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Conserved domains on  [gi|2065799468|gb|KAG7567928|]
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Cyclin N-terminal [Arabidopsis thaliana x Arabidopsis arenosa]

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 2.89e-81

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: 245.90  E-value: 2.89e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  21 SRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQ 100
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2065799468 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 1.88e-70

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: 217.04  E-value: 1.88e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 150 HVEHPHKFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSSI 229
Cdd:cd20594     1 HVEHPHKFILNYLAMLMAPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKVFDAEKAEI 80

                          90       100
                  ....*....|....*....|.
gi 2065799468 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 ...
 335-417 2.83e-11

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: 64.94  E-value: 2.83e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 335 GERERESGREKERSRERDRTRShrgRDSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDKSRHhsSRDRDYRESSHSSKD 414
Cdd:TIGR01622   1 RYRDRERERLRDSSSAGDRDRR---RDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERR--SRSRRPNRRYRPREK 75


                  ...
gi 2065799468 415 RRR 417
Cdd:TIGR01622  76 RRR 78
MSCRAMM_ClfA super family cl41352
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 253-414 3.27e-05

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


The actual alignment was detected with superfamily member NF033609:

Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 46.44  E-value: 3.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 253 DGKPFTFSSRSGNSQAQSATKDvlPGVGDAVDTKCAPGSANNDSKDGMVISPHEKGTDSKK-SDTESNSqpivgDSRNGK 331
Cdd:NF033609  568 DSGSDSSNSDSGSDSGSDSTSD--SGSDSASDSDSASDSDSASDSDSASDSDSASDSDSASdSDSASDS-----DSASDS 640

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 332 SKVGERERESGREKERSRERDrtrSHRGRDSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDK-SRHHSSRDRDYRESSH 410
Cdd:NF033609  641 DSDSDSDSDSDSDSDSDSDSD---SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSdSDSDSDSDSDSDSDSD 717


                  ....
gi 2065799468 411 SSKD 414
Cdd:NF033609  718 SDSD 721
 
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 2.89e-81

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: 245.90  E-value: 2.89e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  21 SRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQ 100
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2065799468 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 1.88e-70

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: 217.04  E-value: 1.88e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 150 HVEHPHKFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSSI 229
Cdd:cd20594     1 HVEHPHKFILNYLAMLMAPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKVFDAEKAEI 80

                          90       100
                  ....*....|....*....|.
gi 2065799468 230 DEVCRVLAHLYSLPKAQYISV 250
Cdd:cd20594    81 DVVCKVLADLYRQPKARYIEV 101
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 31-230 2.61e-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: 104.81  E-value: 2.61e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  31 EISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPkkarqviiVFHRMEC 110
Cdd:COG5333    41 ELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTP--------RDISIES 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 111 RRENlplehlDMYAKKFSELKVELSRTERHILKEMGFVCHVEHPHKFISNYLATLET--PPELRQEAWNLANDSLRTTLC 188
Cdd:COG5333   113 FEAR------DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEkdKYKLLQIAWKIINDALRTDLC 186

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2065799468 189 VRFRSEVVACGVVYAAARRFQVPLPENppWWKAFDADKSSID 230
Cdd:COG5333   187 LLYPPHIIALAALLIACEVLGMPIIKL--LDFVSYETKEEVI 226
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 335-417 2.83e-11

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: 64.94  E-value: 2.83e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 335 GERERESGREKERSRERDRTRShrgRDSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDKSRHhsSRDRDYRESSHSSKD 414
Cdd:TIGR01622   1 RYRDRERERLRDSSSAGDRDRR---RDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERR--SRSRRPNRRYRPREK 75


                  ...
gi 2065799468 415 RRR 417
Cdd:TIGR01622  76 RRR 78
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 40-143 2.65e-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: 53.75  E-value: 2.65e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468   40 DLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEEnpkkarqviivfhrmecrrENLPLEH 119
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEE-------------------TPPWTKE 61

                           90       100
                   ....*....|....*....|....
gi 2065799468  120 LDMYAKKFSElkVELSRTERHILK 143
Cdd:smart00385  62 LVHYTGYFTE--EEILRMERLLLE 83
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 8-93 2.63e-08

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: 52.13  E-value: 2.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468   8 NFYLTDEqlKASPSRKDGIDETTEISL--RIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCV 85
Cdd:pfam00134   4 QYLRELE--LKYLPKPDYMDQQPDINPkmRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCL 81


                  ....*...
gi 2065799468  86 WLASKLEE 93
Cdd:pfam00134  82 FIAAKYEE 89
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 156-241 1.69e-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: 1.69e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  156 KFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPeNPPWWKAfdADKSSIDEVCRV 235
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPW-TKELVHY--TGYFTEEEILRM 77


                   ....*.
gi 2065799468  236 LAHLYS 241
Cdd:smart00385  78 ERLLLE 83
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 253-414 3.27e-05

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 46.44  E-value: 3.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 253 DGKPFTFSSRSGNSQAQSATKDvlPGVGDAVDTKCAPGSANNDSKDGMVISPHEKGTDSKK-SDTESNSqpivgDSRNGK 331
Cdd:NF033609  568 DSGSDSSNSDSGSDSGSDSTSD--SGSDSASDSDSASDSDSASDSDSASDSDSASDSDSASdSDSASDS-----DSASDS 640

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 332 SKVGERERESGREKERSRERDrtrSHRGRDSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDK-SRHHSSRDRDYRESSH 410
Cdd:NF033609  641 DSDSDSDSDSDSDSDSDSDSD---SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSdSDSDSDSDSDSDSDSD 717


                  ....
gi 2065799468 411 SSKD 414
Cdd:NF033609  718 SDSD 721
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 308-417 6.39e-05

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 45.28  E-value: 6.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 308 GTDSKKSDTESNSQPIVGDSRNGKSKVGERERESGREKERSRERDRTRSHRGRDSDKESDRERDKLKDRSHHRSRDRL-K 386
Cdd:PRK12678  159 DAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRdA 238

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2065799468 387 DSDGHSDKSRHHSSRDRDYRESSHSSKDRRR 417
Cdd:PRK12678  239 RGDDNREDRGDRDGDDGEGRGGRRGRRFRDR 269
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 51-213 8.69e-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: 44.05  E-value: 8.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  51 LPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIivfhrmecrrENL---PLEHLDmyakkf 127
Cdd:TIGR00569  74 MPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFV----------GNLketPLKALE------ 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 128 SELKVELSrterhILKEMGFVCHVEHPHK----F---ISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGV 200
Cdd:TIGR00569 138 QVLEYELL-----LIQQLNFHLIVHNPYRplegFlidIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAA 212

                         170
                  ....*....|...
gi 2065799468 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 ...
 335-419 1.07e-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: 40.91  E-value: 1.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 335 GERERESGREKERSRERDRTRSHRGRDSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDKSRHHSSRDRDYRESSHSSKD 414
Cdd:pfam12871  13 EEEEDEEEDEEASDESERASLSRKRRSRSRRRSSTRDRSRSRSRSRSRDRRSRGTRDRRRDRDRDRYRSLRSRSRDRSRD 92


                  ....*
gi 2065799468 415 RRRHH 419
Cdd:pfam12871  93 RDRDR 97
 
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 2.89e-81

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: 245.90  E-value: 2.89e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  21 SRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQ 100
Cdd:cd20591     1 SRKDGIDEDTEITLRIFGCELIQESGILLKLPQAVMATGQVLFQRFYCKKSFARFNVKRVAASCVWLAAKLEESPRKIRQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2065799468 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 1.88e-70

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: 217.04  E-value: 1.88e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 150 HVEHPHKFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSSI 229
Cdd:cd20594     1 HVEHPHKFILNYLAMLMAPPELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQVPLPENPPWWKVFDAEKAEI 80

                          90       100
                  ....*....|....*....|.
gi 2065799468 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 5.69e-69

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: 213.96  E-value: 5.69e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  24 DGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVII 103
Cdd:cd20532     1 DGIDEETEIDLRIYGCELIQDAGILLKLPQVVMATAQVLFHRFYYRKSLRKFDVKIVAMACLFLASKIEETPRRLRDVIN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2065799468 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 2065799468 153 HPHKFISNYLATLET--PPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSSID 230
Cdd:cd20533     1 HPHKFILMYLQVLEGedNKKLAQTAWNYMNDSLRTDLCVRYPPEVIACACIYLAARELGIPLPLPPPWWELFDVSKEDIE 80

                          90
                  ....*....|.
gi 2065799468 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 4.81e-41

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: 142.84  E-value: 4.81e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468   2 IYTAIDNFYLTDEQLKASPSRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVA 81
Cdd:cd20590    11 VLITLENCLLPEERLRFTPSMSSGLDVDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVKHSMEHVS 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2065799468  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 7.68e-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: 136.03  E-value: 7.68e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  24 DGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVII 103
Cdd:cd20589     1 DGLDHETETDLRILGCELIQTAGILLRLPQVAMATGQVLFQRFFYSKSFVKHSMEIVAMACINLASKIEEAPRRIRDVIN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2065799468 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 8.76e-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: 8.76e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 152 EHPHKFISNYLATLETP--PELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSSI 229
Cdd:cd20592     1 KHPHKIIVMYLQVLECErnQTLVQTAWNYMNDSLRTNVFVRFQPETIACACIYLAARALQIPLPNRPHWFLLFGATEEEI 80

                          90
                  ....*....|....*...
gi 2065799468 230 DEVCRVLAHLYSLPKAQY 247
Cdd:cd20592    81 QEICITTLKLYTRKKPNY 98
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 31-230 2.61e-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: 104.81  E-value: 2.61e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  31 EISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPkkarqviiVFHRMEC 110
Cdd:COG5333    41 ELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTP--------RDISIES 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 111 RRENlplehlDMYAKKFSELKVELSRTERHILKEMGFVCHVEHPHKFISNYLATLET--PPELRQEAWNLANDSLRTTLC 188
Cdd:COG5333   113 FEAR------DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEkdKYKLLQIAWKIINDALRTDLC 186

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2065799468 189 VRFRSEVVACGVVYAAARRFQVPLPENppWWKAFDADKSSID 230
Cdd:COG5333   187 LLYPPHIIALAALLIACEVLGMPIIKL--LDFVSYETKEEVI 226
CYCLIN_CCNT_rpt1 cd20538
first cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 9-147 1.13e-24

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: 98.62  E-value: 1.13e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468   9 FYLTDEQLKASPSRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLA 88
Cdd:cd20538     2 WYFTREQLENTPSRRCGVDPDKELSYRQQAANLIQEMGQRLQVSQLCINTAIVYMHRFYMFHSFTKFHRNSIAAAALFLA 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2065799468  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 1.52e-24

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: 97.30  E-value: 1.52e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  25 GIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIIV 104
Cdd:cd20530     1 GIDPETEARYRREGARFIQDVGTKLGLPYDTIATGIVYFHRFYMFHSFKDFDRYVTAACCLFLAGKVEETPKKCKDIIKT 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2065799468 105 FHRmecrrenlpLEHLDMYAKKFSELKVELSRTERHILKEMGF 147
Cdd:cd20530    81 ARS---------LLNDKQFAQFGDDPKEEVMVLERILLQTIKF 114
CYCLIN_CCNL2_rpt2 cd20593
second cyclin box found in cyclin-2 (CCNL2) and similar proteins; CCNL2 is a novel RNA ...
 153-245 1.18e-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: 1.18e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 153 HPHKFISNYLATLETP--PELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENPPWWKAFDADKSSID 230
Cdd:cd20593     1 HPHKIIVMYLQVLECErnRHLVQTSWNYMNDSLRTDVFVRFNPETIACACIYLAARTLEIPLPNRPHWFLLFGATEEEIQ 80

                          90
                  ....*....|....*
gi 2065799468 231 EVCRVLAHLYSLPKA 245
Cdd:cd20593    81 EICLKILQLYTRKKV 95
CYCLIN_CCNT1_rpt1 cd20595
first cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 9-147 3.08e-22

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: 92.04  E-value: 3.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468   9 FYLTDEQLKASPSRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLA 88
Cdd:cd20595     3 WYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALFLA 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2065799468  89 SKLEENPKKARQVIIVFHRMECRRENLPLEHLDMYAKKFSELKVelsrTERHILKEMGF 147
Cdd:cd20595    83 AKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVI----LESIILQTLGF 137
CYCLIN_CCNT2_rpt1 cd20596
first cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit ...
 9-147 1.78e-21

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


Pssm-ID: 410299 [Multi-domain]  Cd Length: 139  Bit Score: 89.72  E-value: 1.78e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468   9 FYLTDEQLKASPSRKDGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLA 88
Cdd:cd20596     4 WFFTREQLENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFHRNIISPTALFLA 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  89 SKLEENPKKARQVIIVFHrmECRRenlPLE-HLDMYAKKFSELKVELSRTERHILKEMGF 147
Cdd:cd20596    84 AKVEEQPRKLEHVIKVAH--ACLN---PLEpQLDTKSDAYLQQAQELVILETIMLQTLGF 138
CYCLIN_CCNM_CCNQ_rpt1 cd20534
first cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 39-147 3.05e-21

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: 88.00  E-value: 3.05e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  39 CDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIIVFHRMeCRRENLPLE 118
Cdd:cd20534     6 LRFIREAGLKLELSSVTIATACVLYHRFYRELSLEDYDPYLVAMACLYLAGKAEEQPRRLRDIINVSYRI-LHPDKPPLE 84

                          90       100
                  ....*....|....*....|....*....
gi 2065799468 119 HLDMYakkfSELKVELSRTERHILKEMGF 147
Cdd:cd20534    85 LDDEY----WELRDSIVNCELLLLRILKF 109
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 153-241 7.38e-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: 7.38e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 153 HPHKFISNYLATLETP--PELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENP-----PWWKAFDAD 225
Cdd:cd20546     1 HPYQYLIKFAKKLGVSdpKELAQLAWAFLNDSYRTPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPneklnEWWELFGVD 80

                          90
                  ....*....|....*.
gi 2065799468 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 3.66e-18

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


Pssm-ID: 410290 [Multi-domain]  Cd Length: 124  Bit Score: 79.87  E-value: 3.66e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  24 DGIDETTEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVII 103
Cdd:cd20587     1 DGIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKNDRQTIATVCMFLAGKVEETPRPLKDVIV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2065799468 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 2.61e-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: 2.61e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 152 EHPHKFISNYLATL----ETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAAR--RFQVPLPENPP----WWKA 221
Cdd:cd20531     1 EHPYKYLLKYAKQLkgdkNKIQKLVQMAWTFVNDSLCTTLCLQWEPEIIAVALMYLAAKlsKFDLQDWTSKPpgkrWWEQ 80

                          90       100
                  ....*....|....*....|.
gi 2065799468 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 2.96e-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: 73.78  E-value: 2.96e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2065799468  34 LRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKAR 99
Cdd:cd20513     1 LHIFFANFIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECPSHAR 66
CYCLIN_SpCG1C-like_rpt1 cd20545
first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar ...
 31-147 4.53e-16

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: 74.00  E-value: 4.53e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  31 EISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIIVFHRMEC 110
Cdd:cd20545     1 EQEDRSKGVNFIIRVGSRLKLPQTTLFTAATYFHRFYMRNSLKKYHYYEIAATCLFLATKVEESGRKLRDIVIACAKVAQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2065799468 111 RRENLpleHLDMYAKKFSELKVELSRTERHILKEMGF 147
Cdd:cd20545    81 KNPNL---VIDEQSKEVWRWRDSILYNEEVLLETLCF 114
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 152-240 2.05e-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: 2.05e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 152 EHPHKFISNYLATLE-TPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPEN--PPWWKAFDADKSS 228
Cdd:cd20588     1 EHPYKPLVAAIKKFNvAQNALAQAAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPCDgrKVWWQEFDVTPRQ 80

                          90
                  ....*....|..
gi 2065799468 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 3.10e-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: 3.10e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 153 HPHKFISNYLATLE--TPPE------LRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPENP----PWWK 220
Cdd:cd20535     1 LPHKYLLHYLKSLRdwLNPEfwsrspIAKTAWSLLRDFYHSPLCLQFKPQHIALAVIYLALQVYGVKVPPEEeaekPWWQ 80

                          90       100
                  ....*....|....*....|....
gi 2065799468 221 AF--DADKSSIDEVCRVLAHLYSL 242
Cdd:cd20535    81 AFceDLTKETIDEIIEDIINVYDL 104
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 335-417 2.83e-11

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: 64.94  E-value: 2.83e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 335 GERERESGREKERSRERDRTRShrgRDSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDKSRHhsSRDRDYRESSHSSKD 414
Cdd:TIGR01622   1 RYRDRERERLRDSSSAGDRDRR---RDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERR--SRSRRPNRRYRPREK 75


                  ...
gi 2065799468 415 RRR 417
Cdd:TIGR01622  76 RRR 78
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 37-106 4.74e-11

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: 58.58  E-value: 4.74e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  37 YGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIIVFH 106
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSG 70
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 337-417 6.80e-10

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: 60.68  E-value: 6.80e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 337 RERESGREKERSRERDRTRShrgrdSDKESDRERDKLKDRS-HHRSRDRLKDSDG-HSDKSRHHSSRDRDYRESSH-SSK 413
Cdd:TIGR01642   1 RDEEPDREREKSRGRDRDRS-----SERPRRRSRDRSRFRDrHRRSRERSYREDSrPRDRRRYDSRSPRSLRYSSVrRSR 75


                  ....
gi 2065799468 414 DRRR 417
Cdd:TIGR01642  76 DRPR 79
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 326-417 1.89e-09

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: 59.52  E-value: 1.89e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 326 DSRNGKSKVGERERESGREKERSRERDRTRSHRGRDsdkESDRERDKLKDRSHHRSRDRLKDSDGHSDKSRHHSsrDRDY 405
Cdd:TIGR01642   8 EREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRE---RSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRP--RRRS 82

                          90
                  ....*....|..
gi 2065799468 406 RESSHSSKDRRR 417
Cdd:TIGR01642  83 RSVRSIEQHRRR 94
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 40-143 2.65e-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: 53.75  E-value: 2.65e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468   40 DLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEEnpkkarqviivfhrmecrrENLPLEH 119
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEE-------------------TPPWTKE 61

                           90       100
                   ....*....|....*....|....
gi 2065799468  120 LDMYAKKFSElkVELSRTERHILK 143
Cdd:smart00385  62 LVHYTGYFTE--EEILRMERLLLE 83
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 34-108 3.63e-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: 3.63e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065799468  34 LRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIIVFHRM 108
Cdd:cd20547     1 LRLAAFQFISQLCKKLKFPRRTLGTAMLLYQRFHLFNPFTDSSNYEVALACLFLASKIEDTQKKSKDILAASYNL 75
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 326-416 8.98e-09

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: 57.24  E-value: 8.98e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 326 DSRNGKSKVGERERESGREKERSRERDRTRShrgRDSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDKSRHHSSRDRDY 405
Cdd:TIGR01622   4 DRERERLRDSSSAGDRDRRRDKGRERSRDRS---RDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYRPREKRRRRG 80

                          90
                  ....*....|.
gi 2065799468 406 RESSHSSKDRR 416
Cdd:TIGR01622  81 DSYRRRRDDRR 91
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 153-238 1.04e-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: 52.28  E-value: 1.04e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 153 HPHKFISNYLATLE-TPPELRQEAWNLANDSLR-TTLCVRFRSEVVACGVVYAAAR--RFQVPLP-ENPPWWKAFdaDKS 227
Cdd:cd20539     1 HPHTHVLKICNLVKaGSKDLAQTAYFLATNSLHlTTFCLQYKPTVIACVCIHLACKwsNWEIPRSsEGKDWYEYV--DPS 78

                          90
                  ....*....|.
gi 2065799468 228 SIDEVCRVLAH 238
Cdd:cd20539    79 LTLEELDELTS 89
CYCLIN_CCNH_rpt1 cd20524
first cyclin box found in cyclin-H (CCNH) and similar proteins; CCNH, also called ...
 49-95 1.47e-08

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


Pssm-ID: 410228  Cd Length: 150  Bit Score: 53.37  E-value: 1.47e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2065799468  49 LKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENP 95
Cdd:cd20524    69 FKLPDSVLATALTYFKRFYLKNSVMEYHPKEIMLTCLYLACKVEEFN 115
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 8-93 2.63e-08

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: 52.13  E-value: 2.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468   8 NFYLTDEqlKASPSRKDGIDETTEISL--RIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCV 85
Cdd:pfam00134   4 QYLRELE--LKYLPKPDYMDQQPDINPkmRAILIDWLVEVHEKFKLLPETLYLAVNYLDRFLSKKSVPKNKLQLVGVTCL 81


                  ....*...
gi 2065799468  86 WLASKLEE 93
Cdd:pfam00134  82 FIAAKYEE 89
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 326-416 3.47e-08

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: 55.28  E-value: 3.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 326 DSRnGKSKVGERERESGREKERSRERDRTR---------SHRGRDSDKESDRERDKLKDRSHHRSRDRL-KDSDGHSDKS 395
Cdd:TIGR01642  11 KSR-GRDRDRSSERPRRRSRDRSRFRDRHRrsrersyreDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPrRRSRSVRSIE 89

                          90       100
                  ....*....|....*....|..
gi 2065799468 396 RH-HSSRDRDYRESSHSSKDRR 416
Cdd:TIGR01642  90 QHrRRLRDRSPSNQWRKDDKKR 111
CYCLIN_AtCycC_rpt1 cd20571
first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins; ...
 34-108 7.50e-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: 50.24  E-value: 7.50e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065799468  34 LRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIIVFHRM 108
Cdd:cd20571     6 IKIHMSNYIKKLAQHIKVRQRVVATAITYFRRVYTRKSFTEYDPRLVAPTCLYLASKAEESTVQAKLLVFYMKRL 80
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 156-241 1.69e-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: 1.69e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  156 KFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPeNPPWWKAfdADKSSIDEVCRV 235
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPW-TKELVHY--TGYFTEEEILRM 77


                   ....*.
gi 2065799468  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 2.13e-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: 2.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 153 HPHKFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFQVPLPEnppWWKAFDADKSSIDEV 232
Cdd:cd20514     1 HPYRPLTQYVQDAGLDDELLPLAWRIVNDSYRTDVCLLYPPYLIALACLHMACVLLQKDARQ---WFAELNVDMDKILEI 77

                          90
                  ....*....|..
gi 2065799468 233 CRVLAHLYSLPK 244
Cdd:cd20514    78 TREILSLYELWK 89
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 325-417 8.62e-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: 51.07  E-value: 8.62e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 325 GDSRNgKSKVGERERESGREKERSRERDRTRShRGRDSDKESDRERDKLKDRsHHRSRDRLKDSDGHS-DKSRHHSSRDR 403
Cdd:TIGR01622   8 ERLRD-SSSAGDRDRRRDKGRERSRDRSRDRE-RSRSRRRDRHRDRDYYRGR-ERRSRSRRPNRRYRPrEKRRRRGDSYR 84

                          90
                  ....*....|....
gi 2065799468 404 DYRESSHSSKDRRR 417
Cdd:TIGR01622  85 RRRDDRRSRREKPR 98
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 153-235 2.11e-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: 2.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 153 HPHKFISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGVVYAAARRFqvplpENPPWWKAF-DADKSSIDE 231
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLE-----ELPRTLKEIaKVSGVSEKE 75


                  ....
gi 2065799468 232 VCRV 235
Cdd:cd00043    76 LRKA 79
CYCLIN_AcCycH_rpt1 cd20585
first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins; CycH ...
 26-121 8.24e-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: 45.97  E-value: 8.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  26 IDEttEISLRIYGCDLIQEGGILLKLPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQV---I 102
Cdd:cd20585    71 ADE--ELLMLKYYEQKIQEVCRALRLPNKIQATALLYFKRFYLQWSVMEHDPKRIMLTCIYLACKVEEYHVSAEELgkgI 148

                          90
                  ....*....|....*....
gi 2065799468 103 IVFHRMECRRENLPLEHLD 121
Cdd:cd20585   149 QQDHQLILKNELALLQGLN 167
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 336-417 8.57e-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: 47.99  E-value: 8.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 336 ERERESGREKERSRERDRTRSH-RGRDSDKE----SDRERDKLKDRSHHRSRDRLKDSDghsdksRHHSSRDRDYRESSH 410
Cdd:TIGR01622  20 DRRRDKGRERSRDRSRDRERSRsRRRDRHRDrdyyRGRERRSRSRRPNRRYRPREKRRR------RGDSYRRRRDDRRSR 93


                  ....*..
gi 2065799468 411 SSKDRRR 417
Cdd:TIGR01622  94 REKPRAR 100
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 253-414 3.27e-05

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 46.44  E-value: 3.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 253 DGKPFTFSSRSGNSQAQSATKDvlPGVGDAVDTKCAPGSANNDSKDGMVISPHEKGTDSKK-SDTESNSqpivgDSRNGK 331
Cdd:NF033609  568 DSGSDSSNSDSGSDSGSDSTSD--SGSDSASDSDSASDSDSASDSDSASDSDSASDSDSASdSDSASDS-----DSASDS 640

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 332 SKVGERERESGREKERSRERDrtrSHRGRDSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDK-SRHHSSRDRDYRESSH 410
Cdd:NF033609  641 DSDSDSDSDSDSDSDSDSDSD---SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSdSDSDSDSDSDSDSDSD 717


                  ....
gi 2065799468 411 SSKD 414
Cdd:NF033609  718 SDSD 721
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 308-417 6.39e-05

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 45.28  E-value: 6.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 308 GTDSKKSDTESNSQPIVGDSRNGKSKVGERERESGREKERSRERDRTRSHRGRDSDKESDRERDKLKDRSHHRSRDRL-K 386
Cdd:PRK12678  159 DAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRdA 238

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2065799468 387 DSDGHSDKSRHHSSRDRDYRESSHSSKDRRR 417
Cdd:PRK12678  239 RGDDNREDRGDRDGDDGEGRGGRRGRRFRDR 269
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 310-417 7.67e-05

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 44.89  E-value: 7.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 310 DSKKSDTESNSQPIVGDSRNGKSKVGERERESGREKERSRERDRTRSHRGRDSDKESDRERDKLKDRSHHRSRDRLKDSD 389
Cdd:PRK12678  140 GAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERG 219

                          90       100
                  ....*....|....*....|....*...
gi 2065799468 390 GHSDKSRHHSSRDRDYRESSHSSKDRRR 417
Cdd:PRK12678  220 RRDGGDRRGRRRRRDRRDARGDDNREDR 247
ccl1 TIGR00569
cyclin ccl1; All proteins in this family for which functions are known are cyclins that are ...
 51-213 8.69e-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: 44.05  E-value: 8.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  51 LPQAVMATGQVLFHRFYCKKSLAKFDVKIVAASCVWLASKLEENPKKARQVIivfhrmecrrENL---PLEHLDmyakkf 127
Cdd:TIGR00569  74 MPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFV----------GNLketPLKALE------ 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 128 SELKVELSrterhILKEMGFVCHVEHPHK----F---ISNYLATLETPPELRQEAWNLANDSLRTTLCVRFRSEVVACGV 200
Cdd:TIGR00569 138 QVLEYELL-----LIQQLNFHLIVHNPYRplegFlidIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAA 212

                         170
                  ....*....|...
gi 2065799468 201 VYAAARRFQVPLP 213
Cdd:TIGR00569 213 ILHTASRAGLNME 225
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 306-417 9.53e-05

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 44.51  E-value: 9.53e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 306 EKGTDSKKSDTESNSQPIVGDSRNGKSKVGERERESGREKERSRERDRTRSHRGRDSDKESDRERDKLKDRSHHRSRDRL 385
Cdd:PRK12678  141 AARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGR 220

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2065799468 386 KDSDGHSDKSRHHSSRDRDYRESSHSSKDRRR 417
Cdd:PRK12678  221 RDGGDRRGRRRRRDRRDARGDDNREDRGDRDG 252
PRP38_assoc pfam12871
Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region ...
 335-419 1.07e-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: 40.91  E-value: 1.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 335 GERERESGREKERSRERDRTRSHRGRDSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDKSRHHSSRDRDYRESSHSSKD 414
Cdd:pfam12871  13 EEEEDEEEDEEASDESERASLSRKRRSRSRRRSSTRDRSRSRSRSRSRDRRSRGTRDRRRDRDRDRYRSLRSRSRDRSRD 92


                  ....*
gi 2065799468 415 RRRHH 419
Cdd:pfam12871  93 RDRDR 97
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 304-417 1.27e-04

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 44.12  E-value: 1.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 304 PHEKGTDSKKSDTESNSQPIVGDSRNGKSKVGERERESGREKERSRERDRTRSHRGRDSDKESDRERDKLKDRSHHRSRD 383
Cdd:PRK12678  145 AGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGG 224

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2065799468 384 RLKDSDGHSDKSRHHSSRDRDYRESSHSSKDRRR 417
Cdd:PRK12678  225 DRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGR 258
NRP1_C pfam20427
Nuclear speckle splicing regulatory protein 1, RS-like domain; This domain found at the ...
 326-419 1.94e-04

Nuclear speckle splicing regulatory protein 1, RS-like domain; This domain found at the C-terminal of Nuclear speckle splicing regulatory protein 1 (NRP1, also known as Nuclear speckle-related protein 70 and Coiled-coil domain-containing protein 55). This is the RS-like domain, that resembles the arginine/serine-rich (RS) domain in other SR proteins, interacts with two SR proteins and with target mRNA, being essential for NRP1 activity. NRP1 is a RNA-binding protein that mediates pre-mRNA alternative splicing regulation.


Pssm-ID: 466576 [Multi-domain]  Cd Length: 174  Bit Score: 41.75  E-value: 1.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 326 DSRNGKSKVGERERESGREKERSRE--RDRTRSHRGRDSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDK-----SRHH 398
Cdd:pfam20427  71 DKLRGRDQRERNDREWKREKYSSREqeRDRQRNDHDRHSEKGEKEEKSKEKEEHMKGRKERYENSDKYRDRekqevSVQS 150

                          90       100
                  ....*....|....*....|.
gi 2065799468 399 SSRDRDYRESSHSSKDRRRHH 419
Cdd:pfam20427 151 SERNRDRKESSPNSRAKDEFL 171
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 349-418 3.00e-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: 42.98  E-value: 3.00e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 349 RERDRTRshrGRDSDKESDRERDKLKDRSHHRSRDRlkdsdghsdksrhhsSRDRDyresSHSSKDRRRH 418
Cdd:TIGR01622   1 RYRDRER---ERLRDSSSAGDRDRRRDKGRERSRDR---------------SRDRE----RSRSRRRDRH 48
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 367-418 6.67e-04

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: 41.80  E-value: 6.67e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 367 DRERDKLKDRShhRSRDRLKDSDGHSDKS--------RHHSSRDRDYRESSHSSKDRRRH 418
Cdd:TIGR01642   2 DEEPDREREKS--RGRDRDRSSERPRRRSrdrsrfrdRHRRSRERSYREDSRPRDRRRYD 59
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 301-418 8.56e-04

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 41.43  E-value: 8.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 301 VISPHEKGTDSKKSDTESNSQPIVGDS--RNGKSKVGERERESGREKERSRERDRTRSHRGRDSDKESDRERDKLKDRSH 378
Cdd:PRK12678  110 AAAAAAAEAASAPEAAQARERRERGEAarRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGE 189

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2065799468 379 HRSRDRLKDSDGHSDKSRHHSSRDRDYRESSHSSKDRRRH 418
Cdd:PRK12678  190 RGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGR 229
PRP38_assoc pfam12871
Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region ...
 335-408 1.11e-03

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: 38.22  E-value: 1.11e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2065799468 335 GERERESGREKERSRERDRTRShRGRDSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDKSRHHSSRDRDYRES 408
Cdd:pfam12871  26 DESERASLSRKRRSRSRRRSST-RDRSRSRSRSRSRDRRSRGTRDRRRDRDRDRYRSLRSRSRDRSRDRDRDRR 98
EIF4E-T pfam10477
Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E; EIF4E-T is the transporter ...
 331-418 1.23e-03

Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E; EIF4E-T is the transporter protein for shuttling the mRNA cap-binding protein EIF4E protein, targeting it for nuclear import. EIF4E-T contains several key binding domains including two functional leucine-rich NESs (nuclear export signals) between residues 438-447 and 613-638 in the human protein. The other two binding domains are an EIF4E-binding site, between residues 27-42 in Q9EST3, and a bipartite NLS (nuclear localization signals) between 194-211, and these lie in family EIF4E-T_N. EIF4E is the eukaryotic translation initiation factor 4E that is the rate-limiting factor for cap-dependent translation initiation.


Pssm-ID: 371079  Cd Length: 646  Bit Score: 41.15  E-value: 1.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 331 KSKVGEREReSGREKERSRERDRTRSHRGRDSDKESDRERD-KLKDRSHHRSRDRLKDSDGHSDKSRHHSSRDRDYRESS 409
Cdd:pfam10477 159 RSPNGSGSS-RQDEEDQRNNQQNLRTFSGRHNERGRDGDRRsKRNRRTFGRFQYDGKKPVDRGRRISNKDKFSFQDRGKR 237


                  ....*....
gi 2065799468 410 HSskDRRRH 418
Cdd:pfam10477 238 YN--SRRRN 244
PRP38_assoc pfam12871
Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region ...
 308-389 1.25e-03

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: 37.83  E-value: 1.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 308 GTDSKKSDTESNSQPIVGDSRNGKSKVGERERESGREKERSRERDRTRSHRGR---DSDKESDRERDK-LKDRSHHRSRD 383
Cdd:pfam12871  13 EEEEDEEEDEEASDESERASLSRKRRSRSRRRSSTRDRSRSRSRSRSRDRRSRgtrDRRRDRDRDRYRsLRSRSRDRSRD 92


                  ....*.
gi 2065799468 384 RLKDSD 389
Cdd:pfam12871  93 RDRDRR 98
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
 152-223 1.87e-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: 1.87e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2065799468 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 1.99e-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: 1.99e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2065799468 152 EHPHKFISNYLATLETPPELRQEAWNLANDSLR-TTLCVRFRSEVVACGVVYAAAR--RFQVPLP-ENPPWWKAFDA 224
Cdd:cd20597     1 DHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHlTTFSLQYTPPVVACVCIHLACKwsNWEIPVStDGKHWWEYVDA 77
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 260-419 2.18e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 40.27  E-value: 2.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 260 SSRSGNSQAQSATKDVLPGVGDAVDTKCAPGSANNDSKDGMVISPHEKGTDSKKSDTESNSQPIVGDSRNGKskvGERER 339
Cdd:PRK12678   89 QAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADA---AERTE 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 340 ESGREKERsRERDRTRSHRGRDSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDKSRHHSSRDRDYRESSHSSKDRRRHH 419
Cdd:PRK12678  166 EEERDERR-RRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNR 244
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 326-387 4.03e-03

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: 39.52  E-value: 4.03e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2065799468 326 DSRNGKSKVGERERE----SGREKERSRERDRTRSHRGRDSDKESDRERDKLKDRSHHRSRDRLKD 387
Cdd:TIGR01622  36 DRERSRSRRRDRHRDrdyyRGRERRSRSRRPNRRYRPREKRRRRGDSYRRRRDDRRSRREKPRARD 101
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 325-416 6.13e-03

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: 38.75  E-value: 6.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468 325 GDSRNGKSKVGERERESGREKERSRERDRTRSHRgrdSDKESDRERDKLKDRSHHRSRDRLKDSDGHSDKSRHhsSRDRD 404
Cdd:TIGR01622  29 RSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSR---SRRPNRRYRPREKRRRRGDSYRRRRDDRRSRREKPR--ARDGT 103

                          90
                  ....*....|..
gi 2065799468 405 YRESSHSSKDRR 416
Cdd:TIGR01622 104 PEPLTEDERDRR 115
CYCLIN_ScCLN_like cd20559
cyclin box found in Saccharomyces cerevisiae G1/S-specific cyclins (ScCLNs) and similar ...
 60-143 8.07e-03

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


Pssm-ID: 410262 [Multi-domain]  Cd Length: 95  Bit Score: 35.44  E-value: 8.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065799468  60 QVLFH------RFYCKKSLAKFDVKIVAASCVWLASKLEENpkKARQVIIVFHRMECRRENlplehldmYAKKFSELkve 133
Cdd:cd20559    18 QTFFLsvnlidRYCSKRIVLKKHYQLVGCTCLWIASKFWES--KARVPLLSELSKMCCNSY--------GEELFIQM--- 84

                          90
                  ....*....|
gi 2065799468 134 lsrtERHILK 143
Cdd:cd20559    85 ----EMHILN 90
 
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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