Citrus Sinensis ID: 027897

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-------
MGTLALDTESVGTDIYRMLGLKDLGKGTVGSPKILSLIGRLLEKSVQKNEMLLDTIKTKDVTIFHGLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQKTDGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRLQVNVETFHKFCSQLGKEAAEGLQIDRPIQACKIKENWSSKGDAACVPTIAR
cccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHcccccccccccHHHHcccccHHHHHHHHHHHHHHccccEEEcHHHHHHHHHHHHHHHHHcccccccHHHHHHHccccccccccccccccc
ccccccccccccHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEcccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccEEccHHHHHHHHHHHHHHHHHHHHccccccHEEEEccccHHHHHHHHHHHHHHcccEEEEcHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccc
mgtlaldtesvgTDIYRMLglkdlgkgtvgspkILSLIGRLLEKSVQKNEMLLdtiktkdvtifhglraptisIQQYIDRIFkygacspsCFVIAHIYMdrflqktdghltslNVHRLLITSVMVAAKFIddaffnnayyarvggvstaEMNRMEVKFLFSLDFRLQVNVETFHKFCSQLGKEAAeglqidrpiqackikenwsskgdaacvptiar
mgtlaldtesvgtDIYRMLglkdlgkgtvgsPKILSLIGRLLEKSVQKNEMLLdtiktkdvtifhgLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQKTDGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRLQVNVETFHKFCSQLGKEAAEGLQIDRPIQAckikenwsskgdaacvptiar
MGTLALDTESVGTDIYRMLGLKDLGKGTVGSPKILSLIGRLLEKSVQKNEMLLDTIKTKDVTIFHGLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQKTDGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRLQVNVETFHKFCSQLGKEAAEGLQIDRPIQACKIKENWSSKGDAACVPTIAR
*********SVGTDIYRMLGLKDLGKGTVGSPKILSLIGRLLEKSVQKNEMLLDTIKTKDVTIFHGLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQKTDGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRLQVNVETFHKFCSQLGKEAAEGLQIDRPIQACKIKENWS*************
********************************KILSLIGRLLEKSVQ*******************LRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQKTDGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRLQVNVETFHKFCSQLGKEAA********************************
MGTLALDTESVGTDIYRMLGLKDLGKGTVGSPKILSLIGRLLEKSVQKNEMLLDTIKTKDVTIFHGLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQKTDGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRLQVNVETFHKFCSQLGKEAAEGLQIDRPIQACKIKENWSSKGDAACVPTIAR
*********SVGTDIYRMLGLKDLGKGTVGSPKILSLIGRLLEKSVQKNEMLLDTIKTKDVTIFHGLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQKTDGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRLQVNVETFHKFCSQLGKEAAEGL*****************************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MGTLALDTESVGTDIYRMLGLKDLGKGTVGSPKILSLIGRLLEKSVQKNEMLLDTIKTKDVTIFHGLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQKTDGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRLQVNVETFHKFCSQLGKEAAEGLQIDRPIQACKIKENWSSKGDAACVPTIAR
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 ?
Query217 2.2.26 [Sep-21-2011]
Q75HV0236 Cyclin-P3-1 OS=Oryza sati yes no 0.894 0.822 0.590 7e-59
Q8LB60221 Cyclin-U3-1 OS=Arabidopsi yes no 0.990 0.972 0.515 1e-53
O80513202 Cyclin-U4-1 OS=Arabidopsi no no 0.746 0.801 0.503 3e-43
Q9LJ45210 Cyclin-U1-1 OS=Arabidopsi no no 0.764 0.790 0.477 1e-38
Q9LY16216 Cyclin-U4-2 OS=Arabidopsi no no 0.700 0.703 0.448 1e-36
Q7XC35212 Cyclin-P4-1 OS=Oryza sati no no 0.838 0.858 0.392 1e-35
Q9FKF6219 Cyclin-U4-3 OS=Arabidopsi no no 0.695 0.689 0.458 1e-35
Q9SHD3222 Cyclin-U2-1 OS=Arabidopsi no no 0.880 0.860 0.356 9e-34
Q9M205230 Cyclin-U2-2 OS=Arabidopsi no no 0.774 0.730 0.363 5e-32
Q7FAT5217 Cyclin-P2-1 OS=Oryza sati no no 0.843 0.843 0.322 6e-26
>sp|Q75HV0|CCP31_ORYSJ Cyclin-P3-1 OS=Oryza sativa subsp. japonica GN=CYCP3-1 PE=3 SV=1 Back     alignment and function desciption
 Score =  226 bits (577), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 117/198 (59%), Positives = 143/198 (72%), Gaps = 4/198 (2%)

Query: 1   MGTLALDTESVGTDIYRMLGL--KDLGKGTVGSPKILSLIGRLLEKSVQKNEMLLDTIKT 58
           MGT   D      + Y  LGL      K     PK+L L+   L++SVQKNE LLD+ K 
Sbjct: 3   MGTFTTDESDKHEESYLSLGLTVSQSKKNNTEYPKVLLLLAAYLDRSVQKNEDLLDSNKI 62

Query: 59  KDV-TIFHGLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQKTDGHLTSLNVHR 117
           KD  TIFHG RAP +SI+ Y +RIFKY  CSPSCFV+A IYM+R+LQ+   ++TSL+VHR
Sbjct: 63  KDSSTIFHGHRAPDLSIKLYAERIFKYSECSPSCFVLALIYMERYLQQPHVYMTSLSVHR 122

Query: 118 LLITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRLQVNVETFHKFC 177
           LLITSV+VAAKF DDAFFNNA+YARVGG+ST EMNR+E+  LF+LDFRL+V++ETF  +C
Sbjct: 123 LLITSVVVAAKFTDDAFFNNAFYARVGGISTVEMNRLELDLLFNLDFRLKVDLETFGSYC 182

Query: 178 SQLGKEAAEGLQIDRPIQ 195
            QL KE    L IDRPIQ
Sbjct: 183 LQLEKETM-VLVIDRPIQ 199

Oryza sativa subsp. japonica (taxid: 39947)
>sp|Q8LB60|CCU31_ARATH Cyclin-U3-1 OS=Arabidopsis thaliana GN=CYCU3-1 PE=1 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|Q9LJ45|CCU11_ARATH Cyclin-U1-1 OS=Arabidopsis thaliana GN=CYCU1-1 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|Q7XC35|CCP41_ORYSJ Cyclin-P4-1 OS=Oryza sativa subsp. japonica GN=CYCP4-1 PE=2 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
>sp|Q9SHD3|CCU21_ARATH Cyclin-U2-1 OS=Arabidopsis thaliana GN=CYCU2-1 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|Q7FAT5|CCP21_ORYSJ Cyclin-P2-1 OS=Oryza sativa subsp. japonica GN=CYCP2-1 PE=2 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 ?
Query217
255559444219 cyclin-dependent protein kinase, putativ 1.0 0.990 0.721 4e-90
225436916226 PREDICTED: cyclin-P3-1-like isoform 1 [V 0.995 0.955 0.738 2e-89
225436914247 PREDICTED: cyclin-P3-1-like isoform 2 [V 0.995 0.874 0.738 2e-89
224082636219 predicted protein [Populus trichocarpa] 1.0 0.990 0.716 2e-89
224066505219 predicted protein [Populus trichocarpa] 1.0 0.990 0.689 3e-86
388504686218 unknown [Medicago truncatula] 0.995 0.990 0.678 9e-81
356572186246 PREDICTED: cyclin-P3-1-like [Glycine max 0.995 0.878 0.678 3e-80
255645377246 unknown [Glycine max] 0.995 0.878 0.678 9e-80
388503884214 unknown [Lotus japonicus] 0.981 0.995 0.678 1e-79
449462330218 PREDICTED: cyclin-P3-1-like [Cucumis sat 1.0 0.995 0.637 1e-79
>gi|255559444|ref|XP_002520742.1| cyclin-dependent protein kinase, putative [Ricinus communis] gi|223540127|gb|EEF41704.1| cyclin-dependent protein kinase, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  336 bits (861), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 158/219 (72%), Positives = 188/219 (85%), Gaps = 2/219 (0%)

Query: 1   MGTLALDTESVGTDIYRMLGLKDLGKGTVGSPKILSLIGRLLEKSVQKNEMLLDTIKTKD 60
           MGTLALDTE+V  D+Y  LGLK LGK  +G+P+ L+L+  LLE+SVQKNEMLL+T +  D
Sbjct: 1   MGTLALDTENVDLDVYLTLGLKALGKRILGTPRALTLLSSLLERSVQKNEMLLETTQIND 60

Query: 61  V-TIFHGLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQKTDGHLTSLNVHRLL 119
             T FHG RAPT+SI+QYIDRIFKY  CSPSCF++AHIY+DRF+Q TD HLTSLNVHRLL
Sbjct: 61  SRTEFHGSRAPTVSIRQYIDRIFKYSGCSPSCFIVAHIYVDRFIQNTDIHLTSLNVHRLL 120

Query: 120 ITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRLQVNVETFHKFCSQ 179
           ITSVMVAAKFIDDAFFNNAYYA+VGGVST E+N++E+KFLFS+DFRLQV+V TF ++CSQ
Sbjct: 121 ITSVMVAAKFIDDAFFNNAYYAKVGGVSTEELNKLEMKFLFSIDFRLQVSVNTFGRYCSQ 180

Query: 180 LGKEAAEGLQIDRPIQACKIKENWSSKGDAA-CVPTIAR 217
           L KEAAEG QI+RPIQ C+IKE+WS+K D+  C PTIAR
Sbjct: 181 LEKEAAEGHQIERPIQVCRIKESWSNKDDSTPCAPTIAR 219

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225436916|ref|XP_002274682.1| PREDICTED: cyclin-P3-1-like isoform 1 [Vitis vinifera] Back     alignment and taxonomy information
>gi|225436914|ref|XP_002274732.1| PREDICTED: cyclin-P3-1-like isoform 2 [Vitis vinifera] Back     alignment and taxonomy information
>gi|224082636|ref|XP_002306774.1| predicted protein [Populus trichocarpa] gi|222856223|gb|EEE93770.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224066505|ref|XP_002302113.1| predicted protein [Populus trichocarpa] gi|222843839|gb|EEE81386.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|388504686|gb|AFK40409.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|356572186|ref|XP_003554251.1| PREDICTED: cyclin-P3-1-like [Glycine max] Back     alignment and taxonomy information
>gi|255645377|gb|ACU23185.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|388503884|gb|AFK40008.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|449462330|ref|XP_004148894.1| PREDICTED: cyclin-P3-1-like [Cucumis sativus] gi|449491500|ref|XP_004158917.1| PREDICTED: cyclin-P3-1-like isoform 2 [Cucumis sativus] 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 ?
Query217
TAIR|locus:2099192221 CYCP1;1 "cyclin p1;1" [Arabido 1.0 0.981 0.515 2.1e-52
TAIR|locus:2088743210 CYCP2;1 "cyclin p2;1" [Arabido 0.705 0.728 0.506 5.3e-40
TAIR|locus:2042421202 CYCP4;1 "AT2G44740" [Arabidops 0.695 0.747 0.522 6.8e-40
TAIR|locus:1009023243212 AT3G05327 [Arabidopsis thalian 0.801 0.820 0.469 2.9e-39
TAIR|locus:2183394216 CYCP4;3 "cyclin p4;3" [Arabido 0.700 0.703 0.448 5.1e-35
TAIR|locus:2151656219 CYCP4;2 "CYCLIN P4;2" [Arabido 0.695 0.689 0.458 1.2e-33
TAIR|locus:2055552222 cycp3;1 "cyclin p3;1" [Arabido 0.894 0.873 0.356 3.2e-33
TAIR|locus:2103391230 CYCP3;2 "cyclin p3;2" [Arabido 0.774 0.730 0.369 6.9e-31
DICTYBASE|DDB_G0277481 391 DDB_G0277481 [Dictyostelium di 0.672 0.373 0.384 1.9e-26
DICTYBASE|DDB_G0280425333 DDB_G0280425 [Dictyostelium di 0.691 0.450 0.381 4.6e-25
TAIR|locus:2099192 CYCP1;1 "cyclin p1;1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 114/221 (51%), Positives = 147/221 (66%)

Query:     1 MGTLALDTESVGTDIYRMLGLKDLGKGTVGSPKILSLIGRLLEKSVQKNEMLLDTIKTKD 60
             M +LA D   + +D+Y  LGL   GK     P +LS +   LE+S+  N      + + D
Sbjct:     1 MDSLATDPAFIDSDVYLRLGLIIEGKRLKKPPTVLSRLSSSLERSLLLNHDDKILLGSPD 60

Query:    61 -VTIFHGLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQKTDGHLTSLNVHRLL 119
              VT+F G   P ISI  Y+DRIFKY  CSPSCFVIAHIY+D FL KT   L  LNVHRL+
Sbjct:    61 SVTVFDGRSPPEISIAHYLDRIFKYSCCSPSCFVIAHIYIDHFLHKTRALLKPLNVHRLI 120

Query:   120 ITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRLQVNVETFHKFCSQ 179
             IT+VM+AAK  DD +FNNAYYARVGGV+T E+NR+E++ LF+LDF+LQV+ +TFH  C Q
Sbjct:   121 ITTVMLAAKVFDDRYFNNAYYARVGGVTTRELNRLEMELLFTLDFKLQVDPQTFHTHCCQ 180

Query:   180 LGKEAAEGLQIDRPI-QACKI-KENWSSKG-DAACVPTIAR 217
             L K+  +G QI+ PI +AC+  KE W  +  D+ C  T AR
Sbjct:   181 LEKQNRDGFQIEWPIKEACRANKETWQKRTPDSLCSQTTAR 221
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:0010440 "stomatal lineage progression" evidence=RCA
TAIR|locus:2088743 CYCP2;1 "cyclin p2;1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2042421 CYCP4;1 "AT2G44740" [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: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
TAIR|locus:2055552 cycp3;1 "cyclin p3;1" [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
DICTYBASE|DDB_G0277481 DDB_G0277481 [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0280425 DDB_G0280425 [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 number0.59090.89400.8220yesno
Q8LB60CCU31_ARATHNo assigned EC number0.51560.99070.9728yesno

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:
estExt_fgenesh4_pg.C_LG_V1250
SubName- Full=Putative uncharacterized protein; (219 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 ?
Query217
pfam08613140 pfam08613, Cyclin, Cyclin 8e-36
pfam00134127 pfam00134, Cyclin_N, Cyclin, N-terminal domain 5e-12
>gnl|CDD|204002 pfam08613, Cyclin, Cyclin Back     alignment and domain information 
 Score =  122 bits (309), Expect = 8e-36
 Identities = 48/106 (45%), Positives = 71/106 (66%), Gaps = 3/106 (2%)

Query: 64  FHGLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQ---KTDGHLTSLNVHRLLI 120
           F+    P+IS+ QY+ RI KY   SP   + A IY+DR ++   K    +TSLNVHRLL+
Sbjct: 35  FYSKAVPSISLTQYLSRIQKYCPTSPDVLLSALIYLDRIVKRCDKPTITVTSLNVHRLLL 94

Query: 121 TSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRL 166
           T++ VA KF+ D  ++N+ +A+VGG+S  E+N +E+ FLF +DF L
Sbjct: 95  TALTVATKFLSDGSYSNSRFAKVGGISLHELNHLEIDFLFLVDFDL 140

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 217
PF08613149 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu 100.0
KOG1674218 consensus Cyclin [General function prediction only 99.96
KOG1675343 consensus Predicted cyclin [General function predi 99.61
PF00134127 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR 99.32
cd0004388 CYCLIN Cyclin box fold. Protein binding domain fun 98.83
smart0038583 CYCLIN domain present in cyclins, TFIIB and Retino 98.6
KOG0656 335 consensus G1/S-specific cyclin D [Cell cycle contr 98.23
KOG0653391 consensus Cyclin B and related kinase-activating p 97.7
TIGR00569305 ccl1 cyclin ccl1. University). 97.55
KOG0655 408 consensus G1/S-specific cyclin E [Cell cycle contr 97.39
COG5333297 CCL1 Cdk activating kinase (CAK)/RNA polymerase II 97.07
COG5024440 Cyclin [Cell division and chromosome partitioning] 96.85
KOG4164497 consensus Cyclin ik3-1/CABLES [Cell cycle control, 96.17
KOG0794264 consensus CDK8 kinase-activating protein cyclin C 94.49
KOG0834 323 consensus CDK9 kinase-activating protein cyclin T 93.77
PRK00423310 tfb transcription initiation factor IIB; Reviewed 93.72
KOG0835 367 consensus Cyclin L [General function prediction on 91.24
KOG1674218 consensus Cyclin [General function prediction only 90.17
PRK00423310 tfb transcription initiation factor IIB; Reviewed 89.98
KOG2496 325 consensus Cdk activating kinase (CAK)/RNA polymera 88.24
PF0038271 TFIIB: Transcription factor TFIIB repeat; InterPro 83.19
>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=7e-35  Score=236.24  Aligned_cols=134  Identities=40%  Similarity=0.758  Sum_probs=101.0

Q ss_pred             hHHHHHHHHHHHHHHhhhccccccCC-----------CCcccccCCCCCchhHHHHHHHHHHHcCCCchHHHHHHHHHHH
Q 027897           33 KILSLIGRLLEKSVQKNEMLLDTIKT-----------KDVTIFHGLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDR  101 (217)
Q Consensus        33 ~~l~~ia~~Le~~i~~nd~~~~~~~~-----------~~~~~F~~~~~P~isi~~yl~rI~~~~~~s~~~~ilALiYidR  101 (217)
                      +++..|+.++++++..|+.....++.           ...+.|++..+|+++|.+|+.||+++++|+++|+++|++||+|
T Consensus         2 ~~~~~i~~~l~~~~~~n~~~~~~s~~~~~~~~~~~~~~~~~~F~~~~~p~i~i~~fl~ri~~~~~~s~~~~i~aliYl~R   81 (149)
T PF08613_consen    2 KLVQSIARQLDRLINNNESTAQSSSSSSSPSSPFQQSPKISQFHSQSVPSISIRDFLSRILKYTQCSPECLILALIYLDR   81 (149)
T ss_dssp             HHHHHHHHHHHHHHHHHH--------------T---------T--SS--SS-HHHHHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccCchhhhhcccccccccccccccccccccCCCCCCCcHHHHHHHHHHHcCCChHHHHHHHHHHHH
Confidence            57899999999999999876443211           1267899999999999999999999999999999999999999


Q ss_pred             Hhc---cCCCccccccHHHHHHHHHHhhhhhcccCcccccccccccCCCHHHHHHHHHHHHHhCCCce
Q 027897          102 FLQ---KTDGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRL  166 (217)
Q Consensus       102 l~~---~~~~~i~~~n~hRL~ltal~lAsKf~dD~~~sN~~~akv~gvs~~eLN~LE~~FL~lLd~~L  166 (217)
                      +.+   .+.+.+++.|+||++++|+|||+||+||.+|+|++||+++|++++|||.||++||.+|||+|
T Consensus        82 l~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~eln~lE~~fL~~l~~~L  149 (149)
T PF08613_consen   82 LRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKELNELEREFLKLLDYNL  149 (149)
T ss_dssp             HHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHHHHHHHHHHHHHTTT--
T ss_pred             HHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHHHHHHHHHHHHHCCCcC
Confidence            998   68899999999999999999999999999999999999999999999999999999999997

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
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>TIGR00569 ccl1 cyclin ccl1 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
>COG5024 Cyclin [Cell division and chromosome partitioning] Back     alignment and domain information
>KOG4164 consensus Cyclin ik3-1/CABLES [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
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>PRK00423 tfb transcription initiation factor IIB; Reviewed 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
>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
>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 ?
Query217
2pk9_B293 Structure Of The Pho85-pho80 Cdk-cyclin Complex Of 4e-13
>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 = 71.2 bits (173), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 49/138 (35%), Positives = 74/138 (53%), Gaps = 7/138 (5%)
Query: 34  ILSLIGRLLEKSVQKNEMLLDTIKTKD---VTIFHGLRAPTISIQQYIDRIFKYGACSPS 90
           ++ LI R+L   +  NE    T K+ D   +T +H    P ISI  Y  R+ K+ +    
Sbjct: 35  LVVLISRMLVSLIAINENSA-TKKSDDQITLTRYHSKIPPNISIFNYFIRLTKFSSLE-H 92
Query: 91  CFVIAHIYMDRFLQKT--DGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVGGVST 148
           C ++  +Y    LQ    D  L SL  HR L+T+  VA K + D+F  NA+YA+VGGV  
Sbjct: 93  CVLMTSLYYIDLLQTVYPDFTLNSLTAHRFLLTATTVATKGLCDSFSTNAHYAKVGGVRC 152
Query: 149 AEMNRMEVKFLFSLDFRL 166
            E+N +E  FL  +++R+
Sbjct: 153 HELNILENDFLKRVNYRI 170

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query217
2pmi_B293 PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de 7e-47
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-08
3g33_B306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 5e-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 =  155 bits (392), Expect = 7e-47
 Identities = 43/156 (27%), Positives = 70/156 (44%), Gaps = 3/156 (1%)

Query: 32  PKILSLIGRLLEKSVQKNEMLLDTIK--TKDVTIFHGLRAPTISIQQYIDRIFKYGACSP 89
             ++ LI R+L   +  NE            +T +H    P ISI  Y  R+ K+ +   
Sbjct: 33  TDLVVLISRMLVSLIAINENSATKKSDDQITLTRYHSKIPPNISIFNYFIRLTKFSSLEH 92

Query: 90  SCFVIAHIYMDRFLQKTDGH-LTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVGGVST 148
              + +  Y+D          L SL  HR L+T+  VA K + D+F  NA+YA+VGGV  
Sbjct: 93  CVLMTSLYYIDLLQTVYPDFTLNSLTAHRFLLTATTVATKGLCDSFSTNAHYAKVGGVRC 152

Query: 149 AEMNRMEVKFLFSLDFRLQVNVETFHKFCSQLGKEA 184
            E+N +E  FL  +++R+            +  ++ 
Sbjct: 153 HELNILENDFLKRVNYRIIPRDHNITLCSIEQKQKK 188
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query217
2pmi_B293 PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de 100.0
1f5q_B252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 98.77
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 98.73
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 98.71
3g33_B306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 98.71
2w96_A271 G1/S-specific cyclin-D1; serine/threonine-protein 98.68
2b9r_A269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 98.67
2cch_B260 Cyclin A2, cyclin-A; complex(transferase/cell divi 98.65
1w98_B283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 98.65
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 98.3
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 98.3
2ivx_A257 Cyclin-T2; transcription regulation, cell division 98.23
3rgf_B285 Cyclin-C; protein kinase complex, transferase,tran 98.12
2pk2_A 358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 97.99
1jkw_A 323 Cyclin H; cell cycle, cell division, nuclear prote 97.92
1c9b_A207 General transcription factor IIB; protein-DNA comp 97.86
1ais_B200 TFB TFIIB, protein (transcription initiation facto 97.4
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 93.7
1ais_B200 TFB TFIIB, protein (transcription initiation facto 92.92
1c9b_A207 General transcription factor IIB; protein-DNA comp 91.62
4bbr_M345 Transcription initiation factor IIB; RNA polymeras 84.17
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 81.08
2ivx_A257 Cyclin-T2; transcription regulation, cell division 80.89
3rgf_B285 Cyclin-C; protein kinase complex, transferase,tran 80.08
>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=4.1e-39  Score=284.48  Aligned_cols=152  Identities=29%  Similarity=0.405  Sum_probs=138.2

Q ss_pred             CchhHHHHHHHHHHHHHHhhhccccccC--CCCcccccCCCCCchhHHHHHHHHHHHcCCCchHHHHHHHHHHHHhc-cC
Q 027897           30 GSPKILSLIGRLLEKSVQKNEMLLDTIK--TKDVTIFHGLRAPTISIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQ-KT  106 (217)
Q Consensus        30 ~~p~~l~~ia~~Le~~i~~nd~~~~~~~--~~~~~~F~~~~~P~isi~~yl~rI~~~~~~s~~~~ilALiYidRl~~-~~  106 (217)
                      +..+++.+||.+|+++|+.||..+...+  ...++.||+..+|+|+|++|+.||+++++|+++|+++|++||+|+.. .+
T Consensus        31 ~~~dlv~~IA~~L~~LI~~Nd~~~~~~~~~~~~~t~F~~~~~P~ISI~~Yl~RI~k~t~ls~~~ll~ALvYLdRL~~~~p  110 (293)
T 2pmi_B           31 SRTDLVVLISRMLVSLIAINENSATKKSDDQITLTRYHSKIPPNISIFNYFIRLTKFSSLEHCVLMTSLYYIDLLQTVYP  110 (293)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHCC--------CCCCTTCCSSCCSSCHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHCT
T ss_pred             CHHHHHHHHHHHHHHHHHcCccccccccccccccccccCCCCCCCcHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhCC
Confidence            3458999999999999999998754322  12488999999999999999999999999999999999999999997 58


Q ss_pred             CCccccccHHHHHHHHHHhhhhhcccCcccccccccccCCCHHHHHHHHHHHHHhCCCceeecHHHHHHHHHHHH
Q 027897          107 DGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVGGVSTAEMNRMEVKFLFSLDFRLQVNVETFHKFCSQLG  181 (217)
Q Consensus       107 ~~~i~~~n~hRL~ltal~lAsKf~dD~~~sN~~~akv~gvs~~eLN~LE~~FL~lLd~~L~Vs~~e~~~y~~~L~  181 (217)
                      ++.+++.||||+|++|+|||+||+||.+|+|++||+|||++++|||.||++||.+|||+|+|+.++|..|+.++.
T Consensus       111 ~~~l~~~nvHRLlLtALmlAsK~ldD~~ysN~~wAkVgGisl~ELN~LE~eFL~lLdf~L~V~~ee~~~cy~E~~  185 (293)
T 2pmi_B          111 DFTLNSLTAHRFLLTATTVATKGLCDSFSTNAHYAKVGGVRCHELNILENDFLKRVNYRIIPRDHNITLCSIEQK  185 (293)
T ss_dssp             TCCCSTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTTTCCSCCTTHHHHHHHHSC
T ss_pred             CCccCCchHHHHHHHHHHHHHHhccccccChhHhhhccCcCHHHHHHHHHHHHHHcCCceeeCHHHHHHHHHHHh
Confidence            899999999999999999999999999999999999999999999999999999999999999999999887653
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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

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 217
d1bu2a1127 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saim 2e-06
d1w98b2140 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human 3e-06
d1g3nc1132 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma 1e-05
d2cchb1128 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [T 5e-05
d2i53a1144 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) 2e-04
>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} Length = 127 Back     information, alignment and structure

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Herpesvirus saimiri [TaxId: 10381]

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 14/83 (16%), Positives = 31/83 (37%), Gaps = 4/83 (4%)

Query: 87  CSPSCFVIAHIYMDRFLQKTDGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARV--G 144
              S F ++   +DR+L K  G   +L   ++    V++ +K         +    +   
Sbjct: 47  LDKSVFPLSVSILDRYLCKKQGTKKTL--QKIGAACVLIGSKIRTVKPMTVSKLTYLSCD 104

Query: 145 GVSTAEMNRMEVKFLFSLDFRLQ 167
             +  E+   E   L +L +  +
Sbjct: 105 CFTNLELINQEKDILEALKWDTE 127
>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
>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
>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Length = 144 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 ?
Query217
d1w98b2140 G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax 99.0
d2cchb1128 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 98.95
d1bu2a1127 Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} 98.93
d1g3nc1132 Viral cyclin {Kaposi's sarcoma-associated herpesvi 98.9
d1f5qb1141 Viral cyclin {Murine herpesvirus 68 [TaxId: 33708] 98.84
d2i53a1144 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 98.57
d1jkwa1151 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 98.34
d2ivxa1143 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 98.3
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 95.55
d1aisb295 Transcription factor IIB (TFIIB), core domain {Arc 94.97
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 94.85
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 93.31
>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=99.00  E-value=7.8e-10  Score=85.45  Aligned_cols=93  Identities=19%  Similarity=0.279  Sum_probs=81.1

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHhc-cCCCccccccHHHHHHHHHHhhhhhcccCccccccccccc--CCCHH
Q 027897           73 SIQQYIDRIFKYGACSPSCFVIAHIYMDRFLQ-KTDGHLTSLNVHRLLITSVMVAAKFIDDAFFNNAYYARVG--GVSTA  149 (217)
Q Consensus        73 si~~yl~rI~~~~~~s~~~~ilALiYidRl~~-~~~~~i~~~n~hRL~ltal~lAsKf~dD~~~sN~~~akv~--gvs~~  149 (217)
                      .+-+++.++....+++++++.+|..|+||+.. ++.  +.....+-+-++|+.||+|+.+......+.+..++  .++.+
T Consensus        45 ~lidW~~~v~~~~~l~~et~~lAv~llDryl~~~~~--v~~~~lqL~a~acL~IAsK~ee~~~~~~~~l~~~~~~~~t~~  122 (140)
T d1w98b2          45 ILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQEN--VVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGD  122 (140)
T ss_dssp             HHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCC--CCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTSSCHH
T ss_pred             HHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhcccc--ccHHHHhHHHHHHHHHHHHHcccCCCCHHHHHHHHcCCCCHH
Confidence            37789999999999999999999999999975 332  34567889999999999999988888888887764  48999


Q ss_pred             HHHHHHHHHHHhCCCcee
Q 027897          150 EMNRMEVKFLFSLDFRLQ  167 (217)
Q Consensus       150 eLN~LE~~FL~lLd~~L~  167 (217)
                      |+..||+..|..|+|+|+
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
>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} 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
>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