Citrus Sinensis ID: 018657

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-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350--
MSAESLDNSHSSSLYCGEEDAAAAADGGSDMVSCDTTDTWIFHNQSPAFDVVDDADADDVVSRLIDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLSSHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMSVLNWRLNSITPFDYLHYFISKLPASSSEPGSFTRFLWSSSDLIIRTTRVVNFLGFAPSTIAAAAVLCAAGESLDSPAICHQRLNEEMVRSCHQLMEEYLIDTCPSAQVKDQSEEPQVAPPSPVGVLDAAACGSCDTRSDNPGSSNQVEAELCAKRLRSSAPDVQQP
cccccccccccccEEccccccHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHcccccccccccEEEcccccccHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHccccccHHHHHcccccccccccccHHcccccccccccccccccccccccccccccccccccccccc
ccccHHcccccHHHHccHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHcccccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHcccccHccEEEEEEcccccHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHcHHHcccHHHHHHHHHHHHHHHcccccHHHHccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHccccccccccccccHHHcccccccccEEccccccccccEEEccccccccccc
msaesldnshssslycgeedaaaaadggsdmvscdttdtwifhnqspafdvvddadadDVVSRLIDresethhmlhpdylhrfrdcSVFVTARQDSINWILNVhanykfrpvTALLSVNYFDRflsshflplangwplqLLSVACLSLAAKMEETQVpllldlqifdprfvfepktvQRMELRVMSVLNWRlnsitpfdYLHYFISklpasssepgsftrflwsssdliiRTTRVvnflgfapSTIAAAAVLCAagesldspaichQRLNEEMVRSCHQLMEEYlidtcpsaqvkdqseepqvappspvgvldaaacgscdtrsdnpgssnQVEAELCAKRLrssapdvqqp
msaesldnshsssLYCGEEDAAAAADGGSDMVSCDTTDTWIFHNQSpafdvvddADADDVVSRLIDresethhmlhpdylHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLSSHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMSVLNWRLNSITPFDYLHYFISKLPASSSEPGSFTRFLWSSSDLIIRTTRVVNFLGFAPSTIAAAAVLCAAGESLDSPAICHQRLNEEMVRSCHQLMEEYLIDTCPSAQVKDQSEEPQVAPPSPVGVLDAAACGSCDtrsdnpgssNQVEAELCAKRlrssapdvqqp
MSAESLDNSHSSSLYCgeedaaaaadggSDMVSCDTTDTWIFHNQSPAFdvvddadaddvvSRLIDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLSSHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMSVLNWRLNSITPFDYLHYFISKLPASSSEPGSFTRFLWSSSDLIIRTTRVVNFLGFAPSTIAAAAVLCAAGESLDSPAICHQRLNEEMVRSCHQLMEEYLIDTCPSAQVKDQSEEPQVAPPSPVGVLDAAACGSCDTRSDNPGSSNQVEAELCAKRLRSSAPDVQQP
******************************MVSCDTTDTWIFHNQSPAFDVVDDADADDVVSRLIDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLSSHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMSVLNWRLNSITPFDYLHYFISKLP******GSFTRFLWSSSDLIIRTTRVVNFLGFAPSTIAAAAVLCAAGESLDSPAICHQRLNEEMVRSCHQLMEEYLIDTC***************************************************************
*********HSSSLYCGEEDAAAAADGGSDMVSCDTTDTWIFHNQSPAFDVVDDADADDVVSRLIDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLSSHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMSVLNWRLNSITPFDYLHYFISKLPASSSEPGSFTRFLWSSSDLIIRTTRVVNFLGFAPSTIAAAAVLCAAGESLDSPAICHQRLNEEMVRSCHQLMEEYL*************************VLDAAAC***********************************
*************LYCGEED**********MVSCDTTDTWIFHNQSPAFDVVDDADADDVVSRLIDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLSSHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMSVLNWRLNSITPFDYLHYFISKLPASSSEPGSFTRFLWSSSDLIIRTTRVVNFLGFAPSTIAAAAVLCAAGESLDSPAICHQRLNEEMVRSCHQLMEEYLIDTCPSA**************SPVGVLDAAACGSC*************EAELCAKRL**********
*****************EEDA*A*******MVSCDTTDTWIFHNQSPAFDVVDDADADDVVSRLIDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLSSHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMSVLNWRLNSITPFDYLHYFISKLPASSSEPGSFTRFLWSSSDLIIRTTRVVNFLGFAPSTIAAAAVLCAAGESLDSPAICHQRLNEEMVRSCHQLMEEYLIDTCPSAQVKDQSEEPQVAPPSPVGVLDAAACGSCDT*S****************************
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MSAESLDNSHSSSLYCGEEDAAAAADGGSDMVSCDTTDTWIFHNQSPAFDVVDDADADDVVSRLIDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLSSHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMSVLNWRLNSITPFDYLHYFISKLPASSSEPGSFTRFLWSSSDLIIRTTRVVNFLGFAPSTIAAAAVLCAAGESLDSPAICHQRLNEEMVRSCHQLMEEYLIDTCPSAQVKDQSEEPQVAPPSPVGVLDAAACGSCDTRSDNPGSSNQVEAELCAKRLRSSAPDVQQP
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 ?
Query352 2.2.26 [Sep-21-2011]
P42751339 Cyclin-D1-1 OS=Arabidopsi yes no 0.738 0.766 0.406 7e-52
Q6YXH8356 Cyclin-D4-1 OS=Oryza sati yes no 0.75 0.741 0.437 2e-48
Q69QB8342 Cyclin-D3-1 OS=Oryza sati no no 0.909 0.935 0.380 9e-48
Q8LGA1308 Cyclin-D4-1 OS=Arabidopsi no no 0.693 0.792 0.381 7e-47
Q8LHA8356 Cyclin-D2-2 OS=Oryza sati no no 0.801 0.792 0.385 3e-46
Q0J233308 Cyclin-D2-1 OS=Oryza sati no no 0.730 0.834 0.400 7e-46
Q8H339354 Cyclin-D1-2 OS=Oryza sati no no 0.633 0.629 0.440 8e-46
Q4KYM5383 Cyclin-D4-2 OS=Oryza sati no no 0.559 0.514 0.485 1e-44
Q0WQN9298 Cyclin-D4-2 OS=Arabidopsi no no 0.633 0.748 0.419 1e-43
P42752361 Cyclin-D2-1 OS=Arabidopsi no no 0.650 0.634 0.394 6e-42
>sp|P42751|CCD11_ARATH Cyclin-D1-1 OS=Arabidopsis thaliana GN=CYCD1-1 PE=1 SV=3 Back     alignment and function desciption
 Score =  204 bits (520), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 119/293 (40%), Positives = 174/293 (59%), Gaps = 33/293 (11%)

Query: 5   SLDNSHSSSLYCGEEDAAAAADGGSDMVSCDTTDTWIFHNQSPAFDVVDDADADDVVSRL 64
           S+  S+   L+CGE+    + +   D  S +  D+W                  D ++  
Sbjct: 13  SVSFSNDMDLFCGEDSGVFSGESTVDFSSSEV-DSW----------------PGDSIACF 55

Query: 65  IDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRF 124
           I  E E H +   DYL RF+  S+  +AR+DS+ WIL V A Y F+P+TA L+VNY DRF
Sbjct: 56  I--EDERHFVPGHDYLSRFQTRSLDASAREDSVAWILKVQAYYNFQPLTAYLAVNYMDRF 113

Query: 125 LSSHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRV 184
           L +  LP  +GWP+QLL+VACLSLAAKMEE  VP L D Q+   +++FE KT++RMEL V
Sbjct: 114 LYARRLPETSGWPMQLLAVACLSLAAKMEEILVPSLFDFQVAGVKYLFEAKTIKRMELLV 173

Query: 185 MSVLNWRLNSITPFDYLHYFISKLPASSSEPGSFTRFLWS-SSDLIIRTTRVVNFLGFAP 243
           +SVL+WRL S+TPFD++ +F  K+  S    G+F  F  S ++++I+   +  +FL + P
Sbjct: 174 LSVLDWRLRSVTPFDFISFFAYKIDPS----GTFLGFFISHATEIILSNIKEASFLEYWP 229

Query: 244 STIAAAAVLCAAGE--SL-------DSPAICHQRLNEEMVRSCHQLMEEYLID 287
           S+IAAAA+LC A E  SL       +SP      L++E +  C++LM+   I+
Sbjct: 230 SSIAAAAILCVANELPSLSSVVNPHESPETWCDGLSKEKIVRCYRLMKAMAIE 282
May activate cell cycle in the root apical meristem (RAM) and promote embryonic root (radicle) protrusion.
Arabidopsis thaliana (taxid: 3702)
>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|Q69QB8|CCD31_ORYSJ Cyclin-D3-1 OS=Oryza sativa subsp. japonica GN=CYCD3-1 PE=2 SV=2 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|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|Q8H339|CCD12_ORYSJ Cyclin-D1-2 OS=Oryza sativa subsp. japonica GN=CYCD1-2 PE=3 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|Q0WQN9|CCD42_ARATH Cyclin-D4-2 OS=Arabidopsis thaliana GN=CYCD4-2 PE=1 SV=2 Back     alignment and function description
>sp|P42752|CCD21_ARATH Cyclin-D2-1 OS=Arabidopsis thaliana GN=CYCD2-1 PE=1 SV=3 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 ?
Query352
224056262400 predicted protein [Populus trichocarpa] 0.931 0.82 0.607 1e-103
307135950347 cyclin d protein [Cucumis melo subsp. me 0.849 0.861 0.65 1e-97
225429023354 PREDICTED: cyclin-D4-1 [Vitis vinifera] 0.917 0.912 0.583 5e-93
356574327324 PREDICTED: cyclin-D4-1-like [Glycine max 0.798 0.867 0.635 3e-91
147767172334 hypothetical protein VITISV_043227 [Viti 0.880 0.928 0.583 6e-90
449465087330 PREDICTED: cyclin-D1-1-like [Cucumis sat 0.829 0.884 0.613 3e-89
356534274299 PREDICTED: cyclin-D1-1-like [Glycine max 0.801 0.943 0.634 7e-89
224056264262 predicted protein [Populus trichocarpa] 0.713 0.958 0.661 7e-86
224103775285 predicted protein [Populus trichocarpa] 0.670 0.828 0.647 3e-80
374349348334 cyclin D-type [Persea americana] 0.767 0.808 0.546 3e-77
>gi|224056262|ref|XP_002298781.1| predicted protein [Populus trichocarpa] gi|222846039|gb|EEE83586.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 217/357 (60%), Positives = 266/357 (74%), Gaps = 29/357 (8%)

Query: 12  SSLYCGEEDAAAAADGGSDMVSCDTTDTWI-----FHNQSPAFDVVDDADADDVVSRLID 66
           +SLYCGE+         S++V  D  DTWI     F   SP+  V   +D ++ +++LID
Sbjct: 57  NSLYCGED--------VSEVVQRDA-DTWISSHLQFPPPSPSIIVSPPSD-ENTITKLID 106

Query: 67  RESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLS 126
             SE+H M   DYLHR R  S+ +TARQDSINWIL V+A+Y+FRP+TALLSVNYFDRFLS
Sbjct: 107 --SESHFMPLSDYLHRCRHRSIDITARQDSINWILKVYAHYEFRPLTALLSVNYFDRFLS 164

Query: 127 SHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMS 186
           S+ LP  NGWP QLLSVACLSLAAKMEE  VPLLLDLQI +P F+FEPK +Q+MELRVM+
Sbjct: 165 SYSLP-ENGWPFQLLSVACLSLAAKMEEPDVPLLLDLQILEPGFIFEPKNIQKMELRVMA 223

Query: 187 VLNWRLNSITPFDYLHYFISKLPA-SSSEPGSFTRFLWSSSDLIIRTTRVVNFLGFAPST 245
            LNWRL S TPFDYL YFISKLP+ SS++P +F R L  S+DLI+ TTRV++FLGFAPST
Sbjct: 224 NLNWRLRSTTPFDYLDYFISKLPSCSSTKPENFDRVLKKSADLILNTTRVIDFLGFAPST 283

Query: 246 IAAAAVLCAAGESLDSPAI-------CHQRLNEEMVRSCHQLMEEYLIDTCPSAQVKDQS 298
           +AAAAV+ AAG++ D+  +        H+R+N EMVRSCHQL+EEYLIDTCP+A++KD S
Sbjct: 284 VAAAAVISAAGKNFDTIPLKAGVGQFFHERVNREMVRSCHQLIEEYLIDTCPTARLKDLS 343

Query: 299 EEPQVAPPSPVGVLD-AAACGSCDTRSDNP--GSSNQVEAELCAKRLRSSAPDVQQP 352
           ++  V P SP GVLD AAACGSC TRS+NP   SS   E E   KRLRS+A DVQ+P
Sbjct: 344 DDALVDPASPAGVLDAAAACGSCSTRSENPISASSQAPETEPIIKRLRSTATDVQEP 400

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|307135950|gb|ADN33810.1| cyclin d protein [Cucumis melo subsp. melo] Back     alignment and taxonomy information
>gi|225429023|ref|XP_002267356.1| PREDICTED: cyclin-D4-1 [Vitis vinifera] gi|296083031|emb|CBI22435.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|356574327|ref|XP_003555300.1| PREDICTED: cyclin-D4-1-like [Glycine max] Back     alignment and taxonomy information
>gi|147767172|emb|CAN66965.1| hypothetical protein VITISV_043227 [Vitis vinifera] Back     alignment and taxonomy information
>gi|449465087|ref|XP_004150260.1| PREDICTED: cyclin-D1-1-like [Cucumis sativus] gi|449521665|ref|XP_004167850.1| PREDICTED: cyclin-D1-1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|356534274|ref|XP_003535682.1| PREDICTED: cyclin-D1-1-like [Glycine max] Back     alignment and taxonomy information
>gi|224056264|ref|XP_002298782.1| predicted protein [Populus trichocarpa] gi|159025703|emb|CAN88852.1| D1-type cyclin [Populus trichocarpa] gi|222846040|gb|EEE83587.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224103775|ref|XP_002313188.1| predicted protein [Populus trichocarpa] gi|159025701|emb|CAN88851.1| D1-type cyclin [Populus trichocarpa] gi|222849596|gb|EEE87143.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|374349348|gb|AEZ35254.1| cyclin D-type [Persea americana] 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 ?
Query352
TAIR|locus:2020663339 CYCD1;1 "CYCLIN D1;1" [Arabido 0.613 0.637 0.465 1.2e-47
TAIR|locus:2142504298 CYCD4;2 "AT5G10440" [Arabidops 0.605 0.714 0.437 5.9e-41
TAIR|locus:2124331376 CYCD3;1 "CYCLIN D3;1" [Arabido 0.727 0.680 0.339 5.7e-36
TAIR|locus:2157172367 CYCD3;2 "AT5G67260" [Arabidops 0.775 0.743 0.328 2.2e-34
TAIR|locus:2083128361 CYCD3;3 "AT3G50070" [Arabidops 0.701 0.684 0.348 5.8e-34
TAIR|locus:2120081323 CYCD5;1 "AT4G37630" [Arabidops 0.775 0.845 0.311 3.5e-27
TAIR|locus:2125522302 CYCD6;1 "AT4G03270" [Arabidops 0.738 0.860 0.314 8.4e-26
UNIPROTKB|Q10QA2345 CYCD5-3 "Cyclin-D5-3" [Oryza s 0.696 0.710 0.314 2e-24
UNIPROTKB|P50755291 ccnd1 "G1/S-specific cyclin-D1 0.613 0.742 0.305 3.6e-18
ZFIN|ZDB-GENE-980526-176291 ccnd1 "cyclin D1" [Danio rerio 0.644 0.780 0.3 9.1e-17
TAIR|locus:2020663 CYCD1;1 "CYCLIN D1;1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 498 (180.4 bits), Expect = 1.2e-47, P = 1.2e-47
 Identities = 107/230 (46%), Positives = 152/230 (66%)

Query:    68 ESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLSS 127
             E E H +   DYL RF+  S+  +AR+DS+ WIL V A Y F+P+TA L+VNY DRFL +
Sbjct:    57 EDERHFVPGHDYLSRFQTRSLDASAREDSVAWILKVQAYYNFQPLTAYLAVNYMDRFLYA 116

Query:   128 HFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMSV 187
               LP  +GWP+QLL+VACLSLAAKMEE  VP L D Q+   +++FE KT++RMEL V+SV
Sbjct:   117 RRLPETSGWPMQLLAVACLSLAAKMEEILVPSLFDFQVAGVKYLFEAKTIKRMELLVLSV 176

Query:   188 LNWRLNSITPFDYLHYFISKLPASSSEPGSFTRFLWS-SSDLIIRTTRVVNFLGFAPSTI 246
             L+WRL S+TPFD++ +F  K+  S    G+F  F  S ++++I+   +  +FL + PS+I
Sbjct:   177 LDWRLRSVTPFDFISFFAYKIDPS----GTFLGFFISHATEIILSNIKEASFLEYWPSSI 232

Query:   247 AAAAVLCAAGE--SLDSPAICHQR-------LNEEMVRSCHQLMEEYLID 287
             AAAA+LC A E  SL S    H+        L++E +  C++LM+   I+
Sbjct:   233 AAAAILCVANELPSLSSVVNPHESPETWCDGLSKEKIVRCYRLMKAMAIE 282
GO:0005634 "nucleus" evidence=ISM;IEA
GO:0016538 "cyclin-dependent protein serine/threonine kinase regulator activity" evidence=ISS
GO:0051726 "regulation of cell cycle" evidence=ISS
GO:0005515 "protein binding" evidence=IPI
GO:0000278 "mitotic cell cycle" evidence=RCA
GO:0010440 "stomatal lineage progression" evidence=RCA
GO:0042023 "DNA endoreduplication" evidence=RCA
GO:0045736 "negative regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=RCA
TAIR|locus:2142504 CYCD4;2 "AT5G10440" [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
TAIR|locus:2120081 CYCD5;1 "AT4G37630" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2125522 CYCD6;1 "AT4G03270" [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
UNIPROTKB|P50755 ccnd1 "G1/S-specific cyclin-D1" [Xenopus laevis (taxid:8355)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-980526-176 ccnd1 "cyclin D1" [Danio rerio (taxid:7955)] 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:
grail3.0017029801
SubName- Full=D1-type cyclin; (262 aa)
(Populus trichocarpa)
Predicted Functional Partners:
gw1.IV.1616.1
synthase/transferase (EC-2.4.1.21) (1017 aa)
      • 0.510
gw1.I.2314.1
hypothetical protein (887 aa)
      • 0.510
fgenesh4_pg.C_LG_V001651
SubName- Full=Starch branching enzyme I; (701 aa)
      • 0.510
eugene3.00280310
SubName- Full=Starch branching enzyme II; (730 aa)
      • 0.510

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 ?
Query352
pfam00134127 pfam00134, Cyclin_N, Cyclin, N-terminal domain 1e-37
cd0004388 cd00043, CYCLIN, Cyclin box fold 8e-15
smart0038583 smart00385, CYCLIN, domain present in cyclins, TFI 1e-13
COG5024440 COG5024, COG5024, Cyclin [Cell division and chromo 8e-13
COG5333297 COG5333, CCL1, Cdk activating kinase (CAK)/RNA pol 5e-07
pfam02984117 pfam02984, Cyclin_C, Cyclin, C-terminal domain 0.004
>gnl|CDD|215740 pfam00134, Cyclin_N, Cyclin, N-terminal domain Back     alignment and domain information 
 Score =  130 bits (330), Expect = 1e-37
 Identities = 48/127 (37%), Positives = 65/127 (51%), Gaps = 6/127 (4%)

Query: 67  RESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLS 126
           RE E      PDYL +  D  +    R   I+W++ VH  +K  P T  L+VNY DRFLS
Sbjct: 7   RELEEEDRPPPDYLDQQPD--INPKMRAILIDWLVEVHEEFKLLPETLYLAVNYLDRFLS 64

Query: 127 SHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMS 186
              +P      LQL+ V CL +AAK EE   P + D         +  + + RMEL ++S
Sbjct: 65  KQPVPR---TKLQLVGVTCLLIAAKYEEIYPPSVEDFVYIT-DNAYTKEEILRMELLILS 120

Query: 187 VLNWRLN 193
            LNW L+
Sbjct: 121 TLNWDLS 127

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
>gnl|CDD|227640 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
>gnl|CDD|217307 pfam02984, Cyclin_C, Cyclin, C-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 352
KOG0656335 consensus G1/S-specific cyclin D [Cell cycle contr 100.0
KOG0655408 consensus G1/S-specific cyclin E [Cell cycle contr 100.0
KOG0653391 consensus Cyclin B and related kinase-activating p 100.0
COG5024440 Cyclin [Cell division and chromosome partitioning] 99.97
KOG0654359 consensus G2/Mitotic-specific cyclin A [Cell cycle 99.93
PF00134127 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR 99.91
TIGR00569305 ccl1 cyclin ccl1. University). 99.89
PRK00423310 tfb transcription initiation factor IIB; Reviewed 99.86
KOG0834323 consensus CDK9 kinase-activating protein cyclin T 99.85
KOG1597308 consensus Transcription initiation factor TFIIB [T 99.81
KOG0835367 consensus Cyclin L [General function prediction on 99.78
COG5333297 CCL1 Cdk activating kinase (CAK)/RNA polymerase II 99.68
KOG0794264 consensus CDK8 kinase-activating protein cyclin C 99.65
cd0004388 CYCLIN Cyclin box fold. Protein binding domain fun 99.47
COG1405285 SUA7 Transcription initiation factor TFIIIB, Brf1 99.44
smart0038583 CYCLIN domain present in cyclins, TFIIB and Retino 99.42
KOG2496325 consensus Cdk activating kinase (CAK)/RNA polymera 99.25
PF02984118 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR 99.16
PF08613149 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu 98.51
KOG1598 521 consensus Transcription initiation factor TFIIIB, 98.48
KOG4164497 consensus Cyclin ik3-1/CABLES [Cell cycle control, 98.15
smart0038583 CYCLIN domain present in cyclins, TFIIB and Retino 97.6
cd0004388 CYCLIN Cyclin box fold. Protein binding domain fun 97.59
PF0038271 TFIIB: Transcription factor TFIIB repeat; InterPro 97.13
KOG1674218 consensus Cyclin [General function prediction only 95.97
PRK00423310 tfb transcription initiation factor IIB; Reviewed 95.93
PF0038271 TFIIB: Transcription factor TFIIB repeat; InterPro 92.59
PF02984118 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR 87.35
COG1405285 SUA7 Transcription initiation factor TFIIIB, Brf1 87.24
KOG0834323 consensus CDK9 kinase-activating protein cyclin T 86.21
PF0827143 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013 81.8
KOG1675343 consensus Predicted cyclin [General function predi 80.89
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information 
Probab=100.00  E-value=1.1e-52  Score=393.21  Aligned_cols=220  Identities=40%  Similarity=0.650  Sum_probs=199.3

Q ss_pred             CCChHHHHHHHHHHhhhhccCCCccccccccCCCCCHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHhhhhcccccCC
Q 018657           54 DADADDVVSRLIDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLSSHFLPLA  133 (352)
Q Consensus        54 ~~~~~e~l~~ll~rE~E~~~~p~~~yl~~~~~~~i~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAv~~lDRfls~~~i~~~  133 (352)
                      -.+++|++.+|++  +|..|.|..+|.... +..+.+.+|.++++||++|+++++++++|++||+||||||++.+.+++.
T Consensus        42 ~~~~e~~i~~ll~--kEe~~~p~~~~~~~~-~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~  118 (335)
T KOG0656|consen   42 LLWDERVLANLLE--KEEQHNPSLDYFLCV-QKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKD  118 (335)
T ss_pred             ccccHHHHHHHHH--HHHHhCCCCchhhhc-ccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCC
Confidence            4588999999999  888999999876544 4678889999999999999999999999999999999999999999999


Q ss_pred             CCCchHHHHHHHHHHHhhhhccCCCcchhhhhhCCCCccCHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHhCCCCCC
Q 018657          134 NGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMSVLNWRLNSITPFDYLHYFISKLPASSS  213 (352)
Q Consensus       134 ~~~~lqLlavaCL~LAaK~eE~~~p~~~dl~~~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~  213 (352)
                      ++|++||+|+|||+||||+||+.+|.+.|++++++++.|.+++|+|||++||++|+|||+++||++|+++|+++++..  
T Consensus       119 k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~--  196 (335)
T KOG0656|consen  119 KPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQK--  196 (335)
T ss_pred             chHHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcc--
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999987  


Q ss_pred             CcchHHHHHHHHHHHHHHhcchhhhcCccHHHHHHHHHHHHHhccCCCCC-------ccccCCCHHHHHHHHH
Q 018657          214 EPGSFTRFLWSSSDLIIRTTRVVNFLGFAPSTIAAAAVLCAAGESLDSPA-------ICHQRLNEEMVRSCHQ  279 (352)
Q Consensus       214 ~~~~~~~~~~~~~~l~l~~~~~~~fl~~~PS~iAaAai~~a~~~~~~~~~-------~~~~~~~~e~l~~C~~  279 (352)
                       .+....+..++..+++.++.+++|++|+||+||||+++.+...+.+...       ..+.+++++.+..|++
T Consensus       197 -~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~  268 (335)
T KOG0656|consen  197 -DHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD  268 (335)
T ss_pred             -cchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence             3445678889999999999999999999999999999888765544321       1266788888888888

>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
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, 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
>TIGR00569 ccl1 cyclin ccl1 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
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>KOG0835 consensus Cyclin L [General function prediction only] 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
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription] Back     alignment and domain information
>cd00043 CYCLIN Cyclin box fold Back     alignment and domain information
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma 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
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 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
>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
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription] Back     alignment and domain information
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>cd00043 CYCLIN Cyclin box fold 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
>KOG1674 consensus Cyclin [General function prediction only] 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
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 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
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [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
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>KOG1675 consensus Predicted 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 ?
Query352
4bcq_B262 Structure Of Cdk2 In Complex With Cyclin A And A 2- 3e-10
4bco_B262 Structure Of Cdk2 In Complex With Cyclin A And A 2- 3e-10
4bcq_D262 Structure Of Cdk2 In Complex With Cyclin A And A 2- 4e-10
3dog_B264 Structure Of Thr 160 Phosphorylated Cdk2CYCLIN A IN 4e-10
3ddq_B269 Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN 5e-10
3ddp_B268 Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN 5e-10
3bht_B262 Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN 5e-10
2g9x_B262 Structure Of Thr 160 Phosphorylated Cdk2CYCLIN A IN 5e-10
1vin_A268 Bovine Cyclin A3 Length = 268 5e-10
3f5x_B256 Cdk-2-Cyclin Complex With Indazole Inhibitor 9 Boun 7e-10
1vyw_B265 Structure Of Cdk2CYCLIN A WITH PNU-292137 Length = 7e-10
1fin_B260 Cyclin A-Cyclin-Dependent Kinase 2 Complex Length = 7e-10
2x1n_B261 Truncation And Optimisation Of Peptide Inhibitors O 7e-10
1ogu_B260 Structure Of Human Thr160-phospho Cdk2/cyclin A Com 7e-10
1qmz_B259 Phosphorylated Cdk2-Cyclyin A-Substrate Peptide Com 7e-10
1jst_B258 Phosphorylated Cyclin-Dependent Kinase-2 Bound To C 7e-10
1e9h_B261 Thr 160 Phosphorylated Cdk2-Human Cyclin A3 Complex 9e-10
4i3z_B257 Structure Of Pcdk2CYCLINA BOUND TO ADP AND 2 MAGNES 2e-09
3qhr_B261 Structure Of A Pcdk2CYCLINA TRANSITION-State Mimic 3e-09
4ii5_B258 Structure Of Pcdk2/cyclina Bound To Adp And 1 Magne 3e-09
2w96_A271 Crystal Structure Of Cdk4 In Complex With A D-Type 4e-09
2w9z_A257 Crystal Structure Of Cdk4 In Complex With A D-Type 6e-09
2jgz_B260 Crystal Structure Of Phospho-Cdk2 In Complex With C 1e-08
2b9r_A269 Crystal Structure Of Human Cyclin B1 Length = 269 2e-07
3g33_B306 Crystal Structure Of Cdk4CYCLIN D3 Length = 306 2e-07
1w98_B283 The Structural Basis Of Cdk2 Activation By Cyclin E 2e-05
>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 
Iteration: 1

 Score = 62.8 bits (151), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 53/155 (34%), Positives = 79/155 (50%), Gaps = 11/155 (7%)
Query: 97  INWILNVHANYKFRPVTALLSVNYFDRFLSSHFLPLANGWPLQLLSVACLSLAAKMEETQ 156
           ++W++ V   YK +  T  L+VNY DRFLSS  + +  G  LQL+  A + LA+K EE  
Sbjct: 45  VDWLVEVGEEYKLQNETLHLAVNYIDRFLSS--MSVLRG-KLQLVGTAAMLLASKFEEIY 101
Query: 157 VPLLLDLQIFDPRFVFEPKTVQRMELRVMSVLNWRLNSITPFDYL-HYFISKLPASSSEP 215
            P + +  ++     +  K V RME  V+ VL + L + T   +L  YF+ + PA + + 
Sbjct: 102 PPEVAEF-VYITDDTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPA-NCKV 159
Query: 216 GSFTRFLWSSSDLIIRTTRVVNFLGFAPSTIAAAA 250
            S   FL   S           +L + PS IAAAA
Sbjct: 160 ESLAMFLGELS-----LIDADPYLKYLPSVIAAAA 189
>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|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|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|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|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|3F5X|B Chain B, Cdk-2-Cyclin Complex With Indazole Inhibitor 9 Bound At Its Active Site Length = 256 Back     alignment and structure
>pdb|1VYW|B Chain B, Structure Of Cdk2CYCLIN A WITH PNU-292137 Length = 265 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|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|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|4I3Z|B Chain B, Structure Of Pcdk2CYCLINA BOUND TO ADP AND 2 MAGNESIUM IONS Length = 257 Back     alignment and structure
>pdb|3QHR|B Chain B, Structure Of A Pcdk2CYCLINA TRANSITION-State Mimic Length = 261 Back     alignment and structure
>pdb|4II5|B Chain B, Structure Of Pcdk2/cyclina Bound To Adp And 1 Magnesium Ion Length = 258 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|2W9Z|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin Length = 257 Back     alignment and structure
>pdb|2JGZ|B Chain B, Crystal Structure Of Phospho-Cdk2 In Complex With Cyclin B Length = 260 Back     alignment and structure
>pdb|2B9R|A Chain A, Crystal Structure Of Human Cyclin B1 Length = 269 Back     alignment and structure
>pdb|3G33|B Chain B, Crystal Structure Of Cdk4CYCLIN D3 Length = 306 Back     alignment and structure
>pdb|1W98|B Chain B, The Structural Basis Of Cdk2 Activation By Cyclin E Length = 283 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 ?
Query352
2w96_A271 G1/S-specific cyclin-D1; serine/threonine-protein 2e-47
3g33_B306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 4e-47
2cch_B260 Cyclin A2, cyclin-A; complex(transferase/cell divi 3e-33
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 1e-32
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 1e-31
1f5q_B252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 2e-31
1w98_B283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 1e-30
2b9r_A269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 2e-29
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 2e-17
1jkw_A323 Cyclin H; cell cycle, cell division, nuclear prote 3e-14
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 1e-13
2pk2_A358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 3e-10
2ivx_A257 Cyclin-T2; transcription regulation, cell division 1e-08
3rgf_B285 Cyclin-C; protein kinase complex, transferase,tran 6e-08
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-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 =  160 bits (407), Expect = 2e-47
 Identities = 60/250 (24%), Positives = 109/250 (43%), Gaps = 23/250 (9%)

Query: 57  ADDVVSRLIDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALL 116
            D V+  +   ++E        Y    +   V  + R+    W+L V    K       L
Sbjct: 24  NDRVLRAM--LKAEETCAPSVSYFKCVQK-EVLPSMRKIVATWMLEVCEEQKCEEEVFPL 80

Query: 117 SVNYFDRFLSSHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKT 176
           ++NY DRFLS   +  +    LQLL   C+ +A+KM+ET +PL  +           P+ 
Sbjct: 81  AMNYLDRFLSLEPVKKSR---LQLLGATCMFVASKMKET-IPLTAEKLCIYTDNSIRPEE 136

Query: 177 VQRMELRVMSVLNWRLNSITPFDYLHYFISKLPASSSEPGSFTRFLWSSSDLIIRTTRVV 236
           + +MEL +++ L W L ++TP D++ +F+SK+P  + E     R    +   +      V
Sbjct: 137 LLQMELLLVNKLKWNLAAMTPHDFIEHFLSKMPE-AEENKQIIRKH--AQTFVALCATDV 193

Query: 237 NFLGFAPSTIAAAAVLCAA---GESLDSPAICHQ----------RLNEEMVRSCHQLMEE 283
            F+   PS +AA +V+ A         +  + +           + + + +R+C + +E 
Sbjct: 194 KFISNPPSMVAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSRVIKCDPDCLRACQEQIEA 253

Query: 284 YLIDTCPSAQ 293
            L  +   AQ
Sbjct: 254 LLESSLRQAQ 263
>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
>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
>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
>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
>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
>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
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Length = 269 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
>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 Length = 323 Back     alignment and structure
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Length = 235 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
>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* Length = 257 Back     alignment and structure
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens} Length = 285 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
>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 ?
Query352
3g33_B306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 100.0
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 100.0
2w96_A271 G1/S-specific cyclin-D1; serine/threonine-protein 100.0
1f5q_B252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 100.0
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 100.0
2cch_B260 Cyclin A2, cyclin-A; complex(transferase/cell divi 100.0
1w98_B283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 100.0
2b9r_A269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 100.0
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 100.0
2ivx_A257 Cyclin-T2; transcription regulation, cell division 100.0
3rgf_B285 Cyclin-C; protein kinase complex, transferase,tran 100.0
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 99.98
2pk2_A358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 99.97
1jkw_A323 Cyclin H; cell cycle, cell division, nuclear prote 99.96
1c9b_A207 General transcription factor IIB; protein-DNA comp 99.93
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 99.87
1ais_B200 TFB TFIIB, protein (transcription initiation facto 99.87
4bbr_M345 Transcription initiation factor IIB; RNA polymeras 99.76
2pmi_B293 PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de 98.48
1ais_B200 TFB TFIIB, protein (transcription initiation facto 96.94
1c9b_A207 General transcription factor IIB; protein-DNA comp 95.25
3h4c_A260 Transcription factor TFIIB-like; cyclin, transcrip 94.6
1dl6_A58 Transcription factor II B (TFIIB); zinc ribbon, ge 94.45
3k1f_M197 Transcription initiation factor IIB; RNA polymeras 91.01
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 89.72
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 89.44
2ivx_A257 Cyclin-T2; transcription regulation, cell division 88.98
1pft_A50 TFIIB, PFTFIIBN; N-terminal domain, transcription 88.6
3rgf_B285 Cyclin-C; protein kinase complex, transferase,tran 85.67
2pk2_A358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 85.2
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 82.52
4bbr_M345 Transcription initiation factor IIB; RNA polymeras 80.07
>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
Probab=100.00  E-value=4.7e-46  Score=352.39  Aligned_cols=224  Identities=21%  Similarity=0.337  Sum_probs=192.4

Q ss_pred             CChHHHHHHHHHHhhhhccCCCccccccccCCCCCHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHhhhhcccccCCC
Q 018657           55 ADADDVVSRLIDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLSSHFLPLAN  134 (352)
Q Consensus        55 ~~~~e~l~~ll~rE~E~~~~p~~~yl~~~~~~~i~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAv~~lDRfls~~~i~~~~  134 (352)
                      .|++|++.+|++  +|.++.|.++|+... +.++++.+|.++|+||++|+.+|+++++|+++||+|||||+++..+.+. 
T Consensus        36 ~~~~~i~~~l~~--~E~~~~p~~~y~~~~-q~~i~~~~R~~lvdwl~ev~~~~~l~~~t~~lAv~~lDRfls~~~v~~~-  111 (306)
T 3g33_B           36 LGDQRVLQSLLR--LEERYVPRASYFQCV-QREIKPHMRKMLAYWMLEVCEEQRCEEEVFPLAMNYLDRYLSCVPTRKA-  111 (306)
T ss_dssp             -CHHHHHHHHHH--HGGGGSCSSCCTTTS-TTTCCHHHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHCCCCGG-
T ss_pred             cchHHHHHHHHH--HHHHhCCCcHHHhhc-CccCCHHHHHHHHHHHHHHHHHhCCcHhHHHHHHHHHHHHHhcCCCcHH-
Confidence            378999999999  888999999999754 4689999999999999999999999999999999999999999998875 


Q ss_pred             CCchHHHHHHHHHHHhhhhccCCCcchhhhhhCCCCccCHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHhCCCCCCC
Q 018657          135 GWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMSVLNWRLNSITPFDYLHYFISKLPASSSE  214 (352)
Q Consensus       135 ~~~lqLlavaCL~LAaK~eE~~~p~~~dl~~~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~~  214 (352)
                        ++||+|+|||+||+|+||..+|.+.+++.. +++.|++++|++||+.||++|+|++++|||++||.+|+..++.....
T Consensus       112 --~lqLv~~tcL~lAsK~eE~~p~~~~~l~~~-~~~~~~~~~i~~mE~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~  188 (306)
T 3g33_B          112 --QLQLLGAVCMLLASKLRETTPLTIEKLCIY-TDHAVSPRQLRDWEVLVLGKLKWDLAAVIAHDFLAFILHRLSLPRDR  188 (306)
T ss_dssp             --GHHHHHHHHHHHHHHHHCSSCCCTTHHHHH-TTTSSCHHHHHHHHHHHHHHTTTCCCCCCGGGGHHHHHHTSSCCTTT
T ss_pred             --HHHHHHHHHHHHHHHhccCCCCCHHHHHHH-hccCccHHHHHHHHHHHHHHcCCccCCCCHHHHHHHHHHHcCCChhH
Confidence              999999999999999999999999999876 67899999999999999999999999999999999999998765322


Q ss_pred             cchHHHHHHHHHHHHHHhcchhhhcCccHHHHHHHHHHHHHhccCCCCCc---------cccCCCHHHHHHHHHHHHHHH
Q 018657          215 PGSFTRFLWSSSDLIIRTTRVVNFLGFAPSTIAAAAVLCAAGESLDSPAI---------CHQRLNEEMVRSCHQLMEEYL  285 (352)
Q Consensus       215 ~~~~~~~~~~~~~l~l~~~~~~~fl~~~PS~iAaAai~~a~~~~~~~~~~---------~~~~~~~e~l~~C~~~i~~~~  285 (352)
                         ...+...+..++..++.++.|+.|+||.||||||++|+......+.|         .++||++++|.+|++.|.+++
T Consensus       189 ---~~~~~~~a~~~l~lsl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~w~~~w~~~L~~~tg~~~~~l~~c~~~I~~l~  265 (306)
T 3g33_B          189 ---QALVKKHAQTFLALCATDYTFAMYPPSMIATGSIGAAVQGLGACSMSGDELTELLAGITGTEVDCLRACQEQIEAAL  265 (306)
T ss_dssp             ---HHHHHHHHHHHHHHHHHCGGGTTSCHHHHHHHHHHHHHHTCC---CCHHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHHHHHHHhhhhhccCCHHHHHHHHHHHHHHHhcCCCCchhhHHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence               22222333344445667899999999999999999997655443333         178999999999999999998


Q ss_pred             Hhh
Q 018657          286 IDT  288 (352)
Q Consensus       286 ~~~  288 (352)
                      .+.
T Consensus       266 ~~~  268 (306)
T 3g33_B          266 RES  268 (306)
T ss_dssp             HTC
T ss_pred             HHH
Confidence            763
>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
>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
>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
>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
>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
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_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
>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
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} 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
>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
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M 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
>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
>3h4c_A Transcription factor TFIIB-like; cyclin, transcription factor TFIIB repeat; 2.30A {Trypanosoma brucei brucei} Back     alignment and structure
>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A Back     alignment and structure
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} 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
>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
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1 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
>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
>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 352
d1w98b2140 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human 3e-29
d2cchb1128 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [T 8e-28
d1g3nc1132 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma 2e-25
d1f5qb1141 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesviru 2e-25
d1bu2a1127 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saim 2e-22
d2i53a1144 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) 3e-20
d2ivxa1143 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) 4e-18
d1jkwa1151 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo s 7e-17
>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 =  107 bits (269), Expect = 3e-29
 Identities = 33/139 (23%), Positives = 62/139 (44%), Gaps = 7/139 (5%)

Query: 55  ADADDVVSRLIDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTA 114
           A+ ++V   +     E  ++    +L +     +    R   ++W++ V   YK    T 
Sbjct: 9   ANREEVWKIM--LNKEKTYLRDQHFLEQHPL--LQPKMRAILLDWLMEVCEVYKLHRETF 64

Query: 115 LLSVNYFDRFLSSHFLPLANGWPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEP 174
            L+ ++FDR++++          LQL+ ++ L +AAK+EE   P L     +        
Sbjct: 65  YLAQDFFDRYMATQENV--VKTLLQLIGISSLFIAAKLEEIYPPKLHQF-AYVTDGACSG 121

Query: 175 KTVQRMELRVMSVLNWRLN 193
             +  MEL +M  L WRL+
Sbjct: 122 DEILTMELMIMKALKWRLS 140
>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Length = 128 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
>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Length = 141 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
>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 ?
Query352
d1g3nc1132 Viral cyclin {Kaposi's sarcoma-associated herpesvi 99.98
d1w98b2140 G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax 99.97
d2cchb1128 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 99.97
d1bu2a1127 Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} 99.96
d1f5qb1141 Viral cyclin {Murine herpesvirus 68 [TaxId: 33708] 99.95
d2i53a1144 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 99.82
d1jkwa1151 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 99.77
d2ivxa1143 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 99.77
d2cchb2124 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 99.06
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 98.18
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 98.08
d2i53a2110 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 98.03
d1w98b1130 G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax 97.97
d2ivxa2113 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 97.85
d1aisb295 Transcription factor IIB (TFIIB), core domain {Arc 97.77
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 97.66
d1aisb295 Transcription factor IIB (TFIIB), core domain {Arc 97.6
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 97.25
d1jkwa2126 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 96.87
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 96.49
d2ivxa2113 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 96.49
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 96.36
d1dl6a_58 Transcription initiation factor TFIIB, N-terminal 94.77
d1pfta_50 Transcription initiation factor TFIIB, N-terminal 93.78
d2i53a2110 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 92.83
d1f5qb2106 Viral cyclin {Murine herpesvirus 68 [TaxId: 33708] 84.16
>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=99.98  E-value=1e-32  Score=227.70  Aligned_cols=131  Identities=20%  Similarity=0.304  Sum_probs=123.1

Q ss_pred             ChHHHHHHHHHHhhhhccCCCccccccccCCCCCHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHhhhhcccccCCCC
Q 018657           56 DADDVVSRLIDRESETHHMLHPDYLHRFRDCSVFVTARQDSINWILNVHANYKFRPVTALLSVNYFDRFLSSHFLPLANG  135 (352)
Q Consensus        56 ~~~e~l~~ll~rE~E~~~~p~~~yl~~~~~~~i~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAv~~lDRfls~~~i~~~~~  135 (352)
                      ++++++++|++  .|.+++|..+|+...+ .++++.+|..+|+||.+|+..++++++|+++||+|||||+++..++++  
T Consensus         2 ~~~~i~~~l~~--~E~~~~p~~~y~~~~q-~~it~~~R~~lidWl~~v~~~~~l~~et~~lAv~llDrfls~~~v~~~--   76 (132)
T d1g3nc1           2 CEDRIFYNILE--IEPRFLTSDSVFGTFQ-QSLTSHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKE--   76 (132)
T ss_dssp             HHHHHHHHHHH--HGGGGCCCGGGHHHHT-SSCCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHH--
T ss_pred             chHHHHHHHHH--HHHHHCCChHHHHhcC-ccCCHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCcccCcHH--
Confidence            47899999999  8999999999998764 689999999999999999999999999999999999999999999887  


Q ss_pred             CchHHHHHHHHHHHhhhhccCCCcchhhhhhCCCCccCHHHHHHHHHHHHHHcCcccc
Q 018657          136 WPLQLLSVACLSLAAKMEETQVPLLLDLQIFDPRFVFEPKTVQRMELRVMSVLNWRLN  193 (352)
Q Consensus       136 ~~lqLlavaCL~LAaK~eE~~~p~~~dl~~~~~~~~f~~~~I~~mE~~IL~~L~w~l~  193 (352)
                       .+||+|+|||+||+|+||..+|.+.++... +++.|+.++|.+||+.||++|+|++.
T Consensus        77 -~lqLia~tcl~iAsK~ee~~~~~~~~l~~~-~~~~~t~~ei~~mE~~IL~~L~w~l~  132 (132)
T d1g3nc1          77 -HFQKTGSACLLVASKLRSLTPISTSSLCYA-AADSFSRQELIDQEKELLEKLAWRTE  132 (132)
T ss_dssp             -HHHHHHHHHHHHHHHHHCSSCCCHHHHHHH-TTTCSCHHHHHHHHHHHHHHTTTCCC
T ss_pred             -HHHHHHHHHHHHHHHhcccCCCCHHHHHHH-HcCCCCHHHHHHHHHHHHHHcCCcCC
Confidence             999999999999999999999999999876 67899999999999999999999974
>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>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
>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
>d2cchb2 a.74.1.1 (B:309-432) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 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
>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} 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
>d1w98b1 a.74.1.1 (B:228-357) G1/S-specific cyclin-E1 {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
>d1aisb2 a.74.1.2 (B:1206-1300) 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
>d1aisb2 a.74.1.2 (B:1206-1300) 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
>d1jkwa2 a.74.1.1 (A:162-287) 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
>d2ivxa2 a.74.1.1 (A:150-262) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 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
>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} 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
>d1f5qb2 a.74.1.1 (B:147-252) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Back     information, alignment and structure