Citrus Sinensis ID: 041949

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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-------220-----
Protein Sequence
MAVASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSIGGGYHIERTLRCAEEIKSRQTEDRIFNHIARLTL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHccccccccccEEEEccccHHHHHHHHHHHHHHcccccEEcHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHccHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEcccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccEEccHHHHHHHHHHHHHHHHHHHHccccccHEEEEccccHHHHHHHHHHHHHHcccEEEccHHHHHHHHHHHHHHHHccccccccHHHcccccccccccHHHHHHHHHEHcc
Coil and Loop (DISEMBL)
mavasaslvisprklrsdvysysyendsntpLVISVLASLIERTMARNERIARNCRRAlskdsrsrvfdsheipdmTIQSYLERIFRYTKAGPSVYVVAYVYIDRfcqanpgfrihaTNVHRLLITTIMVASKYVEDLNYRNSYFArvggletnelnKLELDFLFLMGFKMHVNVSVFESYCChlerevsigggyhiERTLRCAEEIKSRQTEDRIFNHIARLTL
Flexible Loop (DISEMBL)
mavasaslvisprklrSDVYSysyendsntplVISVLASLIERTMarneriarncrralskdsrsrvfdsheipdmtiQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSIGGGYHIERTLRCAEEiksrqtedrifnhiarltl
Low Complexity Region (SEG)
MAVASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSIGGGYHIERTLRCAEEIKSRQTEDRIFNHIARLTL
Disordered region (IsUnstruct)
*****************DVYSYSYENDSNTPLVISVLASLIERTMARNERIARNC************FDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSIGGGYHIERTLRCAEEIK******RIFNHI*****
Disordered Region (DISOPRED)
*******************************LVISVLASLIERTMARN************************IPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSI******************************RL**
Disordered Region (DISEMBL)
MAVASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRR*********VFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSIGGGYHIERTLRCAEEIKSRQTEDRIFNHIARLTL
Disordered Region (DISPRO)
*************KLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSIGGGYHIERTLRCAEEIKSRQTEDRIFNHIARLTL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAVASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSIGGGYHIERTLRCAEEIKSRQTEDRIFNHIARLTL
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	225	2.2.26 [Sep-21-2011]
Q9M205	230	Cyclin-U2-2 OS=Arabidopsi	yes	no	0.933	0.913	0.800	4e-97
Q9SHD3	222	Cyclin-U2-1 OS=Arabidopsi	no	no	0.893	0.905	0.815	3e-94
Q7FAT5	217	Cyclin-P2-1 OS=Oryza sati	yes	no	0.857	0.889	0.527	1e-49
O80513	202	Cyclin-U4-1 OS=Arabidopsi	no	no	0.724	0.806	0.467	3e-39
Q9LY16	216	Cyclin-U4-2 OS=Arabidopsi	no	no	0.715	0.745	0.418	1e-36
Q9FKF6	219	Cyclin-U4-3 OS=Arabidopsi	no	no	0.68	0.698	0.422	9e-36
Q75HV0	236	Cyclin-P3-1 OS=Oryza sati	no	no	0.737	0.703	0.397	2e-33
Q7XC35	212	Cyclin-P4-1 OS=Oryza sati	no	no	0.711	0.754	0.428	4e-33
Q9LJ45	210	Cyclin-U1-1 OS=Arabidopsi	no	no	0.724	0.776	0.421	4e-32
Q8LB60	221	Cyclin-U3-1 OS=Arabidopsi	no	no	0.688	0.701	0.396	2e-29

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

 Score =  353 bits (907), Expect = 4e-97,   Method: Compositional matrix adjust.
 Identities = 169/211 (80%), Positives = 187/211 (88%), Gaps = 1/211 (0%)

Query: 1   MAVASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALS 60
           MAV S SL ISPRKLRSD+YSYSY+N+S TPLVISVL+SLI+RT+ RNERI+R    +  
Sbjct: 1   MAV-SNSLTISPRKLRSDLYSYSYQNNSKTPLVISVLSSLIDRTLTRNERISRRALPSSG 59

Query: 61  KDSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNV 120
              ++++FD  EIPDMTIQSYL RIFRYTKAGPSVYVVAYVYIDRFCQ NPGFRI  TNV
Sbjct: 60  AGGKTQIFDCREIPDMTIQSYLGRIFRYTKAGPSVYVVAYVYIDRFCQTNPGFRISLTNV 119

Query: 121 HRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFES 180
           HRLLITTIM+ASKYVEDLNYRNSYFA+VGGLET +LNKLEL+FLFLMGFK+HVNVSVFES
Sbjct: 120 HRLLITTIMIASKYVEDLNYRNSYFAKVGGLETEDLNKLELEFLFLMGFKLHVNVSVFES 179

Query: 181 YCCHLEREVSIGGGYHIERTLRCAEEIKSRQ 211
           YCCHLEREVS GGGY IE+ LRCAEEIKSRQ
Sbjct: 180 YCCHLEREVSFGGGYQIEKALRCAEEIKSRQ 210

Arabidopsis thaliana (taxid: 3702)

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

 Score =  344 bits (882), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 168/206 (81%), Positives = 185/206 (89%), Gaps = 5/206 (2%)

Query: 7   SLVISPRKLRSDVYSYSYENDSNT-PLVISVLASLIERTMARNERIARNCRRALSKDSRS 65
           SL ISPRKLRSD+YSYSY++DSNT PLVISVL+SLIERT+ARNERI+R    +     ++
Sbjct: 3   SLAISPRKLRSDLYSYSYQDDSNTVPLVISVLSSLIERTLARNERISR----SYGGFGKT 58

Query: 66  RVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLI 125
           RVFD  EIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQ N GFRI  TNVHRLLI
Sbjct: 59  RVFDCREIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQNNQGFRISLTNVHRLLI 118

Query: 126 TTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHL 185
           TTIM+ASKYVED+NY+NSYFA+VGGLET +LN LEL+FLFLMGFK+HVNVSVFESYCCHL
Sbjct: 119 TTIMIASKYVEDMNYKNSYFAKVGGLETEDLNNLELEFLFLMGFKLHVNVSVFESYCCHL 178

Query: 186 EREVSIGGGYHIERTLRCAEEIKSRQ 211
           EREVSIGGGY IE+ LRCAEEIKSRQ
Sbjct: 179 EREVSIGGGYQIEKALRCAEEIKSRQ 204

Arabidopsis thaliana (taxid: 3702)

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

 Score =  196 bits (498), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 105/199 (52%), Positives = 138/199 (69%), Gaps = 6/199 (3%)

Query: 10  ISPRKLRSDVYSYSYENDS----NTPLVISVLASLIERTMARNERIARNCRRALSKDSRS 65
           ++  +L SDVY+    +D     +TP+V+SVLASL+ER +ARNER  +          R+
Sbjct: 1   MASTELASDVYALPCGDDGTTALSTPVVVSVLASLLERHIARNER-DQAAAADGEAARRA 59

Query: 66  RVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLI 125
           R FDS  + DM++ ++LER  RY    P VYVVAY Y+DR  + + G R+ + N  RLL 
Sbjct: 60  RAFDSGTVLDMSLHAFLERFSRYANVSPQVYVVAYAYLDRLRRGD-GVRVVSANAQRLLT 118

Query: 126 TTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHL 185
           T I+VASK+VED NY+NSYFA VGGL   EL+ LELDFLFLM F+++V+VSVF+SYC HL
Sbjct: 119 TAILVASKFVEDRNYKNSYFAAVGGLTAAELSSLELDFLFLMQFRLNVSVSVFQSYCRHL 178

Query: 186 EREVSIGGGYHIERTLRCA 204
           EREVS GGGY +ER L+ A
Sbjct: 179 EREVSYGGGYQVERCLKKA 197

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  161 bits (408), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 78/167 (46%), Positives = 114/167 (68%), Gaps = 4/167 (2%)

Query: 25  ENDSNTPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLER 84
           EN S    +I+ L+SL+ER    N+      RR  ++  R  VF     P +TIQSYLER
Sbjct: 5   ENPSVMSKLIAFLSSLLERVAESNDL----TRRVATQSQRVSVFHGLSRPTITIQSYLER 60

Query: 85  IFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSY 144
           IF+Y    PS +VVAYVY+DRF    P   I++ NVHRLLIT++MVA+K+++DL Y N+Y
Sbjct: 61  IFKYANCSPSCFVVAYVYLDRFTHRQPSLPINSFNVHRLLITSVMVAAKFLDDLYYNNAY 120

Query: 145 FARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSI 191
           +A+VGG+ T E+N LELDFLF +GF+++V  + F +Y  +L++E+++
Sbjct: 121 YAKVGGISTKEMNFLELDFLFGLGFELNVTPNTFNAYFSYLQKEMTL 167

Arabidopsis thaliana (taxid: 3702)

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

 Score =  152 bits (385), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 69/165 (41%), Positives = 114/165 (69%), Gaps = 4/165 (2%)

Query: 31  PLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIFRYTK 90
           P VI+ ++SL++R    N+ ++R  R    +  R   F++   P ++I+SY+ERIF+Y  
Sbjct: 21  PNVITAMSSLLQRVSETNDDLSRPFR----EHKRISAFNAVTKPSISIRSYMERIFKYAD 76

Query: 91  AGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGG 150
              S Y+VAY+Y+DRF Q  P   I ++NVHRL+IT+++V++K+++DL Y N+++A+VGG
Sbjct: 77  CSDSCYIVAYIYLDRFIQKQPLLPIDSSNVHRLIITSVLVSAKFMDDLCYNNAFYAKVGG 136

Query: 151 LETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSIGGGY 195
           + T E+N LELDFLF +GF+++V +S +  YC  L+RE+ +   Y
Sbjct: 137 ITTEEMNLLELDFLFGIGFQLNVTISTYNDYCSSLQREMVMRTMY 181

Arabidopsis thaliana (taxid: 3702)

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

 Score =  150 bits (378), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 68/161 (42%), Positives = 109/161 (67%), Gaps = 8/161 (4%)

Query: 31  PLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIFRYTK 90
           P V++ ++ L++R    N+         LS+  +   F     P ++I+SYLERIF Y  
Sbjct: 23  PSVLTAMSYLLQRVSETNDN--------LSQKQKPSSFTGVTKPSISIRSYLERIFEYAN 74

Query: 91  AGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGG 150
              S Y+VAY+Y+DRF +  P   I++ NVHRL+IT+++V++K+++DL+Y N Y+A+VGG
Sbjct: 75  CSYSCYIVAYIYLDRFVKKQPFLPINSFNVHRLIITSVLVSAKFMDDLSYNNEYYAKVGG 134

Query: 151 LETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSI 191
           +   E+N LELDFLF +GF+++V VS F +YCC L+RE+++
Sbjct: 135 ISREEMNMLELDFLFGIGFELNVTVSTFNNYCCFLQREMAM 175

Arabidopsis thaliana (taxid: 3702)

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

 Score =  142 bits (357), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 68/171 (39%), Positives = 118/171 (69%), Gaps = 5/171 (2%)

Query: 21  SYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQS 80
           S S +N++  P V+ +LA+ ++R++ +NE +  + +    KDS S +F  H  PD++I+ 
Sbjct: 26  SQSKKNNTEYPKVLLLLAAYLDRSVQKNEDLLDSNK---IKDS-STIFHGHRAPDLSIKL 81

Query: 81  YLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNY 140
           Y ERIF+Y++  PS +V+A +Y++R+ Q  P   + + +VHRLLIT+++VA+K+ +D  +
Sbjct: 82  YAERIFKYSECSPSCFVLALIYMERYLQ-QPHVYMTSLSVHRLLITSVVVAAKFTDDAFF 140

Query: 141 RNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSI 191
            N+++ARVGG+ T E+N+LELD LF + F++ V++  F SYC  LE+E  +
Sbjct: 141 NNAFYARVGGISTVEMNRLELDLLFNLDFRLKVDLETFGSYCLQLEKETMV 191

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  141 bits (355), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 69/161 (42%), Positives = 102/161 (63%), Gaps = 1/161 (0%)

Query: 30  TPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIFRYT 89
            P V+++L+SL++R   RN+  A          + S  F     P ++I  YLERIFR+ 
Sbjct: 10  VPRVVAILSSLLQRVAERNDAAAAAAAVGEEAAAVS-AFQGLTKPAISIGGYLERIFRFA 68

Query: 90  KAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG 149
              PS YVVAY+Y+DRF +  P   + + NVHRLLIT+++ A K+V+D+ Y N+YFARVG
Sbjct: 69  NCSPSCYVVAYIYLDRFLRRRPALAVDSFNVHRLLITSVLTAVKFVDDICYNNAYFARVG 128

Query: 150 GLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVS 190
           G+   E+N LE+DFLF + F ++V  + F SYC  L+ E++
Sbjct: 129 GISLMEMNYLEVDFLFGIAFDLNVTPAAFASYCAVLQSEMT 169

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  138 bits (347), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 70/166 (42%), Positives = 115/166 (69%), Gaps = 3/166 (1%)

Query: 26  NDSNTPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERI 85
            ++ TP V+++++ ++E+ +ARNE +A+  +    K   +  F     P ++I  YLERI
Sbjct: 20  TEAATPRVLTIISHVMEKLVARNEWLAKQTK-GFGKSLEA--FHGVRAPSISIAKYLERI 76

Query: 86  FRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYF 145
           ++YTK  P+ +VV YVYIDR    +PG  + + NVHRLL+T +M+A+K ++D++Y N ++
Sbjct: 77  YKYTKCSPACFVVGYVYIDRLAHKHPGSLVVSLNVHRLLVTCVMIAAKILDDVHYNNEFY 136

Query: 146 ARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSI 191
           ARVGG+   +LNK+EL+ LFL+ F++ V+  VFESYC HLE+E+ +
Sbjct: 137 ARVGGVSNADLNKMELELLFLLDFRVTVSFRVFESYCFHLEKEMQL 182

Arabidopsis thaliana (taxid: 3702)

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

 Score =  129 bits (324), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 63/159 (39%), Positives = 100/159 (62%), Gaps = 4/159 (2%)

Query: 60  SKDSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATN 119
           S DS + VFD    P+++I  YL+RIF+Y+   PS +V+A++YID F        +   N
Sbjct: 58  SPDSVT-VFDGRSPPEISIAHYLDRIFKYSCCSPSCFVIAHIYIDHFLHKTRAL-LKPLN 115

Query: 120 VHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFE 179
           VHRL+ITT+M+A+K  +D  + N+Y+ARVGG+ T ELN+LE++ LF + FK+ V+   F 
Sbjct: 116 VHRLIITTVMLAAKVFDDRYFNNAYYARVGGVTTRELNRLEMELLFTLDFKLQVDPQTFH 175

Query: 180 SYCCHLEREVSIGGG--YHIERTLRCAEEIKSRQTEDRI 216
           ++CC LE++   G    + I+   R  +E   ++T D +
Sbjct: 176 THCCQLEKQNRDGFQIEWPIKEACRANKETWQKRTPDSL 214

Arabidopsis thaliana (taxid: 3702)

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	225
224063681	223	predicted protein [Populus trichocarpa]	0.991	1.0	0.838	1e-109
224129942	223	predicted protein [Populus trichocarpa]	0.991	1.0	0.829	1e-108
255541168	224	Nuc-1 negative regulatory protein preg,	0.991	0.995	0.843	1e-107
225453521	229	PREDICTED: cyclin-U2-1 [Vitis vinifera]	0.973	0.956	0.821	1e-102
217072958	224	unknown [Medicago truncatula] gi|3885225	0.991	0.995	0.781	2e-98
297817366	227	CYCP3_2 [Arabidopsis lyrata subsp. lyrat	0.995	0.986	0.754	2e-95
15232360	230	cyclin-U2-2 [Arabidopsis thaliana] gi|75	0.933	0.913	0.800	2e-95
297824545	222	CYCP3_1 [Arabidopsis lyrata subsp. lyrat	0.893	0.905	0.820	1e-92
15225402	222	cyclin-U2-1 [Arabidopsis thaliana] gi|75	0.893	0.905	0.815	2e-92
356496316	224	PREDICTED: cyclin-U2-1-like [Glycine max	0.986	0.991	0.783	2e-91

>gi|224063681|ref|XP_002301262.1| predicted protein [Populus trichocarpa] gi|222842988|gb|EEE80535.1| predicted protein [Populus trichocarpa]

 Score =  398 bits (1023), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 187/223 (83%), Positives = 208/223 (93%)

Query: 3   VASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALSKD 62
           +A++SL ISPRKLRSD+YSYSY+NDSNTPLVISVLASLIERTMARNERI +NC  ALSKD
Sbjct: 1   MATSSLAISPRKLRSDLYSYSYQNDSNTPLVISVLASLIERTMARNERIVKNCTWALSKD 60

Query: 63  SRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHR 122
            R+RVFD HE PD+TIQSYLER+FRYT+AGPSVYVVAYVYIDRFCQANPGFRI++ NVHR
Sbjct: 61  IRTRVFDCHETPDLTIQSYLERVFRYTRAGPSVYVVAYVYIDRFCQANPGFRINSRNVHR 120

Query: 123 LLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYC 182
           LLITTIMVASKYVED+NYRNSYFARVGGL TNELNKLEL+F+FLMGFK+HVNVSVFESYC
Sbjct: 121 LLITTIMVASKYVEDMNYRNSYFARVGGLTTNELNKLELEFVFLMGFKLHVNVSVFESYC 180

Query: 183 CHLEREVSIGGGYHIERTLRCAEEIKSRQTEDRIFNHIARLTL 225
           CHLEREV IGGGYHIE+TLRCAEEIKS Q E++ +N IAR+ L
Sbjct: 181 CHLEREVGIGGGYHIEKTLRCAEEIKSGQQEEKRYNQIARIML 223

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224129942|ref|XP_002320709.1| predicted protein [Populus trichocarpa] gi|222861482|gb|EEE99024.1| predicted protein [Populus trichocarpa]

 Score =  395 bits (1016), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 185/223 (82%), Positives = 207/223 (92%)

Query: 3   VASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALSKD 62
           +A++SL ISPRKLRSD+YSYSY+NDSNTPLVI+VLASLIERTMARNERI +NC  ALSKD
Sbjct: 1   MATSSLAISPRKLRSDLYSYSYQNDSNTPLVIAVLASLIERTMARNERIVKNCTWALSKD 60

Query: 63  SRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHR 122
           +R+RVFD HE PD+TIQSYLERIFRYT+AGPSVYVVAYVYIDRFCQANP FRI+A NVHR
Sbjct: 61  TRTRVFDCHETPDLTIQSYLERIFRYTRAGPSVYVVAYVYIDRFCQANPEFRINARNVHR 120

Query: 123 LLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYC 182
           LLITTIMVASKYVED+NYRNSYFARVGGL  N +NK+EL+FLFLMGFK+HVNVSVFESYC
Sbjct: 121 LLITTIMVASKYVEDMNYRNSYFARVGGLTANVMNKMELEFLFLMGFKLHVNVSVFESYC 180

Query: 183 CHLEREVSIGGGYHIERTLRCAEEIKSRQTEDRIFNHIARLTL 225
           CHLEREV IGGGYHIE+TLRCAEEIKSRQ E++ +N IAR+ L
Sbjct: 181 CHLEREVGIGGGYHIEKTLRCAEEIKSRQQEEKGYNQIARIML 223

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255541168|ref|XP_002511648.1| Nuc-1 negative regulatory protein preg, putative [Ricinus communis] gi|223548828|gb|EEF50317.1| Nuc-1 negative regulatory protein preg, putative [Ricinus communis]

 Score =  394 bits (1012), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 189/224 (84%), Positives = 206/224 (91%), Gaps = 1/224 (0%)

Query: 3   VASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALSKD 62
           +A++SL ISPRKLRSD+YSYSY+NDS+ PLVISVLASLIERTMARNERIA+NC  ALSKD
Sbjct: 1   MAASSLAISPRKLRSDLYSYSYQNDSSIPLVISVLASLIERTMARNERIAKNCSWALSKD 60

Query: 63  SRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHR 122
            ++RVFD +E PDMTIQSYLERIFRYT+ GPSVYVVAYVYIDRFCQANPGFRI A NVHR
Sbjct: 61  IKTRVFDCYETPDMTIQSYLERIFRYTRTGPSVYVVAYVYIDRFCQANPGFRISARNVHR 120

Query: 123 LLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYC 182
           LLITT+MVASKYVED+NYRNSYFARVGGL TNELNKLEL+FLF+MGFKMHVNVSVFESYC
Sbjct: 121 LLITTVMVASKYVEDMNYRNSYFARVGGLTTNELNKLELEFLFMMGFKMHVNVSVFESYC 180

Query: 183 CHLEREVSIGGGYHIERTLRCAEEIKSRQTED-RIFNHIARLTL 225
            HLEREVSIGGGYHIE+TLRCAEEIKS QTED R  N IAR+ L
Sbjct: 181 SHLEREVSIGGGYHIEKTLRCAEEIKSGQTEDKRYINQIARIML 224

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453521|ref|XP_002275585.1| PREDICTED: cyclin-U2-1 [Vitis vinifera] gi|297734540|emb|CBI16591.3| unnamed protein product [Vitis vinifera]

 Score =  376 bits (965), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 180/219 (82%), Positives = 200/219 (91%)

Query: 7   SLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALSKDSRSR 66
           +L ISPRKLR+D+YSYSY+ DSNTPLVISVLASLIERTMARNERIA+N  R LS+  R+ 
Sbjct: 11  ALTISPRKLRTDLYSYSYQEDSNTPLVISVLASLIERTMARNERIAKNSPRGLSRYLRTG 70

Query: 67  VFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLIT 126
           VFD HE PDMTIQSYLERIFRYT+AGPSVYVVAYVYIDRFCQ NPGFRI A+NVH LLIT
Sbjct: 71  VFDCHETPDMTIQSYLERIFRYTRAGPSVYVVAYVYIDRFCQINPGFRISASNVHGLLIT 130

Query: 127 TIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLE 186
           TIMVASKYVED+NYRNSY+ARVGGL TNE+N+LE++FLFLMGFK+HVNVSVFESYC HLE
Sbjct: 131 TIMVASKYVEDMNYRNSYYARVGGLTTNEMNELEVEFLFLMGFKLHVNVSVFESYCSHLE 190

Query: 187 REVSIGGGYHIERTLRCAEEIKSRQTEDRIFNHIARLTL 225
           REVSIGGGYHIE+TLRCAEEIKSRQ  +R +N IAR+TL
Sbjct: 191 REVSIGGGYHIEKTLRCAEEIKSRQIVERRYNRIARVTL 229

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217072958|gb|ACJ84839.1| unknown [Medicago truncatula] gi|388522547|gb|AFK49335.1| unknown [Medicago truncatula]

 Score =  364 bits (934), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 175/224 (78%), Positives = 198/224 (88%), Gaps = 1/224 (0%)

Query: 3   VASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALSKD 62
           +AS+SL ISPRKLRSDVYS+SY+ DS+TPLVI+VLASLIER MAR +RI +NC R+LSK 
Sbjct: 1   MASSSLTISPRKLRSDVYSFSYQQDSSTPLVINVLASLIERNMARTKRIVKNCSRSLSKA 60

Query: 63  SRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHR 122
             + +FD  EIPD+TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQ NPGFRI+A NVHR
Sbjct: 61  ISTNIFDCREIPDLTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQINPGFRINARNVHR 120

Query: 123 LLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYC 182
           LLITTIMVASKYVEDLNYRNSYF RVGGL T+E+NKLEL+FLF+MGFK+HVNVSVFESYC
Sbjct: 121 LLITTIMVASKYVEDLNYRNSYFGRVGGLTTSEINKLELEFLFMMGFKLHVNVSVFESYC 180

Query: 183 CHLEREVSIGGGYHIERTLRCAEEIKSRQTED-RIFNHIARLTL 225
            HLEREV IGGGYHIE+TLRCAEEIK+R  E+ R +  I R+ L
Sbjct: 181 SHLEREVGIGGGYHIEKTLRCAEEIKARHREEIRGYAQIPRVML 224

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297817366|ref|XP_002876566.1| CYCP3_2 [Arabidopsis lyrata subsp. lyrata] gi|297322404|gb|EFH52825.1| CYCP3_2 [Arabidopsis lyrata subsp. lyrata]

 Score =  353 bits (907), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 172/228 (75%), Positives = 196/228 (85%), Gaps = 4/228 (1%)

Query: 1   MAVASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALS 60
           MAV S SL ISPRKLRSD+YSYSY+N+S TPLVISVL+SLI+RT+ RNERI+R    +  
Sbjct: 1   MAV-SNSLTISPRKLRSDLYSYSYQNNSETPLVISVLSSLIDRTLTRNERISRRALPSSG 59

Query: 61  KDSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNV 120
              ++++FD  EIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQ NP FRI  TNV
Sbjct: 60  AGGKTQIFDCREIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQTNPSFRISLTNV 119

Query: 121 HRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFES 180
           HRLLITTIM+ASKYVEDLNYRNSYFA+VGGLET +LNKLEL+FLFLMGFK+HVNV+VFES
Sbjct: 120 HRLLITTIMIASKYVEDLNYRNSYFAKVGGLETEDLNKLELEFLFLMGFKLHVNVTVFES 179

Query: 181 YCCHLEREVSIGGGYHIERTLRCAEEIKSRQ---TEDRIFNHIARLTL 225
           YCCHLEREVSIGGGY IE+ LRCAEEIKS+Q    + +  +H AR+ L
Sbjct: 180 YCCHLEREVSIGGGYQIEKALRCAEEIKSKQMIVQDPKHHHHFARILL 227

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15232360|ref|NP_191614.1| cyclin-U2-2 [Arabidopsis thaliana] gi|75311794|sp|Q9M205.1|CCU22_ARATH RecName: Full=Cyclin-U2-2; Short=CycU2;2; AltName: Full=Cyclin-P3.2; Short=CycP3;2 gi|7288003|emb|CAB81841.1| regulatory protein-like [Arabidopsis thaliana] gi|45825149|gb|AAS77482.1| At3g60550 [Arabidopsis thaliana] gi|332646557|gb|AEE80078.1| cyclin-U2-2 [Arabidopsis thaliana]

 Score =  353 bits (907), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 169/211 (80%), Positives = 187/211 (88%), Gaps = 1/211 (0%)

Query: 1   MAVASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALS 60
           MAV S SL ISPRKLRSD+YSYSY+N+S TPLVISVL+SLI+RT+ RNERI+R    +  
Sbjct: 1   MAV-SNSLTISPRKLRSDLYSYSYQNNSKTPLVISVLSSLIDRTLTRNERISRRALPSSG 59

Query: 61  KDSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNV 120
              ++++FD  EIPDMTIQSYL RIFRYTKAGPSVYVVAYVYIDRFCQ NPGFRI  TNV
Sbjct: 60  AGGKTQIFDCREIPDMTIQSYLGRIFRYTKAGPSVYVVAYVYIDRFCQTNPGFRISLTNV 119

Query: 121 HRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFES 180
           HRLLITTIM+ASKYVEDLNYRNSYFA+VGGLET +LNKLEL+FLFLMGFK+HVNVSVFES
Sbjct: 120 HRLLITTIMIASKYVEDLNYRNSYFAKVGGLETEDLNKLELEFLFLMGFKLHVNVSVFES 179

Query: 181 YCCHLEREVSIGGGYHIERTLRCAEEIKSRQ 211
           YCCHLEREVS GGGY IE+ LRCAEEIKSRQ
Sbjct: 180 YCCHLEREVSFGGGYQIEKALRCAEEIKSRQ 210

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297824545|ref|XP_002880155.1| CYCP3_1 [Arabidopsis lyrata subsp. lyrata] gi|297325994|gb|EFH56414.1| CYCP3_1 [Arabidopsis lyrata subsp. lyrata]

 Score =  345 bits (884), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 169/206 (82%), Positives = 185/206 (89%), Gaps = 5/206 (2%)

Query: 7   SLVISPRKLRSDVYSYSYENDSNT-PLVISVLASLIERTMARNERIARNCRRALSKDSRS 65
           SL ISPRKLRSD+YSYSY++DSNT PLVISVL+SLIERT+ARNERI+R    +     ++
Sbjct: 3   SLAISPRKLRSDLYSYSYQDDSNTVPLVISVLSSLIERTLARNERISR----SYGGFGKT 58

Query: 66  RVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLI 125
           RVFD  EIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQ N GFRI  TNVHRLLI
Sbjct: 59  RVFDCREIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQNNQGFRISLTNVHRLLI 118

Query: 126 TTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHL 185
           TTIM+ASKYVED+NYRNSYFA+VGGLET +LN LEL+FLFLMGFK+HVNVSVFESYCCHL
Sbjct: 119 TTIMIASKYVEDMNYRNSYFAKVGGLETEDLNNLELEFLFLMGFKLHVNVSVFESYCCHL 178

Query: 186 EREVSIGGGYHIERTLRCAEEIKSRQ 211
           EREVSIGGGY IE+ LRCAEEIKSRQ
Sbjct: 179 EREVSIGGGYQIEKALRCAEEIKSRQ 204

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15225402|ref|NP_182034.1| cyclin-U2-1 [Arabidopsis thaliana] gi|75313451|sp|Q9SHD3.1|CCU21_ARATH RecName: Full=Cyclin-U2-1; Short=CycU2;1; AltName: Full=Cyclin-P3.1; Short=CycP3;1 gi|18491283|gb|AAL69466.1| At2g45080/T14P1.11 [Arabidopsis thaliana] gi|330255412|gb|AEC10506.1| cyclin-U2-1 [Arabidopsis thaliana]

 Score =  344 bits (882), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 168/206 (81%), Positives = 185/206 (89%), Gaps = 5/206 (2%)

Query: 7   SLVISPRKLRSDVYSYSYENDSNT-PLVISVLASLIERTMARNERIARNCRRALSKDSRS 65
           SL ISPRKLRSD+YSYSY++DSNT PLVISVL+SLIERT+ARNERI+R    +     ++
Sbjct: 3   SLAISPRKLRSDLYSYSYQDDSNTVPLVISVLSSLIERTLARNERISR----SYGGFGKT 58

Query: 66  RVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLI 125
           RVFD  EIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQ N GFRI  TNVHRLLI
Sbjct: 59  RVFDCREIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQNNQGFRISLTNVHRLLI 118

Query: 126 TTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHL 185
           TTIM+ASKYVED+NY+NSYFA+VGGLET +LN LEL+FLFLMGFK+HVNVSVFESYCCHL
Sbjct: 119 TTIMIASKYVEDMNYKNSYFAKVGGLETEDLNNLELEFLFLMGFKLHVNVSVFESYCCHL 178

Query: 186 EREVSIGGGYHIERTLRCAEEIKSRQ 211
           EREVSIGGGY IE+ LRCAEEIKSRQ
Sbjct: 179 EREVSIGGGYQIEKALRCAEEIKSRQ 204

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496316|ref|XP_003517014.1| PREDICTED: cyclin-U2-1-like [Glycine max]

 Score =  340 bits (873), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 174/222 (78%), Positives = 198/222 (89%)

Query: 4   ASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALSKDS 63
           +S++L ISPRKLR D+YSYSY+ DSNTPLVI+VLASLIER+MAR +RI +NC  ALSK  
Sbjct: 3   SSSTLTISPRKLRYDLYSYSYKEDSNTPLVINVLASLIERSMARTQRIVKNCSNALSKVI 62

Query: 64  RSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRL 123
            + +FD  EIPDMTI+SYLERIFRYT+AGPSVYVVAYVYIDRFCQ NPGFRI+  NVHRL
Sbjct: 63  STNIFDCREIPDMTIESYLERIFRYTRAGPSVYVVAYVYIDRFCQNNPGFRINTRNVHRL 122

Query: 124 LITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCC 183
           LITTIMVASKYVED+N+RNSYFARVGGL TNELN+LEL+FLFLMGFK+HVNVSVFESYCC
Sbjct: 123 LITTIMVASKYVEDMNFRNSYFARVGGLRTNELNELELEFLFLMGFKLHVNVSVFESYCC 182

Query: 184 HLEREVSIGGGYHIERTLRCAEEIKSRQTEDRIFNHIARLTL 225
           HLEREVSIGGGYHIERTLRCAEEIK++  E+R +  I R+ L
Sbjct: 183 HLEREVSIGGGYHIERTLRCAEEIKAKNIEERGYTQITRVML 224

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	225
TAIR|locus:2103391	230	CYCP3;2 "cyclin p3;2" [Arabido	0.933	0.913	0.796	1.1e-87
TAIR|locus:2055552	222	cycp3;1 "cyclin p3;1" [Arabido	0.928	0.941	0.790	6.9e-86
TAIR|locus:2042421	202	CYCP4;1 "AT2G44740" [Arabidops	0.724	0.806	0.467	8e-37
TAIR|locus:2088743	210	CYCP2;1 "cyclin p2;1" [Arabido	0.72	0.771	0.424	4.4e-36
TAIR|locus:2183394	216	CYCP4;3 "cyclin p4;3" [Arabido	0.688	0.717	0.427	2.2e-34
TAIR|locus:2151656	219	CYCP4;2 "CYCLIN P4;2" [Arabido	0.68	0.698	0.422	9.5e-34
TAIR|locus:2099192	221	CYCP1;1 "cyclin p1;1" [Arabido	0.911	0.927	0.354	8.8e-31
TAIR|locus:1009023243	212	AT3G05327 [Arabidopsis thalian	0.706	0.75	0.361	5.2e-26
DICTYBASE|DDB_G0277391	798	DDB_G0277391 "cyclin-related 2	0.657	0.185	0.324	1.5e-23
DICTYBASE|DDB_G0286485	398	DDB_G0286485 "PHO85 cyclin-2"	0.644	0.364	0.333	1.4e-21

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

 Score = 876 (313.4 bits), Expect = 1.1e-87, P = 1.1e-87
 Identities = 168/211 (79%), Positives = 188/211 (89%)

Query:     1 MAVASASLVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALS 60
             MAV++ SL ISPRKLRSD+YSYSY+N+S TPLVISVL+SLI+RT+ RNERI+R    +  
Sbjct:     1 MAVSN-SLTISPRKLRSDLYSYSYQNNSKTPLVISVLSSLIDRTLTRNERISRRALPSSG 59

Query:    61 KDSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNV 120
                ++++FD  EIPDMTIQSYL RIFRYTKAGPSVYVVAYVYIDRFCQ NPGFRI  TNV
Sbjct:    60 AGGKTQIFDCREIPDMTIQSYLGRIFRYTKAGPSVYVVAYVYIDRFCQTNPGFRISLTNV 119

Query:   121 HRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFES 180
             HRLLITTIM+ASKYVEDLNYRNSYFA+VGGLET +LNKLEL+FLFLMGFK+HVNVSVFES
Sbjct:   120 HRLLITTIMIASKYVEDLNYRNSYFAKVGGLETEDLNKLELEFLFLMGFKLHVNVSVFES 179

Query:   181 YCCHLEREVSIGGGYHIERTLRCAEEIKSRQ 211
             YCCHLEREVS GGGY IE+ LRCAEEIKSRQ
Sbjct:   180 YCCHLEREVSFGGGYQIEKALRCAEEIKSRQ 210

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

 Score = 859 (307.4 bits), Expect = 6.9e-86, P = 6.9e-86
 Identities = 170/215 (79%), Positives = 189/215 (87%)

Query:     7 SLVISPRKLRSDVYSYSYENDSNT-PLVISVLASLIERTMARNERIARNCRRALSKDSRS 65
             SL ISPRKLRSD+YSYSY++DSNT PLVISVL+SLIERT+ARNERI+R+         ++
Sbjct:     3 SLAISPRKLRSDLYSYSYQDDSNTVPLVISVLSSLIERTLARNERISRS----YGGFGKT 58

Query:    66 RVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLI 125
             RVFD  EIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQ N GFRI  TNVHRLLI
Sbjct:    59 RVFDCREIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQNNQGFRISLTNVHRLLI 118

Query:   126 TTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHL 185
             TTIM+ASKYVED+NY+NSYFA+VGGLET +LN LEL+FLFLMGFK+HVNVSVFESYCCHL
Sbjct:   119 TTIMIASKYVEDMNYKNSYFAKVGGLETEDLNNLELEFLFLMGFKLHVNVSVFESYCCHL 178

Query:   186 EREVSIGGGYHIERTLRCAEEIKSRQ-TEDRIFNH 219
             EREVSIGGGY IE+ LRCAEEIKSRQ  +D   +H
Sbjct:   179 EREVSIGGGYQIEKALRCAEEIKSRQIVQDPKHHH 213

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

 Score = 396 (144.5 bits), Expect = 8.0e-37, P = 8.0e-37
 Identities = 78/167 (46%), Positives = 114/167 (68%)

Query:    25 ENDSNTPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLER 84
             EN S    +I+ L+SL+ER    N+      RR  ++  R  VF     P +TIQSYLER
Sbjct:     5 ENPSVMSKLIAFLSSLLERVAESNDLT----RRVATQSQRVSVFHGLSRPTITIQSYLER 60

Query:    85 IFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSY 144
             IF+Y    PS +VVAYVY+DRF    P   I++ NVHRLLIT++MVA+K+++DL Y N+Y
Sbjct:    61 IFKYANCSPSCFVVAYVYLDRFTHRQPSLPINSFNVHRLLITSVMVAAKFLDDLYYNNAY 120

Query:   145 FARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSI 191
             +A+VGG+ T E+N LELDFLF +GF+++V  + F +Y  +L++E+++
Sbjct:   121 YAKVGGISTKEMNFLELDFLFGLGFELNVTPNTFNAYFSYLQKEMTL 167

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

 Score = 389 (142.0 bits), Expect = 4.4e-36, P = 4.4e-36
 Identities = 70/165 (42%), Positives = 115/165 (69%)

Query:    27 DSNTPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIF 86
             ++ TP V+++++ ++E+ +ARNE +A+  +    K   +  F     P ++I  YLERI+
Sbjct:    21 EAATPRVLTIISHVMEKLVARNEWLAKQTK-GFGKSLEA--FHGVRAPSISIAKYLERIY 77

Query:    87 RYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFA 146
             +YTK  P+ +VV YVYIDR    +PG  + + NVHRLL+T +M+A+K ++D++Y N ++A
Sbjct:    78 KYTKCSPACFVVGYVYIDRLAHKHPGSLVVSLNVHRLLVTCVMIAAKILDDVHYNNEFYA 137

Query:   147 RVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSI 191
             RVGG+   +LNK+EL+ LFL+ F++ V+  VFESYC HLE+E+ +
Sbjct:   138 RVGGVSNADLNKMELELLFLLDFRVTVSFRVFESYCFHLEKEMQL 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:2183394 CYCP4;3 "cyclin p4;3" [Arabidopsis thaliana (taxid:3702)]

 Score = 373 (136.4 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 68/159 (42%), Positives = 112/159 (70%)

Query:    31 PLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIFRYTK 90
             P VI+ ++SL++R    N+ ++R  R    +  R   F++   P ++I+SY+ERIF+Y  
Sbjct:    21 PNVITAMSSLLQRVSETNDDLSRPFR----EHKRISAFNAVTKPSISIRSYMERIFKYAD 76

Query:    91 AGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGG 150
                S Y+VAY+Y+DRF Q  P   I ++NVHRL+IT+++V++K+++DL Y N+++A+VGG
Sbjct:    77 CSDSCYIVAYIYLDRFIQKQPLLPIDSSNVHRLIITSVLVSAKFMDDLCYNNAFYAKVGG 136

Query:   151 LETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREV 189
             + T E+N LELDFLF +GF+++V +S +  YC  L+RE+
Sbjct:   137 ITTEEMNLLELDFLFGIGFQLNVTISTYNDYCSSLQREM 175

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 = 367 (134.2 bits), Expect = 9.5e-34, P = 9.5e-34
 Identities = 68/161 (42%), Positives = 109/161 (67%)

Query:    31 PLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIFRYTK 90
             P V++ ++ L++R    N+         LS+  +   F     P ++I+SYLERIF Y  
Sbjct:    23 PSVLTAMSYLLQRVSETNDN--------LSQKQKPSSFTGVTKPSISIRSYLERIFEYAN 74

Query:    91 AGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGG 150
                S Y+VAY+Y+DRF +  P   I++ NVHRL+IT+++V++K+++DL+Y N Y+A+VGG
Sbjct:    75 CSYSCYIVAYIYLDRFVKKQPFLPINSFNVHRLIITSVLVSAKFMDDLSYNNEYYAKVGG 134

Query:   151 LETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSI 191
             +   E+N LELDFLF +GF+++V VS F +YCC L+RE+++
Sbjct:   135 ISREEMNMLELDFLFGIGFELNVTVSTFNNYCCFLQREMAM 175

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

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 77/217 (35%), Positives = 121/217 (55%)

Query:     7 SLVISPRKLRSDVY---SYSYEND--SNTPLVISVLASLIERTMARNERIARNCRRALSK 61
             SL   P  + SDVY       E       P V+S L+S +ER++  N     + +  L  
Sbjct:     3 SLATDPAFIDSDVYLRLGLIIEGKRLKKPPTVLSRLSSSLERSLLLNH----DDKILLGS 58

Query:    62 DSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVH 121
                  VFD    P+++I  YL+RIF+Y+   PS +V+A++YID F        +   NVH
Sbjct:    59 PDSVTVFDGRSPPEISIAHYLDRIFKYSCCSPSCFVIAHIYIDHFLHKTRAL-LKPLNVH 117

Query:   122 RLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESY 181
             RL+ITT+M+A+K  +D  + N+Y+ARVGG+ T ELN+LE++ LF + FK+ V+   F ++
Sbjct:   118 RLIITTVMLAAKVFDDRYFNNAYYARVGGVTTRELNRLEMELLFTLDFKLQVDPQTFHTH 177

Query:   182 CCHLEREVSIGGG--YHIERTLRCAEEIKSRQTEDRI 216
             CC LE++   G    + I+   R  +E   ++T D +
Sbjct:   178 CCQLEKQNRDGFQIEWPIKEACRANKETWQKRTPDSL 214

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:1009023243 AT3G05327 [Arabidopsis thaliana (taxid:3702)]

 Score = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 60/166 (36%), Positives = 102/166 (61%)

Query:    27 DSNTPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIF 86
             DS  P VI++LAS +E+ + +N++   + R   +K     +F   + P ++I  Y ERI 
Sbjct:    27 DSTPPRVITLLASTLEKMIQKNKK-KFHTRH--NKADEITMFHGSKAPSLSIYRYTERIH 83

Query:    87 RYTKAGPSVYVVAYVYIDRFCQ----ANPGFRIHATNVHRLLITTIMVASKYVEDLNYRN 142
             RY +  P  +V A+ YI R+ Q     +   R+ + NVHRLLIT+++VA+K++E   Y N
Sbjct:    84 RYAQCSPVCFVAAFAYILRYLQRPEATSTARRLTSLNVHRLLITSLLVAAKFLERQCYNN 143

Query:   143 SYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLERE 188
             +Y+A++GG+ T E+N+LE  FL  + F++++    FE +C  L++E
Sbjct:   144 AYYAKIGGVSTEEMNRLERTFLVDVDFRLYITTETFEKHCLMLQKE 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_G0277391 DDB_G0277391 "cyclin-related 2 family protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 281 (104.0 bits), Expect = 1.5e-23, P = 1.5e-23
 Identities = 48/148 (32%), Positives = 94/148 (63%)

Query:    44 TMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYI 103
             T A     ++    +LS   + +VF+  +IP+++I++Y+ER+F+Y   G  +++ + +Y+
Sbjct:   320 TTATTTTTSKTATSSLSTIEKFQVFNVDQIPEISIEAYIERVFKYLPFGTDIFIFSTIYL 379

Query:   104 DRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDF 163
             DR  Q N   +I   N+HRL + +I+VASK+  D    N Y+A+VGG+   E+N+LE+ F
Sbjct:   380 DRLIQWNQEIQISPLNIHRLFMASIIVASKFHNDKALNNRYYAQVGGISLFEMNQLEIHF 439

Query:   164 LFLMGFKMHVNVSVFESYCCHLEREVSI 191
             L L+ +K+H++  +F+++   ++ ++ I
Sbjct:   440 LLLLNWKLHIDPEIFDAFKTSIQSKIDI 467

GO:0006972 "hyperosmotic response" evidence=IEP

GO:0019901 "protein kinase binding" evidence=IEA

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

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

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

 Score = 254 (94.5 bits), Expect = 1.4e-21, P = 1.4e-21
 Identities = 51/153 (33%), Positives = 93/153 (60%)

Query:    36 VLASLIERTMARNERIARNCRRALSKDSRSRVFDSH-EIPDMTIQSYLERIFRYTKAGPS 94
             +L SL+   MA N+ ++ N +     ++ S+    H ++P +TI+ Y+ RI +Y+     
Sbjct:    95 LLRSLV---MAINQMLSVNDQ---FPNNHSQFLPEHMKLPMITIEGYISRIIKYSPCSKE 148

Query:    95 VYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETN 154
              +++  +YIDR  Q    F +++ N+HR+LIT ++VA+KY++D+ Y N ++++VGG+   
Sbjct:   149 CFIIILMYIDRLIQKR-NFIVNSYNIHRILITCVLVAAKYLDDIFYNNQFYSQVGGVSVK 207

Query:   155 ELNKLELDFLFLMGFKMHVNVSVFESYCCHLER 187
             E+N +ELDFL L+ F +  N  V+  Y    E+
Sbjct:   208 EINVMELDFLKLLSFDVSANTDVYSVYLEFFEK 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)
Q9M205	CCU22_ARATH	No assigned EC number	0.8009	0.9333	0.9130	yes	no
Q7FAT5	CCP21_ORYSJ	No assigned EC number	0.5276	0.8577	0.8894	yes	no
Q9SHD3	CCU21_ARATH	No assigned EC number	0.8155	0.8933	0.9054	no	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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	225
pfam08613	140	pfam08613, Cyclin, Cyclin	1e-31
pfam00134	127	pfam00134, Cyclin_N, Cyclin, N-terminal domain	6e-09

>gnl|CDD|204002 pfam08613, Cyclin, Cyclin

 Score =  112 bits (282), Expect = 1e-31
 Identities = 49/143 (34%), Positives = 82/143 (57%), Gaps = 5/143 (3%)

Query: 31  PLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIFRYTK 90
             +I  ++ +++R  A N+  +     + +       F S  +P +++  YL RI +Y  
Sbjct: 1   DELIESISRVLDRIPALND--STATASSSASSPLEP-FYSKAVPSISLTQYLSRIQKYCP 57

Query: 91  AGPSVYVVAYVYIDRFCQAN--PGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARV 148
             P V + A +Y+DR  +    P   + + NVHRLL+T + VA+K++ D +Y NS FA+V
Sbjct: 58  TSPDVLLSALIYLDRIVKRCDKPTITVTSLNVHRLLLTALTVATKFLSDGSYSNSRFAKV 117

Query: 149 GGLETNELNKLELDFLFLMGFKM 171
           GG+  +ELN LE+DFLFL+ F +
Sbjct: 118 GGISLHELNHLEIDFLFLVDFDL 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 = 52.2 bits (126), Expect = 6e-09
 Identities = 21/93 (22%), Positives = 39/93 (41%), Gaps = 5/93 (5%)

Query: 81  YLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNY 140
           +L  +    K  P    +A  Y+DRF    P  R   T +  + +T +++A+KY E    
Sbjct: 37  WLVEVHEEFKLLPETLYLAVNYLDRFLSKQPVPR---TKLQLVGVTCLLIAAKYEEIYPP 93

Query: 141 RNSYFARV--GGLETNELNKLELDFLFLMGFKM 171
               F  +        E+ ++EL  L  + + +
Sbjct: 94  SVEDFVYITDNAYTKEEILRMELLILSTLNWDL 126

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	225
PF08613	149	Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu	100.0
KOG1674	218	consensus Cyclin [General function prediction only	99.97
KOG1675	343	consensus Predicted cyclin [General function predi	99.78
PF00134	127	Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR	99.35
cd00043	88	CYCLIN Cyclin box fold. Protein binding domain fun	98.86
smart00385	83	CYCLIN domain present in cyclins, TFIIB and Retino	98.64
KOG0656	335	consensus G1/S-specific cyclin D [Cell cycle contr	98.27
KOG0653	391	consensus Cyclin B and related kinase-activating p	97.93
KOG0655	408	consensus G1/S-specific cyclin E [Cell cycle contr	97.64
TIGR00569	305	ccl1 cyclin ccl1. University).	97.43
COG5024	440	Cyclin [Cell division and chromosome partitioning]	96.97
COG5333	297	CCL1 Cdk activating kinase (CAK)/RNA polymerase II	96.92
KOG4164	497	consensus Cyclin ik3-1/CABLES [Cell cycle control,	96.68
KOG0834	323	consensus CDK9 kinase-activating protein cyclin T	94.32
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	93.07
KOG0794	264	consensus CDK8 kinase-activating protein cyclin C	92.84
KOG0835	367	consensus Cyclin L [General function prediction on	92.11
KOG2496	325	consensus Cdk activating kinase (CAK)/RNA polymera	89.96
KOG1674	218	consensus Cyclin [General function prediction only	89.82
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	89.71
PF00382	71	TFIIB: Transcription factor TFIIB repeat; InterPro	82.8

>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=8.5e-35  Score=237.67  Aligned_cols=140  Identities=31%  Similarity=0.699  Sum_probs=101.5

Q ss_pred             hHHHHHHHHHHHHHHHhhhhhhhhccc------cCCCCCcccccCCCCCchhHHHHHHHHHHHcCCCchHHHHHHHHHHH
Q 041949           32 LVISVLASLIERTMARNERIARNCRRA------LSKDSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDR  105 (225)
Q Consensus        32 ~~i~~la~lle~~i~~n~~~~~~~~~~------~~~~~~~~~F~~~~~P~isi~~fl~rI~~~~~~s~~~~llAliYldR  105 (225)
                      .++..|+.++++.+..|+......+..      .......+.|++..+|++++.+|+.||+++++|+++|+++|++||+|
T Consensus         2 ~~~~~i~~~l~~~~~~n~~~~~~s~~~~~~~~~~~~~~~~~~F~~~~~p~i~i~~fl~ri~~~~~~s~~~~i~aliYl~R   81 (149)
T PF08613_consen    2 KLVQSIARQLDRLINNNESTAQSSSSSSSPSSPFQQSPKISQFHSQSVPSISIRDFLSRILKYTQCSPECLILALIYLDR   81 (149)
T ss_dssp             HHHHHHHHHHHHHHHHHH--------------T---------T--SS--SS-HHHHHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccCchhhhhcccccccccccccccccccccCCCCCCCcHHHHHHHHHHHcCCChHHHHHHHHHHHH
Confidence            478999999999999998765433211      12345677899999999999999999999999999999999999999


Q ss_pred             HHh--hCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCHHHHHHHHHHHHHhCCCce
Q 041949          106 FCQ--ANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKM  171 (225)
Q Consensus       106 l~~--~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~eLN~LE~~FL~lLdf~L  171 (225)
                      +..  ..+.+.+++.|+||++++|+|||+||+||.+|+|++||+|||++++|||.||++||.+|||+|
T Consensus        82 l~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~eln~lE~~fL~~l~~~L  149 (149)
T PF08613_consen   82 LRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKELNELEREFLKLLDYNL  149 (149)
T ss_dssp             HHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHHHHHHHHHHHHHTTT--
T ss_pred             HHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHHHHHHHHHHHHHCCCcC
Confidence            999  568899999999999999999999999999999999999999999999999999999999997

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=99.97  E-value=1.2e-31  Score=232.07  Aligned_cols=186  Identities=43%  Similarity=0.735  Sum_probs=168.7

Q ss_pred             cccccccccccccccccCccCCCCC-ChhHHHHHHHHHHHHHHHhhhhhhhhccccCCCCCcccccCCCCCchhHHHHHH
Q 041949            5 SASLVISPRKLRSDVYSYSYENDSN-TPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLE   83 (225)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~d~~-~p~~i~~la~lle~~i~~n~~~~~~~~~~~~~~~~~~~F~~~~~P~isi~~fl~   83 (225)
                      +++..++|.++.+|....+...... .|.++..++.++++..+.|+.....  .+.+....++.|++...|+|++++|++
T Consensus         6 ~~s~~~~~~~~~~~~~~~~~~~~ss~~p~~l~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~f~~~~~p~isi~~yle   83 (218)
T KOG1674|consen    6 TMSVYINPDKLRLNLPDNPTGRNSSITPIFLTCLSSLLKRLNDSNENLSRE--NNKSWASPTTGFDGVSTPNISIRQYLE   83 (218)
T ss_pred             HhHhhcCccchhhccCcccccccccccchHHHHHHHHHHHHHhcChhhhcc--cccccccccccccCCCCCCcchHHHHH
Confidence            3567889999999988887766655 7999999999999999999876532  233456778899999999999999999


Q ss_pred             HHHHHcCCCchHHHHHHHHHHHHHhh------CCCccccccc-hHHHHHHHHHHhhhhcccCCcccccccccCCCCHHHH
Q 041949           84 RIFRYTKAGPSVYVVAYVYIDRFCQA------NPGFRIHATN-VHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNEL  156 (225)
Q Consensus        84 rI~~~~~~s~~~~llAliYldRl~~~------~~~~~l~~~n-~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~eL  156 (225)
                      ||.++++|+++|+++|++|+||+.++      .|...+++.| +||++++++++|+||.+|.+|+|++||++||++.+||
T Consensus        84 ri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y~n~~~a~vggl~~~el  163 (218)
T KOG1674|consen   84 RIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYYSNAYYAKVGGLTTDEL  163 (218)
T ss_pred             HHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchhhhHHHHHHhCCCChHhh
Confidence            99999999999999999999999996      6888999999 9999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCceeeCHHHHHHHHHHHHHhhhhC
Q 041949          157 NKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSIG  192 (225)
Q Consensus       157 N~LE~~FL~lLdf~L~Vs~~ef~~y~~~L~~~~~~~  192 (225)
                      |.||.+||..+||+|.|+.++|+.|+..++++...+
T Consensus       164 n~lE~~~l~~~~~~l~i~~~~~~~~~~~~~~~~~~~  199 (218)
T KOG1674|consen  164 NKLELDLLFLLDFRLIISRSEFNLYEDLLEREENLN  199 (218)
T ss_pred             hhhhHHHHhhCCeEEEechhHHHHHHHHHHHHHhcc
Confidence            999999999999999999999999999999887654

>KOG1675 consensus Predicted cyclin [General function prediction only]

Probab=99.78  E-value=1.3e-19  Score=162.00  Aligned_cols=145  Identities=20%  Similarity=0.281  Sum_probs=132.1

Q ss_pred             CCCCchhHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC-
Q 041949           71 HEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG-  149 (225)
Q Consensus        71 ~~~P~isi~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg-  149 (225)
                      ..+|..-+..|+.-.+.+.+++.+|-++.++|++|+... .+..+++.||+|....++++|+|.|+|..++|-.|+++. 
T Consensus       186 ~~~~~~ri~k~v~~l~~~~qlta~~aiitL~~~erl~~~-~e~~~~p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlK  264 (343)
T KOG1675|consen  186 SHPGLVRIKKFVRILFSWAQLTAECDIITLVYAERLLWL-AERDPCPRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILK  264 (343)
T ss_pred             cCcchhheehhhhhHhhhhhhhhccchHHHHhhHhhhhH-hhcCCCcchhhhhhhhhheehhhhhhhhhcccHHHHHHHh
Confidence            344556788899999999999999999999999999984 456688999999999999999999999999999999995 


Q ss_pred             CCCHHHHHHHHHHHHHhCCCceeeCHHHHHHHHHHHHHhhhhCCCcccchhhc--chH--HHHhhhhhhhh
Q 041949          150 GLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLEREVSIGGGYHIERTLR--CAE--EIKSRQTEDRI  216 (225)
Q Consensus       150 Gis~~eLN~LE~~FL~lLdf~L~Vs~~ef~~y~~~L~~~~~~~~~~~~~~~~~--~~~--e~~~~~~~~~~  216 (225)
                      .+++.+||.|||+||.+|+||+.|+..+|.+||..|...+..+...+...|+.  .++  ||++|.|||||
T Consensus       265 d~tveDmNe~ERqfLelLqfNinvp~svYAKyYfdlr~Lae~n~L~f~~ePlsKeRaqkleA~sr~~EDkd  335 (343)
T KOG1675|consen  265 DQSVDDMNALERQFLELLQFNINVPSSEYAKYYFDLRCLAEANPLLFPCEPLSKERAQKLEAMGRDAEDKD  335 (343)
T ss_pred             hccHhhHHHHHHHHHHHHhhccCccHHHHHHHHHHHhhhccccccccccccchhhHHHHHHHHhhhhccch
Confidence            69999999999999999999999999999999999999988888888888884  454  89999999998

>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=99.35  E-value=3.5e-12  Score=99.18  Aligned_cols=93  Identities=19%  Similarity=0.358  Sum_probs=79.9

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC--CCCHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG--GLETN  154 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg--Gis~~  154 (225)
                      .+.+|+.++....++++.++..|+.|+||+..+.+   +...+++.+.++|+++|+|+.++...+...|..++  .++.+
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            57789999999999999999999999999998653   67889999999999999999999888888888875  47999


Q ss_pred             HHHHHHHHHHHhCCCcee
Q 041949          155 ELNKLELDFLFLMGFKMH  172 (225)
Q Consensus       155 eLN~LE~~FL~lLdf~L~  172 (225)
                      ++.+||+.+|..|+|+|+
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            999999999999999985

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=98.86  E-value=1.7e-08  Score=71.96  Aligned_cols=84  Identities=19%  Similarity=0.220  Sum_probs=77.0

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCC-CHHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGL-ETNE  155 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGi-s~~e  155 (225)
                      ...+|+.++.+..++++.+...|..|+||+...++   +...+.+.+.++|+.+|+|+.++ ..+++.+.+++|. +.++
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            67899999999999999999999999999998653   34788999999999999999988 8899999999999 9999


Q ss_pred             HHHHHHHHH
Q 041949          156 LNKLELDFL  164 (225)
Q Consensus       156 LN~LE~~FL  164 (225)
                      +..+|.++|
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=98.64  E-value=1.9e-07  Score=65.80  Aligned_cols=82  Identities=18%  Similarity=0.220  Sum_probs=72.5

Q ss_pred             HHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCC-CHHHHHH
Q 041949           80 SYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGL-ETNELNK  158 (225)
Q Consensus        80 ~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGi-s~~eLN~  158 (225)
                      +|+.++.+..++++.+...|..++||+...+. +  ...+.+.+..+|+.+|+|..+.. .+++.+.++.|+ +.+++..
T Consensus         1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~-~--~~~~~~~ia~a~l~lA~k~~~~~-~~~~~~~~~~~~~~~~~i~~   76 (83)
T smart00385        1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYK-F--LKYSPSLIAAAALYLAAKTEEIP-PWTKELVHYTGYFTEEEILR   76 (83)
T ss_pred             CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhh-c--ccCCHHHHHHHHHHHHHHHhcCC-CCchhHhHhhCCCCHHHHHH
Confidence            48999999999999999999999999988532 2  34889999999999999999876 688899999888 9999999


Q ss_pred             HHHHHHH
Q 041949          159 LELDFLF  165 (225)
Q Consensus       159 LE~~FL~  165 (225)
                      +|+++|.
T Consensus        77 ~~~~il~   83 (83)
T smart00385       77 MEKLLLE   83 (83)
T ss_pred             HHHHHhC
Confidence            9999873

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=98.27  E-value=5.1e-06  Score=76.42  Aligned_cols=107  Identities=17%  Similarity=0.171  Sum_probs=84.6

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC---CCCH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG---GLET  153 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg---Gis~  153 (225)
                      --.+|+-++.++-+|++.|+.+|.-|+|||....+--.-.++-..-+-++|+-+|+|+-+-....-..+--.+   -+..
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            3568999999999999999999999999999854322233455788999999999999876533333332221   2689


Q ss_pred             HHHHHHHHHHHHhCCCcee-eCHHHHHHHHH
Q 041949          154 NELNKLELDFLFLMGFKMH-VNVSVFESYCC  183 (225)
Q Consensus       154 ~eLN~LE~~FL~lLdf~L~-Vs~~ef~~y~~  183 (225)
                      +.|-+||+-.|..|+|++. |++-.|-+|.-
T Consensus       160 ktI~rmELLVLstL~Wrl~aVTP~sF~~~fl  190 (335)
T KOG0656|consen  160 KTIQRMELLVLSTLKWRLRAVTPFSFIDHFL  190 (335)
T ss_pred             HHHHHHHHHHHhhccccccCCCchHHHHHHH
Confidence            9999999999999999998 78888888763

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

Probab=97.93  E-value=7.7e-05  Score=69.97  Aligned_cols=94  Identities=18%  Similarity=0.337  Sum_probs=77.8

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHH-HhhhhcccCC-ccccccccc--CCCC
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIM-VASKYVEDLN-YRNSYFARV--GGLE  152 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~-lAsK~~dD~~-~~N~~~AkV--gGis  152 (225)
                      -+.+|+..++.+.+++++++-+|+-++|||....+   +...-..-+-++|++ +|+|| ++.. ..-..+.-+  +.++
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            46789999999999999999999999999999743   445556677788867 99999 4443 334555555  6689


Q ss_pred             HHHHHHHHHHHHHhCCCceeeC
Q 041949          153 TNELNKLELDFLFLMGFKMHVN  174 (225)
Q Consensus       153 ~~eLN~LE~~FL~lLdf~L~Vs  174 (225)
                      .+++-.||...|..|+|++.++
T Consensus       236 ~~~il~mE~~il~~L~f~l~~p  257 (391)
T KOG0653|consen  236 REEILRMEKYILNVLEFDLSVP  257 (391)
T ss_pred             hHHHHHHHHHHHhccCeeecCC
Confidence            9999999999999999999997

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

Probab=97.64  E-value=0.00017  Score=66.25  Aligned_cols=102  Identities=22%  Similarity=0.339  Sum_probs=87.2

Q ss_pred             cCCCCCchh--HHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCccccccc
Q 041949           69 DSHEIPDMT--IQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFA  146 (225)
Q Consensus        69 ~~~~~P~is--i~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~A  146 (225)
                      |..-.|+..  +.||+-.+..-.++-.++|-+|.=|+||+....  ..++..|..-+-++|+.+|+|+-+=....-..||
T Consensus       137 Hpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~--~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFA  214 (408)
T KOG0655|consen  137 HPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQ--VEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFA  214 (408)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH--HHhhhhhHHHhhHHHHHHHHHHhhccCcccccee
Confidence            444456543  678999999999999999999999999999964  4556778888999999999998776667778899


Q ss_pred             cc--CCCCHHHHHHHHHHHHHhCCCcee
Q 041949          147 RV--GGLETNELNKLELDFLFLMGFKMH  172 (225)
Q Consensus       147 kV--gGis~~eLN~LE~~FL~lLdf~L~  172 (225)
                      -|  |..|-.+|-.||+-+|+.|+|+|.
T Consensus       215 yvTDgAcs~ddIltmE~iilkal~W~l~  242 (408)
T KOG0655|consen  215 YVTDGACSEDDILTMELIILKALKWELS  242 (408)
T ss_pred             eeccCccchHHHHHHHHHHHHHhccccc
Confidence            88  679999999999999999999996

>TIGR00569 ccl1 cyclin ccl1

Probab=97.43  E-value=0.00069  Score=61.84  Aligned_cols=91  Identities=20%  Similarity=0.185  Sum_probs=72.1

Q ss_pred             HHHHHHHHHcC--CCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC-CC---CH
Q 041949           80 SYLERIFRYTK--AGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG-GL---ET  153 (225)
Q Consensus        80 ~fl~rI~~~~~--~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg-Gi---s~  153 (225)
                      .++.++....+  ++..+.-.|.+|++||..++.   +.....+-+.+||+.+|+|+-+-. .+-..+.+.. +-   ..
T Consensus        61 ~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~S---v~~~~p~~Ia~tclfLA~KvEE~~-~si~~fv~~~~~~~~~~~  136 (305)
T TIGR00569        61 KRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNS---VMEYHPKIIMLTCVFLACKVEEFN-VSIDQFVGNLKETPLKAL  136 (305)
T ss_pred             HHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCc---hhhcCHHHHHHHHHHHHHhccccC-cCHHHHHhhccCCchhhH
Confidence            45677778888  999999999999999988642   446778999999999999976543 3444444332 22   35


Q ss_pred             HHHHHHHHHHHHhCCCceeeC
Q 041949          154 NELNKLELDFLFLMGFKMHVN  174 (225)
Q Consensus       154 ~eLN~LE~~FL~lLdf~L~Vs  174 (225)
                      .+|-.+|..+|..|+|+|.|.
T Consensus       137 ~~Il~~E~~lL~~L~F~L~V~  157 (305)
T TIGR00569       137 EQVLEYELLLIQQLNFHLIVH  157 (305)
T ss_pred             HHHHHHHHHHHHHCCCcEEee
Confidence            899999999999999999987

University).

>COG5024 Cyclin [Cell division and chromosome partitioning]

Probab=96.97  E-value=0.0023  Score=61.11  Aligned_cols=98  Identities=18%  Similarity=0.216  Sum_probs=81.7

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccch-HHHHHHHHHHhhhhcccCCccccccccc--CCCCH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNV-HRLLITTIMVASKYVEDLNYRNSYFARV--GGLET  153 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~-hRL~ltsl~lAsK~~dD~~~~N~~~AkV--gGis~  153 (225)
                      .|-+|+..++...++.|+++.+|.-.+||+.... .+.   .+. .-+-++|+.+|+||-+=.+..-+.|+-+  |.++.
T Consensus       215 ~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~-~v~---l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~  290 (440)
T COG5024         215 ILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSR-VVS---LEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTR  290 (440)
T ss_pred             HHHHHHHHhcccccccchHHHHHHHHHHHHhccC-ccc---HHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccH
Confidence            4778999999999999999999999999999963 333   343 4455789999999987777677776665  78999


Q ss_pred             HHHHHHHHHHHHhCCCceeeC-HHHH
Q 041949          154 NELNKLELDFLFLMGFKMHVN-VSVF  178 (225)
Q Consensus       154 ~eLN~LE~~FL~lLdf~L~Vs-~~ef  178 (225)
                      +++..+|+..|..++|++..+ +.-|
T Consensus       291 ~~i~~aE~~ml~~l~f~is~P~P~sF  316 (440)
T COG5024         291 DDIIRAERYMLEVLDFNISWPSPMSF  316 (440)
T ss_pred             HHHHHHHHHHhhhcccccCCCChHHH
Confidence            999999999999999999877 5555

>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=96.92  E-value=0.0042  Score=56.43  Aligned_cols=98  Identities=14%  Similarity=0.262  Sum_probs=81.9

Q ss_pred             HHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcc---cC----CcccccccccCCCC
Q 041949           80 SYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVE---DL----NYRNSYFARVGGLE  152 (225)
Q Consensus        80 ~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~d---D~----~~~N~~~AkVgGis  152 (225)
                      .++.++-.+.+++..+.-.|.+|.+|+.-+++   +...+.+-+..||+.+|.|+-|   |.    +.-+.-|+..---+
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            67888889999999999999999999988643   6778899999999999999877   21    23344577777789


Q ss_pred             HHHHHHHHHHHHHhCCCceeeC-HHHHHH
Q 041949          153 TNELNKLELDFLFLMGFKMHVN-VSVFES  180 (225)
Q Consensus       153 ~~eLN~LE~~FL~lLdf~L~Vs-~~ef~~  180 (225)
                      .+.+-.+|.+.|+.|+|++.|. +-.+..
T Consensus       127 r~~Il~~E~~lLEaL~fd~~V~hPy~~l~  155 (297)
T COG5333         127 RERILEYEFELLEALDFDLHVHHPYKYLE  155 (297)
T ss_pred             HHHHHHHHHHHHHHcccceEeccccHHHH
Confidence            9999999999999999999997 444443

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

Probab=96.68  E-value=0.0029  Score=59.45  Aligned_cols=109  Identities=15%  Similarity=0.162  Sum_probs=89.4

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCccccccc----ccCCCC
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFA----RVGGLE  152 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~A----kVgGis  152 (225)
                      |+..-+.++-.-|++...+.-.|.||++++.-++   .++..|-+-.--+|+++|.|+-|=.--.-+.+-    ..+..+
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            6778888888899999999999999999999863   356777888888999999999833333333322    246788


Q ss_pred             HHHHHHHHHHHHHhCCCceeeCHHHHHHHHHHHHHh
Q 041949          153 TNELNKLELDFLFLMGFKMHVNVSVFESYCCHLERE  188 (225)
Q Consensus       153 ~~eLN~LE~~FL~lLdf~L~Vs~~ef~~y~~~L~~~  188 (225)
                      .+||-..|.-.|..|+|.|+++.+|..-.|+.|+.+
T Consensus       461 rrdLia~Ef~VlvaLefaL~~~~~eVlPHy~RL~~e  496 (497)
T KOG4164|consen  461 RRDLIAFEFPVLVALEFALHLPEHEVLPHYRRLQQE  496 (497)
T ss_pred             HHhhhhhhhhHHHhhhhhccCChhhcchHHHHHhhc
Confidence            999999999999999999999999999888888754

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

Probab=94.32  E-value=0.17  Score=46.80  Aligned_cols=111  Identities=16%  Similarity=0.174  Sum_probs=79.5

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccC------C-cccccccccC
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDL------N-YRNSYFARVG  149 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~------~-~~N~~~AkVg  149 (225)
                      ....||..+-.+.+++.-++-.|.+|..||...+   .+.....+-+-.+|+.+|.|.-|--      . -+++++....
T Consensus        41 ~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~---s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~  117 (323)
T KOG0834|consen   41 EGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFH---SFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKD  117 (323)
T ss_pred             HHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhc---ccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCccc
Confidence            4557999999999999999999999999998853   2344445667888999999974332      1 1222222110


Q ss_pred             -------CCCHHHHHHHHHHHHHhCCCceeeC-HHHHH-HHHHHHHHhhh
Q 041949          150 -------GLETNELNKLELDFLFLMGFKMHVN-VSVFE-SYCCHLEREVS  190 (225)
Q Consensus       150 -------Gis~~eLN~LE~~FL~lLdf~L~Vs-~~ef~-~y~~~L~~~~~  190 (225)
                             -=..+++-.+|+-.|..|+|++.|. +..|. +|+..+.....
T Consensus       118 ~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~  167 (323)
T KOG0834|consen  118 LELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADEN  167 (323)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhh
Confidence                   0136889999999999999999998 35554 67777765543

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=93.07  E-value=1  Score=40.99  Aligned_cols=102  Identities=16%  Similarity=0.144  Sum_probs=80.1

Q ss_pred             HHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCHHHHHHH
Q 041949           80 SYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKL  159 (225)
Q Consensus        80 ~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~eLN~L  159 (225)
                      ..|.++....+++..+.=-|..+..++....  . +...+..-+..+|+-+|.|. +....+-+..+.+.+++.+++.+.
T Consensus       127 ~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~--~-~rgrs~~~i~AAclYiACR~-~~~prtl~eI~~~~~v~~k~i~~~  202 (310)
T PRK00423        127 SELDRIASQLGLPRSVREEAAVIYRKAVEKG--L-IRGRSIEGVVAAALYAACRR-CKVPRTLDEIAEVSRVSRKEIGRC  202 (310)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC--c-ccCCCHHHHHHHHHHHHHHH-cCCCcCHHHHHHHhCCCHHHHHHH
Confidence            4567777888899888888888888887742  2 34556778888889899886 777788889999999999999999


Q ss_pred             HHHHHHhCCCceeeC-HHHHH-HHHHHH
Q 041949          160 ELDFLFLMGFKMHVN-VSVFE-SYCCHL  185 (225)
Q Consensus       160 E~~FL~lLdf~L~Vs-~~ef~-~y~~~L  185 (225)
                      ++.+++.|++++-.. +++|. +|+..|
T Consensus       203 ~~~l~k~L~~~~~~~~p~~~i~r~~~~L  230 (310)
T PRK00423        203 YRFLLRELNLKLPPTDPIDYVPRFASEL  230 (310)
T ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHc
Confidence            999999999887553 55554 455544

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

Probab=92.84  E-value=0.15  Score=45.13  Aligned_cols=96  Identities=18%  Similarity=0.203  Sum_probs=76.6

Q ss_pred             hhHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccC-Cc-------ccc----
Q 041949           76 MTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDL-NY-------RNS----  143 (225)
Q Consensus        76 isi~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~-~~-------~N~----  143 (225)
                      |-..+++..+-.+.++--.++-.|.+|+.|+..+..   +...+..-+..||+-+|+|.-+-- .+       .+.    
T Consensus        42 i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S---~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~  118 (264)
T KOG0794|consen   42 IFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKS---LKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTR  118 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh---hhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhh
Confidence            445577888888889999999999999999998743   456778899999999999986552 11       111    


Q ss_pred             --cccccCCCCHHHHHHHHHHHHHhCCCceeeC
Q 041949          144 --YFARVGGLETNELNKLELDFLFLMGFKMHVN  174 (225)
Q Consensus       144 --~~AkVgGis~~eLN~LE~~FL~lLdf~L~Vs  174 (225)
                        +|..-.....+.+-.+|...|..||+-|.|-
T Consensus       119 f~~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVh  151 (264)
T KOG0794|consen  119 FSYWPEKFPYERKDILEMEFYLLEALDCYLIVH  151 (264)
T ss_pred             cccchhhcCCCcCcchhhhhhHHhhhceeEEEe
Confidence              4666667788999999999999999999884

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=92.11  E-value=1.3  Score=41.10  Aligned_cols=97  Identities=19%  Similarity=0.216  Sum_probs=67.4

Q ss_pred             HHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcc--------------------ccccc
Q 041949           87 RYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYR--------------------NSYFA  146 (225)
Q Consensus        87 ~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~--------------------N~~~A  146 (225)
                      --.+++-.|...++|++.|++...+.   -..+..-+..+|+.+|||.-+.-.--                    ...++
T Consensus        35 ILL~L~q~a~atgqVLFqRf~~~ks~---v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~~~~~~~~~~~~  111 (367)
T KOG0835|consen   35 ILLNLPQVAMATGQVLFQRFCYSKSF---VRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRRESEAAEHLILA  111 (367)
T ss_pred             HhhcCcHHHHHHHHHHHHHHHhcccc---ccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHHhccCcchhhhh
Confidence            44568889999999999999996432   23567789999999999986543210                    00011


Q ss_pred             ccCCCCHHHHHHHHHHHHHhCCCceeeC--HHHHHHHHHHHH
Q 041949          147 RVGGLETNELNKLELDFLFLMGFKMHVN--VSVFESYCCHLE  186 (225)
Q Consensus       147 kVgGis~~eLN~LE~~FL~lLdf~L~Vs--~~ef~~y~~~L~  186 (225)
                      +-.-=-....-..|++.|..|+|.++|.  -..+..|...|+
T Consensus       112 ~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~  153 (367)
T KOG0835|consen  112 RLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQ  153 (367)
T ss_pred             hHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhc
Confidence            1100013456788999999999999987  556678887765

>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=89.96  E-value=2.7  Score=38.62  Aligned_cols=81  Identities=20%  Similarity=0.239  Sum_probs=64.3

Q ss_pred             CCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCC----CCHHHHHHHHHHHHH
Q 041949           90 KAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGG----LETNELNKLELDFLF  165 (225)
Q Consensus        90 ~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgG----is~~eLN~LE~~FL~  165 (225)
                      .+++++.-.|+.|..|+.-.+.   +......-++.||+.+|.|. ++.+.+-..|.+-..    =+...+-..|...|+
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            5788889999999999987542   34566788999999999995 466666666665432    468889999999999


Q ss_pred             hCCCceeeC
Q 041949          166 LMGFKMHVN  174 (225)
Q Consensus       166 lLdf~L~Vs  174 (225)
                      .|+|+|.|-
T Consensus       149 sL~f~L~vh  157 (325)
T KOG2496|consen  149 SLKFSLTVH  157 (325)
T ss_pred             hhhhhheec
Confidence            999999985

>KOG1674 consensus Cyclin [General function prediction only]

Probab=89.82  E-value=0.2  Score=43.66  Aligned_cols=94  Identities=16%  Similarity=0.102  Sum_probs=72.8

Q ss_pred             HHHHHHHHHH--HHHhhCCCcc-ccccchHHHHHHHHHHhhhhcccCCc-----ccccccc-cCC-CCHHHHHHHHHHHH
Q 041949           95 VYVVAYVYID--RFCQANPGFR-IHATNVHRLLITTIMVASKYVEDLNY-----RNSYFAR-VGG-LETNELNKLELDFL  164 (225)
Q Consensus        95 ~~llAliYld--Rl~~~~~~~~-l~~~n~hRL~ltsl~lAsK~~dD~~~-----~N~~~Ak-VgG-is~~eLN~LE~~FL  164 (225)
                      +.+.+..|++  |+....+... ....+.++.++++++.+.|...|..-     +++.|+. +.| ......|.+|+++|
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            5667788888  8877544321 23456899999999999999988876     7888985 334 46888999999999


Q ss_pred             HhCCCceeeCHHHHHHHHHHHHHh
Q 041949          165 FLMGFKMHVNVSVFESYCCHLERE  188 (225)
Q Consensus       165 ~lLdf~L~Vs~~ef~~y~~~L~~~  188 (225)
                      ..++|...+++++|..=+-.+.+.
T Consensus        83 eri~k~~~~s~~~lv~al~Yldr~  106 (218)
T KOG1674|consen   83 ERIFKYSKCSPECLVLALVYLDRF  106 (218)
T ss_pred             HHHHHHhcCCchhhhhhhhhhhhh
Confidence            999999999999998644444443

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=89.71  E-value=3  Score=37.99  Aligned_cols=95  Identities=15%  Similarity=0.132  Sum_probs=76.2

Q ss_pred             CCCchhHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCC
Q 041949           72 EIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGL  151 (225)
Q Consensus        72 ~~P~isi~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGi  151 (225)
                      ..|.++-.+|+.|+....+++..+.-.|...+.+....  ++ ....++.-+..+|+-+|++... ..-+.+..+++.|+
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            46677889999999999999999988888777777653  33 3567889999999999999764 44678889999999


Q ss_pred             CHHHHHHHHHHHHHhCCCc
Q 041949          152 ETNELNKLELDFLFLMGFK  170 (225)
Q Consensus       152 s~~eLN~LE~~FL~lLdf~  170 (225)
                      +...+..-=.++...++..
T Consensus       289 s~~tI~~~ykel~~~l~~~  307 (310)
T PRK00423        289 TEVTVRNRYKELAEKLDIK  307 (310)
T ss_pred             CHHHHHHHHHHHHHHhCcc
Confidence            9999887666666666543

>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=82.80  E-value=8.9  Score=26.83  Aligned_cols=71  Identities=11%  Similarity=0.104  Sum_probs=54.2

Q ss_pred             HHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCHHHH
Q 041949           82 LERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNEL  156 (225)
Q Consensus        82 l~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~eL  156 (225)
                      +.|+....+++..+.=.|..+.++.....  + ....+..-+..+|+-+|.+.. +...+-+..+.+.||+.+++
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            56888899999999999998888887742  2 345667888889999998765 66678888999999998775

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	225
2pk9_B	293	Structure Of The Pho85-pho80 Cdk-cyclin Complex Of		1e-09

>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 = 60.1 bits (144), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 57/98 (58%)
Query: 74  PDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASK 133
           P+++I +Y  R+ +++     V + +  YID      P F +++   HR L+T   VA+K
Sbjct: 73  PNISIFNYFIRLTKFSSLEHCVLMTSLYYIDLLQTVYPDFTLNSLTAHRFLLTATTVATK 132
Query: 134 YVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKM 171
            + D    N+++A+VGG+  +ELN LE DFL  + +++
Sbjct: 133 GLCDSFSTNAHYAKVGGVRCHELNILENDFLKRVNYRI 170

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	225
2pmi_B	293	PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de	3e-41
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-08

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

 Score =  141 bits (355), Expect = 3e-41
 Identities = 39/179 (21%), Positives = 80/179 (44%), Gaps = 3/179 (1%)

Query: 10  ISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFD 69
           I   +    V   +  N  +   ++ +++ ++   +A NE  A               + 
Sbjct: 12  IHEDQGIPKVILPADFNKCSRTDLVVLISRMLVSLIAINENSATK---KSDDQITLTRYH 68

Query: 70  SHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIM 129
           S   P+++I +Y  R+ +++     V + +  YID      P F +++   HR L+T   
Sbjct: 69  SKIPPNISIFNYFIRLTKFSSLEHCVLMTSLYYIDLLQTVYPDFTLNSLTAHRFLLTATT 128

Query: 130 VASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLERE 188
           VA+K + D    N+++A+VGG+  +ELN LE DFL  + +++              +++
Sbjct: 129 VATKGLCDSFSTNAHYAKVGGVRCHELNILENDFLKRVNYRIIPRDHNITLCSIEQKQK 187

>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 = 51.8 bits (123), Expect = 6e-08
 Identities = 33/207 (15%), Positives = 63/207 (30%), Gaps = 62/207 (29%)

Query: 8   LVISPRKLRSDVYSYSYENDSNTPLVISVLASLIERTMARNE-----------RIARNCR 56
           L   P+ L  +V + +       P  +S++A  I   +A  +            I  +  
Sbjct: 311 LDCRPQDLPREVLTTN-------PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL 363

Query: 57  RALS-KDSRSR-----VF-DSHEIPDMTIQSY---------------LER---IFRYTKA 91
             L   + R       VF  S  IP + +                  L +   + +  K 
Sbjct: 364 NVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK- 422

Query: 92  GPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVED---LNYRNSYFAR- 147
             S   +  +Y++   +       +   +HR ++    +   +  D     Y + YF   
Sbjct: 423 -ESTISIPSIYLELKVKLE-----NEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH 476

Query: 148 VG--------GLETNELNKLELDFLFL 166
           +G                 + LDF FL
Sbjct: 477 IGHHLKNIEHPERMTLFRMVFLDFRFL 503

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	225
2pmi_B	293	PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de	100.0
1f5q_B	252	Gamma herpesvirus cyclin; herpesviral cyclin, cycl	98.89
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	98.83
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	98.82
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	98.78
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	98.76
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	98.74
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	98.74
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	98.74
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	98.38
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	98.36
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	98.3
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	98.22
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	98.04
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	98.01
1c9b_A	207	General transcription factor IIB; protein-DNA comp	97.97
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	97.39
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	93.83
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	93.66
1c9b_A	207	General transcription factor IIB; protein-DNA comp	91.61
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	82.06

>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=1.7e-39  Score=289.41  Aligned_cols=154  Identities=23%  Similarity=0.359  Sum_probs=139.9

Q ss_pred             ChhHHHHHHHHHHHHHHHhhhhhhhhccccCCCCCcccccCCCCCchhHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhh
Q 041949           30 TPLVISVLASLIERTMARNERIARNCRRALSKDSRSRVFDSHEIPDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQA  109 (225)
Q Consensus        30 ~p~~i~~la~lle~~i~~n~~~~~~~~~~~~~~~~~~~F~~~~~P~isi~~fl~rI~~~~~~s~~~~llAliYldRl~~~  109 (225)
                      ...++.+||.+|+++|+.||....+.   ...+..++.||+..+|+|+|++|+.||+++++|+++|+++|++||||+..+
T Consensus        32 ~~dlv~~IA~~L~~LI~~Nd~~~~~~---~~~~~~~t~F~~~~~P~ISI~~Yl~RI~k~t~ls~~~ll~ALvYLdRL~~~  108 (293)
T 2pmi_B           32 RTDLVVLISRMLVSLIAINENSATKK---SDDQITLTRYHSKIPPNISIFNYFIRLTKFSSLEHCVLMTSLYYIDLLQTV  108 (293)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCC-----------CCCCTTCCSSCCSSCHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCccccccc---cccccccccccCCCCCCCcHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhh
Confidence            45799999999999999999876432   123457789999999999999999999999999999999999999999999


Q ss_pred             CCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCHHHHHHHHHHHHHhCCCceeeCHHHHHHHHHHHH
Q 041949          110 NPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNKLELDFLFLMGFKMHVNVSVFESYCCHLE  186 (225)
Q Consensus       110 ~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~eLN~LE~~FL~lLdf~L~Vs~~ef~~y~~~L~  186 (225)
                      +|++.+++.||||++++|+|||+||+||.+|+|++||+|||++++|||.||++||.+|||+|+|+.++|..|+..+.
T Consensus       109 ~p~~~l~~~nvHRLlLtALmlAsK~ldD~~ysN~~wAkVgGisl~ELN~LE~eFL~lLdf~L~V~~ee~~~cy~E~~  185 (293)
T 2pmi_B          109 YPDFTLNSLTAHRFLLTATTVATKGLCDSFSTNAHYAKVGGVRCHELNILENDFLKRVNYRIIPRDHNITLCSIEQK  185 (293)
T ss_dssp             CTTCCCSTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTTTCCSCCTTHHHHHHHHSC
T ss_pred             CCCCccCCchHHHHHHHHHHHHHHhccccccChhHhhhccCcCHHHHHHHHHHHHHHcCCceeeCHHHHHHHHHHHh
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999886653

>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=98.89  E-value=1.5e-08  Score=88.22  Aligned_cols=104  Identities=13%  Similarity=0.204  Sum_probs=88.7

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCccccccccc--CCCCHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARV--GGLETN  154 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkV--gGis~~  154 (225)
                      -+.+|+..+....+++++++.+|..|+||+..+.+   +.....+-+-++|+.+|+|+-+-....-+.+..+  +.++.+
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            47789999999999999999999999999999753   4567789999999999999988766666666655  468999


Q ss_pred             HHHHHHHHHHHhCCCceeeC-HHHHHHHHH
Q 041949          155 ELNKLELDFLFLMGFKMHVN-VSVFESYCC  183 (225)
Q Consensus       155 eLN~LE~~FL~lLdf~L~Vs-~~ef~~y~~  183 (225)
                      |+.+||+..|..|+|+|.++ +-.|..++.
T Consensus       128 ~i~~mE~~IL~~L~w~l~~pTp~~FL~~~l  157 (252)
T 1f5q_B          128 KLLTLEVKSLDTLSWVADRCLSTDLICYIL  157 (252)
T ss_dssp             HHHHHHHHHHHHTTTCCCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCccCCCCHHHHHHHHH
Confidence            99999999999999999965 777776543

>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=98.83  E-value=3.4e-08  Score=85.35  Aligned_cols=102  Identities=13%  Similarity=0.142  Sum_probs=87.0

Q ss_pred             HHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC--CCCHHH
Q 041949           78 IQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG--GLETNE  155 (225)
Q Consensus        78 i~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg--Gis~~e  155 (225)
                      +.+|+..+....+++++++.+|..|+||+..+.   .+.....+-+.++|+.+|+|+-+-...+-+.+..++  .++.+|
T Consensus        55 lvdwl~~v~~~~~l~~etl~lAv~~~DRfls~~---~v~~~~lqLv~~acl~iA~K~eE~~~p~~~d~~~~~~~~~~~~~  131 (254)
T 2f2c_A           55 LLTWMHLLCESFELDKSVFPLSVSILDRYLCKK---QGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSCDCFTNLE  131 (254)
T ss_dssp             HHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTS---CCCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHSTTC---CCHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHHHccC---CcCHHHccHHHHHHHHHHHHhcccCCCCHHHHHHHhCCCCCHHH
Confidence            678999999999999999999999999999864   356677899999999999999887777777777773  489999


Q ss_pred             HHHHHHHHHHhCCCceeeC-HHHHHHHH
Q 041949          156 LNKLELDFLFLMGFKMHVN-VSVFESYC  182 (225)
Q Consensus       156 LN~LE~~FL~lLdf~L~Vs-~~ef~~y~  182 (225)
                      +.+||+..|+.|+|++.+. +..|-.++
T Consensus       132 i~~mE~~IL~~L~~~l~~~tp~~fl~~~  159 (254)
T 2f2c_A          132 LINQEKDILEALKWDTEAVLATDFLIPL  159 (254)
T ss_dssp             HHHHHHHHHHHTTTCCCCCCGGGSHHHH
T ss_pred             HHHHHHHHHHHCCCcCCCCCHHHHHHHH
Confidence            9999999999999999865 66665543

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

Probab=98.82  E-value=2.3e-08  Score=89.20  Aligned_cols=103  Identities=15%  Similarity=0.232  Sum_probs=88.5

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC--CCCHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG--GLETN  154 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg--Gis~~  154 (225)
                      .+.+|+.++....+++++++.+|..|+||+..+.+   +.....+.+-++|+.+|+|+-+-...+-+.+..++  .++.+
T Consensus        73 ~lvdwl~ev~~~~~l~~~t~~lAv~~lDRfls~~~---v~~~~lqLv~~tcL~lAsK~eE~~p~~~~~l~~~~~~~~~~~  149 (306)
T 3g33_B           73 MLAYWMLEVCEEQRCEEEVFPLAMNYLDRYLSCVP---TRKAQLQLLGAVCMLLASKLRETTPLTIEKLCIYTDHAVSPR  149 (306)
T ss_dssp             HHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHCC---CCGGGHHHHHHHHHHHHHHHHCSSCCCTTHHHHHTTTSSCHH
T ss_pred             HHHHHHHHHHHHhCCcHhHHHHHHHHHHHHHhcCC---CcHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHhccCccHH
Confidence            36789999999999999999999999999999753   56788999999999999999887766777777764  48999


Q ss_pred             HHHHHHHHHHHhCCCceeeC-HHHHHHHH
Q 041949          155 ELNKLELDFLFLMGFKMHVN-VSVFESYC  182 (225)
Q Consensus       155 eLN~LE~~FL~lLdf~L~Vs-~~ef~~y~  182 (225)
                      ++.+||+.+|..|+|+|.+. +..|..++
T Consensus       150 ~i~~mE~~IL~~L~f~l~~~tp~~fl~~~  178 (306)
T 3g33_B          150 QLRDWEVLVLGKLKWDLAAVIAHDFLAFI  178 (306)
T ss_dssp             HHHHHHHHHHHHTTTCCCCCCGGGGHHHH
T ss_pred             HHHHHHHHHHHHcCCccCCCCHHHHHHHH
Confidence            99999999999999999875 66665444

>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=98.78  E-value=3.7e-08  Score=85.19  Aligned_cols=103  Identities=15%  Similarity=0.199  Sum_probs=88.4

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCccccccccc--CCCCHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARV--GGLETN  154 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkV--gGis~~  154 (225)
                      .+.+|+..+....+++++++.+|..|+||+..+.   .+.....+-+.++|+.+|+|+-+-...+-+.+..+  +.++.+
T Consensus        53 ~lvdwl~ev~~~~~l~~etl~lAv~~~DRfls~~---~v~~~~lqLv~~acl~iA~K~eE~~~p~~~d~~~~~~~~~~~~  129 (257)
T 1g3n_C           53 LLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIK---QVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQ  129 (257)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTC---CCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTCSCHH
T ss_pred             HHHHHHHHHHHHhCCCccHHHHHHHHHHHHHccC---CCCHHHHHHHHHHHHHHHHHHccccCCCHHHHHHHHCCCCCHH
Confidence            3678999999999999999999999999999864   35567788999999999999987766677777777  448999


Q ss_pred             HHHHHHHHHHHhCCCceeeC-HHHHHHHH
Q 041949          155 ELNKLELDFLFLMGFKMHVN-VSVFESYC  182 (225)
Q Consensus       155 eLN~LE~~FL~lLdf~L~Vs-~~ef~~y~  182 (225)
                      |+.+||+..|..|+|++.+. +..|..++
T Consensus       130 ~i~~mE~~iL~~L~~~l~~~tp~~fl~~~  158 (257)
T 1g3n_C          130 ELIDQEKELLEKLAWRTEAVLATDVTSFL  158 (257)
T ss_dssp             HHHHHHHHHHHHTTTCCCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCcCCCCCHHHHHHHH
Confidence            99999999999999999865 77776544

>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=98.76  E-value=4.8e-08  Score=84.64  Aligned_cols=103  Identities=17%  Similarity=0.217  Sum_probs=87.9

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC--CCCHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG--GLETN  154 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg--Gis~~  154 (225)
                      .+.+|+.++....+++++++.+|..|+||+..+.+   +...+.+-+.++|+.+|+|+-+-...+-+.+..++  .++.+
T Consensus        41 ~lvdwl~~v~~~~~l~~~tl~lAv~~lDRfls~~~---v~~~~lqlv~~acl~iA~K~ee~~~~~~~d~~~i~~~~~~~~  117 (260)
T 2cch_B           41 ILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMS---VLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKK  117 (260)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCC---CCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTSSSCHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccCC---CCHHHHhHHHHHHHHHHHHhcccCCCCHHHHHHHHcCCcCHH
Confidence            36689999999999999999999999999999753   45677889999999999999887666777777764  48999


Q ss_pred             HHHHHHHHHHHhCCCceeeC-HHHHHHHH
Q 041949          155 ELNKLELDFLFLMGFKMHVN-VSVFESYC  182 (225)
Q Consensus       155 eLN~LE~~FL~lLdf~L~Vs-~~ef~~y~  182 (225)
                      |+.+||+..|..|+|++.+. +..|..++
T Consensus       118 ~i~~mE~~iL~~L~~~l~~~tp~~fl~~~  146 (260)
T 2cch_B          118 QVLRMEHLVLKVLTFDLAAPTVNQFLTQY  146 (260)
T ss_dssp             HHHHHHHHHHHHTTTCCCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCccCCCCHHHHHHHH
Confidence            99999999999999999865 66665443

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

Probab=98.74  E-value=7.8e-08  Score=83.86  Aligned_cols=102  Identities=20%  Similarity=0.230  Sum_probs=87.5

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC--CCCHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG--GLETN  154 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg--Gis~~  154 (225)
                      .+.+|+.++....+++++++.+|..|+||+....+   +...+.+-+.++|+.+|+|+-+-...+-+.+..++  .++.+
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            36789999999999999999999999999999653   56678999999999999999877666677777775  48999


Q ss_pred             HHHHHHHHHHHhCCCceeeC-HHHHHHH
Q 041949          155 ELNKLELDFLFLMGFKMHVN-VSVFESY  181 (225)
Q Consensus       155 eLN~LE~~FL~lLdf~L~Vs-~~ef~~y  181 (225)
                      |+.+||+..|..|+|++.+. +..|...
T Consensus       117 eI~~mE~~IL~~L~f~l~~~tp~~fl~~  144 (269)
T 2b9r_A          117 QIRQMEMKILRALNFGLGRPLPLHFLRR  144 (269)
T ss_dssp             HHHHHHHHHHHHTTSCCCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCccCCCCHHHHHHH
Confidence            99999999999999999865 6666544

>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=98.74  E-value=8e-08  Score=83.71  Aligned_cols=103  Identities=18%  Similarity=0.276  Sum_probs=86.9

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCccccccccc--CCCCHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARV--GGLETN  154 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkV--gGis~~  154 (225)
                      .+.+|+.++..+.+++++++.+|..|+||+..+.   .+...+.+-+.++|+.+|+|+-+-...+-+.+..+  +.++.+
T Consensus        59 ~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~---~v~~~~lqlv~~acL~iAsK~EE~~p~~~~~~~~~~~~~~~~~  135 (271)
T 2w96_A           59 IVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLE---PVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPE  135 (271)
T ss_dssp             HHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHTTS---CCCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTSSCHH
T ss_pred             HHHHHHHHHHHHHCCchhHHHHHHHHHHHhCCcC---CcCHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCHH
Confidence            3668899999999999999999999999999965   34567799999999999999987656666677766  358999


Q ss_pred             HHHHHHHHHHHhCCCceeeC-HHHHHHHH
Q 041949          155 ELNKLELDFLFLMGFKMHVN-VSVFESYC  182 (225)
Q Consensus       155 eLN~LE~~FL~lLdf~L~Vs-~~ef~~y~  182 (225)
                      |+.+||+.+|+.|+|++.+. +..|..++
T Consensus       136 eI~~mE~~IL~~L~~~l~~~tp~~fl~~~  164 (271)
T 2w96_A          136 ELLQMELLLVNKLKWNLAAMTPHDFIEHF  164 (271)
T ss_dssp             HHHHHHHHHHHHTTTCCCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCccCCCCHHHHHHHH
Confidence            99999999999999999865 66666433

>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=98.74  E-value=9.1e-08  Score=84.19  Aligned_cols=106  Identities=15%  Similarity=0.226  Sum_probs=89.9

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC--CCCHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG--GLETN  154 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg--Gis~~  154 (225)
                      .+.+|+.++....+++++++.+|..|+||+.....  .+...+.+-+.++|+.+|+|+-+-...+-+.+..++  .++.+
T Consensus        52 ~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~--~v~~~~lqlv~~acL~iA~K~eE~~~p~l~~~~~i~~~~~~~~  129 (283)
T 1w98_B           52 ILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQE--NVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGD  129 (283)
T ss_dssp             HHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCC--CCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTSSCHH
T ss_pred             HHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHhCC--CCCHHHHHHHHHHHHHHHHHhcccCCCcHHHHHHHHcCCCCHH
Confidence            35689999999999999999999999999998632  245678999999999999999887666777777774  58999


Q ss_pred             HHHHHHHHHHHhCCCceeeC-HHHHHHHHHH
Q 041949          155 ELNKLELDFLFLMGFKMHVN-VSVFESYCCH  184 (225)
Q Consensus       155 eLN~LE~~FL~lLdf~L~Vs-~~ef~~y~~~  184 (225)
                      |+.+||+..|..|+|+|.+. +..|..++..
T Consensus       130 ei~~mE~~IL~~L~~~l~~~tp~~fL~~f~~  160 (283)
T 1w98_B          130 EILTMELMIMKALKWRLSPLTIVSWLNVYMQ  160 (283)
T ss_dssp             HHHHHHHHHHHHTTTCCCCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcCCCCCHHHHHHHHHH
Confidence            99999999999999999865 7777765543

>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=98.38  E-value=1.2e-06  Score=75.21  Aligned_cols=99  Identities=14%  Similarity=0.086  Sum_probs=78.9

Q ss_pred             HHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccc----------
Q 041949           78 IQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFAR----------  147 (225)
Q Consensus        78 i~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~Ak----------  147 (225)
                      ..+|+.++....+++.+++-.|..|+||+..++   .+...+.+-+.++|+.+|+|+-+ ...+-+.+.+          
T Consensus        44 ~~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~---~~~~~~~qlv~~acL~lA~K~eE-~~~~l~d~~~~~~~~~~~~~  119 (258)
T 2i53_A           44 GARFIFDVGTRLGLHYDTLATGIIYFHRFYMFH---SFKQFPRYVTGACCLFLAGKVEE-TPKKCKDIIKTARSLLNDVQ  119 (258)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTS---CTTTSCHHHHHHHHHHHHHHHTT-CCCCHHHHHHHHHHHSCHHH
T ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhC---ChhhcCHHHHHHHHHHHHHcccc-ccccHHHHHHHHHHHhchhh
Confidence            458899999999999999999999999998864   24567788899999999999876 4433333332          


Q ss_pred             ---cCCCCHHHHHHHHHHHHHhCCCceeeC-HHHHHH
Q 041949          148 ---VGGLETNELNKLELDFLFLMGFKMHVN-VSVFES  180 (225)
Q Consensus       148 ---VgGis~~eLN~LE~~FL~lLdf~L~Vs-~~ef~~  180 (225)
                         .+.-+.+++-.||+.+|..|+|++.+. +..|..
T Consensus       120 ~~~~~~~~~~~i~~~E~~iL~~L~f~l~~~~P~~fl~  156 (258)
T 2i53_A          120 FGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLL  156 (258)
T ss_dssp             HGGGCSCHHHHHHHHHHHHHHHTTTCCCCCCHHHHHH
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHCCCceeccChHHHHH
Confidence               223357899999999999999999976 666653

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

Probab=98.36  E-value=2.9e-06  Score=72.21  Aligned_cols=100  Identities=12%  Similarity=0.113  Sum_probs=82.5

Q ss_pred             hhHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccc-cchHHHHHHHHHHhhhhcccCCcccccccccC-----
Q 041949           76 MTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHA-TNVHRLLITTIMVASKYVEDLNYRNSYFARVG-----  149 (225)
Q Consensus        76 isi~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~-~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg-----  149 (225)
                      ....+++.++....+++..++-.|..|+||+..++.   +.. .+.+-+.++|+.+|+|+-+ ...+-+.+..+.     
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            346688999999999999999999999999999753   345 7789999999999999976 444545555443     


Q ss_pred             ---CCCHHHHHHHHHHHHHhCCCceeeC-HHHHH
Q 041949          150 ---GLETNELNKLELDFLFLMGFKMHVN-VSVFE  179 (225)
Q Consensus       150 ---Gis~~eLN~LE~~FL~lLdf~L~Vs-~~ef~  179 (225)
                         .++.+++-+||+.+|+.|+|++.+. +..|.
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               5789999999999999999999975 55554

>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=98.30  E-value=4.4e-06  Score=71.83  Aligned_cols=99  Identities=19%  Similarity=0.210  Sum_probs=80.0

Q ss_pred             HHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC--------
Q 041949           78 IQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG--------  149 (225)
Q Consensus        78 i~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg--------  149 (225)
                      ..+|+.++....+++..++-.|..|+||+..++   .+...+.+-+.++|+.+|+|+-+- ..+-+.+.++.        
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            568899999999999999999999999998864   345678899999999999999765 44444554332        


Q ss_pred             ---C-----CC--HHHHHHHHHHHHHhCCCceeeC-HHHHHH
Q 041949          150 ---G-----LE--TNELNKLELDFLFLMGFKMHVN-VSVFES  180 (225)
Q Consensus       150 ---G-----is--~~eLN~LE~~FL~lLdf~L~Vs-~~ef~~  180 (225)
                         .     +.  .+++-.||+.+|..|+|++.+. +..|..
T Consensus       110 ~~~~~~~~~y~~~~~~I~~~E~~iL~~L~f~l~~~~P~~fl~  151 (257)
T 2ivx_A          110 PLLDTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVV  151 (257)
T ss_dssp             CCCCTTSHHHHHHHHHHHHHHHHHHHHTTTCCCCCCHHHHHH
T ss_pred             CCCCcchHHHHHHHHHHHHHHHHHHHHcccceEeeCcHHHHH
Confidence               1     12  8999999999999999999976 666654

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

Probab=98.22  E-value=1.1e-05  Score=70.84  Aligned_cols=106  Identities=19%  Similarity=0.117  Sum_probs=82.1

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCccccccccc--------
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARV--------  148 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkV--------  148 (225)
                      -..+||.++....+++..++-.|.+|+||+..++.   +...+.+-+.++|+.+|+|+-+-...+.+....+        
T Consensus        45 ~~~~~I~~v~~~l~L~~~t~~tA~~~~~RF~~~~s---~~~~~~~lva~acLfLA~K~EE~~~~~~~di~~~~~~~~k~~  121 (285)
T 3rgf_B           45 FFTNVIQALGEHLKLRQQVIATATVYFKRFYARYS---LKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTR  121 (285)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHSC---TTTSCHHHHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhCC---chhcCHHHHHHHHHHHHHhhhccccccHHHHHHHHHHHHccc
Confidence            35688999999999999999999999999999753   4567889999999999999865543332222211        


Q ss_pred             --------CCCCHHHHHHHHHHHHHhCCCceeeC-HHHHH-HHHHHH
Q 041949          149 --------GGLETNELNKLELDFLFLMGFKMHVN-VSVFE-SYCCHL  185 (225)
Q Consensus       149 --------gGis~~eLN~LE~~FL~lLdf~L~Vs-~~ef~-~y~~~L  185 (225)
                              ...+.+++-.||+.+|..|+|++.+. +..|. .|+..+
T Consensus       122 ~~~~~~~~~~~~~~~Il~~E~~iL~~L~f~l~v~~P~~fL~~~~~~l  168 (285)
T 3rgf_B          122 FSYAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDM  168 (285)
T ss_dssp             CTTTCCSCCCCCHHHHHHHHHHHHHHTTTCCCCCCSHHHHHHHHHHH
T ss_pred             ccccCchhhHHHHHHHHHHHHHHHHHcCCCeEeCChHHHHHHHHHHh
Confidence                    12578999999999999999999876 55544 555555

>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=98.04  E-value=4e-06  Score=76.29  Aligned_cols=100  Identities=16%  Similarity=0.196  Sum_probs=78.7

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCC------
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGG------  150 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgG------  150 (225)
                      ...+||.++....+++..++-.|..|+||+...+   .+...+.+-+.++||.+|+|+-+- ..+-+.+..+..      
T Consensus        40 ~~v~wI~ev~~~l~L~~~t~~tAv~~~dRFl~~~---sv~~~~~qlva~acLfLA~K~EE~-p~~l~d~v~v~~~~~~~~  115 (358)
T 2pk2_A           40 QAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQ---SFTRFPGNSVAPAALFLAAKVEEQ-PKKLEHVIKVAHTCLHPQ  115 (358)
T ss_dssp             HHHHHHHHHHTTTTCCHHHHHHHHHHHHHHTTTS---CTTTSCHHHHHHHHHHHHHHHTTC-CCCHHHHHTTHHHHHCSS
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC---CcccccHHHHHHHHHHHHHhhccC-CCCHHHHHHHHHHHhccc
Confidence            3668899999999999999999999999999864   345678899999999999999765 433334433220      


Q ss_pred             ----------C--CHHHHHHHHHHHHHhCCCceeeC-HHHHHH
Q 041949          151 ----------L--ETNELNKLELDFLFLMGFKMHVN-VSVFES  180 (225)
Q Consensus       151 ----------i--s~~eLN~LE~~FL~lLdf~L~Vs-~~ef~~  180 (225)
                                +  ..++|-.||+.+|..|+|+|.+. +..|..
T Consensus       116 ~~~~~~~~~~y~~~~~~Il~~E~~IL~~L~f~L~v~~P~~fL~  158 (358)
T 2pk2_A          116 ESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVV  158 (358)
T ss_dssp             SCCCCTTSHHHHGGGTGGGTHHHHHHHHTTTCCCCCCTTHHHH
T ss_pred             cccccccchhhhHHHHHHHHHHHHHHHHcCCceeCCCHHHHHH
Confidence                      1  26889999999999999999976 555543

>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=98.01  E-value=7.4e-05  Score=66.86  Aligned_cols=103  Identities=19%  Similarity=0.166  Sum_probs=81.1

Q ss_pred             HHHHHHHHHcC--CCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCC------
Q 041949           80 SYLERIFRYTK--AGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGL------  151 (225)
Q Consensus        80 ~fl~rI~~~~~--~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGi------  151 (225)
                      ++|.++....+  ++..++-.|.+|+||+...+.   +...+.+-+.++|+.+|+|+-+- ..+-+.+..+...      
T Consensus        62 ~~I~ev~~~l~~~Lp~~t~~tA~~~~~RF~~~~s---~~~~~~~lva~acLfLA~K~EE~-~~~l~d~v~~~~~~p~~~~  137 (323)
T 1jkw_A           62 KRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNS---VMEYHPRIIMLTCAFLACKVDEF-NVSSPQFVGNLRESPLGQE  137 (323)
T ss_dssp             HHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSC---TTTSCHHHHHHHHHHHHHHHTTC-CCCHHHHGGGSSSCHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhhCC---hhhcCHHHHHHHHHHHHHhhhcC-CCCHHHHHHHhccChhhhH
Confidence            56888888999  999999999999999998653   45678899999999999998654 4455555554332      


Q ss_pred             -CHHHHHHHHHHHHHhCCCceeeC-HHHHH-HHHHHHH
Q 041949          152 -ETNELNKLELDFLFLMGFKMHVN-VSVFE-SYCCHLE  186 (225)
Q Consensus       152 -s~~eLN~LE~~FL~lLdf~L~Vs-~~ef~-~y~~~L~  186 (225)
                       +.+++-.||+.+|..|+|+|.|. +..|. .|+..+.
T Consensus       138 ~~~~~Il~~E~~iL~~L~f~l~v~~P~~~L~~~l~~l~  175 (323)
T 1jkw_A          138 KALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLK  175 (323)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCCCCCCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCcEEcCChHHHHHHHHHHHH
Confidence             36899999999999999999976 55554 4665554

>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=97.97  E-value=7.8e-05  Score=61.95  Aligned_cols=104  Identities=6%  Similarity=0.076  Sum_probs=86.7

Q ss_pred             HHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCHHHHH
Q 041949           78 IQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELN  157 (225)
Q Consensus        78 i~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~eLN  157 (225)
                      -.+++.++....+++..+.-.|..|++|+...+.   +...+..-+..+|+.+|+|.-+ ...+-+.++.+.+++.+++.
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            3568889999999999999999999999998742   3456788999999999999855 57788899999999999999


Q ss_pred             HHHHHHHHhCCCceeeC-H-HHHHHHHHHH
Q 041949          158 KLELDFLFLMGFKMHVN-V-SVFESYCCHL  185 (225)
Q Consensus       158 ~LE~~FL~lLdf~L~Vs-~-~ef~~y~~~L  185 (225)
                      ++|+.+|+.|+|++.+. + .-..+|+..|
T Consensus        84 ~~~~~ll~~L~~~l~~~~p~~~l~r~~~~l  113 (207)
T 1c9b_A           84 RCFKLILKALETSVDLITTGDFMSRFCSNL  113 (207)
T ss_dssp             HHHHHHHHHTTCCCCCCCTHHHHHHHHHHT
T ss_pred             HHHHHHHHHHCCCcCcCCHHHHHHHHHHHC
Confidence            99999999999999765 3 3344555544

>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=97.39  E-value=0.00082  Score=55.31  Aligned_cols=105  Identities=11%  Similarity=0.096  Sum_probs=87.3

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCHHHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNEL  156 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~eL  156 (225)
                      .-.+++.++....+++..+.=.|..|.+|+...+  . +...+..-+..+|+-+|+|..+ ...+-+..+.+.|++.+++
T Consensus        11 ~a~~~I~~~~~~L~L~~~v~~~A~~l~~~~~~~~--~-~~gr~~~~vaaAclylAcr~~~-~p~~l~di~~~~~v~~~~i   86 (200)
T 1ais_B           11 FALSELDRITAQLKLPRHVEEEAARLYREAVRKG--L-IRGRSIESVMAACVYAACRLLK-VPRTLDEIADIARVDKKEI   86 (200)
T ss_dssp             HHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTT--T-TTTCCHHHHHHHHHHHHHHHHT-CCCCHHHHHHHTTSCHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhCC--C-cCCCCHHHHHHHHHHHHHHHcC-CCCCHHHHHHHHCCCHHHH
Confidence            4567899999999999999999999999998853  2 2456688899999999999866 6788889999999999999


Q ss_pred             HHHHHHHHHhCCCceee---CHHHHH-HHHHHH
Q 041949          157 NKLELDFLFLMGFKMHV---NVSVFE-SYCCHL  185 (225)
Q Consensus       157 N~LE~~FL~lLdf~L~V---s~~ef~-~y~~~L  185 (225)
                      ..+|+.+++.++|++.+   ++..|- +|+..|
T Consensus        87 ~~~~~~l~~~L~~~~~~~~~~p~~~i~r~~~~L  119 (200)
T 1ais_B           87 GRSYRFIARNLNLTPKKLFVKPTDYVNKFADEL  119 (200)
T ss_dssp             HHHHHHHHHHTTCCTTTTCCCGGGGHHHHHHHH
T ss_pred             HHHHHHHHHHhcccCCcCCCCHHHHHHHHHHHc
Confidence            99999999999999875   454443 555554

>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=93.83  E-value=0.2  Score=40.74  Aligned_cols=95  Identities=11%  Similarity=0.069  Sum_probs=76.8

Q ss_pred             CCc--hhHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCC
Q 041949           73 IPD--MTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGG  150 (225)
Q Consensus        73 ~P~--isi~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgG  150 (225)
                      .|.  ++-.+|+.|+.+..+++..+.-.|..++.+.....  . ....++.-+..+|+-+|++..+ ...+.+.++++.|
T Consensus       101 ~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~-~~gr~P~~iAaAaly~A~~~~~-~~~t~~ei~~~~~  176 (200)
T 1ais_B          101 PKKLFVKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRG--L-TSGKSPAGLVAAALYIASLLEG-EKRTQREVAEVAR  176 (200)
T ss_dssp             TTTTCCCGGGGHHHHHHHHTCCHHHHHHHHHHHHHHHHTT--C-CTTSCHHHHHHHHHHHHHHHTT-CCCCHHHHHHHHT
T ss_pred             CCcCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcC--c-ccCCCHHHHHHHHHHHHHHHhC-CCCCHHHHHHHhC
Confidence            444  67789999999999999999888988888877742  2 3457788999999999999865 4467788999999


Q ss_pred             CCHHHHHHHHHHHHHhCCCce
Q 041949          151 LETNELNKLELDFLFLMGFKM  171 (225)
Q Consensus       151 is~~eLN~LE~~FL~lLdf~L  171 (225)
                      ++..++..-=.++...++-++
T Consensus       177 vs~~ti~~~~~~l~~~l~~~~  197 (200)
T 1ais_B          177 VTEVTVRNRYKELVEKLKIKV  197 (200)
T ss_dssp             CCHHHHHHHHHHHHHHHTCCC
T ss_pred             CCHHHHHHHHHHHHHHcCCCC
Confidence            999999888888887776443

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

Probab=93.66  E-value=0.052  Score=48.64  Aligned_cols=106  Identities=9%  Similarity=0.096  Sum_probs=73.5

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCHHHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNEL  156 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~eL  156 (225)
                      ....+|.++....+++..+.=.|..|..|+...+   .+...+..-+..+|+.+|.| .+....+-+.++.+.+++.+|+
T Consensus       128 ~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~~~~~~---~~kgr~~~~vaaAclyiAcR-~e~~prtl~ei~~~~~v~~keI  203 (345)
T 3k7a_M          128 AAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEK---TLKGKSMESIMAASILIGCR-RAEVARTFKEIQSLIHVKTKEF  203 (345)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHTHHHHHHHHHSSSC---SSCCCCSHHHHTTTTTTTSB-TTBSSCCHHHHHHSSSCCSHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC---cccCCcHHHHHHHHHHHHHH-HcCCCccHHHHHHHHCCCHHHH
Confidence            3457788888899999999999999999987743   13445678888999999999 4566788889999999999999


Q ss_pred             HHHHHHHHHhCC------------Cceee-CHHHHH-HHHHHHH
Q 041949          157 NKLELDFLFLMG------------FKMHV-NVSVFE-SYCCHLE  186 (225)
Q Consensus       157 N~LE~~FL~lLd------------f~L~V-s~~ef~-~y~~~L~  186 (225)
                      .+.++.+++.|+            +++.+ ++..|. +|+..|.
T Consensus       204 gr~~~~l~~~L~~~~~~~~~~~~~~~~~~~~p~~~i~Rf~~~L~  247 (345)
T 3k7a_M          204 GKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLG  247 (345)
T ss_dssp             HHHHHHHHHHHTCC------------------------------
T ss_pred             HHHHHHHHHHHhhhhccccccccccccCCCCHHHHHHHHHHHcC
Confidence            999999999998            66653 355554 5666554

>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=91.61  E-value=0.59  Score=38.13  Aligned_cols=88  Identities=9%  Similarity=0.042  Sum_probs=68.6

Q ss_pred             CchhHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCH
Q 041949           74 PDMTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLET  153 (225)
Q Consensus        74 P~isi~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~  153 (225)
                      |...-.+|+.|+.+..+++..+.-.|...+.+....  +. ....+++-+..+|+.+|++..+ ...+.+.|+++.|++.
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            345668999999999999998888888777776653  22 3457789999999999999875 5567788999999998


Q ss_pred             HHHHHHHHHHHH
Q 041949          154 NELNKLELDFLF  165 (225)
Q Consensus       154 ~eLN~LE~~FL~  165 (225)
                      .++..-=++++.
T Consensus       174 ~tI~~~~~~l~~  185 (207)
T 1c9b_A          174 VTIRQSYRLIYP  185 (207)
T ss_dssp             HHHHHHHHHHGG
T ss_pred             HHHHHHHHHHHH
Confidence            888766555444

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

Probab=82.06  E-value=3.5  Score=36.83  Aligned_cols=91  Identities=8%  Similarity=0.015  Sum_probs=72.9

Q ss_pred             hhHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCHHH
Q 041949           76 MTIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNE  155 (225)
Q Consensus        76 isi~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~e  155 (225)
                      ..-...|.++....+++..+.=.|..+..|+....  + +...+..-+..+|+.+|.|- +....+-+..+.+.+++.+|
T Consensus       127 ~~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~a~~~~--~-~rGrs~e~vaAAclYiACR~-~~~prtl~eI~~~~~v~~ke  202 (345)
T 4bbr_M          127 QAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEK--T-LKGKSMESIMAASILIGCRR-AEVARTFKEIQSLIHVKTKE  202 (345)
T ss_dssp             THHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCT--T-TTTCCHHHHHHHHHHHHHHH-TCCBCCHHHHHHHHTCCTTH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC--C-ccCCCHHHHHHHHHHHHHHh-cCCCccHHHHHHHhCCCHHH
Confidence            35667788899999999999999988888887742  2 23456788888999999985 56778888899999999999


Q ss_pred             HHHHHHHHHHhCCCc
Q 041949          156 LNKLELDFLFLMGFK  170 (225)
Q Consensus       156 LN~LE~~FL~lLdf~  170 (225)
                      |.+..+.+.+.|+..
T Consensus       203 igr~~k~l~~~L~l~  217 (345)
T 4bbr_M          203 FGKTLNIMKNILRGK  217 (345)
T ss_dssp             HHHHHHHHHHCC---
T ss_pred             HHHHHHHHHHHhCcc
Confidence            999999999999864

---

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	225
d1w98b2	140	G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax	99.09
d2cchb1	128	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	99.03
d1bu2a1	127	Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}	98.99
d1g3nc1	132	Viral cyclin {Kaposi's sarcoma-associated herpesvi	98.99
d1f5qb1	141	Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]	98.98
d2i53a1	144	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	98.64
d2ivxa1	143	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	98.42
d1jkwa1	151	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	98.41
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	95.6
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	95.35
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	94.83
d1vola2	109	Transcription factor IIB (TFIIB), core domain {Hum	93.36

>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=99.09  E-value=2.8e-10  Score=88.79  Aligned_cols=94  Identities=18%  Similarity=0.294  Sum_probs=83.1

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCccccccccc--CCCCHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARV--GGLETN  154 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkV--gGis~~  154 (225)
                      .+.+|+.++..+.+++++++.+|.-|+||+....+.  +...+.+.+.++|++||+|+.+......+.+.++  +.++.+
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            477899999999999999999999999999875432  4567789999999999999998888888888876  458999


Q ss_pred             HHHHHHHHHHHhCCCcee
Q 041949          155 ELNKLELDFLFLMGFKMH  172 (225)
Q Consensus       155 eLN~LE~~FL~lLdf~L~  172 (225)
                      |+.+||+..|..|+|+|+
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=5.4e-10  Score=85.66  Aligned_cols=93  Identities=17%  Similarity=0.220  Sum_probs=81.8

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC--CCCHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG--GLETN  154 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg--Gis~~  154 (225)
                      .+.+|+.++.++.+++++++.+|..|+||+....+   +...+.+-+.++|+++|+|+-+.....-+.+.+++  .++.+
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            36799999999999999999999999999998642   45678899999999999999988777777777763  47999


Q ss_pred             HHHHHHHHHHHhCCCcee
Q 041949          155 ELNKLELDFLFLMGFKMH  172 (225)
Q Consensus       155 eLN~LE~~FL~lLdf~L~  172 (225)
                      |+.+||+..|..|+|+|.
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=98.99  E-value=1.1e-09  Score=84.21  Aligned_cols=91  Identities=13%  Similarity=0.178  Sum_probs=81.5

Q ss_pred             HHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC--CCCHHH
Q 041949           78 IQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG--GLETNE  155 (225)
Q Consensus        78 i~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg--Gis~~e  155 (225)
                      +.+|+.++..+.+++++++.+|..|+||+....   .++..+.+-+-++|+++|+|+-+-...+-+.+.+++  .++.+|
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            679999999999999999999999999999853   356788999999999999999887777777777774  479999


Q ss_pred             HHHHHHHHHHhCCCce
Q 041949          156 LNKLELDFLFLMGFKM  171 (225)
Q Consensus       156 LN~LE~~FL~lLdf~L  171 (225)
                      +.+||+..|..|+||+
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=98.99  E-value=7.3e-10  Score=85.66  Aligned_cols=92  Identities=15%  Similarity=0.212  Sum_probs=81.0

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCccccccccc--CCCCHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARV--GGLETN  154 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkV--gGis~~  154 (225)
                      .+.+|+.++..+.+++++++.+|..|+||+....   .++....+.+-++|+.+|+|+-+....+-+.+.++  +.++.+
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            4779999999999999999999999999999854   35677889999999999999977666666777766  468999


Q ss_pred             HHHHHHHHHHHhCCCce
Q 041949          155 ELNKLELDFLFLMGFKM  171 (225)
Q Consensus       155 eLN~LE~~FL~lLdf~L  171 (225)
                      |+.+||..+|..|+|+|
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=98.98  E-value=1.5e-09  Score=84.89  Aligned_cols=92  Identities=14%  Similarity=0.235  Sum_probs=82.8

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCccccccccc--CCCCHH
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARV--GGLETN  154 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkV--gGis~~  154 (225)
                      .+.+|+.++..+.+++++++.+|..|+||+....+   ++..+.+-+-++|+.+|+|+-+........+..+  +.++.+
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            68899999999999999999999999999998643   5677899999999999999998877777777776  458999


Q ss_pred             HHHHHHHHHHHhCCCce
Q 041949          155 ELNKLELDFLFLMGFKM  171 (225)
Q Consensus       155 eLN~LE~~FL~lLdf~L  171 (225)
                      |+..||...|..|+|.+
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=98.64  E-value=4.7e-08  Score=75.68  Aligned_cols=93  Identities=15%  Similarity=0.131  Sum_probs=73.6

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCccccc------------
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSY------------  144 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~------------  144 (225)
                      .+.+|+..+....+++..++..|..|+||+..++   .+...+.+-+.+||+.+|+|+-+... .-+.            
T Consensus        39 ~~~~~i~~~~~~l~l~~~t~~~A~~~~dRf~~~~---~~~~~~~~lva~acl~LA~K~eE~~~-~l~~vi~~~~~~~~~~  114 (144)
T d2i53a1          39 EGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFH---SFKQFPRYVTGACCLFLAGKVEETPK-KCKDIIKTARSLLNDV  114 (144)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTS---CTTTSCHHHHHHHHHHHHHHHTTCCC-CHHHHHHHHHHHSCHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhhC---cccchhHHHHHHHHHHHHHHhhcccc-cHHHHHHHHHHHhhhh
Confidence            4668999999999999999999999999998864   35567899999999999999866421 1111            


Q ss_pred             -ccccCCCCHHHHHHHHHHHHHhCCCceee
Q 041949          145 -FARVGGLETNELNKLELDFLFLMGFKMHV  173 (225)
Q Consensus       145 -~AkVgGis~~eLN~LE~~FL~lLdf~L~V  173 (225)
                       ....+..+.+++-.||+..|..|+|+|+|
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             11112235688999999999999999986

>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=3.5e-07  Score=70.29  Aligned_cols=93  Identities=19%  Similarity=0.207  Sum_probs=72.3

Q ss_pred             hHHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccc---------
Q 041949           77 TIQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFAR---------  147 (225)
Q Consensus        77 si~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~Ak---------  147 (225)
                      ...+|+.++..+.+++..++..|.+|+||+..++   .+...+++-+.+||+.+|+|+-+...- -++...         
T Consensus        33 ~~~~~i~~~~~~l~l~~~t~~~A~~l~~Rf~~~~---s~~~~~~~~va~acl~LA~K~eE~~~~-~~~ii~~~~~~~~~~  108 (143)
T d2ivxa1          33 QAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHH---SFTKFNKNIISSTALFLAAKVEEQARK-LEHVIKVAHACLHPL  108 (143)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTS---CTTTSCHHHHHHHHHHHHHHHTTCCCC-HHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhC---CccccCHHHHHHHHHHHHHHhcccccc-HHHHHHHHHHHhccc
Confidence            3457888899999999999999999999998864   356778999999999999999775321 111000         


Q ss_pred             ---------cCCCCHHHHHHHHHHHHHhCCCceee
Q 041949          148 ---------VGGLETNELNKLELDFLFLMGFKMHV  173 (225)
Q Consensus       148 ---------VgGis~~eLN~LE~~FL~lLdf~L~V  173 (225)
                               ......+++..||+..|+.|+|++.|
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                     00124678999999999999999986

>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=98.41  E-value=7.2e-07  Score=69.45  Aligned_cols=90  Identities=21%  Similarity=0.231  Sum_probs=69.6

Q ss_pred             HHHHHHHHHcC--CCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccC-------C
Q 041949           80 SYLERIFRYTK--AGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVG-------G  150 (225)
Q Consensus        80 ~fl~rI~~~~~--~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVg-------G  150 (225)
                      +++.++..+.+  ++..++-.|.+|++|+..++.   +...+.+-+.++|+.+|+|+-+ ...+-+.+.+..       .
T Consensus        52 ~~l~~~~~~~k~~l~~~~~~tA~~~~~RF~~~~s---~~~~~~~li~~acl~LA~K~ee-~~~~~~~~~~~~~~~~~~~~  127 (151)
T d1jkwa1          52 KRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNS---VMEYHPRIIMLTCAFLACKVDE-FNVSSPQFVGNLRESPLGQE  127 (151)
T ss_dssp             HHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSC---TTTSCHHHHHHHHHHHHHHHTT-CCCCHHHHGGGSSSCHHHHH
T ss_pred             HHHHHHHHHHccCCCHHHHHHHHHHHHHHhhcCc---cccccHHHHHHHHHHHHHHHcc-cCCCHHHHHHHHHhhccccc
Confidence            45666666544  889999999999999999753   5677889999999999999855 333333333221       1


Q ss_pred             CCHHHHHHHHHHHHHhCCCceee
Q 041949          151 LETNELNKLELDFLFLMGFKMHV  173 (225)
Q Consensus       151 is~~eLN~LE~~FL~lLdf~L~V  173 (225)
                      .+.+++..||...|..|+|+|.|
T Consensus       128 ~~~~~i~~~E~~iL~~L~f~L~V  150 (151)
T d1jkwa1         128 KALEQILEYELLLIQQLNFHLIV  150 (151)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             ccHHHHHHHHHHHHHHcCCeeee
Confidence            46889999999999999999987

>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=95.60  E-value=0.069  Score=37.04  Aligned_cols=90  Identities=6%  Similarity=-0.017  Sum_probs=76.3

Q ss_pred             HHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCHHHHH
Q 041949           78 IQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELN  157 (225)
Q Consensus        78 i~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~eLN  157 (225)
                      ....++++....++++.+.=-|..+..+..+..  + ....+..-+..+|+-+|.+. .+...+-+..+++.|++.++++
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            456799999999999999999988888887742  2 24566788999999999985 5677888899999999999999


Q ss_pred             HHHHHHHHhCCCce
Q 041949          158 KLELDFLFLMGFKM  171 (225)
Q Consensus       158 ~LE~~FL~lLdf~L  171 (225)
                      +.-+.+.+.++.++
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=95.35  E-value=0.037  Score=38.62  Aligned_cols=90  Identities=12%  Similarity=0.092  Sum_probs=74.1

Q ss_pred             HHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCHHHHHH
Q 041949           79 QSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNK  158 (225)
Q Consensus        79 ~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~eLN~  158 (225)
                      .+|+.|+....+++..+.=.|..+..+..+.  + .+...+..-+..+|+-+|++.. +...+-+..+++.|+|...++.
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            4899999999999999888887777776663  2 2456778899999999999876 4556788999999999999999


Q ss_pred             HHHHHHHhCCCcee
Q 041949          159 LELDFLFLMGFKMH  172 (225)
Q Consensus       159 LE~~FL~lLdf~L~  172 (225)
                      -=+++...++.++=
T Consensus        80 ~yk~l~~~l~~~~p   93 (95)
T d1aisb2          80 RYKELVEKLKIKVP   93 (95)
T ss_dssp             HHHHHHHHHTCCCC
T ss_pred             HHHHHHHHhCCCCC
Confidence            99999988887653

>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=94.83  E-value=0.12  Score=35.92  Aligned_cols=86  Identities=14%  Similarity=0.125  Sum_probs=71.2

Q ss_pred             HHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCHHHHHH
Q 041949           79 QSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELNK  158 (225)
Q Consensus        79 ~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~eLN~  158 (225)
                      ...++|+.+..+++..+.=-|.-+..+..+.  ++ ....+..-+..+|+-+|.+.. +...+-+..|++.|++..++.+
T Consensus         6 ~~~I~~~~~~L~L~~~i~~~A~~i~k~~~~~--~~-~~g~~~~~iaaA~iY~Acr~~-~~~~t~~eIa~~~~is~~ti~k   81 (98)
T d1aisb1           6 LSELDRITAQLKLPRHVEEEAARLYREAVRK--GL-IRGRSIESVMAACVYAACRLL-KVPRTLDEIADIARVDKKEIGR   81 (98)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHHHHTT--TT-TTTCCHHHHHHHHHHHHHHHH-TCCCCHHHHHHHTTSCHHHHHH
T ss_pred             HHHHHHHHHHcCcCHHHHHHHHHHHHHHHHh--hh-hcCCCHHHHHHHHHHHHHHHc-CCCCCHHHHHHHHCCCHHHHHH
Confidence            4568899999999999988888777777663  22 245667888889999999865 7778889999999999999999


Q ss_pred             HHHHHHHhCC
Q 041949          159 LELDFLFLMG  168 (225)
Q Consensus       159 LE~~FL~lLd  168 (225)
                      ..+.+++.|+
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=93.36  E-value=0.072  Score=38.06  Aligned_cols=83  Identities=8%  Similarity=0.071  Sum_probs=67.2

Q ss_pred             HHHHHHHHHHHcCCCchHHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhcccCCcccccccccCCCCHHHHH
Q 041949           78 IQSYLERIFRYTKAGPSVYVVAYVYIDRFCQANPGFRIHATNVHRLLITTIMVASKYVEDLNYRNSYFARVGGLETNELN  157 (225)
Q Consensus        78 i~~fl~rI~~~~~~s~~~~llAliYldRl~~~~~~~~l~~~n~hRL~ltsl~lAsK~~dD~~~~N~~~AkVgGis~~eLN  157 (225)
                      -.+|+.|+....+++..+.=.|..+..++.+.+  + ....+..-+..+|+.+|++. .+...+-+..|+++|++..++.
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            358999999999999998888888888887742  2 35677888999999999985 4567788899999999999998


Q ss_pred             HHHHHHH
Q 041949          158 KLELDFL  164 (225)
Q Consensus       158 ~LE~~FL  164 (225)
                      +.=+.+.
T Consensus        80 k~yk~l~   86 (109)
T d1vola2          80 QSYRLIY   86 (109)
T ss_dssp             HHHHHHG
T ss_pred             HHHHHHH
Confidence            7655553