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Conserved domains on  [gi|556962862|ref|XP_005991486|]
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cyclin-T1 isoform X1 [Latimeria chalumnae]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
12-149 3.46e-101

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: 308.52  E-value: 3.46e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  12 RKWYFTREQIENSPSRRAGQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLF 91
Cdd:cd20595    1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 556962862  92 LAAKVEEQPRKLEHVIKVTHACLNPQEPSPDIRSEAYLQQAQDLVILENIILQTLGFE 149
Cdd:cd20595   81 LAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 138
CYCLIN_SF super family cl40454
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
153-302 5.35e-66

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 cd20597:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 109  Bit Score: 214.56  E-value: 5.35e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 153 DHPHTHVVKCTQLVReqvtawttvvegyphcpanvsypssgmgarelfslhacsmcASKDLAQTSYFMATNSLHLTTFSL 232
Cdd:cd20597    1 DHPHTHVVKCTQLVR-----------------------------------------ASKDLAQTSYFMATNSLHLTTFSL 39
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 233 QYSPPIVACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRLKRIKNWR 302
Cdd:cd20597   40 QYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIWNWR 109
 
Name Accession Description Interval E-value
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
12-149 3.46e-101

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: 308.52  E-value: 3.46e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  12 RKWYFTREQIENSPSRRAGQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLF 91
Cdd:cd20595    1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 556962862  92 LAAKVEEQPRKLEHVIKVTHACLNPQEPSPDIRSEAYLQQAQDLVILENIILQTLGFE 149
Cdd:cd20595   81 LAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 138
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
153-302 5.35e-66

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: 214.56  E-value: 5.35e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 153 DHPHTHVVKCTQLVReqvtawttvvegyphcpanvsypssgmgarelfslhacsmcASKDLAQTSYFMATNSLHLTTFSL 232
Cdd:cd20597    1 DHPHTHVVKCTQLVR-----------------------------------------ASKDLAQTSYFMATNSLHLTTFSL 39
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 233 QYSPPIVACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRLKRIKNWR 302
Cdd:cd20597   40 QYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIWNWR 109
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
14-151 1.49e-18

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: 82.18  E-value: 1.49e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862   14 WYFTREQIENSPSRR-AGQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFL 92
Cdd:pfam00134   4 QYLRELELKYLPKPDyMDQQPDINPKMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFI 83
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862   93 AAKVEE-QPRKLEHVIKVThaclnpqepspDirsEAYlqQAQDLVILENIILQTLGFEIT 151
Cdd:pfam00134  84 AAKYEEiYPPTVEDLVYIT-----------D---NAY--TREEILRMERLILETLNFDLS 127
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
45-144 6.01e-14

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: 67.62  E-value: 6.01e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862    45 NLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKLEHVIKVTHAClnpqepspdir 124
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYF----------- 69
                           90       100
                   ....*....|....*....|
gi 556962862   125 seaylqQAQDLVILENIILQ 144
Cdd:smart00385  70 ------TEEEILRMERLLLE 83
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
34-260 6.45e-14

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: 73.23  E-value: 6.45e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  34 DKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKlehvIKVTHAC 113
Cdd:COG5333   39 EKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRD----ISIESFE 114
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 114 LNpqepspDIRSEAYLQQAQDLVILENIILQTLGFEITIDHPHTHVVKctqlvreqvtawttvvegyphcpanvsypssg 193
Cdd:COG5333  115 AR------DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEG-------------------------------- 156
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556962862 194 mgarelfSLHACSMCASKDLAQTSYFMATNSLHlTTFSLQYSPPIVACVCIHLACK------WSNWEIPVSTD 260
Cdd:COG5333  157 -------FLKDLQEKDKYKLLQIAWKIINDALR-TDLCLLYPPHIIALAALLIACEvlgmpiIKLLDFVSYET 221
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
33-155 2.84e-05

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: 46.75  E-value: 2.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862   33 PDKELSYRQQAANLLQDMGQRLNVSQLT--INTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEeqprklEHVIKVT 110
Cdd:TIGR00569  49 PEEELDLVKYYEKRLLDFCSAFKPTMPTsvVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVE------EFNVSID 122
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 556962862  111 HACLNPQEpSPDIRSEAYLQqaqdlviLENIILQTLGFEITIDHP 155
Cdd:TIGR00569 123 QFVGNLKE-TPLKALEQVLE-------YELLLIQQLNFHLIVHNP 159
 
Name Accession Description Interval E-value
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
12-149 3.46e-101

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: 308.52  E-value: 3.46e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  12 RKWYFTREQIENSPSRRAGQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLF 91
Cdd:cd20595    1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 556962862  92 LAAKVEEQPRKLEHVIKVTHACLNPQEPSPDIRSEAYLQQAQDLVILENIILQTLGFE 149
Cdd:cd20595   81 LAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 138
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
13-149 4.05e-93

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: 287.37  E-value: 4.05e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  13 KWYFTREQIENSPSRRAGQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFL 92
Cdd:cd20538    1 RWYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFL 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 556962862  93 AAKVEEQPRKLEHVIKVTHACLNPQEPSPDIRSEAYLQQAQDLVILENIILQTLGFE 149
Cdd:cd20538   81 AAKVEEQPRKLEHVIKVAHACLHRGEPDLDTKSEAYLQQAQELVINENILLQTLGFE 137
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
11-149 6.69e-86

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: 268.45  E-value: 6.69e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  11 ARKWYFTREQIENSPSRRAGQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVL 90
Cdd:cd20596    1 SSRWFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTAL 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 556962862  91 FLAAKVEEQPRKLEHVIKVTHACLNPQEPSPDIRSEAYLQQAQDLVILENIILQTLGFE 149
Cdd:cd20596   81 FLAAKVEEQPRKLEHVIKVAHACLNPLEPQLDTKSDAYLQQAQELVILETIMLQTLGFE 139
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
153-302 5.35e-66

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: 214.56  E-value: 5.35e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 153 DHPHTHVVKCTQLVReqvtawttvvegyphcpanvsypssgmgarelfslhacsmcASKDLAQTSYFMATNSLHLTTFSL 232
Cdd:cd20597    1 DHPHTHVVKCTQLVR-----------------------------------------ASKDLAQTSYFMATNSLHLTTFSL 39
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 233 QYSPPIVACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRLKRIKNWR 302
Cdd:cd20597   40 QYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIWNWR 109
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
153-307 1.09e-63

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: 208.40  E-value: 1.09e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 153 DHPHTHVVKCTQLVReqvtawttvvegyphcpanvsypssgmgarelfslhacsmcASKDLAQTSYFMATNSLHLTTFSL 232
Cdd:cd20598    1 EHPHTDVVKCTQLVR-----------------------------------------ASKDLAQTSYFMATNSLHLTTFCL 39
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556962862 233 QYSPPIVACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRLKRIKNWRAGQAA 307
Cdd:cd20598   40 QYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPSRLKRIRNWRANQAA 114
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
154-285 1.15e-49

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: 169.38  E-value: 1.15e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 154 HPHTHVVKCTQLVREQvtawttvvegyphcpanvsypssgmgarelfslhacsmcaSKDLAQTSYFMATNSLHLTTFSLQ 233
Cdd:cd20539    1 HPHTHVLKICNLVKAG----------------------------------------SKDLAQTAYFLATNSLHLTTFCLQ 40
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 556962862 234 YSPPIVACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFL 285
Cdd:cd20539   41 YKPTVIACVCIHLACKWSNWEIPRSSEGKDWYEYVDPSLTLEELDELTSEFL 92
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
30-149 3.31e-36

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: 132.36  E-value: 3.31e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  30 GQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKLEHVIKV 109
Cdd:cd20530    1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 556962862 110 THACLNpqepspDIRSEAYLQQAQDLVI-LENIILQTLGFE 149
Cdd:cd20530   81 ARSLLN------DKQFAQFGDDPKEEVMvLERILLQTIKFD 115
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
30-149 3.13e-28

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: 109.92  E-value: 3.13e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  30 GQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKLEHVIKV 109
Cdd:cd20587    2 GIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIVV 81
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 556962862 110 THACLNPQEPSPDIR---SEAYLQQAQDLVILENIILQTLGFE 149
Cdd:cd20587   82 SYEIIFKKDPSAAQRikqKEVYEQQKELVLNGEKLVLSTLGFD 124
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
30-148 4.67e-24

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: 98.02  E-value: 4.67e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  30 GQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKLEHVIKV 109
Cdd:cd20532    2 GIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVINV 81
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 556962862 110 THACLNPQEPSP------DIRSEAYLQQAQDLVILENIILQTLGF 148
Cdd:cd20532   82 FHRLLQRRLGKPaevlplDIGSAEYEELKNDIIKAERRILKELGF 126
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
14-151 1.49e-18

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: 82.18  E-value: 1.49e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862   14 WYFTREQIENSPSRR-AGQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFL 92
Cdd:pfam00134   4 QYLRELELKYLPKPDyMDQQPDINPKMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFI 83
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862   93 AAKVEE-QPRKLEHVIKVThaclnpqepspDirsEAYlqQAQDLVILENIILQTLGFEIT 151
Cdd:pfam00134  84 AAKYEEiYPPTVEDLVYIT-----------D---NAY--TREEILRMERLILETLNFDLS 127
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
36-150 2.47e-18

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: 81.32  E-value: 2.47e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  36 ELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKLEHVIKVThACLN 115
Cdd:cd20545    1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIAC-AKVA 79
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 556962862 116 PQEPSPDI-RSEAYLQQAQDLVIL-ENIILQTLGFEI 150
Cdd:cd20545   80 QKNPNLVIdEQSKEVWRWRDSILYnEEVLLETLCFDL 116
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
40-149 3.71e-18

first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ancient conserved domain proteins (ACDPs), are evolutionarily conserved Mg2+ transporters. CCNM, also called cyclin-Q (CCNQ), or CDK10-activating cyclin, or cyclin-related protein FAM58A, associates with CDK10 to promote its kinase activity. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410237 [Multi-domain]  Cd Length: 110  Bit Score: 80.68  E-value: 3.71e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  40 RQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKLEHVIKVTHACLNPQEP 119
Cdd:cd20534    2 HFKVLRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRILHPDKP 81
                         90       100       110
                 ....*....|....*....|....*....|
gi 556962862 120 SPDIrSEAYLQQAQDLVILENIILQTLGFE 149
Cdd:cd20534   82 PLEL-DDEYWELRDSIVNCELLLLRILKFD 110
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
26-148 8.44e-18

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: 80.26  E-value: 8.44e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  26 SRRAGQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKLEH 105
Cdd:cd20591    1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 556962862 106 VIKVTHACLNPQEPSP----DIRSEAYLQQAQDLVILENIILQTLGF 148
Cdd:cd20591   81 VLMVFHRMECRRENLPleplEPESKKYDEMKEDLIRTERHLLKEMGF 127
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
19-148 1.35e-15

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: 74.66  E-value: 1.35e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  19 EQIENSPSRRAGQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEE 98
Cdd:cd20590   23 ERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVKHSMEHVSMACVHLASKIEE 102
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 556962862  99 QPRKLEHVIKVTH---ACLNPQEPSPDIRSEAYLQQAQDLVILENIILQTLGF 148
Cdd:cd20590  103 APRRIRDVINVFHrlrQLREKKKPVPLILDQEYVNLKNQIIKAERRVLKELGF 155
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
44-115 2.82e-15

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: 72.24  E-value: 2.82e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556962862  44 ANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRklehVIKVTHACLN 115
Cdd:cd20513    6 ANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPS----HARLIVAEAK 73
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
45-144 6.01e-14

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: 67.62  E-value: 6.01e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862    45 NLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKLEHVIKVTHAClnpqepspdir 124
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYF----------- 69
                           90       100
                   ....*....|....*....|
gi 556962862   125 seaylqQAQDLVILENIILQ 144
Cdd:smart00385  70 ------TEEEILRMERLLLE 83
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
34-260 6.45e-14

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: 73.23  E-value: 6.45e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  34 DKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKlehvIKVTHAC 113
Cdd:COG5333   39 EKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRD----ISIESFE 114
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 114 LNpqepspDIRSEAYLQQAQDLVILENIILQTLGFEITIDHPHTHVVKctqlvreqvtawttvvegyphcpanvsypssg 193
Cdd:COG5333  115 AR------DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEG-------------------------------- 156
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556962862 194 mgarelfSLHACSMCASKDLAQTSYFMATNSLHlTTFSLQYSPPIVACVCIHLACK------WSNWEIPVSTD 260
Cdd:COG5333  157 -------FLKDLQEKDKYKLLQIAWKIINDALR-TDLCLLYPPHIIALAALLIACEvlgmpiIKLLDFVSYET 221
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
42-111 1.10e-13

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: 67.05  E-value: 1.10e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  42 QAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKLEHVIKVTH 111
Cdd:cd00043    1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSG 70
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
30-148 4.13e-13

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


Pssm-ID: 410292 [Multi-domain]  Cd Length: 124  Bit Score: 66.69  E-value: 4.13e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  30 GQDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKLEHVIKV 109
Cdd:cd20589    2 GLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVINV 81
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 556962862 110 TH---ACLNPQEPSPDIRSEAYLQQAQDLVILENIILQTLGF 148
Cdd:cd20589   82 FHhikQVRGKRTISPLILDQNYINLKNQVIKAERRVLKELGF 123
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
39-148 2.96e-12

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: 63.90  E-value: 2.96e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  39 YRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKLEHVIKVTHACLNPQE 118
Cdd:cd20547    1 LRLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNLRHPDK 80
                         90       100       110
                 ....*....|....*....|....*....|.
gi 556962862 119 PSPDIRseaYLQQAQDLVI-LENIILQTLGF 148
Cdd:cd20547   81 ISVDDQ---MLEEFRKAILgLERLLLETICF 108
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
213-289 6.21e-12

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: 62.74  E-value: 6.21e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 213 LAQTSYFMATNSLHlTTFSLQYSPPIVACVCIHLACKWSNWEIP---VSTDGKHWWEYVDPTVTLELLDELTHeflQILE 289
Cdd:cd20531   24 LVQMAWTFVNDSLC-TTLCLQWEPEIIAVALMYLAAKLSKFDLQdwtSKPPGKRWWEQFVEDVSLEVLEDICH---QVLD 99
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
209-286 9.35e-09

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: 53.52  E-value: 9.35e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 209 ASKDLAQTSYFMATNSLHlTTFSLQYSPPIVACVCIHLACKWSNWEIPVSTDGKH--WWEYVDptVTLELLDELTHEFLQ 286
Cdd:cd20546   17 DPKELAQLAWAFLNDSYR-TPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPNEKLneWWELFG--VDEEEIADAINEILD 93
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
42-98 4.22e-08

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


Pssm-ID: 410274 [Multi-domain]  Cd Length: 107  Bit Score: 51.78  E-value: 4.22e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 556962862  42 QAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEE 98
Cdd:cd20571    9 HMSNYIKKLAQHIKVRQRVVATAITYFRRVYTRKSFTEYDPRLVAPTCLYLASKAEE 65
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
210-289 5.44e-08

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: 51.06  E-value: 5.44e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 210 SKDLAQTSY-FMatNSLHLTTFSLQYSPPIVACVCIHLACKWSNWEIPvstDGKHWWEYVDptVTLELLDELThefLQIL 288
Cdd:cd20533   18 NKKLAQTAWnYM--NDSLRTDLCVRYPPEVIACACIYLAARELGIPLP---LPPPWWELFD--VSKEDIEEIC---LTIL 87

                 .
gi 556962862 289 E 289
Cdd:cd20533   88 E 88
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
12-150 2.55e-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: 50.67  E-value: 2.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862  12 RKWYFT----------------REQIENSPSRRAGQD----PDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRF 71
Cdd:cd20524    7 KHWIFSseeelaelraeanekaREKLKESLKEEDAEPkfltPEEELLLVRYYEKKLLEFCRAFKLPDSVLATALTYFKRF 86
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556962862  72 YMIQSFTRFHRNAVAPAVLFLAAKVEEQPRKLEHVIKVthacLNPQEPSPDIrseaylqqaqdLVILENIILQTLGFEI 150
Cdd:cd20524   87 YLKNSVMEYHPKEIMLTCLYLACKVEEFNISIDQFVGN----IKESEKTAEI-----------ILEYELLLLQGLNFHL 150
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
213-287 3.18e-06

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: 46.48  E-value: 3.18e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556962862 213 LAQTSYFMATNSLHlTTFSLQYSPPIVACVCIHLACKWSNWEIPVSTDG-KHWWEYVDPTVTLELLDELTHEFLQI 287
Cdd:cd20535   27 IAKTAWSLLRDFYH-SPLCLQFKPQHIALAVIYLALQVYGVKVPPEEEAeKPWWQAFCEDLTKETIDEIIEDIINV 101
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
206-289 5.39e-06

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: 45.60  E-value: 5.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862 206 SMCASKDLAQTSYFMATNSLHlTTFSLQYSPPIVACVCIHLACKWSNWEIPVSTDgKHWWEYVDptVTLELLDELTHEFL 285
Cdd:cd20588   14 FNVAQNALAQAAWNFVNDGLR-TSLCLQFKPHHIAAGAIFLAAKFLKVKLPCDGR-KVWWQEFD--VTPRQLEEVSNQML 89

                 ....
gi 556962862 286 QILE 289
Cdd:cd20588   90 ELYE 93
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
33-155 2.84e-05

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: 46.75  E-value: 2.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556962862   33 PDKELSYRQQAANLLQDMGQRLNVSQLT--INTAIVYMHRFYMIQSFTRFHRNAVAPAVLFLAAKVEeqprklEHVIKVT 110
Cdd:TIGR00569  49 PEEELDLVKYYEKRLLDFCSAFKPTMPTsvVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVE------EFNVSID 122
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 556962862  111 HACLNPQEpSPDIRSEAYLQqaqdlviLENIILQTLGFEITIDHP 155
Cdd:TIGR00569 123 QFVGNLKE-TPLKALEQVLE-------YELLLIQQLNFHLIVHNP 159
 
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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