Citrus Sinensis ID: 020177

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
MSVTCSGSFPDLLCGEDSGIFAGESSPACSSSDLESSASIEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLSLVNPEHAESWCDGLSKEKIISCYRLMQRLVLNDSRRKQPKVIPQLRVTIRARMRSSCDSSSSSSSSSSPTYKRRKLNNYLWVGDDKGGSE
cccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHccccccccccEEEEcccccccHHHHHHHHHHHHHHccccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHccccccccHHHHHHHcccccHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccc
cccccccccHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHccccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHcccccHccEEEEEEcccccHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHcHHHcccHHHHHHHHHHHHHHHHccccccccccHHHHHccccHHHHHHHHHHHHHHHHHccccccccEEcccccccccHHHccccccccccccccccccEEccccEEEEcccccccc
msvtcsgsfpdllcgedsgifagesspacsssdlessaSIEESIAGFiedernfvpgfdyltrfqthsldasAREESVAWILKVQAYYNFLPLTSYLSVNYMDrflysrrlpdnngwpwQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWrlrsvtpfsFIYFFAckldptgtfMGFLISRATKIILSNIQeasfleyrpsSIAAAAILCAAneipnlslvnpehaeswcdglskekIISCYRLMQRLVlndsrrkqpkvipQLRVTIRARMrsscdssssssssssptykrrklnnylwvgddkggse
msvtcsgsfpdLLCGEDSGIFAGESSPACSSSDLESSASIEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLSLVNPEHAESWCDGLSKEKIISCYRLMQRlvlndsrrkqpkvipqlrvtirarmrsscdssssssssssptykrrklnnylwvgddkggse
MSVTCSGSFPDLLCGEDSGIFAGesspacsssdlessasieesiagfieDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSiaaaailcaaNEIPNLSLVNPEHAESWCDGLSKEKIISCYRLMQRLVLNDSRRKQPKVIPQLRVTIRARMRsscdssssssssssPTYKRRKLNNYLWVGDDKGGSE
************LC*****************************IAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLSLVNPEHAESWCDGLSKEKIISCYRLMQRLVLND*******************************************NNYLWV********
******G**PDLLCGEDSGIFAGESSPACSSSDLESSASIEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLSLVNPEHAESWCDGLSKEKIISCYRLMQR**************************************************************
********FPDLLCGEDSGIFAG****************IEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLSLVNPEHAESWCDGLSKEKIISCYRLMQRLVLNDSRRKQPKVIPQLRVTIRA********************KRRKLNNYLWVGDDKGGSE
*****SGSFPDLLCGEDSGIFAGESSPACSSSDLESSASIEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLSLVNPEHAESWCDGLSKEKIISCYRLMQRLVLNDSRRKQPKVIPQLRVTIR*******************TYKRRKLNNYLWVGD******
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MSVTCSGSFPDLLCGEDSGIFAGESSPACSSSDLESSASIEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLSLVNPEHAESWCDGLSKEKIISCYRLMQRLVLNDSRRKQPKVIPQLRVTIRARMRSSCDSSSSSSSSSSPTYKRRKLNNYLWVGDDKGGSE
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 ?
Query330 2.2.26 [Sep-21-2011]
P42751339 Cyclin-D1-1 OS=Arabidopsi yes no 0.984 0.958 0.691 1e-122
Q0J233308 Cyclin-D2-1 OS=Oryza sati yes no 0.754 0.808 0.535 6e-72
Q8H339354 Cyclin-D1-2 OS=Oryza sati yes no 0.690 0.644 0.562 3e-66
Q67V81363 Cyclin-D1-1 OS=Oryza sati yes no 0.615 0.559 0.578 4e-57
P42752361 Cyclin-D2-1 OS=Arabidopsi no no 0.751 0.686 0.434 5e-47
Q8LHA8356 Cyclin-D2-2 OS=Oryza sati no no 0.833 0.772 0.389 1e-45
Q10K98405 Putative cyclin-D2-3 OS=O no no 0.675 0.550 0.413 2e-44
Q8LGA1308 Cyclin-D4-1 OS=Arabidopsi no no 0.690 0.740 0.415 2e-44
Q4KYM5383 Cyclin-D4-2 OS=Oryza sati no no 0.678 0.584 0.432 5e-44
Q6YXH8356 Cyclin-D4-1 OS=Oryza sati no no 0.757 0.702 0.398 8e-43
>sp|P42751|CCD11_ARATH Cyclin-D1-1 OS=Arabidopsis thaliana GN=CYCD1-1 PE=1 SV=3 Back     alignment and function desciption
 Score =  436 bits (1122), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 229/331 (69%), Positives = 270/331 (81%), Gaps = 6/331 (1%)

Query: 1   MSVTCSGSFPDLLCGEDSGIFAGESSPACSSSDLESSASIEESIAGFIEDERNFVPGFDY 60
           MSV+ S    DL CGEDSG+F+GES+   SSS+++S     +SIA FIEDER+FVPG DY
Sbjct: 12  MSVSFSNDM-DLFCGEDSGVFSGESTVDFSSSEVDSWPG--DSIACFIEDERHFVPGHDY 68

Query: 61  LTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQ 120
           L+RFQT SLDASARE+SVAWILKVQAYYNF PLT+YL+VNYMDRFLY+RRLP+ +GWP Q
Sbjct: 69  LSRFQTRSLDASAREDSVAWILKVQAYYNFQPLTAYLAVNYMDRFLYARRLPETSGWPMQ 128

Query: 121 LLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFS 180
           LL+VACLSLAAKMEE +VPSL D QV G KY+FE KTI+RMELLVLSVLDWRLRSVTPF 
Sbjct: 129 LLAVACLSLAAKMEEILVPSLFDFQVAGVKYLFEAKTIKRMELLVLSVLDWRLRSVTPFD 188

Query: 181 FIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNL- 239
           FI FFA K+DP+GTF+GF IS AT+IILSNI+EASFLEY PSSIAAAAILC ANE+P+L 
Sbjct: 189 FISFFAYKIDPSGTFLGFFISHATEIILSNIKEASFLEYWPSSIAAAAILCVANELPSLS 248

Query: 240 SLVNP-EHAESWCDGLSKEKIISCYRLMQRLVLNDSRRKQPKVIPQLRVTIRARMRSSCD 298
           S+VNP E  E+WCDGLSKEKI+ CYRLM+ + + ++R   PKVI +LRV++RA    +  
Sbjct: 249 SVVNPHESPETWCDGLSKEKIVRCYRLMKAMAIENNRLNTPKVIAKLRVSVRASSTLTRP 308

Query: 299 SSSSSSSSSSPTYKRRKLNNYLWVGDDKGGS 329
           S  SS SSSSP  KRRKL+ Y WVGD+   S
Sbjct: 309 SDESSFSSSSPC-KRRKLSGYSWVGDETSTS 338
May activate cell cycle in the root apical meristem (RAM) and promote embryonic root (radicle) protrusion.
Arabidopsis thaliana (taxid: 3702)
>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|Q67V81|CCD11_ORYSJ Cyclin-D1-1 OS=Oryza sativa subsp. japonica GN=CYCD1-1 PE=3 SV=1 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
>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|Q10K98|CCD23_ORYSJ Putative cyclin-D2-3 OS=Oryza sativa subsp. japonica GN=CYCD2-3 PE=3 SV=1 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|Q4KYM5|CCD42_ORYSJ Cyclin-D4-2 OS=Oryza sativa subsp. japonica GN=CYCD4-2 PE=2 SV=2 Back     alignment and function description
>sp|Q6YXH8|CCD41_ORYSJ Cyclin-D4-1 OS=Oryza sativa subsp. japonica GN=CYCD4-1 PE=2 SV=2 Back     alignment and function description

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 ?
Query330
225424764324 PREDICTED: cyclin-D1-1 [Vitis vinifera] 0.981 1.0 0.784 1e-132
356501290339 PREDICTED: cyclin-D1-1-like [Glycine max 0.990 0.964 0.751 1e-130
224108117327 predicted protein [Populus trichocarpa] 0.972 0.981 0.798 1e-130
359359230327 D1-type cyclin [Populus x canadensis] 0.972 0.981 0.801 1e-130
224102013328 predicted protein [Populus trichocarpa] 0.972 0.978 0.805 1e-129
296046565331 cyclin D1 [Passiflora morifolia] 0.993 0.990 0.786 1e-126
255581192386 cyclin d, putative [Ricinus communis] gi 0.996 0.852 0.75 1e-124
356498000339 PREDICTED: cyclin-D1-1-like [Glycine max 0.993 0.967 0.747 1e-121
2995130335 cyclin delta-1 [Arabidopsis thaliana] 0.972 0.958 0.685 1e-121
15223075339 cyclin-D1-1 [Arabidopsis thaliana] gi|59 0.984 0.958 0.691 1e-120
>gi|225424764|ref|XP_002268394.1| PREDICTED: cyclin-D1-1 [Vitis vinifera] gi|296086502|emb|CBI32091.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  476 bits (1225), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 259/330 (78%), Positives = 288/330 (87%), Gaps = 6/330 (1%)

Query: 1   MSVTCSGSFPDLLCGEDSGIFAGESSPACSSSDLESSASIEESIAGFIEDERNFVPGFDY 60
           MS++ S  F DLLCGEDS I +G+  P CSS DLES   IEESIAGFIEDERNFVPGFDY
Sbjct: 1   MSLSYSDRFSDLLCGEDSSILSGDL-PECSS-DLESPTDIEESIAGFIEDERNFVPGFDY 58

Query: 61  LTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQ 120
           L RF++HSLDASAREESVAWILKVQAY+ F PLT+YLSVNY+DRFLYSRRLP  NGWP Q
Sbjct: 59  LARFRSHSLDASAREESVAWILKVQAYHGFQPLTAYLSVNYLDRFLYSRRLPQTNGWPLQ 118

Query: 121 LLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFS 180
           LLSVACLSLAAKMEE +VPSLLDLQVEGAK+IFE+KTIRRMELLVL VLDWRLRS+TPFS
Sbjct: 119 LLSVACLSLAAKMEEPLVPSLLDLQVEGAKFIFESKTIRRMELLVLGVLDWRLRSITPFS 178

Query: 181 FIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLS 240
           FI FFA KLD +G+ +GFLISRAT+IILSNIQEASFLEY PS IAAAAILCAANEIP LS
Sbjct: 179 FIGFFAYKLDSSGSVIGFLISRATQIILSNIQEASFLEYWPSCIAAAAILCAANEIPKLS 238

Query: 241 LVNPEHAESWCDGLSKEKIISCYRLMQRLVLNDSRRKQPKVIPQLRVTIRARMRSSCDSS 300
           LV+PE AESWCDGLSKEKIISCY+LMQ + ++++RRK PK++PQLRVTIRAR+R    SS
Sbjct: 239 LVDPERAESWCDGLSKEKIISCYQLMQEITVDNNRRKPPKLLPQLRVTIRARVR----SS 294

Query: 301 SSSSSSSSPTYKRRKLNNYLWVGDDKGGSE 330
            SSSSSSS +YKRRKLNN LWV DDKG  +
Sbjct: 295 GSSSSSSSSSYKRRKLNNCLWVDDDKGNGD 324

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|356501290|ref|XP_003519458.1| PREDICTED: cyclin-D1-1-like [Glycine max] Back     alignment and taxonomy information
>gi|224108117|ref|XP_002314728.1| predicted protein [Populus trichocarpa] gi|159025699|emb|CAN88850.1| D1-type cyclin [Populus trichocarpa] gi|222863768|gb|EEF00899.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|359359230|gb|AEV41133.1| D1-type cyclin [Populus x canadensis] Back     alignment and taxonomy information
>gi|224102013|ref|XP_002312511.1| predicted protein [Populus trichocarpa] gi|159025697|emb|CAN88849.1| D1-type cyclin [Populus trichocarpa] gi|222852331|gb|EEE89878.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|296046565|gb|ADG86424.1| cyclin D1 [Passiflora morifolia] Back     alignment and taxonomy information
>gi|255581192|ref|XP_002531409.1| cyclin d, putative [Ricinus communis] gi|223529002|gb|EEF30993.1| cyclin d, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|356498000|ref|XP_003517843.1| PREDICTED: cyclin-D1-1-like [Glycine max] Back     alignment and taxonomy information
>gi|2995130|emb|CAA58285.1| cyclin delta-1 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|15223075|ref|NP_177178.1| cyclin-D1-1 [Arabidopsis thaliana] gi|59802916|sp|P42751.3|CCD11_ARATH RecName: Full=Cyclin-D1-1; AltName: Full=Cyclin-delta-1; Short=Cyclin-d1; AltName: Full=G1/S-specific cyclin-D1-1; Short=CycD1;1 gi|2194121|gb|AAB61096.1| Strong similarity to Arabidopsis cyclin delta-1 (gb|ATCD1). EST gb|ATTS4338 comes from this gene [Arabidopsis thaliana] gi|26449478|dbj|BAC41865.1| unknown protein [Arabidopsis thaliana] gi|28950911|gb|AAO63379.1| At1g70210 [Arabidopsis thaliana] gi|332196913|gb|AEE35034.1| cyclin-D1-1 [Arabidopsis thaliana] 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 ?
Query330
TAIR|locus:2020663339 CYCD1;1 "CYCLIN D1;1" [Arabido 0.984 0.958 0.607 2.1e-100
TAIR|locus:2124331376 CYCD3;1 "CYCLIN D3;1" [Arabido 0.593 0.521 0.392 3.6e-34
TAIR|locus:2142504298 CYCD4;2 "AT5G10440" [Arabidops 0.560 0.620 0.424 1.5e-33
TAIR|locus:2083128361 CYCD3;3 "AT3G50070" [Arabidops 0.575 0.526 0.423 4.1e-33
TAIR|locus:2157172367 CYCD3;2 "AT5G67260" [Arabidops 0.639 0.574 0.375 4.1e-33
TAIR|locus:2120081323 CYCD5;1 "AT4G37630" [Arabidops 0.669 0.684 0.317 3.6e-25
TAIR|locus:2125522302 CYCD6;1 "AT4G03270" [Arabidops 0.642 0.701 0.319 2.6e-24
UNIPROTKB|Q10QA2345 CYCD5-3 "Cyclin-D5-3" [Oryza s 0.596 0.571 0.330 1.1e-23
TAIR|locus:2185178341 CYCD7;1 "AT5G02110" [Arabidops 0.593 0.574 0.270 1.6e-20
TAIR|locus:2031407442 CYCA1;2 "CYCLIN A1;2" [Arabido 0.490 0.366 0.331 7.4e-12
TAIR|locus:2020663 CYCD1;1 "CYCLIN D1;1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 996 (355.7 bits), Expect = 2.1e-100, P = 2.1e-100
 Identities = 201/331 (60%), Positives = 236/331 (71%)

Query:     1 MSVTCSGSFPDLLCGEDSGIFAGXXXXXXXXXXXXXXXXXXXXXXXXXXDERNFVPGFDY 60
             MSV+ S    DL CGEDSG+F+G                          DER+FVPG DY
Sbjct:    12 MSVSFSNDM-DLFCGEDSGVFSGESTVDFSSSEVDSWPGDSIACFIE--DERHFVPGHDY 68

Query:    61 LTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQ 120
             L+RFQT SLDASARE+SVAWILKVQAYYNF PLT+YL+VNYMDRFLY+RRLP+ +GWP Q
Sbjct:    69 LSRFQTRSLDASAREDSVAWILKVQAYYNFQPLTAYLAVNYMDRFLYARRLPETSGWPMQ 128

Query:   121 LLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFS 180
             LL+VACLSLAAKMEE +VPSL D QV G KY+FE KTI+RMELLVLSVLDWRLRSVTPF 
Sbjct:   129 LLAVACLSLAAKMEEILVPSLFDFQVAGVKYLFEAKTIKRMELLVLSVLDWRLRSVTPFD 188

Query:   181 FIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSXXXXXXXXXXNEIPNLS 240
             FI FFA K+DP+GTF+GF IS AT+IILSNI+EASFLEY PSS          NE+P+LS
Sbjct:   189 FISFFAYKIDPSGTFLGFFISHATEIILSNIKEASFLEYWPSSIAAAAILCVANELPSLS 248

Query:   241 -LVNP-EHAESWCDGLSKEKIISCYRLMQRLVLNDSRRKQPKVIPQLRVTIRARMRXXXX 298
              +VNP E  E+WCDGLSKEKI+ CYRLM+ + + ++R   PKVI +LRV++RA       
Sbjct:   249 SVVNPHESPETWCDGLSKEKIVRCYRLMKAMAIENNRLNTPKVIAKLRVSVRASSTLTRP 308

Query:   299 XXXXXXXXXXPTYKRRKLNNYLWVGDDKGGS 329
                       P  KRRKL+ Y WVGD+   S
Sbjct:   309 SDESSFSSSSPC-KRRKLSGYSWVGDETSTS 338
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:2124331 CYCD3;1 "CYCLIN D3;1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2142504 CYCD4;2 "AT5G10440" [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:2157172 CYCD3;2 "AT5G67260" [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
TAIR|locus:2185178 CYCD7;1 "AT5G02110" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2031407 CYCA1;2 "CYCLIN A1;2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
P42751CCD11_ARATHNo assigned EC number0.69180.98480.9587yesno
Q0J233CCD21_ORYSJNo assigned EC number0.53590.75450.8084yesno
Q8H339CCD12_ORYSJNo assigned EC number0.56220.69090.6440yesno

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

Fail to connect to STRING server

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 ?
Query330
pfam00134127 pfam00134, Cyclin_N, Cyclin, N-terminal domain 4e-36
COG5024440 COG5024, COG5024, Cyclin [Cell division and chromo 2e-15
cd0004388 cd00043, CYCLIN, Cyclin box fold 6e-14
smart0038583 smart00385, CYCLIN, domain present in cyclins, TFI 9e-14
pfam02984117 pfam02984, Cyclin_C, Cyclin, C-terminal domain 7e-09
>gnl|CDD|215740 pfam00134, Cyclin_N, Cyclin, N-terminal domain Back     alignment and domain information 
 Score =  126 bits (319), Expect = 4e-36
 Identities = 47/133 (35%), Positives = 67/133 (50%), Gaps = 6/133 (4%)

Query: 42  ESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNY 101
           +  A   E E    P  DYL +     ++   R   + W+++V   +  LP T YL+VNY
Sbjct: 1   DIYAYLRELEEEDRPPPDYLDQQPD--INPKMRAILIDWLVEVHEEFKLLPETLYLAVNY 58

Query: 102 MDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRM 161
           +DRFL  + +P       QL+ V CL +AAK EE   PS+ D         +  + I RM
Sbjct: 59  LDRFLSKQPVPRTK---LQLVGVTCLLIAAKYEEIYPPSVEDFVYI-TDNAYTKEEILRM 114

Query: 162 ELLVLSVLDWRLR 174
           ELL+LS L+W L 
Sbjct: 115 ELLILSTLNWDLS 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|227357 COG5024, COG5024, Cyclin [Cell division and chromosome partitioning] Back     alignment and domain information
>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|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 330
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] 100.0
KOG0654359 consensus G2/Mitotic-specific cyclin A [Cell cycle 99.96
PF00134127 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR 99.93
TIGR00569305 ccl1 cyclin ccl1. University). 99.92
KOG0834323 consensus CDK9 kinase-activating protein cyclin T 99.92
KOG0835367 consensus Cyclin L [General function prediction on 99.87
KOG0794264 consensus CDK8 kinase-activating protein cyclin C 99.81
COG5333297 CCL1 Cdk activating kinase (CAK)/RNA polymerase II 99.76
PRK00423310 tfb transcription initiation factor IIB; Reviewed 99.58
cd0004388 CYCLIN Cyclin box fold. Protein binding domain fun 99.47
PF02984118 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR 99.45
smart0038583 CYCLIN domain present in cyclins, TFIIB and Retino 99.4
KOG2496325 consensus Cdk activating kinase (CAK)/RNA polymera 99.39
COG1405285 SUA7 Transcription initiation factor TFIIIB, Brf1 98.98
KOG1597308 consensus Transcription initiation factor TFIIB [T 98.86
PF08613149 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu 98.42
smart0038583 CYCLIN domain present in cyclins, TFIIB and Retino 98.18
cd0004388 CYCLIN Cyclin box fold. Protein binding domain fun 98.18
KOG4164497 consensus Cyclin ik3-1/CABLES [Cell cycle control, 98.05
KOG1598 521 consensus Transcription initiation factor TFIIIB, 97.68
PF0038271 TFIIB: Transcription factor TFIIB repeat; InterPro 96.13
KOG1674218 consensus Cyclin [General function prediction only 96.06
PF0038271 TFIIB: Transcription factor TFIIB repeat; InterPro 95.78
PRK00423310 tfb transcription initiation factor IIB; Reviewed 93.45
KOG1675343 consensus Predicted cyclin [General function predi 86.7
PF02984118 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR 84.67
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information 
Probab=100.00  E-value=3.5e-52  Score=388.51  Aligned_cols=254  Identities=44%  Similarity=0.670  Sum_probs=223.9

Q ss_pred             cccccccccccccC---CCCCCCCCCCCCC---CCChHHHHHHHHHHHhccCCCCCccccccCCCCCHHHHHHHHHHHHH
Q 020177           10 PDLLCGEDSGIFAG---ESSPACSSSDLES---SASIEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILK   83 (330)
Q Consensus        10 ~~l~c~ed~~~~~~---~~~~~~~~~~~~~---~~~~~e~l~~ll~~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~   83 (330)
                      +.|+|+|++....+   .+|+.-+..++..   -.++||.+.+|+++|.++.|+.+|...+| ..+++.+|.++++||++
T Consensus         9 ~~l~c~E~~~~~~~~~~~~D~~~~~~~~~~~~~~~~~e~~i~~ll~kEe~~~p~~~~~~~~~-~~~~~~~R~~A~~WIl~   87 (335)
T KOG0656|consen    9 SQLLCHEESTSDEQDRADNDESSTESSIPQLGFLLWDERVLANLLEKEEQHNPSLDYFLCVQ-KLILSSMRKQALDWILK   87 (335)
T ss_pred             cccccCCCCcccccccccCCcccccccccccccccccHHHHHHHHHHHHHhCCCCchhhhcc-cccccHHHHHHHHHHHH
Confidence            44899998875542   1112111112221   25899999999999999999999776654 46889999999999999


Q ss_pred             HHHHhCCchhHHHHHHHHHHHHhcCCCcCCCCCCchhHHHHHHhhhhhhhccccCCchhhhhHhcccccccHHHHHHHHH
Q 020177           84 VQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMEL  163 (330)
Q Consensus        84 v~~~~~l~~~t~~lAv~~~DRfls~~~i~~~~~~~lqLla~aCL~LAsK~eE~~~p~l~~l~~~~~~~~~~~~~I~~mE~  163 (330)
                      |++++++.++|+++|+||||||++.+.+++.++|++||+|+|||+||||+||+.+|.+.|+++.+.+|.|.+++|++||+
T Consensus        88 V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~rmEL  167 (335)
T KOG0656|consen   88 VCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQRMEL  167 (335)
T ss_pred             HHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHcCccccCCChHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHhhchhcccCccHHHHHHHHHHHHHhhCCCCCCCC
Q 020177          164 LVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLSLVN  243 (330)
Q Consensus       164 ~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~~~~~~~~~a~~ll~~~l~d~~~l~~~PS~iAaAai~~A~~~~~~~~~~~  243 (330)
                      +||++|+|||+.+||++|+++|+++++..+...+.++.++..++..+..|.+|++|+||+||+|++..+...+.......
T Consensus       168 LVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~~~~~l~~~~  247 (335)
T KOG0656|consen  168 LVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVSASVDGLDFRE  247 (335)
T ss_pred             HHHhhccccccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHHHhhcchhhhh
Confidence            99999999999999999999999999998888899999999999999999999999999999999999988776554444


Q ss_pred             ccccchhccCCCHHHHHHHHH
Q 020177          244 PEHAESWCDGLSKEKIISCYR  264 (330)
Q Consensus       244 ~~~~l~~~~~~~~e~l~~c~~  264 (330)
                      .++.+.++.+++++.+..|+.
T Consensus       248 ~~~~~~~~~~l~~e~~~~~~~  268 (335)
T KOG0656|consen  248 YENNLLSLLSLSKEKVNRCYD  268 (335)
T ss_pred             hhHHHHHHHHhhHHhhhcchh
Confidence            456778889999999999998

>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
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>KOG0835 consensus Cyclin L [General function prediction only] Back     alignment and domain information
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription] Back     alignment and domain information
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair] Back     alignment and domain information
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>cd00043 CYCLIN Cyclin box fold 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
>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
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription] 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
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>cd00043 CYCLIN Cyclin box fold Back     alignment and domain information
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription] 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
>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
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>KOG1675 consensus Predicted cyclin [General function prediction only] 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query330
1vyw_B265 Structure Of Cdk2CYCLIN A WITH PNU-292137 Length = 2e-08
2x1n_B261 Truncation And Optimisation Of Peptide Inhibitors O 2e-08
3f5x_B256 Cdk-2-Cyclin Complex With Indazole Inhibitor 9 Boun 3e-08
1qmz_B259 Phosphorylated Cdk2-Cyclyin A-Substrate Peptide Com 3e-08
4bco_B262 Structure Of Cdk2 In Complex With Cyclin A And A 2- 3e-08
1jst_B258 Phosphorylated Cyclin-Dependent Kinase-2 Bound To C 3e-08
4bcq_B262 Structure Of Cdk2 In Complex With Cyclin A And A 2- 3e-08
1fin_B260 Cyclin A-Cyclin-Dependent Kinase 2 Complex Length = 3e-08
1e9h_B261 Thr 160 Phosphorylated Cdk2-Human Cyclin A3 Complex 3e-08
1ogu_B260 Structure Of Human Thr160-phospho Cdk2/cyclin A Com 3e-08
4bcq_D262 Structure Of Cdk2 In Complex With Cyclin A And A 2- 3e-08
3qhr_B261 Structure Of A Pcdk2CYCLINA TRANSITION-State Mimic 3e-08
4i3z_B257 Structure Of Pcdk2CYCLINA BOUND TO ADP AND 2 MAGNES 4e-08
4ii5_B258 Structure Of Pcdk2/cyclina Bound To Adp And 1 Magne 4e-08
2g9x_B262 Structure Of Thr 160 Phosphorylated Cdk2CYCLIN A IN 4e-08
1vin_A268 Bovine Cyclin A3 Length = 268 4e-08
3ddq_B269 Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN 4e-08
3ddp_B268 Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN 4e-08
3bht_B262 Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN 4e-08
3dog_B264 Structure Of Thr 160 Phosphorylated Cdk2CYCLIN A IN 4e-08
2b9r_A269 Crystal Structure Of Human Cyclin B1 Length = 269 7e-06
2jgz_B260 Crystal Structure Of Phospho-Cdk2 In Complex With C 1e-05
3g33_B306 Crystal Structure Of Cdk4CYCLIN D3 Length = 306 2e-05
2w96_A271 Crystal Structure Of Cdk4 In Complex With A D-Type 3e-04
2w9z_A257 Crystal Structure Of Cdk4 In Complex With A D-Type 3e-04
1w98_B283 The Structural Basis Of Cdk2 Activation By Cyclin E 7e-04
>pdb|1VYW|B Chain B, Structure Of Cdk2CYCLIN A WITH PNU-292137 Length = 265 Back     alignment and structure 
Iteration: 1

 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 73/158 (46%), Gaps = 20/158 (12%)
Query: 72  SAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAA 131
           S R   V W+++V   Y     T +L+VNY+DRFL S  +        QL+  A + LA+
Sbjct: 42  SMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGK---LQLVGTAAMLLAS 98
Query: 132 KMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFI--YFFA--- 186
           K EE   P + +  V      +  K + RME LVL VL + L + T   F+  YF     
Sbjct: 99  KFEEIYPPEVAEF-VYITDDTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQP 157
Query: 187 --CKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPS 222
             CK++    F+G          LS I    +L+Y PS
Sbjct: 158 ANCKVESLAMFLGE---------LSLIDADPYLKYLPS 186
>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|3F5X|B Chain B, Cdk-2-Cyclin Complex With Indazole Inhibitor 9 Bound At Its Active Site Length = 256 Back     alignment and structure
>pdb|1QMZ|B Chain B, Phosphorylated Cdk2-Cyclyin A-Substrate Peptide Complex Length = 259 Back     alignment and structure
>pdb|4BCO|B Chain B, Structure Of Cdk2 In Complex With Cyclin A And A 2-amino-4- Heteroaryl-pyrimidine Inhibitor Length = 262 Back     alignment and structure
>pdb|1JST|B Chain B, Phosphorylated Cyclin-Dependent Kinase-2 Bound To Cyclin A Length = 258 Back     alignment and structure
>pdb|4BCQ|B Chain B, Structure Of Cdk2 In Complex With Cyclin A And A 2-amino-4- Heteroaryl-pyrimidine Inhibitor Length = 262 Back     alignment and structure
>pdb|1FIN|B Chain B, Cyclin A-Cyclin-Dependent Kinase 2 Complex Length = 260 Back     alignment and structure
>pdb|1E9H|B Chain B, Thr 160 Phosphorylated Cdk2-Human Cyclin A3 Complex With The Inhibitor Indirubin-5-Sulphonate Bound Length = 261 Back     alignment and structure
>pdb|1OGU|B Chain B, Structure Of Human Thr160-phospho Cdk2/cyclin A Complexed With A 2-arylamino-4-cyclohexylmethyl-5-nitroso-6- aminopyrimidine Inhibitor Length = 260 Back     alignment and structure
>pdb|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|3QHR|B Chain B, Structure Of A Pcdk2CYCLINA TRANSITION-State Mimic 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|4II5|B Chain B, Structure Of Pcdk2/cyclina Bound To Adp And 1 Magnesium Ion Length = 258 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|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|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|2B9R|A Chain A, Crystal Structure Of Human Cyclin B1 Length = 269 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|3G33|B Chain B, Crystal Structure Of Cdk4CYCLIN D3 Length = 306 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|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 ?
Query330
3g33_B306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 2e-53
2w96_A271 G1/S-specific cyclin-D1; serine/threonine-protein 2e-50
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 9e-36
2cch_B260 Cyclin A2, cyclin-A; complex(transferase/cell divi 2e-33
1f5q_B252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 1e-32
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 4e-31
2b9r_A269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 4e-31
1w98_B283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 1e-29
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 3e-16
1jkw_A323 Cyclin H; cell cycle, cell division, nuclear prote 5e-14
2pk2_A358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 1e-13
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 1e-13
2ivx_A257 Cyclin-T2; transcription regulation, cell division 1e-10
3rgf_B285 Cyclin-C; protein kinase complex, transferase,tran 7e-10
>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
 Score =  176 bits (448), Expect = 2e-53
 Identities = 56/300 (18%), Positives = 100/300 (33%), Gaps = 22/300 (7%)

Query: 11  DLLCGEDSGIFAGESSPACSSSDLESSASIEESIAGFIEDERNFVPGFDYLTRFQTHSLD 70
           +LLC E +         A  +         +  +   +  E  +VP   Y    Q   + 
Sbjct: 16  ELLCCEGT-------RHAPRAGPDPRLLGDQRVLQSLLRLEERYVPRASYFQCVQRE-IK 67

Query: 71  ASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLA 130
              R+    W+L+V            L++NY+DR+L             QLL   C+ LA
Sbjct: 68  PHMRKMLAYWMLEVCEEQRCEEEVFPLAMNYLDRYLSCVPTRKAQ---LQLLGAVCMLLA 124

Query: 131 AKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLD 190
           +K+ ET   ++  L      +    + +R  E+LVL  L W L +V    F+ F   +L 
Sbjct: 125 SKLRETTPLTIEKL-CIYTDHAVSPRQLRDWEVLVLGKLKWDLAAVIAHDFLAFILHRLS 183

Query: 191 PTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLSLVNPEHAESW 250
                   +   A   +     + +F  Y PS IA  +I  A   +           +  
Sbjct: 184 LPRDRQALVKKHAQTFLALCATDYTFAMYPPSMIATGSIGAAVQGLGA----CSMSGDEL 239

Query: 251 CD------GLSKEKIISCYRLMQRLVLNDSRRKQPKVIPQLRVTIRARMRSSCDSSSSSS 304
            +      G   + + +C   ++  +    R              R         +S+ +
Sbjct: 240 TELLAGITGTEVDCLRACQEQIEAALRESLREAAQTSSSPAPKAPRGSSSQGPSQTSTPT 299
>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
>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
>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
>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
>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
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Length = 269 Back     alignment and structure
>1w98_B Cyclin E, G1/S-specific cyclin E1; cell cycle, transferase; HET: TPO; 2.15A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Length = 283 Back     alignment and structure
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Length = 258 Back     alignment and structure
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query330
3g33_B306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 100.0
2w96_A271 G1/S-specific cyclin-D1; serine/threonine-protein 100.0
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 100.0
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 100.0
1f5q_B252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 100.0
2cch_B260 Cyclin A2, cyclin-A; complex(transferase/cell divi 100.0
2b9r_A269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 100.0
1w98_B283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 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; 100.0
2pk2_A358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 100.0
1jkw_A323 Cyclin H; cell cycle, cell division, nuclear prote 99.97
1c9b_A207 General transcription factor IIB; protein-DNA comp 99.94
1ais_B200 TFB TFIIB, protein (transcription initiation facto 99.89
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 99.73
4bbr_M345 Transcription initiation factor IIB; RNA polymeras 99.37
2pmi_B293 PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de 98.38
1ais_B200 TFB TFIIB, protein (transcription initiation facto 96.14
1c9b_A207 General transcription factor IIB; protein-DNA comp 95.01
4bbr_M345 Transcription initiation factor IIB; RNA polymeras 90.64
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 89.22
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 86.87
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 85.04
3h4c_A260 Transcription factor TFIIB-like; cyclin, transcrip 83.91
3rgf_B285 Cyclin-C; protein kinase complex, transferase,tran 81.75
2ivx_A257 Cyclin-T2; transcription regulation, cell division 81.64
>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=4.5e-50  Score=377.56  Aligned_cols=255  Identities=23%  Similarity=0.348  Sum_probs=206.8

Q ss_pred             cCcccccccccccc--cccCCCCCCCCCCCCCCCCChHHHHHHHHHHHhccCCCCCccccccCCCCCHHHHHHHHHHHHH
Q 020177            6 SGSFPDLLCGEDSG--IFAGESSPACSSSDLESSASIEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILK   83 (330)
Q Consensus         6 ~~~~~~l~c~ed~~--~~~~~~~~~~~~~~~~~~~~~~e~l~~ll~~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~   83 (330)
                      |..| +|+|+|+..  ...+.+ |.-.        +++|++.+|+++|.++.|+++|+... ++++++.+|..+|+||++
T Consensus        12 ~~~~-~l~~~e~~~~~~~a~~d-p~l~--------~~~~i~~~l~~~E~~~~p~~~y~~~~-q~~i~~~~R~~lvdwl~e   80 (306)
T 3g33_B           12 GGSM-ELLCCEGTRHAPRAGPD-PRLL--------GDQRVLQSLLRLEERYVPRASYFQCV-QREIKPHMRKMLAYWMLE   80 (306)
T ss_dssp             -----------------------------------CHHHHHHHHHHHGGGGSCSSCCTTTS-TTTCCHHHHHHHHHHHHH
T ss_pred             CCCc-ceeeecccccccccCCC-Cccc--------chHHHHHHHHHHHHHhCCCcHHHhhc-CccCCHHHHHHHHHHHHH
Confidence            3445 699999443  555666 4322        78899999999999999999999865 467999999999999999


Q ss_pred             HHHHhCCchhHHHHHHHHHHHHhcCCCcCCCCCCchhHHHHHHhhhhhhhccccCCchhhhhHhcccccccHHHHHHHHH
Q 020177           84 VQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMEL  163 (330)
Q Consensus        84 v~~~~~l~~~t~~lAv~~~DRfls~~~i~~~~~~~lqLla~aCL~LAsK~eE~~~p~l~~l~~~~~~~~~~~~~I~~mE~  163 (330)
                      |+.+|+++++|+++||+|||||+++..+.+.   ++||+|+||||||+|+||..+|.+.++... +++.|++++|++||+
T Consensus        81 v~~~~~l~~~t~~lAv~~lDRfls~~~v~~~---~lqLv~~tcL~lAsK~eE~~p~~~~~l~~~-~~~~~~~~~i~~mE~  156 (306)
T 3g33_B           81 VCEEQRCEEEVFPLAMNYLDRYLSCVPTRKA---QLQLLGAVCMLLASKLRETTPLTIEKLCIY-TDHAVSPRQLRDWEV  156 (306)
T ss_dssp             HHHHTTCCTTHHHHHHHHHHHHHHHCCCCGG---GHHHHHHHHHHHHHHHHCSSCCCTTHHHHH-TTTSSCHHHHHHHHH
T ss_pred             HHHHhCCcHhHHHHHHHHHHHHHhcCCCcHH---HHHHHHHHHHHHHHHhccCCCCCHHHHHHH-hccCccHHHHHHHHH
Confidence            9999999999999999999999999998776   899999999999999999999999999655 778999999999999


Q ss_pred             HHHHHcCccccCCChHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHhhchhcccCccHHHHHHHHHHHHHhhCCCCCCCC
Q 020177          164 LVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLSLVN  243 (330)
Q Consensus       164 ~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~~~~~~~~~a~~ll~~~l~d~~~l~~~PS~iAaAai~~A~~~~~~~~~~~  243 (330)
                      .||++|+|+++.|||++||.+|++.++........+...++++++.++.++.|++|+||.||||||++|+..++..+.|.
T Consensus       157 ~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~lsl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~w~  236 (306)
T 3g33_B          157 LVLGKLKWDLAAVIAHDFLAFILHRLSLPRDRQALVKKHAQTFLALCATDYTFAMYPPSMIATGSIGAAVQGLGACSMSG  236 (306)
T ss_dssp             HHHHHTTTCCCCCCGGGGHHHHHHTSSCCTTTHHHHHHHHHHHHHHHHHCGGGTTSCHHHHHHHHHHHHHHTCC---CCH
T ss_pred             HHHHHcCCccCCCCHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhhhhhccCCHHHHHHHHHHHHHHHhcCCCCch
Confidence            99999999999999999999999988877666666777899999999999999999999999999999999887543331


Q ss_pred             --ccccchhccCCCHHHHHHHHHHHHHHHhhcCC
Q 020177          244 --PEHAESWCDGLSKEKIISCYRLMQRLVLNDSR  275 (330)
Q Consensus       244 --~~~~l~~~~~~~~e~l~~c~~~l~~l~~~~~~  275 (330)
                        ....+..++||++++|.+|++.|.+++.+..+
T Consensus       237 ~~w~~~L~~~tg~~~~~l~~c~~~I~~l~~~~l~  270 (306)
T 3g33_B          237 DELTELLAGITGTEVDCLRACQEQIEAALRESLR  270 (306)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTC--
T ss_pred             hhHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence              12345667899999999999999999987443
>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A Back     alignment and structure
>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A Back     alignment and structure
>1g3n_C V-cyclin; cyclin-dependent kinase, INK4 inhibitor, viral cyclin, cell cycle, signaling protein; 2.90A {Human herpesvirus 8} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>1f5q_B Gamma herpesvirus cyclin; herpesviral cyclin, cyclin dependent kinase. protein/protein complex, transferase; 2.50A {Murid herpesvirus 4} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>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
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Back     alignment and structure
>1w98_B Cyclin E, G1/S-specific cyclin E1; cell cycle, transferase; HET: TPO; 2.15A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>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
>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
>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
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M 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
>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
>3h4c_A Transcription factor TFIIB-like; cyclin, transcription factor TFIIB repeat; 2.30A {Trypanosoma brucei brucei} Back     alignment and structure
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens} 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

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 330
d2cchb1128 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [T 2e-27
d1g3nc1132 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma 3e-27
d1bu2a1127 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saim 5e-26
d1w98b2140 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human 8e-26
d1f5qb1141 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesviru 3e-24
d2i53a1144 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) 8e-20
d2ivxa1143 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) 6e-17
d1jkwa1151 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo s 3e-15
d2cchb2124 a.74.1.1 (B:309-432) Cyclin A {Cow (Bos taurus) [T 0.001
>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Length = 128 Back     information, alignment and structure

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin A
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  101 bits (254), Expect = 2e-27
 Identities = 41/127 (32%), Positives = 60/127 (47%), Gaps = 6/127 (4%)

Query: 49  EDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYS 108
           E E    P   Y+ + Q   +  S R   V W+++V   Y     T +L+VNY+DRFL S
Sbjct: 8   EMEVKCKPKVGYMKK-QPD-ITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSS 65

Query: 109 RRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSV 168
             +        QL+  A + LA+K EE   P + +  V      +  K + RME LVL V
Sbjct: 66  MSVLR---GKLQLVGTAAMLLASKFEEIYPPEVAEF-VYITDDTYTKKQVLRMEHLVLKV 121

Query: 169 LDWRLRS 175
           L + L +
Sbjct: 122 LTFDLAA 128
>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]} Length = 132 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
>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
>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Length = 141 Back     information, alignment and structure
>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Length = 144 Back     information, alignment and structure
>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Length = 143 Back     information, alignment and structure
>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Length = 151 Back     information, alignment and structure
>d2cchb2 a.74.1.1 (B:309-432) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Length = 124 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 ?
Query330
d1g3nc1132 Viral cyclin {Kaposi's sarcoma-associated herpesvi 100.0
d2cchb1128 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 99.98
d1w98b2140 G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax 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]} 99.83
d1jkwa1151 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 99.8
d2ivxa1143 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 99.79
d2cchb2124 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 99.43
d2i53a2110 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 98.92
d2ivxa2113 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 98.66
d1w98b1130 G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax 98.39
d1aisb295 Transcription factor IIB (TFIIB), core domain {Arc 97.98
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 97.83
d1jkwa2126 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 97.83
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 97.8
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 97.73
d1aisb295 Transcription factor IIB (TFIIB), core domain {Arc 97.26
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 97.23
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 97.21
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 96.45
d2ivxa2113 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 95.35
d2i53a2110 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 91.72
d1f5qb2106 Viral cyclin {Murine herpesvirus 68 [TaxId: 33708] 91.45
>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=100.00  E-value=3.3e-33  Score=229.67  Aligned_cols=130  Identities=25%  Similarity=0.361  Sum_probs=123.1

Q ss_pred             hHHHHHHHHHHHhccCCCCCccccccCCCCCHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCCcCCCCCCch
Q 020177           40 IEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPW  119 (330)
Q Consensus        40 ~~e~l~~ll~~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~~t~~lAv~~~DRfls~~~i~~~~~~~l  119 (330)
                      +|+++.+|++.|.+++|+++|+..+|. ++|+.+|..+|+||.+|+..|+++++|+|+||+|||||+++..+++.   ++
T Consensus         3 ~~~i~~~l~~~E~~~~p~~~y~~~~q~-~it~~~R~~lidWl~~v~~~~~l~~et~~lAv~llDrfls~~~v~~~---~l   78 (132)
T d1g3nc1           3 EDRIFYNILEIEPRFLTSDSVFGTFQQ-SLTSHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKE---HF   78 (132)
T ss_dssp             HHHHHHHHHHHGGGGCCCGGGHHHHTS-SCCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHH---HH
T ss_pred             hHHHHHHHHHHHHHHCCChHHHHhcCc-cCCHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCcccCcHH---HH
Confidence            679999999999999999999998765 69999999999999999999999999999999999999999999988   79


Q ss_pred             hHHHHHHhhhhhhhccccCCchhhhhHhcccccccHHHHHHHHHHHHHHcCcccc
Q 020177          120 QLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLR  174 (330)
Q Consensus       120 qLla~aCL~LAsK~eE~~~p~l~~l~~~~~~~~~~~~~I~~mE~~IL~~L~w~l~  174 (330)
                      ||+|+||||||+|+||..+|.+.++... +++.|++++|.+||+.||++|+|++.
T Consensus        79 qLia~tcl~iAsK~ee~~~~~~~~l~~~-~~~~~t~~ei~~mE~~IL~~L~w~l~  132 (132)
T d1g3nc1          79 QKTGSACLLVASKLRSLTPISTSSLCYA-AADSFSRQELIDQEKELLEKLAWRTE  132 (132)
T ss_dssp             HHHHHHHHHHHHHHHCSSCCCHHHHHHH-TTTCSCHHHHHHHHHHHHHHTTTCCC
T ss_pred             HHHHHHHHHHHHHhcccCCCCHHHHHHH-HcCCCCHHHHHHHHHHHHHHcCCcCC
Confidence            9999999999999999999999999644 77899999999999999999999974
>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} Back     information, alignment and structure
>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Back     information, alignment and structure
>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>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
>d2i53a2 a.74.1.1 (A:158-267) Cyclin K {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
>d1w98b1 a.74.1.1 (B:228-357) G1/S-specific cyclin-E1 {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
>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} 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
>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
>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ivxa2 a.74.1.1 (A:150-262) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2i53a2 a.74.1.1 (A:158-267) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1f5qb2 a.74.1.1 (B:147-252) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Back     information, alignment and structure