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Conserved domains on  [gi|2019495587|ref|XP_040268467|]
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cyclin-K [Bufo bufo]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 40-154 1.82e-79

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: 245.22  E-value: 1.82e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  40 GLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDIIKT 119
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2019495587 120 ARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFD 154
Cdd:cd20530    81 ARSLLNDKQFAQFGDDPKEEVMVLERILLQTIKFD 115
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 158-258 6.12e-71

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


:

Pssm-ID: 410234 [Multi-domain]  Cd Length: 101  Bit Score: 222.60  E-value: 6.12e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 158 EHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQ 237
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDWTSKPPGKRWWEQ 80

                          90       100
                  ....*....|....*....|.
gi 2019495587 238 FVQDVPVDVLEDICHQILDLY 258
Cdd:cd20531    81 FVEDVSLEVLEDICHQVLDLY 101
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 281-398 3.02e-05

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 47.24  E-value: 3.02e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  281 IAAVQPLQPTDSQTA---QQKDPPQPGGQQTKKPSPQSSPPKQTKRPLPTSPKDDGKAQDQPLTKMAKVEAPHPPLPPVI 357
Cdd:PHA03247  2886 LARPAVSRSTESFALppdQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLG 2965

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 2019495587  358 TPVE-RKPVAPALVPGEGDPVGIPEAAdltklqIPPPTHPSA 398
Cdd:PHA03247  2966 ALVPgRVAVPRFRVPQPAPSREAPASS------TPPLTGHSL 3001
 
Name Accession Description Interval E-value
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 40-154 1.82e-79

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: 245.22  E-value: 1.82e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  40 GLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDIIKT 119
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2019495587 120 ARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFD 154
Cdd:cd20530    81 ARSLLNDKQFAQFGDDPKEEVMVLERILLQTIKFD 115
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 158-258 6.12e-71

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


Pssm-ID: 410234 [Multi-domain]  Cd Length: 101  Bit Score: 222.60  E-value: 6.12e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 158 EHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQ 237
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDWTSKPPGKRWWEQ 80

                          90       100
                  ....*....|....*....|.
gi 2019495587 238 FVQDVPVDVLEDICHQILDLY 258
Cdd:cd20531    81 FVEDVSLEVLEDICHQVLDLY 101
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 25-217 1.35e-27

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: 112.52  E-value: 1.35e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  25 YWDKKDLAH--TPSQQEGLDPAT----EARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGAC 98
Cdd:COG5333    14 PLLSFDSSQnaIELDLLVLEPELtlekELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTT 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  99 CLFLAGKVEETPKKckdiIKTARSLLNDVQFGQFGDDPkEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKi 178
Cdd:COG5333    94 CVYLACKVEDTPRD----ISIESFEARDLWSEEPKSSR-ERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKY- 167

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2019495587 179 qKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRL 217
Cdd:COG5333   168 -KLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEV 205
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 55-149 4.78e-15

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: 70.31  E-value: 4.78e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587   55 RFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDIIKTArsllndvqfgqfGD 134
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT------------GY 68

                           90
                   ....*....|....*
gi 2019495587  135 DPKEEVMVLERILLQ 149
Cdd:smart00385  69 FTEEEILRMERLLLE 83
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 23-155 5.40e-12

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: 62.92  E-value: 5.40e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  23 CWYWDKKDLAHTPS-----QQEGLDPateaRYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGA 97
Cdd:pfam00134   3 FQYLRELELKYLPKpdymdQQPDINP----KMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2019495587  98 CCLFLAGKVEET-PKKCKDIIktarsLLNDVQFgqfgddPKEEVMVLERILLQTIKFDL 155
Cdd:pfam00134  79 TCLFIAAKYEEIyPPTVEDLV-----YITDNAY------TREEILRMERLILETLNFDL 126
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 71-224 1.74e-10

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: 62.16  E-value: 1.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  71 LATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEE----TPKKCKDIIKTARSLLndvqfgqfgddpkEEVMVLERI 146
Cdd:TIGR00569  79 VGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEfnvsIDQFVGNLKETPLKAL-------------EQVLEYELL 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 147 LLQTIKFDLQVEHPYQ----FLLKYAKQLKGDKNKiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAV-AVMYLAGRLC-KF 220
Cdd:TIGR00569 146 LIQQLNFHLIVHNPYRplegFLIDIKTRLPGLENP-EYLRKHADKFLNRTLLTDAYLLYTPSQIALaAILHTASRAGlNM 224


                  ....
gi 2019495587 221 EIQE 224
Cdd:TIGR00569 225 ESYL 228
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 162-256 2.99e-06

domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 45.28  E-value: 2.99e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  162 QFLLKYAKQLKGDknkiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCkfEIQEWTSKpmyrrwWEQFVQD 241
Cdd:smart00385   1 DFLRRVCKALNLD----PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTE--ETPPWTKE------LVHYTGY 68

                           90
                   ....*....|....*
gi 2019495587  242 VPVDVLEDICHQILD 256
Cdd:smart00385  69 FTEEEILRMERLLLE 83
PHA03247 PHA03247
large tegument protein UL36; Provisional
 281-398 3.02e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 47.24  E-value: 3.02e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  281 IAAVQPLQPTDSQTA---QQKDPPQPGGQQTKKPSPQSSPPKQTKRPLPTSPKDDGKAQDQPLTKMAKVEAPHPPLPPVI 357
Cdd:PHA03247  2886 LARPAVSRSTESFALppdQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLG 2965

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 2019495587  358 TPVE-RKPVAPALVPGEGDPVGIPEAAdltklqIPPPTHPSA 398
Cdd:PHA03247  2966 ALVPgRVAVPRFRVPQPAPSREAPASS------TPPLTGHSL 3001
TALPID3 pfam15324
Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for ...
 286-396 4.55e-04

Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.


Pssm-ID: 434634 [Multi-domain]  Cd Length: 1288  Bit Score: 43.34  E-value: 4.55e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  286 PLQPTDSQTAQQKDPPQPGGQQTKKPSPQSSPPKQTKRPLPTSPKD----DGKAQDQPlTKMAKVEAPHPPLP------- 354
Cdd:pfam15324  968 PVAASVPGDLPTKETLLPTPVPTPQPTPPCSPPSPLKEPSPVKTPDsspcVSEHDFFP-VKEIPPEKGADTGPavslvit 1046

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 2019495587  355 PVITPVERKPVAPALVPGEGDpvgipEAADLTKLQIPPPTHP 396
Cdd:pfam15324 1047 PTVTPIATPPPAATPTPPLSE-----NSIDKLKSPSPELPKP 1083
 
Name Accession Description Interval E-value
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 40-154 1.82e-79

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: 245.22  E-value: 1.82e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  40 GLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDIIKT 119
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2019495587 120 ARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFD 154
Cdd:cd20530    81 ARSLLNDKQFAQFGDDPKEEVMVLERILLQTIKFD 115
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 158-258 6.12e-71

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


Pssm-ID: 410234 [Multi-domain]  Cd Length: 101  Bit Score: 222.60  E-value: 6.12e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 158 EHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQ 237
Cdd:cd20531     1 EHPYKYLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKLSKFDLQDWTSKPPGKRWWEQ 80

                          90       100
                  ....*....|....*....|.
gi 2019495587 238 FVQDVPVDVLEDICHQILDLY 258
Cdd:cd20531    81 FVEDVSLEVLEDICHQVLDLY 101
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 24-154 8.12e-39

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: 138.68  E-value: 8.12e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  24 WYWDKKDLAHTPSQQEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLA 103
Cdd:cd20538     2 WYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFLA 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2019495587 104 GKVEETPKKCKDIIKTARSLLNDvqfGQFGDDPKEEV--------MVLERILLQTIKFD 154
Cdd:cd20538    82 AKVEEQPRKLEHVIKVAHACLHR---GEPDLDTKSEAylqqaqelVINENILLQTLGFE 137
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
 24-154 1.21e-30

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: 116.30  E-value: 1.21e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  24 WYWDKKDLAHTPSQQEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLA 103
Cdd:cd20596     4 WFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTALFLA 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2019495587 104 GKVEETPKKCKDIIKTARSLLNDV--QFGQFGD---DPKEEVMVLERILLQTIKFD 154
Cdd:cd20596    84 AKVEEQPRKLEHVIKVAHACLNPLepQLDTKSDaylQQAQELVILETIMLQTLGFE 139
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 24-154 1.39e-30

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: 116.31  E-value: 1.39e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  24 WYWDKKDLAHTPSQQEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLA 103
Cdd:cd20595     3 WYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALFLA 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2019495587 104 GKVEETPKKCKDIIKTARSLLN------DVQFGQFGDDpKEEVMVLERILLQTIKFD 154
Cdd:cd20595    83 AKVEEQPKKLEHVIKVAHTCLHpqeslpDTRSEAYLQQ-VQDLVILESIILQTLGFE 138
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 159-260 1.97e-29

second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2), and similar proteins; Cyclin pch1 is essential for progression through the whole cell cycle. It is a homolog of cyclin T; it forms a heterodimer with its partner kinase, cyclin-dependent kinase 9 (CDK9), that can phosphorylate both the pol II C-terminal domain (CTD) and the CTD of transcription elongation factor Spt5. Yeast Cdk9/Pch1, with mRNA capping enzyme Pct1, may also form an elongation checkpoint for mRNA quality control. CTK2, also called CTD kinase subunit beta, CTDK-I subunit beta, or CTD kinase 38 kDa subunit, is the cyclin subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. This group also includes yeast RNA polymerase II holoenzyme cyclin-like subunit, a component of the SRB8-11 complex, a regulatory module of the Mediator complex which is involved in regulation of basal and activated RNA polymerase II-dependent transcription. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410249 [Multi-domain]  Cd Length: 97  Bit Score: 111.69  E-value: 1.97e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 159 HPYQFLLKYAKQLKGDKNKiqKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMyRRWWEQF 238
Cdd:cd20546     1 HPYQYLIKFAKKLGVSDPK--ELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPNEKL-NEWWELF 77

                          90       100
                  ....*....|....*....|..
gi 2019495587 239 vqDVPVDVLEDICHQILDLYSQ 260
Cdd:cd20546    78 --GVDEEEIADAINEILDLYSS 97
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 25-217 1.35e-27

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: 112.52  E-value: 1.35e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  25 YWDKKDLAH--TPSQQEGLDPAT----EARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGAC 98
Cdd:COG5333    14 PLLSFDSSQnaIELDLLVLEPELtlekELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTT 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  99 CLFLAGKVEETPKKckdiIKTARSLLNDVQFGQFGDDPkEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKi 178
Cdd:COG5333    94 CVYLACKVEDTPRD----ISIESFEARDLWSEEPKSSR-ERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKY- 167

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2019495587 179 qKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRL 217
Cdd:COG5333   168 -KLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEV 205
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 159-259 3.41e-25

second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 and CCNL2. CCNL1 is involved in regulation of RNA polymerase II (pol II) transcription. It functions in association with cyclin-dependent kinases (CDKs). CCNL2 is a novel RNA polymerase II-associated cyclin involved in pre-mRNA splicing. It may induce cell death, possibly by acting on the transcription and RNA processing of apoptosis-related factors. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410236 [Multi-domain]  Cd Length: 92  Bit Score: 99.60  E-value: 3.41e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 159 HPYQFLLKYAKQLKGDKNKiqKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEwtSKPmyrrWWEQF 238
Cdd:cd20533     1 HPHKFILMYLQVLEGEDNK--KLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAARELGIPLPL--PPP----WWELF 72

                          90       100
                  ....*....|....*....|.
gi 2019495587 239 vqDVPVDVLEDICHQILDLYS 259
Cdd:cd20533    73 --DVSKEDIEEICLTILELYT 91
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 50-154 1.17e-23

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: 95.70  E-value: 1.17e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  50 RREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDIIKTARSLLN-DVQ 128
Cdd:cd20534     2 HFKVLRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRILHpDKP 81

                          90       100
                  ....*....|....*....|....*....
gi 2019495587 129 FGQFGDD---PKEEVMVLERILLQTIKFD 154
Cdd:cd20534    82 PLELDDEyweLRDSIVNCELLLLRILKFD 110
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 46-155 1.46e-23

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: 95.57  E-value: 1.46e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  46 EARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDII----KTAR 121
Cdd:cd20545     1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIViacaKVAQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2019495587 122 SLLNDVQFGQFGDDPKEEVMVL--ERILLQTIKFDL 155
Cdd:cd20545    81 KNPNLVIDEQSKEVWRWRDSILynEEVLLETLCFDL 116
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 49-154 2.40e-21

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: 89.33  E-value: 2.40e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  49 YRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQ 128
Cdd:cd20547     1 LRLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNLRHPDK 80

                          90       100
                  ....*....|....*....|....*....
gi 2019495587 129 FG---QFGDDPKEEVMVLERILLQTIKFD 154
Cdd:cd20547    81 ISvddQMLEEFRKAILGLERLLLETICFD 109
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 158-258 3.51e-19

second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; CycTs associate with their partner cyclin-dependent kinases (CDKs) to trigger their kinase activity. CycTs show high sequence similarity with metazoan cyclin-K (CCNK). CycTs contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410291 [Multi-domain]  Cd Length: 93  Bit Score: 82.58  E-value: 3.51e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 158 EHPYQFLLKYAKQLKGDKNKiqkLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQewtsKPMYRRWWEQ 237
Cdd:cd20588     1 EHPYKPLVAAIKKFNVAQNA---LAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLP----CDGRKVWWQE 73

                          90       100
                  ....*....|....*....|.
gi 2019495587 238 FvqDVPVDVLEDICHQILDLY 258
Cdd:cd20588    74 F--DVTPRQLEEVSNQMLELY 92
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 39-153 4.57e-19

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: 83.38  E-value: 4.57e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  39 EGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDII- 117
Cdd:cd20532     1 DGIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVIn 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2019495587 118 -----------KTARSLLNDVqFGQFGDDPKEEVMVLERILLQTIKF 153
Cdd:cd20532    81 vfhrllqrrlgKPAEVLPLDI-GSAEYEELKNDIIKAERRILKELGF 126
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 159-260 5.78e-19

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


Pssm-ID: 410238 [Multi-domain]  Cd Length: 104  Bit Score: 82.30  E-value: 5.78e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 159 HPYQFLLKYAKQLK----GDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMyrRW 234
Cdd:cd20535     1 LPHKYLLHYLKSLRdwlnPEFWSRSPIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQVYGVKVPPEEEAEK--PW 78

                          90       100
                  ....*....|....*....|....*.
gi 2019495587 235 WEQFVQDVPVDVLEDICHQILDLYSQ 260
Cdd:cd20535    79 WQAFCEDLTKETIDEIIEDIINVYDL 104
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 39-154 5.66e-18

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: 80.26  E-value: 5.66e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  39 EGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDIIK 118
Cdd:cd20587     1 DGIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2019495587 119 TARSLLND--------VQFGQFGDDPKEEVMVLERILLQTIKFD 154
Cdd:cd20587    81 VSYEIIFKkdpsaaqrIKQKEVYEQQKELVLNGEKLVLSTLGFD 124
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 157-264 2.75e-15

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


Pssm-ID: 410297 [Multi-domain]  Cd Length: 101  Bit Score: 71.82  E-value: 2.75e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 157 VEHPYQFLLKYAKQLKgdknKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRlcKFEIqewtSKPMYRRWWE 236
Cdd:cd20594     2 VEHPHKFILNYLAMLM----APPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAAR--RFQV----PLPENPPWWK 71

                          90       100
                  ....*....|....*....|....*...
gi 2019495587 237 QFvqDVPVDVLEDICHQILDLYSQGKQQ 264
Cdd:cd20594    72 VF--DAEKAEIDVVCKVLADLYRQPKAR 97
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 55-149 4.78e-15

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: 70.31  E-value: 4.78e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587   55 RFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDIIKTArsllndvqfgqfGD 134
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT------------GY 68

                           90
                   ....*....|....*
gi 2019495587  135 DPKEEVMVLERILLQ 149
Cdd:smart00385  69 FTEEEILRMERLLLE 83
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
 36-153 7.30e-15

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: 71.41  E-value: 7.30e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  36 SQQEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKD 115
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2019495587 116 II----------KTARSLLNDVQFGQFgDDPKEEVMVLERILLQTIKF 153
Cdd:cd20591    81 VLmvfhrmecrrENLPLEPLEPESKKY-DEMKEDLIRTERHLLKEMGF 127
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 159-264 2.41e-14

second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or SRB11, is a component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. It mediates stress-induced mitochondrial fission and apoptosis. CCNC contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410218 [Multi-domain]  Cd Length: 92  Bit Score: 68.80  E-value: 2.41e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 159 HPYQFLLKYAKQLKGDKNkiqkLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKpmyrrwweqf 238
Cdd:cd20514     1 HPYRPLTQYVQDAGLDDE----LLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDARQWFAE---------- 66

                          90       100
                  ....*....|....*....|....*.
gi 2019495587 239 vQDVPVDVLEDICHQILDLYSQGKQQ 264
Cdd:cd20514    67 -LNVDMDKILEITREILSLYELWKTF 91
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 56-148 2.69e-13

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: 66.08  E-value: 2.69e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  56 FIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDvQFGQFGDD 135
Cdd:cd20513     8 FIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPSHARLIVAEAKVLKTK-FSYEFPYR 86

                          90
                  ....*....|...
gi 2019495587 136 PKeEVMVLERILL 148
Cdd:cd20513    87 VN-DILECEFYLL 98
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 158-268 3.12e-13

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


Pssm-ID: 410295 [Multi-domain]  Cd Length: 123  Bit Score: 66.56  E-value: 3.12e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 158 EHPYQFLLKYAKQLKGDKNkiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIqewTSKPmyrRWWEQ 237
Cdd:cd20592     1 KHPHKIIVMYLQVLECERN--QTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPL---PNRP---HWFLL 72

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2019495587 238 FvqDVPVDVLEDICHQILDLYSQGKqqmPHH 268
Cdd:cd20592    73 F--GATEEEIQEICITTLKLYTRKK---PNY 98
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 159-267 4.98e-13

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


Pssm-ID: 410296 [Multi-domain]  Cd Length: 123  Bit Score: 66.14  E-value: 4.98e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 159 HPYQFLLKYAKQLKGDKNkiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIqewtskPMYRRWWEQF 238
Cdd:cd20593     1 HPHKIIVMYLQVLECERN--RHLVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEIPL------PNRPHWFLLF 72

                          90       100
                  ....*....|....*....|....*....
gi 2019495587 239 vqDVPVDVLEDICHQILDLYSQGKQQMPH 267
Cdd:cd20593    73 --GATEEEIQEICLKILQLYTRKKVDLEH 99
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 52-128 8.20e-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: 63.97  E-value: 8.20e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2019495587  52 EGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQ 128
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELR 77
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 14-117 3.06e-12

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: 64.64  E-value: 3.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  14 SGTLDHSKPCWYWDKKdLAHTPSQQEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARY 93
Cdd:cd20590     9 SGVLITLENCLLPEER-LRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVKHSME 87

                          90       100
                  ....*....|....*....|....
gi 2019495587  94 VTGACCLFLAGKVEETPKKCKDII 117
Cdd:cd20590    88 HVSMACVHLASKIEEAPRRIRDVI 111
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 23-155 5.40e-12

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: 62.92  E-value: 5.40e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  23 CWYWDKKDLAHTPS-----QQEGLDPateaRYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGA 97
Cdd:pfam00134   3 FQYLRELELKYLPKpdymdQQPDINP----KMRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2019495587  98 CCLFLAGKVEET-PKKCKDIIktarsLLNDVQFgqfgddPKEEVMVLERILLQTIKFDL 155
Cdd:pfam00134  79 TCLFIAAKYEEIyPPTVEDLV-----YITDNAY------TREEILRMERLILETLNFDL 126
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 71-224 1.74e-10

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: 62.16  E-value: 1.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  71 LATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEE----TPKKCKDIIKTARSLLndvqfgqfgddpkEEVMVLERI 146
Cdd:TIGR00569  79 VGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEfnvsIDQFVGNLKETPLKAL-------------EQVLEYELL 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 147 LLQTIKFDLQVEHPYQ----FLLKYAKQLKGDKNKiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAV-AVMYLAGRLC-KF 220
Cdd:TIGR00569 146 LIQQLNFHLIVHNPYRplegFLIDIKTRLPGLENP-EYLRKHADKFLNRTLLTDAYLLYTPSQIALaAILHTASRAGlNM 224


                  ....
gi 2019495587 221 EIQE 224
Cdd:TIGR00569 225 ESYL 228
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
 39-117 4.38e-10

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: 57.45  E-value: 4.38e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2019495587  39 EGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDII 117
Cdd:cd20589     1 DGLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVI 79
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 28-155 8.54e-09

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: 54.52  E-value: 8.54e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  28 KKDLAHTPSQQEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVE 107
Cdd:cd20524    33 KESLKEEDAEPKFLTPEEELLLVRYYEKKLLEFCRAFKLPDSVLATALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVE 112

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2019495587 108 ETP-------KKCKDIIKTARSLLNdvqfgqfgddpkeevmvLERILLQTIKFDL 155
Cdd:cd20524   113 EFNisidqfvGNIKESEKTAEIILE-----------------YELLLLQGLNFHL 150
CYCLIN_AtCycC_rpt2 cd20572
second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 159-258 5.02e-07

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


Pssm-ID: 410275 [Multi-domain]  Cd Length: 102  Bit Score: 48.23  E-value: 5.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 159 HPYQFLLkyakQLKGDKNkIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIqewtskpmyRRWWEQF 238
Cdd:cd20572     1 HPYRPLI----QLLQDAG-LTDMTQFTWSIVNDTYRTDLILIHPPYMIALACIYIASVHKEKDI---------TLWFEEL 66

                          90       100
                  ....*....|....*....|
gi 2019495587 239 VQDvpVDVLEDICHQILDLY 258
Cdd:cd20572    67 RVD--MNIIKNIAMEILDFY 84
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 162-256 2.99e-06

domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 45.28  E-value: 2.99e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  162 QFLLKYAKQLKGDknkiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCkfEIQEWTSKpmyrrwWEQFVQD 241
Cdd:smart00385   1 DFLRRVCKALNLD----PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTE--ETPPWTKE------LVHYTGY 68

                           90
                   ....*....|....*
gi 2019495587  242 VPVDVLEDICHQILD 256
Cdd:smart00385  69 FTEEEILRMERLLLE 83
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 159-255 1.21e-05

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: 43.80  E-value: 1.21e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 159 HPYQFLLKYAKQLK-GDKNkiqkLVQMAWTFVNDSL-CTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKpmyRRWWE 236
Cdd:cd20539     1 HPHTHVLKICNLVKaGSKD----LAQTAYFLATNSLhLTTFCLQYKPTVIACVCIHLACKWSNWEIPRSSEG---KDWYE 73

                          90
                  ....*....|....*....
gi 2019495587 237 QFVQDVPVDVLEDICHQIL 255
Cdd:cd20539    74 YVDPSLTLEELDELTSEFL 92
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
 158-257 1.28e-05

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


Pssm-ID: 410301 [Multi-domain]  Cd Length: 114  Bit Score: 44.69  E-value: 1.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 158 EHPYQFLLKYAKQLKGDKNkiqkLVQMAWTFVNDSL-CTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKpmyRRWWE 236
Cdd:cd20598     1 EHPHTDVVKCTQLVRASKD----LAQTSYFMATNSLhLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDG---KHWWE 73

                          90       100
                  ....*....|....*....|.
gi 2019495587 237 QFVQDVPVDVLEDICHQILDL 257
Cdd:cd20598    74 YVDPTVTLELLDELTHEFLQI 94
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 158-257 1.76e-05

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: 43.91  E-value: 1.76e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 158 EHPYQFLLKYAKQLKGDKNkiqkLVQMAWTFVNDSL-CTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKpmyRRWWE 236
Cdd:cd20597     1 DHPHTHVVKCTQLVRASKD----LAQTSYFMATNSLhLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDG---KHWWE 73

                          90       100
                  ....*....|....*....|.
gi 2019495587 237 QFVQDVPVDVLEDICHQILDL 257
Cdd:cd20597    74 YVDATVTLELLDELTHEFLQI 94
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
 71-155 2.97e-05

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: 44.82  E-value: 2.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  71 LATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDIiktarsllndvqfGQFGDDPKEEVMVLERILLQT 150
Cdd:cd20585    99 QATALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEEYHVSAEEL-------------GKGIQQDHQLILKNELALLQG 165


                  ....*
gi 2019495587 151 IKFDL 155
Cdd:cd20585   166 LNFDL 170
PHA03247 PHA03247
large tegument protein UL36; Provisional
 281-398 3.02e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 47.24  E-value: 3.02e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  281 IAAVQPLQPTDSQTA---QQKDPPQPGGQQTKKPSPQSSPPKQTKRPLPTSPKDDGKAQDQPLTKMAKVEAPHPPLPPVI 357
Cdd:PHA03247  2886 LARPAVSRSTESFALppdQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLG 2965

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 2019495587  358 TPVE-RKPVAPALVPGEGDPVGIPEAAdltklqIPPPTHPSA 398
Cdd:PHA03247  2966 ALVPgRVAVPRFRVPQPAPSREAPASS------TPPLTGHSL 3001
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 159-222 1.24e-04

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


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 40.86  E-value: 1.24e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2019495587 159 HPYQFLLKYAKQLKGDknkiQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEI 222
Cdd:cd00043     1 KAVDFIRRLCSKLGLP----EEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPR 60
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 283-389 3.01e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 43.64  E-value: 3.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 283 AVQPLQPTDSQTAQQKDPPQPGgQQTKKPSPQSSPPKQTKRPLPTSPKDDGKAQDQPLTKmakVEAPHPPLPPVITPVER 362
Cdd:PRK14950  365 APQPAKPTAAAPSPVRPTPAPS-TRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPH---TPESAPKLTRAAIPVDE 440

                          90       100
                  ....*....|....*....|....*...
gi 2019495587 363 KPVAPALVP-GEGDPVGIPEAADLTKLQ 389
Cdd:PRK14950  441 KPKYTPPAPpKEEEKALIADGDVLEQLE 468
TALPID3 pfam15324
Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for ...
 286-396 4.55e-04

Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.


Pssm-ID: 434634 [Multi-domain]  Cd Length: 1288  Bit Score: 43.34  E-value: 4.55e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  286 PLQPTDSQTAQQKDPPQPGGQQTKKPSPQSSPPKQTKRPLPTSPKD----DGKAQDQPlTKMAKVEAPHPPLP------- 354
Cdd:pfam15324  968 PVAASVPGDLPTKETLLPTPVPTPQPTPPCSPPSPLKEPSPVKTPDsspcVSEHDFFP-VKEIPPEKGADTGPavslvit 1046

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 2019495587  355 PVITPVERKPVAPALVPGEGDpvgipEAADLTKLQIPPPTHP 396
Cdd:pfam15324 1047 PTVTPIATPPPAATPTPPLSE-----NSIDKLKSPSPELPKP 1083
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 56-129 9.03e-04

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: 39.07  E-value: 9.03e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2019495587  56 FIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFARYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQF 129
Cdd:cd20571    13 YIKKLAQHIKVRQRVVATAITYFRRVYTRKSFTEYDPRLVAPTCLYLASKAEESTVQAKLLVFYMKRLYADEYH 86
CYCLIN_CCNO-like_rpt2 cd20537
second cyclin box found in cyclin-O (CCNO) and similar proteins; This subfamily is composed of ...
 159-260 1.13e-03

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


Pssm-ID: 410240 [Multi-domain]  Cd Length: 91  Bit Score: 38.44  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 159 HPYQFLLKYAKQLKGDKnkiqKLVQMAWtFVND-SLCTTLSLQWEPEIIAVAVMYLAGRLCKfeIQEWTSKPMYRRWWEQ 237
Cdd:cd20537     2 TPLSFLRRYLSLLGLDE----KVRHLAR-YLLElSLLDYEFLKYRPSLIAAAALYLARKILG--EPPPSPQLLQLVTGYS 74

                          90       100
                  ....*....|....*....|...
gi 2019495587 238 FvqdvpvDVLEDICHQILDLYSQ 260
Cdd:cd20537    75 E------NDLQECAKELLELLAQ 91
CYCLIN_CCNJ-like_rpt1 cd20528
first cyclin box found in cyclin-J (CCNJ) family; The CCNJ family includes two cyclins, CCNJ ...
 49-153 1.22e-03

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: 38.35  E-value: 1.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  49 YRREGARFIFDVGTRLGLHYDT--LAtgiIYFHRFYMFH---SFKQFarYVTGACCLFLAGKVEEtpkKCKDIIKTARsl 123
Cdd:cd20528     6 LRRYLVDWLAVVSERLKLSDTTlhLA---VYLLDRFMDRydiSEDQL--HLVALTCLLLAAKFEE---LDDNIPKISD-- 75

                          90       100       110
                  ....*....|....*....|....*....|
gi 2019495587 124 LNdvQFGQFGDDPKEEVMVLERILLQTIKF 153
Cdd:cd20528    76 LN--RYLCNSVYSKQEYLQMELLILEFFQW 103
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 303-398 7.14e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 39.31  E-value: 7.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 303 PGGQQTKKPSPQSSPPKQTKRPLPTspkddgkAQDQPLTKMAKVEAPHPPL--PPVITPVERKPVAPALVPGEGDPVGIP 380
Cdd:PRK14951  366 PAAAAEAAAPAEKKTPARPEAAAPA-------AAPVAQAAAAPAPAAAPAAaaSAPAAPPAAAPPAPVAAPAAAAPAAAP 438

                          90
                  ....*....|....*...
gi 2019495587 381 EAADLTKLQIPPPTHPSA 398
Cdd:PRK14951  439 AAAPAAVALAPAPPAQAA 456
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 265-355 8.63e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 39.30  E-value: 8.63e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587  265 MPHHGAQQQSPQVQAQIAAVQPLQPTDS-QTAQQKDPPQPGGQQTKKP---SPQSSPPKQtkrplPTSPKDDGKAQDQPL 340
Cdd:PRK10263   750 EPVQQPQQPVAPQQQYQQPQQPVAPQPQyQQPQQPVAPQPQYQQPQQPvapQPQYQQPQQ-----PVAPQPQYQQPQQPV 824

                           90
                   ....*....|....*
gi 2019495587  341 TKMAKVEAPHPPLPP 355
Cdd:PRK10263   825 APQPQYQQPQQPVAP 839
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
266-398 9.11e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 39.06  E-value: 9.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019495587 266 PHHGAQQQSPQVQAQIAAVQPLQPTDSQTAQQKDPPQPGGQQTKKPSPQSSPPKQTKRPLPTSPKDDGKAQDQPLTKMAK 345
Cdd:PRK07003  412 PKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFE 491

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2019495587 346 VEAPHPPLPPVITPVERKPVAPALVPGEGDPVGIPEAADLTKLQIPPPTHPSA 398
Cdd:PRK07003  492 PAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTPAAAAPAA 544
 
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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