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Conserved domains on  [gi|1443061903|ref|XP_025879236|]
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cyclin-T1-2 isoform X2 [Oryza sativa Japonica Group]

Protein Classification

cyclin family protein( domain architecture ID 1750054)

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

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CYCLIN_SF super family cl40454
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
2-94 2.84e-44

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 cd20587:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 124  Bit Score: 153.06  E-value: 2.84e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPATARRIHQKDVFEKQKALIL 81
Cdd:cd20587    32 TIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIVVSYEIIFKKDPSAAQRIKQKEVYEQQKELVL 111
                          90
                  ....*....|...
gi 1443061903  82 TGERLVLTTVRFD 94
Cdd:cd20587   112 NGEKLVLSTLGFD 124
CYCLIN_SF super family cl40454
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
98-188 1.06e-38

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 cd20588:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 93  Bit Score: 136.89  E-value: 1.06e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  98 QHPYRPLLDAMEKLGISQKEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLPVHGGHVWWHQFDVAPKP 177
Cdd:cd20588     1 EHPYKPLVAAIKKFNVAQNALAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPCDGRKVWWQEFDVTPRQ 80
                          90
                  ....*....|.
gi 1443061903 178 LEAVLQQMREM 188
Cdd:cd20588    81 LEEVSNQMLEL 91
 
Name Accession Description Interval E-value
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
2-94 2.84e-44

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: 153.06  E-value: 2.84e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPATARRIHQKDVFEKQKALIL 81
Cdd:cd20587    32 TIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIVVSYEIIFKKDPSAAQRIKQKEVYEQQKELVL 111
                          90
                  ....*....|...
gi 1443061903  82 TGERLVLTTVRFD 94
Cdd:cd20587   112 NGEKLVLSTLGFD 124
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
98-188 1.06e-38

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: 136.89  E-value: 1.06e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  98 QHPYRPLLDAMEKLGISQKEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLPVHGGHVWWHQFDVAPKP 177
Cdd:cd20588     1 EHPYKPLVAAIKKFNVAQNALAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPCDGRKVWWQEFDVTPRQ 80
                          90
                  ....*....|.
gi 1443061903 178 LEAVLQQMREM 188
Cdd:cd20588    81 LEEVSNQMLEL 91
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
2-160 4.07e-24

Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair];


Pssm-ID: 227640 [Multi-domain]  Cd Length: 297  Bit Score: 102.50  E-value: 4.07e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDtpCPLDQVIRVAygtmyrrdpatARRIHQKDVFEKQKALIL 81
Cdd:COG5333    65 VLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVED--TPRDISIESF-----------EARDLWSEEPKSSRERIL 131
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  82 TGERLVLTTVRFDFNIQHPYRPLLDAMEKLGISQK-EVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLP 160
Cdd:COG5333   132 EYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKyKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPII 211
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
3-160 2.77e-11

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


Pssm-ID: 129660 [Multi-domain]  Cd Length: 305  Bit Score: 64.86  E-value: 2.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   3 IATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPAtarrihqkdvfekqkalILT 82
Cdd:TIGR00569  79 VGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKETPLKALEQ-----------------VLE 141
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  83 GERLVLTTVRFDFNIQHPYRP----LLDAMEKLGISQKE--VKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQN 156
Cdd:TIGR00569 142 YELLLIQQLNFHLIVHNPYRPlegfLIDIKTRLPGLENPeyLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAG 221

                  ....
gi 1443061903 157 VKLP 160
Cdd:TIGR00569 222 LNME 225
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
2-96 9.83e-10

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: 56.76  E-value: 9.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCP-LDQVIRVAYGTMYRRDpatarrihqkdvfekqkalI 80
Cdd:pfam00134  51 TLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYEEIYPPtVEDLVYITDNAYTREE-------------------I 111
                          90
                  ....*....|....*.
gi 1443061903  81 LTGERLVLTTVRFDFN 96
Cdd:pfam00134 112 LRMERLILETLNFDLS 127
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
116-160 1.88e-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: 46.05  E-value: 1.88e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443061903  116 KEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLP 160
Cdd:smart00385  14 PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPW 58
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
2-52 3.06e-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: 3.06e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443061903    2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVA 52
Cdd:smart00385  16 TLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT 66
 
Name Accession Description Interval E-value
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
2-94 2.84e-44

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: 153.06  E-value: 2.84e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPATARRIHQKDVFEKQKALIL 81
Cdd:cd20587    32 TIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIVVSYEIIFKKDPSAAQRIKQKEVYEQQKELVL 111
                          90
                  ....*....|...
gi 1443061903  82 TGERLVLTTVRFD 94
Cdd:cd20587   112 NGEKLVLSTLGFD 124
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
98-188 1.06e-38

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: 136.89  E-value: 1.06e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  98 QHPYRPLLDAMEKLGISQKEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLPVHGGHVWWHQFDVAPKP 177
Cdd:cd20588     1 EHPYKPLVAAIKKFNVAQNALAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPCDGRKVWWQEFDVTPRQ 80
                          90
                  ....*....|.
gi 1443061903 178 LEAVLQQMREM 188
Cdd:cd20588    81 LEEVSNQMLEL 91
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
98-185 8.33e-25

second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase II-associated C-type cyclin possessing both carboxy-terminal domain kinase and Cdk-activating kinase activity. It is a regulatory subunit of cyclin-dependent kinases that mediates the activation of these target kinases. It plays a role in transcriptional regulation by controlling the phosphorylation of the C-terminal domain (CTD) of the large subunit of RNA polymerase II (POLR2A). CCNK contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410234 [Multi-domain]  Cd Length: 101  Bit Score: 98.56  E-value: 8.33e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  98 QHPYRPLLDAMEKLGISQKEVK---QVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLPVHG----GHVWWHQ 170
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQklvQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDWTskppGKRWWEQ 80
                          90
                  ....*....|....*..
gi 1443061903 171 F--DVAPKPLEAVLQQM 185
Cdd:cd20531    81 FveDVSLEVLEDICHQV 97
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
2-94 3.21e-24

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: 97.69  E-value: 3.21e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPATarrihqkdVFEKQKALIL 81
Cdd:cd20530    31 TIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKTARSLLNDKQFAQ--------FGDDPKEEVM 102
                          90
                  ....*....|...
gi 1443061903  82 TGERLVLTTVRFD 94
Cdd:cd20530   103 VLERILLQTIKFD 115
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
2-160 4.07e-24

Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair];


Pssm-ID: 227640 [Multi-domain]  Cd Length: 297  Bit Score: 102.50  E-value: 4.07e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDtpCPLDQVIRVAygtmyrrdpatARRIHQKDVFEKQKALIL 81
Cdd:COG5333    65 VLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVED--TPRDISIESF-----------EARDLWSEEPKSSRERIL 131
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  82 TGERLVLTTVRFDFNIQHPYRPLLDAMEKLGISQK-EVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLP 160
Cdd:COG5333   132 EYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKyKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPII 211
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
99-188 1.22e-19

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: 83.95  E-value: 1.22e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  99 HPYRPLLDAMEKLGISQ-KEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLPVHGGHV---WWHQFDVA 174
Cdd:cd20546     1 HPYQYLIKFAKKLGVSDpKELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPNEKlneWWELFGVD 80
                          90
                  ....*....|....
gi 1443061903 175 PKPLEAVLQQMREM 188
Cdd:cd20546    81 EEEIADAINEILDL 94
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
99-188 1.86e-16

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: 74.56  E-value: 1.86e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  99 HPYRPLLDAMEKL-GISQKEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLPVHGGhvWWHQFDVAPKP 177
Cdd:cd20533     1 HPHKFILMYLQVLeGEDNKKLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAARELGIPLPLPPP--WWELFDVSKED 78
                          90
                  ....*....|.
gi 1443061903 178 LEAVLQQMREM 188
Cdd:cd20533    79 IEEICLTILEL 89
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
1-94 2.58e-15

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: 72.81  E-value: 2.58e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   1 MTIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPataRRIHQKDVFEKQKALI 80
Cdd:cd20538    47 LCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFLAAKVEEQPRKLEHVIKVAHACLHRGEP---DLDTKSEAYLQQAQEL 123
                          90
                  ....*....|....
gi 1443061903  81 LTGERLVLTTVRFD 94
Cdd:cd20538   124 VINENILLQTLGFE 137
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
96-173 7.33e-14

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: 67.58  E-value: 7.33e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1443061903  96 NIQHPYRPLLDAMEKLGiSQKEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLPVHGGhvWWHQFDV 173
Cdd:cd20594     1 HVEHPHKFILNYLAMLM-APPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPP--WWKVFDA 75
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
2-95 8.77e-14

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: 67.76  E-value: 8.77e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYgTMYRRDPATArrihQKDVFEKQKALIL 81
Cdd:cd20547    22 TLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASY-NLRHPDKISV----DDQMLEEFRKAIL 96
                          90
                  ....*....|....
gi 1443061903  82 TGERLVLTTVRFDF 95
Cdd:cd20547    97 GLERLLLETICFDF 110
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
1-94 1.05e-13

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: 68.54  E-value: 1.05e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   1 MTIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPATARRihqKDVFEKQKALI 80
Cdd:cd20595    48 LTINTAIVYMHRFYMIQSFTQFHRNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTR---SEAYLQQVQDL 124
                          90
                  ....*....|....
gi 1443061903  81 LTGERLVLTTVRFD 94
Cdd:cd20595   125 VILESIILQTLGFE 138
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
99-185 5.35e-13

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: 64.95  E-value: 5.35e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  99 HPYRPLLDAMEKLGISqKEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLpvhggHVWWHQFDVAPKPL 178
Cdd:cd20514     1 HPYRPLTQYVQDAGLD-DELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDA-----RQWFAELNVDMDKI 74

                  ....*..
gi 1443061903 179 EAVLQQM 185
Cdd:cd20514    75 LEITREI 81
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
1-94 6.22e-13

first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to production elongation by phosphorylating the CTD (carboxy-terminal domain) of the large subunit of RNA polymerase II (RNAP II). CCNT2 contains two cyclin boxs. The model responds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410299 [Multi-domain]  Cd Length: 139  Bit Score: 66.22  E-value: 6.22e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   1 MTIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPATARRihqKDVFEKQKALI 80
Cdd:cd20596    49 LTINTAIVYMHRFYMHHSFTKFHRNIISPTALFLAAKVEEQPRKLEHVIKVAHACLNPLEPQLDTK---SDAYLQQAQEL 125
                          90
                  ....*....|....
gi 1443061903  81 LTGERLVLTTVRFD 94
Cdd:cd20596   126 VILETIMLQTLGFE 139
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
2-93 7.00e-13

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: 65.66  E-value: 7.00e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRD--PATARRIHQKD-VFEKQKA 78
Cdd:cd20532    32 VMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVINVFHRLLQRRLgkPAEVLPLDIGSaEYEELKN 111
                          90
                  ....*....|....*
gi 1443061903  79 LILTGERLVLTTVRF 93
Cdd:cd20532   112 DIIKAERRILKELGF 126
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
1-94 2.81e-12

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: 63.34  E-value: 2.81e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   1 MTIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPATARrihqKDVFEKQKALI 80
Cdd:cd20534    21 VTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRILHPDKPPLEL----DDEYWELRDSI 96
                          90
                  ....*....|....
gi 1443061903  81 LTGERLVLTTVRFD 94
Cdd:cd20534    97 VNCELLLLRILKFD 110
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
3-160 2.77e-11

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


Pssm-ID: 129660 [Multi-domain]  Cd Length: 305  Bit Score: 64.86  E-value: 2.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   3 IATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPAtarrihqkdvfekqkalILT 82
Cdd:TIGR00569  79 VGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKETPLKALEQ-----------------VLE 141
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  83 GERLVLTTVRFDFNIQHPYRP----LLDAMEKLGISQKE--VKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQN 156
Cdd:TIGR00569 142 YELLLIQQLNFHLIVHNPYRPlegfLIDIKTRLPGLENPeyLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAG 221

                  ....
gi 1443061903 157 VKLP 160
Cdd:TIGR00569 222 LNME 225
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
2-95 6.01e-11

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: 59.74  E-value: 6.01e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDpaTARRIHQKDVFEKQKALIL 81
Cdd:cd20545    25 TLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQKNP--NLVIDEQSKEVWRWRDSIL 102
                          90
                  ....*....|....
gi 1443061903  82 TGERLVLTTVRFDF 95
Cdd:cd20545   103 YNEEVLLETLCFDL 116
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
2-96 9.83e-10

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: 56.76  E-value: 9.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCP-LDQVIRVAYGTMYRRDpatarrihqkdvfekqkalI 80
Cdd:pfam00134  51 TLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYEEIYPPtVEDLVYITDNAYTREE-------------------I 111
                          90
                  ....*....|....*.
gi 1443061903  81 LTGERLVLTTVRFDFN 96
Cdd:pfam00134 112 LRMERLILETLNFDLS 127
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
99-172 1.37e-09

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: 54.97  E-value: 1.37e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443061903  99 HPYRPLLDAMEKLGISQKEVKQVAWNFVNDWLK-TTLCLQYKPQYIAAGSLYLAAKFQNVKLPV--HGGHvWWHQFD 172
Cdd:cd20539     1 HPHTHVLKICNLVKAGSKDLAQTAYFLATNSLHlTTFCLQYKPTVIACVCIHLACKWSNWEIPRssEGKD-WYEYVD 76
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
2-59 1.39e-08

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


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 52.03  E-value: 1.39e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1443061903   2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGT------MYRR 59
Cdd:cd00043    19 VLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSekelrkAEKE 82
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
4-95 1.20e-07

first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called MO15-associated protein, p34, or p37, is normally associated with the cyclin-dependent kinase cdk7, the catalytic subunit of the CDK-activating kinase (CAK) enzymatic complex. CCNH contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410228  Cd Length: 150  Bit Score: 51.06  E-value: 1.20e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   4 ATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVirvaygtmyrrdpatARRIHQKDVFEKQkalILTG 83
Cdd:cd20524    77 ATALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVEEFNISIDQF---------------VGNIKESEKTAEI---ILEY 138
                          90
                  ....*....|..
gi 1443061903  84 ERLVLTTVRFDF 95
Cdd:cd20524   139 ELLLLQGLNFHL 150
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
99-161 3.29e-07

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: 48.18  E-value: 3.29e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443061903  99 HPYRPLLDAMEKLGISQkEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLPV 161
Cdd:cd00043     1 KAVDFIRRLCSKLGLPE-EVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTL 62
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
99-172 4.21e-07

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: 48.41  E-value: 4.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  99 HPY-----RPLLDAMEKLGISQKEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLP--VHGGHVWWHQF 171
Cdd:cd20535     3 HKYllhylKSLRDWLNPEFWSRSPIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQVYGVKVPpeEEAEKPWWQAF 82

                  .
gi 1443061903 172 D 172
Cdd:cd20535    83 C 83
CYCLIN_AtCycC_rpt2 cd20572
second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
99-152 5.59e-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: 48.23  E-value: 5.59e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1443061903  99 HPYRPLLDAMEKLGISqkEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAA 152
Cdd:cd20572     1 HPYRPLIQLLQDAGLT--DMTQFTWSIVNDTYRTDLILIHPPYMIALACIYIAS 52
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
98-160 6.48e-07

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: 48.45  E-value: 6.48e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1443061903  98 QHPYRPLLDAMEKLGISQKE-VKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLP 160
Cdd:cd20592     1 KHPHKIIVMYLQVLECERNQtLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLP 64
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
3-74 9.09e-07

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: 47.20  E-value: 9.09e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443061903   3 IATAIMFCHRFYLYQSLAK-NGWQtIATVCIFLASKVEDTPcpldQVIRVAYgtmyrrdpATARRIHQKDVFE 74
Cdd:cd20513    23 IATAIVYFKRFYARNSFKDiDPRL-VAPTCLYLASKVEECP----SHARLIV--------AEAKVLKTKFSYE 82
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
3-93 9.32e-07

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: 48.29  E-value: 9.32e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   3 IATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRD--PATARRIHQKDvFEKQKALI 80
Cdd:cd20591    36 MATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQVLMVFHRMECRREnlPLEPLEPESKK-YDEMKEDL 114
                          90
                  ....*....|...
gi 1443061903  81 LTGERLVLTTVRF 93
Cdd:cd20591   115 IRTERHLLKEMGF 127
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
99-160 1.66e-06

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: 47.27  E-value: 1.66e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443061903  99 HPYRPLLDAMEKLGISQ-KEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLP 160
Cdd:cd20593     1 HPHKIIVMYLQVLECERnRHLVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEIPLP 63
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
116-160 1.88e-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: 46.05  E-value: 1.88e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443061903  116 KEVKQVAWNFVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQNVKLP 160
Cdd:smart00385  14 PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPW 58
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
2-52 3.06e-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: 3.06e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443061903    2 TIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVA 52
Cdd:smart00385  16 TLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT 66
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
98-190 2.83e-05

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: 43.53  E-value: 2.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  98 QHPYRPLLDAMEkLGISQKEVKQVAWNFVNDWLK-TTLCLQYKPQYIAAGSLYLAAKFQNVKLPVHG-GHVWWHQFDVAp 175
Cdd:cd20598     1 EHPHTDVVKCTQ-LVRASKDLAQTSYFMATNSLHlTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTdGKHWWEYVDPT- 78
                          90
                  ....*....|....*
gi 1443061903 176 kpleAVLQQMREMVH 190
Cdd:cd20598    79 ----VTLELLDELTH 89
CYCLIN_CCNH_rpt2 cd20525
second cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
99-189 3.24e-05

second 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 second one. The cyclin box is a protein binding domain.


Pssm-ID: 410229  Cd Length: 126  Bit Score: 43.82  E-value: 3.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  99 HPYRPL----LDAMEKLGISQKEVKQVAWN----FVNDWLKTTLCLQYKPQYIAAGSLYLAAKFQN--------VKLPVH 162
Cdd:cd20525     2 HPYRPLegflLDLKTRLPDLKAENLEKLYKeareFLNRSLLTDAPLLYPPSQIALAALLLAASEAGidveeylsEKLPGS 81
                          90       100
                  ....*....|....*....|....*..
gi 1443061903 163 GGHVWWHQfdvapkpLEAVLQQMREMV 189
Cdd:cd20525    82 EESEELEK-------LLEIIREIKKLV 101
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
3-93 4.43e-05

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: 43.20  E-value: 4.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   3 IATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPATARRIHQKDVFEKQKALILT 82
Cdd:cd20589    33 MATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVINVFHHIKQVRGKRTISPLILDQNYINLKNQVIK 112
                          90
                  ....*....|.
gi 1443061903  83 GERLVLTTVRF 93
Cdd:cd20589   113 AERRVLKELGF 123
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
1-93 2.05e-04

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: 41.92  E-value: 2.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903   1 MTIATAIMFCHRFYLYQSLAKNGWQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPATARRIHQKDVFEKQKALI 80
Cdd:cd20590    63 VAMATGQVLFQRFFYTKSFVKHSMEHVSMACVHLASKIEEAPRRIRDVINVFHRLRQLREKKKPVPLILDQEYVNLKNQI 142
                          90
                  ....*....|...
gi 1443061903  81 LTGERLVLTTVRF 93
Cdd:cd20590   143 IKAERRVLKELGF 155
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
99-190 1.13e-03

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


Pssm-ID: 410300 [Multi-domain]  Cd Length: 109  Bit Score: 38.91  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061903  99 HPYRPLLDAMEkLGISQKEVKQVAWNFVNDWLK-TTLCLQYKPQYIAAGSLYLAAKFQNVKLPVH-GGHVWWHQFDVApk 176
Cdd:cd20597     2 HPHTHVVKCTQ-LVRASKDLAQTSYFMATNSLHlTTFSLQYTPPVVACVCIHLACKWSNWEIPVStDGKHWWEYVDAT-- 78
                          90
                  ....*....|....
gi 1443061903 177 pleAVLQQMREMVH 190
Cdd:cd20597    79 ---VTLELLDELTH 89
 
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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