd:cd20572    67 RVD--MNIIKNIAMEILDFY 84
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
4-71 1.34e-06

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: 47.55  E-value: 1.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867   4 SFKQFPRYVTGACCLFLAGKVEETPKKCKDII------------KTARSLLNDVqFGQFGDDPKEEVMVLERILLQTIKF 71
Cdd:cd20532    48 SLRKFDVKIVAMACLFLASKIEETPRRLRDVInvfhrllqrrlgKPAEVLPLDI-GSAEYEELKNDIIKAERRILKELGF 126
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
1-67 2.55e-06

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: 45.28  E-value: 2.55e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1334650867    1 MFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTArsllndvqfgqfGDDPKEEVMVLERILLQ 67
Cdd:smart00385  29 SDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT------------GYFTEEEILRMERLLLE 83
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
80-174 2.76e-06

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: 45.28  E-value: 2.76e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867   80 QFLLKYAKQLKGDknkiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCkfEIQEWTSKpmyrrwWEQFVQD 159
Cdd:smart00385   1 DFLRRVCKALNLD----PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTE--ETPPWTKE------LVHYTGY 68
                           90
                   ....*....|....*
gi 1334650867  160 VPVDVLEDICHQILD 174
Cdd:smart00385  69 FTEEEILRMERLLLE 83
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
17-72 3.14e-06

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: 46.36  E-value: 3.14e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1334650867  17 CLFLAGKVEETPKKCKDIIKTARSLLND--------VQFGQFGDDPKEEVMVLERILLQTIKFD 72
Cdd:cd20587    61 CMFLAGKVEETPRPLKDVIVVSYEIIFKkdpsaaqrIKQKEVYEQQKELVLNGEKLVLSTLGFD 124
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
76-193 6.11e-06

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: 45.07  E-value: 6.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  76 EHPYQFLLKYAKQLKGDKNkiqkLVQMAWTFVNDSL-CTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKpmyRRWWE 154
Cdd:cd20597     1 DHPHTHVVKCTQLVRASKD----LAQTSYFMATNSLhLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDG---KHWWE 73
                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1334650867 155 QFVQDVPVDVLEDICHQILdlysqgkqQMPHHTPHQLQQ 193
Cdd:cd20597    74 YVDATVTLELLDELTHEFL--------QILEKTPNRLKR 104
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
76-193 7.01e-06

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: 45.07  E-value: 7.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  76 EHPYQFLLKYAKQLKGDKNkiqkLVQMAWTFVNDSL-CTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKpmyRRWWE 154
Cdd:cd20598     1 EHPHTDVVKCTQLVRASKD----LAQTSYFMATNSLhLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDG---KHWWE 73
                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1334650867 155 QFVQDVPVDVLEDICHQILdlysqgkqQMPHHTPHQLQQ 193
Cdd:cd20598    74 YVDPTVTLELLDELTHEFL--------QILEKTPSRLKR 104
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
2-142 8.46e-06

cyclin ccl1; All proteins in this family for which functions are known are cyclins that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, StanfordUniversity). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129660 [Multi-domain]  Cd Length: 305  Bit Score: 47.91  E-value: 8.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867   2 FHSFKQF----------PRYVTgACCLFLAGKVEE----TPKKCKDIIKTARSLLndvqfgqfgddpkEEVMVLERILLQ 67
Cdd:TIGR00569  83 IMYFKRFylnnsvmeyhPKIIM-LTCVFLACKVEEfnvsIDQFVGNLKETPLKAL-------------EQVLEYELLLIQ 148
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  68 TIKFDLQVEHPYQ----FLLKYAKQLKGDKNKiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAV-AVMYLAGRLC-KFEIQ 141
Cdd:TIGR00569 149 QLNFHLIVHNPYRplegFLIDIKTRLPGLENP-EYLRKHADKFLNRTLLTDAYLLYTPSQIALaAILHTASRAGlNMESY 227

                  .
gi 1334650867 142 E 142
Cdd:TIGR00569 228 L 228
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
77-173 9.05e-06

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


Pssm-ID: 410242 [Multi-domain]  Cd Length: 92  Bit Score: 44.19  E-value: 9.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  77 HPYQFLLKYAKQLK-GDKNkiqkLVQMAWTFVNDSL-CTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKpmyRRWWE 154
Cdd:cd20539     1 HPHTHVLKICNLVKaGSKD----LAQTAYFLATNSLhLTTFCLQYKPTVIACVCIHLACKWSNWEIPRSSEG---KDWYE 73
                          90
                  ....*....|....*....
gi 1334650867 155 QFVQDVPVDVLEDICHQIL 173
Cdd:cd20539    74 YVDPSLTLEELDELTSEFL 92
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
77-140 1.14e-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: 40.86  E-value: 1.14e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1334650867  77 HPYQFLLKYAKQLKGDknkiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEI 140
Cdd:cd00043     1 KAVDFIRRLCSKLGLP----EEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPR 60
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
3-46 2.89e-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: 39.70  E-value: 2.89e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1334650867   3 HSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQ 46
Cdd:cd00043    34 GLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELR 77
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
2-73 2.06e-03

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: 38.27  E-value: 2.06e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1334650867   2 FHSFKQFPRY---VTGACCLFLAGKVEET-PKKCKDIIktarsLLNDVQFgqfgddPKEEVMVLERILLQTIKFDL 73
Cdd:pfam00134  62 FLSKKSVPKNklqLVGVTCLFIAAKYEEIyPPTVEDLV-----YITDNAY------TREEILRMERLILETLNFDL 126
CYCLIN_CCNO-like_rpt2 cd20537
second cyclin box found in cyclin-O (CCNO) and similar proteins; This subfamily is composed of ...
77-178 2.22e-03

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


Pssm-ID: 410240 [Multi-domain]  Cd Length: 91  Bit Score: 37.29  E-value: 2.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334650867  77 HPYQFLLKYAKQLKGDKnkiqKLVQMAWtFVND-SLCTTLSLQWEPEIIAVAVMYLAGRLCKfeIQEWTSKPMYRRWWEQ 155
Cdd:cd20537     2 TPLSFLRRYLSLLGLDE----KVRHLAR-YLLElSLLDYEFLKYRPSLIAAAALYLARKILG--EPPPSPQLLQLVTGYS 74
                          90       100
                  ....*....|....*....|...
gi 1334650867 156 FvqdvpvDVLEDICHQILDLYSQ 178
Cdd:cd20537    75 E------NDLQECAKELLELLAQ 91
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
4-71 2.38e-03

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: 38.28  E-value: 2.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1334650867   4 SFKQFPRYVTGACCLFLAGKVEETPKKCKDII----------KTARSLLNDVQFGQFgDDPKEEVMVLERILLQTIKF 71
Cdd:cd20591    51 SFARFNVKRVAASCVWLAAKLEESPRKIRQVLmvfhrmecrrENLPLEPLEPESKKY-DEMKEDLIRTERHLLKEMGF 127
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
3-66 2.78e-03

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: 37.19  E-value: 2.78e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1334650867   3 HSFKQF-PRYVtGACCLFLAGKVEETPKKCKDIIKTARSLLNDvQFGQFGDDPKeEVMVLERILL 66
Cdd:cd20513    37 NSFKDIdPRLV-APTCLYLASKVEECPSHARLIVAEAKVLKTK-FSYEFPYRVN-DILECEFYLL 98
 
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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