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Conserved domains on  [gi|157831652|pdb|1KXU|A]
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Chain A, CYCLIN H

Protein Classification

ccl1 family protein( domain architecture ID 11489237)

ccl1 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 12-318 2.03e-179

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: 498.20  E-value: 2.03e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A         12 YHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVG 91
Cdd:TIGR00569   1 YRNSSQKRHWTFTSEEQLQEKRADANAKFREAHEEEEKVLEAKPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A         92 TACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLgqeKALEQILEYELLLIQQLNFHLIVH 171
Cdd:TIGR00569  81 TAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKETPL---KALEQVLEYELLLIQQLNFHLIVH 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A        172 NPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKEN 251
Cdd:TIGR00569 158 NPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMESYLTEQLSVPGN 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
1KXU_A        252 RTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALN-VITKKRKGYEDDDYVSKKSK 318
Cdd:TIGR00569 238 REELPQLIDIMRELRILVKKYEEPRSEKVAALKKKLDECHSIEENLSsVKIRKRKGYEDDTYISKKAK 305
 
Name Accession Description Interval E-value
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 12-318 2.03e-179

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: 498.20  E-value: 2.03e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A         12 YHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVG 91
Cdd:TIGR00569   1 YRNSSQKRHWTFTSEEQLQEKRADANAKFREAHEEEEKVLEAKPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A         92 TACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLgqeKALEQILEYELLLIQQLNFHLIVH 171
Cdd:TIGR00569  81 TAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKETPL---KALEQVLEYELLLIQQLNFHLIVH 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A        172 NPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKEN 251
Cdd:TIGR00569 158 NPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMESYLTEQLSVPGN 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
1KXU_A        252 RTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALN-VITKKRKGYEDDDYVSKKSK 318
Cdd:TIGR00569 238 REELPQLIDIMRELRILVKKYEEPRSEKVAALKKKLDECHSIEENLSsVKIRKRKGYEDDTYISKKAK 305
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 13-168 2.83e-77

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: 233.26  E-value: 2.83e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A       13 HNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKpaMPRSVVGT 92
Cdd:cd20524   1 HTSTQRKHWIFSSEEELAELRAEANEKAREKLKESLKEEDAEPKFLTPEEELLLVRYYEKKLLEFCRAFK--LPDSVLAT 78

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
1KXU_A       93 ACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESplgqEKALEQILEYELLLIQQLNFHL 168
Cdd:cd20524  79 ALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVEEFNISIDQFVGNIKES----EKTAEIILEYELLLLQGLNFHL 150
Cyclin_C_2 pfam16899
Cyclin C-terminal domain; Cyclins contain two domains of similar all-alpha fold, this family ...
 172-270 2.68e-37

Cyclin C-terminal domain; Cyclins contain two domains of similar all-alpha fold, this family corresponds with the C-terminal domain of some cyclins including cyclin C and cyclin H.


Pssm-ID: 465303  Cd Length: 98  Bit Score: 128.81  E-value: 2.68e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A        172 NPYRPFEGFLIDLKTRYPILE-NPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGitmESYLSESLMLKE 250
Cdd:pfam16899   1 HPFRPLEGFLLDLKTRPPLLEdRIESLYKRAREILKSALLTDAYFLYTPSQIALAALLLADSPLA---EFYLTEKFGLPE 77

                          90       100
                  ....*....|....*....|.
1KXU_A        251 NRT-CLSQLLDIMKSMRNLVK 270
Cdd:pfam16899  78 DREtKLEKLLDTIESCRNLLK 98
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 58-232 1.27e-26

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: 106.74  E-value: 1.27e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A       58 LEPHEEMT----LCKYYEKRLLEFCSVFKPamPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEF--NVS 131
Cdd:COG5333  32 LEPELTLEkelnLVIYYLKLIMDLCTRLNL--PQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTprDIS 109

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A      132 SPQFVGNLRESPLgQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKtrypILENPEILrKTADDFLNRIALT 211
Cdd:COG5333 110 IESFEARDLWSEE-PKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQ----EKDKYKLL-QIAWKIINDALRT 183

                       170       180
                ....*....|....*....|.
1KXU_A      212 DAYLLYTPSQIALTAILSSAS 232
Cdd:COG5333 184 DLCLLYPPHIIALAALLIACE 204
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 72-162 2.40e-10

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: 56.06  E-value: 2.40e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A          72 KRLLEFCSVFKpaMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLresplgQEKALE 151
Cdd:smart00385   1 DFLRRVCKALN--LDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT------GYFTEE 72

                           90
                   ....*....|.
1KXU_A         152 QILEYELLLIQ 162
Cdd:smart00385  73 EILRMERLLLE 83
 
Name Accession Description Interval E-value
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 12-318 2.03e-179

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: 498.20  E-value: 2.03e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A         12 YHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVG 91
Cdd:TIGR00569   1 YRNSSQKRHWTFTSEEQLQEKRADANAKFREAHEEEEKVLEAKPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A         92 TACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLgqeKALEQILEYELLLIQQLNFHLIVH 171
Cdd:TIGR00569  81 TAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKETPL---KALEQVLEYELLLIQQLNFHLIVH 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A        172 NPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKEN 251
Cdd:TIGR00569 158 NPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMESYLTEQLSVPGN 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
1KXU_A        252 RTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALN-VITKKRKGYEDDDYVSKKSK 318
Cdd:TIGR00569 238 REELPQLIDIMRELRILVKKYEEPRSEKVAALKKKLDECHSIEENLSsVKIRKRKGYEDDTYISKKAK 305
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 13-168 2.83e-77

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: 233.26  E-value: 2.83e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A       13 HNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKpaMPRSVVGT 92
Cdd:cd20524   1 HTSTQRKHWIFSSEEELAELRAEANEKAREKLKESLKEEDAEPKFLTPEEELLLVRYYEKKLLEFCRAFK--LPDSVLAT 78

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
1KXU_A       93 ACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESplgqEKALEQILEYELLLIQQLNFHL 168
Cdd:cd20524  79 ALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVEEFNISIDQFVGNIKES----EKTAEIILEYELLLLQGLNFHL 150
CYCLIN_CCNH_rpt2 cd20525
second cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 171-292 4.39e-46

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: 152.83  E-value: 4.39e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A      171 HNPYRPFEGFLIDLKTRYPIL--ENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLML 248
Cdd:cd20525   1 HHPYRPLEGFLLDLKTRLPDLkaENLEKLYKEAREFLNRSLLTDAPLLYPPSQIALAALLLAASEAGIDVEEYLSEKLPG 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
1KXU_A      249 KENRTCLSQLLDIMKSMRNLVKKYE-PPRSEEVAVLKQKLERCHS 292
Cdd:cd20525  81 SEESEELEKLLEIIREIKKLVKKYEgPPDKEEVKALDKKLKKCRN 125
Cyclin_C_2 pfam16899
Cyclin C-terminal domain; Cyclins contain two domains of similar all-alpha fold, this family ...
 172-270 2.68e-37

Cyclin C-terminal domain; Cyclins contain two domains of similar all-alpha fold, this family corresponds with the C-terminal domain of some cyclins including cyclin C and cyclin H.


Pssm-ID: 465303  Cd Length: 98  Bit Score: 128.81  E-value: 2.68e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A        172 NPYRPFEGFLIDLKTRYPILE-NPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGitmESYLSESLMLKE 250
Cdd:pfam16899   1 HPFRPLEGFLLDLKTRPPLLEdRIESLYKRAREILKSALLTDAYFLYTPSQIALAALLLADSPLA---EFYLTEKFGLPE 77

                          90       100
                  ....*....|....*....|.
1KXU_A        251 NRT-CLSQLLDIMKSMRNLVK 270
Cdd:pfam16899  78 DREtKLEKLLDTIESCRNLLK 98
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
 15-168 2.25e-27

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: 105.29  E-value: 2.25e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A       15 SSQKRHWTFSSEeQLARLRADAN----------RKFRCKAVANGKVLP-------NDPVFLEPH-----EEMTLCKYYEK 72
Cdd:cd20585   5 STHRQRWIFTPQ-DLTEKREAANqravdalqqcGATRVEAQAAGSLGGgaevggsNGKAAKLPEplsadEELLMLKYYEQ 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A       73 RLLEFCSVFkpAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPlgqekalEQ 152
Cdd:cd20585  84 KIQEVCRAL--RLPNKIQATALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEEYHVSAEELGKGIQQDH-------QL 154

                       170
                ....*....|....*.
1KXU_A      153 ILEYELLLIQQLNFHL 168
Cdd:cd20585 155 ILKNELALLQGLNFDL 170
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 58-232 1.27e-26

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: 106.74  E-value: 1.27e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A       58 LEPHEEMT----LCKYYEKRLLEFCSVFKPamPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEF--NVS 131
Cdd:COG5333  32 LEPELTLEkelnLVIYYLKLIMDLCTRLNL--PQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTprDIS 109

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A      132 SPQFVGNLRESPLgQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKtrypILENPEILrKTADDFLNRIALT 211
Cdd:COG5333 110 IESFEARDLWSEE-PKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQ----EKDKYKLL-QIAWKIINDALRT 183

                       170       180
                ....*....|....*....|.
1KXU_A      212 DAYLLYTPSQIALTAILSSAS 232
Cdd:COG5333 184 DLCLLYPPHIIALAALLIACE 204
CYCLIN_AcCycH_rpt2 cd20586
second cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; ...
 171-290 1.43e-15

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


Pssm-ID: 410289 [Multi-domain]  Cd Length: 132  Bit Score: 72.46  E-value: 1.43e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A      171 HNPYRPFEGFLIDLKTRYPILENPEI-----LRKTADDFLNRIALTDAYLLYTPSQIALTAILSSA-SRAGITMESYLsE 244
Cdd:cd20586   1 YAPYRALEGFVQDLEEFLAAGSGPDSqglqeLRKAALAAVDKLMLTDAPLLYPPGQLALAALRSANkAKGGVDFDRYL-E 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
1KXU_A      245 SLM----LKENRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERC 290
Cdd:cd20586  80 RVAaraaSKMPDDPAAALTAVLDEIEYLVSEGARPEVAEVKEIDRKLKEC 129
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 89-164 4.23e-12

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: 61.84  E-value: 4.23e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A       89 VVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLREspLGQEKALE------QILEYELLLIQ 162
Cdd:cd20513  22 VIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPSHARLIVAEAKV--LKTKFSYEfpyrvnDILECEFYLLE 99


                ..
1KXU_A      163 QL 164
Cdd:cd20513 100 AL 101
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 72-162 2.40e-10

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: 56.06  E-value: 2.40e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A          72 KRLLEFCSVFKpaMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLresplgQEKALE 151
Cdd:smart00385   1 DFLRRVCKALN--LDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYT------GYFTEE 72

                           90
                   ....*....|.
1KXU_A         152 QILEYELLLIQ 162
Cdd:smart00385  73 EILRMERLLLE 83
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 85-127 2.75e-09

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: 54.35  E-value: 2.75e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
1KXU_A       85 MPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDE 127
Cdd:cd20545  21 LPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEE 63
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 89-167 1.34e-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: 52.17  E-value: 1.34e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A       89 VVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRE--SPLGQEKALEQILEYELLLIQQLNF 166
Cdd:cd20571  27 VVATAITYFRRVYTRKSFTEYDPRLVAPTCLYLASKAEESTVQAKLLVFYMKRlyADEYHRYEIKDILEMEMKLLEALDY 106


                .
1KXU_A      167 H 167
Cdd:cd20571 107 Y 107
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 72-136 3.00e-07

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


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 47.41  E-value: 3.00e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
1KXU_A       72 KRLLEFCSVFKpaMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFV 136
Cdd:cd00043   4 DFIRRLCSKLG--LPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIA 66
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 85-127 3.10e-07

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: 48.71  E-value: 3.10e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
1KXU_A       85 MPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDE 127
Cdd:cd20532  28 LPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEE 70
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 92-167 7.88e-07

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: 47.16  E-value: 7.88e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A       92 TACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDE--------FNVS--------SPQFVG----NLRESplgqekale 151
Cdd:cd20534  25 TACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEqprrlrdiINVSyrilhpdkPPLELDdeywELRDS--------- 95

                        90
                ....*....|....*.
1KXU_A      152 qILEYELLLIQQLNFH 167
Cdd:cd20534  96 -IVNCELLLLRILKFD 110
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 86-166 4.14e-06

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: 45.03  E-value: 4.14e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A       86 PRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDE------------FNVSSPQFVGNLRESPLGQEKAleqI 153
Cdd:cd20547  19 PRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDtqkkskdilaasYNLRHPDKISVDDQMLEEFRKA---I 95

                        90
                ....*....|...
1KXU_A      154 LEYELLLIQQLNF 166
Cdd:cd20547  96 LGLERLLLETICF 108
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
 90-127 5.85e-04

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: 39.65  E-value: 5.85e-04
                        10        20        30
                ....*....|....*....|....*....|....*...
1KXU_A       90 VGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDE 127
Cdd:cd20596  51 INTAIVYMHRFYMHHSFTKFHRNIISPTALFLAAKVEE 88
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
 86-166 7.30e-04

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: 38.75  E-value: 7.30e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A       86 PRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFN------VSSPQFVGNLRESPLGQEKALEQILEYELL 159
Cdd:cd20530  28 PYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPkkckdiIKTARSLLNDKQFAQFGDDPKEEVMVLERI 107


                ....*..
1KXU_A      160 LIQQLNF 166
Cdd:cd20530 108 LLQTIKF 114
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 92-166 1.81e-03

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: 38.14  E-value: 1.81e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KXU_A       92 TACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEfnvsSPQFVGNL---------RESPLGQEKA------LEQILEY 156
Cdd:cd20538  51 TAIVYMHRFYMFHSFTKFHRNSIAAAALFLAAKVEE----QPRKLEHVikvahaclhRGEPDLDTKSeaylqqAQELVIN 126

                        90
                ....*....|
1KXU_A      157 ELLLIQQLNF 166
Cdd:cd20538 127 ENILLQTLGF 136
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 96-168 3.43e-03

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: 37.11  E-value: 3.43e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
1KXU_A         96 YFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEfnVSSPQfvgnLRESPLGQEKAL--EQILEYELLLIQQLNFHL 168
Cdd:pfam00134  58 YLDRFLSKKSVPKNKLQLVGVTCLFIAAKYEE--IYPPT----VEDLVYITDNAYtrEEILRMERLILETLNFDL 126
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 86-127 5.77e-03

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: 36.34  E-value: 5.77e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
1KXU_A       86 PRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDE 127
Cdd:cd20587  29 PQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEE 70
 
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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