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Conserved domains on  [gi|18401127|ref|NP_565622|]
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arginine-rich cyclin 1 [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
21-148 9.61e-82

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: 246.67  E-value: 9.61e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  21 SRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQ 100
Cdd:cd20591   1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 18401127 101 VIIVFHRMECRRENLPLEHLDMYAKKFSELKVELSRTERHILKEMGFV 148
Cdd:cd20591  81 VLMVFHRMECRRENLPLEPLEPESKKYDEMKEDLIRTERHLLKEMGFI 128
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
150-250 9.45e-71

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: 217.81  E-value: 9.45e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 150 HVEHPHKFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSSI 229
Cdd:cd20594   1 HVEHPHKFILNYLAMLMAPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKVFDAEKAEI 80
                        90       100
                ....*....|....*....|.
gi 18401127 230 DEVCRVLAHLYSLPKAQYISV 250
Cdd:cd20594  81 DVVCKVLADLYRQPKARYIEV 101
SF-CC1 super family cl36939
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
336-414 1.09e-07

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


The actual alignment was detected with superfamily member TIGR01622:

Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 53.77  E-value: 1.09e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18401127   336 DRERESDREKErgrerdrgrSHRGRDSDRDSDRERDKLKDRSHHRSRDRLKDSGGHSDKSRHHSSRDRDYRDSSKDRRR 414
Cdd:TIGR01622   4 DRERERLRDSS---------SAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYRPR 73
 
Name Accession Description Interval E-value
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
21-148 9.61e-82

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: 246.67  E-value: 9.61e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  21 SRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQ 100
Cdd:cd20591   1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 18401127 101 VIIVFHRMECRRENLPLEHLDMYAKKFSELKVELSRTERHILKEMGFV 148
Cdd:cd20591  81 VLMVFHRMECRRENLPLEPLEPESKKYDEMKEDLIRTERHLLKEMGFI 128
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
150-250 9.45e-71

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: 217.81  E-value: 9.45e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 150 HVEHPHKFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSSI 229
Cdd:cd20594   1 HVEHPHKFILNYLAMLMAPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKVFDAEKAEI 80
                        90       100
                ....*....|....*....|.
gi 18401127 230 DEVCRVLAHLYSLPKAQYISV 250
Cdd:cd20594  81 DVVCKVLADLYRQPKARYIEV 101
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
31-230 3.63e-25

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: 104.04  E-value: 3.63e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  31 EISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPkkarqviiVFHRMEC 110
Cdd:COG5333  41 ELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTP--------RDISIES 112
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 111 RRENlplehlDMYAKKFSELKVELSRTERHILKEMGFVCHVEHPHKFISNYLATLET--PPELRQEAWNLANDSLRTTLC 188
Cdd:COG5333 113 FEAR------DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEkdKYKLLQIAWKIINDALRTDLC 186
                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 18401127 189 VRFRSEVVACGVVYAAARRFQVPLPENppWWKAFDADKSSID 230
Cdd:COG5333 187 LLYPPHIIALAALLIACEVLGMPIIKL--LDFVSYETKEEVI 226
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
40-143 2.82e-09

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: 53.37  E-value: 2.82e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127     40 DLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEEnpkkarqviivfhrmecrrENLPLEH 119
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEE-------------------TPPWTKE 61
                           90       100
                   ....*....|....*....|....
gi 18401127    120 LDMYAKKFSElkVELSRTERHILK 143
Cdd:smart00385  62 LVHYTGYFTE--EEILRMERLLLE 83
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
336-414 1.09e-07

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 53.77  E-value: 1.09e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18401127   336 DRERESDREKErgrerdrgrSHRGRDSDRDSDRERDKLKDRSHHRSRDRLKDSGGHSDKSRHHSSRDRDYRDSSKDRRR 414
Cdd:TIGR01622   4 DRERERLRDSS---------SAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYRPR 73
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
156-241 2.04e-07

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: 48.36  E-value: 2.04e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127    156 KFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPeNPPWWKAfdADKSSIDEVCRV 235
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPW-TKELVHY--TGYFTEEEILRM 77

                   ....*.
gi 18401127    236 LAHLYS 241
Cdd:smart00385  78 ERLLLE 83
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
8-93 3.91e-07

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: 48.67  E-value: 3.91e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127     8 NFYLSDEqlKASPSRKDGIDETTEISL--RIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCV 85
Cdd:pfam00134   4 QYLRELE--LKYLPKPDYMDQQPDINPkmRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCL 81

                  ....*...
gi 18401127    86 WLASKLEE 93
Cdd:pfam00134  82 FIAAKYEE 89
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
51-213 3.78e-05

cyclin ccl1; All proteins in this family for which functions are known are cyclins that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, StanfordUniversity). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129660 [Multi-domain]  Cd Length: 305  Bit Score: 45.21  E-value: 3.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127    51 LPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIivfhrmecrrENL---PLEHLDmyakkf 127
Cdd:TIGR00569  74 MPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFV----------GNLketPLKALE------ 137
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127   128 SELKVELSrterhILKEMGFVCHVEHPHK----F---ISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGV 200
Cdd:TIGR00569 138 QVLEYELL-----LIQQLNFHLIVHNPYRplegFlidIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAA 212
                         170
                  ....*....|...
gi 18401127   201 VYAAARRFQVPLP 213
Cdd:TIGR00569 213 ILHTASRAGLNME 225
PRP38_assoc pfam12871
Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region ...
330-416 3.84e-04

Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known.


Pssm-ID: 463734 [Multi-domain]  Cd Length: 98  Bit Score: 39.37  E-value: 3.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127   330 ERSKVGDRERESDREKERGRERDRGRSHRGRDSDRDSDRERDKlkDRSHHRSRDRLKDSGGHSDKSRHHSSRDRDyRDSS 409
Cdd:pfam12871  14 EEEDEEEDEEASDESERASLSRKRRSRSRRRSSTRDRSRSRSR--SRSRDRRSRGTRDRRRDRDRDRYRSLRSRS-RDRS 90

                  ....*..
gi 18401127   410 KDRRRHH 416
Cdd:pfam12871  91 RDRDRDR 97
PRK12678 PRK12678
transcription termination factor Rho; Provisional
306-416 1.55e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 40.66  E-value: 1.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  306 EKATDSKKSGTESNSQPIVGDSSYERSKVGDRERESDREKERGRERDRGRSHRGRDSDRDSDRERDKLKDRSHHRSRDRL 385
Cdd:PRK12678 141 AARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGR 220
                         90       100       110
                 ....*....|....*....|....*....|.
gi 18401127  386 KDSGGHSDKSRHHSSRDRDYRDSSKDRRRHH 416
Cdd:PRK12678 221 RDGGDRRGRRRRRDRRDARGDDNREDRGDRD 251
 
Name Accession Description Interval E-value
CYCLIN_AcCycL_rpt1 cd20591
first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
21-148 9.61e-82

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: 246.67  E-value: 9.61e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  21 SRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQ 100
Cdd:cd20591   1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 18401127 101 VIIVFHRMECRRENLPLEHLDMYAKKFSELKVELSRTERHILKEMGFV 148
Cdd:cd20591  81 VLMVFHRMECRRENLPLEPLEPESKKYDEMKEDLIRTERHLLKEMGFI 128
CYCLIN_AcCycL_rpt2 cd20594
second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins; ...
150-250 9.45e-71

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: 217.81  E-value: 9.45e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 150 HVEHPHKFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSSI 229
Cdd:cd20594   1 HVEHPHKFILNYLAMLMAPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKVFDAEKAEI 80
                        90       100
                ....*....|....*....|.
gi 18401127 230 DEVCRVLAHLYSLPKAQYISV 250
Cdd:cd20594  81 DVVCKVLADLYRQPKARYIEV 101
CYCLIN_CCNL_rpt1 cd20532
first cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
24-148 1.23e-68

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: 213.19  E-value: 1.23e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  24 DGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVII 103
Cdd:cd20532   1 DGIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVIN 80
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 18401127 104 VFHRMECRRENLPLEH--LDMYAKKFSELKVELSRTERHILKEMGFV 148
Cdd:cd20532  81 VFHRLLQRRLGKPAEVlpLDIGSAEYEELKNDIIKAERRILKELGFC 127
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
153-241 1.04e-44

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: 150.06  E-value: 1.04e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 153 HPHKFISNYLATLET--PPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSSID 230
Cdd:cd20533   1 HPHKFILMYLQVLEGedNKKLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAARELGIPLPLPPPWWELFDVSKEDIE 80
                        90
                ....*....|.
gi 18401127 231 EVCRVLAHLYS 241
Cdd:cd20533  81 EICLTILELYT 91
CYCLIN_CCNL2_rpt1 cd20590
first cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
2-147 4.09e-42

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: 145.53  E-value: 4.09e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127   2 IYTAIDNFYLSDEQLKASPSRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVA 81
Cdd:cd20590  11 VLITLENCLLPEERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVKHSMEHVS 90
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18401127  82 ASCVWLASKLEENPKKARQVIIVFHRMECRREN---LPLehldMYAKKFSELKVELSRTERHILKEMGF 147
Cdd:cd20590  91 MACVHLASKIEEAPRRIRDVINVFHRLRQLREKkkpVPL----ILDQEYVNLKNQIIKAERRVLKELGF 155
CYCLIN_CCNL1_rpt1 cd20589
first cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
24-147 2.85e-39

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: 137.18  E-value: 2.85e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  24 DGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVII 103
Cdd:cd20589   1 DGLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVIN 80
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 18401127 104 VFHRMECRRENLPLEHLdMYAKKFSELKVELSRTERHILKEMGF 147
Cdd:cd20589  81 VFHHIKQVRGKRTISPL-ILDQNYINLKNQVIKAERRVLKELGF 123
CYCLIN_CCNL1_rpt2 cd20592
second cyclin box found in cyclin-L1 (CCNL1) and similar proteins; CCNL1 is an L-type cyclin ...
152-247 8.48e-26

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: 101.23  E-value: 8.48e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 152 EHPHKFISNYLATLETP--PELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSSI 229
Cdd:cd20592   1 KHPHKIIVMYLQVLECErnQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPNRPHWFLLFGATEEEI 80
                        90
                ....*....|....*...
gi 18401127 230 DEVCRVLAHLYSLPKAQY 247
Cdd:cd20592  81 QEICITTLKLYTRKKPNY 98
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
31-230 3.63e-25

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: 104.04  E-value: 3.63e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  31 EISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPkkarqviiVFHRMEC 110
Cdd:COG5333  41 ELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTP--------RDISIES 112
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 111 RRENlplehlDMYAKKFSELKVELSRTERHILKEMGFVCHVEHPHKFISNYLATLET--PPELRQEAWNLANDSLRTTLC 188
Cdd:COG5333 113 FEAR------DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEkdKYKLLQIAWKIINDALRTDLC 186
                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 18401127 189 VRFRSEVVACGVVYAAARRFQVPLPENppWWKAFDADKSSID 230
Cdd:COG5333 187 LLYPPHIIALAALLIACEVLGMPIIKL--LDFVSYETKEEVI 226
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
153-245 1.15e-23

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: 95.42  E-value: 1.15e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 153 HPHKFISNYLATLETP--PELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSSID 230
Cdd:cd20593   1 HPHKIIVMYLQVLECErnRHLVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEIPLPNRPHWFLLFGATEEEIQ 80
                        90
                ....*....|....*
gi 18401127 231 EVCRVLAHLYSLPKA 245
Cdd:cd20593  81 EICLKILQLYTRKKV 95
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
9-147 3.84e-23

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: 94.38  E-value: 3.84e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127   9 FYLSDEQLKASPSRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLA 88
Cdd:cd20538   2 WYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFLA 81
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 18401127  89 SKLEENPKKARQVIIVFHRMECRRENLPLEHLDMYAKKFSELKVelsrTERHILKEMGF 147
Cdd:cd20538  82 AKVEEQPRKLEHVIKVAHACLHRGEPDLDTKSEAYLQQAQELVI----NENILLQTLGF 136
CYCLIN_CCNK_rpt1 cd20530
first cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase ...
25-147 4.23e-23

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: 93.45  E-value: 4.23e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  25 GIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIIV 104
Cdd:cd20530   1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80
                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 18401127 105 FHRmecrrenlpLEHLDMYAKKFSELKVELSRTERHILKEMGF 147
Cdd:cd20530  81 ARS---------LLNDKQFAQFGDDPKEEVMVLERILLQTIKF 114
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
9-147 1.17e-20

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: 87.42  E-value: 1.17e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127   9 FYLSDEQLKASPSRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLA 88
Cdd:cd20595   3 WYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALFLA 82
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 18401127  89 SKLEENPKKARQVIIVFHRMECRRENLPLEHLDMYAKKFSELKVelsrTERHILKEMGF 147
Cdd:cd20595  83 AKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVI----LESIILQTLGF 137
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
39-147 2.99e-20

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: 85.30  E-value: 2.99e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  39 CDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIIVFHRMeCRRENLPLE 118
Cdd:cd20534   6 LRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRI-LHPDKPPLE 84
                        90       100
                ....*....|....*....|....*....
gi 18401127 119 HLDMYakkfSELKVELSRTERHILKEMGF 147
Cdd:cd20534  85 LDDEY----WELRDSIVNCELLLLRILKF 109
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
9-147 6.73e-20

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: 85.48  E-value: 6.73e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127   9 FYLSDEQLKASPSRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLA 88
Cdd:cd20596   4 WFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTALFLA 83
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  89 SKLEENPKKARQVIIVFHrmECRRenlPLE-HLDMYAKKFSELKVELSRTERHILKEMGF 147
Cdd:cd20596  84 AKVEEQPRKLEHVIKVAH--ACLN---PLEpQLDTKSDAYLQQAQELVILETIMLQTLGF 138
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
153-241 7.25e-19

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: 81.26  E-value: 7.25e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 153 HPHKFISNYLATLETP--PELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENP-----PWWKAFDAD 225
Cdd:cd20546   1 HPYQYLIKFAKKLGVSdpKELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPneklnEWWELFGVD 80
                        90
                ....*....|....*.
gi 18401127 226 KSSIDEVCRVLAHLYS 241
Cdd:cd20546  81 EEEIADAINEILDLYS 96
CYCLIN_AcCycT_rpt1 cd20587
first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
24-147 1.95e-17

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: 77.94  E-value: 1.95e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  24 DGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVII 103
Cdd:cd20587   1 DGIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIV 80
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 18401127 104 VFHRMECRREnlPLEHLDMYAKK-FSELKVELSRTERHILKEMGF 147
Cdd:cd20587  81 VSYEIIFKKD--PSAAQRIKQKEvYEQQKELVLNGEKLVLSTLGF 123
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
152-240 2.57e-17

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: 76.99  E-value: 2.57e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 152 EHPHKFISNYLATL----ETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAAR--RFQVPLPENPP----WWKA 221
Cdd:cd20531   1 EHPYKYLLKYAKQLkgdkNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKlsKFDLQDWTSKPpgkrWWEQ 80
                        90       100
                ....*....|....*....|.
gi 18401127 222 FDADKSS--IDEVCRVLAHLY 240
Cdd:cd20531  81 FVEDVSLevLEDICHQVLDLY 101
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
34-99 1.70e-16

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: 74.55  E-value: 1.70e-16
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18401127  34 LRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKAR 99
Cdd:cd20513   1 LHIFFANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPSHAR 66
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
152-240 2.02e-15

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: 71.41  E-value: 2.02e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 152 EHPHKFISNYLATLE-TPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPEN--PPWWKAFDADKSS 228
Cdd:cd20588   1 EHPYKPLVAAIKKFNvAQNALAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPCDgrKVWWQEFDVTPRQ 80
                        90
                ....*....|..
gi 18401127 229 IDEVCRVLAHLY 240
Cdd:cd20588  81 LEEVSNQMLELY 92
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
153-242 3.35e-15

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: 71.13  E-value: 3.35e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 153 HPHKFISNYLATLE--TPPE------LRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENP----PWWK 220
Cdd:cd20535   1 LPHKYLLHYLKSLRdwLNPEfwsrspIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQVYGVKVPPEEeaekPWWQ 80
                        90       100
                ....*....|....*....|....
gi 18401127 221 AF--DADKSSIDEVCRVLAHLYSL 242
Cdd:cd20535  81 AFceDLTKETIDEIIEDIINVYDL 104
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
31-147 3.41e-15

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: 71.30  E-value: 3.41e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  31 EISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIIVFHRMEC 110
Cdd:cd20545   1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQ 80
                        90       100       110
                ....*....|....*....|....*....|....*..
gi 18401127 111 RRENLpleHLDMYAKKFSELKVELSRTERHILKEMGF 147
Cdd:cd20545  81 KNPNL---VIDEQSKEVWRWRDSILYNEEVLLETLCF 114
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
37-106 1.09e-10

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: 57.42  E-value: 1.09e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  37 YGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIIVFH 106
Cdd:cd00043   1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSG 70
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
40-143 2.82e-09

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: 53.37  E-value: 2.82e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127     40 DLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEEnpkkarqviivfhrmecrrENLPLEH 119
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEE-------------------TPPWTKE 61
                           90       100
                   ....*....|....*....|....
gi 18401127    120 LDMYAKKFSElkVELSRTERHILK 143
Cdd:smart00385  62 LVHYTGYFTE--EEILRMERLLLE 83
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
49-95 2.99e-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: 55.29  E-value: 2.99e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 18401127  49 LKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENP 95
Cdd:cd20524  69 FKLPDSVLATALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVEEFN 115
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
34-108 4.05e-09

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: 53.89  E-value: 4.05e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18401127  34 LRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIIVFHRM 108
Cdd:cd20547   1 LRLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNL 75
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
153-238 1.24e-08

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: 51.89  E-value: 1.24e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 153 HPHKFISNYLATLE-TPPELRQEAWNLANDSLR-TTLCVRFRSEVVACGVVYAAAR--RFQVPLP-ENPPWWKAFdaDKS 227
Cdd:cd20539   1 HPHTHVLKICNLVKaGSKDLAQTAYFLATNSLHlTTFCLQYKPTVIACVCIHLACKwsNWEIPRSsEGKDWYEYV--DPS 78
                        90
                ....*....|.
gi 18401127 228 SIDEVCRVLAH 238
Cdd:cd20539  79 LTLEELDELTS 89
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
34-108 4.71e-08

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


Pssm-ID: 410274 [Multi-domain]  Cd Length: 107  Bit Score: 51.01  E-value: 4.71e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18401127  34 LRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIIVFHRM 108
Cdd:cd20571   6 IKIHMSNYIKKLAQHIKVRQRVVATAITYFRRVYTRKSFTEYDPRLVAPTCLYLASKAEESTVQAKLLVFYMKRL 80
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
336-414 1.09e-07

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 53.77  E-value: 1.09e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18401127   336 DRERESDREKErgrerdrgrSHRGRDSDRDSDRERDKLKDRSHHRSRDRLKDSGGHSDKSRHHSSRDRDYRDSSKDRRR 414
Cdd:TIGR01622   4 DRERERLRDSS---------SAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYRPR 73
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
156-241 2.04e-07

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: 48.36  E-value: 2.04e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127    156 KFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPeNPPWWKAfdADKSSIDEVCRV 235
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPW-TKELVHY--TGYFTEEEILRM 77

                   ....*.
gi 18401127    236 LAHLYS 241
Cdd:smart00385  78 ERLLLE 83
CYCLIN_CCNC_rpt2 cd20514
second cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
153-244 2.15e-07

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: 48.38  E-value: 2.15e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 153 HPHKFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPEnppWWKAFDADKSSIDEV 232
Cdd:cd20514   1 HPYRPLTQYVQDAGLDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDARQ---WFAELNVDMDKILEI 77
                        90
                ....*....|..
gi 18401127 233 CRVLAHLYSLPK 244
Cdd:cd20514  78 TREILSLYELWK 89
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
8-93 3.91e-07

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: 48.67  E-value: 3.91e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127     8 NFYLSDEqlKASPSRKDGIDETTEISL--RIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCV 85
Cdd:pfam00134   4 QYLRELE--LKYLPKPDYMDQQPDINPkmRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCL 81

                  ....*...
gi 18401127    86 WLASKLEE 93
Cdd:pfam00134  82 FIAAKYEE 89
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
336-414 7.14e-07

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 51.05  E-value: 7.14e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18401127   336 DRERESDREKErgrerdrgrshrgRDSDRDSDRERDklKDRSHHRSRDRlkdsgghsdkSRHHSSRDRDYRDSSKDRRR 414
Cdd:TIGR01642   2 DEEPDREREKS-------------RGRDRDRSSERP--RRRSRDRSRFR----------DRHRRSRERSYREDSRPRDR 55
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
337-415 7.46e-07

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 51.05  E-value: 7.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127   337 RERESDREKERGRERDrgrshRGRDSDRDSDRERDKLKDRS-HHRSRDR--LKDSgGHSDKSRHHSSRDRDYRDSSKDRR 413
Cdd:TIGR01642   1 RDEEPDREREKSRGRD-----RDRSSERPRRRSRDRSRFRDrHRRSRERsyREDS-RPRDRRRYDSRSPRSLRYSSVRRS 74

                  ..
gi 18401127   414 RH 415
Cdd:TIGR01642  75 RD 76
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
153-235 2.09e-06

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: 45.48  E-value: 2.09e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127 153 HPHKFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFqvplpENPPWWKAF-DADKSSIDE 231
Cdd:cd00043   1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLE-----ELPRTLKEIaKVSGVSEKE 75

                ....
gi 18401127 232 VCRV 235
Cdd:cd00043  76 LRKA 79
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
331-414 2.38e-06

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 49.53  E-value: 2.38e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127   331 RSKVGDRERESDREKERGRERDRGrshRGRDSDRDSDRERDKLKDRSHHRSRDRLKDSGGHSDK----SRHHSSRDRDYR 406
Cdd:TIGR01622   3 RDRERERLRDSSSAGDRDRRRDKG---RERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSrrpnRRYRPREKRRRR 79

                  ....*...
gi 18401127   407 DSSKDRRR 414
Cdd:TIGR01622  80 GDSYRRRR 87
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
26-121 4.09e-06

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: 46.74  E-value: 4.09e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  26 IDEttEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQV---I 102
Cdd:cd20585  71 ADE--ELLMLKYYEQKIQEVCRALRLPNKIQATALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEEYHVSAEELgkgI 148
                        90
                ....*....|....*....
gi 18401127 103 IVFHRMECRRENLPLEHLD 121
Cdd:cd20585 149 QQDHQLILKNELALLQGLN 167
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
310-414 2.04e-05

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 46.81  E-value: 2.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127   310 DSKKSGTESNSQPIVGDSSYERSKVGDRERESDRE-KERGRERDRGRSHRGRDSDRDSDRERDKLKDRSHHRSRDRL-KD 387
Cdd:TIGR01642   2 DEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDrHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPrRR 81
                          90       100       110
                  ....*....|....*....|....*....|
gi 18401127   388 SGGHSDKSRH-HSSRDRDYRDSSK--DRRR 414
Cdd:TIGR01642  82 SRSVRSIEQHrRRLRDRSPSNQWRkdDKKR 111
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
51-213 3.78e-05

cyclin ccl1; All proteins in this family for which functions are known are cyclins that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, StanfordUniversity). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129660 [Multi-domain]  Cd Length: 305  Bit Score: 45.21  E-value: 3.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127    51 LPQAVMATGQVLFQRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIivfhrmecrrENL---PLEHLDmyakkf 127
Cdd:TIGR00569  74 MPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFV----------GNLketPLKALE------ 137
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127   128 SELKVELSrterhILKEMGFVCHVEHPHK----F---ISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGV 200
Cdd:TIGR00569 138 QVLEYELL-----LIQQLNFHLIVHNPYRplegFlidIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAA 212
                         170
                  ....*....|...
gi 18401127   201 VYAAARRFQVPLP 213
Cdd:TIGR00569 213 ILHTASRAGLNME 225
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
330-413 1.31e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 44.14  E-value: 1.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127   330 ERSKVGDRERESDREKERGrerdrgrshRGRDSDRDSDRERDKLKDRsHHRSRDRLKDSGGHS-DKSRHHSSRDRDYRDS 408
Cdd:TIGR01622  20 DRRRDKGRERSRDRSRDRE---------RSRSRRRDRHRDRDYYRGR-ERRSRSRRPNRRYRPrEKRRRRGDSYRRRRDD 89

                  ....*
gi 18401127   409 SKDRR 413
Cdd:TIGR01622  90 RRSRR 94
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
364-415 3.82e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 42.60  E-value: 3.82e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 18401127   364 RDSDRERDklKDRSHHRSRDRLKDSGGHSDKSRhhsSRDRDyRDSSKDRRRH 415
Cdd:TIGR01622   3 RDRERERL--RDSSSAGDRDRRRDKGRERSRDR---SRDRE-RSRSRRRDRH 48
PRP38_assoc pfam12871
Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region ...
330-416 3.84e-04

Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known.


Pssm-ID: 463734 [Multi-domain]  Cd Length: 98  Bit Score: 39.37  E-value: 3.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127   330 ERSKVGDRERESDREKERGRERDRGRSHRGRDSDRDSDRERDKlkDRSHHRSRDRLKDSGGHSDKSRHHSSRDRDyRDSS 409
Cdd:pfam12871  14 EEEDEEEDEEASDESERASLSRKRRSRSRRRSSTRDRSRSRSR--SRSRDRRSRGTRDRRRDRDRDRYRSLRSRS-RDRS 90

                  ....*..
gi 18401127   410 KDRRRHH 416
Cdd:pfam12871  91 RDRDRDR 97
PRK12678 PRK12678
transcription termination factor Rho; Provisional
306-416 1.55e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 40.66  E-value: 1.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  306 EKATDSKKSGTESNSQPIVGDSSYERSKVGDRERESDREKERGRERDRGRSHRGRDSDRDSDRERDKLKDRSHHRSRDRL 385
Cdd:PRK12678 141 AARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGR 220
                         90       100       110
                 ....*....|....*....|....*....|.
gi 18401127  386 KDSGGHSDKSRHHSSRDRDYRDSSKDRRRHH 416
Cdd:PRK12678 221 RDGGDRRGRRRRRDRRDARGDDNREDRGDRD 251
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
152-223 1.84e-03

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: 37.75  E-value: 1.84e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18401127 152 EHPHKFISNYLATLETPPELRQEAWNLANDSLR-TTLCVRFRSEVVACGVVYAAAR--RFQVPLP-ENPPWWKAFD 223
Cdd:cd20598   1 EHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHlTTFCLQYKPTVIACVCIHLACKwsNWEIPVStDGKHWWEYVD 76
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
152-224 1.88e-03

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: 37.75  E-value: 1.88e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18401127 152 EHPHKFISNYLATLETPPELRQEAWNLANDSLR-TTLCVRFRSEVVACGVVYAAAR--RFQVPLP-ENPPWWKAFDA 224
Cdd:cd20597   1 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHlTTFSLQYTPPVVACVCIHLACKwsNWEIPVStDGKHWWEYVDA 77
PRK12678 PRK12678
transcription termination factor Rho; Provisional
310-415 7.01e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 38.73  E-value: 7.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18401127  310 DSKKSGTESNSQPIVGDSSYERSKVGDRERESDREKERGRERDRGRSHRGRDSDRDSDRERDKLKDRSHHRSRDRLKDSG 389
Cdd:PRK12678 140 GAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERG 219
                         90       100
                 ....*....|....*....|....*.
gi 18401127  390 GHSDKSRHHSSRDRDYRDSSKDRRRH 415
Cdd:PRK12678 220 RRDGGDRRGRRRRRDRRDARGDDNRE 245
 
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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