Psyllid ID: psy17187

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---
MSAFAISIQTNVFLYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVEDLVYYSDYTFSPHTLKTTEKPAVYLNNTHVIMKKVKDLVGTSMATFS
cccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHccccccccccEEEEccccccHHHHHHHHHHHHHHcccEEccccHHHHHHHHccccc
ccHEEEcHcHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHccccccHHHEEEEEcccccHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcc
MSAFAISIQTNVFLYSSLLQLCEErhceyqvfpYAVSIMDRflcycpmeksqLQLTASACLLIASKIRECHALCVEDLvyysdytfsphtlkttekpavylnNTHVIMKKVKDLVgtsmatfs
msafaisiqtNVFLYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVEDLVYYSDYTFSphtlkttekpavYLNNTHVIMKKVKDLVGTSMATFS
MSAFAISIQTNVFLYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVEDLVYYSDYTFSPHTLKTTEKPAVYLNNTHVIMKKVKDLVGTSMATFS
***FAISIQTNVFLYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVEDLVYYSDYTFSPHTLKTTEKPAVYLNNTHVIMKKVKDLVG*******
**AFAISIQTNVFLYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVEDLVYYSDYTFSPHTLKTTEKPAVYLNNTHVIMKKVKDLVGTSMAT**
MSAFAISIQTNVFLYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVEDLVYYSDYTFSPHTLKTTEKPAVYLNNTHVIMKKVKDLVGTSMATFS
MSAFAISIQTNVFLYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVEDLVYYSDYTFSPHTLKTTEKPAVYLNNTHVIMKKVKDLVGTSMATFS
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSAFAISIQTNVFLYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVEDLVYYSDYTFSPHTLKTTEKPAVYLNNTHVIMKKVKDLVGTSMATFS
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 ?
Query123 2.2.26 [Sep-21-2011]
Q3MHH5 292 G1/S-specific cyclin-D3 O yes N/A 0.634 0.267 0.448 4e-15
P30281 292 G1/S-specific cyclin-D3 O yes N/A 0.634 0.267 0.448 6e-15
P48961 293 G1/S-specific cyclin-D3 O yes N/A 0.634 0.266 0.448 3e-14
P30282 292 G1/S-specific cyclin-D3 O yes N/A 0.634 0.267 0.448 4e-14
P55169 292 G1/S-specific cyclin-D1 O no N/A 0.601 0.253 0.432 3e-13
P30279 289 G1/S-specific cyclin-D2 O no N/A 0.601 0.256 0.432 1e-12
Q2KI22 295 G1/S-specific cyclin-D1 O no N/A 0.601 0.250 0.432 1e-12
Q0P5D3 289 G1/S-specific cyclin-D2 O no N/A 0.601 0.256 0.418 1e-12
P50755 291 G1/S-specific cyclin-D1 O N/A N/A 0.601 0.254 0.432 1e-12
P39948 295 G1/S-specific cyclin-D1 O no N/A 0.577 0.240 0.436 1e-12
>sp|Q3MHH5|CCND3_BOVIN G1/S-specific cyclin-D3 OS=Bos taurus GN=CCND3 PE=2 SV=1 Back     alignment and function desciption
 Score = 80.1 bits (196), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 35/78 (44%), Positives = 54/78 (69%)

Query: 18  LLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVED 77
           +L++CEE+ CE +VFP A++ +DR+L   P  K+QLQL  + C+L+ASK+RE   L +E 
Sbjct: 64  MLEVCEEQRCEEEVFPLAMNYLDRYLSCVPTRKAQLQLLGAVCMLLASKLRETTPLTIEK 123

Query: 78  LVYYSDYTFSPHTLKTTE 95
           L  Y+D++ SP  L+  E
Sbjct: 124 LCIYTDHSVSPRQLRDWE 141
Regulatory component of the cyclin D3-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family including RB1 and regulates the cell-cycle during G(1)/S transition. Phosphorylation of RB1 allows dissociation of the transcription factor E2F from the RB/E2F complex and the subsequent transcription of E2F target genes which are responsible for the progression through the G(1) phase. Hypophosphorylates RB1 in early G(1) phase. Cyclin D-CDK4 complexes are major integrators of various mitogenenic and antimitogenic signals. Also substrate for SMAD3, phosphorylating SMAD3 in a cell-cycle-dependent manner and repressing its transcriptional activity. Component of the ternary complex, cyclin D3/CDK4/CDKN1B, required for nuclear translocation and activity of the cyclin D-CDK4 complex.
Bos taurus (taxid: 9913)
>sp|P30281|CCND3_HUMAN G1/S-specific cyclin-D3 OS=Homo sapiens GN=CCND3 PE=1 SV=2 Back     alignment and function description
>sp|P48961|CCND3_RAT G1/S-specific cyclin-D3 OS=Rattus norvegicus GN=Ccnd3 PE=2 SV=1 Back     alignment and function description
>sp|P30282|CCND3_MOUSE G1/S-specific cyclin-D3 OS=Mus musculus GN=Ccnd3 PE=2 SV=1 Back     alignment and function description
>sp|P55169|CCND1_CHICK G1/S-specific cyclin-D1 OS=Gallus gallus GN=CCND1 PE=2 SV=1 Back     alignment and function description
>sp|P30279|CCND2_HUMAN G1/S-specific cyclin-D2 OS=Homo sapiens GN=CCND2 PE=1 SV=1 Back     alignment and function description
>sp|Q2KI22|CCND1_BOVIN G1/S-specific cyclin-D1 OS=Bos taurus GN=CCND1 PE=2 SV=1 Back     alignment and function description
>sp|Q0P5D3|CCND2_BOVIN G1/S-specific cyclin-D2 OS=Bos taurus GN=CCND2 PE=2 SV=1 Back     alignment and function description
>sp|P50755|CCND1_XENLA G1/S-specific cyclin-D1 OS=Xenopus laevis GN=ccnd1 PE=2 SV=1 Back     alignment and function description
>sp|P39948|CCND1_RAT G1/S-specific cyclin-D1 OS=Rattus norvegicus GN=Ccnd1 PE=2 SV=1 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query123
193716056 291 PREDICTED: g1/S-specific cyclin-D2-like 0.634 0.268 0.487 2e-16
270005146199 hypothetical protein TcasGA2_TC007158 [T 0.634 0.391 0.474 6e-15
91081481 285 PREDICTED: similar to cyclin d [Triboliu 0.634 0.273 0.474 7e-15
444725484 286 G1/S-specific cyclin-D3 [Tupaia chinensi 0.634 0.272 0.461 3e-14
340717114 311 PREDICTED: g1/S-specific cyclin-D2-like 0.642 0.254 0.468 4e-14
348575846 624 PREDICTED: hypothetical protein LOC10071 0.617 0.121 0.447 5e-14
328778614 309 PREDICTED: g1/S-specific cyclin-D2 [Apis 0.642 0.255 0.468 7e-14
383858650 309 PREDICTED: G1/S-specific cyclin-D2-like 0.642 0.255 0.468 7e-14
60822866 292 cyclin D3 [synthetic construct] 0.634 0.267 0.448 1e-13
242003411208 G1/S-specific cyclin-D2, putative [Pedic 0.650 0.384 0.45 1e-13
>gi|193716056|ref|XP_001952350.1| PREDICTED: g1/S-specific cyclin-D2-like [Acyrthosiphon pisum] Back     alignment and taxonomy information
 Score = 89.4 bits (220), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/78 (48%), Positives = 57/78 (73%)

Query: 18  LLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVED 77
           +L +CEE+ CE QVFP +V+ +DRFLC C + K+ LQLT + CLL+ASK+R+C AL +E 
Sbjct: 66  MLDVCEEQRCEDQVFPLSVNFLDRFLCACDISKTHLQLTGAVCLLLASKVRQCTALSIEL 125

Query: 78  LVYYSDYTFSPHTLKTTE 95
           L YY++ + +P  ++  E
Sbjct: 126 LCYYTENSVTPEEMREWE 143

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|270005146|gb|EFA01594.1| hypothetical protein TcasGA2_TC007158 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|91081481|ref|XP_974376.1| PREDICTED: similar to cyclin d [Tribolium castaneum] Back     alignment and taxonomy information
>gi|444725484|gb|ELW66048.1| G1/S-specific cyclin-D3 [Tupaia chinensis] Back     alignment and taxonomy information
>gi|340717114|ref|XP_003397033.1| PREDICTED: g1/S-specific cyclin-D2-like [Bombus terrestris] gi|350416388|ref|XP_003490931.1| PREDICTED: G1/S-specific cyclin-D2-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|348575846|ref|XP_003473699.1| PREDICTED: hypothetical protein LOC100718785 [Cavia porcellus] Back     alignment and taxonomy information
>gi|328778614|ref|XP_396634.2| PREDICTED: g1/S-specific cyclin-D2 [Apis mellifera] gi|380015123|ref|XP_003691559.1| PREDICTED: G1/S-specific cyclin-D2-like [Apis florea] Back     alignment and taxonomy information
>gi|383858650|ref|XP_003704812.1| PREDICTED: G1/S-specific cyclin-D2-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|60822866|gb|AAX36623.1| cyclin D3 [synthetic construct] Back     alignment and taxonomy information
>gi|242003411|ref|XP_002422725.1| G1/S-specific cyclin-D2, putative [Pediculus humanus corporis] gi|212505547|gb|EEB09987.1| G1/S-specific cyclin-D2, putative [Pediculus humanus corporis] 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 ?
Query123
UNIPROTKB|F1MV86 292 CCND3 "G1/S-specific cyclin-D3 0.634 0.267 0.448 2e-15
UNIPROTKB|Q3MHH5 292 CCND3 "G1/S-specific cyclin-D3 0.634 0.267 0.448 2e-15
UNIPROTKB|P30281 292 CCND3 "G1/S-specific cyclin-D3 0.634 0.267 0.448 2.6e-15
UNIPROTKB|F1PC17 394 CCND3 "Uncharacterized protein 0.634 0.197 0.448 8e-15
UNIPROTKB|Q5T8J1 242 CCND3 "G1/S-specific cyclin-D3 0.617 0.314 0.447 1.4e-14
RGD|2293 293 Ccnd3 "cyclin D3" [Rattus norv 0.634 0.266 0.448 1.7e-14
UNIPROTKB|H0Y8M4176 CCND3 "G1/S-specific cyclin-D3 0.609 0.426 0.453 1.8e-14
MGI|MGI:88315 292 Ccnd3 "cyclin D3" [Mus musculu 0.634 0.267 0.448 2.3e-14
UNIPROTKB|Q5ZKI9 292 CCND3 "Uncharacterized protein 0.601 0.253 0.445 9e-14
UNIPROTKB|F1NS84 292 CCND1 "G1/S-specific cyclin-D1 0.634 0.267 0.423 1.5e-13
UNIPROTKB|F1MV86 CCND3 "G1/S-specific cyclin-D3" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
 Score = 194 (73.4 bits), Expect = 2.0e-15, P = 2.0e-15
 Identities = 35/78 (44%), Positives = 54/78 (69%)

Query:    18 LLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVED 77
             +L++CEE+ CE +VFP A++ +DR+L   P  K+QLQL  + C+L+ASK+RE   L +E 
Sbjct:    64 MLEVCEEQRCEEEVFPLAMNYLDRYLSCVPTRKAQLQLLGAVCMLLASKLRETTPLTIEK 123

Query:    78 LVYYSDYTFSPHTLKTTE 95
             L  Y+D++ SP  L+  E
Sbjct:   124 LCIYTDHSVSPRQLRDWE 141
GO:0045737 "positive regulation of cyclin-dependent protein kinase activity" evidence=IEA
GO:0042098 "T cell proliferation" evidence=IEA
GO:0019901 "protein kinase binding" evidence=IEA
GO:0007165 "signal transduction" evidence=IEA
GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=IEA
GO:0000307 "cyclin-dependent protein kinase holoenzyme complex" evidence=IEA
GO:0051301 "cell division" evidence=IEA
GO:0005634 "nucleus" evidence=IEA
UNIPROTKB|Q3MHH5 CCND3 "G1/S-specific cyclin-D3" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|P30281 CCND3 "G1/S-specific cyclin-D3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1PC17 CCND3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q5T8J1 CCND3 "G1/S-specific cyclin-D3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
RGD|2293 Ccnd3 "cyclin D3" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|H0Y8M4 CCND3 "G1/S-specific cyclin-D3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:88315 Ccnd3 "cyclin D3" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|Q5ZKI9 CCND3 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1NS84 CCND1 "G1/S-specific cyclin-D1" [Gallus gallus (taxid:9031)] 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 EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query123
pfam00134127 pfam00134, Cyclin_N, Cyclin, N-terminal domain 1e-19
cd0004388 cd00043, CYCLIN, Cyclin box fold 5e-10
smart0038583 smart00385, CYCLIN, domain present in cyclins, TFI 2e-08
COG5024 440 COG5024, COG5024, Cyclin [Cell division and chromo 2e-06
>gnl|CDD|215740 pfam00134, Cyclin_N, Cyclin, N-terminal domain Back     alignment and domain information 
 Score = 77.2 bits (191), Expect = 1e-19
 Identities = 28/83 (33%), Positives = 44/83 (53%)

Query: 14  LYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHAL 73
           L   L+++ EE     +    AV+ +DRFL   P+ +++LQL    CLLIA+K  E +  
Sbjct: 34  LIDWLVEVHEEFKLLPETLYLAVNYLDRFLSKQPVPRTKLQLVGVTCLLIAAKYEEIYPP 93

Query: 74  CVEDLVYYSDYTFSPHTLKTTEK 96
            VED VY +D  ++   +   E 
Sbjct: 94  SVEDFVYITDNAYTKEEILRMEL 116

Cyclins regulate cyclin dependent kinases (CDKs). Human cyclin-O is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain. Length = 127
>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold Back     alignment and domain information
>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>gnl|CDD|227357 COG5024, COG5024, Cyclin [Cell division and chromosome partitioning] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 123
KOG0655|consensus 408 99.97
KOG0653|consensus 391 99.96
KOG0656|consensus 335 99.96
PF00134127 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR 99.94
COG5024 440 Cyclin [Cell division and chromosome partitioning] 99.94
KOG0654|consensus 359 99.78
cd0004388 CYCLIN Cyclin box fold. Protein binding domain fun 99.74
smart0038583 CYCLIN domain present in cyclins, TFIIB and Retino 99.7
TIGR00569 305 ccl1 cyclin ccl1. University). 99.69
KOG0834|consensus 323 99.44
COG5333 297 CCL1 Cdk activating kinase (CAK)/RNA polymerase II 99.16
KOG0794|consensus264 99.15
PF08613149 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu 98.99
KOG0835|consensus 367 98.68
PRK00423310 tfb transcription initiation factor IIB; Reviewed 98.35
KOG2496|consensus 325 98.26
KOG4164|consensus497 97.76
PF0038271 TFIIB: Transcription factor TFIIB repeat; InterPro 97.23
COG1405285 SUA7 Transcription initiation factor TFIIIB, Brf1 96.53
KOG1674|consensus218 96.51
KOG1597|consensus308 96.41
PRK00423310 tfb transcription initiation factor IIB; Reviewed 96.14
KOG0834|consensus323 95.63
PF02984118 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR 94.32
KOG1675|consensus343 89.3
COG1405285 SUA7 Transcription initiation factor TFIIIB, Brf1 87.26
>KOG0655|consensus Back     alignment and domain information 
Probab=99.97  E-value=1.4e-31  Score=207.04  Aligned_cols=114  Identities=22%  Similarity=0.257  Sum_probs=107.0

Q ss_pred             CCCHHHHHHHHHHHHHHhHhcCCchhhHHHHHHHHHHcccc-CCccCcCceehhhhhHHHHhhhhhccCCCHHhHHHhhc
Q psy17187          5 AISIQTNVFLYSSLLQLCEERHCEYQVFPYAVSIMDRFLCY-CPMEKSQLQLTASACLLIASKIRECHALCVEDLVYYSD   83 (123)
Q Consensus         5 ~Is~~~R~~li~W~~~v~~~~~l~~~tl~lAv~~lDr~ls~-~~i~~~~lqLlg~tcL~iAsK~eE~~~~~~~~l~~~~~   83 (123)
                      .+.|++|++|+|||.|||+.|+|.+||+|||+-|+|||+.. ..+.+..+||+|++|||||||+||..||++.+|.++++
T Consensus       139 dlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTD  218 (408)
T KOG0655|consen  139 DLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTD  218 (408)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeecc
Confidence            36799999999999999999999999999999999999977 47999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHhHhcCCceehhhhhHHhccc
Q psy17187         84 YTFSPHTLKTTEKPAVYLNNTHVIMKKVKDLVGTS  118 (123)
Q Consensus        84 ~~~t~~ei~~mE~~IL~~ln~~i~~~~~~d~~~~~  118 (123)
                      ++||.++|+.||..||+.|+|++-.-|+.--+++=
T Consensus       219 gAcs~ddIltmE~iilkal~W~l~PiTii~WL~vy  253 (408)
T KOG0655|consen  219 GACSEDDILTMELIILKALKWELSPITIISWLNVY  253 (408)
T ss_pred             CccchHHHHHHHHHHHHHhcccccceehHHHHHHH
Confidence            99999999999999999999999888877666543

>KOG0653|consensus Back     alignment and domain information
>KOG0656|consensus 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
>COG5024 Cyclin [Cell division and chromosome partitioning] Back     alignment and domain information
>KOG0654|consensus Back     alignment and domain information
>cd00043 CYCLIN Cyclin box fold Back     alignment and domain information
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>TIGR00569 ccl1 cyclin ccl1 Back     alignment and domain information
>KOG0834|consensus 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 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
>KOG0835|consensus Back     alignment and domain information
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>KOG2496|consensus Back     alignment and domain information
>KOG4164|consensus 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
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>KOG1674|consensus Back     alignment and domain information
>KOG1597|consensus Back     alignment and domain information
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>KOG0834|consensus 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
>KOG1675|consensus Back     alignment and domain information
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] 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 ?
Query123
3g33_B 306 Crystal Structure Of Cdk4CYCLIN D3 Length = 306 4e-16
2w9z_A 257 Crystal Structure Of Cdk4 In Complex With A D-Type 1e-13
2w96_A 271 Crystal Structure Of Cdk4 In Complex With A D-Type 2e-13
1jow_A254 Crystal Structure Of A Complex Of Human Cdk6 And A 2e-09
1bu2_A229 X-Ray Structure Of A Viral Cyclin From Herpesvirus 2e-09
4ii5_B 258 Structure Of Pcdk2/cyclina Bound To Adp And 1 Magne 3e-06
4i3z_B 257 Structure Of Pcdk2CYCLINA BOUND TO ADP AND 2 MAGNES 3e-06
3qhr_B 261 Structure Of A Pcdk2CYCLINA TRANSITION-State Mimic 3e-06
4bcq_D 262 Structure Of Cdk2 In Complex With Cyclin A And A 2- 3e-06
1vyw_B 265 Structure Of Cdk2CYCLIN A WITH PNU-292137 Length = 4e-06
1fin_B 260 Cyclin A-Cyclin-Dependent Kinase 2 Complex Length = 4e-06
2x1n_B 261 Truncation And Optimisation Of Peptide Inhibitors O 4e-06
4bcq_B 262 Structure Of Cdk2 In Complex With Cyclin A And A 2- 4e-06
1e9h_B 261 Thr 160 Phosphorylated Cdk2-Human Cyclin A3 Complex 4e-06
1ogu_B 260 Structure Of Human Thr160-phospho Cdk2/cyclin A Com 4e-06
1jst_B 258 Phosphorylated Cyclin-Dependent Kinase-2 Bound To C 4e-06
3f5x_B 256 Cdk-2-Cyclin Complex With Indazole Inhibitor 9 Boun 4e-06
4bco_B 262 Structure Of Cdk2 In Complex With Cyclin A And A 2- 4e-06
1qmz_B 259 Phosphorylated Cdk2-Cyclyin A-Substrate Peptide Com 4e-06
3ddq_B 269 Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN 4e-06
3ddp_B 268 Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN 4e-06
3bht_B 262 Structure Of Phosphorylated Thr160 Cdk2CYCLIN A IN 4e-06
2g9x_B 262 Structure Of Thr 160 Phosphorylated Cdk2CYCLIN A IN 4e-06
1vin_A 268 Bovine Cyclin A3 Length = 268 4e-06
3dog_B 264 Structure Of Thr 160 Phosphorylated Cdk2CYCLIN A IN 5e-06
2b9r_A 269 Crystal Structure Of Human Cyclin B1 Length = 269 3e-05
2jgz_B 260 Crystal Structure Of Phospho-Cdk2 In Complex With C 1e-04
>pdb|3G33|B Chain B, Crystal Structure Of Cdk4CYCLIN D3 Length = 306 Back     alignment and structure 
Iteration: 1

 Score = 79.7 bits (195), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 35/78 (44%), Positives = 53/78 (67%)
Query: 18  LLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVED 77
           +L++CEE+ CE +VFP A++ +DR+L   P  K+QLQL  + C+L+ASK+RE   L +E 
Sbjct: 78  MLEVCEEQRCEEEVFPLAMNYLDRYLSCVPTRKAQLQLLGAVCMLLASKLRETTPLTIEK 137
Query: 78  LVYYSDYTFSPHTLKTTE 95
           L  Y+D+  SP  L+  E
Sbjct: 138 LCIYTDHAVSPRQLRDWE 155
>pdb|2W9Z|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin Length = 257 Back     alignment and structure
>pdb|2W96|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin Length = 271 Back     alignment and structure
>pdb|1JOW|A Chain A, Crystal Structure Of A Complex Of Human Cdk6 And A Viral Cyclin Length = 254 Back     alignment and structure
>pdb|1BU2|A Chain A, X-Ray Structure Of A Viral Cyclin From Herpesvirus Saimiri Length = 229 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|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|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|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|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|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|1JST|B Chain B, Phosphorylated Cyclin-Dependent Kinase-2 Bound To Cyclin A Length = 258 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|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|1QMZ|B Chain B, Phosphorylated Cdk2-Cyclyin A-Substrate Peptide Complex Length = 259 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|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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query123
1f5q_B252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 2e-21
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 3e-21
3g33_B 306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 4e-21
2w96_A 271 G1/S-specific cyclin-D1; serine/threonine-protein 4e-21
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 2e-20
1w98_B 283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 5e-16
2cch_B 260 Cyclin A2, cyclin-A; complex(transferase/cell divi 1e-13
2b9r_A 269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 2e-13
>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
 Score = 84.5 bits (209), Expect = 2e-21
 Identities = 20/79 (25%), Positives = 35/79 (44%)

Query: 18  LLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVED 77
           +  +C++   +  VFP AV+++D       +++   Q TA+  L IA K+R    +    
Sbjct: 56  MFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQ 115

Query: 78  LVYYSDYTFSPHTLKTTEK 96
           L Y      +   L T E 
Sbjct: 116 LAYLCGGATTADKLLTLEV 134
>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
>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
>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
>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A Length = 254 Back     alignment and structure
>1w98_B Cyclin E, G1/S-specific cyclin E1; cell cycle, transferase; HET: TPO; 2.15A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Length = 283 Back     alignment and structure
>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ... Length = 260 Back     alignment and structure
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Length = 269 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query123
1f5q_B252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 100.0
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 100.0
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 100.0
2b9r_A 269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 100.0
3g33_B 306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 100.0
2w96_A 271 G1/S-specific cyclin-D1; serine/threonine-protein 99.97
2cch_B 260 Cyclin A2, cyclin-A; complex(transferase/cell divi 99.97
1w98_B 283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 99.97
2ivx_A257 Cyclin-T2; transcription regulation, cell division 99.93
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 99.93
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 99.91
3rgf_B 285 Cyclin-C; protein kinase complex, transferase,tran 99.91
2pk2_A 358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 99.91
1jkw_A 323 Cyclin H; cell cycle, cell division, nuclear prote 99.88
1c9b_A207 General transcription factor IIB; protein-DNA comp 99.72
1ais_B200 TFB TFIIB, protein (transcription initiation facto 99.47
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 99.0
2pmi_B 293 PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de 98.62
4bbr_M 345 Transcription initiation factor IIB; RNA polymeras 98.11
1ais_B200 TFB TFIIB, protein (transcription initiation facto 97.42
1c9b_A207 General transcription factor IIB; protein-DNA comp 96.22
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 93.25
2ivx_A257 Cyclin-T2; transcription regulation, cell division 93.1
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 92.67
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 92.56
3rgf_B285 Cyclin-C; protein kinase complex, transferase,tran 91.46
2cch_B260 Cyclin A2, cyclin-A; complex(transferase/cell divi 91.26
2pk2_A358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 91.09
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 90.6
2b9r_A269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 88.75
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 87.11
3g33_B306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 85.38
4bbr_M345 Transcription initiation factor IIB; RNA polymeras 84.54
2w96_A271 G1/S-specific cyclin-D1; serine/threonine-protein 84.37
3h4c_A 260 Transcription factor TFIIB-like; cyclin, transcrip 80.25
>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
Probab=100.00  E-value=2e-36  Score=228.74  Aligned_cols=114  Identities=21%  Similarity=0.255  Sum_probs=110.2

Q ss_pred             CCCHHHHHHHHHHHHHHhHhcCCchhhHHHHHHHHHHccccCCccCcCceehhhhhHHHHhhhhhccCCCHHhHHHhhcC
Q psy17187          5 AISIQTNVFLYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVEDLVYYSDY   84 (123)
Q Consensus         5 ~Is~~~R~~li~W~~~v~~~~~l~~~tl~lAv~~lDr~ls~~~i~~~~lqLlg~tcL~iAsK~eE~~~~~~~~l~~~~~~   84 (123)
                      .|++.+|.++++||.+|+..|+++++|+|+||+|+|||++..+++++++||+|+|||+||+|+||..||+++++++++++
T Consensus        43 ~i~~~~R~~lvdWl~ev~~~~~l~~eT~~lAv~~lDRfLs~~~v~~~~lqLvg~tcl~iAsK~eE~~p~~~~~l~~~~~~  122 (252)
T 1f5q_B           43 HFTSQYRKVLTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLCGG  122 (252)
T ss_dssp             HHHCSHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHCT
T ss_pred             CCCHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCC
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhHhcCCceehhhhhHHhccc
Q psy17187         85 TFSPHTLKTTEKPAVYLNNTHVIMKKVKDLVGTS  118 (123)
Q Consensus        85 ~~t~~ei~~mE~~IL~~ln~~i~~~~~~d~~~~~  118 (123)
                      .|+++||++||+.||++|||++..||+++|++--
T Consensus       123 ~yt~~~i~~mE~~IL~~L~w~l~~pTp~~FL~~~  156 (252)
T 1f5q_B          123 ATTADKLLTLEVKSLDTLSWVADRCLSTDLICYI  156 (252)
T ss_dssp             TCCHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHCCCccCCCCHHHHHHHH
Confidence            9999999999999999999999999999998643
>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
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Back     alignment and structure
>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens} Back     alignment and structure
>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A Back     alignment and structure
>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
>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B* Back     alignment and structure
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Back     alignment and structure
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens} Back     alignment and structure
>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C Back     alignment and structure
>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A Back     alignment and structure
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A* Back     alignment and structure
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Back     alignment and structure
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae} Back     alignment and structure
>2pmi_B PHO85 cyclin PHO80, aminoglycoside anti; cyclin-dependent kinase, signaling protein,transfera cycle complex; HET: MES AGS; 2.90A {Saccharomyces cerevisiae} PDB: 2pk9_B* Back     alignment and structure
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M Back     alignment and structure
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Back     alignment and structure
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A* Back     alignment and structure
>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
>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
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Back     alignment and structure
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens} 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
>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
>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
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_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
>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
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M 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
>3h4c_A Transcription factor TFIIB-like; cyclin, transcription factor TFIIB repeat; 2.30A {Trypanosoma brucei brucei} 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 123
d1bu2a1127 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saim 3e-18
d1f5qb1141 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesviru 2e-17
d1g3nc1132 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma 1e-16
d2cchb1128 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [T 6e-15
d1w98b2140 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human 1e-14
d2i53a1144 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) 2e-08
d1jkwa1151 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo s 2e-08
d2ivxa1143 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) 4e-08
>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} Length = 127 Back     information, alignment and structure

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

 Score = 72.2 bits (177), Expect = 3e-18
 Identities = 32/79 (40%), Positives = 41/79 (51%)

Query: 18  LLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVED 77
           +  LCE    +  VFP +VSI+DR+LC     K  LQ   +AC+LI SKIR    + V  
Sbjct: 38  MHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSK 97

Query: 78  LVYYSDYTFSPHTLKTTEK 96
           L Y S   F+   L   EK
Sbjct: 98  LTYLSCDCFTNLELINQEK 116
>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Length = 141 Back     information, alignment and structure
>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]} Length = 132 Back     information, alignment and structure
>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Length = 128 Back     information, alignment and structure
>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
>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Length = 144 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
>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Length = 143 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 ?
Query123
d1bu2a1127 Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} 100.0
d1g3nc1132 Viral cyclin {Kaposi's sarcoma-associated herpesvi 100.0
d2cchb1128 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 100.0
d1w98b2140 G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax 100.0
d1f5qb1141 Viral cyclin {Murine herpesvirus 68 [TaxId: 33708] 100.0
d2i53a1144 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 99.9
d1jkwa1151 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 99.88
d2ivxa1143 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 99.84
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 98.28
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 98.28
d1aisb295 Transcription factor IIB (TFIIB), core domain {Arc 97.92
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 97.54
d2ivxa2113 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 96.57
d2i53a2110 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 95.87
d2cchb2124 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 85.03
>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} Back     information, alignment and structure
class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Herpesvirus saimiri [TaxId: 10381]

Probab=100.00  E-value=2.1e-36  Score=206.25  Aligned_cols=103  Identities=32%  Similarity=0.474  Sum_probs=100.9

Q ss_pred             cCCCHHHHHHHHHHHHHHhHhcCCchhhHHHHHHHHHHccccCCccCcCceehhhhhHHHHhhhhhccCCCHHhHHHhhc
Q psy17187          4 FAISIQTNVFLYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVEDLVYYSD   83 (123)
Q Consensus         4 ~~Is~~~R~~li~W~~~v~~~~~l~~~tl~lAv~~lDr~ls~~~i~~~~lqLlg~tcL~iAsK~eE~~~~~~~~l~~~~~   83 (123)
                      -.|++++|.+++|||.+++.+++++++|+|+||+++|||++..+++++++||+|+|||+||+|++|..||++++++++|+
T Consensus        24 ~~it~~~R~~lidWl~~v~~~~~l~~eTl~lAv~llDryl~~~~i~~~~lqLi~~tcL~IAsK~ee~~~~~l~~l~~~~~  103 (127)
T d1bu2a1          24 TEVTVDNRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSC  103 (127)
T ss_dssp             SSSCHHHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSCCCTTTHHHHHHHHHHHHHHHSSSSCCCHHHHHHTTT
T ss_pred             CcCCHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHc
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHhHhcCCce
Q psy17187         84 YTFSPHTLKTTEKPAVYLNNTHV  106 (123)
Q Consensus        84 ~~~t~~ei~~mE~~IL~~ln~~i  106 (123)
                      +.||++|+.+||..||++|||++
T Consensus       104 ~~~t~~ei~~mE~~IL~~L~~dl  126 (127)
T d1bu2a1         104 DCFTNLELINQEKDILEALKWDT  126 (127)
T ss_dssp             TSSCHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCC
Confidence            99999999999999999999996
>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]} 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
>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]} 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
>d1aisb1 a.74.1.2 (B:1108-1205) 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
>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
>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
>d2cchb2 a.74.1.1 (B:309-432) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure