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Conserved domains on  [gi|1880356786|ref|XP_035512610|]
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cyclin-T1 isoform X1 [Morone saxatilis]

Protein Classification

cyclin-T1( domain architecture ID 15334822)

cyclin-T1 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)

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 ...
 14-151 1.26e-98

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: 298.89  E-value: 1.26e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  14 NKWYYSRQQIDNSPSRRAGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALF 93
Cdd:cd20595     1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1880356786  94 LAAKVEEQPRKLEHVIKVAHACLNPQDPSPDVRSDAYLQQAQDLVILESIILQTLAFE 151
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 ...
 155-266 1.49e-74

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: 235.36  E-value: 1.49e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 155 DHPHTHVVKCTQLVRvvpASKDLAQTSYFMATNSLHLTTFCLQYSPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDP 234
Cdd:cd20597     1 DHPHTHVVKCTQLVR---ASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDA 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1880356786 235 TVTLELLDELTHEFLQILEKTPSRLKRIRNWK 266
Cdd:cd20597    78 TVTLELLDELTHEFLQILEKTPNRLKRIWNWR 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 ...
 14-151 1.26e-98

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: 298.89  E-value: 1.26e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  14 NKWYYSRQQIDNSPSRRAGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALF 93
Cdd:cd20595     1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1880356786  94 LAAKVEEQPRKLEHVIKVAHACLNPQDPSPDVRSDAYLQQAQDLVILESIILQTLAFE 151
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 ...
 155-266 1.49e-74

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: 235.36  E-value: 1.49e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 155 DHPHTHVVKCTQLVRvvpASKDLAQTSYFMATNSLHLTTFCLQYSPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDP 234
Cdd:cd20597     1 DHPHTHVVKCTQLVR---ASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDA 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1880356786 235 TVTLELLDELTHEFLQILEKTPSRLKRIRNWK 266
Cdd:cd20597    78 TVTLELLDELTHEFLQILEKTPNRLKRIWNWR 109
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 8-224 1.27e-19

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: 89.79  E-value: 1.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786   8 VPASCNNKWYYSRQQIDNSPS-RRAGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNV 86
Cdd:COG5333    10 VSSRPLLSFDSSQNAIELDLLvLEPELTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYS 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  87 ISPAALFLAAKVEEQPRKlehvIKVAHACLNpqdpspDVRSDAYLQQAQDLVILESIILQTLAFEITIDHPHT---HVVK 163
Cdd:COG5333    90 VVTTCVYLACKVEDTPRD----ISIESFEAR------DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKyleGFLK 159

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1880356786 164 CTQLVrvvpASKDLAQTSYFMATNSLHlTTFCLQYSPPVVACVCIHLACK------WSNWEIPVSTD 224
Cdd:COG5333   160 DLQEK----DKYKLLQIAWKIINDALR-TDLCLLYPPHIIALAALLIACEvlgmpiIKLLDFVSYET 221
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 16-153 1.28e-17

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: 79.48  E-value: 1.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  16 WYYSRQQIDNSPSRRaGLD--PDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALF 93
Cdd:pfam00134   4 QYLRELELKYLPKPD-YMDqqPDINPKMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLF 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1880356786  94 LAAKVEE-QPRKLEHVIKVAhaclnpqDpspdvrsDAYlqQAQDLVILESIILQTLAFEIT 153
Cdd:pfam00134  83 IAAKYEEiYPPTVEDLVYIT-------D-------NAY--TREEILRMERLILETLNFDLS 127
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 47-115 5.82e-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: 5.82e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1880356786   47 NLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRKLEHVIKVAHAC 115
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYF 69
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 33-204 2.75e-08

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: 56.00  E-value: 2.75e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  33 LDPDKELSYRQQAANLLQDMGQRLNVSQLT--INTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEeqprklEHVIK 110
Cdd:TIGR00569  47 LTPEEELDLVKYYEKRLLDFCSAFKPTMPTsvVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVE------EFNVS 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 111 VAHACLNPQDpSPDVRSDAYLQqaqdlviLESIILQTLAFEITIDHP----HTHVVKCtQLVRVVPASKDLAQTSYFMAT 186
Cdd:TIGR00569 121 IDQFVGNLKE-TPLKALEQVLE-------YELLLIQQLNFHLIVHNPyrplEGFLIDI-KTRLPGLENPEYLRKHADKFL 191

                         170
                  ....*....|....*...
gi 1880356786 187 NSLHLTTFCLQYSPPVVA 204
Cdd:TIGR00569 192 NRTLLTDAYLLYTPSQIA 209
 
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 ...
 14-151 1.26e-98

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: 298.89  E-value: 1.26e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  14 NKWYYSRQQIDNSPSRRAGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALF 93
Cdd:cd20595     1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1880356786  94 LAAKVEEQPRKLEHVIKVAHACLNPQDPSPDVRSDAYLQQAQDLVILESIILQTLAFE 151
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, ...
 15-151 6.17e-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: 284.28  E-value: 6.17e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  15 KWYYSRQQIDNSPSRRAGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFL 94
Cdd:cd20538     1 RWYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1880356786  95 AAKVEEQPRKLEHVIKVAHACLNPQDPSPDVRSDAYLQQAQDLVILESIILQTLAFE 151
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 ...
 14-151 7.01e-88

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: 271.15  E-value: 7.01e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  14 NKWYYSRQQIDNSPSRRAGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALF 93
Cdd:cd20596     2 SRWFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTALF 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1880356786  94 LAAKVEEQPRKLEHVIKVAHACLNPQDPSPDVRSDAYLQQAQDLVILESIILQTLAFE 151
Cdd:cd20596    82 LAAKVEEQPRKLEHVIKVAHACLNPLEPQLDTKSDAYLQQAQELVILETIMLQTLGFE 139
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 155-266 1.49e-74

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: 235.36  E-value: 1.49e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 155 DHPHTHVVKCTQLVRvvpASKDLAQTSYFMATNSLHLTTFCLQYSPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDP 234
Cdd:cd20597     1 DHPHTHVVKCTQLVR---ASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDA 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1880356786 235 TVTLELLDELTHEFLQILEKTPSRLKRIRNWK 266
Cdd:cd20597    78 TVTLELLDELTHEFLQILEKTPNRLKRIWNWR 109
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
 155-267 1.69e-70

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: 224.96  E-value: 1.69e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 155 DHPHTHVVKCTQLVRvvpASKDLAQTSYFMATNSLHLTTFCLQYSPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDP 234
Cdd:cd20598     1 EHPHTDVVKCTQLVR---ASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDP 77

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1880356786 235 TVTLELLDELTHEFLQILEKTPSRLKRIRNWKA 267
Cdd:cd20598    78 TVTLELLDELTHEFLQILEKTPSRLKRIRNWRA 110
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 156-249 3.95e-57

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: 188.25  E-value: 3.95e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 156 HPHTHVVKCTQLVRVvpASKDLAQTSYFMATNSLHLTTFCLQYSPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDPT 235
Cdd:cd20539     1 HPHTHVLKICNLVKA--GSKDLAQTAYFLATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPRSSEGKDWYEYVDPS 78

                          90
                  ....*....|....
gi 1880356786 236 VTLELLDELTHEFL 249
Cdd:cd20539    79 LTLEELDELTSEFL 92
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 32-151 1.32e-38

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: 138.52  E-value: 1.32e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  32 GLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRKLEHVIKV 111
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1880356786 112 AHACLNPQDPSpdvrsdAYLQQAQDLVI-LESIILQTLAFE 151
Cdd:cd20530    81 ARSLLNDKQFA------QFGDDPKEEVMvLERILLQTIKFD 115
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 32-151 7.27e-29

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: 111.46  E-value: 7.27e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  32 GLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRKLEHVIKV 111
Cdd:cd20587     2 GIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIVV 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1880356786 112 AHACLNPQDPSPDVR---SDAYLQQAQDLVILESIILQTLAFE 151
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 ...
 32-150 7.64e-25

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: 99.94  E-value: 7.64e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  32 GLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRKLEHVIKV 111
Cdd:cd20532     2 GIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVINV 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1880356786 112 AHACLN------PQDPSPDVRSDAYLQQAQDLVILESIILQTLAF 150
Cdd:cd20532    82 FHRLLQrrlgkpAEVLPLDIGSAEYEELKNDIIKAERRILKELGF 126
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 8-224 1.27e-19

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: 89.79  E-value: 1.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786   8 VPASCNNKWYYSRQQIDNSPS-RRAGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNV 86
Cdd:COG5333    10 VSSRPLLSFDSSQNAIELDLLvLEPELTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYS 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  87 ISPAALFLAAKVEEQPRKlehvIKVAHACLNpqdpspDVRSDAYLQQAQDLVILESIILQTLAFEITIDHPHT---HVVK 163
Cdd:COG5333    90 VVTTCVYLACKVEDTPRD----ISIESFEAR------DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKyleGFLK 159

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1880356786 164 CTQLVrvvpASKDLAQTSYFMATNSLHlTTFCLQYSPPVVACVCIHLACK------WSNWEIPVSTD 224
Cdd:COG5333   160 DLQEK----DKYKLLQIAWKIINDALR-TDLCLLYPPHIIALAALLIACEvlgmpiIKLLDFVSYET 221
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 42-151 1.45e-19

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: 84.53  E-value: 1.45e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  42 RQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRKLEHVIKVAHACLNPQDP 121
Cdd:cd20534     2 HFKVLRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRILHPDKP 81

                          90       100       110
                  ....*....|....*....|....*....|
gi 1880356786 122 SPDVrSDAYLQQAQDLVILESIILQTLAFE 151
Cdd:cd20534    82 PLEL-DDEYWELRDSIVNCELLLLRILKFD 110
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 38-152 6.28e-19

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: 82.86  E-value: 6.28e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  38 ELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRKLEHVIKVAhACLN 117
Cdd:cd20545     1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIAC-AKVA 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1880356786 118 PQDPSPDV-RSDAYLQQAQDLVIL-ESIILQTLAFEI 152
Cdd:cd20545    80 QKNPNLVIdEQSKEVWRWRDSILYnEEVLLETLCFDL 116
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 16-153 1.28e-17

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: 79.48  E-value: 1.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  16 WYYSRQQIDNSPSRRaGLD--PDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALF 93
Cdd:pfam00134   4 QYLRELELKYLPKPD-YMDqqPDINPKMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLF 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1880356786  94 LAAKVEE-QPRKLEHVIKVAhaclnpqDpspdvrsDAYlqQAQDLVILESIILQTLAFEIT 153
Cdd:pfam00134  83 IAAKYEEiYPPTVEDLVYIT-------D-------NAY--TREEILRMERLILETLNFDLS 127
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 28-150 2.15e-16

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


Pssm-ID: 410294 [Multi-domain]  Cd Length: 128  Bit Score: 76.03  E-value: 2.15e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  28 SRRAGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRKLEH 107
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1880356786 108 VIKVAHACLNPQDPSP----DVRSDAYLQQAQDLVILESIILQTLAF 150
Cdd:cd20591    81 VLMVFHRMECRRENLPleplEPESKKYDEMKEDLIRTERHLLKEMGF 127
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 155-253 1.61e-15

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: 72.76  E-value: 1.61e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 155 DHPHTHVVK-CTQLVRVVPASKDLAQTSYFMATNSLHlTTFCLQYSPPVVACVCIHLACKWSNWEIP---VSTDGKHWWE 230
Cdd:cd20531     1 EHPYKYLLKyAKQLKGDKNKIQKLVQMAWTFVNDSLC-TTLCLQWEPEIIAVALMYLAAKLSKFDLQdwtSKPPGKRWWE 79

                          90       100
                  ....*....|....*....|...
gi 1880356786 231 YVDPTVTLELLDELTHeflQILE 253
Cdd:cd20531    80 QFVEDVSLEVLEDICH---QVLD 99
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 46-117 5.33e-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: 71.09  E-value: 5.33e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1880356786  46 ANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRklehVIKVAHACLN 117
Cdd:cd20513     6 ANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPS----HARLIVAEAK 73
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 26-150 1.58e-14

first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA polymerase II-associated cyclin that is involved in pre-mRNA splicing. It may induce cell death, possibly by acting on the transcription and RNA processing of apoptosis-related factors. CCNL2 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410293 [Multi-domain]  Cd Length: 156  Bit Score: 71.58  E-value: 1.58e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  26 SPSRRAGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRKL 105
Cdd:cd20590    28 TPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVKHSMEHVSMACVHLASKIEEAPRRI 107

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1880356786 106 EHVIKVAH---ACLNPQDPSPDVRSDAYLQQAQDLVILESIILQTLAF 150
Cdd:cd20590   108 RDVINVFHrlrQLREKKKPVPLILDQEYVNLKNQIIKAERRVLKELGF 155
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 156-250 3.34e-14

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: 68.55  E-value: 3.34e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 156 HPHTHVVKCTQLVrVVPASKDLAQTSYFMATNSLHlTTFCLQYSPPVVACVCIHLACKWSNWEIPVSTDGKH--WWEYVD 233
Cdd:cd20546     1 HPYQYLIKFAKKL-GVSDPKELAQLAWAFLNDSYR-TPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPNEKLneWWELFG 78

                          90
                  ....*....|....*..
gi 1880356786 234 ptVTLELLDELTHEFLQ 250
Cdd:cd20546    79 --VDEEEIADAINEILD 93
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 47-115 5.82e-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: 5.82e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1880356786   47 NLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRKLEHVIKVAHAC 115
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYF 69
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 44-113 1.05e-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: 66.67  E-value: 1.05e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  44 QAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRKLEHVIKVAH 113
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 ...
 32-150 2.27e-12

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: 64.38  E-value: 2.27e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  32 GLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRKLEHVIKV 111
Cdd:cd20589     2 GLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVINV 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1880356786 112 AH---ACLNPQDPSPDVRSDAYLQQAQDLVILESIILQTLAF 150
Cdd:cd20589    82 FHhikQVRGKRTISPLILDQNYINLKNQVIKAERRVLKELGF 123
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 41-150 4.97e-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: 62.75  E-value: 4.97e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  41 YRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEEQPRKLEHVIKVAHACLNPQD 120
Cdd:cd20547     1 LRLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNLRHPDK 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1880356786 121 PSPDvrsDAYLQQAQDLVI-LESIILQTLAF 150
Cdd:cd20547    81 ISVD---DQMLEEFRKAILgLERLLLETICF 108
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 156-253 1.51e-11

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: 61.08  E-value: 1.51e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 156 HPHTHVVKCTQLVRVVPaSKDLAQTSY-FMatNSLHLTTFCLQYSPPVVACVCIHLACKWSNWEIPvstDGKHWWEYVDp 234
Cdd:cd20533     1 HPHKFILMYLQVLEGED-NKKLAQTAWnYM--NDSLRTDLCVRYPPEVIACACIYLAARELGIPLP---LPPPWWELFD- 73

                          90
                  ....*....|....*....
gi 1880356786 235 tVTLELLDELThefLQILE 253
Cdd:cd20533    74 -VSKEDIEEIC---LTILE 88
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 156-253 1.02e-08

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: 52.92  E-value: 1.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 156 HPHTHVVKCtqLVRVVPASKDLAQTSYFMATNSLHlTTFCLQYSPPVVACVCIHLACKWSNWEIPVSTDgKHWWEYVDpt 235
Cdd:cd20588     2 HPYKPLVAA--IKKFNVAQNALAQAAWNFVNDGLR-TSLCLQFKPHHIAAGAIFLAAKFLKVKLPCDGR-KVWWQEFD-- 75

                          90
                  ....*....|....*...
gi 1880356786 236 VTLELLDELTHEFLQILE 253
Cdd:cd20588    76 VTPRQLEEVSNQMLELYE 93
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 33-204 2.75e-08

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: 56.00  E-value: 2.75e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  33 LDPDKELSYRQQAANLLQDMGQRLNVSQLT--INTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEeqprklEHVIK 110
Cdd:TIGR00569  47 LTPEEELDLVKYYEKRLLDFCSAFKPTMPTsvVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVE------EFNVS 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 111 VAHACLNPQDpSPDVRSDAYLQqaqdlviLESIILQTLAFEITIDHP----HTHVVKCtQLVRVVPASKDLAQTSYFMAT 186
Cdd:TIGR00569 121 IDQFVGNLKE-TPLKALEQVLE-------YELLLIQQLNFHLIVHNPyrplEGFLIDI-KTRLPGLENPEYLRKHADKFL 191

                         170
                  ....*....|....*...
gi 1880356786 187 NSLHLTTFCLQYSPPVVA 204
Cdd:TIGR00569 192 NRTLLTDAYLLYTPSQIA 209
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 10-106 3.41e-08

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


Pssm-ID: 410228  Cd Length: 150  Bit Score: 52.98  E-value: 3.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786  10 ASCNNKwYYSR--QQIDNSPSRRAGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVI 87
Cdd:cd20524    22 AEANEK-AREKlkESLKEEDAEPKFLTPEEELLLVRYYEKKLLEFCRAFKLPDSVLATALTYFKRFYLKNSVMEYHPKEI 100

                          90
                  ....*....|....*....
gi 1880356786  88 SPAALFLAAKVEEQPRKLE 106
Cdd:cd20524   101 MLTCLYLACKVEEFNISID 119
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 44-100 1.01e-07

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: 50.63  E-value: 1.01e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1880356786  44 QAANLLQDMGQRLNVSQLTINTAIVYMHRFYMVQSFTRFHRNVISPAALFLAAKVEE 100
Cdd:cd20571     9 HMSNYIKKLAQHIKVRQRVVATAITYFRRVYTRKSFTEYDPRLVAPTCLYLASKAEE 65
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 156-251 1.10e-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: 50.33  E-value: 1.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 156 HPHTHVVKCTQLVR-VVPASK----DLAQTSYFMATNSLHlTTFCLQYSPPVVACVCIHLACKWSNWEIPVSTDG-KHWW 229
Cdd:cd20535     1 LPHKYLLHYLKSLRdWLNPEFwsrsPIAKTAWSLLRDFYH-SPLCLQFKPQHIALAVIYLALQVYGVKVPPEEEAeKPWW 79

                          90       100
                  ....*....|....*....|..
gi 1880356786 230 EYVDPTVTLELLDELTHEFLQI 251
Cdd:cd20535    80 QAFCEDLTKETIDEIIEDIINV 101
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 156-277 2.81e-05

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: 44.19  E-value: 2.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 156 HPHTHVVKCTQLVRVvPASKDLAQTSYFMATNSLHLTTFcLQYSPPVVACVCIHLACKwsNWEIPVStDGKHWWEYVDpt 235
Cdd:cd20593     1 HPHKIIVMYLQVLEC-ERNRHLVQTSWNYMNDSLRTDVF-VRFNPETIACACIYLAAR--TLEIPLP-NRPHWFLLFG-- 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1880356786 236 VTLELLDELTHEFLQILEKTPSRLK----RIRNWKAGGQTPKAKTK 277
Cdd:cd20593    74 ATEEEIQEICLKILQLYTRKKVDLEhlesKVEKRKLAIEEAKAKAK 119
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 154-233 5.32e-04

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: 39.85  E-value: 5.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 154 IDHPHTHVVKCTQLVRVVPAskdLAQTSYFMATNSLHlTTFCLQYSPPVVACVCIHLACKWSNWEIPvstDGKHWWEYVD 233
Cdd:cd20594     2 VEHPHKFILNYLAMLMAPPE---LRQEAWNLANDSLR-TTLCVRFKSEVVACGVVYAAARRFQVPLP---ENPPWWKVFD 74
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 156-244 2.07e-03

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: 37.98  E-value: 2.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1880356786 156 HPHTHVvkcTQLVRVVPASKDLAQTSYFMATNSLHlTTFCLQYSPPVVACVCIHLACkwsnweIPVSTDGKHWWE--YVD 233
Cdd:cd20514     1 HPYRPL---TQYVQDAGLDDELLPLAWRIVNDSYR-TDVCLLYPPYLIALACLHMAC------VLLQKDARQWFAelNVD 70

                          90
                  ....*....|.
gi 1880356786 234 PTVTLELLDEL 244
Cdd:cd20514    71 MDKILEITREI 81
 
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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