Citrus Sinensis ID: 027733

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------22
Protein Sequence
MADHHHHHHLQLGTNIILEGHQEEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGRQLKQYHCCFSEDDCAHQKQLAV
Secondary Structure (PSIPRED)
ccccccccccccccccccccccHHHccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHccccEEEcHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHHcccEEccccccccHccccccHHHHHHHHHHHHHHHHHHHHHccccccccEEEEcccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccccEEccHHHHHHHHHHHHHHHHHHHHcccccHHHEEEccccHHHHHHHHHHHHHHcccEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
madhhhhhhlqlgTNIILEGHQEEAAVMPKLITVLSSLLQRVAesndlsqrfhpqkisvfhgltrptisIHSYLERIFKyancspscFVVAYVYLDrfaqkqpslpinsfnVHRLLITSVLVSAKfmddiyynnaFYAKVGGISTTEMNLLEVDFLFDLgfqlnvtpAAFYTYCSYLQREmflqsplqleeplnvgrqlkqyhccfseddcahqkqlav
Flexible Loop (DISEMBL)
MADHHHHHHLQLGTNIILEGHQEEAAVMPKLITVLSSLLQRVAESNdlsqrfhpqkisvfhgltrPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGRQLKQYHCCFSEDDCAHQKQLAV
Low Complexity Region (SEG)
MADhhhhhhLQLGTNIILEGHQEEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGRQLKQYHCCFSEDDCAHQKQLAV
Disordered region (IsUnstruct)
**************NIILEGHQEEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGRQLKQYHCCFSEDD*********
Disordered Region (DISOPRED)
*****************************KLITVLSSLLQRVA*********************RPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQ*****************************************
Disordered Region (DISEMBL)
**********QLGTNIILEGHQEEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGRQLKQYHCCFSEDDCAHQKQLAV
Disordered Region (DISPRO)
*********LQLGTNIILEGHQEEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQS****EEPLNVGRQ*KQ******************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MADHHHHHHLQLGTNIILEGHQEEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGRQLKQYHCCFSEDDCAHQKQLAV
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	219	2.2.26 [Sep-21-2011]
O80513	202	Cyclin-U4-1 OS=Arabidopsi	yes	no	0.849	0.920	0.678	2e-70
Q9LY16	216	Cyclin-U4-2 OS=Arabidopsi	no	no	0.762	0.773	0.672	5e-61
Q9FKF6	219	Cyclin-U4-3 OS=Arabidopsi	no	no	0.703	0.703	0.689	1e-59
Q7XC35	212	Cyclin-P4-1 OS=Oryza sati	yes	no	0.844	0.872	0.565	3e-57
Q75HV0	236	Cyclin-P3-1 OS=Oryza sati	no	no	0.899	0.834	0.424	1e-40
Q9SHD3	222	Cyclin-U2-1 OS=Arabidopsi	no	no	0.867	0.855	0.395	8e-39
Q9M205	230	Cyclin-U2-2 OS=Arabidopsi	no	no	0.785	0.747	0.421	3e-37
Q9LJ45	210	Cyclin-U1-1 OS=Arabidopsi	no	no	0.726	0.757	0.438	2e-35
Q8LB60	221	Cyclin-U3-1 OS=Arabidopsi	no	no	0.630	0.624	0.482	4e-35
Q7FAT5	217	Cyclin-P2-1 OS=Oryza sati	no	no	0.789	0.797	0.378	1e-28

>sp|O80513|CCU41_ARATH Cyclin-U4-1 OS=Arabidopsis thaliana GN=CYCU4-1 PE=1 SV=1

 Score =  265 bits (677), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 131/193 (67%), Positives = 153/193 (79%), Gaps = 7/193 (3%)

Query: 23  EEAAVMPKLITVLSSLLQRVAESNDLSQRF--HPQKISVFHGLTRPTISIHSYLERIFKY 80
           E  +VM KLI  LSSLL+RVAESNDL++R     Q++SVFHGL+RPTI+I SYLERIFKY
Sbjct: 5   ENPSVMSKLIAFLSSLLERVAESNDLTRRVATQSQRVSVFHGLSRPTITIQSYLERIFKY 64

Query: 81  ANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKV 140
           ANCSPSCFVVAYVYLDRF  +QPSLPINSFNVHRLLITSV+V+AKF+DD+YYNNA+YAKV
Sbjct: 65  ANCSPSCFVVAYVYLDRFTHRQPSLPINSFNVHRLLITSVMVAAKFLDDLYYNNAYYAKV 124

Query: 141 GGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGRQLK 200
           GGIST EMN LE+DFLF LGF+LNVTP  F  Y SYLQ+EM L  PL L     V     
Sbjct: 125 GGISTKEMNFLELDFLFGLGFELNVTPNTFNAYFSYLQKEMTLLQPLSL-----VVVPSS 179

Query: 201 QYHCCFSEDDCAH 213
           +    F++D+ +H
Sbjct: 180 RSLITFNDDEASH 192

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LY16|CCU42_ARATH Cyclin-U4-2 OS=Arabidopsis thaliana GN=CYCU4-2 PE=1 SV=1

 Score =  233 bits (595), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 117/174 (67%), Positives = 143/174 (82%), Gaps = 7/174 (4%)

Query: 21  HQEE--AAVMPKLITVLSSLLQRVAESND-LSQRFHPQK-ISVFHGLTRPTISIHSYLER 76
           H +E  A +MP +IT +SSLLQRV+E+ND LS+ F   K IS F+ +T+P+ISI SY+ER
Sbjct: 11  HDQEPMAEIMPNVITAMSSLLQRVSETNDDLSRPFREHKRISAFNAVTKPSISIRSYMER 70

Query: 77  IFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAF 136
           IFKYA+CS SC++VAY+YLDRF QKQP LPI+S NVHRL+ITSVLVSAKFMDD+ YNNAF
Sbjct: 71  IFKYADCSDSCYIVAYIYLDRFIQKQPLLPIDSSNVHRLIITSVLVSAKFMDDLCYNNAF 130

Query: 137 YAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQ---SPL 187
           YAKVGGI+T EMNLLE+DFLF +GFQLNVT + +  YCS LQREM ++   SPL
Sbjct: 131 YAKVGGITTEEMNLLELDFLFGIGFQLNVTISTYNDYCSSLQREMVMRTMYSPL 184

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKF6|CCU43_ARATH Cyclin-U4-3 OS=Arabidopsis thaliana GN=CYCU4-3 PE=1 SV=1

 Score =  229 bits (583), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 109/158 (68%), Positives = 133/158 (84%), Gaps = 4/158 (2%)

Query: 25  AAVMPKLITVLSSLLQRVAESND-LSQRFHPQKISVFHGLTRPTISIHSYLERIFKYANC 83
           A +MP ++T +S LLQRV+E+ND LSQ+   QK S F G+T+P+ISI SYLERIF+YANC
Sbjct: 19  AEIMPSVLTAMSYLLQRVSETNDNLSQK---QKPSSFTGVTKPSISIRSYLERIFEYANC 75

Query: 84  SPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGI 143
           S SC++VAY+YLDRF +KQP LPINSFNVHRL+ITSVLVSAKFMDD+ YNN +YAKVGGI
Sbjct: 76  SYSCYIVAYIYLDRFVKKQPFLPINSFNVHRLIITSVLVSAKFMDDLSYNNEYYAKVGGI 135

Query: 144 STTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREM 181
           S  EMN+LE+DFLF +GF+LNVT + F  YC +LQREM
Sbjct: 136 SREEMNMLELDFLFGIGFELNVTVSTFNNYCCFLQREM 173

Arabidopsis thaliana (taxid: 3702)

>sp|Q7XC35|CCP41_ORYSJ Cyclin-P4-1 OS=Oryza sativa subsp. japonica GN=CYCP4-1 PE=2 SV=1

 Score =  221 bits (563), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 113/200 (56%), Positives = 142/200 (71%), Gaps = 15/200 (7%)

Query: 23  EEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKI-----SVFHGLTRPTISIHSYLERI 77
           E A  +P+++ +LSSLLQRVAE ND +             S F GLT+P ISI  YLERI
Sbjct: 5   EVAEAVPRVVAILSSLLQRVAERNDAAAAAAAVGEEAAAVSAFQGLTKPAISIGGYLERI 64

Query: 78  FKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFY 137
           F++ANCSPSC+VVAY+YLDRF +++P+L ++SFNVHRLLITSVL + KF+DDI YNNA++
Sbjct: 65  FRFANCSPSCYVVAYIYLDRFLRRRPALAVDSFNVHRLLITSVLTAVKFVDDICYNNAYF 124

Query: 138 AKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGR 197
           A+VGGIS  EMN LEVDFLF + F LNVTPAAF +YC+ LQ EM       LE+P  V  
Sbjct: 125 ARVGGISLMEMNYLEVDFLFGIAFDLNVTPAAFASYCAVLQSEM-----TYLEQPPAV-- 177

Query: 198 QLKQYHCCFSEDD---CAHQ 214
            L + HCC S+ D   C H+
Sbjct: 178 DLPRLHCCPSDQDDAGCHHK 197

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q75HV0|CCP31_ORYSJ Cyclin-P3-1 OS=Oryza sativa subsp. japonica GN=CYCP3-1 PE=3 SV=1

 Score =  166 bits (420), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 87/205 (42%), Positives = 129/205 (62%), Gaps = 8/205 (3%)

Query: 2   ADHHHHHHLQLGTNIILEGHQEEAAVMPKLITVLSSLLQRVAESND--LSQRFHPQKISV 59
           +D H   +L LG  + +   ++     PK++ +L++ L R  + N+  L         ++
Sbjct: 11  SDKHEESYLSLG--LTVSQSKKNNTEYPKVLLLLAAYLDRSVQKNEDLLDSNKIKDSSTI 68

Query: 60  FHGLTRPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITS 119
           FHG   P +SI  Y ERIFKY+ CSPSCFV+A +Y++R+ Q QP + + S +VHRLLITS
Sbjct: 69  FHGHRAPDLSIKLYAERIFKYSECSPSCFVLALIYMERYLQ-QPHVYMTSLSVHRLLITS 127

Query: 120 VLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQR 179
           V+V+AKF DD ++NNAFYA+VGGIST EMN LE+D LF+L F+L V    F +YC  L++
Sbjct: 128 VVVAAKFTDDAFFNNAFYARVGGISTVEMNRLELDLLFNLDFRLKVDLETFGSYCLQLEK 187

Query: 180 E---MFLQSPLQLEEPLNVGRQLKQ 201
           E   + +  P+Q    +N  + L +
Sbjct: 188 ETMVLVIDRPIQQVHGVNSTKDLSR 212

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SHD3|CCU21_ARATH Cyclin-U2-1 OS=Arabidopsis thaliana GN=CYCU2-1 PE=1 SV=1

 Score =  160 bits (404), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 76/192 (39%), Positives = 128/192 (66%), Gaps = 2/192 (1%)

Query: 11  QLGTNIILEGHQEEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQ--KISVFHGLTRPTI 68
           +L +++    +Q+++  +P +I+VLSSL++R    N+   R +    K  VF     P +
Sbjct: 10  KLRSDLYSYSYQDDSNTVPLVISVLSSLIERTLARNERISRSYGGFGKTRVFDCREIPDM 69

Query: 69  SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMD 128
           +I SYLERIF+Y    PS +VVAYVY+DRF Q      I+  NVHRLLIT++++++K+++
Sbjct: 70  TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQNNQGFRISLTNVHRLLITTIMIASKYVE 129

Query: 129 DIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQ 188
           D+ Y N+++AKVGG+ T ++N LE++FLF +GF+L+V  + F +YC +L+RE+ +    Q
Sbjct: 130 DMNYKNSYFAKVGGLETEDLNNLELEFLFLMGFKLHVNVSVFESYCCHLEREVSIGGGYQ 189

Query: 189 LEEPLNVGRQLK 200
           +E+ L    ++K
Sbjct: 190 IEKALRCAEEIK 201

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M205|CCU22_ARATH Cyclin-U2-2 OS=Arabidopsis thaliana GN=CYCU2-2 PE=1 SV=1

 Score =  155 bits (391), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 75/178 (42%), Positives = 118/178 (66%), Gaps = 6/178 (3%)

Query: 29  PKLITVLSSLLQRVAESND-LSQRFHPQ-----KISVFHGLTRPTISIHSYLERIFKYAN 82
           P +I+VLSSL+ R    N+ +S+R  P      K  +F     P ++I SYL RIF+Y  
Sbjct: 30  PLVISVLSSLIDRTLTRNERISRRALPSSGAGGKTQIFDCREIPDMTIQSYLGRIFRYTK 89

Query: 83  CSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG 142
             PS +VVAYVY+DRF Q  P   I+  NVHRLLIT++++++K+++D+ Y N+++AKVGG
Sbjct: 90  AGPSVYVVAYVYIDRFCQTNPGFRISLTNVHRLLITTIMIASKYVEDLNYRNSYFAKVGG 149

Query: 143 ISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGRQLK 200
           + T ++N LE++FLF +GF+L+V  + F +YC +L+RE+      Q+E+ L    ++K
Sbjct: 150 LETEDLNKLELEFLFLMGFKLHVNVSVFESYCCHLEREVSFGGGYQIEKALRCAEEIK 207

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LJ45|CCU11_ARATH Cyclin-U1-1 OS=Arabidopsis thaliana GN=CYCU1-1 PE=1 SV=1

 Score =  149 bits (376), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 71/162 (43%), Positives = 112/162 (69%), Gaps = 3/162 (1%)

Query: 26  AVMPKLITVLSSLLQRVAESNDL---SQRFHPQKISVFHGLTRPTISIHSYLERIFKYAN 82
           A  P+++T++S +++++   N+      +   + +  FHG+  P+ISI  YLERI+KY  
Sbjct: 22  AATPRVLTIISHVMEKLVARNEWLAKQTKGFGKSLEAFHGVRAPSISIAKYLERIYKYTK 81

Query: 83  CSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG 142
           CSP+CFVV YVY+DR A K P   + S NVHRLL+T V+++AK +DD++YNN FYA+VGG
Sbjct: 82  CSPACFVVGYVYIDRLAHKHPGSLVVSLNVHRLLVTCVMIAAKILDDVHYNNEFYARVGG 141

Query: 143 ISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQ 184
           +S  ++N +E++ LF L F++ V+   F +YC +L++EM L 
Sbjct: 142 VSNADLNKMELELLFLLDFRVTVSFRVFESYCFHLEKEMQLN 183

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LB60|CCU31_ARATH Cyclin-U3-1 OS=Arabidopsis thaliana GN=CYCU3-1 PE=1 SV=2

 Score =  147 bits (372), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 68/141 (48%), Positives = 101/141 (71%), Gaps = 3/141 (2%)

Query: 54  PQKISVFHGLTRPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVH 113
           P  ++VF G + P ISI  YL+RIFKY+ CSPSCFV+A++Y+D F  K  +L +   NVH
Sbjct: 59  PDSVTVFDGRSPPEISIAHYLDRIFKYSCCSPSCFVIAHIYIDHFLHKTRAL-LKPLNVH 117

Query: 114 RLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTY 173
           RL+IT+V+++AK  DD Y+NNA+YA+VGG++T E+N LE++ LF L F+L V P  F+T+
Sbjct: 118 RLIITTVMLAAKVFDDRYFNNAYYARVGGVTTRELNRLEMELLFTLDFKLQVDPQTFHTH 177

Query: 174 CSYLQREMFLQSPLQLEEPLN 194
           C  L+++   +   Q+E P+ 
Sbjct: 178 CCQLEKQN--RDGFQIEWPIK 196

Arabidopsis thaliana (taxid: 3702)

>sp|Q7FAT5|CCP21_ORYSJ Cyclin-P2-1 OS=Oryza sativa subsp. japonica GN=CYCP2-1 PE=2 SV=1

 Score =  126 bits (317), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 70/185 (37%), Positives = 111/185 (60%), Gaps = 12/185 (6%)

Query: 29  PKLITVLSSLLQRVAESNDLSQRFHPQKISV-----FHGLTRPTISIHSYLERIFKYANC 83
           P +++VL+SLL+R    N+  Q       +      F   T   +S+H++LER  +YAN 
Sbjct: 26  PVVVSVLASLLERHIARNERDQAAAADGEAARRARAFDSGTVLDMSLHAFLERFSRYANV 85

Query: 84  SPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGI 143
           SP  +VVAY YLDR  ++   + + S N  RLL T++LV++KF++D  Y N+++A VGG+
Sbjct: 86  SPQVYVVAYAYLDRL-RRGDGVRVVSANAQRLLTTAILVASKFVEDRNYKNSYFAAVGGL 144

Query: 144 STTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGRQLKQYH 203
           +  E++ LE+DFLF + F+LNV+ + F +YC +L+RE+      Q+E      R LK+  
Sbjct: 145 TAAELSSLELDFLFLMQFRLNVSVSVFQSYCRHLEREVSYGGGYQVE------RCLKKAL 198

Query: 204 CCFSE 208
            C  E
Sbjct: 199 VCSGE 203

Oryza sativa subsp. japonica (taxid: 39947)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	219
255539923	203	cyclin-dependent protein kinase, putativ	0.899	0.970	0.79	6e-88
224136408	201	predicted protein [Populus trichocarpa]	0.890	0.970	0.791	2e-86
224114603	201	predicted protein [Populus trichocarpa]	0.890	0.970	0.786	3e-86
224137114	202	predicted protein [Populus trichocarpa]	0.894	0.970	0.783	3e-83
255571045	203	cyclin-dependent protein kinase, putativ	0.894	0.965	0.78	3e-83
356520736	202	PREDICTED: cyclin-U4-1-like [Glycine max	0.885	0.960	0.723	2e-76
225453342	204	PREDICTED: cyclin-U4-1 [Vitis vinifera]	0.881	0.946	0.730	6e-76
356568557	205	PREDICTED: cyclin-U4-1-like [Glycine max	0.876	0.936	0.717	1e-74
388507758	207	unknown [Lotus japonicus]	0.863	0.913	0.707	2e-73
449432309	211	PREDICTED: cyclin-U4-1-like [Cucumis sat	0.881	0.914	0.709	4e-73

>gi|255539923|ref|XP_002511026.1| cyclin-dependent protein kinase, putative [Ricinus communis] gi|223550141|gb|EEF51628.1| cyclin-dependent protein kinase, putative [Ricinus communis]

 Score =  329 bits (843), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 158/200 (79%), Positives = 175/200 (87%), Gaps = 3/200 (1%)

Query: 22  QEEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFKYA 81
           +    VMPK++T LSSLLQRVAESNDLS + HPQ+ISVFHGLTRP+IS+ SYLERIFKYA
Sbjct: 5   EATVVVMPKVVTFLSSLLQRVAESNDLSHQLHPQRISVFHGLTRPSISVQSYLERIFKYA 64

Query: 82  NCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG 141
           NCSPSCFV+AYVYLDRFAQ+QPS PINSFNVHRLLITSVLVSAKFMDDIYYNNA+YAKVG
Sbjct: 65  NCSPSCFVIAYVYLDRFAQRQPSFPINSFNVHRLLITSVLVSAKFMDDIYYNNAYYAKVG 124

Query: 142 GISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQ--LEEPLNVGRQL 199
           GIST+EMN+LEVDFLF LGFQLNVTP  F+TYCSYLQREM +QS     +E PLN+ R L
Sbjct: 125 GISTSEMNILEVDFLFGLGFQLNVTPNTFHTYCSYLQREMLVQSSQHQLVEPPLNMARAL 184

Query: 200 KQYHCCFSEDDCAHQKQLAV 219
           K  HCCFSED+  HQKQLAV
Sbjct: 185 K-IHCCFSEDESTHQKQLAV 203

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224136408|ref|XP_002322322.1| predicted protein [Populus trichocarpa] gi|222869318|gb|EEF06449.1| predicted protein [Populus trichocarpa]

 Score =  323 bits (829), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 156/197 (79%), Positives = 173/197 (87%), Gaps = 2/197 (1%)

Query: 24  EAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFKYANC 83
           E AVMPK+IT LSSLLQRVAESND+S + +PQK S+FHGLTRPTISI +YLERIFKY+NC
Sbjct: 6   ETAVMPKVITFLSSLLQRVAESNDISHQLYPQKASIFHGLTRPTISIQNYLERIFKYSNC 65

Query: 84  SPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGI 143
           SPSCFVVAYVYLDRF+Q+Q   P+NSFNVHRLLITSVLVS KFMDDIYYNNAFYAKVGGI
Sbjct: 66  SPSCFVVAYVYLDRFSQRQSCFPLNSFNVHRLLITSVLVSVKFMDDIYYNNAFYAKVGGI 125

Query: 144 STTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQL-EEPLNVGRQLKQY 202
           ST EMNLLEVDFLF LGFQLNVTP  F+ YCSYLQREM +QSPLQ+ + PLN+ R LK  
Sbjct: 126 STREMNLLEVDFLFGLGFQLNVTPTTFHLYCSYLQREMSIQSPLQIVDTPLNIARPLK-I 184

Query: 203 HCCFSEDDCAHQKQLAV 219
           HCCF+ED+  HQKQLAV
Sbjct: 185 HCCFNEDESTHQKQLAV 201

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114603|ref|XP_002332321.1| predicted protein [Populus trichocarpa] gi|222832568|gb|EEE71045.1| predicted protein [Populus trichocarpa]

 Score =  323 bits (828), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 155/197 (78%), Positives = 173/197 (87%), Gaps = 2/197 (1%)

Query: 24  EAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFKYANC 83
           E  VMPK+IT LSSLLQRVAESNDLSQ+ +PQK+S+FHGL+RP ISI +YLERIFKYANC
Sbjct: 6   ETTVMPKVITFLSSLLQRVAESNDLSQQLYPQKVSIFHGLSRPPISIQNYLERIFKYANC 65

Query: 84  SPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGI 143
           SPSCFVVAYVYLDRFAQ+Q   PINSFNVHRLLITSVL+S KFMDDIYYNNAFYAKVGGI
Sbjct: 66  SPSCFVVAYVYLDRFAQRQSCFPINSFNVHRLLITSVLISVKFMDDIYYNNAFYAKVGGI 125

Query: 144 STTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEE-PLNVGRQLKQY 202
           ST EMNLLEVDFLF LGFQLNVTP  F+ YCSYLQREM +QSPL + + PLN+ R L++ 
Sbjct: 126 STAEMNLLEVDFLFGLGFQLNVTPTMFHAYCSYLQREMLIQSPLPIVDLPLNMAR-LQKT 184

Query: 203 HCCFSEDDCAHQKQLAV 219
           HCCF+ED+  HQKQLAV
Sbjct: 185 HCCFNEDESTHQKQLAV 201

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224137114|ref|XP_002327025.1| predicted protein [Populus trichocarpa] gi|222835340|gb|EEE73775.1| predicted protein [Populus trichocarpa]

 Score =  313 bits (802), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 156/199 (78%), Positives = 170/199 (85%), Gaps = 3/199 (1%)

Query: 23  EEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFKYAN 82
           E   +MPK IT LSSLLQRVA+SNDL++ F PQKISVFHGLTRPTISI SYLERIFKYAN
Sbjct: 5   ESTKMMPKSITFLSSLLQRVADSNDLNREFQPQKISVFHGLTRPTISIQSYLERIFKYAN 64

Query: 83  CSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG 142
           CSPSCFVVAYVYLDRFAQ+QPSLPINS NVHRLLITSVLVSAKFMDD+YYNNA+YA+VGG
Sbjct: 65  CSPSCFVVAYVYLDRFAQRQPSLPINSLNVHRLLITSVLVSAKFMDDMYYNNAYYARVGG 124

Query: 143 ISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQL-EEPLNVGRQLKQ 201
           IST EMN LEVDFLF LGF LNVTP  F+TYCSYLQREM  Q  L L E  LN+GR LK 
Sbjct: 125 ISTIEMNYLEVDFLFGLGFNLNVTPNTFHTYCSYLQREMMQQPSLNLAESSLNLGRSLK- 183

Query: 202 YHCCFSEDDCAH-QKQLAV 219
            H CF+ED+ +H Q+QLAV
Sbjct: 184 VHLCFNEDETSHQQQQLAV 202

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255571045|ref|XP_002526473.1| cyclin-dependent protein kinase, putative [Ricinus communis] gi|223534148|gb|EEF35864.1| cyclin-dependent protein kinase, putative [Ricinus communis]

 Score =  313 bits (802), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 156/200 (78%), Positives = 172/200 (86%), Gaps = 4/200 (2%)

Query: 23  EEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFKYAN 82
           E   +MPKLIT LSSLLQRVAESNDL+ + H QKISVFHGLTRPTISI +YLERIFKYAN
Sbjct: 5   ESPNLMPKLITFLSSLLQRVAESNDLNLQIHTQKISVFHGLTRPTISIQNYLERIFKYAN 64

Query: 83  CSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG 142
           CSPSCF+VAYVYLDRFAQ+QPSLP+NSFNVHRLLITSV+V+AKFMDD+YYNNA+YAKVGG
Sbjct: 65  CSPSCFIVAYVYLDRFAQRQPSLPLNSFNVHRLLITSVMVAAKFMDDMYYNNAYYAKVGG 124

Query: 143 ISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEP--LNVGRQLK 200
           IST EMN LEVDFLF LGF LNVTP  F+TY SYLQREM LQ PL L E   LN+GR LK
Sbjct: 125 ISTIEMNYLEVDFLFGLGFHLNVTPNTFHTYSSYLQREMMLQPPLSLVESSSLNLGRSLK 184

Query: 201 QYHCCFSEDDCAHQK-QLAV 219
             H CF+ED+ +HQK QLAV
Sbjct: 185 -VHLCFNEDETSHQKQQLAV 203

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356520736|ref|XP_003529016.1| PREDICTED: cyclin-U4-1-like [Glycine max]

 Score =  291 bits (744), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 144/199 (72%), Positives = 164/199 (82%), Gaps = 5/199 (2%)

Query: 20  GHQEEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFK 79
             +E  +VMPK+IT LSSLL+RVAESND +Q+   QKISVFHGLTRP ISIHSYLERIFK
Sbjct: 2   AEEESPSVMPKVITFLSSLLERVAESNDHNQQH--QKISVFHGLTRPNISIHSYLERIFK 59

Query: 80  YANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAK 139
           YANCSPSCFVVAYVYLDRF Q+QPSLPIN+FNVHRLLITSV+V+AKFMDD+YYNNA+YAK
Sbjct: 60  YANCSPSCFVVAYVYLDRFTQRQPSLPINTFNVHRLLITSVMVAAKFMDDMYYNNAYYAK 119

Query: 140 VGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFL-QSPLQL-EEPLNVGR 197
           VGGI+  EMN LE+DFLF LGF LNVTP  F  YC  LQREM L Q PL   +  LN+G+
Sbjct: 120 VGGITKIEMNFLELDFLFGLGFHLNVTPGTFQAYCVNLQREMLLIQQPLNFADSTLNLGK 179

Query: 198 QLKQYHCCFSEDDCAHQKQ 216
            LK  H CF+ED+ +HQKQ
Sbjct: 180 SLKA-HLCFNEDESSHQKQ 197

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453342|ref|XP_002271136.1| PREDICTED: cyclin-U4-1 [Vitis vinifera] gi|297734633|emb|CBI16684.3| unnamed protein product [Vitis vinifera]

 Score =  289 bits (739), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 144/197 (73%), Positives = 160/197 (81%), Gaps = 4/197 (2%)

Query: 23  EEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLERIFKYAN 82
           E    M KLIT LSS+LQRVAESNDL++RF PQKISVFHGLTRP ISI SYLERIF YAN
Sbjct: 5   ENPNFMSKLITFLSSILQRVAESNDLNRRFLPQKISVFHGLTRPNISIQSYLERIFNYAN 64

Query: 83  CSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG 142
           CSPSC+VVAY+YLDRF QKQPSLPINS+NVHRLLIT V+V+AKFMDD+YYNNA+YAKVGG
Sbjct: 65  CSPSCYVVAYIYLDRFVQKQPSLPINSYNVHRLLITGVMVAAKFMDDMYYNNAYYAKVGG 124

Query: 143 ISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEE---PLNVGRQL 199
           IST EMN LEVDFLF L F LNVTP  F+TYC  LQREM LQSPL L +    LN+ R  
Sbjct: 125 ISTREMNFLEVDFLFGLAFDLNVTPTTFHTYCCCLQREMLLQSPLSLPDHHSSLNLARSS 184

Query: 200 KQYHCCFSEDDCAHQKQ 216
           K  H  F+ED+ +H KQ
Sbjct: 185 K-LHLHFNEDEPSHHKQ 200

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356568557|ref|XP_003552477.1| PREDICTED: cyclin-U4-1-like [Glycine max]

 Score =  285 bits (729), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 142/198 (71%), Positives = 164/198 (82%), Gaps = 6/198 (3%)

Query: 23  EEAAVMPKLITVLSSLLQRVAESNDLSQR--FHPQKISVFHGLTRPTISIHSYLERIFKY 80
           E   VMPKLI+ LSSLL+RVAESNDL+Q+   H QK+SVFHGLTRPTISI SYLERIFKY
Sbjct: 5   ESPNVMPKLISFLSSLLKRVAESNDLNQQQLLH-QKVSVFHGLTRPTISIQSYLERIFKY 63

Query: 81  ANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKV 140
           ANCSPSCF+VAYVYLDRF Q+QPSLPIN FNVHRLLITSV+V+AKFMDD+YYNNA+YAKV
Sbjct: 64  ANCSPSCFIVAYVYLDRFTQRQPSLPINFFNVHRLLITSVMVAAKFMDDLYYNNAYYAKV 123

Query: 141 GGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQL-EEPLNVGRQL 199
           GGI+T EMN LEVDFLF LGF LNVTP  F  YC++LQ EM L  PL   +  L++G+ L
Sbjct: 124 GGITTIEMNFLEVDFLFGLGFHLNVTPGTFQAYCAHLQSEMLLMQPLNFADSSLSLGKSL 183

Query: 200 KQYHCCFSEDD-CAHQKQ 216
           K  H C++ED+  +HQKQ
Sbjct: 184 KA-HLCYNEDESSSHQKQ 200

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388507758|gb|AFK41945.1| unknown [Lotus japonicus]

 Score =  280 bits (717), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 138/195 (70%), Positives = 161/195 (82%), Gaps = 6/195 (3%)

Query: 23  EEAAVMPKLITVLSSLLQRVAESNDLSQR---FHPQKISVFHGLTRPTISIHSYLERIFK 79
           E    MPKL+  LSS+L++VAESNDL+Q+    H QKISVFHGLTRPTISI SYLERIFK
Sbjct: 5   ENPNEMPKLLAFLSSMLKKVAESNDLNQQQQLIH-QKISVFHGLTRPTISIQSYLERIFK 63

Query: 80  YANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAK 139
           YANCSPSCF+VAYVYLDRF QKQPSLPINSFNVHRLLITSV+V+AKFMDD+YYNNA+YA+
Sbjct: 64  YANCSPSCFIVAYVYLDRFTQKQPSLPINSFNVHRLLITSVMVAAKFMDDMYYNNAYYAR 123

Query: 140 VGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQL-EEPLNVGRQ 198
           VGGI+T EMN LE+DFLF LGF LNVTP  F  YCS+LQREM L  PL   +  L++G+ 
Sbjct: 124 VGGITTIEMNFLELDFLFGLGFNLNVTPGTFQGYCSHLQREMMLVQPLIFTDSSLSLGKS 183

Query: 199 LKQYHCCFSEDDCAH 213
           +K  H CF+ED+ +H
Sbjct: 184 VKA-HLCFNEDESSH 197

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449432309|ref|XP_004133942.1| PREDICTED: cyclin-U4-1-like [Cucumis sativus] gi|449521166|ref|XP_004167601.1| PREDICTED: cyclin-U4-1-like [Cucumis sativus]

 Score =  280 bits (715), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 144/203 (70%), Positives = 157/203 (77%), Gaps = 10/203 (4%)

Query: 23  EEAAVMPKLITVLSSLLQRVAESND--LSQRFHPQKISVFHGLTRPTISIHSYLERIFKY 80
           E++ VM KLI  LS LLQRVAESND  LS    P KIS FHGLTRP+ISI SYL+RIFKY
Sbjct: 5   EDSTVMAKLIDFLSCLLQRVAESNDRNLSVNLQPHKISAFHGLTRPSISIQSYLDRIFKY 64

Query: 81  ANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKV 140
           ANCSP CFV+AYVYLDRF Q+QPSLPINSFNVHRLLITSVLVSAKFMDD YYNNA+YAKV
Sbjct: 65  ANCSPCCFVIAYVYLDRFVQRQPSLPINSFNVHRLLITSVLVSAKFMDDTYYNNAYYAKV 124

Query: 141 GGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREM-FLQSPLQLEEP------L 193
           GGISTTEMN LEVDFLF LGF LNVTP  F++Y SYLQR+M  LQ PL           L
Sbjct: 125 GGISTTEMNFLEVDFLFGLGFHLNVTPTTFHSYYSYLQRQMLLLQPPLTSSASTKSDLLL 184

Query: 194 NVGRQLKQYHCCFSEDDCAHQKQ 216
              R LK  H CF ED+ +H+KQ
Sbjct: 185 TSSRALKS-HFCFDEDEASHKKQ 206

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	219
TAIR|locus:2042421	202	CYCP4;1 "AT2G44740" [Arabidops	0.863	0.935	0.688	9.4e-66
TAIR|locus:2183394	216	CYCP4;3 "cyclin p4;3" [Arabido	0.762	0.773	0.672	1.6e-56
TAIR|locus:2151656	219	CYCP4;2 "CYCLIN P4;2" [Arabido	0.703	0.703	0.689	1.3e-54
TAIR|locus:2088743	210	CYCP2;1 "cyclin p2;1" [Arabido	0.726	0.757	0.453	7e-38
TAIR|locus:2055552	222	cycp3;1 "cyclin p3;1" [Arabido	0.867	0.855	0.395	4.9e-37
TAIR|locus:2099192	221	CYCP1;1 "cyclin p1;1" [Arabido	0.808	0.800	0.435	3.5e-36
TAIR|locus:2103391	230	CYCP3;2 "cyclin p3;2" [Arabido	0.867	0.826	0.401	7.2e-36
TAIR|locus:1009023243	212	AT3G05327 [Arabidopsis thalian	0.744	0.768	0.431	4.6e-34
DICTYBASE|DDB_G0277481	391	DDB_G0277481 [Dictyostelium di	0.716	0.401	0.408	8.2e-28
DICTYBASE|DDB_G0286485	398	DDB_G0286485 "PHO85 cyclin-2"	0.657	0.361	0.391	1e-27

TAIR|locus:2042421 CYCP4;1 "AT2G44740" [Arabidopsis thaliana (taxid:3702)]

 Score = 669 (240.6 bits), Expect = 9.4e-66, P = 9.4e-66
 Identities = 135/196 (68%), Positives = 157/196 (80%)

Query:    23 EEAAVMPKLITVLSSLLQRVAESNDLSQRF--HPQKISVFHGLTRPTISIHSYLERIFKY 80
             E  +VM KLI  LSSLL+RVAESNDL++R     Q++SVFHGL+RPTI+I SYLERIFKY
Sbjct:     5 ENPSVMSKLIAFLSSLLERVAESNDLTRRVATQSQRVSVFHGLSRPTITIQSYLERIFKY 64

Query:    81 ANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKV 140
             ANCSPSCFVVAYVYLDRF  +QPSLPINSFNVHRLLITSV+V+AKF+DD+YYNNA+YAKV
Sbjct:    65 ANCSPSCFVVAYVYLDRFTHRQPSLPINSFNVHRLLITSVMVAAKFLDDLYYNNAYYAKV 124

Query:   141 GGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGRQLK 200
             GGIST EMN LE+DFLF LGF+LNVTP  F  Y SYLQ+EM L  PL L   +   R L 
Sbjct:   125 GGISTKEMNFLELDFLFGLGFELNVTPNTFNAYFSYLQKEMTLLQPLSLVV-VPSSRSL- 182

Query:   201 QYHCCFSEDDCAHQKQ 216
                  F++D+ +HQKQ
Sbjct:   183 ---ITFNDDEASHQKQ 195

GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=ISS

GO:0051726 "regulation of cell cycle" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0010440 "stomatal lineage progression" evidence=RCA

TAIR|locus:2183394 CYCP4;3 "cyclin p4;3" [Arabidopsis thaliana (taxid:3702)]

 Score = 582 (209.9 bits), Expect = 1.6e-56, P = 1.6e-56
 Identities = 117/174 (67%), Positives = 143/174 (82%)

Query:    21 HQEE--AAVMPKLITVLSSLLQRVAESND-LSQRFHPQK-ISVFHGLTRPTISIHSYLER 76
             H +E  A +MP +IT +SSLLQRV+E+ND LS+ F   K IS F+ +T+P+ISI SY+ER
Sbjct:    11 HDQEPMAEIMPNVITAMSSLLQRVSETNDDLSRPFREHKRISAFNAVTKPSISIRSYMER 70

Query:    77 IFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAF 136
             IFKYA+CS SC++VAY+YLDRF QKQP LPI+S NVHRL+ITSVLVSAKFMDD+ YNNAF
Sbjct:    71 IFKYADCSDSCYIVAYIYLDRFIQKQPLLPIDSSNVHRLIITSVLVSAKFMDDLCYNNAF 130

Query:   137 YAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQ---SPL 187
             YAKVGGI+T EMNLLE+DFLF +GFQLNVT + +  YCS LQREM ++   SPL
Sbjct:   131 YAKVGGITTEEMNLLELDFLFGIGFQLNVTISTYNDYCSSLQREMVMRTMYSPL 184

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0019901 "protein kinase binding" evidence=IEA

GO:0051726 "regulation of cell cycle" evidence=ISS

GO:0010440 "stomatal lineage progression" evidence=RCA

TAIR|locus:2151656 CYCP4;2 "CYCLIN P4;2" [Arabidopsis thaliana (taxid:3702)]

 Score = 564 (203.6 bits), Expect = 1.3e-54, P = 1.3e-54
 Identities = 109/158 (68%), Positives = 133/158 (84%)

Query:    25 AAVMPKLITVLSSLLQRVAESND-LSQRFHPQKISVFHGLTRPTISIHSYLERIFKYANC 83
             A +MP ++T +S LLQRV+E+ND LSQ+   QK S F G+T+P+ISI SYLERIF+YANC
Sbjct:    19 AEIMPSVLTAMSYLLQRVSETNDNLSQK---QKPSSFTGVTKPSISIRSYLERIFEYANC 75

Query:    84 SPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGI 143
             S SC++VAY+YLDRF +KQP LPINSFNVHRL+ITSVLVSAKFMDD+ YNN +YAKVGGI
Sbjct:    76 SYSCYIVAYIYLDRFVKKQPFLPINSFNVHRLIITSVLVSAKFMDDLSYNNEYYAKVGGI 135

Query:   144 STTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREM 181
             S  EMN+LE+DFLF +GF+LNVT + F  YC +LQREM
Sbjct:   136 SREEMNMLELDFLFGIGFELNVTVSTFNNYCCFLQREM 173

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0019901 "protein kinase binding" evidence=IEA

GO:0051726 "regulation of cell cycle" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0010054 "trichoblast differentiation" evidence=RCA

GO:0010440 "stomatal lineage progression" evidence=RCA

TAIR|locus:2088743 CYCP2;1 "cyclin p2;1" [Arabidopsis thaliana (taxid:3702)]

 Score = 406 (148.0 bits), Expect = 7.0e-38, P = 7.0e-38
 Identities = 74/163 (45%), Positives = 117/163 (71%)

Query:    24 EAAVMPKLITVLSSLLQRVAESND-LSQRFHP--QKISVFHGLTRPTISIHSYLERIFKY 80
             EAA  P+++T++S +++++   N+ L+++     + +  FHG+  P+ISI  YLERI+KY
Sbjct:    21 EAAT-PRVLTIISHVMEKLVARNEWLAKQTKGFGKSLEAFHGVRAPSISIAKYLERIYKY 79

Query:    81 ANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKV 140
               CSP+CFVV YVY+DR A K P   + S NVHRLL+T V+++AK +DD++YNN FYA+V
Sbjct:    80 TKCSPACFVVGYVYIDRLAHKHPGSLVVSLNVHRLLVTCVMIAAKILDDVHYNNEFYARV 139

Query:   141 GGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFL 183
             GG+S  ++N +E++ LF L F++ V+   F +YC +L++EM L
Sbjct:   140 GGVSNADLNKMELELLFLLDFRVTVSFRVFESYCFHLEKEMQL 182

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0019901 "protein kinase binding" evidence=IEA

GO:0051726 "regulation of cell cycle" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0010440 "stomatal lineage progression" evidence=RCA

TAIR|locus:2055552 cycp3;1 "cyclin p3;1" [Arabidopsis thaliana (taxid:3702)]

 Score = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 76/192 (39%), Positives = 128/192 (66%)

Query:    11 QLGTNIILEGHQEEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQ--KISVFHGLTRPTI 68
             +L +++    +Q+++  +P +I+VLSSL++R    N+   R +    K  VF     P +
Sbjct:    10 KLRSDLYSYSYQDDSNTVPLVISVLSSLIERTLARNERISRSYGGFGKTRVFDCREIPDM 69

Query:    69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMD 128
             +I SYLERIF+Y    PS +VVAYVY+DRF Q      I+  NVHRLLIT++++++K+++
Sbjct:    70 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQNNQGFRISLTNVHRLLITTIMIASKYVE 129

Query:   129 DIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQ 188
             D+ Y N+++AKVGG+ T ++N LE++FLF +GF+L+V  + F +YC +L+RE+ +    Q
Sbjct:   130 DMNYKNSYFAKVGGLETEDLNNLELEFLFLMGFKLHVNVSVFESYCCHLEREVSIGGGYQ 189

Query:   189 LEEPLNVGRQLK 200
             +E+ L    ++K
Sbjct:   190 IEKALRCAEEIK 201

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0019901 "protein kinase binding" evidence=IEA

GO:0051726 "regulation of cell cycle" evidence=ISS

GO:0010440 "stomatal lineage progression" evidence=RCA

TAIR|locus:2099192 CYCP1;1 "cyclin p1;1" [Arabidopsis thaliana (taxid:3702)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 81/186 (43%), Positives = 125/186 (67%)

Query:    10 LQLGTNIILEGHQEEAAVMPKLITVLSSLLQR--VAESNDLSQRFHPQKISVFHGLTRPT 67
             L+LG  +I+EG + +    P +++ LSS L+R  +   +D      P  ++VF G + P 
Sbjct:    17 LRLG--LIIEGKRLKKP--PTVLSRLSSSLERSLLLNHDDKILLGSPDSVTVFDGRSPPE 72

Query:    68 ISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFM 127
             ISI  YL+RIFKY+ CSPSCFV+A++Y+D F  K  +L +   NVHRL+IT+V+++AK  
Sbjct:    73 ISIAHYLDRIFKYSCCSPSCFVIAHIYIDHFLHKTRAL-LKPLNVHRLIITTVMLAAKVF 131

Query:   128 DDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPL 187
             DD Y+NNA+YA+VGG++T E+N LE++ LF L F+L V P  F+T+C  L+++   +   
Sbjct:   132 DDRYFNNAYYARVGGVTTRELNRLEMELLFTLDFKLQVDPQTFHTHCCQLEKQN--RDGF 189

Query:   188 QLEEPL 193
             Q+E P+
Sbjct:   190 QIEWPI 195

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0019901 "protein kinase binding" evidence=IEA

GO:0051726 "regulation of cell cycle" evidence=ISS

GO:0010440 "stomatal lineage progression" evidence=RCA

TAIR|locus:2103391 CYCP3;2 "cyclin p3;2" [Arabidopsis thaliana (taxid:3702)]

 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 79/197 (40%), Positives = 123/197 (62%)

Query:    29 PKLITVLSSLLQRVAESND-LSQRFHPQ-----KISVFHGLTRPTISIHSYLERIFKYAN 82
             P +I+VLSSL+ R    N+ +S+R  P      K  +F     P ++I SYL RIF+Y  
Sbjct:    30 PLVISVLSSLIDRTLTRNERISRRALPSSGAGGKTQIFDCREIPDMTIQSYLGRIFRYTK 89

Query:    83 CSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG 142
               PS +VVAYVY+DRF Q  P   I+  NVHRLLIT++++++K+++D+ Y N+++AKVGG
Sbjct:    90 AGPSVYVVAYVYIDRFCQTNPGFRISLTNVHRLLITTIMIASKYVEDLNYRNSYFAKVGG 149

Query:   143 ISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGRQLKQY 202
             + T ++N LE++FLF +GF+L+V  + F +YC +L+RE+      Q+E+ L    ++K  
Sbjct:   150 LETEDLNKLELEFLFLMGFKLHVNVSVFESYCCHLEREVSFGGGYQIEKALRCAEEIKSR 209

Query:   203 HCCFSEDDCAHQK-QLA 218
                  +    H   QLA
Sbjct:   210 QMIIQDPKHHHHHHQLA 226

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=ISS

GO:0019901 "protein kinase binding" evidence=IEA

GO:0051726 "regulation of cell cycle" evidence=ISS

GO:0010440 "stomatal lineage progression" evidence=RCA

TAIR|locus:1009023243 AT3G05327 [Arabidopsis thaliana (taxid:3702)]

 Score = 370 (135.3 bits), Expect = 4.6e-34, P = 4.6e-34
 Identities = 75/174 (43%), Positives = 115/174 (66%)

Query:    16 IILEGHQEEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQ-----KISVFHGLTRPTISI 70
             ++ +  Q   +  P++IT+L+S L+++ + N   ++FH +     +I++FHG   P++SI
Sbjct:    18 LLEDSDQPPDSTPPRVITLLASTLEKMIQKN--KKKFHTRHNKADEITMFHGSKAPSLSI 75

Query:    71 HSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLP----INSFNVHRLLITSVLVSAKF 126
             + Y ERI +YA CSP CFV A+ Y+ R+ Q+  +      + S NVHRLLITS+LV+AKF
Sbjct:    76 YRYTERIHRYAQCSPVCFVAAFAYILRYLQRPEATSTARRLTSLNVHRLLITSLLVAAKF 135

Query:   127 MDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQRE 180
             ++   YNNA+YAK+GG+ST EMN LE  FL D+ F+L +T   F  +C  LQ+E
Sbjct:   136 LERQCYNNAYYAKIGGVSTEEMNRLERTFLVDVDFRLYITTETFEKHCLMLQKE 189

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0019901 "protein kinase binding" evidence=IEA

GO:0010440 "stomatal lineage progression" evidence=RCA

DICTYBASE|DDB_G0277481 DDB_G0277481 [Dictyostelium discoideum (taxid:44689)]

 Score = 311 (114.5 bits), Expect = 8.2e-28, P = 8.2e-28
 Identities = 67/164 (40%), Positives = 102/164 (62%)

Query:    16 IILEGHQEEAAVMPKLITVLSSLLQRVAESNDLSQRFHPQKISVFHGLTRPTISIHSYLE 75
             II +   ++  ++  L TV++ L+    +S +  + F+P           PTI I +YL 
Sbjct:    20 IIPKRDTKDNILLDVLCTVINKLITNGDKSKNDRREFYPPNRKP------PTIGIDAYLA 73

Query:    76 RIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNA 135
             R+ KY+ CS  CFV++ VY+DRF  KQ  L +NS N+HRL+ITS+L+S K++DDI+YNN 
Sbjct:    74 RLLKYSPCSKECFVMSLVYIDRFL-KQCDLTVNSMNIHRLVITSLLISTKYLDDIFYNNE 132

Query:   136 FYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQR 179
             FY++VGGIS  EMN LEV FL  + + +N +   F  Y   +++
Sbjct:   133 FYSQVGGISLKEMNGLEVCFLSMMDYTVNCSLDEFDMYSKQVEK 176

GO:0019901 "protein kinase binding" evidence=IEA

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

DICTYBASE|DDB_G0286485 DDB_G0286485 "PHO85 cyclin-2" [Dictyostelium discoideum (taxid:44689)]

 Score = 310 (114.2 bits), Expect = 1.0e-27, P = 1.0e-27
 Identities = 58/148 (39%), Positives = 96/148 (64%)

Query:    34 VLSSLLQRVAESNDLSQRFHPQKISVF--HGLTRPTISIHSYLERIFKYANCSPSCFVVA 91
             +L SL+  + +   ++ +F P   S F    +  P I+I  Y+ RI KY+ CS  CF++ 
Sbjct:    95 LLRSLVMAINQMLSVNDQF-PNNHSQFLPEHMKLPMITIEGYISRIIKYSPCSKECFIII 153

Query:    92 YVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLL 151
              +Y+DR  QK+  + +NS+N+HR+LIT VLV+AK++DDI+YNN FY++VGG+S  E+N++
Sbjct:   154 LMYIDRLIQKRNFI-VNSYNIHRILITCVLVAAKYLDDIFYNNQFYSQVGGVSVKEINVM 212

Query:   152 EVDFLFDLGFQLNVTPAAFYTYCSYLQR 179
             E+DFL  L F ++     +  Y  + ++
Sbjct:   213 ELDFLKLLSFDVSANTDVYSVYLEFFEK 240

GO:0019901 "protein kinase binding" evidence=IEA

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

---

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)
O80513	CCU41_ARATH	No assigned EC number	0.6787	0.8493	0.9207	yes	no
Q7XC35	CCP41_ORYSJ	No assigned EC number	0.565	0.8447	0.8726	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_fgenesh4_pg.C_LG_XV0856 hypothetical protein (201 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	219
pfam08613	140	pfam08613, Cyclin, Cyclin	6e-39
pfam00134	127	pfam00134, Cyclin_N, Cyclin, N-terminal domain	3e-10

>gnl|CDD|204002 pfam08613, Cyclin, Cyclin

 Score =  130 bits (330), Expect = 6e-39
 Identities = 56/140 (40%), Positives = 82/140 (58%), Gaps = 5/140 (3%)

Query: 29  PKLITVLSSLLQRVAESND---LSQRFHPQKISVFHGLTRPTISIHSYLERIFKYANCSP 85
            +LI  +S +L R+   ND    +       +  F+    P+IS+  YL RI KY   SP
Sbjct: 1   DELIESISRVLDRIPALNDSTATASSSASSPLEPFYSKAVPSISLTQYLSRIQKYCPTSP 60

Query: 86  SCFVVAYVYLDRF--AQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGI 143
              + A +YLDR      +P++ + S NVHRLL+T++ V+ KF+ D  Y+N+ +AKVGGI
Sbjct: 61  DVLLSALIYLDRIVKRCDKPTITVTSLNVHRLLLTALTVATKFLSDGSYSNSRFAKVGGI 120

Query: 144 STTEMNLLEVDFLFDLGFQL 163
           S  E+N LE+DFLF + F L
Sbjct: 121 SLHELNHLEIDFLFLVDFDL 140

This family includes many different cyclin proteins. Members include the G1/S-specific cyclin pas1, and the phosphate system cyclin PHO80/PHO85. Length = 140

>gnl|CDD|215740 pfam00134, Cyclin_N, Cyclin, N-terminal domain

 Score = 56.0 bits (136), Expect = 3e-10
 Identities = 20/94 (21%), Positives = 42/94 (44%), Gaps = 5/94 (5%)

Query: 73  YLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYY 132
           +L  + +     P    +A  YLDRF  KQ   P+    +  + +T +L++AK+ +    
Sbjct: 37  WLVEVHEEFKLLPETLYLAVNYLDRFLSKQ---PVPRTKLQLVGVTCLLIAAKYEEIYPP 93

Query: 133 NNAFYAKV--GGISTTEMNLLEVDFLFDLGFQLN 164
           +   +  +     +  E+  +E+  L  L + L+
Sbjct: 94  SVEDFVYITDNAYTKEEILRMELLILSTLNWDLS 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	219
PF08613	149	Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu	100.0
KOG1674	218	consensus Cyclin [General function prediction only	99.96
KOG1675	343	consensus Predicted cyclin [General function predi	99.61
PF00134	127	Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR	99.37
cd00043	88	CYCLIN Cyclin box fold. Protein binding domain fun	98.92
smart00385	83	CYCLIN domain present in cyclins, TFIIB and Retino	98.62
KOG0656	335	consensus G1/S-specific cyclin D [Cell cycle contr	98.13
KOG0653	391	consensus Cyclin B and related kinase-activating p	97.68
TIGR00569	305	ccl1 cyclin ccl1. University).	97.36
KOG0655	408	consensus G1/S-specific cyclin E [Cell cycle contr	97.35
COG5333	297	CCL1 Cdk activating kinase (CAK)/RNA polymerase II	96.9
KOG4164	497	consensus Cyclin ik3-1/CABLES [Cell cycle control,	96.67
COG5024	440	Cyclin [Cell division and chromosome partitioning]	96.62
KOG1674	218	consensus Cyclin [General function prediction only	94.17
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	93.77
KOG0794	264	consensus CDK8 kinase-activating protein cyclin C	92.64
KOG0834	323	consensus CDK9 kinase-activating protein cyclin T	92.07
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	91.07
KOG2496	325	consensus Cdk activating kinase (CAK)/RNA polymera	90.76
PF00382	71	TFIIB: Transcription factor TFIIB repeat; InterPro	87.73
PF02984	118	Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR	86.55
KOG0835	367	consensus Cyclin L [General function prediction on	86.14

>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)

Probab=100.00  E-value=2.4e-35  Score=240.40  Aligned_cols=135  Identities=44%  Similarity=0.816  Sum_probs=101.5

Q ss_pred             cHHHHHHHHHHHHHHHhccccccc------------CCCCcccccCCCCCChhHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 027733           29 PKLITVLSSLLQRVAESNDLSQRF------------HPQKISVFHGLTRPTISIHSYLERIFKYANCSPSCFVVAYVYLD   96 (219)
Q Consensus        29 p~~l~~ia~lLe~~i~~nd~~~~~------------~~~~~~~F~~~~~P~Isi~~yl~rI~~~~~~s~~~~l~ALiYId   96 (219)
                      +++++.|+.++++++..|+.....            .....+.|++..+|++++.+|+.||.++++|+++|+++|++||+
T Consensus         1 ~~~~~~i~~~l~~~~~~n~~~~~~s~~~~~~~~~~~~~~~~~~F~~~~~p~i~i~~fl~ri~~~~~~s~~~~i~aliYl~   80 (149)
T PF08613_consen    1 DKLVQSIARQLDRLINNNESTAQSSSSSSSPSSPFQQSPKISQFHSQSVPSISIRDFLSRILKYTQCSPECLILALIYLD   80 (149)
T ss_dssp             -HHHHHHHHHHHHHHHHHH--------------T---------T--SS--SS-HHHHHHHHHHHTT--HHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHhccCchhhhhcccccccccccccccccccccCCCCCCCcHHHHHHHHHHHcCCChHHHHHHHHHHH
Confidence            368999999999999988776532            11345789999999999999999999999999999999999999


Q ss_pred             HHhh--hCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHHHHHHHHHHHhcCCce
Q 027733           97 RFAQ--KQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQL  163 (219)
Q Consensus        97 RL~~--~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~ELN~LE~~FL~lLdf~L  163 (219)
                      |+..  ..+.+.+++.|+||+|++|+|||+||+||.+|+|++||++||++++|||.||++||.+|||+|
T Consensus        81 Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~eln~lE~~fL~~l~~~L  149 (149)
T PF08613_consen   81 RLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKELNELEREFLKLLDYNL  149 (149)
T ss_dssp             HHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHHHHHHHHHHHHHTTT--
T ss_pred             HHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHHHHHHHHHHHHHCCCcC
Confidence            9999  567889999999999999999999999999999999999999999999999999999999997

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.

>KOG1674 consensus Cyclin [General function prediction only]

Probab=99.96  E-value=3.9e-29  Score=216.22  Aligned_cols=160  Identities=52%  Similarity=0.886  Sum_probs=148.1

Q ss_pred             ccccHHHHHHHHHHHHHHHhcccccc----cCCCCcccccCCCCCChhHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhh
Q 027733           26 AVMPKLITVLSSLLQRVAESNDLSQR----FHPQKISVFHGLTRPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQK  101 (219)
Q Consensus        26 ~~~p~~l~~ia~lLe~~i~~nd~~~~----~~~~~~~~F~~~~~P~Isi~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~  101 (219)
                      ..+|.++..++.+++++.+.|+....    .....++.|++...|+|++.+|++||.++++|+++|+++|++||||+.+.
T Consensus        30 s~~p~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~p~isi~~yleri~k~~~~s~~~lv~al~Yldr~~~~  109 (218)
T KOG1674|consen   30 SITPIFLTCLSSLLKRLNDSNENLSRENNKSWASPTTGFDGVSTPNISIRQYLERIFKYSKCSPECLVLALVYLDRFVKQ  109 (218)
T ss_pred             cccchHHHHHHHHHHHHHhcChhhhcccccccccccccccCCCCCCcchHHHHHHHHHHhcCCchhhhhhhhhhhhhhhh
Confidence            34799999999999999999985542    12245789999999999999999999999999999999999999999997


Q ss_pred             ------CCCCCCCCcc-HHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHHHHHHHHHHHhcCCceeeCHHHHHHHH
Q 027733          102 ------QPSLPINSFN-VHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYC  174 (219)
Q Consensus       102 ------~p~~~i~~~n-~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~ELN~LE~~FL~lLdf~L~Vs~eey~~Y~  174 (219)
                            .|...+++.| +||++++++++|+||.+|.+|+|++||++||++..|||.||.+||..+||+|.|+.++|..|+
T Consensus       110 ~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y~n~~~a~vggl~~~eln~lE~~~l~~~~~~l~i~~~~~~~~~  189 (218)
T KOG1674|consen  110 PQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYYSNAYYAKVGGLTTDELNKLELDLLFLLDFRLIISRSEFNLYE  189 (218)
T ss_pred             hcccccCcccccccchhHHHHHHHHHHHHHhhccchhhhHHHHHHhCCCChHhhhhhhHHHHhhCCeEEEechhHHHHHH
Confidence                  6888999999 999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcC
Q 027733          175 SYLQREMFLQS  185 (219)
Q Consensus       175 ~~L~~~~~~~~  185 (219)
                      ..+++++....
T Consensus       190 ~~~~~~~~~~~  200 (218)
T KOG1674|consen  190 DLLEREENLNK  200 (218)
T ss_pred             HHHHHHHhccc
Confidence            99999888774

>KOG1675 consensus Predicted cyclin [General function prediction only]

Probab=99.61  E-value=8.6e-16  Score=137.87  Aligned_cols=129  Identities=26%  Similarity=0.328  Sum_probs=116.8

Q ss_pred             CCChhHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccC-C
Q 027733           65 RPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG-I  143 (219)
Q Consensus        65 ~P~Isi~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgG-i  143 (219)
                      +|..-+..|+...+.+.+++.+|-++.|+|++|+.... ...+.+.||+|..+.++++|+|.|+|..++|..|+.+.. +
T Consensus       188 ~~~~ri~k~v~~l~~~~qlta~~aiitL~~~erl~~~~-e~~~~p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd~  266 (343)
T KOG1675|consen  188 PGLVRIKKFVRILFSWAQLTAECDIITLVYAERLLWLA-ERDPCPRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKDQ  266 (343)
T ss_pred             cchhheehhhhhHhhhhhhhhccchHHHHhhHhhhhHh-hcCCCcchhhhhhhhhheehhhhhhhhhcccHHHHHHHhhc
Confidence            34445888999999999999999999999999999854 445789999999999999999999999999999999975 9


Q ss_pred             CHHHHHHHHHHHHHhcCCceeeCHHHHHHHHHHHHHHHHhcCCCCCCccch
Q 027733          144 STTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLN  194 (219)
Q Consensus       144 s~~ELN~LE~~FL~lLdf~L~Vs~eey~~Y~~~L~~~~~~~~~~~~~~~~~  194 (219)
                      ++.+||.|||+||.+|+||+.|...+|.+|+..|...+-.-..-++.+|+.
T Consensus       267 tveDmNe~ERqfLelLqfNinvp~svYAKyYfdlr~Lae~n~L~f~~ePls  317 (343)
T KOG1675|consen  267 SVDDMNALERQFLELLQFNINVPSSEYAKYYFDLRCLAEANPLLFPCEPLS  317 (343)
T ss_pred             cHhhHHHHHHHHHHHHhhccCccHHHHHHHHHHHhhhccccccccccccch
Confidence            999999999999999999999999999999999987777777777888765

>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)

Probab=99.37  E-value=3.7e-12  Score=98.68  Aligned_cols=93  Identities=19%  Similarity=0.346  Sum_probs=80.6

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhcc--CCCHH
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG--GISTT  146 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVg--Gis~~  146 (219)
                      .+.+|+.++....++++.++..|+.|+||+..+.+   +...+++.+.++|+++|+|+.++...+...|..++  .++.+
T Consensus        33 ~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~---~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~  109 (127)
T PF00134_consen   33 IIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRP---VNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKK  109 (127)
T ss_dssp             HHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS----TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHH
T ss_pred             HHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcc---cccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHH
Confidence            48899999999999999999999999999998764   77899999999999999999999888899998876  48999


Q ss_pred             HHHHHHHHHHHhcCCcee
Q 027733          147 EMNLLEVDFLFDLGFQLN  164 (219)
Q Consensus       147 ELN~LE~~FL~lLdf~L~  164 (219)
                      ++..||+.+|..|+|+|+
T Consensus       110 ~i~~~E~~iL~~L~f~ln  127 (127)
T PF00134_consen  110 DILEMEREILSALNFDLN  127 (127)
T ss_dssp             HHHHHHHHHHHHTTT---
T ss_pred             HHHHHHHHHHHHCCCCcC
Confidence            999999999999999984

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....

>cd00043 CYCLIN Cyclin box fold

Probab=98.92  E-value=1.3e-08  Score=72.18  Aligned_cols=84  Identities=20%  Similarity=0.174  Sum_probs=77.3

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCC-CHHH
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGI-STTE  147 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGi-s~~E  147 (219)
                      +..+|+.++.+..++++.+...|..|++|+....+   +...+++.+..+|+.+|+|+.++ ..+++.+.+++|. +.++
T Consensus         4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~---~~~~~~~~ia~a~l~lA~k~~~~-~~~~~~~~~~~~~~~~~~   79 (88)
T cd00043           4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYS---VLGRSPSLVAAAALYLAAKVEEI-PPWLKDLVHVTGYATEEE   79 (88)
T ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcc---cccCChHHHHHHHHHHHHHHcCC-CCCHHHHhHHhCCCCHHH
Confidence            57899999999999999999999999999998654   34789999999999999999998 8899999999999 9999


Q ss_pred             HHHHHHHHH
Q 027733          148 MNLLEVDFL  156 (219)
Q Consensus       148 LN~LE~~FL  156 (219)
                      +..+|..+|
T Consensus        80 i~~~e~~il   88 (88)
T cd00043          80 ILRMEKLLL   88 (88)
T ss_pred             HHHHHHHhC
Confidence            999999874

Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.

>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma

Probab=98.62  E-value=3.6e-07  Score=64.13  Aligned_cols=81  Identities=20%  Similarity=0.219  Sum_probs=72.2

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCC-CHHHHHH
Q 027733           72 SYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGI-STTEMNL  150 (219)
Q Consensus        72 ~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGi-s~~ELN~  150 (219)
                      +|+.|+.+..++++.+.-.|..|++|.....+   +...+++.+..+|+.+|+|+.+.. .+++.+.++.|+ +.+++..
T Consensus         1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~---~~~~~~~~ia~a~l~lA~k~~~~~-~~~~~~~~~~~~~~~~~i~~   76 (83)
T smart00385        1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYK---FLKYSPSLIAAAALYLAAKTEEIP-PWTKELVHYTGYFTEEEILR   76 (83)
T ss_pred             CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhh---cccCCHHHHHHHHHHHHHHHhcCC-CCchhHhHhhCCCCHHHHHH
Confidence            48999999999999999999999999988532   234899999999999999999876 678889999888 9999999


Q ss_pred             HHHHHH
Q 027733          151 LEVDFL  156 (219)
Q Consensus       151 LE~~FL  156 (219)
                      +|+.+|
T Consensus        77 ~~~~il   82 (83)
T smart00385       77 MEKLLL   82 (83)
T ss_pred             HHHHHh
Confidence            999987

A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.

>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]

Probab=98.13  E-value=1.9e-05  Score=72.79  Aligned_cols=107  Identities=20%  Similarity=0.232  Sum_probs=84.4

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhc---cCCCH
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKV---GGIST  145 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkV---gGis~  145 (219)
                      -..++|.++.++-+|++.|+.+|.=|+||+....+--.-.++...-+-++||-+|+|+=+-....-..+--.   .-+..
T Consensus        80 ~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~fea  159 (335)
T KOG0656|consen   80 QALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEA  159 (335)
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccH
Confidence            367899999999999999999999999999986542222345577788899999999987653322222221   13789


Q ss_pred             HHHHHHHHHHHHhcCCcee-eCHHHHHHHHH
Q 027733          146 TEMNLLEVDFLFDLGFQLN-VTPAAFYTYCS  175 (219)
Q Consensus       146 ~ELN~LE~~FL~lLdf~L~-Vs~eey~~Y~~  175 (219)
                      +.|-+||+-.|..|+|++. ||+-.|.+|.-
T Consensus       160 ktI~rmELLVLstL~Wrl~aVTP~sF~~~fl  190 (335)
T KOG0656|consen  160 KTIQRMELLVLSTLKWRLRAVTPFSFIDHFL  190 (335)
T ss_pred             HHHHHHHHHHHhhccccccCCCchHHHHHHH
Confidence            9999999999999999998 99998887753

>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=97.68  E-value=0.00018  Score=67.42  Aligned_cols=95  Identities=21%  Similarity=0.300  Sum_probs=77.1

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHH-HHhhhcccCC-cccchhhhc--cCCC
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVL-VSAKFMDDIY-YNNAFYAKV--GGIS  144 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltali-lAsK~ldD~~-~sN~~~AkV--gGis  144 (219)
                      -+.+|+-.+..+++++++++-+|.-+|||+....+   +...-..-+=++||. ||+|| ++.. ..-+.+..+  +.++
T Consensus       160 iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~---v~~~~lqLvgvsalf~IA~K~-EE~~~P~v~dlv~isd~~~s  235 (391)
T KOG0653|consen  160 ILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVK---VPLKKLQLVGVSALLSIACKY-EEISLPSVEDLVLITDGAYS  235 (391)
T ss_pred             HHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhc---ccHHHhhHHhHHHHHHHHHhh-hhccCCccceeEeeeCCccc
Confidence            38899999999999999999999999999999754   444555556678867 99999 5543 334555555  5599


Q ss_pred             HHHHHHHHHHHHHhcCCceeeCH
Q 027733          145 TTEMNLLEVDFLFDLGFQLNVTP  167 (219)
Q Consensus       145 ~~ELN~LE~~FL~lLdf~L~Vs~  167 (219)
                      .+++-.||+..|..|+|++.+..
T Consensus       236 ~~~il~mE~~il~~L~f~l~~p~  258 (391)
T KOG0653|consen  236 REEILRMEKYILNVLEFDLSVPT  258 (391)
T ss_pred             hHHHHHHHHHHHhccCeeecCCc
Confidence            99999999999999999998754

>TIGR00569 ccl1 cyclin ccl1

Probab=97.36  E-value=0.0013  Score=59.93  Aligned_cols=93  Identities=15%  Similarity=0.193  Sum_probs=73.9

Q ss_pred             HHHHHHHHHHHcC--CCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccC-C---
Q 027733           70 IHSYLERIFKYAN--CSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG-I---  143 (219)
Q Consensus        70 i~~yl~rI~~~~~--~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgG-i---  143 (219)
                      ...++.++....+  ++..+.-.|.+|++|+..++.   +....++-+.+||+.+|+|+=+ .+.+-..+.+..+ -   
T Consensus        59 y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~S---v~~~~p~~Ia~tclfLA~KvEE-~~~si~~fv~~~~~~~~~  134 (305)
T TIGR00569        59 YEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNS---VMEYHPKIIMLTCVFLACKVEE-FNVSIDQFVGNLKETPLK  134 (305)
T ss_pred             HHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCc---hhhcCHHHHHHHHHHHHHhccc-cCcCHHHHHhhccCCchh
Confidence            4456778888889  999999999999999998653   4467889999999999999644 4445555554332 2   


Q ss_pred             CHHHHHHHHHHHHHhcCCceeeC
Q 027733          144 STTEMNLLEVDFLFDLGFQLNVT  166 (219)
Q Consensus       144 s~~ELN~LE~~FL~lLdf~L~Vs  166 (219)
                      ...++-.+|..+|..|+|+|.|.
T Consensus       135 ~~~~Il~~E~~lL~~L~F~L~V~  157 (305)
T TIGR00569       135 ALEQVLEYELLLIQQLNFHLIVH  157 (305)
T ss_pred             hHHHHHHHHHHHHHHCCCcEEee
Confidence            35899999999999999999975

University).

>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]

Probab=97.35  E-value=0.00058  Score=63.00  Aligned_cols=93  Identities=23%  Similarity=0.324  Sum_probs=81.7

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhc--cCCCHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKV--GGISTTE  147 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkV--gGis~~E  147 (219)
                      +.|++-.+..-.++..++|-+|.=|+||+....  ..++..+..-+=++|+.||+|+=+=...+-..||-|  |..|-.+
T Consensus       148 LlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~--~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~dd  225 (408)
T KOG0655|consen  148 LLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQ--VEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDD  225 (408)
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH--HHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHH
Confidence            788999999999999999999999999999875  334556667777899999999877777888889988  5699999


Q ss_pred             HHHHHHHHHHhcCCcee
Q 027733          148 MNLLEVDFLFDLGFQLN  164 (219)
Q Consensus       148 LN~LE~~FL~lLdf~L~  164 (219)
                      +-.||+-.|+.|+|+|.
T Consensus       226 IltmE~iilkal~W~l~  242 (408)
T KOG0655|consen  226 ILTMELIILKALKWELS  242 (408)
T ss_pred             HHHHHHHHHHHhccccc
Confidence            99999999999999986

>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]

Probab=96.90  E-value=0.0023  Score=58.14  Aligned_cols=92  Identities=18%  Similarity=0.322  Sum_probs=79.3

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhccc---C----CcccchhhhccCCC
Q 027733           72 SYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDD---I----YYNNAFYAKVGGIS  144 (219)
Q Consensus        72 ~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD---~----~~sN~~~AkVgGis  144 (219)
                      .++.++..+.+++..++-.|.+|.+|+.-+++   +...+.+-+..|++.+|+|+=|-   .    +-.+.-|++.---+
T Consensus        50 k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~s---v~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~s  126 (297)
T COG5333          50 KLIMDLCTRLNLPQTVLATAILFFSRFYLKNS---VEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSS  126 (297)
T ss_pred             HHHHHHHHhcCCCcchHHHHHHHHHHHHhhcc---cccccHHHHHHhheeeeeecccccchhhHHHHHhhcccccccccc
Confidence            67899999999999999999999999988654   67889999999999999998761   1    23345577788889


Q ss_pred             HHHHHHHHHHHHHhcCCceeeC
Q 027733          145 TTEMNLLEVDFLFDLGFQLNVT  166 (219)
Q Consensus       145 ~~ELN~LE~~FL~lLdf~L~Vs  166 (219)
                      .+.+-.+|...|..|+|++.|.
T Consensus       127 r~~Il~~E~~lLEaL~fd~~V~  148 (297)
T COG5333         127 RERILEYEFELLEALDFDLHVH  148 (297)
T ss_pred             HHHHHHHHHHHHHHcccceEec
Confidence            9999999999999999999974

>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]

Probab=96.67  E-value=0.0031  Score=59.40  Aligned_cols=109  Identities=18%  Similarity=0.180  Sum_probs=88.3

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhh----hccCCC
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYA----KVGGIS  144 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~A----kVgGis  144 (219)
                      ||..-+.+|-.-|+++..+.-+|.+|+++|.-++   .|+-.|-+-.--+|+++|.|+.|=.--.-+.+-    ..+.++
T Consensus       384 SlKREMr~l~~d~~id~~TVa~AyVYFEKliLkg---lisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~n  460 (497)
T KOG4164|consen  384 SLKREMRELGEDCGIDVVTVAMAYVYFEKLILKG---LISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLN  460 (497)
T ss_pred             HHHHHHHHhhhccCccceeehhHHHHHHHHHHhh---hhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhccc
Confidence            5788889999999999999999999999999864   366677777777999999999843333333332    347789


Q ss_pred             HHHHHHHHHHHHHhcCCceeeCHHHHHHHHHHHHHH
Q 027733          145 TTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQRE  180 (219)
Q Consensus       145 ~~ELN~LE~~FL~lLdf~L~Vs~eey~~Y~~~L~~~  180 (219)
                      .+||-..|--.|-.|.|.|+++.+|..--+..|+.+
T Consensus       461 rrdLia~Ef~VlvaLefaL~~~~~eVlPHy~RL~~e  496 (497)
T KOG4164|consen  461 RRDLIAFEFPVLVALEFALHLPEHEVLPHYRRLQQE  496 (497)
T ss_pred             HHhhhhhhhhHHHhhhhhccCChhhcchHHHHHhhc
Confidence            999999999999999999999999988666666544

>COG5024 Cyclin [Cell division and chromosome partitioning]

Probab=96.62  E-value=0.0053  Score=58.67  Aligned_cols=95  Identities=16%  Similarity=0.225  Sum_probs=78.5

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHH-HHHHHHHhhhcccCCcccchhhhc--cCCCHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLL-ITSVLVSAKFMDDIYYNNAFYAKV--GGISTT  146 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~-ltalilAsK~ldD~~~sN~~~AkV--gGis~~  146 (219)
                      |-+|+-.+...+++.|+++.+|.-.+||+..+. .   .+.+...|+ ++|+.||+||=+=..-.-+.|+-+  |.++.+
T Consensus       216 Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~-~---v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~  291 (440)
T COG5024         216 LVDWLVEVHGKFGLLPETLFLAINIIDRFLSSR-V---VSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRD  291 (440)
T ss_pred             HHHHHHHhcccccccchHHHHHHHHHHHHhccC-c---ccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHH
Confidence            889999999999999999999999999999864 3   344555555 689999999866666556666655  779999


Q ss_pred             HHHHHHHHHHHhcCCceeeCHH
Q 027733          147 EMNLLEVDFLFDLGFQLNVTPA  168 (219)
Q Consensus       147 ELN~LE~~FL~lLdf~L~Vs~e  168 (219)
                      ++-.+|+..|..++|++-....
T Consensus       292 ~i~~aE~~ml~~l~f~is~P~P  313 (440)
T COG5024         292 DIIRAERYMLEVLDFNISWPSP  313 (440)
T ss_pred             HHHHHHHHHhhhcccccCCCCh
Confidence            9999999999999999875443

>KOG1674 consensus Cyclin [General function prediction only]

Probab=94.17  E-value=0.039  Score=48.05  Aligned_cols=99  Identities=17%  Similarity=0.207  Sum_probs=79.3

Q ss_pred             HHHHHHHHHH--HHhhhCCCCC-CCCccHHHHHHHHHHHHhhhcccCCc-----ccchhhh-ccC-CCHHHHHHHHHHHH
Q 027733           87 CFVVAYVYLD--RFAQKQPSLP-INSFNVHRLLITSVLVSAKFMDDIYY-----NNAFYAK-VGG-ISTTEMNLLEVDFL  156 (219)
Q Consensus        87 ~~l~ALiYId--RL~~~~p~~~-i~~~n~hRL~ltalilAsK~ldD~~~-----sN~~~Ak-VgG-is~~ELN~LE~~FL  156 (219)
                      +.+++..|++  |+....+... -...+.++.++++++.+.|...|..-     +++.|+. +.| ......|.+|+++|
T Consensus         3 ~~~~~s~~~~~~~~~~~~~~~~~~~~ss~~p~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~p~isi~~yl   82 (218)
T KOG1674|consen    3 TLMTMSVYINPDKLRLNLPDNPTGRNSSITPIFLTCLSSLLKRLNDSNENLSRENNKSWASPTTGFDGVSTPNISIRQYL   82 (218)
T ss_pred             hhhHhHhhcCccchhhccCcccccccccccchHHHHHHHHHHHHHhcChhhhcccccccccccccccCCCCCCcchHHHH
Confidence            6677888998  8887655332 22468899999999999999988876     7888984 444 47899999999999


Q ss_pred             HhcCCceeeCHHHHHHHHHHHHHHHHhcC
Q 027733          157 FDLGFQLNVTPAAFYTYCSYLQREMFLQS  185 (219)
Q Consensus       157 ~lLdf~L~Vs~eey~~Y~~~L~~~~~~~~  185 (219)
                      ..+.|...+++++|..=+-.+.+.....+
T Consensus        83 eri~k~~~~s~~~lv~al~Yldr~~~~~~  111 (218)
T KOG1674|consen   83 ERIFKYSKCSPECLVLALVYLDRFVKQPQ  111 (218)
T ss_pred             HHHHHHhcCCchhhhhhhhhhhhhhhhhc
Confidence            99999999999999877777766665544

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=93.77  E-value=1.1  Score=40.70  Aligned_cols=103  Identities=19%  Similarity=0.171  Sum_probs=81.8

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHHHH
Q 027733           71 HSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNL  150 (219)
Q Consensus        71 ~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~ELN~  150 (219)
                      ...|.++....+++..+.=-|..+..++....  + +...+..-+..+|+-+|.|. ++.+.+-+..+.+.+++.+++.+
T Consensus       126 ~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~--~-~rgrs~~~i~AAclYiACR~-~~~prtl~eI~~~~~v~~k~i~~  201 (310)
T PRK00423        126 LSELDRIASQLGLPRSVREEAAVIYRKAVEKG--L-IRGRSIEGVVAAALYAACRR-CKVPRTLDEIAEVSRVSRKEIGR  201 (310)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC--c-ccCCCHHHHHHHHHHHHHHH-cCCCcCHHHHHHHhCCCHHHHHH
Confidence            34577888888999998888888888887742  2 34567788888999999996 77788999999999999999999


Q ss_pred             HHHHHHHhcCCceee-CHHHHH-HHHHHH
Q 027733          151 LEVDFLFDLGFQLNV-TPAAFY-TYCSYL  177 (219)
Q Consensus       151 LE~~FL~lLdf~L~V-s~eey~-~Y~~~L  177 (219)
                      .++.+++.|++++-+ ++++|. +|+..|
T Consensus       202 ~~~~l~k~L~~~~~~~~p~~~i~r~~~~L  230 (310)
T PRK00423        202 CYRFLLRELNLKLPPTDPIDYVPRFASEL  230 (310)
T ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHHHHc
Confidence            999999999988754 455554 444443

>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]

Probab=92.64  E-value=0.2  Score=44.43  Aligned_cols=94  Identities=14%  Similarity=0.177  Sum_probs=75.2

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccC-Cc-------ccc------
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDI-YY-------NNA------  135 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~-~~-------sN~------  135 (219)
                      ..+++..+.++.++-..++-.|.+|+.|+..+..   +...++.-+..||+-+|+|.=+-- .+       .+.      
T Consensus        44 ~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S---~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~  120 (264)
T KOG0794|consen   44 MANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKS---LKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFS  120 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh---hhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcc
Confidence            4677888889999999999999999999998753   456778888899999999985542 11       111      


Q ss_pred             hhhhccCCCHHHHHHHHHHHHHhcCCceeeC
Q 027733          136 FYAKVGGISTTEMNLLEVDFLFDLGFQLNVT  166 (219)
Q Consensus       136 ~~AkVgGis~~ELN~LE~~FL~lLdf~L~Vs  166 (219)
                      +|..-.....+.+-.+|-..|..||+-|.|-
T Consensus       121 ~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVh  151 (264)
T KOG0794|consen  121 YWPEKFPYERKDILEMEFYLLEALDCYLIVH  151 (264)
T ss_pred             cchhhcCCCcCcchhhhhhHHhhhceeEEEe
Confidence            3666667888999999999999999999884

>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]

Probab=92.07  E-value=0.86  Score=42.14  Aligned_cols=111  Identities=17%  Similarity=0.202  Sum_probs=79.4

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcc--------cchhhh--
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYN--------NAFYAK--  139 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~s--------N~~~Ak--  139 (219)
                      ...||..+-.+.+++.-++-.|.+|..|+.-.+.   +.....+-+-.+|+.+|.|.=| ..-+        ++++..  
T Consensus        42 ~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s---~~~~~~~~vA~sclfLAgKvEe-tp~kl~dIi~~s~~~~~~~~  117 (323)
T KOG0834|consen   42 GAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHS---FKKFDPYTVAASCLFLAGKVEE-TPRKLEDIIKVSYRYLNPKD  117 (323)
T ss_pred             HHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcc---cccCcHHHHHHHHHHHHhhccc-CcccHHHHHHHHHHHcCccc
Confidence            5679999999999999999999999999987542   3444445566788999999733 3221        222221  


Q ss_pred             -----ccCCCHHHHHHHHHHHHHhcCCceeeCH-HH-HHHHHHHHHHHHHhc
Q 027733          140 -----VGGISTTEMNLLEVDFLFDLGFQLNVTP-AA-FYTYCSYLQREMFLQ  184 (219)
Q Consensus       140 -----VgGis~~ELN~LE~~FL~lLdf~L~Vs~-ee-y~~Y~~~L~~~~~~~  184 (219)
                           +.-=..+++-.+|+-.|..|+|++.|.. .. ..+|...+..+....
T Consensus       118 ~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~  169 (323)
T KOG0834|consen  118 LELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLK  169 (323)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhcc
Confidence                 1111467889999999999999999875 33 446777776665544

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=91.07  E-value=3.2  Score=37.73  Aligned_cols=95  Identities=14%  Similarity=0.119  Sum_probs=76.2

Q ss_pred             CCCChhHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCC
Q 027733           64 TRPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGI  143 (219)
Q Consensus        64 ~~P~Isi~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGi  143 (219)
                      ..|.++..+|+.|+....+++..+.-.|...+.+....  ++ ....++.-+..+|+-+|++... ..-+-+..+++.|+
T Consensus       213 ~~~~~~p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~--~l-~~Gr~P~sIAAAaIYlA~~~~g-~~~t~keIa~v~~V  288 (310)
T PRK00423        213 KLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEK--GL-TSGKGPTGLAAAAIYIASLLLG-ERRTQREVAEVAGV  288 (310)
T ss_pred             CCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhc--Cc-ccCCCHHHHHHHHHHHHHHHhC-CCCCHHHHHHHcCC
Confidence            46677889999999999999999888888777766653  22 4668899999999999999764 44678888999999


Q ss_pred             CHHHHHHHHHHHHHhcCCc
Q 027733          144 STTEMNLLEVDFLFDLGFQ  162 (219)
Q Consensus       144 s~~ELN~LE~~FL~lLdf~  162 (219)
                      +..++..-=++++..++..
T Consensus       289 s~~tI~~~ykel~~~l~~~  307 (310)
T PRK00423        289 TEVTVRNRYKELAEKLDIK  307 (310)
T ss_pred             CHHHHHHHHHHHHHHhCcc
Confidence            9999987767777666543

>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]

Probab=90.76  E-value=1  Score=41.37  Aligned_cols=81  Identities=19%  Similarity=0.283  Sum_probs=65.8

Q ss_pred             CCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccC----CCHHHHHHHHHHHHH
Q 027733           82 NCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG----ISTTEMNLLEVDFLF  157 (219)
Q Consensus        82 ~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgG----is~~ELN~LE~~FL~  157 (219)
                      .+++++.-.|+.|+.|+.-.+.   +....+.-++.||+-+|.|. ++.+.+-..|++-..    =....+-..|-..|+
T Consensus        73 ~lp~~Vv~TA~~fFkRffL~ns---vme~~pk~I~~tc~flA~Ki-eef~ISieqFvkn~~~~~~k~~e~vLk~E~~llq  148 (325)
T KOG2496|consen   73 NLPTSVVSTAIEFFKRFFLENS---VMEYSPKIIMATCFFLACKI-EEFYISIEQFVKNMNGRKWKTHEIVLKYEFLLLQ  148 (325)
T ss_pred             CCchHHHHHHHHHHHHHHHhcc---hhhcChHHHHHHHHHHHhhh-HhheecHHHHHhhccCcccccHHHHHhchHHHHH
Confidence            4788999999999999987543   34567788899999999996 467777777776544    568888999999999


Q ss_pred             hcCCceeeC
Q 027733          158 DLGFQLNVT  166 (219)
Q Consensus       158 lLdf~L~Vs  166 (219)
                      .|+|+|.|-
T Consensus       149 sL~f~L~vh  157 (325)
T KOG2496|consen  149 SLKFSLTVH  157 (325)
T ss_pred             hhhhhheec
Confidence            999999864

>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)

Probab=87.73  E-value=6.8  Score=27.44  Aligned_cols=71  Identities=10%  Similarity=0.119  Sum_probs=55.6

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHH
Q 027733           74 LERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEM  148 (219)
Q Consensus        74 l~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~EL  148 (219)
                      +.|+....+++..+.=.|.-+.++.....  + ....++.-+..+|+-+|.+.. +...+-+..+.+.|++.+++
T Consensus         1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~--~-~~Gr~~~~iaAA~iY~acr~~-~~~~t~~eIa~~~~Vs~~tI   71 (71)
T PF00382_consen    1 IPRICSKLGLPEDVRERAKEIYKKAQERG--L-LKGRSPESIAAACIYLACRLN-GVPRTLKEIAEAAGVSEKTI   71 (71)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHHHHHHHTT--T-STTS-HHHHHHHHHHHHHHHT-TSSSSHHHHHHHCTSSHHHH
T ss_pred             ChHHHhHcCCCHHHHHHHHHHHHHHHHcC--C-cccCCHHHHHHHHHHHHHHHc-CCCcCHHHHHHHhCCCCCcC
Confidence            57889999999999999988888887752  2 455778899999999999865 66778899999999998875

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.

>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)

Probab=86.55  E-value=0.43  Score=35.63  Aligned_cols=88  Identities=13%  Similarity=0.066  Sum_probs=57.4

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHH
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEM  148 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~EL  148 (219)
                      +..+|+.++.+..+.+....-+|.+.++--.....   +-...+-.+-.+|+.+|.+.++....++..+.+..|++.+++
T Consensus         2 Tp~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~---fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l   78 (118)
T PF02984_consen    2 TPYDFLRRFLKISNADQEVRNLARYLLELSLLDYE---FLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDL   78 (118)
T ss_dssp             -HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHH---HTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHH
T ss_pred             cHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhcc---ccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHH
Confidence            46789999977777777777777777774333221   223455678889999999998754566666667778877776


Q ss_pred             HHHHHHHHHhc
Q 027733          149 NLLEVDFLFDL  159 (219)
Q Consensus       149 N~LE~~FL~lL  159 (219)
                      ...=..+...+
T Consensus        79 ~~c~~~i~~~~   89 (118)
T PF02984_consen   79 KECIELIQELL   89 (118)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            65544444443

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=86.14  E-value=5.8  Score=37.03  Aligned_cols=103  Identities=17%  Similarity=0.226  Sum_probs=66.8

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCC----------c-----cc--
Q 027733           72 SYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIY----------Y-----NN--  134 (219)
Q Consensus        72 ~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~----------~-----sN--  134 (219)
                      ++|+.-.-..+++..|...++|+++|++-..+-   -..+..-+..+|+.+|+|.=+.-.          |     .+  
T Consensus        28 e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~---v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~~~~~  104 (367)
T KOG0835|consen   28 ELIQEAGILLNLPQVAMATGQVLFQRFCYSKSF---VRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRRESEA  104 (367)
T ss_pred             HHHHhhhHhhcCcHHHHHHHHHHHHHHHhcccc---ccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHHhccC
Confidence            345554455678999999999999999986542   235677799999999999755431          0     00  


Q ss_pred             ---chhhhccCCCHHHHHHHHHHHHHhcCCceeeC--HHHHHHHHHHH
Q 027733          135 ---AFYAKVGGISTTEMNLLEVDFLFDLGFQLNVT--PAAFYTYCSYL  177 (219)
Q Consensus       135 ---~~~AkVgGis~~ELN~LE~~FL~lLdf~L~Vs--~eey~~Y~~~L  177 (219)
                         ...++..-=-....-..|++.|+.|+|..+|.  -..+..|...|
T Consensus       105 ~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL  152 (367)
T KOG0835|consen  105 AEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTL  152 (367)
T ss_pred             cchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHh
Confidence               00111100023456678999999999999863  33444555444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	219
2pk9_B	293	Structure Of The Pho85-pho80 Cdk-cyclin Complex Of		3e-13

>pdb|2PK9|B Chain B, Structure Of The Pho85-pho80 Cdk-cyclin Complex Of The Phosphate-responsive Signal Transduction Pathway Length = 293

Iteration: 1
 Score = 71.6 bits (174), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 39/124 (31%), Positives = 66/124 (53%), Gaps = 1/124 (0%)
Query: 57  ISVFHGLTRPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLL 116
           ++ +H    P ISI +Y  R+ K+++      + +  Y+D      P   +NS   HR L
Sbjct: 64  LTRYHSKIPPNISIFNYFIRLTKFSSLEHCVLMTSLYYIDLLQTVYPDFTLNSLTAHRFL 123
Query: 117 ITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSY 176
           +T+  V+ K + D +  NA YAKVGG+   E+N+LE DFL  + +++ +      T CS 
Sbjct: 124 LTATTVATKGLCDSFSTNAHYAKVGGVRCHELNILENDFLKRVNYRI-IPRDHNITLCSI 182
Query: 177 LQRE 180
            Q++
Sbjct: 183 EQKQ 186

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	219
2pmi_B	293	PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de	5e-49
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05

>2pmi_B PHO85 cyclin PHO80, aminoglycoside anti; cyclin-dependent kinase, signaling protein,transfera cycle complex; HET: MES AGS; 2.90A {Saccharomyces cerevisiae} PDB: 2pk9_B* Length = 293

 Score =  161 bits (407), Expect = 5e-49
 Identities = 41/172 (23%), Positives = 76/172 (44%), Gaps = 3/172 (1%)

Query: 24  EAAVMPKLITVLSSLLQRVAESND---LSQRFHPQKISVFHGLTRPTISIHSYLERIFKY 80
                  L+ ++S +L  +   N+     +      ++ +H    P ISI +Y  R+ K+
Sbjct: 28  NKCSRTDLVVLISRMLVSLIAINENSATKKSDDQITLTRYHSKIPPNISIFNYFIRLTKF 87

Query: 81  ANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKV 140
           ++      + +  Y+D      P   +NS   HR L+T+  V+ K + D +  NA YAKV
Sbjct: 88  SSLEHCVLMTSLYYIDLLQTVYPDFTLNSLTAHRFLLTATTVATKGLCDSFSTNAHYAKV 147

Query: 141 GGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEP 192
           GG+   E+N+LE DFL  + +++              +++ F+     L   
Sbjct: 148 GGVRCHELNILENDFLKRVNYRIIPRDHNITLCSIEQKQKKFVIDKNALGSL 199

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 3e-05
 Identities = 48/269 (17%), Positives = 81/269 (30%), Gaps = 90/269 (33%)

Query: 4   HHHHHHL-------QLGTNIILEGHQEEAAV----------MPKLITVLSSLLQRVAESN 46
           HHHHHH+       Q     IL    E+A V          MPK  ++LS       E +
Sbjct: 1   HHHHHHMDFETGEHQYQYKDILS-VFEDAFVDNFDCKDVQDMPK--SILSK-----EEID 52

Query: 47  DLSQRFHP--QKISVFHGL-TRPTISIHSYLERI-----------FKYANCSPSCFVVAY 92
            +          + +F  L ++    +  ++E +            K     PS     Y
Sbjct: 53  HIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMY 112

Query: 93  V-YLDRFAQKQPSLPINSFNVHRL-------------------------------LITSV 120
           +   DR            +NV RL                               +   V
Sbjct: 113 IEQRDRLYNDNQVFA--KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDV 170

Query: 121 LVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYLQRE 180
            +S K          F+  +   ++ E  +LE+  L  L +Q++          ++  R 
Sbjct: 171 CLSYKV-QCKMDFKIFWLNLKNCNSPE-TVLEM--LQKLLYQID---------PNWTSRS 217

Query: 181 MFLQS-PLQLEEPLNVGRQL---KQYHCC 205
               +  L++       R+L   K Y  C
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENC 246

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	219
2pmi_B	293	PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de	100.0
1f5q_B	252	Gamma herpesvirus cyclin; herpesviral cyclin, cycl	98.77
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	98.73
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	98.7
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	98.69
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	98.69
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	98.67
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	98.66
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	98.66
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	98.31
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	98.29
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	98.2
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	98.1
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	98.06
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	98.0
1c9b_A	207	General transcription factor IIB; protein-DNA comp	97.88
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	97.45
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	94.77
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	94.53
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	93.49
1c9b_A	207	General transcription factor IIB; protein-DNA comp	93.07
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	81.75

>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*

Probab=100.00  E-value=4.9e-40  Score=292.93  Aligned_cols=152  Identities=26%  Similarity=0.438  Sum_probs=140.0

Q ss_pred             ccccHHHHHHHHHHHHHHHhccccccc---CCCCcccccCCCCCChhHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhC
Q 027733           26 AVMPKLITVLSSLLQRVAESNDLSQRF---HPQKISVFHGLTRPTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQ  102 (219)
Q Consensus        26 ~~~p~~l~~ia~lLe~~i~~nd~~~~~---~~~~~~~F~~~~~P~Isi~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~  102 (219)
                      ....+++.+||.+|+++++.||..+..   .+..+++||+.++|+|+|.+|+.||+++++|+++|+++|++||+||..+.
T Consensus        30 ~~~~dlv~~IA~~L~~LI~~Nd~~~~~~~~~~~~~t~F~~~~~P~ISI~~Yl~RI~k~t~ls~~~ll~ALvYLdRL~~~~  109 (293)
T 2pmi_B           30 CSRTDLVVLISRMLVSLIAINENSATKKSDDQITLTRYHSKIPPNISIFNYFIRLTKFSSLEHCVLMTSLYYIDLLQTVY  109 (293)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHCC--------CCCCTTCCSSCCSSCHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHHHHHcCccccccccccccccccccCCCCCCCcHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhC
Confidence            345579999999999999999988632   33467899999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHHHHHHHHHHHhcCCceeeCHHHHHHHHHHH
Q 027733          103 PSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNLLEVDFLFDLGFQLNVTPAAFYTYCSYL  177 (219)
Q Consensus       103 p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~ELN~LE~~FL~lLdf~L~Vs~eey~~Y~~~L  177 (219)
                      |++.+++.|+||+|++|+|||+|||||.+|+|++||+|||++++|||.||++||.+|||+|+|++++|..|+..+
T Consensus       110 p~~~l~~~nvHRLlLtALmlAsK~ldD~~ysN~~wAkVgGisl~ELN~LE~eFL~lLdf~L~V~~ee~~~cy~E~  184 (293)
T 2pmi_B          110 PDFTLNSLTAHRFLLTATTVATKGLCDSFSTNAHYAKVGGVRCHELNILENDFLKRVNYRIIPRDHNITLCSIEQ  184 (293)
T ss_dssp             TTCCCSTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTTTCCSCCTTHHHHHHHHS
T ss_pred             CCCccCCchHHHHHHHHHHHHHHhccccccChhHhhhccCcCHHHHHHHHHHHHHHcCCceeeCHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999999887544

>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

Probab=98.77  E-value=5.1e-08  Score=84.66  Aligned_cols=103  Identities=16%  Similarity=0.181  Sum_probs=88.2

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhc--cCCCHH
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKV--GGISTT  146 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkV--gGis~~  146 (219)
                      .+-+|+..+....+++++++-+|..|+||+..+.+   +......-+-++|+.||+|+-+-...+-+.+..+  +.++.+
T Consensus        51 ~lvdWl~ev~~~~~l~~eT~~lAv~~lDRfLs~~~---v~~~~lqLvg~tcl~iAsK~eE~~p~~~~~l~~~~~~~yt~~  127 (252)
T 1f5q_B           51 VLTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTR---IDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLCGGATTAD  127 (252)
T ss_dssp             HHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSC---CCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHCTTCCHH
T ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHhcCCC---cCHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCCCHH
Confidence            38899999999999999999999999999999763   5667788888999999999988777676777665  358999


Q ss_pred             HHHHHHHHHHHhcCCcee-eCHHHHHHHH
Q 027733          147 EMNLLEVDFLFDLGFQLN-VTPAAFYTYC  174 (219)
Q Consensus       147 ELN~LE~~FL~lLdf~L~-Vs~eey~~Y~  174 (219)
                      |+-+||+..|..|+|+|. +++-.|-.++
T Consensus       128 ~i~~mE~~IL~~L~w~l~~pTp~~FL~~~  156 (252)
T 1f5q_B          128 KLLTLEVKSLDTLSWVADRCLSTDLICYI  156 (252)
T ss_dssp             HHHHHHHHHHHHTTTCCCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCccCCCCHHHHHHHH
Confidence            999999999999999998 5677765443

>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

Probab=98.73  E-value=8.9e-08  Score=82.55  Aligned_cols=101  Identities=15%  Similarity=0.197  Sum_probs=87.8

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhcc--CCCHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG--GISTTE  147 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVg--Gis~~E  147 (219)
                      +.+|+..+....+++++++-+|..|+||+..+.   .+......-+-++|+.||+|+-+-...+-+.+..++  .++.+|
T Consensus        54 lvdwl~ev~~~~~l~~etl~lAv~~~DRfls~~---~v~~~~lqLv~~acl~iA~K~eE~~~p~~~d~~~~~~~~~~~~~  130 (257)
T 1g3n_C           54 LGTWMFSVCQEYNLEPNVVALALNLLDRLLLIK---QVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQE  130 (257)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTC---CCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTCSCHHH
T ss_pred             HHHHHHHHHHHhCCCccHHHHHHHHHHHHHccC---CCCHHHHHHHHHHHHHHHHHHccccCCCHHHHHHHHCCCCCHHH
Confidence            789999999999999999999999999999864   356677888889999999999877777778888774  489999


Q ss_pred             HHHHHHHHHHhcCCcee-eCHHHHHHH
Q 027733          148 MNLLEVDFLFDLGFQLN-VTPAAFYTY  173 (219)
Q Consensus       148 LN~LE~~FL~lLdf~L~-Vs~eey~~Y  173 (219)
                      +-+||+..|..|+|+|. +++..|-.+
T Consensus       131 i~~mE~~iL~~L~~~l~~~tp~~fl~~  157 (257)
T 1g3n_C          131 LIDQEKELLEKLAWRTEAVLATDVTSF  157 (257)
T ss_dssp             HHHHHHHHHHHTTTCCCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCcCCCCCHHHHHHH
Confidence            99999999999999998 566666544

>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens}

Probab=98.70  E-value=8.2e-08  Score=85.33  Aligned_cols=100  Identities=19%  Similarity=0.274  Sum_probs=87.4

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccC--CCHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG--ISTTE  147 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgG--is~~E  147 (219)
                      +.+|+.++....+++++++-+|..|+||+..+.+   +.....+-+-++|+.||+|+-+-...+-+.+..+++  ++.++
T Consensus        74 lvdwl~ev~~~~~l~~~t~~lAv~~lDRfls~~~---v~~~~lqLv~~tcL~lAsK~eE~~p~~~~~l~~~~~~~~~~~~  150 (306)
T 3g33_B           74 LAYWMLEVCEEQRCEEEVFPLAMNYLDRYLSCVP---TRKAQLQLLGAVCMLLASKLRETTPLTIEKLCIYTDHAVSPRQ  150 (306)
T ss_dssp             HHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHCC---CCGGGHHHHHHHHHHHHHHHHCSSCCCTTHHHHHTTTSSCHHH
T ss_pred             HHHHHHHHHHHhCCcHhHHHHHHHHHHHHHhcCC---CcHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHhccCccHHH
Confidence            7889999999999999999999999999999763   567889999999999999998877777777877754  89999


Q ss_pred             HHHHHHHHHHhcCCcee-eCHHHHHH
Q 027733          148 MNLLEVDFLFDLGFQLN-VTPAAFYT  172 (219)
Q Consensus       148 LN~LE~~FL~lLdf~L~-Vs~eey~~  172 (219)
                      +-+||+..|..|+|+|. +++..|-.
T Consensus       151 i~~mE~~IL~~L~f~l~~~tp~~fl~  176 (306)
T 3g33_B          151 LRDWEVLVLGKLKWDLAAVIAHDFLA  176 (306)
T ss_dssp             HHHHHHHHHHHTTTCCCCCCGGGGHH
T ss_pred             HHHHHHHHHHHcCCccCCCCHHHHHH
Confidence            99999999999999997 45555543

>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* ...

Probab=98.69  E-value=1.4e-07  Score=81.45  Aligned_cols=100  Identities=18%  Similarity=0.176  Sum_probs=86.5

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhcc--CCCHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG--GISTTE  147 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVg--Gis~~E  147 (219)
                      +.+|+..+....+++++++-+|..|+||+..+.+   +......-+-++|+.+|+|+-+-...+-+.+..++  .++.++
T Consensus        42 lvdwl~~v~~~~~l~~~tl~lAv~~lDRfls~~~---v~~~~lqlv~~acl~iA~K~ee~~~~~~~d~~~i~~~~~~~~~  118 (260)
T 2cch_B           42 LVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMS---VLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQ  118 (260)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCC---CCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTSSSCHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccCC---CCHHHHhHHHHHHHHHHHHhcccCCCCHHHHHHHHcCCcCHHH
Confidence            7799999999999999999999999999999753   56677888889999999999887677778888775  499999


Q ss_pred             HHHHHHHHHHhcCCcee-eCHHHHHH
Q 027733          148 MNLLEVDFLFDLGFQLN-VTPAAFYT  172 (219)
Q Consensus       148 LN~LE~~FL~lLdf~L~-Vs~eey~~  172 (219)
                      +-+||+..|..|+|++. +++..|-.
T Consensus       119 i~~mE~~iL~~L~~~l~~~tp~~fl~  144 (260)
T 2cch_B          119 VLRMEHLVLKVLTFDLAAPTVNQFLT  144 (260)
T ss_dssp             HHHHHHHHHHHTTTCCCCCCHHHHHH
T ss_pred             HHHHHHHHHHHcCCccCCCCHHHHHH
Confidence            99999999999999987 45555543

>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

Probab=98.69  E-value=1.6e-07  Score=81.56  Aligned_cols=100  Identities=22%  Similarity=0.383  Sum_probs=86.3

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhcc--CCCHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG--GISTTE  147 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVg--Gis~~E  147 (219)
                      +.+|+.++..+.+++++++.+|..|+||+..+.+   +......-+-++|+.+|+|+-+-...+-+.+..++  .++.++
T Consensus        60 lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~---v~~~~lqlv~~acL~iAsK~EE~~p~~~~~~~~~~~~~~~~~e  136 (271)
T 2w96_A           60 VATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEP---VKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPEE  136 (271)
T ss_dssp             HHHHHHHHHHHTTCCTTHHHHHHHHHHHHHTTSC---CCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTSSCHHH
T ss_pred             HHHHHHHHHHHHCCchhHHHHHHHHHHHhCCcCC---cCHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCHHH
Confidence            7789999999999999999999999999998753   55678889999999999999887666777777774  489999


Q ss_pred             HHHHHHHHHHhcCCcee-eCHHHHHH
Q 027733          148 MNLLEVDFLFDLGFQLN-VTPAAFYT  172 (219)
Q Consensus       148 LN~LE~~FL~lLdf~L~-Vs~eey~~  172 (219)
                      +-+||+..|+.|+|++. +++..|-.
T Consensus       137 I~~mE~~IL~~L~~~l~~~tp~~fl~  162 (271)
T 2w96_A          137 LLQMELLLVNKLKWNLAAMTPHDFIE  162 (271)
T ss_dssp             HHHHHHHHHHHTTTCCCCCCHHHHHH
T ss_pred             HHHHHHHHHHHCCCccCCCCHHHHHH
Confidence            99999999999999998 56665653

>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B*

Probab=98.67  E-value=2.5e-07  Score=80.39  Aligned_cols=101  Identities=16%  Similarity=0.225  Sum_probs=87.5

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhcc--CCCHH
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG--GISTT  146 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVg--Gis~~  146 (219)
                      .+.+|+.++....+++++++-+|..|+||+....+   +...+..-+-++|+.+|+|+-+-...+-+.+..++  .++.+
T Consensus        40 ~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfl~~~~---v~~~~lqlv~~acL~iA~K~eE~~~p~~~d~~~~~~~~~~~~  116 (269)
T 2b9r_A           40 ILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQNNS---VPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKH  116 (269)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHTTSC---CCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTCSSSCHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcCCC---CcHHHhhHHHHHHHHHHHhcccccCccHHHHHHHhcCCCCHH
Confidence            37889999999999999999999999999998753   56788999999999999999877666777888775  48999


Q ss_pred             HHHHHHHHHHHhcCCcee-eCHHHHHH
Q 027733          147 EMNLLEVDFLFDLGFQLN-VTPAAFYT  172 (219)
Q Consensus       147 ELN~LE~~FL~lLdf~L~-Vs~eey~~  172 (219)
                      |+-+||+..|..|+|++. +++..|-.
T Consensus       117 eI~~mE~~IL~~L~f~l~~~tp~~fl~  143 (269)
T 2b9r_A          117 QIRQMEMKILRALNFGLGRPLPLHFLR  143 (269)
T ss_dssp             HHHHHHHHHHHHTTSCCCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHcCCccCCCCHHHHHH
Confidence            999999999999999998 56655543

>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

Probab=98.66  E-value=1.2e-07  Score=81.70  Aligned_cols=101  Identities=16%  Similarity=0.174  Sum_probs=87.2

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhcc--CCCHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG--GISTTE  147 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVg--Gis~~E  147 (219)
                      +.+|+..+....+++++++-+|..|+||+..+.+   +......-+-+||+.+|+|+-+-...+-+.+..++  .++.+|
T Consensus        55 lvdwl~~v~~~~~l~~etl~lAv~~~DRfls~~~---v~~~~lqLv~~acl~iA~K~eE~~~p~~~d~~~~~~~~~~~~~  131 (254)
T 2f2c_A           55 LLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQ---GTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSCDCFTNLE  131 (254)
T ss_dssp             HHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSC---CCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHSTTC---CCHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHHHccCC---cCHHHccHHHHHHHHHHHHhcccCCCCHHHHHHHhCCCCCHHH
Confidence            7899999999999999999999999999998643   56678888999999999999887777777888774  489999


Q ss_pred             HHHHHHHHHHhcCCcee-eCHHHHHHH
Q 027733          148 MNLLEVDFLFDLGFQLN-VTPAAFYTY  173 (219)
Q Consensus       148 LN~LE~~FL~lLdf~L~-Vs~eey~~Y  173 (219)
                      +-+||+..|+.|+|++. +++..|-.+
T Consensus       132 i~~mE~~IL~~L~~~l~~~tp~~fl~~  158 (254)
T 2f2c_A          132 LINQEKDILEALKWDTEAVLATDFLIP  158 (254)
T ss_dssp             HHHHHHHHHHHTTTCCCCCCGGGSHHH
T ss_pred             HHHHHHHHHHHCCCcCCCCCHHHHHHH
Confidence            99999999999999998 556555543

>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

Probab=98.66  E-value=3.3e-07  Score=80.36  Aligned_cols=103  Identities=17%  Similarity=0.228  Sum_probs=88.8

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhcc--CCCHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG--GISTTE  147 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVg--Gis~~E  147 (219)
                      +.+|+..+....+++++++-+|..|+||+.....  .+......-+-++|+.+|+|+-+-...+-+.+..++  .++.+|
T Consensus        53 lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~--~v~~~~lqlv~~acL~iA~K~eE~~~p~l~~~~~i~~~~~~~~e  130 (283)
T 1w98_B           53 LLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQE--NVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDE  130 (283)
T ss_dssp             HHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCC--CCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTSSCHHH
T ss_pred             HHHHHHHHHHHhCCCccHHHHHHHHHHHHHHhCC--CCCHHHHHHHHHHHHHHHHHhcccCCCcHHHHHHHHcCCCCHHH
Confidence            7789999999999999999999999999998732  246688899999999999999887677778888875  489999


Q ss_pred             HHHHHHHHHHhcCCcee-eCHHHHHHHH
Q 027733          148 MNLLEVDFLFDLGFQLN-VTPAAFYTYC  174 (219)
Q Consensus       148 LN~LE~~FL~lLdf~L~-Vs~eey~~Y~  174 (219)
                      +.+||+..|+.|+|+|. +++..|-.++
T Consensus       131 i~~mE~~IL~~L~~~l~~~tp~~fL~~f  158 (283)
T 1w98_B          131 ILTMELMIMKALKWRLSPLTIVSWLNVY  158 (283)
T ss_dssp             HHHHHHHHHHHTTTCCCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcCCCCCHHHHHHHH
Confidence            99999999999999998 5666665443

>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe}

Probab=98.31  E-value=4.6e-06  Score=70.73  Aligned_cols=100  Identities=17%  Similarity=0.177  Sum_probs=83.4

Q ss_pred             hhHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCC-ccHHHHHHHHHHHHhhhcccCCcccchhhhcc-----
Q 027733           68 ISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINS-FNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG-----  141 (219)
Q Consensus        68 Isi~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~-~n~hRL~ltalilAsK~ldD~~~sN~~~AkVg-----  141 (219)
                      ....++|.++....++++.++-.|..|++|+..+++   +.. .+..-+.++||.+|+|+-+ ...+-+.++.+.     
T Consensus        29 ~~~~~~i~~v~~~l~L~~~t~~~A~~~~~Rf~~~~~---~~~~~~~~lv~~acL~lA~K~Ee-~~~~l~d~~~~~~~~~~  104 (235)
T 1zp2_A           29 IYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKN---EEKGFSLEALVATCIYLSCKVEE-CPVHIRTICNEANDLWS  104 (235)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCC---SCCCCCHHHHHHHHHHHHHHHTT-CCCCHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcc---cccccCHHHHHHHHHHHHhcccc-CcccHHHHHHHHHHHcc
Confidence            346789999999999999999999999999998753   455 7888999999999999866 555666666553     


Q ss_pred             ---CCCHHHHHHHHHHHHHhcCCceee-CHHHHH
Q 027733          142 ---GISTTEMNLLEVDFLFDLGFQLNV-TPAAFY  171 (219)
Q Consensus       142 ---Gis~~ELN~LE~~FL~lLdf~L~V-s~eey~  171 (219)
                         .++.+++-.||+.+|+.|+|++.+ ++..|-
T Consensus       105 ~~~~~~~~~I~~~E~~iL~~L~f~l~~~~P~~~l  138 (235)
T 1zp2_A          105 LKVKLSRSNISEIEFEIISVLDAFLIVHHPYTSL  138 (235)
T ss_dssp             CSSCCCHHHHHHHHHHHHHHTTTCCCCCCTHHHH
T ss_pred             chhhccHHHHHHHHHHHHHHCCCcEEecChHHHH
Confidence               579999999999999999999985 455553

>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

Probab=98.29  E-value=2.8e-06  Score=72.69  Aligned_cols=98  Identities=16%  Similarity=0.172  Sum_probs=78.7

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhc---------
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKV---------  140 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkV---------  140 (219)
                      ..+++.++....+++++++-.|..|+||+..+.+   +...+.+-+-++|+.+|+|+-+ ...+-+.+..+         
T Consensus        44 ~~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~~---~~~~~~qlv~~acL~lA~K~eE-~~~~l~d~~~~~~~~~~~~~  119 (258)
T 2i53_A           44 GARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHS---FKQFPRYVTGACCLFLAGKVEE-TPKKCKDIIKTARSLLNDVQ  119 (258)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSC---TTTSCHHHHHHHHHHHHHHHTT-CCCCHHHHHHHHHHHSCHHH
T ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCC---hhhcCHHHHHHHHHHHHHcccc-ccccHHHHHHHHHHHhchhh
Confidence            6689999999999999999999999999998653   5567888888999999999866 45444444432         


Q ss_pred             ----cCCCHHHHHHHHHHHHHhcCCceee-CHHHHH
Q 027733          141 ----GGISTTEMNLLEVDFLFDLGFQLNV-TPAAFY  171 (219)
Q Consensus       141 ----gGis~~ELN~LE~~FL~lLdf~L~V-s~eey~  171 (219)
                          +.-+.+++-.||+.+|+.|+|++.+ ++..|-
T Consensus       120 ~~~~~~~~~~~i~~~E~~iL~~L~f~l~~~~P~~fl  155 (258)
T 2i53_A          120 FGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFL  155 (258)
T ss_dssp             HGGGCSCHHHHHHHHHHHHHHHTTTCCCCCCHHHHH
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHCCCceeccChHHHH
Confidence                2235789999999999999999985 455554

>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*

Probab=98.20  E-value=1e-05  Score=69.26  Aligned_cols=98  Identities=23%  Similarity=0.317  Sum_probs=79.9

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccC-------
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG-------  142 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgG-------  142 (219)
                      ..+|+.++....+++++++-.|..|+||+..+.   .+...+.+-+-++|+.+|+|+-+- ..+-+.+.+++.       
T Consensus        34 ~~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~---~~~~~~~qlv~~acL~lA~K~EE~-p~~l~d~~~~~~~~~~~~~  109 (257)
T 2ivx_A           34 AANLIQEMGQRLNVSQLTINTAIVYMHRFYMHH---SFTKFNKNIISSTALFLAAKVEEQ-ARKLEHVIKVAHACLHPLE  109 (257)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTS---CTTTSCHHHHHHHHHHHHHHHTTC-CCCHHHHHHHHHHHHCTTS
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhC---ChhhhCHHHHHHHHHHHHhccccC-CcCHHHHHHHHHHHhccCC
Confidence            678999999999999999999999999999865   356678899999999999999665 555555554431       


Q ss_pred             ---------CC--HHHHHHHHHHHHHhcCCceee-CHHHHH
Q 027733          143 ---------IS--TTEMNLLEVDFLFDLGFQLNV-TPAAFY  171 (219)
Q Consensus       143 ---------is--~~ELN~LE~~FL~lLdf~L~V-s~eey~  171 (219)
                               +.  .+++-.||+.+|..|+|++.+ ++..|-
T Consensus       110 ~~~~~~~~~y~~~~~~I~~~E~~iL~~L~f~l~~~~P~~fl  150 (257)
T 2ivx_A          110 PLLDTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDV  150 (257)
T ss_dssp             CCCCTTSHHHHHHHHHHHHHHHHHHHHTTTCCCCCCHHHHH
T ss_pred             CCCCcchHHHHHHHHHHHHHHHHHHHHcccceEeeCcHHHH
Confidence                     22  899999999999999999984 455554

>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens}

Probab=98.10  E-value=2.4e-05  Score=68.51  Aligned_cols=105  Identities=15%  Similarity=0.105  Sum_probs=80.9

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhc---------
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKV---------  140 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkV---------  140 (219)
                      ..++|.++....++++.++-.|.+|++|+..+..   +...+.+-+.++|+.+|+|+-+-...+.+....+         
T Consensus        46 ~~~~I~~v~~~l~L~~~t~~tA~~~~~RF~~~~s---~~~~~~~lva~acLfLA~K~EE~~~~~~~di~~~~~~~~k~~~  122 (285)
T 3rgf_B           46 FTNVIQALGEHLKLRQQVIATATVYFKRFYARYS---LKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRF  122 (285)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHSC---TTTSCHHHHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhCC---chhcCHHHHHHHHHHHHHhhhccccccHHHHHHHHHHHHcccc
Confidence            6789999999999999999999999999998753   5567889999999999999855433333333221         


Q ss_pred             -------cCCCHHHHHHHHHHHHHhcCCceee-CHHHHH-HHHHHH
Q 027733          141 -------GGISTTEMNLLEVDFLFDLGFQLNV-TPAAFY-TYCSYL  177 (219)
Q Consensus       141 -------gGis~~ELN~LE~~FL~lLdf~L~V-s~eey~-~Y~~~L  177 (219)
                             ...+.+++-.||+.+|..|+|+|.| ++..|- .|...+
T Consensus       123 ~~~~~~~~~~~~~~Il~~E~~iL~~L~f~l~v~~P~~fL~~~~~~l  168 (285)
T 3rgf_B          123 SYAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDM  168 (285)
T ss_dssp             TTTCCSCCCCCHHHHHHHHHHHHHHTTTCCCCCCSHHHHHHHHHHH
T ss_pred             cccCchhhHHHHHHHHHHHHHHHHHcCCCeEeCChHHHHHHHHHHh
Confidence                   1257899999999999999999975 444443 444433

>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

Probab=98.06  E-value=4e-05  Score=68.40  Aligned_cols=104  Identities=15%  Similarity=0.193  Sum_probs=81.1

Q ss_pred             HHHHHHHHHHcC--CCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCC----
Q 027733           71 HSYLERIFKYAN--CSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGIS----  144 (219)
Q Consensus        71 ~~yl~rI~~~~~--~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis----  144 (219)
                      .++|.++....+  ++..++-.|.+|++|+..+++   +...+.+-+.+|||.+|+|+=+- +.+-+.+..+...+    
T Consensus        61 ~~~I~ev~~~l~~~Lp~~t~~tA~~~~~RF~~~~s---~~~~~~~lva~acLfLA~K~EE~-~~~l~d~v~~~~~~p~~~  136 (323)
T 1jkw_A           61 EKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNS---VMEYHPRIIMLTCAFLACKVDEF-NVSSPQFVGNLRESPLGQ  136 (323)
T ss_dssp             HHHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSC---TTTSCHHHHHHHHHHHHHHHTTC-CCCHHHHGGGSSSCHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhhCC---hhhcCHHHHHHHHHHHHHhhhcC-CCCHHHHHHHhccChhhh
Confidence            467888999999  999999999999999998753   55678999999999999998554 55556666544323    


Q ss_pred             ---HHHHHHHHHHHHHhcCCceee-CHHHHH-HHHHHHH
Q 027733          145 ---TTEMNLLEVDFLFDLGFQLNV-TPAAFY-TYCSYLQ  178 (219)
Q Consensus       145 ---~~ELN~LE~~FL~lLdf~L~V-s~eey~-~Y~~~L~  178 (219)
                         .+++-.||+.+|..|+|+|.| ++..|- .|...++
T Consensus       137 ~~~~~~Il~~E~~iL~~L~f~l~v~~P~~~L~~~l~~l~  175 (323)
T 1jkw_A          137 EKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLK  175 (323)
T ss_dssp             HHHHHHHHHHHHHHHHHTTTCCCCCCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCCcEEcCChHHHHHHHHHHHH
Confidence               689999999999999999985 444443 4544443

>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

Probab=98.00  E-value=8.2e-06  Score=74.06  Aligned_cols=98  Identities=22%  Similarity=0.297  Sum_probs=78.4

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccC-------
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG-------  142 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgG-------  142 (219)
                      +.+||.++....+++++++-.|..|+||+..+.+   +...+..-+.++||.||+|+-+. ..+-+.+..+..       
T Consensus        41 ~v~wI~ev~~~l~L~~~t~~tAv~~~dRFl~~~s---v~~~~~qlva~acLfLA~K~EE~-p~~l~d~v~v~~~~~~~~~  116 (358)
T 2pk2_A           41 AANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQS---FTRFPGNSVAPAALFLAAKVEEQ-PKKLEHVIKVAHTCLHPQE  116 (358)
T ss_dssp             HHHHHHHHHTTTTCCHHHHHHHHHHHHHHTTTSC---TTTSCHHHHHHHHHHHHHHHTTC-CCCHHHHHTTHHHHHCSSS
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCC---cccccHHHHHHHHHHHHHhhccC-CCCHHHHHHHHHHHhcccc
Confidence            6789999999999999999999999999998653   56688899999999999999665 444444544321       


Q ss_pred             ---------C--CHHHHHHHHHHHHHhcCCceee-CHHHHH
Q 027733          143 ---------I--STTEMNLLEVDFLFDLGFQLNV-TPAAFY  171 (219)
Q Consensus       143 ---------i--s~~ELN~LE~~FL~lLdf~L~V-s~eey~  171 (219)
                               +  ..++|-.||+.+|..|+|+|.+ ++..|-
T Consensus       117 ~~~~~~~~~y~~~~~~Il~~E~~IL~~L~f~L~v~~P~~fL  157 (358)
T 2pk2_A          117 SLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHV  157 (358)
T ss_dssp             CCCCTTSHHHHGGGTGGGTHHHHHHHHTTTCCCCCCTTHHH
T ss_pred             ccccccchhhhHHHHHHHHHHHHHHHHcCCceeCCCHHHHH
Confidence                     1  2788999999999999999984 444443

>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*

Probab=97.88  E-value=0.00014  Score=60.11  Aligned_cols=92  Identities=8%  Similarity=0.012  Sum_probs=81.7

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMN  149 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~ELN  149 (219)
                      -.++|.++....+++..+.-.|..|++|+...+.   +...+..-+..+|+-+|+|.-+ .+.+-+.++.+.+++.+++.
T Consensus         8 a~~~I~~~~~~L~L~~~v~~~A~~~~~r~~~~~~---~~~~~~~~v~aaclylAcK~ee-~p~~l~di~~~~~~~~~~i~   83 (207)
T 1c9b_A            8 AFKEITTMADRINLPRNIVDRTNNLFKQVYEQKS---LKGRANDAIASACLYIACRQEG-VPRTFKEICAVSRISKKEIG   83 (207)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTC---STTSCHHHHHHHHHHHHHHHTT-CCCCHHHHHHTSSSCHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCC---cCCCCHHHHHHHHHHHHHHhcC-CCCCHHHHHHHHCCCHHHHH
Confidence            3568999999999999999999999999998753   4567888999999999999854 57888999999999999999


Q ss_pred             HHHHHHHHhcCCceee
Q 027733          150 LLEVDFLFDLGFQLNV  165 (219)
Q Consensus       150 ~LE~~FL~lLdf~L~V  165 (219)
                      ++|+.+|+.|+|++.+
T Consensus        84 ~~~~~ll~~L~~~l~~   99 (207)
T 1c9b_A           84 RCFKLILKALETSVDL   99 (207)
T ss_dssp             HHHHHHHHHTTCCCCC
T ss_pred             HHHHHHHHHHCCCcCc
Confidence            9999999999999864

>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*

Probab=97.45  E-value=0.001  Score=54.53  Aligned_cols=104  Identities=13%  Similarity=0.128  Sum_probs=87.2

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMN  149 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~ELN  149 (219)
                      -.+++.++....++++.+.=.|..|++|+....  + +...+..-+..+|+-+|+|..+ .+.+-+..+.+.|++.+++.
T Consensus        12 a~~~I~~~~~~L~L~~~v~~~A~~l~~~~~~~~--~-~~gr~~~~vaaAclylAcr~~~-~p~~l~di~~~~~v~~~~i~   87 (200)
T 1ais_B           12 ALSELDRITAQLKLPRHVEEEAARLYREAVRKG--L-IRGRSIESVMAACVYAACRLLK-VPRTLDEIADIARVDKKEIG   87 (200)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTT--T-TTTCCHHHHHHHHHHHHHHHHT-CCCCHHHHHHHTTSCHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhCC--C-cCCCCHHHHHHHHHHHHHHHcC-CCCCHHHHHHHHCCCHHHHH
Confidence            567899999999999999999999999998863  2 3456788889999999999866 78899999999999999999


Q ss_pred             HHHHHHHHhcCCceee---CHHHHH-HHHHHH
Q 027733          150 LLEVDFLFDLGFQLNV---TPAAFY-TYCSYL  177 (219)
Q Consensus       150 ~LE~~FL~lLdf~L~V---s~eey~-~Y~~~L  177 (219)
                      ..++.+++.|+|++.+   ++..|- +|+..|
T Consensus        88 ~~~~~l~~~L~~~~~~~~~~p~~~i~r~~~~L  119 (200)
T 1ais_B           88 RSYRFIARNLNLTPKKLFVKPTDYVNKFADEL  119 (200)
T ss_dssp             HHHHHHHHHTTCCTTTTCCCGGGGHHHHHHHH
T ss_pred             HHHHHHHHHhcccCCcCCCCHHHHHHHHHHHc
Confidence            9999999999999764   455543 444444

>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*

Probab=94.77  E-value=0.19  Score=40.75  Aligned_cols=92  Identities=11%  Similarity=0.084  Sum_probs=75.5

Q ss_pred             hhHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHH
Q 027733           68 ISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTE  147 (219)
Q Consensus        68 Isi~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~E  147 (219)
                      ++-.+|+.|+.+..+++..+.-.|..++.+.....  . ....++.-+..+|+-+|++..+ ...+.+.++++.|++..+
T Consensus       106 ~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~-~~gr~P~~iAaAaly~A~~~~~-~~~t~~ei~~~~~vs~~t  181 (200)
T 1ais_B          106 VKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRG--L-TSGKSPAGLVAAALYIASLLEG-EKRTQREVAEVARVTEVT  181 (200)
T ss_dssp             CCGGGGHHHHHHHHTCCHHHHHHHHHHHHHHHHTT--C-CTTSCHHHHHHHHHHHHHHHTT-CCCCHHHHHHHHTCCHHH
T ss_pred             CCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcC--c-ccCCCHHHHHHHHHHHHHHHhC-CCCCHHHHHHHhCCCHHH
Confidence            56789999999999999998888888887777642  2 4568888999999999999876 445778899999999999


Q ss_pred             HHHHHHHHHHhcCCce
Q 027733          148 MNLLEVDFLFDLGFQL  163 (219)
Q Consensus       148 LN~LE~~FL~lLdf~L  163 (219)
                      +..-=+++...++.++
T Consensus       182 i~~~~~~l~~~l~~~~  197 (200)
T 1ais_B          182 VRNRYKELVEKLKIKV  197 (200)
T ss_dssp             HHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHHcCCCC
Confidence            9988888887776443

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}

Probab=94.53  E-value=0.045  Score=48.94  Aligned_cols=104  Identities=10%  Similarity=0.068  Sum_probs=75.0

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMN  149 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~ELN  149 (219)
                      ...+|.++....+++..+.=.|..|..|+.....   +...+..-+..+|+-+|.| .+..+.+-+.++.+.+++.+||.
T Consensus       129 a~~~I~~~~~~L~Lp~~v~d~A~~lyk~~~~~~~---~kgr~~~~vaaAclyiAcR-~e~~prtl~ei~~~~~v~~keIg  204 (345)
T 3k7a_M          129 AFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKT---LKGKSMESIMAASILIGCR-RAEVARTFKEIQSLIHVKTKEFG  204 (345)
T ss_dssp             HHHHHHHHHHHTTCCHHHHTHHHHHHHHHSSSCS---SCCCCSHHHHTTTTTTTSB-TTBSSCCHHHHHHSSSCCSHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCc---ccCCcHHHHHHHHHHHHHH-HcCCCccHHHHHHHHCCCHHHHH
Confidence            5678899999999999999999999999877531   3455677888899999999 46678888999999999999999


Q ss_pred             HHHHHHHHhcC------------Ccee-eCHHHHH-HHHHHH
Q 027733          150 LLEVDFLFDLG------------FQLN-VTPAAFY-TYCSYL  177 (219)
Q Consensus       150 ~LE~~FL~lLd------------f~L~-Vs~eey~-~Y~~~L  177 (219)
                      +.++.+++.|+            +++. +++..|. +|+..|
T Consensus       205 r~~~~l~~~L~~~~~~~~~~~~~~~~~~~~p~~~i~Rf~~~L  246 (345)
T 3k7a_M          205 KTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHL  246 (345)
T ss_dssp             HHHHHHHHHHTCC-----------------------------
T ss_pred             HHHHHHHHHHhhhhccccccccccccCCCCHHHHHHHHHHHc
Confidence            99999999998            6654 3444443 455544

>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens}

Probab=93.49  E-value=0.16  Score=43.97  Aligned_cols=119  Identities=8%  Similarity=-0.068  Sum_probs=80.0

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHHHH
Q 027733           71 HSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNL  150 (219)
Q Consensus        71 ~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~ELN~  150 (219)
                      .+|+.++++..+.+....-.|..++...... + . .-...++-+-.+|+.+|.+.++..   ...|....|++.+++..
T Consensus       158 ~~fL~~~~~~l~~~~~~~~~A~~~l~~sl~t-~-~-~l~~~Ps~IAaAaiylA~~~~~~~---~~~W~~~~~~~~~~l~~  231 (285)
T 3rgf_B          158 YRPLLQYVQDMGQEDMLLPLAWRIVNDTYRT-D-L-CLLYPPFMIALACLHVACVVQQKD---ARQWFAELSVDMEKILE  231 (285)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTS-S-H-HHHSCHHHHHHHHHHHHHHHTTCC---CHHHHHTSCSCHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHHHcc-C-h-hhccCHHHHHHHHHHHHHHHcCCC---hhhHHHHHCCCHHHHHH
Confidence            7899999999998888888887777765432 1 1 123677889999999999988643   26788899999999999


Q ss_pred             HHHHHHHhc-CCceeeCHHHHHHHHHHHHHHHHhcCCCCCCccchhhccc
Q 027733          151 LEVDFLFDL-GFQLNVTPAAFYTYCSYLQREMFLQSPLQLEEPLNVGRQL  199 (219)
Q Consensus       151 LE~~FL~lL-df~L~Vs~eey~~Y~~~L~~~~~~~~~~~~~~~~~~~~~~  199 (219)
                      .-.+++.+. .|+-+-..+++..    +.+.|...+++|+.+++.|.|+.
T Consensus       232 ~~~~il~ly~~~~~~~~~~~~~~----~~~k~~~~~~~~~~~~~~~~~~~  277 (285)
T 3rgf_B          232 IIRVILKLYEQWKNFDERKEMAT----ILSKMPKPKPPPNSEGEQGPNGS  277 (285)
T ss_dssp             HHHHHHHHHHHHHHCCHHHHHHH----HHHHSCCCCCCC-----------
T ss_pred             HHHHHHHHHHhcccCchhhhHHH----HHHhCCCCCCCCCCCCCCCCCcc
Confidence            999999886 3555544444432    44666666766666665555543

>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*

Probab=93.07  E-value=0.56  Score=38.17  Aligned_cols=88  Identities=6%  Similarity=0.016  Sum_probs=67.9

Q ss_pred             CChhHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCH
Q 027733           66 PTISIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGIST  145 (219)
Q Consensus        66 P~Isi~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~  145 (219)
                      |...-.+|+.|+.+..+++..+.-.|...+.+....  .+ .....++-+-.+|+-+|++..+ ...+.+.|+++.|++.
T Consensus        98 ~~~~p~~~l~r~~~~l~l~~~~~~~A~~i~~~~~~~--~l-~~g~~P~~IAaAaiylA~~~~~-~~~~~~~i~~~~~v~~  173 (207)
T 1c9b_A           98 DLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVEL--DL-VPGRSPISVAAAAIYMASQASA-EKRTQKEIGDIAGVAD  173 (207)
T ss_dssp             CCCCTHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHT--TC-STTCCHHHHHHHHHHHHHHTSS-SCCCHHHHHHHHTCCH
T ss_pred             CcCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHc--Cc-cCCCChHHHHHHHHHHHHHHHC-CCCCHHHHHHHhCCCH
Confidence            334568999999999999998888887777776653  22 4468899999999999999875 5567788999999998


Q ss_pred             HHHHHHHHHHHH
Q 027733          146 TEMNLLEVDFLF  157 (219)
Q Consensus       146 ~ELN~LE~~FL~  157 (219)
                      .++..-=++++.
T Consensus       174 ~tI~~~~~~l~~  185 (207)
T 1c9b_A          174 VTIRQSYRLIYP  185 (207)
T ss_dssp             HHHHHHHHHHGG
T ss_pred             HHHHHHHHHHHH
Confidence            888765444433

>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M

Probab=81.75  E-value=7.2  Score=34.68  Aligned_cols=90  Identities=8%  Similarity=-0.028  Sum_probs=74.4

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHH
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEM  148 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~EL  148 (219)
                      .....|.++....+++..+.=.|..+..|.....  + +...+..-+..+|+-+|.|. ...+.+-+..+.+.+++.+||
T Consensus       128 ~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~a~~~~--~-~rGrs~e~vaAAclYiACR~-~~~prtl~eI~~~~~v~~kei  203 (345)
T 4bbr_M          128 AAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEK--T-LKGKSMESIMAASILIGCRR-AEVARTFKEIQSLIHVKTKEF  203 (345)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCT--T-TTTCCHHHHHHHHHHHHHHH-TCCBCCHHHHHHHHTCCTTHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC--C-ccCCCHHHHHHHHHHHHHHh-cCCCccHHHHHHHhCCCHHHH
Confidence            4677899999999999999999988888887742  2 34567888889999999995 567888899999999999999


Q ss_pred             HHHHHHHHHhcCCc
Q 027733          149 NLLEVDFLFDLGFQ  162 (219)
Q Consensus       149 N~LE~~FL~lLdf~  162 (219)
                      .+..+.+.+.|+..
T Consensus       204 gr~~k~l~~~L~l~  217 (345)
T 4bbr_M          204 GKTLNIMKNILRGK  217 (345)
T ss_dssp             HHHHHHHHHCC---
T ss_pred             HHHHHHHHHHhCcc
Confidence            99999999999864

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	219
d1w98b2	140	G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax	99.06
d2cchb1	128	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	99.03
d1bu2a1	127	Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}	98.98
d1g3nc1	132	Viral cyclin {Kaposi's sarcoma-associated herpesvi	98.98
d1f5qb1	141	Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]	98.92
d2i53a1	144	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	98.65
d1jkwa1	151	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	98.55
d2ivxa1	143	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	98.42
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	96.04
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	95.96
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	95.41
d1vola2	109	Transcription factor IIB (TFIIB), core domain {Hum	94.69

>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: G1/S-specific cyclin-E1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.06  E-value=6.6e-10  Score=86.40  Aligned_cols=94  Identities=18%  Similarity=0.231  Sum_probs=83.7

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhcc--CCCHH
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG--GISTT  146 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVg--Gis~~  146 (219)
                      .+-+|+.++....+++++++.+|.-|+||+....+.  +.......+-++|+.||+|+-+......+.+.+++  .++.+
T Consensus        45 ~lidW~~~v~~~~~l~~et~~lAv~llDryl~~~~~--v~~~~lqL~a~acL~IAsK~ee~~~~~~~~l~~~~~~~~t~~  122 (140)
T d1w98b2          45 ILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQEN--VVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGD  122 (140)
T ss_dssp             HHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCC--CCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTSSCHH
T ss_pred             HHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhcccc--ccHHHHhHHHHHHHHHHHHHcccCCCCHHHHHHHHcCCCCHH
Confidence            388999999999999999999999999999876543  45678888999999999999998888888888874  48999


Q ss_pred             HHHHHHHHHHHhcCCcee
Q 027733          147 EMNLLEVDFLFDLGFQLN  164 (219)
Q Consensus       147 ELN~LE~~FL~lLdf~L~  164 (219)
                      |+..||+..|..|+|+|.
T Consensus       123 ei~~mE~~IL~~L~~~Ln  140 (140)
T d1w98b2         123 EILTMELMIMKALKWRLS  140 (140)
T ss_dssp             HHHHHHHHHHHHTTTCCC
T ss_pred             HHHHHHHHHHHHCCCcCC
Confidence            999999999999999984

>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]}

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

Probab=99.03  E-value=7.6e-10  Score=84.66  Aligned_cols=93  Identities=16%  Similarity=0.159  Sum_probs=82.9

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccC--CCHH
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG--ISTT  146 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgG--is~~  146 (219)
                      .+-+|+.++.+..+++++++-+|..|+||+....+   +...+.+-+-++|+.||+|+-+.....-+.+.++++  ++.+
T Consensus        33 ~li~W~~~v~~~~~l~~~t~~lAv~llDr~l~~~~---i~~~~~qLi~~~cl~iAsK~ee~~~~~l~~l~~~~~~~~t~~  109 (128)
T d2cchb1          33 ILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMS---VLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKK  109 (128)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCC---CCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTSSSCHH
T ss_pred             HHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcccC---CchHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHcCCCCHH
Confidence            37799999999999999999999999999998653   567788889999999999999888778788877754  8999


Q ss_pred             HHHHHHHHHHHhcCCcee
Q 027733          147 EMNLLEVDFLFDLGFQLN  164 (219)
Q Consensus       147 ELN~LE~~FL~lLdf~L~  164 (219)
                      |+..||+..|..|+|+|.
T Consensus       110 ~i~~mE~~IL~~L~~~l~  127 (128)
T d2cchb1         110 QVLRMEHLVLKVLTFDLA  127 (128)
T ss_dssp             HHHHHHHHHHHHTTTCCC
T ss_pred             HHHHHHHHHHHHCCCeec
Confidence            999999999999999984

>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}

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

Probab=98.98  E-value=1.8e-09  Score=82.84  Aligned_cols=91  Identities=15%  Similarity=0.167  Sum_probs=82.7

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccC--CCHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGG--ISTTE  147 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgG--is~~E  147 (219)
                      +.+|+.++..+.+++++++-+|..|+||+....   .++..+.+-+-++|+.||+|+-+-...+-+.+.++++  ++.+|
T Consensus        34 lidWl~~v~~~~~l~~eTl~lAv~llDryl~~~---~i~~~~lqLi~~tcL~IAsK~ee~~~~~l~~l~~~~~~~~t~~e  110 (127)
T d1bu2a1          34 LLTWMHLLCESFELDKSVFPLSVSILDRYLCKK---QGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSCDCFTNLE  110 (127)
T ss_dssp             HHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTS---CCCTTTHHHHHHHHHHHHHHHSSSSCCCHHHHHHTTTTSSCHHH
T ss_pred             HHHHHHHHHHHHCCChHHHHHHHHHHHHHcccc---cccHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHcCCCCHHH
Confidence            789999999999999999999999999999864   3677889999999999999998877778888888854  89999


Q ss_pred             HHHHHHHHHHhcCCce
Q 027733          148 MNLLEVDFLFDLGFQL  163 (219)
Q Consensus       148 LN~LE~~FL~lLdf~L  163 (219)
                      +-+||+..|..|+||+
T Consensus       111 i~~mE~~IL~~L~~dl  126 (127)
T d1bu2a1         111 LINQEKDILEALKWDT  126 (127)
T ss_dssp             HHHHHHHHHHHTTTCC
T ss_pred             HHHHHHHHHHHcCCCC
Confidence            9999999999999997

>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]

Probab=98.98  E-value=1.4e-09  Score=83.83  Aligned_cols=92  Identities=15%  Similarity=0.178  Sum_probs=81.8

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhcc--CCCHH
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG--GISTT  146 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVg--Gis~~  146 (219)
                      .+.+|+.++....+++++++.+|..|+||+..+.   .+.....+-+-++|+.||+|+-+....+-+.+.+++  .++.+
T Consensus        38 ~lidWl~~v~~~~~l~~et~~lAv~llDrfls~~---~v~~~~lqLia~tcl~iAsK~ee~~~~~~~~l~~~~~~~~t~~  114 (132)
T d1g3nc1          38 LLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIK---QVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQ  114 (132)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTC---CCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTCSCHH
T ss_pred             HHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCcc---cCcHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHcCCCCHH
Confidence            4889999999999999999999999999999764   366778888899999999999777677777777774  48999


Q ss_pred             HHHHHHHHHHHhcCCce
Q 027733          147 EMNLLEVDFLFDLGFQL  163 (219)
Q Consensus       147 ELN~LE~~FL~lLdf~L  163 (219)
                      |+-.||...|..|+|+|
T Consensus       115 ei~~mE~~IL~~L~w~l  131 (132)
T d1g3nc1         115 ELIDQEKELLEKLAWRT  131 (132)
T ss_dssp             HHHHHHHHHHHHTTTCC
T ss_pred             HHHHHHHHHHHHcCCcC
Confidence            99999999999999997

>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Murine herpesvirus 68 [TaxId: 33708]

Probab=98.92  E-value=3.2e-09  Score=82.80  Aligned_cols=92  Identities=15%  Similarity=0.139  Sum_probs=83.5

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhcc--CCCHH
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG--GISTT  146 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVg--Gis~~  146 (219)
                      .+.+|+.++..+.+++++++.+|.-|+||+....+   +.....+-+-++|+.||+|+-+.....-..+.+++  .++.+
T Consensus        46 ~lvdWm~~v~~~~~l~~etl~lAv~llDrfls~~~---i~~~~lqL~a~tcL~IAsK~ee~~~~~~~~l~~~~~~~yt~~  122 (141)
T d1f5qb1          46 VLTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTR---IDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLCGGATTAD  122 (141)
T ss_dssp             HHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSC---CCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHCTTCCHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHHHhhcc---ccHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHhcCCCCHH
Confidence            58999999999999999999999999999998753   66788899999999999999988888888888774  48999


Q ss_pred             HHHHHHHHHHHhcCCce
Q 027733          147 EMNLLEVDFLFDLGFQL  163 (219)
Q Consensus       147 ELN~LE~~FL~lLdf~L  163 (219)
                      |+..||...|..|+|++
T Consensus       123 ei~~mE~~IL~~L~w~~  139 (141)
T d1f5qb1         123 KLLTLEVKSLDTLSWVA  139 (141)
T ss_dssp             HHHHHHHHHHHHTTTCC
T ss_pred             HHHHHHHHHHHHCCccC
Confidence            99999999999999986

>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin K
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.65  E-value=6.9e-08  Score=74.55  Aligned_cols=93  Identities=14%  Similarity=0.163  Sum_probs=74.2

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccch------------
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAF------------  136 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~------------  136 (219)
                      .+.+|+..+....+++..++..|.+|++|+..+.+   +...+.+-+-+||+.+|+|+-+.. ..-+.            
T Consensus        39 ~~~~~i~~~~~~l~l~~~t~~~A~~~~dRf~~~~~---~~~~~~~lva~acl~LA~K~eE~~-~~l~~vi~~~~~~~~~~  114 (144)
T d2i53a1          39 EGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHS---FKQFPRYVTGACCLFLAGKVEETP-KKCKDIIKTARSLLNDV  114 (144)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSC---TTTSCHHHHHHHHHHHHHHHTTCC-CCHHHHHHHHHHHSCHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhhCc---ccchhHHHHHHHHHHHHHHhhccc-ccHHHHHHHHHHHhhhh
Confidence            46789999999999999999999999999998653   566788999999999999986542 11111            


Q ss_pred             -hhhccCCCHHHHHHHHHHHHHhcCCceee
Q 027733          137 -YAKVGGISTTEMNLLEVDFLFDLGFQLNV  165 (219)
Q Consensus       137 -~AkVgGis~~ELN~LE~~FL~lLdf~L~V  165 (219)
                       ....+..+.+++-.||+..|..|+|+|.|
T Consensus       115 ~~~~~~~~~~~~i~~~E~~iL~~L~Fdl~V  144 (144)
T d2i53a1         115 QFGQFGDDPKEEVMVLERILLQTIKFDLQV  144 (144)
T ss_dssp             HHGGGCSCHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             hhhhhchhhHHHHHHHHHHHHHHCCCeeeC
Confidence             11122346688999999999999999976

>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin H (mcs2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.55  E-value=2.7e-07  Score=71.86  Aligned_cols=92  Identities=14%  Similarity=0.198  Sum_probs=72.3

Q ss_pred             HHHHHHHHHHHcC--CCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhcc------
Q 027733           70 IHSYLERIFKYAN--CSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVG------  141 (219)
Q Consensus        70 i~~yl~rI~~~~~--~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVg------  141 (219)
                      ..+++.++..+.+  ++..++-.|.+|++|+..++.   +...+.+-+.++|+.+|+|+-+ ...+-..+.+..      
T Consensus        50 ~~~~l~~~~~~~k~~l~~~~~~tA~~~~~RF~~~~s---~~~~~~~li~~acl~LA~K~ee-~~~~~~~~~~~~~~~~~~  125 (151)
T d1jkwa1          50 YEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNS---VMEYHPRIIMLTCAFLACKVDE-FNVSSPQFVGNLRESPLG  125 (151)
T ss_dssp             HHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSC---TTTSCHHHHHHHHHHHHHHHTT-CCCCHHHHGGGSSSCHHH
T ss_pred             HHHHHHHHHHHHccCCCHHHHHHHHHHHHHHhhcCc---cccccHHHHHHHHHHHHHHHcc-cCCCHHHHHHHHHhhccc
Confidence            3455777777655  889999999999999999753   5678889999999999999854 444444443332      


Q ss_pred             -CCCHHHHHHHHHHHHHhcCCceee
Q 027733          142 -GISTTEMNLLEVDFLFDLGFQLNV  165 (219)
Q Consensus       142 -Gis~~ELN~LE~~FL~lLdf~L~V  165 (219)
                       ..+.+++-.+|...|..|+|+|.|
T Consensus       126 ~~~~~~~i~~~E~~iL~~L~f~L~V  150 (151)
T d1jkwa1         126 QEKALEQILEYELLLIQQLNFHLIV  150 (151)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             ccccHHHHHHHHHHHHHHcCCeeee
Confidence             146889999999999999999987

>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin-T2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.42  E-value=6.4e-07  Score=68.56  Aligned_cols=93  Identities=24%  Similarity=0.311  Sum_probs=73.1

Q ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhc--------
Q 027733           69 SIHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKV--------  140 (219)
Q Consensus        69 si~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkV--------  140 (219)
                      ...+|+..+..+.+++..++..|.+|++|+..+++   +...+++-+.+||+.+|+|+-+... .-.+...+        
T Consensus        33 ~~~~~i~~~~~~l~l~~~t~~~A~~l~~Rf~~~~s---~~~~~~~~va~acl~LA~K~eE~~~-~~~~ii~~~~~~~~~~  108 (143)
T d2ivxa1          33 QAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHS---FTKFNKNIISSTALFLAAKVEEQAR-KLEHVIKVAHACLHPL  108 (143)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSC---TTTSCHHHHHHHHHHHHHHHTTCCC-CHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCC---ccccCHHHHHHHHHHHHHHhccccc-cHHHHHHHHHHHhccc
Confidence            35678999999999999999999999999988653   5678899999999999999976532 11111100        


Q ss_pred             ----------cCCCHHHHHHHHHHHHHhcCCceee
Q 027733          141 ----------GGISTTEMNLLEVDFLFDLGFQLNV  165 (219)
Q Consensus       141 ----------gGis~~ELN~LE~~FL~lLdf~L~V  165 (219)
                                .....+++-.||+..|..|+|+|.|
T Consensus       109 ~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~Fdl~V  143 (143)
T d2ivxa1         109 EPLLDTKCDAYLQQTRELVILETIMLQTLGFEITI  143 (143)
T ss_dssp             SCCCCTTSHHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             chhhhhchhhhHHHHHHHHHHHHHHHHHcCCeeeC
Confidence                      0124678999999999999999976

>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.04  E-value=0.06  Score=37.36  Aligned_cols=90  Identities=8%  Similarity=-0.012  Sum_probs=76.9

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMN  149 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~ELN  149 (219)
                      -...+.|+....++++.+.=-|..+..+.....  + ....++.-+..+|+-+|.+. .+.+.+-+..++++|++..+++
T Consensus         5 a~~~I~~~~~~L~L~~~i~~~A~~i~~~~~~~~--~-~~Gr~~~~i~AA~iY~acr~-~~~p~t~~eIa~~~~i~~~~i~   80 (95)
T d1vola1           5 AFKEITTMADRINLPRNKVDRTNNLFRQAYEQK--S-LKGRANDAIASACLYIACRQ-EGVPRTFKEICAVSRISKKEIG   80 (95)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTC--C-CTTSCHHHHHHHHHHHHHHH-TTCCCCHHHHHTTTCSCHHHHH
T ss_pred             HHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhh--h-hcCCChHHHHHHHHHHHHHH-cCCCCCHHHHHHHhCCCHHHHH
Confidence            356799999999999999999988888887752  2 34568888999999999995 4678888999999999999999


Q ss_pred             HHHHHHHHhcCCce
Q 027733          150 LLEVDFLFDLGFQL  163 (219)
Q Consensus       150 ~LE~~FL~lLdf~L  163 (219)
                      +.-+.+.+.|+.++
T Consensus        81 k~~k~i~~~L~~~v   94 (95)
T d1vola1          81 RCFKLILKALETSV   94 (95)
T ss_dssp             HHHHHHHHHTTCCC
T ss_pred             HHHHHHHHHHCCcC
Confidence            99999999998765

>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=95.96  E-value=0.031  Score=39.02  Aligned_cols=90  Identities=10%  Similarity=0.063  Sum_probs=74.9

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHHHH
Q 027733           71 HSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNL  150 (219)
Q Consensus        71 ~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~ELN~  150 (219)
                      .+|+.|+....+++....=.|..+..+....  + .+...++.-+..+|+-+|.+.. +...+-+..++++|+|..++++
T Consensus         4 ~d~I~R~~~~L~L~~~i~~~A~~i~~~~~~~--~-~~~Gr~p~~vaAA~iY~a~r~~-~~~~t~~eIa~~~~vs~~tI~~   79 (95)
T d1aisb2           4 TDYVNKFADELGLSEKVRRRAIEILDEAYKR--G-LTSGKSPAGLVAAALYIASLLE-GEKRTQREVAEVARVTEVTVRN   79 (95)
T ss_dssp             GGGHHHHHHHHTCCHHHHHHHHHHHHHHHHT--T-CCTTSCHHHHHHHHHHHHHHHT-TCCCCHHHHHHHHTCCHHHHHH
T ss_pred             HHHHHHHHHHcCcCHHHHHHHHHHHHHHHHc--C-CcCCCcHHhHHHHHHHHHHHHc-CCCcCHHHHHHHHCCCHHHHHH
Confidence            4899999999999999888887666666653  2 2456788899999999999876 4557888999999999999999


Q ss_pred             HHHHHHHhcCCcee
Q 027733          151 LEVDFLFDLGFQLN  164 (219)
Q Consensus       151 LE~~FL~lLdf~L~  164 (219)
                      -=+.+...++.++=
T Consensus        80 ~yk~l~~~l~~~~p   93 (95)
T d1aisb2          80 RYKELVEKLKIKVP   93 (95)
T ss_dssp             HHHHHHHHHTCCCC
T ss_pred             HHHHHHHHhCCCCC
Confidence            99999998887653

>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=95.41  E-value=0.12  Score=35.96  Aligned_cols=86  Identities=14%  Similarity=0.087  Sum_probs=72.3

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHHHH
Q 027733           71 HSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMNL  150 (219)
Q Consensus        71 ~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~ELN~  150 (219)
                      ...|.|+....+++..+.=-|.-+..+.....  + ....++.-+..+|+-+|.+.. +.+.+-+..|++.|++..++.+
T Consensus         6 ~~~I~~~~~~L~L~~~i~~~A~~i~k~~~~~~--~-~~g~~~~~iaaA~iY~Acr~~-~~~~t~~eIa~~~~is~~ti~k   81 (98)
T d1aisb1           6 LSELDRITAQLKLPRHVEEEAARLYREAVRKG--L-IRGRSIESVMAACVYAACRLL-KVPRTLDEIADIARVDKKEIGR   81 (98)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTT--T-TTTCCHHHHHHHHHHHHHHHH-TCCCCHHHHHHHTTSCHHHHHH
T ss_pred             HHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhh--h-hcCCCHHHHHHHHHHHHHHHc-CCCCCHHHHHHHHCCCHHHHHH
Confidence            45689999999999998888887777776642  2 345678889999999999866 7778889999999999999999


Q ss_pred             HHHHHHHhcC
Q 027733          151 LEVDFLFDLG  160 (219)
Q Consensus       151 LE~~FL~lLd  160 (219)
                      ..+.++..|+
T Consensus        82 ~yk~i~~~L~   91 (98)
T d1aisb1          82 SYRFIARNLN   91 (98)
T ss_dssp             HHHHHHHHTT
T ss_pred             HHHHHHHHcC
Confidence            9999999876

>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.69  E-value=0.05  Score=38.90  Aligned_cols=83  Identities=5%  Similarity=0.028  Sum_probs=68.3

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhhCCCCCCCCccHHHHHHHHHHHHhhhcccCCcccchhhhccCCCHHHHH
Q 027733           70 IHSYLERIFKYANCSPSCFVVAYVYLDRFAQKQPSLPINSFNVHRLLITSVLVSAKFMDDIYYNNAFYAKVGGISTTEMN  149 (219)
Q Consensus        70 i~~yl~rI~~~~~~s~~~~l~ALiYIdRL~~~~p~~~i~~~n~hRL~ltalilAsK~ldD~~~sN~~~AkVgGis~~ELN  149 (219)
                      -.+|+.|+....+++..+.=.|..+..++.+..  + ....++.-+..+|+-+|++. .+...+-+..|+++|++..+++
T Consensus         4 ~~d~i~Rf~s~L~L~~~i~~~A~~i~~~~~~~~--~-~~Gr~p~~iaAa~iY~a~r~-~~~~~t~~eIa~~~~vs~~tI~   79 (109)
T d1vola2           4 TGDFMSRFCSNLCLPKQVQMAATHIARKAVELD--L-VPGRSPISVAAAAIYMASQA-SAEKRTQKEIGDIAGVADVTIR   79 (109)
T ss_dssp             GGGTHHHHHHHHTCCHHHHHHHHHHHHHHHHTT--C-STTCCHHHHHHHHHHHHHHT-SSSCCCHHHHHHHHTCCHHHHH
T ss_pred             HHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcC--C-cCCCCHHHHHHHHHHHHHHH-cCCCCCHHHHHHHHCCCHHHHH
Confidence            368999999999999998888888888877753  2 45688889999999999985 4567788999999999999998


Q ss_pred             HHHHHHH
Q 027733          150 LLEVDFL  156 (219)
Q Consensus       150 ~LE~~FL  156 (219)
                      +.=+.+.
T Consensus        80 k~yk~l~   86 (109)
T d1vola2          80 QSYRLIY   86 (109)
T ss_dssp             HHHHHHG
T ss_pred             HHHHHHH
Confidence            7665553