Citrus Sinensis ID: 038406

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------12
Protein Sequence
MVLHRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK
Secondary Structure (PSIPRED)
cccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHccccHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccEEEccccccccccccHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHcccEEEEccccHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mvlhrrefspskkdgisfkkdSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYYKQKELILTAErllpatiafdfdiqlpyepLVAAFTRLDLVCDLAKSSMEFHK
Flexible Loop (DISEMBL)
mvlhrrefspskkdgisfkkdsELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK
Low Complexity Region (SEG)
MVLHRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK
Disordered region (IsUnstruct)
*********************SELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLA********
Disordered Region (DISOPRED)
*************DGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFH*
Disordered Region (DISEMBL)
**************GISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLA********
Disordered Region (DISPRO)
*******FSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVLHRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK
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	118	2.2.26 [Sep-21-2011]
Q8LBC0	317	Cyclin-T1-3 OS=Arabidopsi	yes	no	0.923	0.343	0.362	5e-21
Q2QQS5	543	Cyclin-T1-4 OS=Oryza sati	yes	no	0.932	0.202	0.345	8e-21
Q6Z7H3	630	Cyclin-T1-2 OS=Oryza sati	no	no	0.838	0.157	0.36	1e-20
Q0E474	446	Cyclin-T1-1 OS=Oryza sati	no	no	0.822	0.217	0.351	8e-19
Q8GYM6	541	Cyclin-T1-4 OS=Arabidopsi	no	no	0.932	0.203	0.314	3e-18
Q9FKE6	579	Cyclin-T1-5 OS=Arabidopsi	no	no	0.932	0.189	0.314	3e-18
Q2RAC5	490	Cyclin-T1-3 OS=Oryza sati	no	no	0.838	0.202	0.326	1e-17
Q56YF8	460	Cyclin-T1-2 OS=Arabidopsi	no	no	0.796	0.204	0.316	4e-15
Q9C8P7	247	Putative cyclin-T1-1 OS=A	no	no	0.720	0.344	0.290	2e-08
Q9AS36	427	Cyclin-L1-1 OS=Oryza sati	no	no	0.415	0.114	0.469	1e-05

>sp|Q8LBC0|CCT13_ARATH Cyclin-T1-3 OS=Arabidopsis thaliana GN=CYCT1-3 PE=1 SV=2

 Score = 99.8 bits (247), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 58/160 (36%), Positives = 78/160 (48%), Gaps = 51/160 (31%)

Query: 8   FSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH----- 62
           FSPS+KDGI   K+S L   YC+FLQ LG KL + QV ++CAM++CH+FYM Q H     
Sbjct: 44  FSPSRKDGIDLVKESFLRSSYCTFLQRLGMKLHVSQVTISCAMVMCHRFYMRQSHAKNDW 103

Query: 63  ----------------------------------------------DVYYKQKELILTAE 76
                                                         + Y++ KE+IL+ E
Sbjct: 104 QTIATSSLFLACKAEDEPCQLSSVVVASYEIIYEWDPSASIRIHQTECYHEFKEIILSGE 163

Query: 77  RLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEF 116
            LL +T AF  DI+LPY+PL AA  RL+   DLA ++  F
Sbjct: 164 SLLLSTSAFHLDIELPYKPLAAALNRLNAWPDLATAAWNF 203

Arabidopsis thaliana (taxid: 3702)

>sp|Q2QQS5|CCT14_ORYSJ Cyclin-T1-4 OS=Oryza sativa subsp. japonica GN=CYCT1-1 PE=2 SV=1

 Score = 99.0 bits (245), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 56/162 (34%), Positives = 81/162 (50%), Gaps = 52/162 (32%)

Query: 7   EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH---- 62
           E SPS++DGI  KK+S L K YC+FLQ+LG +LK+PQV +A A++ CH+FY+ Q H    
Sbjct: 45  ENSPSRRDGIDLKKESYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFYLRQSHAKND 104

Query: 63  -----------------------------------------------DVYYKQKELILTA 75
                                                          +VY +QKELIL A
Sbjct: 105 RRTIATVCMFLAGKVEETPRPLKDVILVSYEIIHKKDPAAGQRIKQKEVYDQQKELILLA 164

Query: 76  ERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCD-LAKSSMEF 116
           ER++ AT+ FD ++  PY+PLV A  +  +  + LA+ +  F
Sbjct: 165 ERVVLATLGFDLNVHHPYKPLVEAIRKFKVAQNALAQVAWNF 206

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q6Z7H3|CCT12_ORYSJ Cyclin-T1-2 OS=Oryza sativa subsp. japonica GN=CYCT1_2 PE=2 SV=2

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 54/150 (36%), Positives = 79/150 (52%), Gaps = 51/150 (34%)

Query: 7   EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ------ 60
           +FSPS+KDGI+   +SE+ +LYCSF++++G +LKLPQ+ +A A+M CH+FY++Q      
Sbjct: 27  KFSPSRKDGITEIMESEIRQLYCSFIRDVGIRLKLPQMTIATAIMFCHRFYLYQSLAKNG 86

Query: 61  -------------------------------------------LH--DVYYKQKELILTA 75
                                                      +H  DV+ KQK LILT 
Sbjct: 87  WQTIATVCIFLASKVEDTPCPLDQVIRVAYGTMYRRDPATARRIHQKDVFEKQKALILTG 146

Query: 76  ERLLPATIAFDFDIQLPYEPLVAAFTRLDL 105
           ERL+  T+ FDF+IQ PY PL+ A  +L +
Sbjct: 147 ERLVLTTVRFDFNIQHPYRPLLDAMEKLGI 176

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q0E474|CCT11_ORYSJ Cyclin-T1-1 OS=Oryza sativa subsp. japonica GN=CYCT1-1 PE=3 SV=2

 Score = 92.4 bits (228), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 52/148 (35%), Positives = 72/148 (48%), Gaps = 51/148 (34%)

Query: 9   SPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH------ 62
           SPS++DG+   K++EL   YCSF++++G +L+LPQV +A A +LCH+FY+ Q H      
Sbjct: 20  SPSRRDGVGAAKEAELRATYCSFIRDVGLRLQLPQVTIATATLLCHRFYLRQSHAKNEWQ 79

Query: 63  ---------------------------------------------DVYYKQKELILTAER 77
                                                        +V  KQKELIL  E 
Sbjct: 80  TVATVCVFLASKIEDTPCPLQRVIIVAYETMYRKDCNAAHRIYQKEVLEKQKELILVGET 139

Query: 78  LLPATIAFDFDIQLPYEPLVAAFTRLDL 105
           LL +TI FDF+IQ PYEPL  A  +L +
Sbjct: 140 LLLSTIRFDFNIQHPYEPLKLALKKLGI 167

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8GYM6|CCT14_ARATH Cyclin-T1-4 OS=Arabidopsis thaliana GN=CYCT1-4 PE=1 SV=1

 Score = 90.5 bits (223), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 51/162 (31%), Positives = 79/162 (48%), Gaps = 52/162 (32%)

Query: 7   EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH---- 62
           E SPS+ D I  KK++ L K YC+FLQ+LG +LK+PQV +A A++ CH+F++ Q H    
Sbjct: 42  ENSPSRLDSIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIIFCHRFFIRQSHARND 101

Query: 63  -----------------------------------------------DVYYKQKELILTA 75
                                                          +VY +QKELIL  
Sbjct: 102 RRTIATVCMFLAGKVEETPRPLKDVIVVSYEIIHKKDPTTAQKIKQKEVYEQQKELILNG 161

Query: 76  ERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCD-LAKSSMEF 116
           E+++ +T+ FDF++  PY+PLV A  +  +  + LA+ +  F
Sbjct: 162 EKIVLSTLGFDFNVYHPYKPLVEAIKKFKVAQNALAQVAWNF 203

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKE6|CCT15_ARATH Cyclin-T1-5 OS=Arabidopsis thaliana GN=CYCT1-5 PE=2 SV=2

 Score = 90.1 bits (222), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 51/162 (31%), Positives = 78/162 (48%), Gaps = 52/162 (32%)

Query: 7   EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH---- 62
           E SPS+ DGI  KK++ L K YC+FLQ+LG +LK+PQV +A A++ CH+F+  Q H    
Sbjct: 42  ENSPSRLDGIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIIFCHRFFFRQSHAKND 101

Query: 63  -----------------------------------------------DVYYKQKELILTA 75
                                                          +VY +QKELIL  
Sbjct: 102 RRTIATVCMFLAGKVEETPRPLKDVIFVSYEIINKKDPGASQKIKQKEVYEQQKELILNG 161

Query: 76  ERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCD-LAKSSMEF 116
           E+++ +T+ FD ++  PY+PLV A  +  +  + LA+ +  F
Sbjct: 162 EKIVLSTLGFDLNVYHPYKPLVEAIKKFKVAQNALAQVAWNF 203

Arabidopsis thaliana (taxid: 3702)

>sp|Q2RAC5|CCT13_ORYSJ Cyclin-T1-3 OS=Oryza sativa subsp. japonica GN=CYCT1-3 PE=3 SV=2

 Score = 88.6 bits (218), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 49/150 (32%), Positives = 72/150 (48%), Gaps = 51/150 (34%)

Query: 7   EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH---- 62
           E S S++DGI  KK+S L K YC+FLQ+LG +LK+PQV +A A++ CH+F++ Q H    
Sbjct: 46  ENSLSRRDGIDLKKESYLRKSYCTFLQDLGMRLKVPQVTIATAIVFCHRFFLRQSHAKND 105

Query: 63  -----------------------------------------------DVYYKQKELILTA 75
                                                          +VY +QKELIL  
Sbjct: 106 RRTIATVCMFLAGKVEETPRPLKDVILISYEIIHKKDAAAVQRIKQKEVYEQQKELILLG 165

Query: 76  ERLLPATIAFDFDIQLPYEPLVAAFTRLDL 105
           ER++  T+ FD ++  PY+PLV A  +  +
Sbjct: 166 ERVVLVTLGFDLNVHHPYKPLVEAIKKFKV 195

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q56YF8|CCT12_ARATH Cyclin-T1-2 OS=Arabidopsis thaliana GN=CYCT1-2 PE=2 SV=2

 Score = 80.1 bits (196), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 45/142 (31%), Positives = 66/142 (46%), Gaps = 48/142 (33%)

Query: 9   SPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH------ 62
           SPS++DGI  K ++ L   YC+FL+ LG +LK+PQV +A A+  CH+F++ Q H      
Sbjct: 42  SPSRRDGIDLKTETRLRDSYCTFLEILGERLKVPQVTIATAIFFCHRFFLRQSHAKNDRQ 101

Query: 63  ------------------------------------------DVYYKQKELILTAERLLP 80
                                                     +VY +QKEL+L  E L+ 
Sbjct: 102 TIATVCMLLAGKVEETPVTLEDVIIASYERIHKKDLAGAQRKEVYDQQKELVLIGEELVL 161

Query: 81  ATIAFDFDIQLPYEPLVAAFTR 102
           +T+ FD  I  PY+PLV A  +
Sbjct: 162 STLNFDLCISHPYKPLVEAIKK 183

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C8P7|CCT11_ARATH Putative cyclin-T1-1 OS=Arabidopsis thaliana GN=CYCT1-1 PE=3 SV=1

 Score = 57.8 bits (138), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 38/131 (29%), Positives = 60/131 (45%), Gaps = 46/131 (35%)

Query: 9   SPSKKDGISFKKDS-ELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ------- 60
           SPS+ DGI+ K+++ + W  Y SFLQELG +L  PQ  +A A++LC +F+  Q       
Sbjct: 18  SPSRLDGINLKEETFQRWS-YTSFLQELGQRLNNPQKTIATAIVLCQRFFTRQSLTKNDP 76

Query: 61  -------------------------------------LHDVYYKQKELILTAERLLPATI 83
                                                L DV+ + K  +LT E+L+ +T+
Sbjct: 77  KTVAIICMFIAGKVEGSPRPAGDVVFVSYRVLFNKEPLRDVFERLKMTVLTGEKLVLSTL 136

Query: 84  AFDFDIQLPYE 94
             D +I+ PY+
Sbjct: 137 ECDLEIEHPYK 147

Arabidopsis thaliana (taxid: 3702)

>sp|Q9AS36|CCL11_ORYSJ Cyclin-L1-1 OS=Oryza sativa subsp. japonica GN=CYCL1-1 PE=2 SV=1

 Score = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 31/49 (63%)

Query: 9  SPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFY 57
          SPS+KDGI    ++ L    C  +QE G  LKLPQ ++A A +L H+FY
Sbjct: 19 SPSRKDGIDEATETALRVYGCDLIQESGILLKLPQAVMATAQVLFHRFY 67

Oryza sativa subsp. japonica (taxid: 39947)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	118
449532123	230	PREDICTED: cyclin-T1-4-like, partial [Cu	0.915	0.469	0.459	4e-28
224062095	426	predicted protein [Populus trichocarpa]	0.932	0.258	0.416	2e-26
255538732	433	cyclin-dependent protein kinase, putativ	0.915	0.249	0.415	2e-23
449470130	429	PREDICTED: cyclin-T1-3-like [Cucumis sat	0.915	0.251	0.470	2e-21
225458191	442	PREDICTED: cyclin-T1-4 [Vitis vinifera]	0.915	0.244	0.393	9e-20
297845718	317	cyclin family protein [Arabidopsis lyrat	0.923	0.343	0.368	9e-20
302142541	454	unnamed protein product [Vitis vinifera]	0.915	0.237	0.393	9e-20
356576769	568	PREDICTED: cyclin-T1-5-like [Glycine max	0.838	0.174	0.346	1e-19
356521602	567	PREDICTED: cyclin-T1-5-like [Glycine max	0.838	0.174	0.346	1e-19
21618277	317	putative cyclin [Arabidopsis thaliana]	0.923	0.343	0.362	2e-19

>gi|449532123|ref|XP_004173033.1| PREDICTED: cyclin-T1-4-like, partial [Cucumis sativus]

 Score =  128 bits (322), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 73/159 (45%), Positives = 87/159 (54%), Gaps = 51/159 (32%)

Query: 9   SPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH------ 62
           SPS+KDGI FKK+S+L K YCSFLQELG KLK+PQV +A AMMLCH+FYM Q H      
Sbjct: 45  SPSRKDGIDFKKESQLRKSYCSFLQELGMKLKVPQVTIASAMMLCHRFYMRQSHAKNDWQ 104

Query: 63  ---------------------------------------------DVYYKQKELILTAER 77
                                                        +V+ KQKELIL AER
Sbjct: 105 TIGTASIFLACKIEETPRFLNDVVVVAYELTFKWDPSASKRIRQKEVFNKQKELILIAER 164

Query: 78  LLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEF 116
           LL +T+AF+ DIQLPY+PLVAA  RL +  DL K +  F
Sbjct: 165 LLLSTLAFEVDIQLPYKPLVAALKRLGMAADLGKVAWNF 203

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224062095|ref|XP_002300752.1| predicted protein [Populus trichocarpa] gi|222842478|gb|EEE80025.1| predicted protein [Populus trichocarpa]

 Score =  122 bits (307), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 67/161 (41%), Positives = 89/161 (55%), Gaps = 51/161 (31%)

Query: 7   EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD--- 63
           +FSPS++DGI  +K+S+L KLYCSF++ELG KLK+PQV +ACA++LCH+FYM Q H    
Sbjct: 30  DFSPSRRDGIDVEKESQLRKLYCSFIKELGVKLKVPQVTIACALILCHRFYMRQSHAKND 89

Query: 64  ---------------------------VYYK---------------------QKELILTA 75
                                      V Y+                     QKEL++T 
Sbjct: 90  WKTMASASMFLACKLEETPRLLRDVVVVAYELMHKRDPSASHRIRQIGFCSSQKELLVTG 149

Query: 76  ERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEF 116
           ERLL ATI FD D+QLPY+PLV A  +L++  DLAK +  F
Sbjct: 150 ERLLLATIGFDLDVQLPYKPLVNALKKLNIYPDLAKVAWNF 190

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255538732|ref|XP_002510431.1| cyclin-dependent protein kinase, putative [Ricinus communis] gi|223551132|gb|EEF52618.1| cyclin-dependent protein kinase, putative [Ricinus communis]

 Score =  113 bits (282), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 66/159 (41%), Positives = 82/159 (51%), Gaps = 51/159 (32%)

Query: 9   SPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH------ 62
           SPS+KDGI F+K+S+L +LYC F+Q+LG KLK+PQV +ACA+MLCHQFYM Q H      
Sbjct: 36  SPSRKDGIDFEKESQLLRLYCLFIQDLGKKLKIPQVTIACALMLCHQFYMRQSHATNDWQ 95

Query: 63  ---------------------DVYY------------------------KQKELILTAER 77
                                DV                          KQKELI++ E 
Sbjct: 96  TIATVSIFLACKIEDTPRLLRDVVVVAYEMIYKWDPSAPDRIRRTEFCDKQKELIISGET 155

Query: 78  LLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEF 116
           LL  TIAFD  I+LPY PL  A  +L +  DLAK +  F
Sbjct: 156 LLLTTIAFDLGIKLPYRPLFDALKKLKIFPDLAKVAWNF 194

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449470130|ref|XP_004152771.1| PREDICTED: cyclin-T1-3-like [Cucumis sativus]

 Score =  106 bits (264), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 63/134 (47%), Positives = 79/134 (58%), Gaps = 26/134 (19%)

Query: 9   SPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVI------VACAMMLCHQFYMH--- 59
           SPS+KDGI FKK+S+L K YCSFLQELG KLK+ Q I      +AC +    +F      
Sbjct: 45  SPSRKDGIDFKKESQLRKSYCSFLQELGMKLKVLQTIGTASIFLACKIEETPRFLNDVVV 104

Query: 60  -----------------QLHDVYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTR 102
                            +  +V+ KQKELIL AERLL +T+AF+ DIQLPY+PLVAA  R
Sbjct: 105 VAYELTFKWDPSASKRIRQKEVFNKQKELILIAERLLLSTLAFEVDIQLPYKPLVAALKR 164

Query: 103 LDLVCDLAKSSMEF 116
           L +  DL K +  F
Sbjct: 165 LGMAADLGKVAWNF 178

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225458191|ref|XP_002281108.1| PREDICTED: cyclin-T1-4 [Vitis vinifera]

 Score =  100 bits (250), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 63/160 (39%), Positives = 81/160 (50%), Gaps = 52/160 (32%)

Query: 9   SPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ-------- 60
           SPS+KDGI  KK+++  KLYCSFL ELG KLK+PQV +A A+MLCH+FY+ Q        
Sbjct: 45  SPSRKDGIDPKKEAQSRKLYCSFLWELGMKLKVPQVAIATALMLCHRFYLRQSLAKNDWQ 104

Query: 61  -------------------LHDV------------------------YYKQKELILTAER 77
                              L DV                        + KQKELIL  ER
Sbjct: 105 IIATVSMFLACKAEETPRLLRDVIIMAYEMTYRCDPPALKRIKQREFFDKQKELILIGER 164

Query: 78  LLPATIAFDFDIQLPYEPLVAAFTRLDLV-CDLAKSSMEF 116
           LL  TIAFD +I+ PY+P+V A  R+ +   DL K++   
Sbjct: 165 LLLGTIAFDLNIEHPYKPIVDALKRMGISNNDLVKAAQNL 204

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297845718|ref|XP_002890740.1| cyclin family protein [Arabidopsis lyrata subsp. lyrata] gi|297336582|gb|EFH66999.1| cyclin family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  100 bits (250), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 59/160 (36%), Positives = 77/160 (48%), Gaps = 51/160 (31%)

Query: 8   FSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH----- 62
           FSPS+KDGI   K+S L   YC+FLQ LG KL + QV ++CAM++CH+FYM Q H     
Sbjct: 44  FSPSRKDGIDLVKESFLRSSYCTFLQRLGMKLHVSQVTISCAMVMCHRFYMRQSHAKNDW 103

Query: 63  ----------------------------------------------DVYYKQKELILTAE 76
                                                         D Y++ KE+IL  E
Sbjct: 104 QTIGTASLFLACKAEDEPCQLSSVVVASYEIIYEWDPSASIRIHQTDCYHEFKEIILAGE 163

Query: 77  RLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEF 116
            LL +T AF  DI+LPY+PL AA  RL+   DLA ++  F
Sbjct: 164 SLLLSTSAFHLDIELPYKPLAAALNRLNAWPDLATAAWNF 203

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302142541|emb|CBI19744.3| unnamed protein product [Vitis vinifera]

 Score =  100 bits (250), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 63/160 (39%), Positives = 81/160 (50%), Gaps = 52/160 (32%)

Query: 9   SPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ-------- 60
           SPS+KDGI  KK+++  KLYCSFL ELG KLK+PQV +A A+MLCH+FY+ Q        
Sbjct: 45  SPSRKDGIDPKKEAQSRKLYCSFLWELGMKLKVPQVAIATALMLCHRFYLRQSLAKNDWQ 104

Query: 61  -------------------LHDV------------------------YYKQKELILTAER 77
                              L DV                        + KQKELIL  ER
Sbjct: 105 IIATVSMFLACKAEETPRLLRDVIIMAYEMTYRCDPPALKRIKQREFFDKQKELILIGER 164

Query: 78  LLPATIAFDFDIQLPYEPLVAAFTRLDLV-CDLAKSSMEF 116
           LL  TIAFD +I+ PY+P+V A  R+ +   DL K++   
Sbjct: 165 LLLGTIAFDLNIEHPYKPIVDALKRMGISNNDLVKAAQNL 204

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576769|ref|XP_003556502.1| PREDICTED: cyclin-T1-5-like [Glycine max]

 Score =  100 bits (248), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 52/150 (34%), Positives = 76/150 (50%), Gaps = 51/150 (34%)

Query: 7   EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH---- 62
           E SPS+KDGI  KK++ L K YC+FLQ+LG +LK+PQV +A A++ CH+F++ Q H    
Sbjct: 43  EHSPSRKDGIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIIFCHRFFLRQSHAKND 102

Query: 63  -----------------------------------------------DVYYKQKELILTA 75
                                                          +VY +QKELIL  
Sbjct: 103 RRTIATVCMFLAGKVEETPRPLKDVILVSYEIIHKKDPAAAQRIKQKEVYEQQKELILLG 162

Query: 76  ERLLPATIAFDFDIQLPYEPLVAAFTRLDL 105
           ER++ AT+ FD ++Q PY+PLV A  + ++
Sbjct: 163 ERVVLATLGFDLNVQHPYKPLVEAIKKFNV 192

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521602|ref|XP_003529443.1| PREDICTED: cyclin-T1-5-like [Glycine max]

 Score =  100 bits (248), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 52/150 (34%), Positives = 76/150 (50%), Gaps = 51/150 (34%)

Query: 7   EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH---- 62
           E SPS+KDGI  KK++ L K YC+FLQ+LG +LK+PQV +A A++ CH+F++ Q H    
Sbjct: 43  EHSPSRKDGIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIIFCHRFFLRQSHAKND 102

Query: 63  -----------------------------------------------DVYYKQKELILTA 75
                                                          +VY +QKELIL  
Sbjct: 103 RRTIATVCMFLAGKVEETPRPLKDVILVSYEIIHKKDPAAAQRIKQKEVYEQQKELILLG 162

Query: 76  ERLLPATIAFDFDIQLPYEPLVAAFTRLDL 105
           ER++ AT+ FD ++Q PY+PLV A  + ++
Sbjct: 163 ERVVLATLGFDLNVQHPYKPLVEAIKKFNV 192

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21618277|gb|AAM67327.1| putative cyclin [Arabidopsis thaliana]

 Score = 99.8 bits (247), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 58/160 (36%), Positives = 78/160 (48%), Gaps = 51/160 (31%)

Query: 8   FSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH----- 62
           FSPS+KDGI   K+S L   YC+FLQ LG KL + QV ++CAM++CH+FYM Q H     
Sbjct: 44  FSPSRKDGIDLVKESFLRSSYCTFLQRLGMKLHVSQVTISCAMVMCHRFYMRQSHAKNDW 103

Query: 63  ----------------------------------------------DVYYKQKELILTAE 76
                                                         + Y++ KE+IL+ E
Sbjct: 104 QTIATSSLFLACKAEDEPCQLSSVVVASYEIIYEWDPSASIRIHQTECYHEFKEIILSGE 163

Query: 77  RLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEF 116
            LL +T AF  DI+LPY+PL AA  RL+   DLA ++  F
Sbjct: 164 SLLLSTSAFHLDIELPYKPLAAALNRLNAWPDLATAAWNF 203

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	118
TAIR|locus:2196919	317	CYCT1;3 "cyclin T 1;3" [Arabid	0.466	0.173	0.581	5.2e-25
TAIR|locus:2122975	541	CYCT1;4 [Arabidopsis thaliana	0.474	0.103	0.517	4.1e-20
TAIR|locus:2153358	590	AT5G45190 [Arabidopsis thalian	0.474	0.094	0.432	9.9e-16
TAIR|locus:2122940	460	CYCT1;2 [Arabidopsis thaliana	0.771	0.197	0.347	1.3e-10
FB|FBgn0025674	400	CycK "Cyclin K" [Drosophila me	0.440	0.13	0.396	1.9e-08
DICTYBASE|DDB_G0286617	405	cycK "putative K-type cyclin"	0.415	0.120	0.38	1e-07
TAIR|locus:2008698	247	CYCT1;1 "cyclin T1;1" [Arabido	0.432	0.206	0.471	1.3e-07
UNIPROTKB|F1S0D2	692	F1S0D2 "Uncharacterized protei	0.449	0.076	0.301	1.1e-06
UNIPROTKB|E1B6Z5	731	CCNT2 "Uncharacterized protein	0.449	0.072	0.301	1.3e-06
UNIPROTKB|E2RNV9	678	CCNT2 "Uncharacterized protein	0.449	0.078	0.283	2.2e-06

TAIR|locus:2196919 CYCT1;3 "cyclin T 1;3" [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 5.2e-25, Sum P(2) = 5.2e-25
 Identities = 32/55 (58%), Positives = 41/55 (74%)

Query:     8 FSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH 62
             FSPS+KDGI   K+S L   YC+FLQ LG KL + QV ++CAM++CH+FYM Q H
Sbjct:    44 FSPSRKDGIDLVKESFLRSSYCTFLQRLGMKLHVSQVTISCAMVMCHRFYMRQSH 98

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;IDA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

TAIR|locus:2122975 CYCT1;4 [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 4.1e-20, Sum P(2) = 4.1e-20
 Identities = 29/56 (51%), Positives = 42/56 (75%)

Query:     7 EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH 62
             E SPS+ D I  KK++ L K YC+FLQ+LG +LK+PQV +A A++ CH+F++ Q H
Sbjct:    42 ENSPSRLDSIDLKKETYLRKSYCTFLQDLGMRLKVPQVTIATAIIFCHRFFIRQSH 97

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;IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

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

GO:0009615 "response to virus" evidence=IEP

GO:0010090 "trichome morphogenesis" evidence=IMP

GO:0048366 "leaf development" evidence=IGI

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

GO:0008284 "positive regulation of cell proliferation" evidence=RCA

TAIR|locus:2153358 AT5G45190 [Arabidopsis thaliana (taxid:3702)]

 Score = 129 (50.5 bits), Expect = 9.9e-16, Sum P(2) = 9.9e-16
 Identities = 29/67 (43%), Positives = 40/67 (59%)

Query:     7 EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLP-----------QVIVACAMMLCHQ 55
             E SPS+ DGI  KK++ L K YC+FLQ+LG +LKL             V +A A++ CH+
Sbjct:    42 ENSPSRLDGIDLKKETYLRKSYCTFLQDLGMRLKLAWFLDIIAYVCTDVTIATAIIFCHR 101

Query:    56 FYMHQLH 62
             F+  Q H
Sbjct:   102 FFFRQSH 108

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:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

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

GO:0009615 "response to virus" evidence=IEP

GO:0009908 "flower development" evidence=IMP

GO:0010090 "trichome morphogenesis" evidence=IMP

GO:0048366 "leaf development" evidence=IGI

GO:0050792 "regulation of viral reproduction" evidence=IMP

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

GO:0006486 "protein glycosylation" evidence=RCA

GO:0008284 "positive regulation of cell proliferation" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

TAIR|locus:2122940 CYCT1;2 [Arabidopsis thaliana (taxid:3702)]

 Score = 157 (60.3 bits), Expect = 1.3e-10, P = 1.3e-10
 Identities = 33/95 (34%), Positives = 57/95 (60%)

Query:     9 SPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYYKQ 68
             SPS++DGI  K ++ L   YC+FL+ LG +LK+PQV +A A+  CH+F++ Q H      
Sbjct:    42 SPSRRDGIDLKTETRLRDSYCTFLEILGERLKVPQVTIATAIFFCHRFFLRQSHAK--ND 99

Query:    69 KELILTAERLLPATIAFDFDIQLPYEPLVAAFTRL 103
             ++ I T   LL   +  +  + L  + ++A++ R+
Sbjct:   100 RQTIATVCMLLAGKVE-ETPVTLE-DVIIASYERI 132

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:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

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

FB|FBgn0025674 CycK "Cyclin K" [Drosophila melanogaster (taxid:7227)]

 Score = 85 (35.0 bits), Expect = 1.9e-08, Sum P(3) = 1.9e-08
 Identities = 21/53 (39%), Positives = 30/53 (56%)

Query:     6 REFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYM 58
             RE +PS  DGISF+ +    K    F+ E GTK+ L    +A  ++  H+FYM
Sbjct:    12 RE-TPSILDGISFETERRYRKEGARFIMECGTKMGLGHNTMATGVVYFHRFYM 63

GO:0016538 "cyclin-dependent protein serine/threonine kinase regulator activity" evidence=ISS

GO:0019901 "protein kinase binding" evidence=IEA

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0022008 "neurogenesis" evidence=IMP

DICTYBASE|DDB_G0286617 cycK "putative K-type cyclin" [Dictyostelium discoideum (taxid:44689)]

 Score = 96 (38.9 bits), Expect = 1.0e-07, Sum P(2) = 1.0e-07
 Identities = 19/50 (38%), Positives = 32/50 (64%)

Query:    15 GISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYM-HQLHD 63
             GI  K +    +   +F+Q++G KLK+PQ+ +A A+   H+F++ HQL D
Sbjct:    23 GIELKLEVAYRRASAAFIQDVGIKLKMPQLTIATAISYFHRFFIRHQLKD 72

GO:0019901 "protein kinase binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

TAIR|locus:2008698 CYCT1;1 "cyclin T1;1" [Arabidopsis thaliana (taxid:3702)]

 Score = 124 (48.7 bits), Expect = 1.3e-07, P = 1.3e-07
 Identities = 25/53 (47%), Positives = 37/53 (69%)

Query:     9 SPSKKDGISFKKDS-ELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ 60
             SPS+ DGI+ K+++ + W  Y SFLQELG +L  PQ  +A A++LC +F+  Q
Sbjct:    18 SPSRLDGINLKEETFQRWS-YTSFLQELGQRLNNPQKTIATAIVLCQRFFTRQ 69

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:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

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

UNIPROTKB|F1S0D2 F1S0D2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 89 (36.4 bits), Expect = 1.1e-06, Sum P(2) = 1.1e-06
 Identities = 16/53 (30%), Positives = 32/53 (60%)

Query:     7 EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMH 59
             E +PS++ G+   K+    +   + +QE+G +L + Q+ +  A++  H+FYMH
Sbjct:    19 ENTPSRRCGVEADKELSYRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMH 71

GO:0019901 "protein kinase binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

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

UNIPROTKB|E1B6Z5 CCNT2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 89 (36.4 bits), Expect = 1.3e-06, Sum P(2) = 1.3e-06
 Identities = 16/53 (30%), Positives = 32/53 (60%)

Query:     7 EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMH 59
             E +PS++ G+   K+    +   + +QE+G +L + Q+ +  A++  H+FYMH
Sbjct:    19 ENTPSRRCGVEADKELSYRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMH 71

GO:0005634 "nucleus" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

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

UNIPROTKB|E2RNV9 CCNT2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 86 (35.3 bits), Expect = 2.2e-06, Sum P(2) = 2.2e-06
 Identities = 15/53 (28%), Positives = 32/53 (60%)

Query:     7 EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMH 59
             E +PS++ G+   K+    +   + +Q++G +L + Q+ +  A++  H+FYMH
Sbjct:    31 ENTPSRRCGVEADKELSYRQQAANLIQDMGQRLNVSQLTINTAIVYMHRFYMH 83

GO:0019901 "protein kinase binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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	118
COG5333	297	COG5333, CCL1, Cdk activating kinase (CAK)/RNA pol	0.002

>gnl|CDD|227640 COG5333, CCL1, Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 13/42 (30%), Positives = 25/42 (59%)

Query: 16 ISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFY 57
          ++ +K+  L   Y   + +L T+L LPQ ++A A++   +FY
Sbjct: 36 LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFY 77

Length = 297

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	118
KOG0834	323	consensus CDK9 kinase-activating protein cyclin T	100.0
KOG0835	367	consensus Cyclin L [General function prediction on	99.97
TIGR00569	305	ccl1 cyclin ccl1. University).	99.95
COG5333	297	CCL1 Cdk activating kinase (CAK)/RNA polymerase II	99.91
KOG0794	264	consensus CDK8 kinase-activating protein cyclin C	99.89
KOG2496	325	consensus Cdk activating kinase (CAK)/RNA polymera	99.31
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	99.05
PF00134	127	Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR	98.83
KOG0656	335	consensus G1/S-specific cyclin D [Cell cycle contr	97.84
cd00043	88	CYCLIN Cyclin box fold. Protein binding domain fun	97.42
KOG0653	391	consensus Cyclin B and related kinase-activating p	97.26
smart00385	83	CYCLIN domain present in cyclins, TFIIB and Retino	96.66
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	96.21
COG5024	440	Cyclin [Cell division and chromosome partitioning]	95.74
KOG0655	408	consensus G1/S-specific cyclin E [Cell cycle contr	94.71
PF08613	149	Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu	94.38
KOG4164	497	consensus Cyclin ik3-1/CABLES [Cell cycle control,	91.3
KOG1597	308	consensus Transcription initiation factor TFIIB [T	89.85
PF00382	71	TFIIB: Transcription factor TFIIB repeat; InterPro	83.42

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

Probab=100.00  E-value=1.1e-35  Score=231.46  Aligned_cols=116  Identities=36%  Similarity=0.616  Sum_probs=111.2

Q ss_pred             hhhhh-hCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH------------------
Q 038406            3 LHRRE-FSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD------------------   63 (118)
Q Consensus         3 ~~~l~-~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~------------------   63 (118)
                      .++++ +|||+++|++.++|...|..++.||+++|.+|++|+.++|||++||||||+.+|++                  
T Consensus        16 ~e~~~~~tpSr~~g~~~~~E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKv   95 (323)
T KOG0834|consen   16 KEQLEENTPSRRDGIDLKKELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKV   95 (323)
T ss_pred             HHHHccCChhhccCCchhHHHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhc
Confidence            46677 99999999999999999999999999999999999999999999999999999988                  


Q ss_pred             ---------------------------HHHHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCH----HHHHH
Q 038406           64 ---------------------------VYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVC----DLAKS  112 (118)
Q Consensus        64 ---------------------------~~~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~----~l~q~  112 (118)
                                                 .||++|++|+..|.+||++|+|||+|+|||+||++|+++++.++    .+++.
T Consensus        96 Eetp~kl~dIi~~s~~~~~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~  175 (323)
T KOG0834|consen   96 EETPRKLEDIIKVSYRYLNPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQA  175 (323)
T ss_pred             ccCcccHHHHHHHHHHHcCcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHH
Confidence                                       58899999999999999999999999999999999999999985    59999


Q ss_pred             HhhhcC
Q 038406          113 SMEFHK  118 (118)
Q Consensus       113 Aw~~~N  118 (118)
                      ||+|+|
T Consensus       176 Aw~~~n  181 (323)
T KOG0834|consen  176 AWNFVN  181 (323)
T ss_pred             HHHHhc
Confidence            999998

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=99.97  E-value=9.6e-31  Score=202.09  Aligned_cols=115  Identities=28%  Similarity=0.482  Sum_probs=108.0

Q ss_pred             hhhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH--------------------
Q 038406            4 HRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD--------------------   63 (118)
Q Consensus         4 ~~l~~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~--------------------   63 (118)
                      +.+.+|||..||++.+.|..+|..||+|||++|++|+|||.++||++++|+|||..+|+.                    
T Consensus         2 ~~i~~~~s~qd~l~~e~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE   81 (367)
T KOG0835|consen    2 EKIDSTPSLQDGLSLETEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEE   81 (367)
T ss_pred             CcccCchhhhcccccchHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhcc
Confidence            357899999999999999999999999999999999999999999999999999999877                    


Q ss_pred             -------------------------------HHHHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCC--HHHH
Q 038406           64 -------------------------------VYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLV--CDLA  110 (118)
Q Consensus        64 -------------------------------~~~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~--~~l~  110 (118)
                                                     .|..++..++.+|..||++||||++|+|||+.++.|++.|++.  .+|.
T Consensus        82 ~Prr~rdVinVFh~L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~l~  161 (367)
T KOG0835|consen   82 EPRRIRDVINVFHYLEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLKLL  161 (367)
T ss_pred             ccccHhHHHHHHHHHHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchhHH
Confidence                                           3446788999999999999999999999999999999999998  5579


Q ss_pred             HHHhhhcC
Q 038406          111 KSSMEFHK  118 (118)
Q Consensus       111 q~Aw~~~N  118 (118)
                      |.||+|.|
T Consensus       162 Q~~wNfmN  169 (367)
T KOG0835|consen  162 QAAWNFMN  169 (367)
T ss_pred             HHHHHhhh
Confidence            99999998

>TIGR00569 ccl1 cyclin ccl1

Probab=99.95  E-value=1.2e-27  Score=185.69  Aligned_cols=107  Identities=24%  Similarity=0.337  Sum_probs=96.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHhhcC--CCHHHHHHHHHHHHHHhhhcchH--------------------------
Q 038406           12 KKDGISFKKDSELWKLYCSFLQELGTKLK--LPQVIVACAMMLCHQFYMHQLHD--------------------------   63 (118)
Q Consensus        12 ~~~gi~~~~E~~~r~~~~~~I~~~g~~L~--lp~~~~aTA~~~~hRFy~~~S~~--------------------------   63 (118)
                      ...++|+++|..+|.+||.+|+++|.+|+  +|+.|+|||++||||||+++|++                          
T Consensus        43 ~~~~Lt~eeE~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~  122 (305)
T TIGR00569        43 KPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSID  122 (305)
T ss_pred             ccCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHH
Confidence            34699999999999999999999999999  99999999999999999999998                          


Q ss_pred             --------HHHHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCC-------CHHHHHHHhhhcC
Q 038406           64 --------VYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDL-------VCDLAKSSMEFHK  118 (118)
Q Consensus        64 --------~~~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~-------~~~l~q~Aw~~~N  118 (118)
                              ....+++.|+++|+.||++||||+.|+|||+++.+|+.+++.       .+.+.|.||+|+|
T Consensus       123 ~fv~~~~~~~~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~ln  192 (305)
T TIGR00569       123 QFVGNLKETPLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLN  192 (305)
T ss_pred             HHHhhccCCchhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHH
Confidence                    122367999999999999999999999999999999976642       2679999999997

University).

>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=99.91  E-value=5.4e-24  Score=163.53  Aligned_cols=103  Identities=24%  Similarity=0.410  Sum_probs=96.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH--------------------------------
Q 038406           16 ISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD--------------------------------   63 (118)
Q Consensus        16 i~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~--------------------------------   63 (118)
                      ++-++|..+|.+++.+|+++|.+|++|+.+.|||+.||+|||.++|.+                                
T Consensus        36 l~~~~e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~  115 (297)
T COG5333          36 LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEA  115 (297)
T ss_pred             cchhhhhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHh
Confidence            677999999999999999999999999999999999999999999988                                


Q ss_pred             ------HHHHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCC--HHHHHHHhhhcC
Q 038406           64 ------VYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLV--CDLAKSSMEFHK  118 (118)
Q Consensus        64 ------~~~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~--~~l~q~Aw~~~N  118 (118)
                            ..+..|++|+++|+.+|++|+||++|+|||+++.++++++...  .++.+.||+++|
T Consensus       116 ~~~~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~in  178 (297)
T COG5333         116 RDLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIIN  178 (297)
T ss_pred             hccccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence                  2345789999999999999999999999999999999999876  359999999987

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

Probab=99.89  E-value=1.2e-23  Score=156.62  Aligned_cols=106  Identities=23%  Similarity=0.360  Sum_probs=96.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------------------------
Q 038406           13 KDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------------------------   63 (118)
Q Consensus        13 ~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------------------------   63 (118)
                      ..|++.++-..++.+..++|+.+|.+|+++|+|+|||++||+|||.++|++                             
T Consensus        29 ~r~l~~d~~~~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l  108 (264)
T KOG0794|consen   29 LRGLSEDEYSKLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLL  108 (264)
T ss_pred             hhcccHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHH
Confidence            348999999999999999999999999999999999999999999999988                             


Q ss_pred             -----------HHHH-----HHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCC-CHHHHHHHhhhcC
Q 038406           64 -----------VYYK-----QKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDL-VCDLAKSSMEFHK  118 (118)
Q Consensus        64 -----------~~~~-----~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~-~~~l~q~Aw~~~N  118 (118)
                                 .|+.     -+..|+++|+.+|+.|++.+.|+|||++|.+++++.|. +.++.+.||+++|
T Consensus       109 ~~~a~~L~~~f~~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivN  180 (264)
T KOG0794|consen  109 VNEAKVLKTRFSYWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVN  180 (264)
T ss_pred             HHHHHHHhhhcccchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccchhhhhhhHhhhc
Confidence                       0111     13789999999999999999999999999999999999 5779999999998

>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=99.31  E-value=4.2e-12  Score=98.06  Aligned_cols=92  Identities=21%  Similarity=0.418  Sum_probs=74.2

Q ss_pred             hhhCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH----------------------
Q 038406            6 REFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD----------------------   63 (118)
Q Consensus         6 l~~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~----------------------   63 (118)
                      +.-+|+..--++-++|..+-.++..|-.      .+|..|++||+.||.|||+.+|.+                      
T Consensus        45 ~~v~~~ee~tl~k~~E~~l~~f~~k~~p------~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~  118 (325)
T KOG2496|consen   45 VFVLEAEELTLTKEEELSLVNFYSKFKP------NLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFY  118 (325)
T ss_pred             hhccccccccccHHHHHHHHHHHHHhcC------CCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhhe
Confidence            3445555555666666666666555544      899999999999999999999988                      


Q ss_pred             ----HH--------HHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHc
Q 038406           64 ----VY--------YKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRL  103 (118)
Q Consensus        64 ----~~--------~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l  103 (118)
                          .|        |+-.+.|+..|+.+|+.|.|++.|++||+++-+++.++
T Consensus       119 ISieqFvkn~~~~~~k~~e~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D~  170 (325)
T KOG2496|consen  119 ISIEQFVKNMNGRKWKTHEIVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLDM  170 (325)
T ss_pred             ecHHHHHhhccCcccccHHHHHhchHHHHHhhhhhheecCCCCchHHHHHHH
Confidence                11        24468999999999999999999999999999998887

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=99.05  E-value=1.5e-09  Score=84.65  Aligned_cols=93  Identities=17%  Similarity=0.217  Sum_probs=82.9

Q ss_pred             HHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------HH-------------------HHHHHHHHHH
Q 038406           26 KLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------VY-------------------YKQKELILTA   75 (118)
Q Consensus        26 ~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------~~-------------------~~~~~~Il~~   75 (118)
                      ..+.+.|.++|..|++|+.++.+|..+|++++..+.++           .|                   .-.+.+|-..
T Consensus       123 ~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~  202 (310)
T PRK00423        123 AFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRC  202 (310)
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHH
Confidence            56889999999999999999999999999999987766           11                   1236788999


Q ss_pred             HHHHHHHcCcceeecCChHHHHHHHHHcCCCHHHHHHHhhhcC
Q 038406           76 ERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK  118 (118)
Q Consensus        76 E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~l~q~Aw~~~N  118 (118)
                      ++.|++.|++++.+.+|+.++..++..|++++++.+.||.+++
T Consensus       203 ~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~v~~~A~~i~~  245 (310)
T PRK00423        203 YRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQ  245 (310)
T ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999998764

>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=98.83  E-value=1.6e-08  Score=67.93  Aligned_cols=70  Identities=23%  Similarity=0.332  Sum_probs=56.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH---------------------------HH------
Q 038406           19 KKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD---------------------------VY------   65 (118)
Q Consensus        19 ~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~---------------------------~~------   65 (118)
                      +-....|...++||.+++..++++..+.++|+.|++||+.+.++.                           .+      
T Consensus        25 ~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~  104 (127)
T PF00134_consen   25 EITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDN  104 (127)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTT
T ss_pred             hcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcC
Confidence            445588999999999999999999999999999999999988755                           00      


Q ss_pred             HHHHHHHHHHHHHHHHHcCccee
Q 038406           66 YKQKELILTAERLLPATIAFDFD   88 (118)
Q Consensus        66 ~~~~~~Il~~E~~iL~~L~Fdl~   88 (118)
                      .--+++|+++|+.||++|+||++
T Consensus       105 ~~~~~~i~~~E~~iL~~L~f~ln  127 (127)
T PF00134_consen  105 TFTKKDILEMEREILSALNFDLN  127 (127)
T ss_dssp             SSHHHHHHHHHHHHHHHTTT---
T ss_pred             CCCHHHHHHHHHHHHHHCCCCcC
Confidence            01368999999999999999974

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 ....

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

Probab=97.84  E-value=9e-05  Score=58.68  Aligned_cols=83  Identities=12%  Similarity=0.157  Sum_probs=74.0

Q ss_pred             HHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH----------------------------------H---HH
Q 038406           24 LWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD----------------------------------V---YY   66 (118)
Q Consensus        24 ~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~----------------------------------~---~~   66 (118)
                      -|..+..||.+++...+....+..-|+.|+=||-..+++.                                  +   |-
T Consensus        77 ~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~  156 (335)
T KOG0656|consen   77 MRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNV  156 (335)
T ss_pred             HHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcccccc
Confidence            3899999999999999999999999999999998766655                                  1   12


Q ss_pred             HHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCC
Q 038406           67 KQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLV  106 (118)
Q Consensus        67 ~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~  106 (118)
                      --.+.|..+|.+||.+|+-+++--.||.++-.++.+++..
T Consensus       157 feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~  196 (335)
T KOG0656|consen  157 FEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQK  196 (335)
T ss_pred             ccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcc
Confidence            2368999999999999999999999999999999999874

>cd00043 CYCLIN Cyclin box fold

Probab=97.42  E-value=0.00043  Score=42.36  Aligned_cols=39  Identities=18%  Similarity=0.168  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH
Q 038406           25 WKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD   63 (118)
Q Consensus        25 r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~   63 (118)
                      |...++||.+++..+++|..+..+|..++.||+..+++.
T Consensus         2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~   40 (88)
T cd00043           2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVL   40 (88)
T ss_pred             cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccc
Confidence            456789999999999999999999999999999887765

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.

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

Probab=97.26  E-value=0.0016  Score=52.54  Aligned_cols=84  Identities=20%  Similarity=0.272  Sum_probs=73.5

Q ss_pred             HHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------------HHH-----------------HH
Q 038406           23 ELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------------VYY-----------------KQ   68 (118)
Q Consensus        23 ~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------------~~~-----------------~~   68 (118)
                      ..|..-++|+.++-...++...|+..|+-++-||-...+..                 -|+                 --
T Consensus       156 ~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s  235 (391)
T KOG0653|consen  156 KMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYS  235 (391)
T ss_pred             HHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccc
Confidence            56888899999999999999999999999999998876543                 122                 13


Q ss_pred             HHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCC
Q 038406           69 KELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLV  106 (118)
Q Consensus        69 ~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~  106 (118)
                      +++|+.+|..||.+|+|++.+.+|+.+|..+.+..+.+
T Consensus       236 ~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d  273 (391)
T KOG0653|consen  236 REEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYD  273 (391)
T ss_pred             hHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcc
Confidence            69999999999999999999999999999999988754

>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma

Probab=96.66  E-value=0.0045  Score=37.35  Aligned_cols=34  Identities=21%  Similarity=0.223  Sum_probs=29.6

Q ss_pred             HHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH
Q 038406           30 SFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD   63 (118)
Q Consensus        30 ~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~   63 (118)
                      +||.+++..+++|..+..+|..++.||...+++.
T Consensus         1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~   34 (83)
T smart00385        1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFL   34 (83)
T ss_pred             CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcc
Confidence            3789999999999999999999999998855443

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

>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]

Probab=96.21  E-value=0.043  Score=42.73  Aligned_cols=90  Identities=18%  Similarity=0.197  Sum_probs=74.3

Q ss_pred             HHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------HH-------------------HHHHHHHHHHH
Q 038406           27 LYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------VY-------------------YKQKELILTAE   76 (118)
Q Consensus        27 ~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------~~-------------------~~~~~~Il~~E   76 (118)
                      .+.+.|..++..|++|..+.-+|+.+|.+-+..+-..           .|                   .-.+.+|-.+.
T Consensus        99 ~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~~kei~rty  178 (285)
T COG1405          99 TALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVSKKEIGRTY  178 (285)
T ss_pred             HHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCCHHHHHHHH
Confidence            5778899999999999999999999999887655433           11                   12358899999


Q ss_pred             HHHHHHcCcceeecCChHHHHHHHHHcCCCHHHHHHHhhh
Q 038406           77 RLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEF  116 (118)
Q Consensus        77 ~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~l~q~Aw~~  116 (118)
                      +.+.+.|+=.+....|..|+..|+.+|+++.+....|-.+
T Consensus       179 r~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei  218 (285)
T COG1405         179 RLLVRELKLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEI  218 (285)
T ss_pred             HHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            9999999999999999999999999999996666555444

>COG5024 Cyclin [Cell division and chromosome partitioning]

Probab=95.74  E-value=0.069  Score=43.98  Aligned_cols=84  Identities=18%  Similarity=0.230  Sum_probs=70.7

Q ss_pred             HHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH----------------HHH-----------------HHH
Q 038406           23 ELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD----------------VYY-----------------KQK   69 (118)
Q Consensus        23 ~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~----------------~~~-----------------~~~   69 (118)
                      ..|.--.+||.++=..+++-..|.-.|+.+.-||-..+...                -|+                 --+
T Consensus       211 ~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~  290 (440)
T COG5024         211 SMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTR  290 (440)
T ss_pred             hHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccH
Confidence            45777889999999999999999999999999998877654                122                 126


Q ss_pred             HHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCC
Q 038406           70 ELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLV  106 (118)
Q Consensus        70 ~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~  106 (118)
                      ++|+.+|+.+|.+|+|++..-.|+-++..+-+.-+-+
T Consensus       291 ~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dyd  327 (440)
T COG5024         291 DDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDYD  327 (440)
T ss_pred             HHHHHHHHHHhhhcccccCCCChHHHHHHHHhhcccc
Confidence            9999999999999999999999999988877766554

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

Probab=94.71  E-value=0.33  Score=38.92  Aligned_cols=87  Identities=14%  Similarity=0.104  Sum_probs=65.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH------------------HHHH------------
Q 038406           18 FKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD------------------VYYK------------   67 (118)
Q Consensus        18 ~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~------------------~~~~------------   67 (118)
                      +.-+-+.|+--..|+.++|.--+|-..|..-|+-||-||.... .+                  -+++            
T Consensus       138 pdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~-~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyv  216 (408)
T KOG0655|consen  138 PDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQ-VEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYV  216 (408)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH-HHhhhhhHHHhhHHHHHHHHHHhhccCccccceeee
Confidence            3344556777889999999999999999999999999997644 22                  1111            


Q ss_pred             -----HHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCC
Q 038406           68 -----QKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDL  105 (118)
Q Consensus        68 -----~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~  105 (118)
                           --++|+.+|.+||+.|+.++..-.--.-|--|++...+
T Consensus       217 TDgAcs~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~  259 (408)
T KOG0655|consen  217 TDGACSEDDILTMELIILKALKWELSPITIISWLNVYLQVDAL  259 (408)
T ss_pred             ccCccchHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhc
Confidence                 24899999999999999999855444555555555433

>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=94.38  E-value=0.2  Score=34.98  Aligned_cols=60  Identities=8%  Similarity=0.076  Sum_probs=42.7

Q ss_pred             HHHHHHHHHhhcCCCHHHHHHHHHHHHHHhh---hcchH----------------------------HHHH-----HHHH
Q 038406           28 YCSFLQELGTKLKLPQVIVACAMMLCHQFYM---HQLHD----------------------------VYYK-----QKEL   71 (118)
Q Consensus        28 ~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~---~~S~~----------------------------~~~~-----~~~~   71 (118)
                      -.+|+.++....+++..+.-.|.+|+.|+..   ...+.                            .+|.     -.++
T Consensus        54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~e  133 (149)
T PF08613_consen   54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKE  133 (149)
T ss_dssp             HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHH
T ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHH
Confidence            4567888888999999999999999999988   22221                            1121     2579


Q ss_pred             HHHHHHHHHHHcCcce
Q 038406           72 ILTAERLLPATIAFDF   87 (118)
Q Consensus        72 Il~~E~~iL~~L~Fdl   87 (118)
                      +-.+|+..|..|+|+|
T Consensus       134 ln~lE~~fL~~l~~~L  149 (149)
T PF08613_consen  134 LNELEREFLKLLDYNL  149 (149)
T ss_dssp             HHHHHHHHHHHTTT--
T ss_pred             HHHHHHHHHHHCCCcC
Confidence            9999999999999986

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.

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

Probab=91.30  E-value=0.24  Score=40.42  Aligned_cols=59  Identities=17%  Similarity=0.294  Sum_probs=47.9

Q ss_pred             HHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------------------------------HHHHHHHHHHHHH
Q 038406           32 LQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------------------------------VYYKQKELILTAE   76 (118)
Q Consensus        32 I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------------------------------~~~~~~~~Il~~E   76 (118)
                      |.++|.-.++...|+|+|-|||-+--+..-+.                                   .|..-|.+++..|
T Consensus       389 Mr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrrdLia~E  468 (497)
T KOG4164|consen  389 MRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRRDLIAFE  468 (497)
T ss_pred             HHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHHhhhhhh
Confidence            66777777888899999999999888765544                                   2334578999999


Q ss_pred             HHHHHHcCcceeec
Q 038406           77 RLLPATIAFDFDIQ   90 (118)
Q Consensus        77 ~~iL~~L~Fdl~v~   90 (118)
                      +-||-.|.|-|++.
T Consensus       469 f~VlvaLefaL~~~  482 (497)
T KOG4164|consen  469 FPVLVALEFALHLP  482 (497)
T ss_pred             hhHHHhhhhhccCC
Confidence            99999999999754

>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]

Probab=89.85  E-value=6.1  Score=31.14  Aligned_cols=86  Identities=15%  Similarity=0.106  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------------------HHHH-------HHHHHHH
Q 038406           25 WKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------------------VYYK-------QKELILT   74 (118)
Q Consensus        25 r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------------------~~~~-------~~~~Il~   74 (118)
                      -..+..-|..++.+++||..+.-+|.-+|+++...++++                       .|.+       .+++|=.
T Consensus       104 ~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~anv~kKEIgr  183 (308)
T KOG1597|consen  104 LKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVANVSKKEIGR  183 (308)
T ss_pred             HHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHcCCHHHHHH
Confidence            345778899999999999999999999999999766655                       1222       2567777


Q ss_pred             HHHHHHHHcCcceeec--CChHHHHHHHHHcCCCHHHH
Q 038406           75 AERLLPATIAFDFDIQ--LPYEPLVAAFTRLDLVCDLA  110 (118)
Q Consensus        75 ~E~~iL~~L~Fdl~v~--hP~~~l~~~~~~l~~~~~l~  110 (118)
                      +=..|++.|+=.+...  |--.++..|+..|+++++..
T Consensus       184 ~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q  221 (308)
T KOG1597|consen  184 CVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQ  221 (308)
T ss_pred             HHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHH
Confidence            7788888877766544  46778899999999985443

>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=83.42  E-value=1.9  Score=26.00  Aligned_cols=28  Identities=18%  Similarity=0.224  Sum_probs=21.0

Q ss_pred             HHHHHhhcCCCHHHHHHHHHHHHHHhhh
Q 038406           32 LQELGTKLKLPQVIVACAMMLCHQFYMH   59 (118)
Q Consensus        32 I~~~g~~L~lp~~~~aTA~~~~hRFy~~   59 (118)
                      |.++|..|+||..+.-+|.-++++-...
T Consensus         1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~   28 (71)
T PF00382_consen    1 IPRICSKLGLPEDVRERAKEIYKKAQER   28 (71)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHHHHHHHT
T ss_pred             ChHHHhHcCCCHHHHHHHHHHHHHHHHc
Confidence            5678899999999999999988876543

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	118
2ivx_A	257	Crystal Structure Of Human Cyclin T2 At 1.8 A Resol		2e-04

>pdb|2IVX|A Chain A, Crystal Structure Of Human Cyclin T2 At 1.8 A Resolution (Casp Target) Length = 257

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 7  EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYY 66
          E +PS++ G+   K+    +   + +QE+G +L + Q+ +  A++  H+FYMH  H    
Sbjct: 13 ENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMH--HSFTK 70
Query: 67 KQKELILTAERLLPATI 83
            K +I +    L A +
Sbjct: 71 FNKNIISSTALFLAAKV 87

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	118
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	3e-16
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	1e-15
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	1e-12
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	1e-12
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	2e-11
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	6e-11

>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C Length = 358

 Score = 71.8 bits (175), Expect = 3e-16
 Identities = 29/160 (18%), Positives = 58/160 (36%), Gaps = 48/160 (30%)

Query: 7   EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ------ 60
           E SPS++ G+   K+    +   + LQ++G +L + Q+ +  A++  H+FYM Q      
Sbjct: 20  ENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFP 79

Query: 61  ------------------------------------------LHDVYYKQKELILTAERL 78
                                                       + Y +Q + ++  E +
Sbjct: 80  GNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESI 139

Query: 79  LPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK 118
           +  T+ F+  I  P+  +V     +    DLA++S     
Sbjct: 140 ILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMAT 179

>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Length = 258

 Score = 69.2 bits (169), Expect = 1e-15
 Identities = 27/142 (19%), Positives = 50/142 (35%), Gaps = 43/142 (30%)

Query: 7   EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYM-------- 58
             +PS+ +G+    ++   +    F+ ++GT+L L    +A  ++  H+FYM        
Sbjct: 23  AHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFP 82

Query: 59  -----------------------------------HQLHDVYYKQKELILTAERLLPATI 83
                                               Q        KE ++  ER+L  TI
Sbjct: 83  RYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTI 142

Query: 84  AFDFDIQLPYEPLVAAFTRLDL 105
            FD  ++ PY+ L+    +L  
Sbjct: 143 KFDLQVEHPYQFLLKYAKQLKG 164

>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B* Length = 257

 Score = 61.3 bits (148), Expect = 1e-12
 Identities = 29/159 (18%), Positives = 58/159 (36%), Gaps = 48/159 (30%)

Query: 7   EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLH---- 62
           E +PS++ G+   K+    +   + +QE+G +L + Q+ +  A++  H+FYMH       
Sbjct: 13  ENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFN 72

Query: 63  --------------------------------------------DVYYKQKELILTAERL 78
                                                       D Y +Q   ++  E +
Sbjct: 73  KNIISSTALFLAAKVEEQARKLEHVIKVAHACLHPLEPLLDTKCDAYLQQTRELVILETI 132

Query: 79  LPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFH 117
           +  T+ F+  I+ P+  +V     +    DLA++S    
Sbjct: 133 MLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMA 171

>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens} Length = 285

 Score = 61.2 bits (148), Expect = 1e-12
 Identities = 22/158 (13%), Positives = 41/158 (25%), Gaps = 47/158 (29%)

Query: 6   REFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ----- 60
            +        +S ++  +L   + + +Q LG  LKL Q ++A A +   +FY        
Sbjct: 24  LKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSI 83

Query: 61  ------------------------------------------LHDVYYKQKELILTAERL 78
                                                         +  +   IL  E  
Sbjct: 84  DPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRMNHILECEFY 143

Query: 79  LPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEF 116
           L   +     +  PY PL+     +     L   +   
Sbjct: 144 LLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRI 181

>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Length = 235

 Score = 57.7 bits (139), Expect = 2e-11
 Identities = 17/152 (11%), Positives = 40/152 (26%), Gaps = 39/152 (25%)

Query: 4   HRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYM----- 58
             + F  +  + +     S+        +Q  G +L+L Q ++A A++L  ++ +     
Sbjct: 7   LTQLFLSTDLESLEPTCLSKDTIYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEE 66

Query: 59  ----------------------------------HQLHDVYYKQKELILTAERLLPATIA 84
                                                       +  I   E  + + + 
Sbjct: 67  KGFSLEALVATCIYLSCKVEECPVHIRTICNEANDLWSLKVKLSRSNISEIEFEIISVLD 126

Query: 85  FDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEF 116
               +  PY  L  AF    +     + +   
Sbjct: 127 AFLIVHHPYTSLEQAFHDGIINQKQLEFAWSI 158

>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A Length = 323

 Score = 56.6 bits (136), Expect = 6e-11
 Identities = 26/157 (16%), Positives = 44/157 (28%), Gaps = 39/157 (24%)

Query: 1   MVLHRREFSPSKKDGISFKKDSELWKLYCSFLQELGT--KLKLPQVIVACAMMLCHQFYM 58
             +   +  P+    +   ++  L K Y   L E  +  K  +P+ +V  A M   +FY+
Sbjct: 33  KAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYL 92

Query: 59  -------------------------------------HQLHDVYYKQKELILTAERLLPA 81
                                                 +      K  E IL  E LL  
Sbjct: 93  NNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLGQEKALEQILEYELLLIQ 152

Query: 82  TIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK 118
            + F   +  PY P       L     + ++     K
Sbjct: 153 QLNFHLIVHNPYRPFEGFLIDLKTRYPILENPEILRK 189

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	118
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	99.95
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	99.93
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	99.93
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	99.93
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	99.91
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	99.86
1c9b_A	207	General transcription factor IIB; protein-DNA comp	99.74
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	99.6
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	99.55
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	99.54
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	99.53
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	99.51
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	99.47
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	99.43
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	99.3
1f5q_B	252	Gamma herpesvirus cyclin; herpesviral cyclin, cycl	99.25
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	99.17
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	98.49
2pmi_B	293	PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de	92.61

>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=99.95  E-value=3.2e-28  Score=182.37  Aligned_cols=116  Identities=24%  Similarity=0.419  Sum_probs=108.8

Q ss_pred             hhhhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-------------------
Q 038406            3 LHRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-------------------   63 (118)
Q Consensus         3 ~~~l~~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-------------------   63 (118)
                      .+++++|||+++|+++++|...|..++++|.++|..|++|+.|++||++||||||.++|+.                   
T Consensus         9 ~e~l~~~ps~~~g~~~~~e~~~R~~~~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~qlv~~acL~lA~K~E   88 (257)
T 2ivx_A            9 REQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVE   88 (257)
T ss_dssp             HHHHHSCHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhChHhhcCCCHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhCChhhhCHHHHHHHHHHHHhccc
Confidence            4789999999999999999999999999999999999999999999999999999999877                   


Q ss_pred             -------H----------------------HHHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCHHHHHHHh
Q 038406           64 -------V----------------------YYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSM  114 (118)
Q Consensus        64 -------~----------------------~~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~l~q~Aw  114 (118)
                             .                      |+..+++|+.+|+.||++||||+.+.|||.++..+++.++.++++.+.||
T Consensus        89 E~p~~l~d~~~~~~~~~~~~~~~~~~~~~~y~~~~~~I~~~E~~iL~~L~f~l~~~~P~~fl~~~~~~l~~~~~~~~~A~  168 (257)
T 2ivx_A           89 EQARKLEHVIKVAHACLHPLEPLLDTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSY  168 (257)
T ss_dssp             TCCCCHHHHHHHHHHHHCTTSCCCCTTSHHHHHHHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             cCCcCHHHHHHHHHHHhccCCCCCCcchHHHHHHHHHHHHHHHHHHHHcccceEeeCcHHHHHHHHHHhCCCcHHHHHHH
Confidence                   1                      23348999999999999999999999999999999999999999999999


Q ss_pred             hhcC
Q 038406          115 EFHK  118 (118)
Q Consensus       115 ~~~N  118 (118)
                      .++|
T Consensus       169 ~~~~  172 (257)
T 2ivx_A          169 FMAT  172 (257)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9875

>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=99.93  E-value=9.1e-27  Score=182.93  Aligned_cols=116  Identities=25%  Similarity=0.395  Sum_probs=108.3

Q ss_pred             hhhhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-------------------
Q 038406            3 LHRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-------------------   63 (118)
Q Consensus         3 ~~~l~~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-------------------   63 (118)
                      .++|++|||+++|+++++|...|..+++||.++|..|++|+.|++||++||||||.++|+.                   
T Consensus        16 ~eeL~~~pS~~dgi~~~~E~~~R~~~v~wI~ev~~~l~L~~~t~~tAv~~~dRFl~~~sv~~~~~qlva~acLfLA~K~E   95 (358)
T 2pk2_A           16 REQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVE   95 (358)
T ss_dssp             SHHHHTCTTHHHHCCHHHHHHHHHHHHHHHHHHHTTTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhChhhhcCCChHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHhhc
Confidence            3689999999999999999999999999999999999999999999999999999999877                   


Q ss_pred             -------H----------------------HHHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCHHHHHHHh
Q 038406           64 -------V----------------------YYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSM  114 (118)
Q Consensus        64 -------~----------------------~~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~l~q~Aw  114 (118)
                             .                      |+..+++|+.+|+.||++|+||+.+.|||.+|..+++.++.++++.+.||
T Consensus        96 E~p~~l~d~v~v~~~~~~~~~~~~~~~~~~y~~~~~~Il~~E~~IL~~L~f~L~v~~P~~fL~~~~~~l~~~~~l~~~A~  175 (358)
T 2pk2_A           96 EQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSY  175 (358)
T ss_dssp             TCCCCHHHHHTTHHHHHCSSSCCCCTTSHHHHGGGTGGGTHHHHHHHHTTTCCCCCCTTHHHHHHHHHTTCCHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHhccccccccccchhhhHHHHHHHHHHHHHHHHcCCceeCCCHHHHHHHHHHHcCCCHHHHHHHH
Confidence                   0                      22347899999999999999999999999999999999999999999999


Q ss_pred             hhcC
Q 038406          115 EFHK  118 (118)
Q Consensus       115 ~~~N  118 (118)
                      .++|
T Consensus       176 ~ll~  179 (358)
T 2pk2_A          176 FMAT  179 (358)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9875

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

Probab=99.93  E-value=5.3e-26  Score=173.37  Aligned_cols=115  Identities=19%  Similarity=0.169  Sum_probs=105.3

Q ss_pred             hhhhhCCC-CCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-------------------
Q 038406            4 HRREFSPS-KKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-------------------   63 (118)
Q Consensus         4 ~~l~~tPS-~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-------------------   63 (118)
                      +++.++|+ ..+|+++++|...|..++++|+++|.+|++|+.|++||++||||||.++|+.                   
T Consensus        21 ~el~~~~~~~~~~l~~~~e~~~R~~~~~~I~~v~~~l~L~~~t~~tA~~~~~RF~~~~s~~~~~~~lva~acLfLA~K~E  100 (285)
T 3rgf_B           21 QDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVE  100 (285)
T ss_dssp             HHHHHHHTTGGGTSCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHSCTTTSCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhhhcccccCCHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhCCchhcCHHHHHHHHHHHHHhhh
Confidence            57777776 6799999999999999999999999999999999999999999999999987                   


Q ss_pred             --------H----HH----------------HHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCHHHHHHHhh
Q 038406           64 --------V----YY----------------KQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSME  115 (118)
Q Consensus        64 --------~----~~----------------~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~l~q~Aw~  115 (118)
                              .    ..                ..+++|+.+|+.||++||||+.+.|||+++..|++.++.++++.+.||.
T Consensus       101 E~~~~~~~di~~~~~~~~k~~~~~~~~~~~~~~~~~Il~~E~~iL~~L~f~l~v~~P~~fL~~~~~~l~~~~~~~~~A~~  180 (285)
T 3rgf_B          101 EFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWR  180 (285)
T ss_dssp             TSCCCCHHHHHHHHHHHHHHHCTTTCCSCCCCCHHHHHHHHHHHHHHTTTCCCCCCSHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             ccccccHHHHHHHHHHHHcccccccCchhhHHHHHHHHHHHHHHHHHcCCCeEeCChHHHHHHHHHHhCCCHHHHHHHHH
Confidence                    0    10                1358999999999999999999999999999999999999999999999


Q ss_pred             hcC
Q 038406          116 FHK  118 (118)
Q Consensus       116 ~~N  118 (118)
                      ++|
T Consensus       181 ~l~  183 (285)
T 3rgf_B          181 IVN  183 (285)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            986

>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=99.93  E-value=1.2e-25  Score=168.22  Aligned_cols=116  Identities=24%  Similarity=0.386  Sum_probs=106.8

Q ss_pred             hhhhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-------------------
Q 038406            3 LHRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-------------------   63 (118)
Q Consensus         3 ~~~l~~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-------------------   63 (118)
                      .+++++|||+.+|++++.|...|..++++|.++|..+++|+.|++||++||||||.++|+.                   
T Consensus        19 ~~el~~~ps~~~~~~~~~e~~~R~~~~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~qlv~~acL~lA~K~e   98 (258)
T 2i53_A           19 KKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVE   98 (258)
T ss_dssp             GGGGGGCHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhCchhhcCCCHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCChhhcCHHHHHHHHHHHHHccc
Confidence            3789999999999999999999999999999999999999999999999999999999877                   


Q ss_pred             -------HHH-----------------HHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCH----HHHHHHhh
Q 038406           64 -------VYY-----------------KQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVC----DLAKSSME  115 (118)
Q Consensus        64 -------~~~-----------------~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~----~l~q~Aw~  115 (118)
                             .+.                 ..+++|+.+|+.||++|||++.+.|||.++..+++.++.+.    ++.+.||.
T Consensus        99 E~~~~l~d~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~f~l~~~~P~~fl~~~~~~l~~~~~~~~~~~~~A~~  178 (258)
T 2i53_A           99 ETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWT  178 (258)
T ss_dssp             TCCCCHHHHHHHHHHHSCHHHHGGGCSCHHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHHTBCSCHHHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHHhchhhhhhhhhhHHHHHHHHHHHHHHHCCCceeccChHHHHHHHHHHhCCCcchHHHHHHHHHH
Confidence                   111                 03789999999999999999999999999999999999885    79999999


Q ss_pred             hcC
Q 038406          116 FHK  118 (118)
Q Consensus       116 ~~N  118 (118)
                      ++|
T Consensus       179 l~~  181 (258)
T 2i53_A          179 FVN  181 (258)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            875

>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=99.91  E-value=2.5e-24  Score=166.91  Aligned_cols=110  Identities=25%  Similarity=0.327  Sum_probs=99.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcC--CCHHHHHHHHHHHHHHhhhcchH-----------------------
Q 038406            9 SPSKKDGISFKKDSELWKLYCSFLQELGTKLK--LPQVIVACAMMLCHQFYMHQLHD-----------------------   63 (118)
Q Consensus         9 tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~--lp~~~~aTA~~~~hRFy~~~S~~-----------------------   63 (118)
                      .||..+|+|+++|..+|.+++.+|+++|..|+  +|+.|++||++||||||.++|++                       
T Consensus        41 ~~~~~~~lt~eeE~~lr~~~~~~I~ev~~~l~~~Lp~~t~~tA~~~~~RF~~~~s~~~~~~~lva~acLfLA~K~EE~~~  120 (323)
T 1jkw_A           41 LPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNV  120 (323)
T ss_dssp             CTTCTTSCCHHHHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHTTCCC
T ss_pred             CccccCCCCHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhhCChhhcCHHHHHHHHHHHHHhhhcCCC
Confidence            47889999999999999999999999999999  99999999999999999999987                       


Q ss_pred             ---H-----------HHHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHc-------CCCHHHHHHHhhhcC
Q 038406           64 ---V-----------YYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRL-------DLVCDLAKSSMEFHK  118 (118)
Q Consensus        64 ---~-----------~~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l-------~~~~~l~q~Aw~~~N  118 (118)
                         .           ....++.|+.+|+.||++||||+.|.|||+++..|++.+       +.++++.+.||.++|
T Consensus       121 ~l~d~v~~~~~~p~~~~~~~~~Il~~E~~iL~~L~f~l~v~~P~~~L~~~l~~l~~~~~~~~~~~~l~~~A~~~l~  196 (323)
T 1jkw_A          121 SSPQFVGNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYPILENPEILRKTADDFLN  196 (323)
T ss_dssp             CHHHHGGGSSSCHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHhccChhhhHHHHHHHHHHHHHHHHHCCCcEEcCChHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHH
Confidence               1           124579999999999999999999999999999999876       223679999999986

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

Probab=99.86  E-value=2.6e-22  Score=148.74  Aligned_cols=107  Identities=16%  Similarity=0.186  Sum_probs=95.7

Q ss_pred             hhhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH--------------------
Q 038406            4 HRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD--------------------   63 (118)
Q Consensus         4 ~~l~~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~--------------------   63 (118)
                      +++.++||.++|     |   |..++++|.++|..|++|+.|++||++||+|||.++|++                    
T Consensus        15 ~~l~~~~~~~~~-----~---R~~~~~~i~~v~~~l~L~~~t~~~A~~~~~Rf~~~~~~~~~~~~~lv~~acL~lA~K~E   86 (235)
T 1zp2_A           15 DLESLEPTCLSK-----D---TIYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKGFSLEALVATCIYLSCKVE   86 (235)
T ss_dssp             SCTTSSCCCSCH-----H---HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCSCCCCCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHCCcchhH-----H---HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccccCHHHHHHHHHHHHhccc
Confidence            678888887653     2   999999999999999999999999999999999987655                    


Q ss_pred             -------HH------------HHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCHHHHHHHhhhcC
Q 038406           64 -------VY------------YKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK  118 (118)
Q Consensus        64 -------~~------------~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~l~q~Aw~~~N  118 (118)
                             .+            ...+++|+.+|+.||++||||+.+.|||+++..+++.++.++++.+.||.++|
T Consensus        87 e~~~~l~d~~~~~~~~~~~~~~~~~~~I~~~E~~iL~~L~f~l~~~~P~~~l~~~~~~~~~~~~~~~~A~~~l~  160 (235)
T 1zp2_A           87 ECPVHIRTICNEANDLWSLKVKLSRSNISEIEFEIISVLDAFLIVHHPYTSLEQAFHDGIINQKQLEFAWSIVN  160 (235)
T ss_dssp             TCCCCHHHHHHHHHTTCCCSSCCCHHHHHHHHHHHHHHTTTCCCCCCTHHHHHHHHHTTSSCHHHHHHHHHHHH
T ss_pred             cCcccHHHHHHHHHHHccchhhccHHHHHHHHHHHHHHCCCcEEecChHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence                   11            12478999999999999999999999999999999999999999999999986

>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=99.74  E-value=5.9e-18  Score=122.91  Aligned_cols=94  Identities=15%  Similarity=0.152  Sum_probs=84.9

Q ss_pred             HHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------HHH-------------------HHHHHHHH
Q 038406           25 WKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------VYY-------------------KQKELILT   74 (118)
Q Consensus        25 r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------~~~-------------------~~~~~Il~   74 (118)
                      ...|+++|+++|..|++|+.|++||++||||||.+++++           .|-                   --+++|..
T Consensus         5 l~~a~~~I~~~~~~L~L~~~v~~~A~~~~~r~~~~~~~~~~~~~~v~aaclylAcK~ee~p~~l~di~~~~~~~~~~i~~   84 (207)
T 1c9b_A            5 MMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGR   84 (207)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTCSTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHTSSSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHH
Confidence            458999999999999999999999999999999999887           111                   12578999


Q ss_pred             HHHHHHHHcCcceeecCChHHHHHHHHHcCCCHHHHHHHhhhcC
Q 038406           75 AERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK  118 (118)
Q Consensus        75 ~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~l~q~Aw~~~N  118 (118)
                      +|+.||++|||++.+.|||.++..+++.+++++++.+.||.++|
T Consensus        85 ~~~~ll~~L~~~l~~~~p~~~l~r~~~~l~l~~~~~~~A~~i~~  128 (207)
T 1c9b_A           85 CFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIAR  128 (207)
T ss_dssp             HHHHHHHHTTCCCCCCCTHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCcCcCCHHHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999998875

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

Probab=99.60  E-value=1.4e-15  Score=116.91  Aligned_cols=113  Identities=12%  Similarity=0.155  Sum_probs=94.1

Q ss_pred             hhhCCC--CCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH--------------------
Q 038406            6 REFSPS--KKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD--------------------   63 (118)
Q Consensus         6 l~~tPS--~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~--------------------   63 (118)
                      .+..|+  ..+|+..+-+...|...++||.++|..+++++.|+++|+.|++||+.++++.                    
T Consensus        50 ~~~~p~~~y~~~~q~~i~~~~R~~lvdwl~ev~~~~~l~~~t~~lAv~~lDRfls~~~v~~~~lqLv~~tcL~lAsK~eE  129 (306)
T 3g33_B           50 ERYVPRASYFQCVQREIKPHMRKMLAYWMLEVCEEQRCEEEVFPLAMNYLDRYLSCVPTRKAQLQLLGAVCMLLASKLRE  129 (306)
T ss_dssp             GGGSCSSCCTTTSTTTCCHHHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHCCCCGGGHHHHHHHHHHHHHHHHC
T ss_pred             HHhCCCcHHHhhcCccCCHHHHHHHHHHHHHHHHHhCCcHhHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHhcc
Confidence            334444  4466666667789999999999999999999999999999999999988766                    


Q ss_pred             -------HHH------HHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCC----HHHHHHHhhhcC
Q 038406           64 -------VYY------KQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLV----CDLAKSSMEFHK  118 (118)
Q Consensus        64 -------~~~------~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~----~~l~q~Aw~~~N  118 (118)
                             .+.      --+++|+.+|+.||++|+|++.+.+||.++..|++.++.+    ..+.+.||.++|
T Consensus       130 ~~p~~~~~l~~~~~~~~~~~~i~~mE~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~  201 (306)
T 3g33_B          130 TTPLTIEKLCIYTDHAVSPRQLRDWEVLVLGKLKWDLAAVIAHDFLAFILHRLSLPRDRQALVKKHAQTFLA  201 (306)
T ss_dssp             SSCCCTTHHHHHTTTSSCHHHHHHHHHHHHHHTTTCCCCCCGGGGHHHHHHTSSCCTTTHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHhccCccHHHHHHHHHHHHHHcCCccCCCCHHHHHHHHHHHcCCChhHHHHHHHHHHHHHH
Confidence                   111      1268999999999999999999999999999999999876    236688898764

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

Probab=99.55  E-value=1e-14  Score=109.98  Aligned_cols=100  Identities=13%  Similarity=0.132  Sum_probs=88.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH---------------------------HHH-----
Q 038406           19 KKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD---------------------------VYY-----   66 (118)
Q Consensus        19 ~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~---------------------------~~~-----   66 (118)
                      +-....|...++||.++|..+++++.|.++|+.|++||+..+++.                           .+.     
T Consensus        32 ~i~~~~R~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfl~~~~v~~~~lqlv~~acL~iA~K~eE~~~p~~~d~~~~~~~  111 (269)
T 2b9r_A           32 EVTGNMRAILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQNNSVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDN  111 (269)
T ss_dssp             SSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHTTSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTCS
T ss_pred             CCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcCCCCcHHHhhHHHHHHHHHHHhcccccCccHHHHHHHhcC
Confidence            334568999999999999999999999999999999999988766                           111     


Q ss_pred             -HHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCHHHHHHHhhhcC
Q 038406           67 -KQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK  118 (118)
Q Consensus        67 -~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~l~q~Aw~~~N  118 (118)
                       -.+++|+.+|+.||++|+|++.+.+|+.++..+++.++.+.++.+.||.++|
T Consensus       112 ~~~~~eI~~mE~~IL~~L~f~l~~~tp~~fl~~~~~~~~~~~~~~~~a~~l~e  164 (269)
T 2b9r_A          112 TYTKHQIRQMEMKILRALNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLME  164 (269)
T ss_dssp             SSCHHHHHHHHHHHHHHTTSCCCCCCHHHHHHHHHHSSCCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHcCCccCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence             1378999999999999999999999999999999999999889999998864

>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=99.54  E-value=1.1e-14  Score=109.13  Aligned_cols=98  Identities=16%  Similarity=0.207  Sum_probs=87.0

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH---------------------------HHH------H
Q 038406           21 DSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD---------------------------VYY------K   67 (118)
Q Consensus        21 E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~---------------------------~~~------~   67 (118)
                      ....|...++||.++|..+++++.|+++|+.|++||+.++++.                           .+.      -
T Consensus        35 ~~~~R~~lvdwl~~v~~~~~l~~~tl~lAv~~lDRfls~~~v~~~~lqlv~~acl~iA~K~ee~~~~~~~d~~~i~~~~~  114 (260)
T 2cch_B           35 TNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTY  114 (260)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTSSS
T ss_pred             CHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccCCCCHHHHhHHHHHHHHHHHHhcccCCCCHHHHHHHHcCCc
Confidence            3467999999999999999999999999999999999988766                           111      1


Q ss_pred             HHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCH-HHHHHHhhhcC
Q 038406           68 QKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVC-DLAKSSMEFHK  118 (118)
Q Consensus        68 ~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~-~l~q~Aw~~~N  118 (118)
                      .+++|+.+|+.||++|+|++.+.+|+.++..+++.++.+. ++.+.||.++|
T Consensus       115 ~~~~i~~mE~~iL~~L~~~l~~~tp~~fl~~~~~~l~~~~~~~~~~a~~l~e  166 (260)
T 2cch_B          115 TKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGE  166 (260)
T ss_dssp             CHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHTTCSSCCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHcCCccCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHH
Confidence            3789999999999999999999999999999999999875 88999998764

>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=99.53  E-value=1.2e-14  Score=104.78  Aligned_cols=98  Identities=19%  Similarity=0.203  Sum_probs=84.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------HH-------------------HHHH
Q 038406           20 KDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------VY-------------------YKQK   69 (118)
Q Consensus        20 ~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------~~-------------------~~~~   69 (118)
                      .|..+ ..++++|.++|..|++|+.++.||..+|+||+..+++.           .|                   .--+
T Consensus         5 ~er~l-~~a~~~I~~~~~~L~L~~~v~~~A~~l~~~~~~~~~~~gr~~~~vaaAclylAcr~~~~p~~l~di~~~~~v~~   83 (200)
T 1ais_B            5 AERNL-AFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVDK   83 (200)
T ss_dssp             ---CH-HHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTTTTTTCCHHHHHHHHHHHHHHHHTCCCCHHHHHHHTTSCH
T ss_pred             HHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCH
Confidence            34444 48999999999999999999999999999999987766           11                   1125


Q ss_pred             HHHHHHHHHHHHHcCcceee--cCChHHHHHHHHHcCCCHHHHHHHhhhcC
Q 038406           70 ELILTAERLLPATIAFDFDI--QLPYEPLVAAFTRLDLVCDLAKSSMEFHK  118 (118)
Q Consensus        70 ~~Il~~E~~iL~~L~Fdl~v--~hP~~~l~~~~~~l~~~~~l~q~Aw~~~N  118 (118)
                      .+|..+|+.|++.|||++.+  .||+.++..+++.+++++++.+.||.++|
T Consensus        84 ~~i~~~~~~l~~~L~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~  134 (200)
T 1ais_B           84 KEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLSEKVRRRAIEILD  134 (200)
T ss_dssp             HHHHHHHHHHHHHTTCCTTTTCCCGGGGHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcccCCcCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            78999999999999999999  99999999999999999999999999874

>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=99.51  E-value=1.5e-14  Score=108.95  Aligned_cols=98  Identities=14%  Similarity=0.195  Sum_probs=85.0

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH---------------------------HHH------H
Q 038406           21 DSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD---------------------------VYY------K   67 (118)
Q Consensus        21 E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~---------------------------~~~------~   67 (118)
                      ....|...++||.+++..+++++.|+++|+.|++||+.++++.                           .+.      -
T Consensus        53 ~~~~R~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~v~~~~lqlv~~acL~iAsK~EE~~p~~~~~~~~~~~~~~  132 (271)
T 2w96_A           53 LPSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSI  132 (271)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHTTSCCCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTSS
T ss_pred             CHHHHHHHHHHHHHHHHHHCCchhHHHHHHHHHHHhCCcCCcCHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHhcCCC
Confidence            4568999999999999999999999999999999999988766                           111      1


Q ss_pred             HHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCHH----HHHHHhhhcC
Q 038406           68 QKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCD----LAKSSMEFHK  118 (118)
Q Consensus        68 ~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~----l~q~Aw~~~N  118 (118)
                      .+++|+.+|+.||++|+|++.+.+|+.++..+++.++.+.+    +.+.||.++|
T Consensus       133 ~~~eI~~mE~~IL~~L~~~l~~~tp~~fl~~~~~~l~~~~~~~~~~~~~a~~~l~  187 (271)
T 2w96_A          133 RPEELLQMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVA  187 (271)
T ss_dssp             CHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHCCCccCCCCHHHHHHHHHHHcCCCchHHHHHHHHHHHHHH
Confidence            37899999999999999999999999999999999998743    3467888764

>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=99.47  E-value=5.2e-14  Score=105.30  Aligned_cols=114  Identities=13%  Similarity=0.110  Sum_probs=91.1

Q ss_pred             hhhhCCCCC--CCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-------------------
Q 038406            5 RREFSPSKK--DGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-------------------   63 (118)
Q Consensus         5 ~l~~tPS~~--~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-------------------   63 (118)
                      +.+..|+..  ++..++-....|...++||.+++..+++++.|.++|+.|++||+.++++.                   
T Consensus        29 E~~~~p~~~y~~~~q~~i~~~~R~~lvdwl~ev~~~~~l~~etl~lAv~~~DRfls~~~v~~~~lqLv~~acl~iA~K~e  108 (257)
T 1g3n_C           29 EPRFLTSDSVFGTFQQSLTSHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLR  108 (257)
T ss_dssp             GGGGCCCGGGHHHHTSSCCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCChhHHHhcCccCCHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHc
Confidence            445556431  22233344568999999999999999999999999999999999988766                   


Q ss_pred             --------HHH------HHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCH----HHHHHHhhhcC
Q 038406           64 --------VYY------KQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVC----DLAKSSMEFHK  118 (118)
Q Consensus        64 --------~~~------~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~----~l~q~Aw~~~N  118 (118)
                              .+.      --+++|+.+|+.||++|+|++.+.+|+.++..+++.++.+.    .+.+.||.++|
T Consensus       109 E~~~p~~~d~~~~~~~~~~~~~i~~mE~~iL~~L~~~l~~~tp~~fl~~~~~~~~~~~~~~~~~~~~a~~~le  181 (257)
T 1g3n_C          109 SLTPISTSSLCYAAADSFSRQELIDQEKELLEKLAWRTEAVLATDVTSFLLLKLVGGSQHLDFWHHEVNTLIT  181 (257)
T ss_dssp             CSSCCCHHHHHHHTTTCSCHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHHHHSCSSTTHHHHHHHHHHHHH
T ss_pred             cccCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCcCCCCCHHHHHHHHHHHcCCChhHHHHHHHHHHHHHH
Confidence                    111      13689999999999999999999999999999999998762    24677887763

>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=99.43  E-value=2.4e-13  Score=101.46  Aligned_cols=102  Identities=10%  Similarity=0.150  Sum_probs=86.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH----------------HH--------------
Q 038406           16 ISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD----------------VY--------------   65 (118)
Q Consensus        16 i~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~----------------~~--------------   65 (118)
                      ..++-....|...++||.+++..+++++.|.++|+.|+.||+.++++.                -+              
T Consensus        43 ~q~~i~~~~R~~lvdwl~~v~~~~~l~~etl~lAv~~~DRfls~~~v~~~~lqLv~~acl~iA~K~eE~~~p~~~d~~~~  122 (254)
T 2f2c_A           43 IQTEVTVDNRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYL  122 (254)
T ss_dssp             TCSSCCHHHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSCCCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHSTT
T ss_pred             cCccCCHHHHHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHHccCCcCHHHccHHHHHHHHHHHHhcccCCCCHHHHHHH
Confidence            334445678999999999999999999999999999999999988765                01              


Q ss_pred             ---HHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCHH----HHHHHhhhc
Q 038406           66 ---YKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCD----LAKSSMEFH  117 (118)
Q Consensus        66 ---~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~----l~q~Aw~~~  117 (118)
                         .--+++|+.+|+.||++|+|++.+.+|+.++..+++.++.+.+    +.+.||.++
T Consensus       123 ~~~~~~~~~i~~mE~~IL~~L~~~l~~~tp~~fl~~~~~~~~~~~~~~~~~~~~a~~ll  181 (254)
T 2f2c_A          123 SCDCFTNLELINQEKDILEALKWDTEAVLATDFLIPLCNALKIPEDLWPQLYEAASTTI  181 (254)
T ss_dssp             C---CCHHHHHHHHHHHHHHTTTCCCCCCGGGSHHHHHHHTTCCGGGHHHHHHHHHHHH
T ss_pred             hCCCCCHHHHHHHHHHHHHHCCCcCCCCCHHHHHHHHHHHcCCChhhHHHHHHHHHHHH
Confidence               1136899999999999999999999999999999999988733    356788765

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

Probab=99.30  E-value=8.7e-13  Score=102.80  Aligned_cols=93  Identities=10%  Similarity=0.065  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------------------HHHH-------HHHHHHHH
Q 038406           26 KLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------------------VYYK-------QKELILTA   75 (118)
Q Consensus        26 ~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------------------~~~~-------~~~~Il~~   75 (118)
                      ..++..|.++|..|++|+.++.||+.+|+||+..++++                       .+.+       -+++|..+
T Consensus       127 ~~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~~~~~~~~kgr~~~~vaaAclyiAcR~e~~prtl~ei~~~~~v~~keIgr~  206 (345)
T 3k7a_M          127 QAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIHVKTKEFGKT  206 (345)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHTHHHHHHHHHSSSCSSCCCCSHHHHTTTTTTTSBTTBSSCCHHHHHHSSSCCSHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCCHHHHHHH
Confidence            47889999999999999999999999999999988776                       1111       25789999


Q ss_pred             HHHHHHHcC------------cceeecCChHHHHHHHHHcCCCHHHHHHHhhhcC
Q 038406           76 ERLLPATIA------------FDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK  118 (118)
Q Consensus        76 E~~iL~~L~------------Fdl~v~hP~~~l~~~~~~l~~~~~l~q~Aw~~~N  118 (118)
                      ++.|++.|+            |++.+.||+.++..|++.|+++.++.+.||.++|
T Consensus       207 ~~~l~~~L~~~~~~~~~~~~~~~~~~~~p~~~i~Rf~~~L~l~~~v~~~A~~i~~  261 (345)
T 3k7a_M          207 LNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAEYTAK  261 (345)
T ss_dssp             HHHHHHHHTCC--------------------------------------------
T ss_pred             HHHHHHHHhhhhccccccccccccCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            999999999            9999999999999999999999999999999986

>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=99.25  E-value=1.2e-11  Score=92.78  Aligned_cols=99  Identities=12%  Similarity=0.093  Sum_probs=82.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH----------------HHH---------------
Q 038406           18 FKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD----------------VYY---------------   66 (118)
Q Consensus        18 ~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~----------------~~~---------------   66 (118)
                      .+-....|...++||.+++..+++++.|..+|+.|+.||..++++.                -|+               
T Consensus        42 ~~i~~~~R~~lvdWl~ev~~~~~l~~eT~~lAv~~lDRfLs~~~v~~~~lqLvg~tcl~iAsK~eE~~p~~~~~l~~~~~  121 (252)
T 1f5q_B           42 QHFTSQYRKVLTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLCG  121 (252)
T ss_dssp             HHHHCSHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhC
Confidence            3444567999999999999999999999999999999999987765                011               


Q ss_pred             --HHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCHH----HHHHHhhh
Q 038406           67 --KQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCD----LAKSSMEF  116 (118)
Q Consensus        67 --~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~----l~q~Aw~~  116 (118)
                        --+++|+.+|..||++|+|++.+-+|+.++..+++.++.+.+    +.+.|+.+
T Consensus       122 ~~yt~~~i~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~~~~~~~~~~~~~~~a~~~  177 (252)
T 1f5q_B          122 GATTADKLLTLEVKSLDTLSWVADRCLSTDLICYILHIMHAPREDYLNIYNLCRPK  177 (252)
T ss_dssp             TTCCHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHCCCccCCCCHHHHHHHHHHHcCCCcchHHHHHHHHHHH
Confidence              126899999999999999999999999999999999987732    44455544

>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=99.17  E-value=6.7e-11  Score=89.73  Aligned_cols=86  Identities=13%  Similarity=0.070  Sum_probs=74.9

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhh-cchH---------------------------HHH------
Q 038406           21 DSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMH-QLHD---------------------------VYY------   66 (118)
Q Consensus        21 E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~-~S~~---------------------------~~~------   66 (118)
                      ....|...++||.+++..+++++.|+++|+.|++||+.. +++.                           .+.      
T Consensus        46 ~~~~R~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~~v~~~~lqlv~~acL~iA~K~eE~~~p~l~~~~~i~~~~  125 (283)
T 1w98_B           46 QPKMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGA  125 (283)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTS
T ss_pred             CHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcccCCCcHHHHHHHHcCC
Confidence            346899999999999999999999999999999999987 4654                           111      


Q ss_pred             HHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCC
Q 038406           67 KQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLV  106 (118)
Q Consensus        67 ~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~  106 (118)
                      -.+++|+.+|+.||++|+|++.+.+|+.++..+++.++.+
T Consensus       126 ~~~~ei~~mE~~IL~~L~~~l~~~tp~~fL~~f~~~~~~~  165 (283)
T 1w98_B          126 CSGDEILTMELMIMKALKWRLSPLTIVSWLNVYMQVAYLN  165 (283)
T ss_dssp             SCHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHHHHTCC
T ss_pred             CCHHHHHHHHHHHHHHcCCcCCCCCHHHHHHHHHHHhccC
Confidence            1278999999999999999999999999999999987654

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

Probab=98.49  E-value=1e-07  Score=74.32  Aligned_cols=93  Identities=10%  Similarity=0.044  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------HHH-------------------HHHHHHHHH
Q 038406           26 KLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------VYY-------------------KQKELILTA   75 (118)
Q Consensus        26 ~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------~~~-------------------~~~~~Il~~   75 (118)
                      ..+...|.++|..|++|..++.+|..+|+|++..+.++           .|-                   --+.+|-..
T Consensus       127 ~~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~a~~~~~~rGrs~e~vaAAclYiACR~~~~prtl~eI~~~~~v~~keigr~  206 (345)
T 4bbr_M          127 QAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIHVKTKEFGKT  206 (345)
T ss_dssp             THHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCTTTTTCCHHHHHHHHHHHHHHHTCCBCCHHHHHHHHTCCTTHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHH
Confidence            46888999999999999999999999999999877665           121                   124688889


Q ss_pred             HHHHHHHcCcc------------eeecCChHHHHHHHHHcCCCHHHHHHHhhhcC
Q 038406           76 ERLLPATIAFD------------FDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK  118 (118)
Q Consensus        76 E~~iL~~L~Fd------------l~v~hP~~~l~~~~~~l~~~~~l~q~Aw~~~N  118 (118)
                      .+.|.+.|+..            +...+|..|+..|+..|+++.++.+.||.+++
T Consensus       207 ~k~l~~~L~l~~~~~~~~~~~~~~~~~~p~~~i~Rf~s~L~l~~~v~~~A~~i~~  261 (345)
T 4bbr_M          207 LNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAEYTAK  261 (345)
T ss_dssp             HHHHHHCC-----------------------------------------------
T ss_pred             HHHHHHHhCccccccccccccccCCCCCHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            99999999974            66789999999999999999999999998874

>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=92.61  E-value=0.42  Score=36.36  Aligned_cols=72  Identities=6%  Similarity=0.048  Sum_probs=52.7

Q ss_pred             HHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcc-hH----------------------------HHHH-----HHHHHHHH
Q 038406           30 SFLQELGTKLKLPQVIVACAMMLCHQFYMHQL-HD----------------------------VYYK-----QKELILTA   75 (118)
Q Consensus        30 ~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S-~~----------------------------~~~~-----~~~~Il~~   75 (118)
                      +|+.++-..-+++..++-.|.+|+.|+-.++. +.                            .+|.     -.+++-.+
T Consensus        79 ~Yl~RI~k~t~ls~~~ll~ALvYLdRL~~~~p~~~l~~~nvHRLlLtALmlAsK~ldD~~ysN~~wAkVgGisl~ELN~L  158 (293)
T 2pmi_B           79 NYFIRLTKFSSLEHCVLMTSLYYIDLLQTVYPDFTLNSLTAHRFLLTATTVATKGLCDSFSTNAHYAKVGGVRCHELNIL  158 (293)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHHHHHHHCTTCCCSTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHHHhhCCCCccCCchHHHHHHHHHHHHHHhccccccChhHhhhccCcCHHHHHHH
Confidence            57888888888999999999999999977532 11                            2222     15899999


Q ss_pred             HHHHHHHcCcceeecCChHHHHHHHHH
Q 038406           76 ERLLPATIAFDFDIQLPYEPLVAAFTR  102 (118)
Q Consensus        76 E~~iL~~L~Fdl~v~hP~~~l~~~~~~  102 (118)
                      |+..|..|+|++.|. +..+..-++..
T Consensus       159 E~eFL~lLdf~L~V~-~ee~~~cy~E~  184 (293)
T 2pmi_B          159 ENDFLKRVNYRIIPR-DHNITLCSIEQ  184 (293)
T ss_dssp             HHHHHHTTTTCCSCC-TTHHHHHHHHS
T ss_pred             HHHHHHHcCCceeeC-HHHHHHHHHHH
Confidence            999999999999887 33444333333

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	118
d2ivxa1	143	a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens)	9e-11
d2i53a1	144	a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens)	1e-10
d1jkwa1	151	a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo s	3e-06

>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Length = 143

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

 Score = 53.1 bits (127), Expect = 9e-11
 Identities = 16/59 (27%), Positives = 33/59 (55%)

Query: 7  EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVY 65
          E +PS++ G+   K+    +   + +QE+G +L + Q+ +  A++  H+FYMH     +
Sbjct: 13 ENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKF 71

>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Length = 144

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

 Score = 53.1 bits (127), Expect = 1e-10
 Identities = 13/62 (20%), Positives = 30/62 (48%)

Query: 7  EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYY 66
            +PS+ +G+    ++   +    F+ ++GT+L L    +A  ++  H+FYM      + 
Sbjct: 19 AHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFP 78

Query: 67 KQ 68
          + 
Sbjct: 79 RY 80

>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Length = 151

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

 Score = 41.5 bits (97), Expect = 3e-06
 Identities = 14/64 (21%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 7  EFSPSKKDGISFKKDSELWKLYCSFLQELGTKLK--LPQVIVACAMMLCHQFYMHQLHDV 64
          +  P+    +   ++  L K Y   L E  +  K  +P+ +V  A M   +FY++     
Sbjct: 29 KVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVME 88

Query: 65 YYKQ 68
          Y+ +
Sbjct: 89 YHPR 92

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	118
d2ivxa1	143	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	99.93
d2i53a1	144	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	99.91
d1jkwa1	151	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	99.83
d2cchb1	128	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	98.53
d1g3nc1	132	Viral cyclin {Kaposi's sarcoma-associated herpesvi	98.24
d1w98b2	140	G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax	98.12
d1f5qb1	141	Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]	98.12
d1bu2a1	127	Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}	98.1
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	94.42
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	91.17

>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=99.93  E-value=6.6e-27  Score=160.15  Aligned_cols=86  Identities=26%  Similarity=0.524  Sum_probs=82.1

Q ss_pred             hhhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH--------------------
Q 038406            4 HRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD--------------------   63 (118)
Q Consensus         4 ~~l~~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~--------------------   63 (118)
                      +++++|||++||+|+++|..+|..+|+||+++|.+|++|+.|++||++||||||+++|+.                    
T Consensus        10 ~~l~~~pS~~~gi~~~~E~~~R~~~~~~i~~~~~~l~l~~~t~~~A~~l~~Rf~~~~s~~~~~~~~va~acl~LA~K~eE   89 (143)
T d2ivxa1          10 EQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE   89 (143)
T ss_dssp             HHHHSCHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHhCcccccCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHhcc
Confidence            689999999999999999999999999999999999999999999999999999999987                    


Q ss_pred             ----------------------------HHHHHHHHHHHHHHHHHHHcCcceee
Q 038406           64 ----------------------------VYYKQKELILTAERLLPATIAFDFDI   89 (118)
Q Consensus        64 ----------------------------~~~~~~~~Il~~E~~iL~~L~Fdl~v   89 (118)
                                                  .|+.+++.|+.+|+.||++||||++|
T Consensus        90 ~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~Fdl~V  143 (143)
T d2ivxa1          90 QARKLEHVIKVAHACLHPLEPLLDTKCDAYLQQTRELVILETIMLQTLGFEITI  143 (143)
T ss_dssp             CCCCHHHHHHHHHHHHCTTSCCCCTTSHHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             ccccHHHHHHHHHHHhcccchhhhhchhhhHHHHHHHHHHHHHHHHHcCCeeeC
Confidence                                        46678999999999999999999986

>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=99.91  E-value=2.1e-25  Score=153.07  Aligned_cols=86  Identities=26%  Similarity=0.440  Sum_probs=80.1

Q ss_pred             hhhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH--------------------
Q 038406            4 HRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD--------------------   63 (118)
Q Consensus         4 ~~l~~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~--------------------   63 (118)
                      +++++|||+++|+++++|..+|..+++||.++|.+|++|+.|++||++||||||.++|+.                    
T Consensus        16 ~~l~~tps~~~~i~~~~E~~~R~~~~~~i~~~~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~~lva~acl~LA~K~eE   95 (144)
T d2i53a1          16 KDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEE   95 (144)
T ss_dssp             GGGGGCHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHhChhhhcCCChHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhhCcccchhHHHHHHHHHHHHHHhhc
Confidence            679999999999999999999999999999999999999999999999999999999977                    


Q ss_pred             -----------------------HHHHHHHHHHHHHHHHHHHcCcceee
Q 038406           64 -----------------------VYYKQKELILTAERLLPATIAFDFDI   89 (118)
Q Consensus        64 -----------------------~~~~~~~~Il~~E~~iL~~L~Fdl~v   89 (118)
                                             .++..+++|+.+|+.||++||||++|
T Consensus        96 ~~~~l~~vi~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~Fdl~V  144 (144)
T d2i53a1          96 TPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQV  144 (144)
T ss_dssp             CCCCHHHHHHHHHHHSCHHHHGGGCSCHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             ccccHHHHHHHHHHHhhhhhhhhhchhhHHHHHHHHHHHHHHCCCeeeC
Confidence                                   12236789999999999999999986

>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=99.83  E-value=1.5e-20  Score=129.61  Aligned_cols=87  Identities=24%  Similarity=0.292  Sum_probs=79.4

Q ss_pred             hhhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcC--CCHHHHHHHHHHHHHHhhhcchH------------------
Q 038406            4 HRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLK--LPQVIVACAMMLCHQFYMHQLHD------------------   63 (118)
Q Consensus         4 ~~l~~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~--lp~~~~aTA~~~~hRFy~~~S~~------------------   63 (118)
                      +...++|+...++++++|..+|.+++.+|.++|..++  +|+.|+|||++||||||+++|+.                  
T Consensus        26 ~~~~~~~~~~~~l~~~ee~~l~~~~~~~l~~~~~~~k~~l~~~~~~tA~~~~~RF~~~~s~~~~~~~li~~acl~LA~K~  105 (151)
T d1jkwa1          26 ANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKV  105 (151)
T ss_dssp             HTSSSCTTCTTSCCHHHHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHH
T ss_pred             hhcccCcccccCCCHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHhhcCccccccHHHHHHHHHHHHHHH
Confidence            4456789999999999999999999999999999775  99999999999999999999988                  


Q ss_pred             -------------------HHHHHHHHHHHHHHHHHHHcCcceeec
Q 038406           64 -------------------VYYKQKELILTAERLLPATIAFDFDIQ   90 (118)
Q Consensus        64 -------------------~~~~~~~~Il~~E~~iL~~L~Fdl~v~   90 (118)
                                         .++..+++|+.+|..||++|+||+.|+
T Consensus       106 ee~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~f~L~Vh  151 (151)
T d1jkwa1         106 DEFNVSSPQFVGNLRESPLGQEKALEQILEYELLLIQQLNFHLIVH  151 (151)
T ss_dssp             TTCCCCHHHHGGGSSSCHHHHHHHHHHHHHHHHHHHHHTTTCCCCC
T ss_pred             cccCCCHHHHHHHHHhhcccccccHHHHHHHHHHHHHHcCCeeeeC
Confidence                               345678999999999999999999885

>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=98.53  E-value=1.7e-07  Score=61.50  Aligned_cols=71  Identities=20%  Similarity=0.292  Sum_probs=59.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH---------------------------HHH
Q 038406           14 DGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD---------------------------VYY   66 (118)
Q Consensus        14 ~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~---------------------------~~~   66 (118)
                      .++++.    .|...++||.+++..++++..|..+|+.++.||....++.                           .+.
T Consensus        24 ~~i~~~----~R~~li~W~~~v~~~~~l~~~t~~lAv~llDr~l~~~~i~~~~~qLi~~~cl~iAsK~ee~~~~~l~~l~   99 (128)
T d2cchb1          24 PDITNS----MRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFV   99 (128)
T ss_dssp             SSCCHH----HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHH
T ss_pred             CCCCHH----HHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcccCCchHHHHHHHHHHHHHHHHHHhccCCCHHHHH
Confidence            456664    4889999999999999999999999999999999877655                           111


Q ss_pred             H------HHHHHHHHHHHHHHHcCccee
Q 038406           67 K------QKELILTAERLLPATIAFDFD   88 (118)
Q Consensus        67 ~------~~~~Il~~E~~iL~~L~Fdl~   88 (118)
                      .      -+++++.+|..||++|+||+.
T Consensus       100 ~~~~~~~t~~~i~~mE~~IL~~L~~~l~  127 (128)
T d2cchb1         100 YITDDTYTKKQVLRMEHLVLKVLTFDLA  127 (128)
T ss_dssp             HHTTSSSCHHHHHHHHHHHHHHTTTCCC
T ss_pred             HHHcCCCCHHHHHHHHHHHHHHCCCeec
Confidence            1      268999999999999999974

>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=98.24  E-value=1.1e-06  Score=58.08  Aligned_cols=70  Identities=14%  Similarity=0.236  Sum_probs=58.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH---------------------------HHH
Q 038406           14 DGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD---------------------------VYY   66 (118)
Q Consensus        14 ~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~---------------------------~~~   66 (118)
                      .++++.    .|..-++|+.+++..++++..|...|+.|+.||....++.                           .+.
T Consensus        29 ~~it~~----~R~~lidWl~~v~~~~~l~~et~~lAv~llDrfls~~~v~~~~lqLia~tcl~iAsK~ee~~~~~~~~l~  104 (132)
T d1g3nc1          29 QSLTSH----MRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLC  104 (132)
T ss_dssp             SSCCHH----HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHH
T ss_pred             ccCCHH----HHHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCcccCcHHHHHHHHHHHHHHHHHhcccCCCCHHHHH
Confidence            345554    6888999999999999999999999999999999877665                           111


Q ss_pred             H------HHHHHHHHHHHHHHHcCcce
Q 038406           67 K------QKELILTAERLLPATIAFDF   87 (118)
Q Consensus        67 ~------~~~~Il~~E~~iL~~L~Fdl   87 (118)
                      .      -+++|+.+|..||++|+|++
T Consensus       105 ~~~~~~~t~~ei~~mE~~IL~~L~w~l  131 (132)
T d1g3nc1         105 YAAADSFSRQELIDQEKELLEKLAWRT  131 (132)
T ss_dssp             HHTTTCSCHHHHHHHHHHHHHHTTTCC
T ss_pred             HHHcCCCCHHHHHHHHHHHHHHcCCcC
Confidence            1      26899999999999999997

>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=98.12  E-value=2.8e-06  Score=56.42  Aligned_cols=66  Identities=15%  Similarity=0.179  Sum_probs=54.9

Q ss_pred             HHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcc-hH---------------------------HHHH------H
Q 038406           23 ELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQL-HD---------------------------VYYK------Q   68 (118)
Q Consensus        23 ~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S-~~---------------------------~~~~------~   68 (118)
                      ..|..-++|+.+++..++++..|...|+.|+-||...+. ..                           .+..      -
T Consensus        41 ~~R~~lidW~~~v~~~~~l~~et~~lAv~llDryl~~~~~v~~~~lqL~a~acL~IAsK~ee~~~~~~~~l~~~~~~~~t  120 (140)
T d1w98b2          41 KMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACS  120 (140)
T ss_dssp             HHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTSSC
T ss_pred             HHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhccccccHHHHhHHHHHHHHHHHHHcccCCCCHHHHHHHHcCCCC
Confidence            369999999999999999999999999999999976432 22                           1111      2


Q ss_pred             HHHHHHHHHHHHHHcCccee
Q 038406           69 KELILTAERLLPATIAFDFD   88 (118)
Q Consensus        69 ~~~Il~~E~~iL~~L~Fdl~   88 (118)
                      +++|+.+|..||++|+|+++
T Consensus       121 ~~ei~~mE~~IL~~L~~~Ln  140 (140)
T d1w98b2         121 GDEILTMELMIMKALKWRLS  140 (140)
T ss_dssp             HHHHHHHHHHHHHHTTTCCC
T ss_pred             HHHHHHHHHHHHHHCCCcCC
Confidence            68999999999999999974

>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=98.12  E-value=6.2e-07  Score=59.94  Aligned_cols=82  Identities=15%  Similarity=0.203  Sum_probs=64.7

Q ss_pred             hhCCCCCCCCCHHHH--HHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH---------------------
Q 038406            7 EFSPSKKDGISFKKD--SELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD---------------------   63 (118)
Q Consensus         7 ~~tPS~~~gi~~~~E--~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~---------------------   63 (118)
                      +..|++..+.....+  ...|...++|+.+++..++++..|...|+.|+-||....++.                     
T Consensus        24 ~~~~~~~~~~~~~~~it~~~R~~lvdWm~~v~~~~~l~~etl~lAv~llDrfls~~~i~~~~lqL~a~tcL~IAsK~ee~  103 (141)
T d1f5qb1          24 REHDARMVGVNVDQHFTSQYRKVLTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAY  103 (141)
T ss_dssp             HHHHHHHSSSSHHHHHHCSHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHCS
T ss_pred             HHhcccccccccCccCCHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHhc
Confidence            344455455555555  567999999999999999999999999999999998876654                     


Q ss_pred             ------HHH------HHHHHHHHHHHHHHHHcCccee
Q 038406           64 ------VYY------KQKELILTAERLLPATIAFDFD   88 (118)
Q Consensus        64 ------~~~------~~~~~Il~~E~~iL~~L~Fdl~   88 (118)
                            .+-      --+++|..+|..||++|+++++
T Consensus       104 ~~~~~~~l~~~~~~~yt~~ei~~mE~~IL~~L~w~~~  140 (141)
T d1f5qb1         104 MPIKATQLAYLCGGATTADKLLTLEVKSLDTLSWVAD  140 (141)
T ss_dssp             SCCCHHHHHHHHCTTCCHHHHHHHHHHHHHHTTTCCC
T ss_pred             CcccHHHHHHHhcCCCCHHHHHHHHHHHHHHCCccCC
Confidence                  000      1268999999999999999864

>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=98.10  E-value=2.5e-06  Score=55.98  Aligned_cols=69  Identities=6%  Similarity=0.164  Sum_probs=58.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH---------------------------HHHH
Q 038406           15 GISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD---------------------------VYYK   67 (118)
Q Consensus        15 gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~---------------------------~~~~   67 (118)
                      ++|++    .|..-++|+.+++..++++..|...|+.++-||...+++.                           .+..
T Consensus        25 ~it~~----~R~~lidWl~~v~~~~~l~~eTl~lAv~llDryl~~~~i~~~~lqLi~~tcL~IAsK~ee~~~~~l~~l~~  100 (127)
T d1bu2a1          25 EVTVD----NRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTY  100 (127)
T ss_dssp             SSCHH----HHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSCCCTTTHHHHHHHHHHHHHHHSSSSCCCHHHHHH
T ss_pred             cCCHH----HHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            45554    7888999999999999999999999999999999877655                           1111


Q ss_pred             ------HHHHHHHHHHHHHHHcCcce
Q 038406           68 ------QKELILTAERLLPATIAFDF   87 (118)
Q Consensus        68 ------~~~~Il~~E~~iL~~L~Fdl   87 (118)
                            -+++++.+|..||++|+||+
T Consensus       101 ~~~~~~t~~ei~~mE~~IL~~L~~dl  126 (127)
T d1bu2a1         101 LSCDCFTNLELINQEKDILEALKWDT  126 (127)
T ss_dssp             TTTTSSCHHHHHHHHHHHHHHTTTCC
T ss_pred             HHcCCCCHHHHHHHHHHHHHHcCCCC
Confidence                  26899999999999999997

>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=94.42  E-value=0.061  Score=32.14  Aligned_cols=35  Identities=17%  Similarity=0.183  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcc
Q 038406           27 LYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQL   61 (118)
Q Consensus        27 ~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S   61 (118)
                      .+.+.|.++|..|++|..+.-+|..++++.+..+-
T Consensus         4 ~a~~~I~~~~~~L~L~~~i~~~A~~i~~~~~~~~~   38 (95)
T d1vola1           4 NAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKS   38 (95)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhh
Confidence            45678999999999999999999999999876543

>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=91.17  E-value=0.38  Score=28.51  Aligned_cols=34  Identities=24%  Similarity=0.222  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhc
Q 038406           27 LYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ   60 (118)
Q Consensus        27 ~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~   60 (118)
                      .+.+.|.++|..|++|..+.-+|..++.+....+
T Consensus         4 ~a~~~I~~~~~~L~L~~~i~~~A~~i~k~~~~~~   37 (98)
T d1aisb1           4 FALSELDRITAQLKLPRHVEEEAARLYREAVRKG   37 (98)
T ss_dssp             HHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhh
Confidence            4667899999999999999999999998876544