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Conserved domains on  [gi|1246741995|ref|NP_001342735|]
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P-TEFB-associated cyclin T Pch1 [Schizosaccharomyces pombe]

Protein Classification

cyclin( domain architecture ID 11475015)

cyclin is a cell cycle regulator that regulates cyclin dependent kinases (CDKs)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 1-323 2.98e-101

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: 300.11  E-value: 2.98e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995   1 MSEVIKSVPPGSQNTSQWIISKDQLVFTPSaldgIPLDQEEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFS 80
Cdd:COG5333     6 ESNLVSSRPLLSFDSSQNAIELDLLVLEPE----LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  81 LKNYHYYEVAATCIFLATKVEDSvrkLRDIVINCAKVAQKNSnvlvdeqtKEYWRWRDVILYTEEVLLEALCFDFTVEHP 160
Cdd:COG5333    82 VEEISLYSVVTTCVYLACKVEDT---PRDISIESFEARDLWS--------EEPKSSRERILEYEFELLEALDFDLHVHHP 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 161 YPYVLSFIKKFVADDK-NVTKVAWTYINDSTRSIACLLYSPKTIAAAAFQFALEkneinlsttTDGLPVWMEESQVSYED 239
Cdd:COG5333   151 YKYLEGFLKDLQEKDKyKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACE---------VLGMPIIKLLDFVSYET 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 240 VKGVLTLidslykkINPSKQALPIDQKNGSHASSVAPGTPSSLASvSTQATPQHQNSSGRTDSFHSLNTETPSKSTVDDQ 319
Cdd:COG5333   222 KEEVIAL-------NYKSIVKNKIKTFKAEHLSRDLPFTLQNIAE-PQFALDKKPKSEEEADKIPDHNKYLQPSSTITDK 293


                  ....
gi 1246741995 320 ILST 323
Cdd:COG5333   294 NNVQ 297
 
Name Accession Description Interval E-value
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 1-323 2.98e-101

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: 300.11  E-value: 2.98e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995   1 MSEVIKSVPPGSQNTSQWIISKDQLVFTPSaldgIPLDQEEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFS 80
Cdd:COG5333     6 ESNLVSSRPLLSFDSSQNAIELDLLVLEPE----LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  81 LKNYHYYEVAATCIFLATKVEDSvrkLRDIVINCAKVAQKNSnvlvdeqtKEYWRWRDVILYTEEVLLEALCFDFTVEHP 160
Cdd:COG5333    82 VEEISLYSVVTTCVYLACKVEDT---PRDISIESFEARDLWS--------EEPKSSRERILEYEFELLEALDFDLHVHHP 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 161 YPYVLSFIKKFVADDK-NVTKVAWTYINDSTRSIACLLYSPKTIAAAAFQFALEkneinlsttTDGLPVWMEESQVSYED 239
Cdd:COG5333   151 YKYLEGFLKDLQEKDKyKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACE---------VLGMPIIKLLDFVSYET 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 240 VKGVLTLidslykkINPSKQALPIDQKNGSHASSVAPGTPSSLASvSTQATPQHQNSSGRTDSFHSLNTETPSKSTVDDQ 319
Cdd:COG5333   222 KEEVIAL-------NYKSIVKNKIKTFKAEHLSRDLPFTLQNIAE-PQFALDKKPKSEEEADKIPDHNKYLQPSSTITDK 293


                  ....
gi 1246741995 320 ILST 323
Cdd:COG5333   294 NNVQ 297
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 40-155 9.33e-75

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: 226.15  E-value: 9.33e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  40 EEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVINCAKVAQ 119
Cdd:cd20545     1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1246741995 120 KNSNVLVDEQTKEYWRWRDVILYTEEVLLEALCFDF 155
Cdd:cd20545    81 KNPNLVIDEQSKEVWRWRDSILYNEEVLLETLCFDL 116
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 56-207 5.16e-14

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: 71.40  E-value: 5.16e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  56 LRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVINcakvAQKNSNVLVDEqtkeywr 135
Cdd:TIGR00569  70 FKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGN----LKETPLKALEQ------- 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 136 wrdvILYTEEVLLEALCFDFTVEHPY-PyvlsfIKKFVADDKNVT----------KVAWTYINDSTRSIACLLYSPKTIA 204
Cdd:TIGR00569 139 ----VLEYELLLIQQLNFHLIVHNPYrP-----LEGFLIDIKTRLpglenpeylrKHADKFLNRTLLTDAYLLYTPSQIA 209


                  ...
gi 1246741995 205 AAA 207
Cdd:TIGR00569 210 LAA 212
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 49-114 2.71e-12

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: 61.84  E-value: 2.71e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1246741995   49 NFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVINC 114
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT 66
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 48-154 7.27e-10

Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.


Pssm-ID: 459686 [Multi-domain]  Cd Length: 127  Bit Score: 56.37  E-value: 7.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  48 CNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKV-EDSVRKLRDIVINCAKVAQknsnvlv 126
Cdd:pfam00134  35 IDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYeEIYPPTVEDLVYITDNAYT------- 107

                          90       100
                  ....*....|....*....|....*...
gi 1246741995 127 deqtkeywrwRDVILYTEEVLLEALCFD 154
Cdd:pfam00134 108 ----------REEILRMERLILETLNFD 125
 
Name Accession Description Interval E-value
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 1-323 2.98e-101

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: 300.11  E-value: 2.98e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995   1 MSEVIKSVPPGSQNTSQWIISKDQLVFTPSaldgIPLDQEEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFS 80
Cdd:COG5333     6 ESNLVSSRPLLSFDSSQNAIELDLLVLEPE----LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  81 LKNYHYYEVAATCIFLATKVEDSvrkLRDIVINCAKVAQKNSnvlvdeqtKEYWRWRDVILYTEEVLLEALCFDFTVEHP 160
Cdd:COG5333    82 VEEISLYSVVTTCVYLACKVEDT---PRDISIESFEARDLWS--------EEPKSSRERILEYEFELLEALDFDLHVHHP 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 161 YPYVLSFIKKFVADDK-NVTKVAWTYINDSTRSIACLLYSPKTIAAAAFQFALEkneinlsttTDGLPVWMEESQVSYED 239
Cdd:COG5333   151 YKYLEGFLKDLQEKDKyKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACE---------VLGMPIIKLLDFVSYET 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 240 VKGVLTLidslykkINPSKQALPIDQKNGSHASSVAPGTPSSLASvSTQATPQHQNSSGRTDSFHSLNTETPSKSTVDDQ 319
Cdd:COG5333   222 KEEVIAL-------NYKSIVKNKIKTFKAEHLSRDLPFTLQNIAE-PQFALDKKPKSEEEADKIPDHNKYLQPSSTITDK 293


                  ....
gi 1246741995 320 ILST 323
Cdd:COG5333   294 NNVQ 297
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 40-155 9.33e-75

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: 226.15  E-value: 9.33e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  40 EEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVINCAKVAQ 119
Cdd:cd20545     1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1246741995 120 KNSNVLVDEQTKEYWRWRDVILYTEEVLLEALCFDF 155
Cdd:cd20545    81 KNPNLVIDEQSKEVWRWRDSILYNEEVLLETLCFDL 116
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 34-154 1.07e-31

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: 115.02  E-value: 1.07e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  34 GIPLDQEEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVin 113
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDII-- 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1246741995 114 caKVAQknsNVLVDEQTK-EYWRWRDVILYTEEVLLEALCFD 154
Cdd:cd20530    79 --KTAR---SLLNDKQFAqFGDDPKEEVMVLERILLQTIKFD 115
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 33-153 3.93e-29

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: 108.80  E-value: 3.93e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  33 DGIPLDQEEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVI 112
Cdd:cd20532     1 DGIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVIN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1246741995 113 NCAKVAQK-----NSNVLVDEQTKEYWRWRDVILYTEEVLLEALCF 153
Cdd:cd20532    81 VFHRLLQRrlgkpAEVLPLDIGSAEYEELKNDIIKAERRILKELGF 126
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 46-154 1.08e-28

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: 106.87  E-value: 1.08e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  46 KGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVINCAKVAQKNSNVL 125
Cdd:cd20534     4 KVLRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRILHPDKPPL 83

                          90       100
                  ....*....|....*....|....*....
gi 1246741995 126 VDEQtkEYWRWRDVILYTEEVLLEALCFD 154
Cdd:cd20534    84 ELDD--EYWELRDSIVNCELLLLRILKFD 110
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 18-154 8.42e-27

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: 102.85  E-value: 8.42e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  18 WIISKDQLVFTPSALDGIPLDQEEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLA 97
Cdd:cd20538     2 WYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFLA 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1246741995  98 TKVEDSVRKLrDIVINCAKVAQKNSNVLVDEQTKEYWRWRDVILYTEEVLLEALCFD 154
Cdd:cd20538    82 AKVEEQPRKL-EHVIKVAHACLHRGEPDLDTKSEAYLQQAQELVINENILLQTLGFE 137
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 159-252 4.73e-24

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: 94.36  E-value: 4.73e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 159 HPYPYVLSFIKKF-VADDKNVTKVAWTYINDSTRSIACLLYSPKTIAAAAFQFALEKNEINLSTTTDG-LPVWMEESQVS 236
Cdd:cd20546     1 HPYQYLIKFAKKLgVSDPKELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPNEkLNEWWELFGVD 80

                          90
                  ....*....|....*.
gi 1246741995 237 YEDVKGVLTLIDSLYK 252
Cdd:cd20546    81 EEEIADAINEILDLYS 96
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 33-154 1.77e-23

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: 93.74  E-value: 1.77e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  33 DGIPLDQEEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVI 112
Cdd:cd20587     1 DGIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1246741995 113 NCAKVAQKN--SNVLVDEQTKEYWRWRDVILYTEEVLLEALCFD 154
Cdd:cd20587    81 VSYEIIFKKdpSAAQRIKQKEVYEQQKELVLNGEKLVLSTLGFD 124
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 44-155 9.34e-22

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


Pssm-ID: 410250 [Multi-domain]  Cd Length: 110  Bit Score: 88.56  E-value: 9.34e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  44 RSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVInCAKVAQKNSN 123
Cdd:cd20547     2 RLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILA-ASYNLRHPDK 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1246741995 124 VLVDEQTKEywRWRDVILYTEEVLLEALCFDF 155
Cdd:cd20547    81 ISVDDQMLE--EFRKAILGLERLLLETICFDF 110
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 30-153 1.99e-21

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: 88.35  E-value: 1.99e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  30 SALDGIPLDQEEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRD 109
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1246741995 110 IVINCAKVAQKNSNV---LVDEQTKEYWRWRDVILYTEEVLLEALCF 153
Cdd:cd20591    81 VLMVFHRMECRRENLplePLEPESKKYDEMKEDLIRTERHLLKEMGF 127
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
 15-154 2.44e-21

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: 88.57  E-value: 2.44e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  15 TSQWIISKDQLVFTPSALDGIPLDQEEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCI 94
Cdd:cd20596     1 SSRWFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTAL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1246741995  95 FLATKVEDSVRKLRDIVincaKVAQKNSNVL---VDEQTKEYWRWRDVILYTEEVLLEALCFD 154
Cdd:cd20596    81 FLAAKVEEQPRKLEHVI----KVAHACLNPLepqLDTKSDAYLQQAQELVILETIMLQTLGFE 139
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 19-153 1.44e-19

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: 84.29  E-value: 1.44e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  19 IISKDQLVFTPSALDGIPLDQEEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLAT 98
Cdd:cd20590    19 LLPEERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVKHSMEHVSMACVHLAS 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  99 KVEDSVRKLRDIV-----INCAKVAQKNSNVLVDEqtkEYWRWRDVILYTEEVLLEALCF 153
Cdd:cd20590    99 KIEEAPRRIRDVInvfhrLRQLREKKKPVPLILDQ---EYVNLKNQIIKAERRVLKELGF 155
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 16-154 4.10e-19

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: 82.41  E-value: 4.10e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  16 SQWIISKDQLVFTPSALDGIPLDQEEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIF 95
Cdd:cd20595     1 KRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1246741995  96 LATKVEDSVRKLRDiVINCAKVAQKNSNVLVDEQTKEYWRWRDVILYTEEVLLEALCFD 154
Cdd:cd20595    81 LAAKVEEQPKKLEH-VIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFE 138
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 48-151 7.21e-19

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: 80.33  E-value: 7.21e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  48 CNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIViNCAKvaqknsnVLVD 127
Cdd:cd20513     6 ANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPSHARLIV-AEAK-------VLKT 77

                          90       100
                  ....*....|....*....|....
gi 1246741995 128 EQTKEYWRWRDVILYTEEVLLEAL 151
Cdd:cd20513    78 KFSYEFPYRVNDILECEFYLLEAL 101
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 57-155 1.07e-15

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: 73.40  E-value: 1.07e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  57 RLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIvinCAKVAQKNSNVlvdeqtkeywrw 136
Cdd:cd20524    68 AFKLPDSVLATALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVEEFNISIDQF---VGNIKESEKTA------------ 132

                          90
                  ....*....|....*....
gi 1246741995 137 rDVILYTEEVLLEALCFDF 155
Cdd:cd20524   133 -EIILEYELLLLQGLNFHL 150
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 33-123 1.07e-15

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


Pssm-ID: 410292 [Multi-domain]  Cd Length: 124  Bit Score: 72.47  E-value: 1.07e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  33 DGIPLDQEEIQRSKGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVI 112
Cdd:cd20589     1 DGLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVIN 80

                          90
                  ....*....|.
gi 1246741995 113 NCAKVAQKNSN 123
Cdd:cd20589    81 VFHHIKQVRGK 91
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 56-207 5.16e-14

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: 71.40  E-value: 5.16e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  56 LRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVINcakvAQKNSNVLVDEqtkeywr 135
Cdd:TIGR00569  70 FKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGN----LKETPLKALEQ------- 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 136 wrdvILYTEEVLLEALCFDFTVEHPY-PyvlsfIKKFVADDKNVT----------KVAWTYINDSTRSIACLLYSPKTIA 204
Cdd:TIGR00569 139 ----VLEYELLLIQQLNFHLIVHNPYrP-----LEGFLIDIKTRLpglenpeylrKHADKFLNRTLLTDAYLLYTPSQIA 209


                  ...
gi 1246741995 205 AAA 207
Cdd:TIGR00569 210 LAA 212
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 46-111 2.94e-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: 64.35  E-value: 2.94e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1246741995  46 KGCNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIV 111
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIA 66
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 49-114 2.71e-12

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: 61.84  E-value: 2.71e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1246741995   49 NFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVINC 114
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT 66
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 158-232 5.26e-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: 61.59  E-value: 5.26e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 158 EHPYPYVLSFIKKFVADDKNVTK---VAWTYINDSTRSIACLLYSPKTIAAAAFQFA--LEKNEINLSTTTDGLPVWMEE 232
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKlvqMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAakLSKFDLQDWTSKPPGKRWWEQ 80
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 158-251 5.31e-12

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: 61.40  E-value: 5.31e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 158 EHPYPYVLSFIKKFVADDKNVTKVAWTYINDSTRSIACLLYSPKTIAAAAFQFALEKNEINLSttTDGLPVWMEESQVSY 237
Cdd:cd20588     1 EHPYKPLVAAIKKFNVAQNALAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLP--CDGRKVWWQEFDVTP 78

                          90
                  ....*....|....
gi 1246741995 238 EDVKGVLTLIDSLY 251
Cdd:cd20588    79 RQLEEVSNQMLELY 92
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
 58-154 2.88e-11

first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH associates with and activates the cyclin-dependent kinases, CDK-2 and CDK-3. CycH contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410288  Cd Length: 170  Bit Score: 61.38  E-value: 2.88e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  58 LKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIvincAKVAQknsnvlVDEQtkeywrwr 137
Cdd:cd20585    92 LRLPNKIQATALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEEYHVSAEEL----GKGIQ------QDHQ-------- 153

                          90
                  ....*....|....*..
gi 1246741995 138 dVILYTEEVLLEALCFD 154
Cdd:cd20585   154 -LILKNELALLQGLNFD 169
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 159-253 1.00e-10

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: 57.61  E-value: 1.00e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 159 HPYPYVLSFIKK-FVADDKNVTKVAWTYINDSTRSIACLLYSPKTIAAAAFQFALEKNEINLSTTtdglPVWMEESQVSY 237
Cdd:cd20533     1 HPHKFILMYLQVlEGEDNKKLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAARELGIPLPLP----PPWWELFDVSK 76

                          90
                  ....*....|....*.
gi 1246741995 238 EDVKGVLTLIDSLYKK 253
Cdd:cd20533    77 EDIEEICLTILELYTR 92
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 48-154 7.27e-10

Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.


Pssm-ID: 459686 [Multi-domain]  Cd Length: 127  Bit Score: 56.37  E-value: 7.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  48 CNFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKV-EDSVRKLRDIVINCAKVAQknsnvlv 126
Cdd:pfam00134  35 IDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCLFIAAKYeEIYPPTVEDLVYITDNAYT------- 107

                          90       100
                  ....*....|....*....|....*...
gi 1246741995 127 deqtkeywrwRDVILYTEEVLLEALCFD 154
Cdd:pfam00134 108 ----------REEILRMERLILETLNFD 125
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 49-153 3.76e-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: 51.01  E-value: 3.76e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995  49 NFIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVEDSVRKLRDIVINCAKVAQKNSNvlvde 128
Cdd:cd20571    12 NYIKKLAQHIKVRQRVVATAITYFRRVYTRKSFTEYDPRLVAPTCLYLASKAEESTVQAKLLVFYMKRLYADEYH----- 86

                          90       100
                  ....*....|....*....|....*
gi 1246741995 129 qtkeYWRWRDvILYTEEVLLEALCF 153
Cdd:cd20571    87 ----RYEIKD-ILEMEMKLLEALDY 106
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 159-251 8.43e-08

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: 49.54  E-value: 8.43e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 159 HPYPYVLsfikKFVAD---DKNVTKVAWTYINDSTRSIACLLYSPKTIAAAAFQFALEKNEINLSTttdglpvWMEESQV 235
Cdd:cd20514     1 HPYRPLT----QYVQDaglDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDARQ-------WFAELNV 69

                          90
                  ....*....|....*.
gi 1246741995 236 SYEDVKGVLTLIDSLY 251
Cdd:cd20514    70 DMDKILEITREILSLY 85
Cyclin_C pfam02984
Cyclin, C-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 162-270 7.66e-07

Cyclin, C-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 C-terminal domain.


Pssm-ID: 397230  Cd Length: 119  Bit Score: 47.23  E-value: 7.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 162 PYVLSFIKKF-----VADDKNVTKVAWTYINDSTRSIACLLYSPKTIAAAAfqFALEKNEINLSTTTDGLPVWmeeSQVS 236
Cdd:pfam02984   1 PTPLSFLRRFskaadYLHDLELRTLAKYLLELTLLDYDFLKYPPSLIAAAA--VYLARKTLNSPEWTETLEHY---TGYS 75

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1246741995 237 YEDVKGVLTLIDSLYKKINPSKQaLPIDQKNGSH 270
Cdd:pfam02984  76 EEDLKPCVKLLLELLLNAPSSKL-QAVRRKYSSS 108
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 159-255 2.89e-06

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


Pssm-ID: 410296 [Multi-domain]  Cd Length: 123  Bit Score: 45.73  E-value: 2.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 159 HPYPYVLSFIKKFVAD-DKNVTKVAWTYINDSTRSIACLLYSPKTIAAAAFQFALEKNEINLSTTtdglPVWMEESQVSY 237
Cdd:cd20593     1 HPHKIIVMYLQVLECErNRHLVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEIPLPNR----PHWFLLFGATE 76

                          90       100
                  ....*....|....*....|
gi 1246741995 238 EDVKGVLTLIDSLY--KKIN 255
Cdd:cd20593    77 EEIQEICLKILQLYtrKKVD 96
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 158-261 3.86e-06

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


Pssm-ID: 410295 [Multi-domain]  Cd Length: 123  Bit Score: 45.37  E-value: 3.86e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 158 EHPYPYVLSFIKKFVAD-DKNVTKVAWTYINDSTRSIACLLYSPKTIAAAAFQFALEKNEINLSTTtdglPVWMEESQVS 236
Cdd:cd20592     1 KHPHKIIVMYLQVLECErNQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPNR----PHWFLLFGAT 76

                          90       100
                  ....*....|....*....|....*
gi 1246741995 237 YEDVKGVLTLIDSLYKKINPSKQAL 261
Cdd:cd20592    77 EEEIQEICITTLKLYTRKKPNYEFL 101
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 159-213 1.27e-05

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: 43.40  E-value: 1.27e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1246741995 159 HPYPYVLSFIK-------KFVADDKNVTKVAWTYINDSTRSIACLLYSPKTIAAAAFQFALE 213
Cdd:cd20535     1 LPHKYLLHYLKslrdwlnPEFWSRSPIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQ 62
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 157-263 7.65e-05

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: 41.39  E-value: 7.65e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 157 VEHPYPYVLSFIKKFVADDKnVTKVAWTYINDSTRSIACLLYSPKTIA-----AAA--FQFALEKNeinlstttdglPVW 229
Cdd:cd20594     2 VEHPHKFILNYLAMLMAPPE-LRQEAWNLANDSLRTTLCVRFKSEVVAcgvvyAAArrFQVPLPEN-----------PPW 69

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1246741995 230 MEESQVSYEDVKGVLTLIDSLYKKinPSKQALPI 263
Cdd:cd20594    70 WKVFDAEKAEIDVVCKVLADLYRQ--PKARYIEV 101
CYCLIN_CCNJ-like_rpt1 cd20528
first cyclin box found in cyclin-J (CCNJ) family; The CCNJ family includes two cyclins, CCNJ ...
 50-102 6.22e-04

first cyclin box found in cyclin-J (CCNJ) family; The CCNJ family includes two cyclins, CCNJ and CCNJ-like. CCNJ may regulate the cell cycle or transcription. 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: 410231 [Multi-domain]  Cd Length: 103  Bit Score: 38.74  E-value: 6.22e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1246741995  50 FIINVGLRLKLPQTALATANIYFHRFYLRFSLKNYHYYEVAATCIFLATKVED 102
Cdd:cd20528    13 WLAVVSERLKLSDTTLHLAVYLLDRFMDRYDISEDQLHLVALTCLLLAAKFEE 65
CYCLIN_AtCycC_rpt2 cd20572
second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 159-251 1.21e-03

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


Pssm-ID: 410275 [Multi-domain]  Cd Length: 102  Bit Score: 37.83  E-value: 1.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 159 HPYPYVLSFIKKfvADDKNVTKVAWTYINDSTRSIACLLYSPKTIAAAAFQFALEKNEINLSTttdglpvWMEESQVSYE 238
Cdd:cd20572     1 HPYRPLIQLLQD--AGLTDMTQFTWSIVNDTYRTDLILIHPPYMIALACIYIASVHKEKDITL-------WFEELRVDMN 71

                          90
                  ....*....|...
gi 1246741995 239 DVKGVLTLIDSLY 251
Cdd:cd20572    72 IIKNIAMEILDFY 84
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 163-241 2.51e-03

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: 36.23  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 163 YVLSFIKKFVAD---DKNVTKVAWTYINDSTRSIACLLYSPKTIAAAAFQFALEKNEINLStttdgLPVWMEESQVSYED 239
Cdd:cd00043     1 KAVDFIRRLCSKlglPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRT-----LKEIAKVSGVSEKE 75


                  ..
gi 1246741995 240 VK 241
Cdd:cd00043    76 LR 77
CYCLIN_ScCLN_like cd20559
cyclin box found in Saccharomyces cerevisiae G1/S-specific cyclins (ScCLNs) and similar ...
 49-109 6.42e-03

cyclin box found in Saccharomyces cerevisiae G1/S-specific cyclins (ScCLNs) and similar proteins; ScCLNs, including ScCLN1-3, are essential for the control of the cell cycle at the G1/S (start) transition in Saccharomyces. ScCLN1 and ScCLN2 interact with the CDC28 protein kinase to form maturation promoting factor (MPF). ScCLN3 may be an upstream activator of the G1 cyclins that directly initiate G1/S transition. This family also includes Schizosaccharomyces pombe cyclin puc1, which contributes to negative regulation of the timing of sexual development in fission yeast, and functions at the transition between cycling and non-cycling cells. It interacts with protein kinase A. Members of this family contain one cyclin box. The cyclin box is a protein binding domain.


Pssm-ID: 410262 [Multi-domain]  Cd Length: 95  Bit Score: 35.44  E-value: 6.42e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1246741995  49 NFIINVGLRLKL-PQTALATANIYfHRFYLRFSLKNYHYYEVAATCIFLATK-VEDSVRKLRD 109
Cdd:cd20559     4 DFLFELHVELRLsPQTFFLSVNLI-DRYCSKRIVLKKHYQLVGCTCLWIASKfWESKARVPLL 65
CYCLIN_CCNH_rpt2 cd20525
second cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 185-265 9.34e-03

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


Pssm-ID: 410229  Cd Length: 126  Bit Score: 35.73  E-value: 9.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246741995 185 YINDSTRSIACLLYSPKTIAAAAFQFALEKNEINLstttDGLPVWMEESQVSYEDVKGVLTLIDSLYKKINPSKQALPID 264
Cdd:cd20525    36 FLNRSLLTDAPLLYPPSQIALAALLLAASEAGIDV----EEYLSEKLPGSEESEELEKLLEIIREIKKLVKKYEGPPDKE 111


                  .
gi 1246741995 265 Q 265
Cdd:cd20525   112 E 112
 
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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