Citrus Sinensis ID: 030687

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170---
MAENLSDFTASNLTCTESTNTCFDGFDCNATNGDDDDQNSQNHSQDSNFINKRSIFPMGFFPFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVELQV
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHccccccccccccc
cccccHHHHHHHHHccccccHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccHHHHHccccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHccccccHHHccc
maenlsdftasnltctestntcfdgfdcnatngddddqnsqnhsqdsnfinkrsifpmgffpfQTVSEELLREMAVKegellpkhdylnrlrsgdldsRVRREALDWILKAHAhyrfgpmsfclSMNYLDRflsvyelpkgkdwtVQLLTVACLSLAAKMEESEVPLLVELQV
maenlsdftasnltcTESTNTCFDGFDCNATNGDDDDQNSQNHSQDSNFINKRSIFPMGFFPFQTVSEELLREMAVKEgellpkhdylnrlrsgdldsrVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAkmeesevpllvelqv
MAENLSDFTASNLTCTESTNTCFDGFDCNATNGddddqnsqnhsqdsnFINKRSIFPMGFFPFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVELQV
************LTCTESTNTCFDGFDCN*******************FINKRSIFPMGFFPFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKM*************
******D**************C****************************NKRSIFPMGFFPFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVELQV
********TASNLTCTESTNTCFDGFDCNATNGDD*********QDSNFINKRSIFPMGFFPFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVELQV
****LSDFTASNLTCTESTNTCFDGFDCNA*************************FPMGFFPFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVELQV
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MAENLSDFTASNLTCTESTNTCFDGFDCNATNGDDDDQNSQNHSQDSNFINKRSIFPMGFFPFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVELQV
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query173 2.2.26 [Sep-21-2011]
Q0WQN9 298 Cyclin-D4-2 OS=Arabidopsi yes no 0.728 0.422 0.612 8e-38
P42752 361 Cyclin-D2-1 OS=Arabidopsi no no 0.786 0.376 0.576 8e-37
Q8LGA1 308 Cyclin-D4-1 OS=Arabidopsi no no 0.682 0.383 0.628 2e-36
Q6YXH8 356 Cyclin-D4-1 OS=Oryza sati yes no 0.641 0.311 0.556 4e-32
Q4KYM5 383 Cyclin-D4-2 OS=Oryza sati no no 0.647 0.292 0.508 7e-27
Q8LHA8 356 Cyclin-D2-2 OS=Oryza sati no no 0.641 0.311 0.486 6e-25
Q0J233 308 Cyclin-D2-1 OS=Oryza sati no no 0.595 0.334 0.504 8e-24
P42751 339 Cyclin-D1-1 OS=Arabidopsi no no 0.554 0.283 0.5 3e-22
Q69QB8 342 Cyclin-D3-1 OS=Oryza sati no no 0.884 0.447 0.385 8e-21
Q10K98 405 Putative cyclin-D2-3 OS=O no no 0.520 0.222 0.5 1e-18
>sp|Q0WQN9|CCD42_ARATH Cyclin-D4-2 OS=Arabidopsis thaliana GN=CYCD4-2 PE=1 SV=2 Back     alignment and function desciption
 Score =  155 bits (393), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 79/129 (61%), Positives = 98/129 (75%), Gaps = 3/129 (2%)

Query: 45  QDSNFINKRSIFPMGFFPFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREA 104
           + SN ++ RSIF MGF P +  SEE++REM  KE +  P+ DYL RLR+GDLD  VR +A
Sbjct: 16  EKSNSVDTRSIFQMGF-PLE--SEEIVREMIEKERQHSPRDDYLKRLRNGDLDFNVRIQA 72

Query: 105 LDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESE 164
           L WI KA    +FGP+  CL+MNYLDRFLSV++LP GK WTVQLL VACLSLAAK+EE+ 
Sbjct: 73  LGWIWKACEELQFGPLCICLAMNYLDRFLSVHDLPSGKAWTVQLLAVACLSLAAKIEETN 132

Query: 165 VPLLVELQV 173
           VP L++LQV
Sbjct: 133 VPELMQLQV 141
May promote cell division.
Arabidopsis thaliana (taxid: 3702)
>sp|P42752|CCD21_ARATH Cyclin-D2-1 OS=Arabidopsis thaliana GN=CYCD2-1 PE=1 SV=3 Back     alignment and function description
>sp|Q8LGA1|CCD41_ARATH Cyclin-D4-1 OS=Arabidopsis thaliana GN=CYCD4-1 PE=1 SV=2 Back     alignment and function description
>sp|Q6YXH8|CCD41_ORYSJ Cyclin-D4-1 OS=Oryza sativa subsp. japonica GN=CYCD4-1 PE=2 SV=2 Back     alignment and function description
>sp|Q4KYM5|CCD42_ORYSJ Cyclin-D4-2 OS=Oryza sativa subsp. japonica GN=CYCD4-2 PE=2 SV=2 Back     alignment and function description
>sp|Q8LHA8|CCD22_ORYSJ Cyclin-D2-2 OS=Oryza sativa subsp. japonica GN=CYCD2-2 PE=2 SV=1 Back     alignment and function description
>sp|Q0J233|CCD21_ORYSJ Cyclin-D2-1 OS=Oryza sativa subsp. japonica GN=CYCD2-1 PE=3 SV=2 Back     alignment and function description
>sp|P42751|CCD11_ARATH Cyclin-D1-1 OS=Arabidopsis thaliana GN=CYCD1-1 PE=1 SV=3 Back     alignment and function description
>sp|Q69QB8|CCD31_ORYSJ Cyclin-D3-1 OS=Oryza sativa subsp. japonica GN=CYCD3-1 PE=2 SV=2 Back     alignment and function description
>sp|Q10K98|CCD23_ORYSJ Putative cyclin-D2-3 OS=Oryza sativa subsp. japonica GN=CYCD2-3 PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query173
4160298 354 cyclin D2.1 protein [Nicotiana tabacum] 0.959 0.468 0.593 5e-48
225466890 352 PREDICTED: cyclin-D4-1-like [Vitis vinif 0.942 0.463 0.556 5e-44
297735936 353 unnamed protein product [Vitis vinifera] 0.936 0.458 0.554 2e-43
357485601 346 Cyclin D2 [Medicago truncatula] gi|35551 0.947 0.473 0.531 3e-41
255579724 366 cyclin d, putative [Ricinus communis] gi 0.947 0.448 0.550 8e-41
449451605 366 PREDICTED: cyclin-D2-1-like [Cucumis sat 0.890 0.420 0.543 4e-40
356566036 358 PREDICTED: cyclin-D4-1-like [Glycine max 0.936 0.452 0.538 6e-40
356523988 351 PREDICTED: cyclin-D3-1-like [Glycine max 0.936 0.461 0.523 3e-39
356497718 361 PREDICTED: cyclin-D4-1-like [Glycine max 0.982 0.470 0.508 3e-39
255631686182 unknown [Glycine max] 0.942 0.895 0.516 3e-39
>gi|4160298|emb|CAA09852.1| cyclin D2.1 protein [Nicotiana tabacum] Back     alignment and taxonomy information
 Score =  195 bits (496), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 102/172 (59%), Positives = 121/172 (70%), Gaps = 6/172 (3%)

Query: 2   AENLSDFTASNLTCTESTNTCFDGFDCNATNGDDDDQNSQNHSQDSNFINKRSIFPMGFF 61
           A+N+ DF ASNL CTE+ + CFD  D    +     QN +  S+D +F N     P+   
Sbjct: 3   ADNIYDFVASNLLCTETKSLCFDDVDSLTIS----QQNIETKSKDLSFNNGIRSEPLIDL 58

Query: 62  PFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMS 121
           P  ++SEE L  M  +E E LPK DY+ RLRSGDLD  VR+EALDWILKAH HY FG +S
Sbjct: 59  P--SLSEECLSFMVQREMEFLPKDDYVERLRSGDLDLSVRKEALDWILKAHMHYGFGELS 116

Query: 122 FCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVELQV 173
           FCLS+NYLDRFLS+YELP+ K WTVQLL VACLSLAAKMEE  VPL V+LQV
Sbjct: 117 FCLSINYLDRFLSLYELPRSKTWTVQLLAVACLSLAAKMEEINVPLTVDLQV 168

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225466890|ref|XP_002268586.1| PREDICTED: cyclin-D4-1-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|297735936|emb|CBI18712.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|357485601|ref|XP_003613088.1| Cyclin D2 [Medicago truncatula] gi|355514423|gb|AES96046.1| Cyclin D2 [Medicago truncatula] Back     alignment and taxonomy information
>gi|255579724|ref|XP_002530701.1| cyclin d, putative [Ricinus communis] gi|223529757|gb|EEF31696.1| cyclin d, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|449451605|ref|XP_004143552.1| PREDICTED: cyclin-D2-1-like [Cucumis sativus] gi|449527834|ref|XP_004170914.1| PREDICTED: cyclin-D2-1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|356566036|ref|XP_003551241.1| PREDICTED: cyclin-D4-1-like [Glycine max] Back     alignment and taxonomy information
>gi|356523988|ref|XP_003530615.1| PREDICTED: cyclin-D3-1-like [Glycine max] Back     alignment and taxonomy information
>gi|356497718|ref|XP_003517706.1| PREDICTED: cyclin-D4-1-like [Glycine max] Back     alignment and taxonomy information
>gi|255631686|gb|ACU16210.1| unknown [Glycine max] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query173
TAIR|locus:2142504 298 CYCD4;2 "AT5G10440" [Arabidops 0.699 0.406 0.620 6.5e-35
TAIR|locus:2020663 339 CYCD1;1 "CYCLIN D1;1" [Arabido 0.554 0.283 0.5 2.4e-21
TAIR|locus:2124331 376 CYCD3;1 "CYCLIN D3;1" [Arabido 0.421 0.194 0.520 4e-17
TAIR|locus:2157172 367 CYCD3;2 "AT5G67260" [Arabidops 0.699 0.329 0.404 2.2e-16
TAIR|locus:2083128 361 CYCD3;3 "AT3G50070" [Arabidops 0.421 0.202 0.479 4.7e-14
UNIPROTKB|Q10QA2 345 CYCD5-3 "Cyclin-D5-3" [Oryza s 0.421 0.211 0.438 6.7e-11
TAIR|locus:2205871 460 CYCA1;1 "Cyclin A1;1" [Arabido 0.589 0.221 0.330 1.6e-10
SGD|S000003341 380 CLB6 "B-type cyclin involved i 0.589 0.268 0.333 8.2e-10
SGD|S000006324 435 CLB5 "B-type cyclin involved i 0.583 0.232 0.342 4.8e-09
TAIR|locus:2031407 442 CYCA1;2 "CYCLIN A1;2" [Arabido 0.543 0.212 0.326 4.9e-09
TAIR|locus:2142504 CYCD4;2 "AT5G10440" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 378 (138.1 bits), Expect = 6.5e-35, P = 6.5e-35
 Identities = 77/124 (62%), Positives = 95/124 (76%)

Query:    50 INKRSIFPMGFFPFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWIL 109
             ++ RSIF MGF P +  SEE++REM  KE +  P+ DYL RLR+GDLD  VR +AL WI 
Sbjct:    21 VDTRSIFQMGF-PLE--SEEIVREMIEKERQHSPRDDYLKRLRNGDLDFNVRIQALGWIW 77

Query:   110 KAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLV 169
             KA    +FGP+  CL+MNYLDRFLSV++LP GK WTVQLL VACLSLAAK+EE+ VP L+
Sbjct:    78 KACEELQFGPLCICLAMNYLDRFLSVHDLPSGKAWTVQLLAVACLSLAAKIEETNVPELM 137

Query:   170 ELQV 173
             +LQV
Sbjct:   138 QLQV 141
GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=ISS
GO:0005634 "nucleus" evidence=ISM;IEA;IDA
GO:0051726 "regulation of cell cycle" evidence=ISS
GO:0010440 "stomatal lineage progression" evidence=RCA;IMP
GO:0005737 "cytoplasm" evidence=IDA
GO:0005515 "protein binding" evidence=IPI
GO:0000278 "mitotic cell cycle" evidence=RCA
GO:0042023 "DNA endoreduplication" evidence=RCA
GO:0045736 "negative regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=RCA
TAIR|locus:2020663 CYCD1;1 "CYCLIN D1;1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2124331 CYCD3;1 "CYCLIN D3;1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2157172 CYCD3;2 "AT5G67260" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2083128 CYCD3;3 "AT3G50070" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q10QA2 CYCD5-3 "Cyclin-D5-3" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TAIR|locus:2205871 CYCA1;1 "Cyclin A1;1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
SGD|S000003341 CLB6 "B-type cyclin involved in DNA replication during S phase" [Saccharomyces cerevisiae (taxid:4932)] Back     alignment and assigned GO terms
SGD|S000006324 CLB5 "B-type cyclin involved in DNA replication during S phase" [Saccharomyces cerevisiae (taxid:4932)] Back     alignment and assigned GO terms
TAIR|locus:2031407 CYCA1;2 "CYCLIN A1;2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00011072001
SubName- Full=Chromosome undetermined scaffold_1289, whole genome shotgun sequence (Chromosome undetermined scaffold_2101, whole genome shotgun sequence); (352 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query173
pfam00134127 pfam00134, Cyclin_N, Cyclin, N-terminal domain 1e-26
cd0004388 cd00043, CYCLIN, Cyclin box fold 3e-13
smart0038583 smart00385, CYCLIN, domain present in cyclins, TFI 7e-10
COG5024 440 COG5024, COG5024, Cyclin [Cell division and chromo 1e-07
>gnl|CDD|215740 pfam00134, Cyclin_N, Cyclin, N-terminal domain Back     alignment and domain information 
 Score = 97.2 bits (243), Expect = 1e-26
 Identities = 32/105 (30%), Positives = 55/105 (52%), Gaps = 5/105 (4%)

Query: 69  ELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNY 128
           ++   +   E E  P  DYL++    D++ ++R   +DW+++ H  ++  P +  L++NY
Sbjct: 1   DIYAYLRELEEEDRPPPDYLDQQ--PDINPKMRAILIDWLVEVHEEFKLLPETLYLAVNY 58

Query: 129 LDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVELQV 173
           LDRFLS           +QL+ V CL +AAK EE   P + +   
Sbjct: 59  LDRFLSKQ---PVPRTKLQLVGVTCLLIAAKYEEIYPPSVEDFVY 100

Cyclins regulate cyclin dependent kinases (CDKs). Human cyclin-O 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. Length = 127
>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold Back     alignment and domain information
>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>gnl|CDD|227357 COG5024, COG5024, Cyclin [Cell division and chromosome partitioning] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 173
KOG0656 335 consensus G1/S-specific cyclin D [Cell cycle contr 99.98
KOG0655 408 consensus G1/S-specific cyclin E [Cell cycle contr 99.91
KOG0653 391 consensus Cyclin B and related kinase-activating p 99.88
COG5024 440 Cyclin [Cell division and chromosome partitioning] 99.86
PF00134127 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR 99.84
KOG0654 359 consensus G2/Mitotic-specific cyclin A [Cell cycle 99.55
cd0004388 CYCLIN Cyclin box fold. Protein binding domain fun 99.37
smart0038583 CYCLIN domain present in cyclins, TFIIB and Retino 99.22
TIGR00569 305 ccl1 cyclin ccl1. University). 98.8
KOG0834 323 consensus CDK9 kinase-activating protein cyclin T 98.31
KOG0794 264 consensus CDK8 kinase-activating protein cyclin C 97.95
COG5333 297 CCL1 Cdk activating kinase (CAK)/RNA polymerase II 97.87
KOG0835 367 consensus Cyclin L [General function prediction on 97.44
PF08613149 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu 96.54
PF0038271 TFIIB: Transcription factor TFIIB repeat; InterPro 95.17
KOG4164497 consensus Cyclin ik3-1/CABLES [Cell cycle control, 94.56
PRK00423 310 tfb transcription initiation factor IIB; Reviewed 94.42
KOG2496 325 consensus Cdk activating kinase (CAK)/RNA polymera 93.52
PRK00423310 tfb transcription initiation factor IIB; Reviewed 84.41
KOG0834 323 consensus CDK9 kinase-activating protein cyclin T 84.09
KOG1674218 consensus Cyclin [General function prediction only 82.54
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information 
Probab=99.98  E-value=2e-32  Score=236.13  Aligned_cols=111  Identities=51%  Similarity=0.825  Sum_probs=104.6

Q ss_pred             CCCCCHHHHHHHHHHHHhccCCCccchhhccCCCCCHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCC
Q 030687           62 PFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKG  141 (173)
Q Consensus        62 pf~~y~~eil~~L~~~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~  141 (173)
                      +|..+++|++..|+++|+++.|..+|...++ ..+++.+|.++++||++||++++++++|++||||||||||+.+++++.
T Consensus        40 ~~~~~~e~~i~~ll~kEe~~~p~~~~~~~~~-~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~  118 (335)
T KOG0656|consen   40 GFLLWDERVLANLLEKEEQHNPSLDYFLCVQ-KLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKD  118 (335)
T ss_pred             ccccccHHHHHHHHHHHHHhCCCCchhhhcc-cccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCC
Confidence            3567999999999999999999999776654 468889999999999999999999999999999999999999999999


Q ss_pred             CCccchhhHHHHHHhhhhcccccCCCCCCCCC
Q 030687          142 KDWTVQLLTVACLSLAAKMEESEVPLLVELQV  173 (173)
Q Consensus       142 ~~w~lQLlgvaCL~LAaK~EE~~~P~~~dlqv  173 (173)
                      ++|++||||+|||+|||||||+.+|.+.|+||
T Consensus       119 k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v  150 (335)
T KOG0656|consen  119 KPWMLQLLAVACLSLASKMEETDVPLLADLQV  150 (335)
T ss_pred             chHHHHHHHHHHHHHHHhhcCcCCchhhhhhh
Confidence            99999999999999999999999999999997

>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>COG5024 Cyclin [Cell division and chromosome partitioning] Back     alignment and domain information
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) Back     alignment and domain information
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>cd00043 CYCLIN Cyclin box fold Back     alignment and domain information
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>TIGR00569 ccl1 cyclin ccl1 Back     alignment and domain information
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription] Back     alignment and domain information
>COG5333 CCL1 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] Back     alignment and domain information
>KOG0835 consensus Cyclin L [General function prediction only] Back     alignment and domain information
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) Back     alignment and domain information
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) Back     alignment and domain information
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair] Back     alignment and domain information
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>KOG1674 consensus Cyclin [General function prediction only] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query173
3qhr_B 261 Structure Of A Pcdk2CYCLINA TRANSITION-State Mimic 1e-07
4ii5_B 258 Structure Of Pcdk2/cyclina Bound To Adp And 1 Magne 1e-07
4i3z_B 257 Structure Of Pcdk2CYCLINA BOUND TO ADP AND 2 MAGNES 2e-07
4bcq_B 262 Structure Of Cdk2 In Complex With Cyclin A And A 2- 3e-07
1vyw_B 265 Structure Of Cdk2CYCLIN A WITH PNU-292137 Length = 3e-07
3f5x_B 256 Cdk-2-Cyclin Complex With Indazole Inhibitor 9 Boun 3e-07
3dog_B 264 Structure Of Thr 160 Phosphorylated Cdk2CYCLIN A IN 3e-07
2g9x_B 262 Structure Of Thr 160 Phosphorylated Cdk2CYCLIN A IN 3e-07
1vin_A 268 Bovine Cyclin A3 Length = 268 3e-07
1fin_B 260 Cyclin A-Cyclin-Dependent Kinase 2 Complex Length = 3e-07
2x1n_B 261 Truncation And Optimisation Of Peptide Inhibitors O 3e-07
3ddq_B 269 Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN 3e-07
3ddp_B 268 Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN 3e-07
3bht_B 262 Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN 3e-07
4bcq_D 262 Structure Of Cdk2 In Complex With Cyclin A And A 2- 3e-07
4bco_B 262 Structure Of Cdk2 In Complex With Cyclin A And A 2- 3e-07
1e9h_B 261 Thr 160 Phosphorylated Cdk2-Human Cyclin A3 Complex 3e-07
1ogu_B 260 Structure Of Human Thr160-phospho Cdk2/cyclin A Com 3e-07
1qmz_B 259 Phosphorylated Cdk2-Cyclyin A-Substrate Peptide Com 3e-07
1jst_B 258 Phosphorylated Cyclin-Dependent Kinase-2 Bound To C 3e-07
2w9z_A 257 Crystal Structure Of Cdk4 In Complex With A D-Type 1e-06
2w96_A 271 Crystal Structure Of Cdk4 In Complex With A D-Type 1e-06
3g33_B 306 Crystal Structure Of Cdk4CYCLIN D3 Length = 306 6e-05
>pdb|3QHR|B Chain B, Structure Of A Pcdk2CYCLINA TRANSITION-State Mimic Length = 261 Back     alignment and structure 
Iteration: 1

 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/100 (35%), Positives = 55/100 (55%), Gaps = 8/100 (8%)
Query: 71  LREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLD 130
           LREM VK     PK  Y+ R    D+ + +R   +DW+++    Y+    +  L++NY+D
Sbjct: 15  LREMEVK---CKPKVGYMKR--QPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYID 69
Query: 131 RFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVE 170
           RFLS   + +GK   +QL+  A + LA+K EE   P + E
Sbjct: 70  RFLSSMSVLRGK---LQLVGTAAMLLASKFEEIYPPEVAE 106
>pdb|4II5|B Chain B, Structure Of Pcdk2/cyclina Bound To Adp And 1 Magnesium Ion Length = 258 Back     alignment and structure
>pdb|4I3Z|B Chain B, Structure Of Pcdk2CYCLINA BOUND TO ADP AND 2 MAGNESIUM IONS Length = 257 Back     alignment and structure
>pdb|4BCQ|B Chain B, Structure Of Cdk2 In Complex With Cyclin A And A 2-amino-4- Heteroaryl-pyrimidine Inhibitor Length = 262 Back     alignment and structure
>pdb|1VYW|B Chain B, Structure Of Cdk2CYCLIN A WITH PNU-292137 Length = 265 Back     alignment and structure
>pdb|3F5X|B Chain B, Cdk-2-Cyclin Complex With Indazole Inhibitor 9 Bound At Its Active Site Length = 256 Back     alignment and structure
>pdb|3DOG|B Chain B, Structure Of Thr 160 Phosphorylated Cdk2CYCLIN A IN Complex With The Inhibitor N-&-N1 Length = 264 Back     alignment and structure
>pdb|2G9X|B Chain B, Structure Of Thr 160 Phosphorylated Cdk2CYCLIN A IN COMPLEX WITH THE Inhibitor Nu6271 Length = 262 Back     alignment and structure
>pdb|1VIN|A Chain A, Bovine Cyclin A3 Length = 268 Back     alignment and structure
>pdb|1FIN|B Chain B, Cyclin A-Cyclin-Dependent Kinase 2 Complex Length = 260 Back     alignment and structure
>pdb|2X1N|B Chain B, Truncation And Optimisation Of Peptide Inhibitors Of Cdk2, Cyclin A Through Structure Guided Design Length = 261 Back     alignment and structure
>pdb|3DDQ|B Chain B, Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN COMPLEX With The Inhibitor Roscovitine Length = 269 Back     alignment and structure
>pdb|3DDP|B Chain B, Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN COMPLEX With The Inhibitor Cr8 Length = 268 Back     alignment and structure
>pdb|3BHT|B Chain B, Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN COMPLEX WITH THE Inhibitor Meriolin 3 Length = 262 Back     alignment and structure
>pdb|4BCQ|D Chain D, Structure Of Cdk2 In Complex With Cyclin A And A 2-amino-4- Heteroaryl-pyrimidine Inhibitor Length = 262 Back     alignment and structure
>pdb|4BCO|B Chain B, Structure Of Cdk2 In Complex With Cyclin A And A 2-amino-4- Heteroaryl-pyrimidine Inhibitor Length = 262 Back     alignment and structure
>pdb|1E9H|B Chain B, Thr 160 Phosphorylated Cdk2-Human Cyclin A3 Complex With The Inhibitor Indirubin-5-Sulphonate Bound Length = 261 Back     alignment and structure
>pdb|1OGU|B Chain B, Structure Of Human Thr160-phospho Cdk2/cyclin A Complexed With A 2-arylamino-4-cyclohexylmethyl-5-nitroso-6- aminopyrimidine Inhibitor Length = 260 Back     alignment and structure
>pdb|1QMZ|B Chain B, Phosphorylated Cdk2-Cyclyin A-Substrate Peptide Complex Length = 259 Back     alignment and structure
>pdb|1JST|B Chain B, Phosphorylated Cyclin-Dependent Kinase-2 Bound To Cyclin A Length = 258 Back     alignment and structure
>pdb|2W9Z|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin Length = 257 Back     alignment and structure
>pdb|2W96|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin Length = 271 Back     alignment and structure
>pdb|3G33|B Chain B, Crystal Structure Of Cdk4CYCLIN D3 Length = 306 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query173
2w96_A 271 G1/S-specific cyclin-D1; serine/threonine-protein 1e-26
3g33_B 306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 2e-23
1g3n_C 257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 3e-18
1f5q_B 252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 1e-17
2cch_B 260 Cyclin A2, cyclin-A; complex(transferase/cell divi 3e-17
2b9r_A 269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 7e-16
2f2c_A 254 Cyclin homolog, V-cyclin; small molecule inhibitor 8e-16
1w98_B 283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 1e-15
2i53_A 258 Cyclin K; cell cycle, transcription, cyclin BOX, C 2e-05
2pk2_A 358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 3e-04
>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A Length = 271 Back     alignment and structure
 Score =  100 bits (252), Expect = 1e-26
 Identities = 32/110 (29%), Positives = 56/110 (50%), Gaps = 5/110 (4%)

Query: 64  QTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFC 123
             +++ +LR M   E    P   Y   ++  ++   +R+    W+L+     +     F 
Sbjct: 21  NLLNDRVLRAMLKAEETCAPSVSYFKCVQK-EVLPSMRKIVATWMLEVCEEQKCEEEVFP 79

Query: 124 LSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVELQV 173
           L+MNYLDRFLS+  + K +   +QLL   C+ +A+KM+E+ +PL  E   
Sbjct: 80  LAMNYLDRFLSLEPVKKSR---LQLLGATCMFVASKMKET-IPLTAEKLC 125
>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens} Length = 306 Back     alignment and structure
>1g3n_C V-cyclin; cyclin-dependent kinase, INK4 inhibitor, viral cyclin, cell cycle, signaling protein; 2.90A {Human herpesvirus 8} SCOP: a.74.1.1 a.74.1.1 Length = 257 Back     alignment and structure
>1f5q_B Gamma herpesvirus cyclin; herpesviral cyclin, cyclin dependent kinase. protein/protein complex, transferase; 2.50A {Murid herpesvirus 4} SCOP: a.74.1.1 a.74.1.1 Length = 252 Back     alignment and structure
>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ... Length = 260 Back     alignment and structure
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Length = 269 Back     alignment and structure
>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A Length = 254 Back     alignment and structure
>1w98_B Cyclin E, G1/S-specific cyclin E1; cell cycle, transferase; HET: TPO; 2.15A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Length = 283 Back     alignment and structure
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Length = 258 Back     alignment and structure
>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C Length = 358 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query173
2cch_B 260 Cyclin A2, cyclin-A; complex(transferase/cell divi 99.94
2w96_A 271 G1/S-specific cyclin-D1; serine/threonine-protein 99.94
2f2c_A 254 Cyclin homolog, V-cyclin; small molecule inhibitor 99.94
3g33_B 306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 99.93
1w98_B 283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 99.93
1g3n_C 257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 99.93
1f5q_B 252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 99.93
2b9r_A 269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 99.92
2ivx_A 257 Cyclin-T2; transcription regulation, cell division 99.67
2i53_A 258 Cyclin K; cell cycle, transcription, cyclin BOX, C 99.67
2pk2_A 358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 99.62
3rgf_B 285 Cyclin-C; protein kinase complex, transferase,tran 99.59
1zp2_A 235 RNA polymerase II holoenzyme cyclin-like subunit; 99.55
1jkw_A 323 Cyclin H; cell cycle, cell division, nuclear prote 99.45
1c9b_A 207 General transcription factor IIB; protein-DNA comp 98.98
1ais_B 200 TFB TFIIB, protein (transcription initiation facto 98.33
3k7a_M 345 Transcription initiation factor IIB; RNA polymeras 97.15
2pmi_B 293 PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de 95.72
4bbr_M 345 Transcription initiation factor IIB; RNA polymeras 95.21
1ais_B200 TFB TFIIB, protein (transcription initiation facto 92.61
1c9b_A207 General transcription factor IIB; protein-DNA comp 89.89
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 81.98
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 80.12
>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ... Back     alignment and structure
Probab=99.94  E-value=1.5e-27  Score=197.84  Aligned_cols=103  Identities=29%  Similarity=0.516  Sum_probs=98.5

Q ss_pred             CCHHHHHHHHHHHHhccCCCccchhhccCCCCCHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCc
Q 030687           65 TVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDW  144 (173)
Q Consensus        65 ~y~~eil~~L~~~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w  144 (173)
                      +|.+||+++|+++|.++.|.++|+.+  |+++++.+|..+++||.+|+..|++.++|+++||+|+|||++...+++.+  
T Consensus         5 eY~~di~~~l~~~E~~~~p~~~y~~~--q~~i~~~~R~~lvdwl~~v~~~~~l~~~tl~lAv~~lDRfls~~~v~~~~--   80 (260)
T 2cch_B            5 DYHEDIHTYLREMEVKCKPKVGYMKK--QPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGK--   80 (260)
T ss_dssp             TTHHHHHHHHHHHHHHTCCCTTGGGG--CSSCCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCCCHHH--
T ss_pred             hHHHHHHHHHHHHHhhcCCCchhhhc--CCCCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccCCCCHHH--
Confidence            89999999999999999999999986  67899999999999999999999999999999999999999999998887  


Q ss_pred             cchhhHHHHHHhhhhcccccCCCCCCCC
Q 030687          145 TVQLLTVACLSLAAKMEESEVPLLVELQ  172 (173)
Q Consensus       145 ~lQLlgvaCL~LAaK~EE~~~P~~~dlq  172 (173)
                       +||+|+|||+||+|+||+.+|.+.||+
T Consensus        81 -lqlv~~acl~iA~K~ee~~~~~~~d~~  107 (260)
T 2cch_B           81 -LQLVGTAAMLLASKFEEIYPPEVAEFV  107 (260)
T ss_dssp             -HHHHHHHHHHHHHHHHCSSCCCHHHHH
T ss_pred             -HhHHHHHHHHHHHHhcccCCCCHHHHH
Confidence             999999999999999999999987763
>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A Back     alignment and structure
>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A Back     alignment and structure
>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens} Back     alignment and structure
>1w98_B Cyclin E, G1/S-specific cyclin E1; cell cycle, transferase; HET: TPO; 2.15A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>1g3n_C V-cyclin; cyclin-dependent kinase, INK4 inhibitor, viral cyclin, cell cycle, signaling protein; 2.90A {Human herpesvirus 8} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>1f5q_B Gamma herpesvirus cyclin; herpesviral cyclin, cyclin dependent kinase. protein/protein complex, transferase; 2.50A {Murid herpesvirus 4} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Back     alignment and structure
>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B* Back     alignment and structure
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C Back     alignment and structure
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens} Back     alignment and structure
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Back     alignment and structure
>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A Back     alignment and structure
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A* Back     alignment and structure
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Back     alignment and structure
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae} Back     alignment and structure
>2pmi_B PHO85 cyclin PHO80, aminoglycoside anti; cyclin-dependent kinase, signaling protein,transfera cycle complex; HET: MES AGS; 2.90A {Saccharomyces cerevisiae} PDB: 2pk9_B* Back     alignment and structure
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M Back     alignment and structure
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Back     alignment and structure
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A* Back     alignment and structure
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Back     alignment and structure
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 173
d1w98b2140 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human 4e-20
d1g3nc1132 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma 1e-19
d2cchb1128 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [T 8e-18
d1bu2a1127 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saim 7e-17
d1f5qb1141 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesviru 5e-16
d2i53a1144 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) 2e-13
d2ivxa1143 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) 2e-11
d1jkwa1151 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo s 8e-09
>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]} Length = 140 Back     information, alignment and structure

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: G1/S-specific cyclin-E1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 79.3 bits (195), Expect = 4e-20
 Identities = 27/106 (25%), Positives = 51/106 (48%), Gaps = 4/106 (3%)

Query: 67  SEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSM 126
            EE+ + M  KE   L    +L +     L  ++R   LDW+++    Y+    +F L+ 
Sbjct: 11  REEVWKIMLNKEKTYLRDQHFLEQ--HPLLQPKMRAILLDWLMEVCEVYKLHRETFYLAQ 68

Query: 127 NYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVELQ 172
           ++ DR+++           +QL+ ++ L +AAK+EE   P L +  
Sbjct: 69  DFFDRYMATQ--ENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFA 112
>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]} Length = 132 Back     information, alignment and structure
>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Length = 128 Back     information, alignment and structure
>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} Length = 127 Back     information, alignment and structure
>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Length = 141 Back     information, alignment and structure
>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Length = 144 Back     information, alignment and structure
>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Length = 143 Back     information, alignment and structure
>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Length = 151 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query173
d1g3nc1132 Viral cyclin {Kaposi's sarcoma-associated herpesvi 99.96
d2cchb1128 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 99.95
d1w98b2140 G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax 99.95
d1bu2a1127 Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} 99.93
d1f5qb1141 Viral cyclin {Murine herpesvirus 68 [TaxId: 33708] 99.9
d2i53a1144 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 99.61
d2ivxa1143 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 99.53
d1jkwa1151 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 99.49
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 95.42
d1aisb295 Transcription factor IIB (TFIIB), core domain {Arc 95.38
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 95.23
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 94.28
d2ivxa2113 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 94.13
d2i53a2110 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 90.79
>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]} Back     information, alignment and structure
class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]

Probab=99.96  E-value=2.6e-30  Score=194.11  Aligned_cols=102  Identities=22%  Similarity=0.373  Sum_probs=96.3

Q ss_pred             CHHHHHHHHHHHHhccCCCccchhhccCCCCCHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCcc
Q 030687           66 VSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWT  145 (173)
Q Consensus        66 y~~eil~~L~~~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~  145 (173)
                      ++++|+.+|++.|.+++|.++|+..+|. ++++.+|..+|+||.+|+..|+++++|+|+||+|+||||+..++++++   
T Consensus         2 ~~~~i~~~l~~~E~~~~p~~~y~~~~q~-~it~~~R~~lidWl~~v~~~~~l~~et~~lAv~llDrfls~~~v~~~~---   77 (132)
T d1g3nc1           2 CEDRIFYNILEIEPRFLTSDSVFGTFQQ-SLTSHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEH---   77 (132)
T ss_dssp             HHHHHHHHHHHHGGGGCCCGGGHHHHTS-SCCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHHH---
T ss_pred             chHHHHHHHHHHHHHHCCChHHHHhcCc-cCCHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCcccCcHHH---
Confidence            5789999999999999999999988764 799999999999999999999999999999999999999999999888   


Q ss_pred             chhhHHHHHHhhhhcccccCCCCCCC
Q 030687          146 VQLLTVACLSLAAKMEESEVPLLVEL  171 (173)
Q Consensus       146 lQLlgvaCL~LAaK~EE~~~P~~~dl  171 (173)
                      +||+|+|||+||+|+||+.+|.+.++
T Consensus        78 lqLia~tcl~iAsK~ee~~~~~~~~l  103 (132)
T d1g3nc1          78 FQKTGSACLLVASKLRSLTPISTSSL  103 (132)
T ss_dssp             HHHHHHHHHHHHHHHHCSSCCCHHHH
T ss_pred             HHHHHHHHHHHHHHhcccCCCCHHHH
Confidence            99999999999999999998887654
>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} Back     information, alignment and structure
>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Back     information, alignment and structure
>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Back     information, alignment and structure
>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Back     information, alignment and structure
>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ivxa2 a.74.1.1 (A:150-262) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2i53a2 a.74.1.1 (A:158-267) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure