Citrus Sinensis ID: 026696

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-------180-------190-------200-------210-------220-------230-----
MLAATGYSTYQGRLPEPSQNETTTPRVLTIIASVMEKLVARNDRLADSLSRQLTKGNGVFSGSTPIGTSLNTFHGVRAPNISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLVVSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAELNRLELELLFLLDFGVMVSSRVFESYCLHLEKEMLVNGTTSKIEKAFISNPVDDVTEISAENTASCSPLLSIGLS
ccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHccccccccccccEEccccHHHHHHHHHHHHHHccccEEEcHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccc
ccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcHccccHHHcccccccccccEEEEcccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccEEccHHHHHHHHHHHHHHHHHHcHccccccHEEEEccccHHHHHHHHHHHHHHcccEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccEHEcccc
mlaatgystyqgrlpepsqnetttpRVLTIIASVMEKLVARNDRLADSLSRqltkgngvfsgstpigtslntfhgvrapniSIAKYLERIYKytncspscfvVGYVYIDrllhrhpdslvVSLNVHRLLVTSVMVASKtmddvhynnAFYARVGGVSNAELNRLELELLFLLDFGVMVSSRVFESYCLHLEKEMLVNGTTSKIEKAFisnpvddvteisaentascspllsigls
mlaatgystyqgrlpepsqnetttprVLTIIASVMEKLVARNDRLADSLSrqltkgngvfsgstpigtslntfhgvraPNISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLVVSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAELNRLELELLFLLDFGVMVSSRVFESYCLHLEKEMLVNGTTSKIEKAFISNPVDDVTEisaentascspllsigls
MLAATGYSTYQGRLPEPSQNETTTPRVLTIIASVMEKLVARNDRLADSLSRQLTKGNGVFSGSTPIGTSLNTFHGVRAPNISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLVVSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAelnrlelellfllDFGVMVSSRVFESYCLHLEKEMLVNGTTSKIEKAFISNPVDDVTEISAENTASCSPLLSIGLS
*************************RVLTIIASVMEKLVARNDRLA******LTKGNGVFSGSTPIGTSLNTFHGVRAPNISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLVVSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAELNRLELELLFLLDFGVMVSSRVFESYCLHLEKEMLVNGTTSKIEKAFISNPVDDV********************
**************************VLTIIASVMEKLVARNDR********************************RAPNISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLVVSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAELNRLELELLFLLDFGVMVSSRVFESYCLHLE********************************************
MLAATGYSTYQGRLPEPSQNETTTPRVLTIIASVMEKLVARNDRLADSLSRQLTKGNGVFSGSTPIGTSLNTFHGVRAPNISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLVVSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAELNRLELELLFLLDFGVMVSSRVFESYCLHLEKEMLVNGTTSKIEKAFISNPVDDVTEISAENTASCSPLLSIGLS
********TYQGRLPEPSQNETTTPRVLTIIASVMEKLVARNDRLADSLSRQLTKGNGVFSGSTPIGTSLNTFHGVRAPNISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLVVSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAELNRLELELLFLLDFGVMVSSRVFESYCLHLEKEMLVN**************************************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MLAATGYSTYQGRLPEPSQNETTTPRVLTIIASVMEKLVARNDRLADSLSRQLTKGNGVFSGSTPIGTSLNTFHGVRAPNISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLVVSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAELNRLELELLFLLDFGVMVSSRVFESYCLHLEKEMLVNGTTSKIEKAFISNPVDDVTEISAENTASCSPLLSIGLS
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 ?
Query235 2.2.26 [Sep-21-2011]
Q9LJ45210 Cyclin-U1-1 OS=Arabidopsi yes no 0.808 0.904 0.666 6e-64
Q75HV0236 Cyclin-P3-1 OS=Oryza sati yes no 0.846 0.843 0.432 3e-43
Q0J9W0264 Cyclin-P1-1 OS=Oryza sati no no 0.719 0.640 0.488 3e-41
O80513202 Cyclin-U4-1 OS=Arabidopsi no no 0.672 0.782 0.5 1e-40
Q9M205230 Cyclin-U2-2 OS=Arabidopsi no no 0.753 0.769 0.417 3e-37
Q8LB60221 Cyclin-U3-1 OS=Arabidopsi no no 0.527 0.561 0.552 5e-37
Q7XC35212 Cyclin-P4-1 OS=Oryza sati no no 0.680 0.754 0.436 3e-36
Q9SHD3222 Cyclin-U2-1 OS=Arabidopsi no no 0.727 0.770 0.417 1e-35
Q9LY16216 Cyclin-U4-2 OS=Arabidopsi no no 0.8 0.870 0.367 1e-34
Q9FKF6219 Cyclin-U4-3 OS=Arabidopsi no no 0.642 0.689 0.411 2e-34
>sp|Q9LJ45|CCU11_ARATH Cyclin-U1-1 OS=Arabidopsis thaliana GN=CYCU1-1 PE=1 SV=1 Back     alignment and function desciption
 Score =  243 bits (621), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 136/204 (66%), Positives = 152/204 (74%), Gaps = 14/204 (6%)

Query: 1   MLAATGYSTYQGRLPEPSQNETTTPRVLTIIASVMEKLVARNDRLADSLSRQLTKGNGVF 60
           ML A G       +   S  E  TPRVLTII+ VMEKLVARN+ LA     + TKG    
Sbjct: 1   MLTAAGDDELDPVVGPESATEAATPRVLTIISHVMEKLVARNEWLA-----KQTKG---- 51

Query: 61  SGSTPIGTSLNTFHGVRAPNISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLV 120
                 G SL  FHGVRAP+ISIAKYLERIYKYT CSP+CFVVGYVYIDRL H+HP SLV
Sbjct: 52  -----FGKSLEAFHGVRAPSISIAKYLERIYKYTKCSPACFVVGYVYIDRLAHKHPGSLV 106

Query: 121 VSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAELNRLELELLFLLDFGVMVSS 180
           VSLNVHRLLVT VM+A+K +DDVHYNN FYARVGGVSNA+LN++ELELLFLLDF V VS 
Sbjct: 107 VSLNVHRLLVTCVMIAAKILDDVHYNNEFYARVGGVSNADLNKMELELLFLLDFRVTVSF 166

Query: 181 RVFESYCLHLEKEMLVNGTTSKIE 204
           RVFESYC HLEKEM +N   S ++
Sbjct: 167 RVFESYCFHLEKEMQLNDAVSSLK 190

Arabidopsis thaliana (taxid: 3702)
>sp|Q75HV0|CCP31_ORYSJ Cyclin-P3-1 OS=Oryza sativa subsp. japonica GN=CYCP3-1 PE=3 SV=1 Back     alignment and function description
>sp|Q0J9W0|CCP11_ORYSJ Cyclin-P1-1 OS=Oryza sativa subsp. japonica GN=CYCP1-1 PE=3 SV=2 Back     alignment and function description
>sp|O80513|CCU41_ARATH Cyclin-U4-1 OS=Arabidopsis thaliana GN=CYCU4-1 PE=1 SV=1 Back     alignment and function description
>sp|Q9M205|CCU22_ARATH Cyclin-U2-2 OS=Arabidopsis thaliana GN=CYCU2-2 PE=1 SV=1 Back     alignment and function description
>sp|Q8LB60|CCU31_ARATH Cyclin-U3-1 OS=Arabidopsis thaliana GN=CYCU3-1 PE=1 SV=2 Back     alignment and function description
>sp|Q7XC35|CCP41_ORYSJ Cyclin-P4-1 OS=Oryza sativa subsp. japonica GN=CYCP4-1 PE=2 SV=1 Back     alignment and function description
>sp|Q9SHD3|CCU21_ARATH Cyclin-U2-1 OS=Arabidopsis thaliana GN=CYCU2-1 PE=1 SV=1 Back     alignment and function description
>sp|Q9LY16|CCU42_ARATH Cyclin-U4-2 OS=Arabidopsis thaliana GN=CYCU4-2 PE=1 SV=1 Back     alignment and function description
>sp|Q9FKF6|CCU43_ARATH Cyclin-U4-3 OS=Arabidopsis thaliana GN=CYCU4-3 PE=1 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 ?
Query235
255549349230 Nuc-1 negative regulatory protein preg, 0.957 0.978 0.741 2e-94
224095750230 predicted protein [Populus trichocarpa] 0.957 0.978 0.719 8e-93
449468442233 PREDICTED: cyclin-U1-1-like [Cucumis sat 0.961 0.969 0.653 2e-78
449531376213 PREDICTED: LOW QUALITY PROTEIN: cyclin-U 0.872 0.962 0.696 1e-77
351722311232 uncharacterized protein LOC100527137 [Gl 0.957 0.969 0.713 2e-76
356543744232 PREDICTED: cyclin-U1-1-like [Glycine max 0.957 0.969 0.717 2e-76
225447342220 PREDICTED: cyclin-U1-1 [Vitis vinifera] 0.906 0.968 0.678 7e-74
357453505233 Cyclin-U1-1 [Medicago truncatula] gi|355 0.948 0.957 0.685 9e-71
159902359198 putative cyclin-dependent protein kinase 0.834 0.989 0.755 9e-70
297835184210 CYCP2_1 [Arabidopsis lyrata subsp. lyrat 0.744 0.833 0.710 1e-62
>gi|255549349|ref|XP_002515728.1| Nuc-1 negative regulatory protein preg, putative [Ricinus communis] gi|223545165|gb|EEF46675.1| Nuc-1 negative regulatory protein preg, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  350 bits (899), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 169/228 (74%), Positives = 193/228 (84%), Gaps = 3/228 (1%)

Query: 1   MLAATGYSTYQGRLPEPSQNETTTPRVLTIIASVMEKLVARNDRLADSLSRQLTKGNGVF 60
           MLA    +T Q R PEPSQ+E TTPRVLTI+++V+EKLV RNDRL D LS ++   +G+ 
Sbjct: 1   MLARDKLTTSQSRQPEPSQSEQTTPRVLTILSTVIEKLVTRNDRLVDGLSHRV---DGMS 57

Query: 61  SGSTPIGTSLNTFHGVRAPNISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLV 120
           SG T +G SLN FHGVRAP ISI KYLER+YKYTNCSPSCFVVGYVYIDRLLH+HPDSLV
Sbjct: 58  SGLTHLGKSLNAFHGVRAPTISIPKYLERLYKYTNCSPSCFVVGYVYIDRLLHKHPDSLV 117

Query: 121 VSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAELNRLELELLFLLDFGVMVSS 180
           +SLNVHRLLVTSVMVASK +DDVHYNNAFYA+VGGVSNAELNRLE+ELLFLLDFGVMVSS
Sbjct: 118 ISLNVHRLLVTSVMVASKVLDDVHYNNAFYAKVGGVSNAELNRLEIELLFLLDFGVMVSS 177

Query: 181 RVFESYCLHLEKEMLVNGTTSKIEKAFISNPVDDVTEISAENTASCSP 228
           R+FESYCLHLEKEML++G   KIE+   SN +DDVTEI  E+  + SP
Sbjct: 178 RIFESYCLHLEKEMLLHGAIQKIERTIPSNSLDDVTEILVEDMQNSSP 225

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224095750|ref|XP_002310464.1| predicted protein [Populus trichocarpa] gi|222853367|gb|EEE90914.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449468442|ref|XP_004151930.1| PREDICTED: cyclin-U1-1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449531376|ref|XP_004172662.1| PREDICTED: LOW QUALITY PROTEIN: cyclin-U1-1-like, partial [Cucumis sativus] Back     alignment and taxonomy information
>gi|351722311|ref|NP_001235448.1| uncharacterized protein LOC100527137 [Glycine max] gi|255631636|gb|ACU16185.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|356543744|ref|XP_003540320.1| PREDICTED: cyclin-U1-1-like [Glycine max] Back     alignment and taxonomy information
>gi|225447342|ref|XP_002280596.1| PREDICTED: cyclin-U1-1 [Vitis vinifera] Back     alignment and taxonomy information
>gi|357453505|ref|XP_003597030.1| Cyclin-U1-1 [Medicago truncatula] gi|355486078|gb|AES67281.1| Cyclin-U1-1 [Medicago truncatula] Back     alignment and taxonomy information
>gi|159902359|gb|ABX10779.1| putative cyclin-dependent protein kinase [Glycine max] gi|159902361|gb|ABX10780.1| putative cyclin-dependent protein kinase [Glycine soja] Back     alignment and taxonomy information
>gi|297835184|ref|XP_002885474.1| CYCP2_1 [Arabidopsis lyrata subsp. lyrata] gi|297331314|gb|EFH61733.1| CYCP2_1 [Arabidopsis lyrata subsp. lyrata] 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 ?
Query235
TAIR|locus:2088743210 CYCP2;1 "cyclin p2;1" [Arabido 0.808 0.904 0.622 1.6e-56
TAIR|locus:2042421202 CYCP4;1 "AT2G44740" [Arabidops 0.672 0.782 0.450 4.1e-33
TAIR|locus:2103391230 CYCP3;2 "cyclin p3;2" [Arabido 0.748 0.765 0.372 5.6e-29
TAIR|locus:1009023243212 AT3G05327 [Arabidopsis thalian 0.744 0.825 0.373 9.1e-29
TAIR|locus:2099192221 CYCP1;1 "cyclin p1;1" [Arabido 0.621 0.660 0.440 1.5e-28
TAIR|locus:2055552222 cycp3;1 "cyclin p3;1" [Arabido 0.727 0.770 0.368 1e-27
TAIR|locus:2183394216 CYCP4;3 "cyclin p4;3" [Arabido 0.719 0.782 0.356 1.3e-27
TAIR|locus:2151656219 CYCP4;2 "CYCLIN P4;2" [Arabido 0.527 0.566 0.443 7.3e-27
DICTYBASE|DDB_G0277481 391 DDB_G0277481 [Dictyostelium di 0.646 0.388 0.339 1.3e-22
DICTYBASE|DDB_G0286485 398 DDB_G0286485 "PHO85 cyclin-2" 0.493 0.291 0.393 8.1e-19
TAIR|locus:2088743 CYCP2;1 "cyclin p2;1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 582 (209.9 bits), Expect = 1.6e-56, P = 1.6e-56
 Identities = 127/204 (62%), Positives = 140/204 (68%)

Query:     1 MLAATGYSTYQGRLPEPSQNETTTPRVLTIIASVMEKLVARNDRLADSLSRQLTKGNGVF 60
             ML A G       +   S  E  TPRVLTII+ VMEKLVARN+ LA    +Q TKG    
Sbjct:     1 MLTAAGDDELDPVVGPESATEAATPRVLTIISHVMEKLVARNEWLA----KQ-TKG---- 51

Query:    61 SGSTPIGTSLNTFHGVRAPNISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLV 120
                   G SL  FHGVRAP+ISIAKYLERIYKYT CSP+CFVVGYVYIDRL H+HP SLV
Sbjct:    52 -----FGKSLEAFHGVRAPSISIAKYLERIYKYTKCSPACFVVGYVYIDRLAHKHPGSLV 106

Query:   121 VSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAXXXXXXXXXXXXXDFGVMVSS 180
             VSLNVHRLLVT VM+A+K +DDVHYNN FYARVGGVSNA             DF V VS 
Sbjct:   107 VSLNVHRLLVTCVMIAAKILDDVHYNNEFYARVGGVSNADLNKMELELLFLLDFRVTVSF 166

Query:   181 RVFESYCLHLEKEMLVNGTTSKIE 204
             RVFESYC HLEKEM +N   S ++
Sbjct:   167 RVFESYCFHLEKEMQLNDAVSSLK 190
GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA
GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=ISS
GO:0005634 "nucleus" evidence=ISM
GO:0019901 "protein kinase binding" evidence=IEA
GO:0051726 "regulation of cell cycle" evidence=ISS
GO:0005515 "protein binding" evidence=IPI
GO:0010440 "stomatal lineage progression" evidence=RCA
TAIR|locus:2042421 CYCP4;1 "AT2G44740" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2103391 CYCP3;2 "cyclin p3;2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:1009023243 AT3G05327 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2099192 CYCP1;1 "cyclin p1;1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2055552 cycp3;1 "cyclin p3;1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2183394 CYCP4;3 "cyclin p4;3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2151656 CYCP4;2 "CYCLIN P4;2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0277481 DDB_G0277481 [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0286485 DDB_G0286485 "PHO85 cyclin-2" [Dictyostelium discoideum (taxid:44689)] 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q75HV0CCP31_ORYSJNo assigned EC number0.43250.84680.8432yesno
Q9LJ45CCU11_ARATHNo assigned EC number0.66660.80850.9047yesno

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:
eugene3.00070247
hypothetical protein (231 aa)
(Populus trichocarpa)
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 ?
Query235
pfam08613140 pfam08613, Cyclin, Cyclin 7e-36
pfam00134127 pfam00134, Cyclin_N, Cyclin, N-terminal domain 5e-12
>gnl|CDD|204002 pfam08613, Cyclin, Cyclin Back     alignment and domain information 
 Score =  123 bits (311), Expect = 7e-36
 Identities = 56/152 (36%), Positives = 86/152 (56%), Gaps = 16/152 (10%)

Query: 25  PRVLTIIASVMEKLVARNDRLADSLSRQLTKGNGVFSGSTPIGTSLNTFHGVRAPNISIA 84
             ++  I+ V++++ A ND  A +            S S         F+    P+IS+ 
Sbjct: 1   DELIESISRVLDRIPALNDSTATA------------SSSASSPLE--PFYSKAVPSISLT 46

Query: 85  KYLERIYKYTNCSPSCFVVGYVYIDRLLHR--HPDSLVVSLNVHRLLVTSVMVASKTMDD 142
           +YL RI KY   SP   +   +Y+DR++ R   P   V SLNVHRLL+T++ VA+K + D
Sbjct: 47  QYLSRIQKYCPTSPDVLLSALIYLDRIVKRCDKPTITVTSLNVHRLLLTALTVATKFLSD 106

Query: 143 VHYNNAFYARVGGVSNAELNRLELELLFLLDF 174
             Y+N+ +A+VGG+S  ELN LE++ LFL+DF
Sbjct: 107 GSYSNSRFAKVGGISLHELNHLEIDFLFLVDF 138

This family includes many different cyclin proteins. Members include the G1/S-specific cyclin pas1, and the phosphate system cyclin PHO80/PHO85. Length = 140
>gnl|CDD|215740 pfam00134, Cyclin_N, Cyclin, N-terminal domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 235
PF08613149 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu 100.0
KOG1674218 consensus Cyclin [General function prediction only 99.97
KOG1675343 consensus Predicted cyclin [General function predi 99.78
PF00134127 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR 99.3
cd0004388 CYCLIN Cyclin box fold. Protein binding domain fun 98.75
smart0038583 CYCLIN domain present in cyclins, TFIIB and Retino 98.51
KOG0656335 consensus G1/S-specific cyclin D [Cell cycle contr 97.99
TIGR00569305 ccl1 cyclin ccl1. University). 97.55
KOG0653391 consensus Cyclin B and related kinase-activating p 97.47
KOG0655 408 consensus G1/S-specific cyclin E [Cell cycle contr 96.96
COG5333297 CCL1 Cdk activating kinase (CAK)/RNA polymerase II 96.91
KOG4164497 consensus Cyclin ik3-1/CABLES [Cell cycle control, 96.63
COG5024440 Cyclin [Cell division and chromosome partitioning] 96.25
PRK00423310 tfb transcription initiation factor IIB; Reviewed 93.48
KOG0794264 consensus CDK8 kinase-activating protein cyclin C 91.51
KOG0834 323 consensus CDK9 kinase-activating protein cyclin T 91.49
KOG0835 367 consensus Cyclin L [General function prediction on 90.85
KOG1674218 consensus Cyclin [General function prediction only 90.57
KOG2496 325 consensus Cdk activating kinase (CAK)/RNA polymera 89.7
PRK00423310 tfb transcription initiation factor IIB; Reviewed 86.14
PF0038271 TFIIB: Transcription factor TFIIB repeat; InterPro 80.86
>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 
Probab=100.00  E-value=2.7e-36  Score=248.36  Aligned_cols=147  Identities=39%  Similarity=0.689  Sum_probs=102.2

Q ss_pred             hhHHHHHHHHHHHHHHHhcchhhhhhhhhhcCCCccCCCCCCCCccccccCCCCCchhHHHHHHHHHHHcCCChhhHHHH
Q 026696           25 PRVLTIIASVMEKLVARNDRLADSLSRQLTKGNGVFSGSTPIGTSLNTFHGVRAPNISIAKYLERIYKYTNCSPSCFVVG  104 (235)
Q Consensus        25 p~~l~~la~~Le~~~~~nd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~F~~~~~P~isi~~yl~rI~~~~~~s~~~~v~A  104 (235)
                      ++++.+|+.+++++++.|+......++...     ...........+.|++..+|+++|.+|+.||+++++|+++|+++|
T Consensus         1 ~~~~~~i~~~l~~~~~~n~~~~~~s~~~~~-----~~~~~~~~~~~~~F~~~~~p~i~i~~fl~ri~~~~~~s~~~~i~a   75 (149)
T PF08613_consen    1 DKLVQSIARQLDRLINNNESTAQSSSSSSS-----PSSPFQQSPKISQFHSQSVPSISIRDFLSRILKYTQCSPECLILA   75 (149)
T ss_dssp             -HHHHHHHHHHHHHHHHHH-------------------T---------T--SS--SS-HHHHHHHHHHHTT--HHHHHHH
T ss_pred             ChHHHHHHHHHHHHhccCchhhhhcccccc-----cccccccccccccccCCCCCCCcHHHHHHHHHHHcCCChHHHHHH
Confidence            368999999999999999997754322110     001112346788999999999999999999999999999999999


Q ss_pred             HHHHHHHHh--hCCCcccccchhHHHHHHHHHhhcccccCCCccccccccccCCCHHHHHHHHHHHHHhCCCce
Q 026696          105 YVYIDRLLH--RHPDSLVVSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAELNRLELELLFLLDFGV  176 (235)
Q Consensus       105 LiYldRl~~--~~~~~~l~~~n~hRL~ltal~lAsK~ldD~~~~N~~~a~VgGis~~ELN~LE~~FL~lLdf~L  176 (235)
                      ++||+|+..  ..+.+.+++.|+|||+++|+|||+||+||.+|+|++||+|||++++|||+||++||.+|||+|
T Consensus        76 liYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~eln~lE~~fL~~l~~~L  149 (149)
T PF08613_consen   76 LIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKELNELEREFLKLLDYNL  149 (149)
T ss_dssp             HHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHHHHHHHHHHHHHTTT--
T ss_pred             HHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHHHHHHHHHHHHHCCCcC
Confidence            999999999  568899999999999999999999999999999999999999999999999999999999997

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
>KOG1674 consensus Cyclin [General function prediction only] Back     alignment and domain information
>KOG1675 consensus Predicted cyclin [General function prediction only] 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
>cd00043 CYCLIN Cyclin box fold Back     alignment and domain information
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>TIGR00569 ccl1 cyclin ccl1 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
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning] 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
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>COG5024 Cyclin [Cell division and chromosome partitioning] Back     alignment and domain information
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription] 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
>KOG0835 consensus Cyclin L [General function prediction only] Back     alignment and domain information
>KOG1674 consensus Cyclin [General function prediction only] 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
>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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query235
2pk9_B293 Structure Of The Pho85-pho80 Cdk-cyclin Complex Of 4e-10
>pdb|2PK9|B Chain B, Structure Of The Pho85-pho80 Cdk-cyclin Complex Of The Phosphate-responsive Signal Transduction Pathway Length = 293 Back     alignment and structure 
Iteration: 1

 Score = 61.6 bits (148), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 34/88 (38%), Positives = 48/88 (54%)
Query: 69  SLNTFHGVRAPNISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLVVSLNVHRL 128
           +L  +H    PNISI  Y  R+ K+++      +    YID L   +PD  + SL  HR 
Sbjct: 63  TLTRYHSKIPPNISIFNYFIRLTKFSSLEHCVLMTSLYYIDLLQTVYPDFTLNSLTAHRF 122
Query: 129 LVTSVMVASKTMDDVHYNNAFYARVGGV 156
           L+T+  VA+K + D    NA YA+VGGV
Sbjct: 123 LLTATTVATKGLCDSFSTNAHYAKVGGV 150

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query235
2pmi_B293 PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de 2e-44
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-08
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-04
>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* Length = 293 Back     alignment and structure
 Score =  149 bits (377), Expect = 2e-44
 Identities = 48/182 (26%), Positives = 83/182 (45%), Gaps = 14/182 (7%)

Query: 20  NETTTPRVLTIIASVMEKLVARNDRLADSLSRQLTKGNGVFSGSTPIGTSLNTFHGVRAP 79
           N+ +   ++ +I+ ++  L+A N+  A   S                  +L  +H    P
Sbjct: 28  NKCSRTDLVVLISRMLVSLIAINENSATKKSDD--------------QITLTRYHSKIPP 73

Query: 80  NISIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLVVSLNVHRLLVTSVMVASKT 139
           NISI  Y  R+ K+++      +    YID L   +PD  + SL  HR L+T+  VA+K 
Sbjct: 74  NISIFNYFIRLTKFSSLEHCVLMTSLYYIDLLQTVYPDFTLNSLTAHRFLLTATTVATKG 133

Query: 140 MDDVHYNNAFYARVGGVSNAELNRLELELLFLLDFGVMVSSRVFESYCLHLEKEMLVNGT 199
           + D    NA YA+VGGV   ELN LE + L  +++ ++          +  +++  V   
Sbjct: 134 LCDSFSTNAHYAKVGGVRCHELNILENDFLKRVNYRIIPRDHNITLCSIEQKQKKFVIDK 193

Query: 200 TS 201
            +
Sbjct: 194 NA 195
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query235
2pmi_B293 PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de 100.0
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 98.68
1f5q_B252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 98.66
3g33_B306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 98.64
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 98.57
2cch_B260 Cyclin A2, cyclin-A; complex(transferase/cell divi 98.57
2w96_A271 G1/S-specific cyclin-D1; serine/threonine-protein 98.56
2b9r_A269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 98.55
1w98_B283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 98.54
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 98.22
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 98.15
2ivx_A257 Cyclin-T2; transcription regulation, cell division 98.09
3rgf_B285 Cyclin-C; protein kinase complex, transferase,tran 98.0
1jkw_A 323 Cyclin H; cell cycle, cell division, nuclear prote 97.95
1c9b_A207 General transcription factor IIB; protein-DNA comp 97.81
2pk2_A 358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 97.8
1ais_B200 TFB TFIIB, protein (transcription initiation facto 97.22
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 94.43
1ais_B200 TFB TFIIB, protein (transcription initiation facto 91.94
1c9b_A207 General transcription factor IIB; protein-DNA comp 88.91
4bbr_M345 Transcription initiation factor IIB; RNA polymeras 86.98
>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
Probab=100.00  E-value=3e-41  Score=303.05  Aligned_cols=155  Identities=30%  Similarity=0.443  Sum_probs=141.2

Q ss_pred             ChhhHHHHHHHHHHHHHHHhcchhhhhhhhhhcCCCccCCCCCCCCccccccCCCCCchhHHHHHHHHHHHcCCChhhHH
Q 026696           23 TTPRVLTIIASVMEKLVARNDRLADSLSRQLTKGNGVFSGSTPIGTSLNTFHGVRAPNISIAKYLERIYKYTNCSPSCFV  102 (235)
Q Consensus        23 ~~p~~l~~la~~Le~~~~~nd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~F~~~~~P~isi~~yl~rI~~~~~~s~~~~v  102 (235)
                      +..+++.+||.+|+++++.||..+.....              ....+++||+..+|+|+|.+|+.||+++++|+++|++
T Consensus        31 ~~~dlv~~IA~~L~~LI~~Nd~~~~~~~~--------------~~~~~t~F~~~~~P~ISI~~Yl~RI~k~t~ls~~~ll   96 (293)
T 2pmi_B           31 SRTDLVVLISRMLVSLIAINENSATKKSD--------------DQITLTRYHSKIPPNISIFNYFIRLTKFSSLEHCVLM   96 (293)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHCC----------------------CCCCTTCCSSCCSSCHHHHHHHHHHTTTCCHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHcCccccccccc--------------cccccccccCCCCCCCcHHHHHHHHHHHcCCCHHHHH
Confidence            46689999999999999999998643211              1246889999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhCCCcccccchhHHHHHHHHHhhcccccCCCccccccccccCCCHHHHHHHHHHHHHhCCCceeeCHHH
Q 026696          103 VGYVYIDRLLHRHPDSLVVSLNVHRLLVTSVMVASKTMDDVHYNNAFYARVGGVSNAELNRLELELLFLLDFGVMVSSRV  182 (235)
Q Consensus       103 ~ALiYldRl~~~~~~~~l~~~n~hRL~ltal~lAsK~ldD~~~~N~~~a~VgGis~~ELN~LE~~FL~lLdf~L~Vs~~e  182 (235)
                      +|++|||||..++|++.+++.||||||++|+|||+|||||.+|+|++||+||||+++|||.||++||.+|||+|+|+.++
T Consensus        97 ~ALvYLdRL~~~~p~~~l~~~nvHRLlLtALmlAsK~ldD~~ysN~~wAkVgGisl~ELN~LE~eFL~lLdf~L~V~~ee  176 (293)
T 2pmi_B           97 TSLYYIDLLQTVYPDFTLNSLTAHRFLLTATTVATKGLCDSFSTNAHYAKVGGVRCHELNILENDFLKRVNYRIIPRDHN  176 (293)
T ss_dssp             HHHHHHHHHHHHCTTCCCSTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTTTCCSCCTTH
T ss_pred             HHHHHHHHHHhhCCCCccCCchHHHHHHHHHHHHHHhccccccChhHhhhccCcCHHHHHHHHHHHHHHcCCceeeCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHH
Q 026696          183 FESYCLHLE  191 (235)
Q Consensus       183 ~~~y~~~L~  191 (235)
                      |..|+..+.
T Consensus       177 ~~~cy~E~~  185 (293)
T 2pmi_B          177 ITLCSIEQK  185 (293)
T ss_dssp             HHHHHHHSC
T ss_pred             HHHHHHHHh
Confidence            999887653
>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
>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
>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
>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
>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
>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
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* 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
>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
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} 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
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens} 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
>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
>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
>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
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M 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 235
d1w98b2140 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human 3e-04
>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 = 37.7 bits (87), Expect = 3e-04
 Identities = 17/94 (18%), Positives = 39/94 (41%), Gaps = 4/94 (4%)

Query: 83  IAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLVVSLNVHRLLVTSVMVASKTMDD 142
           +  +L  + +        F +   + DR +    +  VV   +  + ++S+ +A+K  + 
Sbjct: 46  LLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQEN--VVKTLLQLIGISSLFIAAKLEEI 103

Query: 143 VHYNNAFYARV--GGVSNAELNRLELELLFLLDF 174
                  +A V  G  S  E+  +EL ++  L +
Sbjct: 104 YPPKLHQFAYVTDGACSGDEILTMELMIMKALKW 137

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query235
d1w98b2140 G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax 98.94
d2cchb1128 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 98.89
d1g3nc1132 Viral cyclin {Kaposi's sarcoma-associated herpesvi 98.82
d1bu2a1127 Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} 98.82
d1f5qb1141 Viral cyclin {Murine herpesvirus 68 [TaxId: 33708] 98.77
d2i53a1144 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 98.58
d1jkwa1151 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 98.39
d2ivxa1143 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 98.32
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 94.8
d1aisb295 Transcription factor IIB (TFIIB), core domain {Arc 94.73
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 93.53
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 92.84
>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]} 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]

Probab=98.94  E-value=1.6e-09  Score=84.95  Aligned_cols=94  Identities=18%  Similarity=0.247  Sum_probs=82.6

Q ss_pred             hHHHHHHHHHHHcCCChhhHHHHHHHHHHHHhhCCCcccccchhHHHHHHHHHhhcccccCCCccccccccc--cCCCHH
Q 026696           82 SIAKYLERIYKYTNCSPSCFVVGYVYIDRLLHRHPDSLVVSLNVHRLLVTSVMVASKTMDDVHYNNAFYARV--GGVSNA  159 (235)
Q Consensus        82 si~~yl~rI~~~~~~s~~~~v~ALiYldRl~~~~~~~~l~~~n~hRL~ltal~lAsK~ldD~~~~N~~~a~V--gGis~~  159 (235)
                      .+-+|+.++..+.+++++++.+|.-|+||+....+  .+.....+.+-++|++||+|+-+......+.+.++  +.++.+
T Consensus        45 ~lidW~~~v~~~~~l~~et~~lAv~llDryl~~~~--~v~~~~lqL~a~acL~IAsK~ee~~~~~~~~l~~~~~~~~t~~  122 (140)
T d1w98b2          45 ILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQE--NVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGD  122 (140)
T ss_dssp             HHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCC--CCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTSSCHH
T ss_pred             HHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhccc--cccHHHHhHHHHHHHHHHHHHcccCCCCHHHHHHHHcCCCCHH
Confidence            58899999999999999999999999999987544  34567788999999999999998877777778775  348999


Q ss_pred             HHHHHHHHHHHhCCCcee
Q 026696          160 ELNRLELELLFLLDFGVM  177 (235)
Q Consensus       160 ELN~LE~~FL~lLdf~L~  177 (235)
                      |+.+||+..|..|+|+|+
T Consensus       123 ei~~mE~~IL~~L~~~Ln  140 (140)
T d1w98b2         123 EILTMELMIMKALKWRLS  140 (140)
T ss_dssp             HHHHHHHHHHHHTTTCCC
T ss_pred             HHHHHHHHHHHHCCCcCC
Confidence            999999999999999984
>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]} 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
>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {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
>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