Psyllid ID: psy1168

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------23
Protein Sequence
MGLISTQGRFYPEWIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIAEVGTLGEVGESFP
Secondary Structure (PSIPRED)
cccccccccccccccccccccHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHccccccccHHHHHHHHHHHHHHccccHHHHHHcHHHHHHHHHHHHHHHHHccccEEEEccHHHHHHHHHHHcccHHHHHHHHHHHHHHcccccEEcccHHHHHHHHHHHHcccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccHHcccEEEcHHHHHcccccccccccHHHHHHHHHHHHHHHHHHccHccccHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHcccEEEEccccHHHHHHHHHHcccHHHHHHHHHHHHcccccEEEEEccHHHHHHHHHHHHHHHccccccccEEEEEcccc
Coil and Loop (DISEMBL)
mglistqgrfypEWIQQWVLDRQDLIRErkhdlsilsdEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYArnslkcidplllaptcvFLASKVEEFGVISSSRLLSTCQTVVKNKLNyayaqefpyrtnhiLECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDslrtdvcllyppyqiaigecsfsftphviaevgtlgevgesfp
Flexible Loop (DISEMBL)
mglistqgrfypewIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIAEVGtlgevgesfp
Low Complexity Region (SEG)
MGLISTQGRFYPEWIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIAEVGTLGEVGESFP
Disordered region (IsUnstruct)
******QGRFYPEWIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIAEVGTLG*******
Disordered Region (DISOPRED)
*********FYPEWIQQWVL*******************EYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIAEVGTLGEVGE***
Disordered Region (DISEMBL)
MGLISTQGRFYPEWIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIAEVGTLGEVGESFP
Disordered Region (DISPRO)
*G*****GRFYPEWIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIAEVGTLGEVGES**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGLISTQGRFYPEWIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIAEVGTLGEVGESFP
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	229	2.2.26 [Sep-21-2011]
Q16JA2	265	Cyclin-C OS=Aedes aegypti	N/A	N/A	0.825	0.713	0.867	7e-96
Q7QB13	266	Cyclin-C OS=Anopheles gam	yes	N/A	0.825	0.710	0.857	3e-95
Q29AI1	267	Cyclin-C OS=Drosophila ps	yes	N/A	0.825	0.707	0.830	9e-93
P25008	267	Cyclin-C OS=Drosophila me	yes	N/A	0.825	0.707	0.830	2e-92
P55168	283	Cyclin-C OS=Gallus gallus	yes	N/A	0.820	0.664	0.712	6e-79
Q4KLA0	283	Cyclin-C OS=Xenopus laevi	N/A	N/A	0.820	0.664	0.712	6e-79
Q28F72	283	Cyclin-C OS=Xenopus tropi	yes	N/A	0.820	0.664	0.712	6e-79
P24863	283	Cyclin-C OS=Homo sapiens	yes	N/A	0.820	0.664	0.707	1e-78
Q62447	283	Cyclin-C OS=Mus musculus	yes	N/A	0.820	0.664	0.707	3e-78
Q3ZCK5	283	Cyclin-C OS=Bos taurus GN	yes	N/A	0.820	0.664	0.696	4e-78

>sp|Q16JA2|CCNC_AEDAE Cyclin-C OS=Aedes aegypti GN=CycC PE=3 SV=1

 Score =  349 bits (896), Expect = 7e-96,   Method: Compositional matrix adjust.
 Identities = 164/189 (86%), Positives = 179/189 (94%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDLIRER+HDL  L++EEYQKIF+FFAN IQ+LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWILDKQDLIRERQHDLKNLTEEEYQKIFMFFANVIQVLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLKCIDPLLLAPTC+ LASKVEEFGVIS+SRL++TCQTV+KNK +YAY QEFPYR
Sbjct: 72  FYARNSLKCIDPLLLAPTCILLASKVEEFGVISNSRLITTCQTVIKNKFSYAYQQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
           TNHILECEFYLLENLDCCLIVYQPYRPLLQL+QDIG EDQLL L WR+INDSLRTDV LL
Sbjct: 132 TNHILECEFYLLENLDCCLIVYQPYRPLLQLIQDIGQEDQLLTLTWRLINDSLRTDVSLL 191

Query: 196 YPPYQIAIG 204
           YPPYQIAIG
Sbjct: 192 YPPYQIAIG 200

Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Binds to and activates cyclin-dependent kinase Cdk8 that phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex.
Aedes aegypti (taxid: 7159)

>sp|Q7QB13|CCNC_ANOGA Cyclin-C OS=Anopheles gambiae GN=CycC PE=3 SV=2

 Score =  347 bits (891), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 162/189 (85%), Positives = 179/189 (94%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDLIRER+HDL  LS+EEYQK+F+FFAN IQ+LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWILDKQDLIRERQHDLKTLSEEEYQKLFMFFANIIQVLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLKCIDPLLLAPTC+ L+SKVEEFGVIS+SRL++TCQTV+KNK +YAY QEFPYR
Sbjct: 72  FYARNSLKCIDPLLLAPTCILLSSKVEEFGVISNSRLITTCQTVIKNKFSYAYQQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
           TNHILECEFYLLENLDCCLIVYQPYRPLLQL+QDIG E+QLL L WR+INDSLRTDV LL
Sbjct: 132 TNHILECEFYLLENLDCCLIVYQPYRPLLQLMQDIGQEEQLLTLTWRLINDSLRTDVSLL 191

Query: 196 YPPYQIAIG 204
           YPPYQIAIG
Sbjct: 192 YPPYQIAIG 200

Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Binds to and activates cyclin-dependent kinase Cdk8 that phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex.

Anopheles gambiae (taxid: 7165)

>sp|Q29AI1|CCNC_DROPS Cyclin-C OS=Drosophila pseudoobscura pseudoobscura GN=CycC PE=3 SV=1

 Score =  339 bits (870), Expect = 9e-93,   Method: Compositional matrix adjust.
 Identities = 157/189 (83%), Positives = 176/189 (93%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDL+RER+HDL  L+++EYQK+FIFFAN IQ+LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWILDKQDLLRERQHDLLSLNEDEYQKVFIFFANVIQVLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLK IDPLLLAPTC+ LASKVEEFGVIS+SRL+S CQ+ +K K +YAY QEFPYR
Sbjct: 72  FYARNSLKNIDPLLLAPTCILLASKVEEFGVISNSRLISICQSAIKTKFSYAYTQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
           TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQD+G EDQLL L+WR++NDSLRTDVCLL
Sbjct: 132 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDMGQEDQLLTLSWRIVNDSLRTDVCLL 191

Query: 196 YPPYQIAIG 204
           YPPYQIAI 
Sbjct: 192 YPPYQIAIA 200

Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Binds to and activates cyclin-dependent kinase Cdk8 that phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex.

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

>sp|P25008|CCNC_DROME Cyclin-C OS=Drosophila melanogaster GN=CycC PE=1 SV=1

 Score =  338 bits (867), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 157/189 (83%), Positives = 176/189 (93%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+ DL+RER+HDL  L+++EYQK+FIFFAN IQ+LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWILDKPDLLRERQHDLLALNEDEYQKVFIFFANVIQVLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLK IDPLLLAPTC+ LASKVEEFGVIS+SRL+S CQ+ +K K +YAYAQEFPYR
Sbjct: 72  FYARNSLKNIDPLLLAPTCILLASKVEEFGVISNSRLISICQSAIKTKFSYAYAQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
           TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQD+G EDQLL L+WR++NDSLRTDVCLL
Sbjct: 132 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDMGQEDQLLTLSWRIVNDSLRTDVCLL 191

Query: 196 YPPYQIAIG 204
           YPPYQIAI 
Sbjct: 192 YPPYQIAIA 200

Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Binds to and activates cyclin-dependent kinase Cdk8 that phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex. Required for leg and eye development and macrochaete specification or differentiation.

Drosophila melanogaster (taxid: 7227)

>sp|P55168|CCNC_CHICK Cyclin-C OS=Gallus gallus GN=CCNC PE=2 SV=1

 Score =  293 bits (751), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 134/188 (71%), Positives = 161/188 (85%)

Query: 17  QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
           QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct: 13  QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 72

Query: 77  YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
           YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL+S   +V+K + +YA+ +EFPYR 
Sbjct: 73  YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLISAATSVLKTRFSYAFPKEFPYRM 132

Query: 137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
           NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct: 133 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 192

Query: 197 PPYQIAIG 204
           PP+ IA+ 
Sbjct: 193 PPFMIALA 200

Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Binds to and activates cyclin-dependent kinase CDK8 that phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex.

Gallus gallus (taxid: 9031)

>sp|Q4KLA0|CCNC_XENLA Cyclin-C OS=Xenopus laevis GN=ccnc PE=2 SV=1

 Score =  293 bits (751), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 134/188 (71%), Positives = 161/188 (85%)

Query: 17  QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
           QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct: 13  QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 72

Query: 77  YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
           YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL+S   +V+K + +YA+ +EFPYR 
Sbjct: 73  YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLISAATSVLKTRFSYAFPKEFPYRM 132

Query: 137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
           NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct: 133 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 192

Query: 197 PPYQIAIG 204
           PP+ IA+ 
Sbjct: 193 PPFMIALA 200

Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Binds to and activates cyclin-dependent kinase cdk8 that phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex.

Xenopus laevis (taxid: 8355)

>sp|Q28F72|CCNC_XENTR Cyclin-C OS=Xenopus tropicalis GN=ccnc PE=2 SV=1

 Score =  293 bits (750), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 134/188 (71%), Positives = 161/188 (85%)

Query: 17  QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
           QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct: 13  QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 72

Query: 77  YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
           YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL+S   +V+K + +YA+ +EFPYR 
Sbjct: 73  YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLISAATSVLKTRFSYAFPKEFPYRM 132

Query: 137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
           NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct: 133 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 192

Query: 197 PPYQIAIG 204
           PP+ IA+ 
Sbjct: 193 PPFMIALA 200

Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Binds to and activates cyclin-dependent kinase cdk8 that phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex.

Xenopus tropicalis (taxid: 8364)

>sp|P24863|CCNC_HUMAN Cyclin-C OS=Homo sapiens GN=CCNC PE=1 SV=2

 Score =  292 bits (748), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 133/188 (70%), Positives = 161/188 (85%)

Query: 17  QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
           QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct: 13  QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 72

Query: 77  YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
           YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL++   +V+K + +YA+ +EFPYR 
Sbjct: 73  YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRM 132

Query: 137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
           NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct: 133 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 192

Query: 197 PPYQIAIG 204
           PP+ IA+ 
Sbjct: 193 PPFMIALA 200

Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Binds to and activates cyclin-dependent kinase CDK8 that phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex.

Homo sapiens (taxid: 9606)

>sp|Q62447|CCNC_MOUSE Cyclin-C OS=Mus musculus GN=Ccnc PE=2 SV=4

 Score =  291 bits (745), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 133/188 (70%), Positives = 161/188 (85%)

Query: 17  QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
           QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct: 13  QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 72

Query: 77  YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
           YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL++   +V+K + +YA+ +EFPYR 
Sbjct: 73  YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAATTSVLKTRFSYAFPKEFPYRM 132

Query: 137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
           NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct: 133 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDVLLPLAWRIVNDTYRTDLCLLY 192

Query: 197 PPYQIAIG 204
           PP+ IA+ 
Sbjct: 193 PPFMIALA 200

Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Binds to and activates cyclin-dependent kinase CDK8 that phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex.

Mus musculus (taxid: 10090)

>sp|Q3ZCK5|CCNC_BOVIN Cyclin-C OS=Bos taurus GN=CCNC PE=2 SV=1

 Score =  290 bits (743), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 131/188 (69%), Positives = 161/188 (85%)

Query: 17  QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
           QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct: 13  QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 72

Query: 77  YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
           YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL++   +V+K + +YA+ +EFPY+ 
Sbjct: 73  YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYKM 132

Query: 137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
           NH+LECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct: 133 NHVLECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 192

Query: 197 PPYQIAIG 204
           PP+ IA+ 
Sbjct: 193 PPFMIALA 200

Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Binds to and activates cyclin-dependent kinase CDK8 that phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex.

Bos taurus (taxid: 9913)

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	229
332376318	266	unknown [Dendroctonus ponderosae]	0.825	0.710	0.878	9e-97
91093000	266	PREDICTED: similar to g1/s-specific cycl	0.825	0.710	0.873	2e-95
242019414	268	G1/S-specific cyclin-C, putative [Pedicu	0.825	0.705	0.863	1e-94
157135767	265	g1/s-specific cyclin c [Aedes aegypti] g	0.825	0.713	0.867	4e-94
170039649	265	G1/S-specific cyclin-C [Culex quinquefas	0.825	0.713	0.867	5e-94
242247391	267	cyclin C-like [Acyrthosiphon pisum] gi|2	0.825	0.707	0.884	8e-94
383852679	266	PREDICTED: cyclin-C-like [Megachile rotu	0.825	0.710	0.862	1e-93
312380568	266	hypothetical protein AND_07358 [Anophele	0.825	0.710	0.862	1e-93
58384260	266	AGAP004240-PA [Anopheles gambiae str. PE	0.825	0.710	0.857	2e-93
307177223	266	Cyclin-C [Camponotus floridanus]	0.825	0.710	0.862	2e-93

>gi|332376318|gb|AEE63299.1| unknown [Dendroctonus ponderosae]

 Score =  358 bits (919), Expect = 9e-97,   Method: Compositional matrix adjust.
 Identities = 166/189 (87%), Positives = 184/189 (97%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDL+RER+HDL+IL+DEEYQKIFIFF++ IQ LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWILDKQDLVRERQHDLAILTDEEYQKIFIFFSSVIQTLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLKCIDPLLLAPTC+FLASKVEEFGVIS++RL+STCQTV+KNK  YAY+QEFPYR
Sbjct: 72  FYARNSLKCIDPLLLAPTCIFLASKVEEFGVISNTRLISTCQTVIKNKFGYAYSQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
           TNHILECEFYLLE+LDCCLIVYQPYRPLLQLVQDIGHE+QLL LAWR++NDSLRTDVCLL
Sbjct: 132 TNHILECEFYLLESLDCCLIVYQPYRPLLQLVQDIGHEEQLLTLAWRIVNDSLRTDVCLL 191

Query: 196 YPPYQIAIG 204
           YPPYQIAIG
Sbjct: 192 YPPYQIAIG 200

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91093000|ref|XP_968481.1| PREDICTED: similar to g1/s-specific cyclin c [Tribolium castaneum] gi|270003157|gb|EEZ99604.1| hypothetical protein TcasGA2_TC002120 [Tribolium castaneum]

 Score =  353 bits (907), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 165/189 (87%), Positives = 183/189 (96%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDLIRER+HDL +L++EEYQKIFIFFA+ IQ LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWLLDKQDLIRERQHDLQLLTEEEYQKIFIFFASVIQTLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYA+NSLKCIDPLLLAPTC+FLASKVEEFGVIS+SRL++TCQTV+KNK +YAY+QEFPYR
Sbjct: 72  FYAKNSLKCIDPLLLAPTCIFLASKVEEFGVISNSRLITTCQTVIKNKFSYAYSQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
           TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQD+G EDQLL LAWR++NDSLRTDVCLL
Sbjct: 132 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDMGQEDQLLTLAWRIVNDSLRTDVCLL 191

Query: 196 YPPYQIAIG 204
           YPPYQIAIG
Sbjct: 192 YPPYQIAIG 200

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242019414|ref|XP_002430156.1| G1/S-specific cyclin-C, putative [Pediculus humanus corporis] gi|212515247|gb|EEB17418.1| G1/S-specific cyclin-C, putative [Pediculus humanus corporis]

 Score =  351 bits (900), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 165/191 (86%), Positives = 182/191 (95%), Gaps = 2/191 (1%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDLIRER HDL IL++EEYQKIFIFF+NFIQ+LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWILDKQDLIRERHHDLQILTEEEYQKIFIFFSNFIQVLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLKCIDPLLLAPTCVFLASKVEEFGVIS++RL++ CQ VVKNK +YAYAQEFPYR
Sbjct: 72  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISNTRLITICQNVVKNKFSYAYAQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDI--GHEDQLLALAWRVINDSLRTDVC 193
           TNHILECEFYLLENLDCCLI+YQPYRPLL L+ DI  GHEDQ++ALAWRV+NDSLRTDVC
Sbjct: 132 TNHILECEFYLLENLDCCLILYQPYRPLLSLIADIGNGHEDQMMALAWRVVNDSLRTDVC 191

Query: 194 LLYPPYQIAIG 204
           LLYPPYQIA+G
Sbjct: 192 LLYPPYQIALG 202

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157135767|ref|XP_001663584.1| g1/s-specific cyclin c [Aedes aegypti] gi|122104845|sp|Q16JA2.1|CCNC_AEDAE RecName: Full=Cyclin-C gi|108870132|gb|EAT34357.1| AAEL013397-PA [Aedes aegypti]

 Score =  349 bits (896), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 164/189 (86%), Positives = 179/189 (94%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDLIRER+HDL  L++EEYQKIF+FFAN IQ+LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWILDKQDLIRERQHDLKNLTEEEYQKIFMFFANVIQVLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLKCIDPLLLAPTC+ LASKVEEFGVIS+SRL++TCQTV+KNK +YAY QEFPYR
Sbjct: 72  FYARNSLKCIDPLLLAPTCILLASKVEEFGVISNSRLITTCQTVIKNKFSYAYQQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
           TNHILECEFYLLENLDCCLIVYQPYRPLLQL+QDIG EDQLL L WR+INDSLRTDV LL
Sbjct: 132 TNHILECEFYLLENLDCCLIVYQPYRPLLQLIQDIGQEDQLLTLTWRLINDSLRTDVSLL 191

Query: 196 YPPYQIAIG 204
           YPPYQIAIG
Sbjct: 192 YPPYQIAIG 200

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170039649|ref|XP_001847640.1| G1/S-specific cyclin-C [Culex quinquefasciatus] gi|167863264|gb|EDS26647.1| G1/S-specific cyclin-C [Culex quinquefasciatus]

 Score =  349 bits (895), Expect = 5e-94,   Method: Compositional matrix adjust.
 Identities = 164/189 (86%), Positives = 178/189 (94%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDLIRER+ DL  L+DEEYQKIF+FFAN IQ+LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWILDKQDLIRERQDDLKTLTDEEYQKIFMFFANVIQVLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLKCIDPLLLAPTC+ LASKVEEFGVIS+SRL++TCQTV+KNK NYAY QEFPYR
Sbjct: 72  FYARNSLKCIDPLLLAPTCILLASKVEEFGVISNSRLITTCQTVIKNKFNYAYQQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
           TNHILECEFYLLENLDCCLIVYQPYRPLLQL+QDIG E+QLL L WR+INDSLRTDV LL
Sbjct: 132 TNHILECEFYLLENLDCCLIVYQPYRPLLQLIQDIGQEEQLLTLTWRLINDSLRTDVSLL 191

Query: 196 YPPYQIAIG 204
           YPPYQIAIG
Sbjct: 192 YPPYQIAIG 200

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242247391|ref|NP_001156079.1| cyclin C-like [Acyrthosiphon pisum] gi|239790160|dbj|BAH71657.1| ACYPI001314 [Acyrthosiphon pisum]

 Score =  348 bits (894), Expect = 8e-94,   Method: Compositional matrix adjust.
 Identities = 168/190 (88%), Positives = 183/190 (96%), Gaps = 1/190 (0%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDL+RER+ DL ILS+EEYQKI IFF+NFIQILGEQLKL+QQVIATATVYFKR
Sbjct: 12  QQWILDKQDLVRERQLDLQILSEEEYQKIGIFFSNFIQILGEQLKLKQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLK IDPLLL+PTCVFLASKVEEFGVIS+SRL++TCQTV+KNKLNYAY QEFPYR
Sbjct: 72  FYARNSLKSIDPLLLSPTCVFLASKVEEFGVISNSRLITTCQTVLKNKLNYAYTQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIG-HEDQLLALAWRVINDSLRTDVCL 194
           TNHILECEFYLLENLDCCLIV+QPYRPLLQLVQDIG HEDQLLALAWRV+NDSLRTD+ L
Sbjct: 132 TNHILECEFYLLENLDCCLIVFQPYRPLLQLVQDIGQHEDQLLALAWRVVNDSLRTDLSL 191

Query: 195 LYPPYQIAIG 204
           LYPPYQIAIG
Sbjct: 192 LYPPYQIAIG 201

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383852679|ref|XP_003701853.1| PREDICTED: cyclin-C-like [Megachile rotundata]

 Score =  348 bits (893), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 163/189 (86%), Positives = 181/189 (95%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDL+RER+HDLSIL++EEYQK+FIFF+N IQ+LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWLLDKQDLVRERQHDLSILTEEEYQKLFIFFSNLIQVLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLKCIDPLLLAPT VFLASKVEEFGVISS RL++TCQTVVK K NYAY+QEFPYR
Sbjct: 72  FYARNSLKCIDPLLLAPTSVFLASKVEEFGVISSHRLVTTCQTVVKTKFNYAYSQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
           TNHILECEFYLLE+LDCCLIVYQPYRPLL L+QD+G ++QLL LAWR+INDSLRTDVCLL
Sbjct: 132 TNHILECEFYLLEHLDCCLIVYQPYRPLLTLIQDVGPDEQLLTLAWRIINDSLRTDVCLL 191

Query: 196 YPPYQIAIG 204
           YPPYQIAIG
Sbjct: 192 YPPYQIAIG 200

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312380568|gb|EFR26526.1| hypothetical protein AND_07358 [Anopheles darlingi]

 Score =  348 bits (893), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 163/189 (86%), Positives = 178/189 (94%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDLIRER+HDL  L++EEYQKIF+FFAN IQ+LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWILDKQDLIRERQHDLKSLTEEEYQKIFMFFANIIQVLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLKCIDPLLLAPTC+ LASKVEEFGVIS+SRL++TCQTV+KNK  YAY QEFPYR
Sbjct: 72  FYARNSLKCIDPLLLAPTCILLASKVEEFGVISNSRLITTCQTVIKNKFGYAYQQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
           TNHILECEFYLLENLDCCLIVYQPYRPLLQL+QDIG E+QLL L WR+INDSLRTDV LL
Sbjct: 132 TNHILECEFYLLENLDCCLIVYQPYRPLLQLMQDIGQEEQLLTLTWRLINDSLRTDVSLL 191

Query: 196 YPPYQIAIG 204
           YPPYQIAIG
Sbjct: 192 YPPYQIAIG 200

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|58384260|ref|XP_313156.2| AGAP004240-PA [Anopheles gambiae str. PEST] gi|74921277|sp|Q7QB13.2|CCNC_ANOGA RecName: Full=Cyclin-C gi|55241371|gb|EAA08619.2| AGAP004240-PA [Anopheles gambiae str. PEST]

 Score =  347 bits (891), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 162/189 (85%), Positives = 179/189 (94%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDLIRER+HDL  LS+EEYQK+F+FFAN IQ+LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWILDKQDLIRERQHDLKTLSEEEYQKLFMFFANIIQVLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLKCIDPLLLAPTC+ L+SKVEEFGVIS+SRL++TCQTV+KNK +YAY QEFPYR
Sbjct: 72  FYARNSLKCIDPLLLAPTCILLSSKVEEFGVISNSRLITTCQTVIKNKFSYAYQQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
           TNHILECEFYLLENLDCCLIVYQPYRPLLQL+QDIG E+QLL L WR+INDSLRTDV LL
Sbjct: 132 TNHILECEFYLLENLDCCLIVYQPYRPLLQLMQDIGQEEQLLTLTWRLINDSLRTDVSLL 191

Query: 196 YPPYQIAIG 204
           YPPYQIAIG
Sbjct: 192 YPPYQIAIG 200

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307177223|gb|EFN66421.1| Cyclin-C [Camponotus floridanus]

 Score =  347 bits (890), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 163/189 (86%), Positives = 180/189 (95%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           QQW+LD+QDL+RER+HDLSIL++EEYQKIFIFF+N IQ+LGEQLKLRQQVIATATVYFKR
Sbjct: 12  QQWLLDKQDLVRERQHDLSILTEEEYQKIFIFFSNMIQMLGEQLKLRQQVIATATVYFKR 71

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYARNSLKCIDPLLLAPT VFLASKVEEFGVIS++RL++T  TVVKNK NYAY QEFPYR
Sbjct: 72  FYARNSLKCIDPLLLAPTAVFLASKVEEFGVISNTRLITTMGTVVKNKFNYAYTQEFPYR 131

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
           TNHILECEFYLLE+LDCCLIVYQPYRPLL L+QD+G +DQLL LAWR+INDSLRTDVCLL
Sbjct: 132 TNHILECEFYLLEHLDCCLIVYQPYRPLLTLIQDVGPDDQLLTLAWRIINDSLRTDVCLL 191

Query: 196 YPPYQIAIG 204
           YPPYQIAIG
Sbjct: 192 YPPYQIAIG 200

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

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	229
UNIPROTKB|Q29AI1	267	CycC "Cyclin-C" [Drosophila ps	0.820	0.704	0.835	5.4e-86
FB|FBgn0004597	267	CycC "Cyclin C" [Drosophila me	0.820	0.704	0.835	6.9e-86
UNIPROTKB|P55168	283	CCNC "Cyclin-C" [Gallus gallus	0.816	0.660	0.716	3.6e-73
UNIPROTKB|Q91031	272	CCNC "Cyclin C" [Gallus gallus	0.816	0.687	0.716	3.6e-73
UNIPROTKB|F1PGM0	284	CCNC "Uncharacterized protein"	0.816	0.658	0.716	3.6e-73
UNIPROTKB|E5RFK5	282	CCNC "Cyclin-C" [Homo sapiens	0.816	0.663	0.711	7.5e-73
UNIPROTKB|G5E954	202	CCNC "Cyclin-C" [Homo sapiens	0.816	0.925	0.711	7.5e-73
UNIPROTKB|P24863	283	CCNC "Cyclin-C" [Homo sapiens	0.816	0.660	0.711	7.5e-73
ZFIN|ZDB-GENE-030131-7369	283	ccnc "cyclin C" [Danio rerio (	0.816	0.660	0.716	7.5e-73
UNIPROTKB|F1LNZ0	333	Ccnc "Cyclin-C" [Rattus norveg	0.868	0.597	0.68	1.2e-72

UNIPROTKB|Q29AI1 CycC "Cyclin-C" [Drosophila pseudoobscura pseudoobscura (taxid:46245)]

 Score = 860 (307.8 bits), Expect = 5.4e-86, P = 5.4e-86
 Identities = 157/188 (83%), Positives = 176/188 (93%)

Query:    16 QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
             QQW+LD+QDL+RER+HDL  L+++EYQK+FIFFAN IQ+LGEQLKLRQQVIATATVYFKR
Sbjct:    12 QQWILDKQDLLRERQHDLLSLNEDEYQKVFIFFANVIQVLGEQLKLRQQVIATATVYFKR 71

Query:    76 FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
             FYARNSLK IDPLLLAPTC+ LASKVEEFGVIS+SRL+S CQ+ +K K +YAY QEFPYR
Sbjct:    72 FYARNSLKNIDPLLLAPTCILLASKVEEFGVISNSRLISICQSAIKTKFSYAYTQEFPYR 131

Query:   136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
             TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQD+G EDQLL L+WR++NDSLRTDVCLL
Sbjct:   132 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDMGQEDQLLTLSWRIVNDSLRTDVCLL 191

Query:   196 YPPYQIAI 203
             YPPYQIAI
Sbjct:   192 YPPYQIAI 199

GO:0001104 "RNA polymerase II transcription cofactor activity" evidence=ISS

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0016592 "mediator complex" evidence=ISS

FB|FBgn0004597 CycC "Cyclin C" [Drosophila melanogaster (taxid:7227)]

 Score = 859 (307.4 bits), Expect = 6.9e-86, P = 6.9e-86
 Identities = 157/188 (83%), Positives = 176/188 (93%)

Query:    16 QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
             QQW+LD+ DL+RER+HDL  L+++EYQK+FIFFAN IQ+LGEQLKLRQQVIATATVYFKR
Sbjct:    12 QQWILDKPDLLRERQHDLLALNEDEYQKVFIFFANVIQVLGEQLKLRQQVIATATVYFKR 71

Query:    76 FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
             FYARNSLK IDPLLLAPTC+ LASKVEEFGVIS+SRL+S CQ+ +K K +YAYAQEFPYR
Sbjct:    72 FYARNSLKNIDPLLLAPTCILLASKVEEFGVISNSRLISICQSAIKTKFSYAYAQEFPYR 131

Query:   136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
             TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQD+G EDQLL L+WR++NDSLRTDVCLL
Sbjct:   132 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDMGQEDQLLTLSWRIVNDSLRTDVCLL 191

Query:   196 YPPYQIAI 203
             YPPYQIAI
Sbjct:   192 YPPYQIAI 199

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

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=NAS

GO:0019908 "nuclear cyclin-dependent protein kinase holoenzyme complex" evidence=NAS

GO:0016592 "mediator complex" evidence=ISS;IPI

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISS

GO:0001104 "RNA polymerase II transcription cofactor activity" evidence=ISS;IMP

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

GO:0019901 "protein kinase binding" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0036011 "imaginal disc-derived leg segmentation" evidence=IMP

GO:0022416 "chaeta development" evidence=IMP

GO:0045498 "sex comb development" evidence=IMP

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IGI

UNIPROTKB|P55168 CCNC "Cyclin-C" [Gallus gallus (taxid:9031)]

 Score = 739 (265.2 bits), Expect = 3.6e-73, P = 3.6e-73
 Identities = 134/187 (71%), Positives = 161/187 (86%)

Query:    17 QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
             QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct:    13 QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 72

Query:    77 YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
             YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL+S   +V+K + +YA+ +EFPYR 
Sbjct:    73 YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLISAATSVLKTRFSYAFPKEFPYRM 132

Query:   137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
             NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct:   133 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 192

Query:   197 PPYQIAI 203
             PP+ IA+
Sbjct:   193 PPFMIAL 199

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

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0016592 "mediator complex" evidence=IEA

UNIPROTKB|Q91031 CCNC "Cyclin C" [Gallus gallus (taxid:9031)]

 Score = 739 (265.2 bits), Expect = 3.6e-73, P = 3.6e-73
 Identities = 134/187 (71%), Positives = 161/187 (86%)

Query:    17 QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
             QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct:     2 QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 61

Query:    77 YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
             YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL+S   +V+K + +YA+ +EFPYR 
Sbjct:    62 YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLISAATSVLKTRFSYAFPKEFPYRM 121

Query:   137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
             NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct:   122 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 181

Query:   197 PPYQIAI 203
             PP+ IA+
Sbjct:   182 PPFMIAL 188

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

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

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0016592 "mediator complex" evidence=IEA

UNIPROTKB|F1PGM0 CCNC "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 739 (265.2 bits), Expect = 3.6e-73, P = 3.6e-73
 Identities = 134/187 (71%), Positives = 161/187 (86%)

Query:    17 QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
             QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct:    14 QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 73

Query:    77 YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
             YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL+S   +V+K + +YA+ +EFPYR 
Sbjct:    74 YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLISAATSVLKTRFSYAFPKEFPYRM 133

Query:   137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
             NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct:   134 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 193

Query:   197 PPYQIAI 203
             PP+ IA+
Sbjct:   194 PPFMIAL 200

GO:0019901 "protein kinase binding" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" 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|E5RFK5 CCNC "Cyclin-C" [Homo sapiens (taxid:9606)]

 Score = 736 (264.1 bits), Expect = 7.5e-73, P = 7.5e-73
 Identities = 133/187 (71%), Positives = 161/187 (86%)

Query:    17 QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
             QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct:    13 QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 72

Query:    77 YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
             YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL++   +V+K + +YA+ +EFPYR 
Sbjct:    73 YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRM 132

Query:   137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
             NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct:   133 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 192

Query:   197 PPYQIAI 203
             PP+ IA+
Sbjct:   193 PPFMIAL 199

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

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

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

UNIPROTKB|G5E954 CCNC "Cyclin-C" [Homo sapiens (taxid:9606)]

 Score = 736 (264.1 bits), Expect = 7.5e-73, P = 7.5e-73
 Identities = 133/187 (71%), Positives = 161/187 (86%)

Query:    17 QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
             QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct:    13 QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 72

Query:    77 YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
             YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL++   +V+K + +YA+ +EFPYR 
Sbjct:    73 YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRM 132

Query:   137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
             NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct:   133 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 192

Query:   197 PPYQIAI 203
             PP+ IA+
Sbjct:   193 PPFMIAL 199

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

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

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

UNIPROTKB|P24863 CCNC "Cyclin-C" [Homo sapiens (taxid:9606)]

 Score = 736 (264.1 bits), Expect = 7.5e-73, P = 7.5e-73
 Identities = 133/187 (71%), Positives = 161/187 (86%)

Query:    17 QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
             QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct:    13 QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 72

Query:    77 YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
             YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL++   +V+K + +YA+ +EFPYR 
Sbjct:    73 YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRM 132

Query:   137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
             NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct:   133 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 192

Query:   197 PPYQIAI 203
             PP+ IA+
Sbjct:   193 PPFMIAL 199

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

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0016592 "mediator complex" evidence=IEA

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006351 "transcription, DNA-dependent" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0007179 "transforming growth factor beta receptor signaling pathway" evidence=TAS

GO:0007219 "Notch signaling pathway" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

ZFIN|ZDB-GENE-030131-7369 ccnc "cyclin C" [Danio rerio (taxid:7955)]

 Score = 736 (264.1 bits), Expect = 7.5e-73, P = 7.5e-73
 Identities = 134/187 (71%), Positives = 162/187 (86%)

Query:    17 QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
             QWVLD+QDL++ER+ DL  L++EEY K+ IFFAN IQ LGE LKLRQQVIATATVYFKRF
Sbjct:    13 QWVLDKQDLMKERQKDLKFLTEEEYWKLQIFFANVIQALGEHLKLRQQVIATATVYFKRF 72

Query:    77 YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
             YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL+S   +V+K + +YA+ +EFP+R 
Sbjct:    73 YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLISAATSVLKTRFSYAFPKEFPFRM 132

Query:   137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
             NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct:   133 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 192

Query:   197 PPYQIAI 203
             PP+ IA+
Sbjct:   193 PPFMIAL 199

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

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

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

UNIPROTKB|F1LNZ0 Ccnc "Cyclin-C" [Rattus norvegicus (taxid:10116)]

 Score = 734 (263.4 bits), Expect = 1.2e-72, P = 1.2e-72
 Identities = 136/200 (68%), Positives = 165/200 (82%)

Query:     5 STQGRFYPE-WIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQ 63
             S  G F+      QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQ
Sbjct:    50 SMAGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQ 109

Query:    64 QVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNK 123
             QVIATATVYFKRFYAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL++   +V+K +
Sbjct:   110 QVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAATTSVLKTR 169

Query:   124 LNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRV 183
              +YA+ +EFPYR NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR+
Sbjct:   170 FSYAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDVLLPLAWRI 229

Query:   184 INDSLRTDVCLLYPPYQIAI 203
             +ND+ RTD+CLLYPP+ IA+
Sbjct:   230 VNDTYRTDLCLLYPPFMIAL 249

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

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

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0016592 "mediator complex" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q28F72	CCNC_XENTR	No assigned EC number	0.7127	0.8209	0.6643	yes	N/A
Q62447	CCNC_MOUSE	No assigned EC number	0.7074	0.8209	0.6643	yes	N/A
P93411	CCC11_ORYSJ	No assigned EC number	0.4638	0.6899	0.6147	yes	N/A
Q16JA2	CCNC_AEDAE	No assigned EC number	0.8677	0.8253	0.7132	N/A	N/A
Q4KLA0	CCNC_XENLA	No assigned EC number	0.7127	0.8209	0.6643	N/A	N/A
P25008	CCNC_DROME	No assigned EC number	0.8306	0.8253	0.7078	yes	N/A
Q86KE7	CCNC_DICDI	No assigned EC number	0.4255	0.7772	0.6980	yes	N/A
P24863	CCNC_HUMAN	No assigned EC number	0.7074	0.8209	0.6643	yes	N/A
Q2UDB2	SSN8_ASPOR	No assigned EC number	0.3415	0.8165	0.6212	yes	N/A
Q9FJK7	CCC12_ARATH	No assigned EC number	0.3578	0.7772	0.7035	yes	N/A
P39947	CCNC_RAT	No assigned EC number	0.6861	0.7991	0.6582	yes	N/A
Q7QB13	CCNC_ANOGA	No assigned EC number	0.8571	0.8253	0.7105	yes	N/A
Q29AI1	CCNC_DROPS	No assigned EC number	0.8306	0.8253	0.7078	yes	N/A
Q3ZCK5	CCNC_BOVIN	No assigned EC number	0.6968	0.8209	0.6643	yes	N/A
Q9TYP2	CCNC_CAEEL	No assigned EC number	0.3632	0.8209	0.6225	yes	N/A
P55168	CCNC_CHICK	No assigned EC number	0.7127	0.8209	0.6643	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	229
COG5333	297	COG5333, CCL1, Cdk activating kinase (CAK)/RNA pol	6e-33
TIGR00569	305	TIGR00569, ccl1, cyclin ccl1	2e-21
cd00043	88	cd00043, CYCLIN, Cyclin box fold	5e-11
pfam00134	127	pfam00134, Cyclin_N, Cyclin, N-terminal domain	1e-10
smart00385	83	smart00385, CYCLIN, domain present in cyclins, TFI	3e-09

>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 =  120 bits (302), Expect = 6e-33
 Identities = 67/173 (38%), Positives = 101/173 (58%), Gaps = 13/173 (7%)

Query: 35  ILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTC 94
            L+ E+   + I++   I  L  +L L Q V+ATA ++F RFY +NS++ I    +  TC
Sbjct: 35  ELTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTC 94

Query: 95  VFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT-NHILECEFYLLENLDCC 153
           V+LA KVE+     + R +S      ++        E P  +   ILE EF LLE LD  
Sbjct: 95  VYLACKVED-----TPRDISIESFEARDL-----WSEEPKSSRERILEYEFELLEALDFD 144

Query: 154 LIVYQPYRPLLQLVQDIGHED--QLLALAWRVINDSLRTDVCLLYPPYQIAIG 204
           L V+ PY+ L   ++D+  +D  +LL +AW++IND+LRTD+CLLYPP+ IA+ 
Sbjct: 145 LHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALA 197

Length = 297

>gnl|CDD|129660 TIGR00569, ccl1, cyclin ccl1

 Score = 89.9 bits (223), Expect = 2e-21
 Identities = 57/178 (32%), Positives = 82/178 (46%), Gaps = 22/178 (12%)

Query: 36  LSDEEYQKIFIFFANFIQILGEQLK--LRQQVIATATVYFKRFYARNSLKCIDPLLLAPT 93
           L+ EE   +  ++   +       K  +   V+ TA +YFKRFY  NS+    P ++  T
Sbjct: 47  LTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLT 106

Query: 94  CVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCC 153
           CVFLA KVEEF V            + +  L              +LE E  L++ L+  
Sbjct: 107 CVFLACKVEEFNVSID----QFVGNLKETPLK---------ALEQVLEYELLLIQQLNFH 153

Query: 154 LIVYQPYRPLLQLVQDI-------GHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIG 204
           LIV+ PYRPL   + DI        + + L   A + +N +L TD  LLY P QIA+ 
Sbjct: 154 LIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALA 211

All proteins in this family for which functions are known are cyclins that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, StanfordUniversity) [DNA metabolism, DNA replication, recombination, and repair]. Length = 305

>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold

 Score = 56.9 bits (138), Expect = 5e-11
 Identities = 23/98 (23%), Positives = 35/98 (35%), Gaps = 16/98 (16%)

Query: 50  NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISS 109
           +F++ + + L L  + +  A     RF    S+    P L+A   ++LA+KVEE      
Sbjct: 7   DFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI----- 61

Query: 110 SRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLL 147
              L     V                   IL  E  LL
Sbjct: 62  PPWLKDLVHVTGY-----------ATEEEILRMEKLLL 88

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. Length = 88

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

 Score = 56.8 bits (138), Expect = 1e-10
 Identities = 23/105 (21%), Positives = 43/105 (40%), Gaps = 14/105 (13%)

Query: 50  NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISS 109
           +++  + E+ KL  + +  A  Y  RF ++  +      L+  TC+ +A+K EE      
Sbjct: 36  DWLVEVHEEFKLLPETLYLAVNYLDRFLSKQPVPRTKLQLVGVTCLLIAAKYEEI----- 90

Query: 110 SRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCL 154
                   +V     ++ Y  +  Y    IL  E  +L  L+  L
Sbjct: 91  -----YPPSV----EDFVYITDNAYTKEEILRMELLILSTLNWDL 126

Cyclins regulate cyclin dependent kinases (CDKs). Human cyclin-O is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain. Length = 127

>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and Retinoblastoma

 Score = 52.2 bits (126), Expect = 3e-09
 Identities = 24/99 (24%), Positives = 35/99 (35%), Gaps = 16/99 (16%)

Query: 50  NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISS 109
           +F++ + + L L  + +  A     RF +        P L+A   ++LASK EE      
Sbjct: 1   DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETP---- 56

Query: 110 SRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLE 148
                        K    Y   F      IL  E  LLE
Sbjct: 57  ----------PWTKELVHYTGYFTE--EEILRMERLLLE 83

A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control. Length = 83

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	229
KOG0794|consensus	264		100.0
TIGR00569	305	ccl1 cyclin ccl1. University).	100.0
KOG0834|consensus	323		100.0
KOG0835|consensus	367		100.0
COG5333	297	CCL1 Cdk activating kinase (CAK)/RNA polymerase II	100.0
KOG2496|consensus	325		99.96
KOG0656|consensus	335		99.92
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	99.91
KOG0653|consensus	391		99.83
KOG0655|consensus	408		99.81
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	99.79
KOG1597|consensus	308		99.78
COG5024	440	Cyclin [Cell division and chromosome partitioning]	99.76
PF00134	127	Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR	99.74
cd00043	88	CYCLIN Cyclin box fold. Protein binding domain fun	99.47
KOG0654|consensus	359		99.42
smart00385	83	CYCLIN domain present in cyclins, TFIIB and Retino	99.34
KOG1598|consensus	521		99.12
PF00382	71	TFIIB: Transcription factor TFIIB repeat; InterPro	98.96
KOG4164|consensus	497		98.55
PF02984	118	Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR	98.48
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	98.24
cd00043	88	CYCLIN Cyclin box fold. Protein binding domain fun	98.18
smart00385	83	CYCLIN domain present in cyclins, TFIIB and Retino	98.15
PF00382	71	TFIIB: Transcription factor TFIIB repeat; InterPro	98.15
PF08613	149	Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu	98.07
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	97.19
KOG1597|consensus	308		96.94
PF01857	135	RB_B: Retinoblastoma-associated protein B domain;	96.09
TIGR00569	305	ccl1 cyclin ccl1. University).	93.3
PF02984	118	Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR	93.21
PF00134	127	Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR	92.4
KOG0835|consensus	367		91.1
KOG1674|consensus	218		88.82
KOG0834|consensus	323		84.38
KOG1598|consensus	521		84.23

>KOG0794|consensus

Probab=100.00  E-value=3.5e-45  Score=286.26  Aligned_cols=209  Identities=54%  Similarity=0.903  Sum_probs=194.6

Q ss_pred             ccccchh-hhccCCcccHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhcccccc
Q psy1168           6 TQGRFYP-EWIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKC   84 (229)
Q Consensus         6 ~~~~~~~-~~~~~w~f~~~~l~~~~~~~~~~~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~   84 (229)
                      |+||||+ +|..+|+|+++++...++.+..+++.+++.+++.+..+.|..+|+++++.+.|++||++||+|||.++|+++
T Consensus         1 MA~NFW~SSh~~qwl~dk~el~k~r~~D~r~l~~d~~~~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~   80 (264)
T KOG0794|consen    1 MAGNFWTSSHYQQWLLDKTELLKERQLDLRGLSEDEYSKLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKE   80 (264)
T ss_pred             CCcchhhhhhhhhHhcCHHHHhhhccchhhcccHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            8999999 999999999999999998888899999999999999999999999999999999999999999999999999


Q ss_pred             CCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHH
Q psy1168          85 IDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLL  164 (229)
Q Consensus        85 ~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~  164 (229)
                      +++.+++.||+|||||+||+| +...+++..+..+++++++ ..++.+....++|..+|+.+|+.|++-|-+.|||+.+.
T Consensus        81 ~~p~lla~TClyLAcKvEE~~-i~~~r~l~~~a~~L~~~f~-~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~  158 (264)
T KOG0794|consen   81 IEPRLLAPTCLYLACKVEECP-IVHIRLLVNEAKVLKTRFS-YWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLL  158 (264)
T ss_pred             cCHHHHHHHHHHHHhhhhhcc-hHHHHHHHHHHHHHhhhcc-cchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHH
Confidence            999999999999999999998 3667777777778887776 44566677789999999999999999999999999999


Q ss_pred             HHHHHhCc-cHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         165 QLVQDIGH-EDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       165 ~~~~~l~~-~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      .++++.|. +....+.+|.++||++++++|+.|+|..||.||+++|+..++-+
T Consensus       159 q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~  211 (264)
T KOG0794|consen  159 QFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKD  211 (264)
T ss_pred             HHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCC
Confidence            99999998 56799999999999999999999999999999999999987644

>TIGR00569 ccl1 cyclin ccl1

Probab=100.00  E-value=3.5e-43  Score=295.17  Aligned_cols=202  Identities=31%  Similarity=0.472  Sum_probs=177.6

Q ss_pred             chh-hhccCCccc-HHHHHHhhh------------------cCCCCCCHHHHHHHHHHHHHHHHHHHHhcC--CCHHHHH
Q psy1168          10 FYP-EWIQQWVLD-RQDLIRERK------------------HDLSILSDEEYQKIFIFFANFIQILGEQLK--LRQQVIA   67 (229)
Q Consensus        10 ~~~-~~~~~w~f~-~~~l~~~~~------------------~~~~~~s~~~e~~~r~~~~~~I~~~~~~l~--l~~~~~~   67 (229)
                      ||. ||.+.|.|| ++||...|.                  ....++++++|..+|.+++.+|.++|.+|+  ||+.|++
T Consensus         1 y~~StQ~r~W~F~~~~~L~~~R~~~N~~~~~~~~~~~~~~~~~~~~Lt~eeE~~l~~~y~~~i~~~~~~lkp~Lpq~via   80 (305)
T TIGR00569         1 YRNSSQKRHWTFTSEEQLQEKRADANAKFREAHEEEEKVLEAKPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVG   80 (305)
T ss_pred             CCCCcccccCcCCCHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHH
Confidence            677 999999999 999998764                  124589999999999999999999999999  9999999


Q ss_pred             HHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhcccccccchhhHHHHHHHHHHHH
Q psy1168          68 TATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLL  147 (229)
Q Consensus        68 ~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL  147 (229)
                      ||++||||||.++|+..+++++|++||+|||||+||.++ ++++++....            +....++++|+.+|..||
T Consensus        81 TAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~-si~~fv~~~~------------~~~~~~~~~Il~~E~~lL  147 (305)
T TIGR00569        81 TAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNV-SIDQFVGNLK------------ETPLKALEQVLEYELLLI  147 (305)
T ss_pred             HHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCc-CHHHHHhhcc------------CCchhhHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999996 8888876321            122245799999999999


Q ss_pred             HHcCcceeecCChHHHHHHHHHhC-------ccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccccCCc
Q psy1168         148 ENLDCCLIVYQPYRPLLQLVQDIG-------HEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIAEVGT  220 (229)
Q Consensus       148 ~~L~fdl~~~~P~~~l~~~~~~l~-------~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~~~~~  220 (229)
                      ++|+|||.++|||+++..|+.+++       ..+.+.+.||.++||++.|+.|+.|+|++||+|||++|+..+++.-.+.
T Consensus       148 ~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~~~~~~~l~~~  227 (305)
T TIGR00569       148 QQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMESY  227 (305)
T ss_pred             HHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHHHHHhCCCCccc
Confidence            999999999999999999997654       2356889999999999999999999999999999999999988764444


Q ss_pred             cccc
Q psy1168         221 LGEV  224 (229)
Q Consensus       221 ~~ev  224 (229)
                      .+|+
T Consensus       228 ~~e~  231 (305)
T TIGR00569       228 LTEQ  231 (305)
T ss_pred             chhh
Confidence            4443

University).

>KOG0834|consensus

Probab=100.00  E-value=3.8e-44  Score=300.48  Aligned_cols=209  Identities=30%  Similarity=0.431  Sum_probs=188.7

Q ss_pred             hhccCCcccHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHH
Q psy1168          13 EWIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAP   92 (229)
Q Consensus        13 ~~~~~w~f~~~~l~~~~~~~~~~~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~   92 (229)
                      ..-+.|+|+++|+++..+...+|++.++|.+.|..++.||.++|.+|++|+.+++||++||||||+.+++++++++.+|+
T Consensus         7 ~~~~~w~~s~e~~~~~tpSr~~g~~~~~E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~   86 (323)
T KOG0834|consen    7 GETSRWYFSKEQLEENTPSRRDGIDLKKELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAA   86 (323)
T ss_pred             ccccccccCHHHHccCChhhccCCchhHHHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHH
Confidence            56789999999999544445678999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcccccccchHHHHHHHHHHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCc
Q psy1168          93 TCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGH  172 (229)
Q Consensus        93 acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~  172 (229)
                      +|+|||+|+||+++ +++|+|.++++..++.. ....+.|+..++.|+..|..+|++|+|||++.+||.|+..|+++++.
T Consensus        87 sclfLAgKvEetp~-kl~dIi~~s~~~~~~~~-~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~  164 (323)
T KOG0834|consen   87 SCLFLAGKVEETPR-KLEDIIKVSYRYLNPKD-LELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKA  164 (323)
T ss_pred             HHHHHHhhcccCcc-cHHHHHHHHHHHcCccc-ccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhh
Confidence            99999999999997 99999999887665321 23346688999999999999999999999999999999999999987


Q ss_pred             cH----HHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccccCCccccc
Q psy1168         173 ED----QLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIAEVGTLGEV  224 (229)
Q Consensus       173 ~~----~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~~~~~~~ev  224 (229)
                      ..    .+.+.||.++||++.+.+|++|+|..||+|||++|+...++ +++..++.
T Consensus       165 ~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~-~~~~~~~~  219 (323)
T KOG0834|consen  165 DENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGV-ELPSDTDK  219 (323)
T ss_pred             hhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCC-CCCCCccc
Confidence            55    49999999999999999999999999999999999999998 55555543

>KOG0835|consensus

Probab=100.00  E-value=1.5e-33  Score=231.14  Aligned_cols=182  Identities=27%  Similarity=0.322  Sum_probs=162.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHH
Q psy1168          32 DLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSR  111 (229)
Q Consensus        32 ~~~~~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~  111 (229)
                      ..++++.+.+..+|..+|.||++-|-.|+||+.+.+|++++|+|||..+++..++...+++||+.||+|+||.|+ ++++
T Consensus        10 ~qd~l~~e~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Pr-r~rd   88 (367)
T KOG0835|consen   10 LQDGLSLETEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPR-RIRD   88 (367)
T ss_pred             hhcccccchHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccc-cHhH
Confidence            456778777778888999999999999999999999999999999999999999999999999999999999997 9999


Q ss_pred             HHHHHHHHHHhhh-----cc-cccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccH--HHHHHHHHH
Q psy1168         112 LLSTCQTVVKNKL-----NY-AYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHED--QLLALAWRV  183 (229)
Q Consensus       112 li~~~~~~~~~~~-----~~-~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~--~i~~~a~~~  183 (229)
                      ++++.... +++.     +. .....+...+..++.+|..||+.|||+..+.+||.++..|++.+++++  .+.|.+|.+
T Consensus        89 VinVFh~L-~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~l~Q~~wNf  167 (367)
T KOG0835|consen   89 VINVFHYL-EQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLKLLQAAWNF  167 (367)
T ss_pred             HHHHHHHH-HHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchhHHHHHHHh
Confidence            99986643 3321     11 123445667889999999999999999999999999999999999864  579999999


Q ss_pred             HHHHhCCcccccccHHHHHHHHHHHhcccCcc
Q psy1168         184 INDSLRTDVCLLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       184 ~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      +||++.|++|..|+|..||+||||+|+...+|
T Consensus       168 mNDslRT~v~vry~pe~iACaciyLaAR~~eI  199 (367)
T KOG0835|consen  168 MNDSLRTDVFVRYSPESIACACIYLAARNLEI  199 (367)
T ss_pred             hhhccccceeeecCHHHHHHHHHHHHHhhhcC
Confidence            99999999999999999999999999998764

>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=100.00  E-value=1.8e-32  Score=224.83  Aligned_cols=172  Identities=37%  Similarity=0.603  Sum_probs=150.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHH
Q psy1168          36 LSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLST  115 (229)
Q Consensus        36 ~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~  115 (229)
                      ++-+++..+|.+++.+|..+|.+|++|+.+.+||+.+|+||+.+++.++.+++.++.||+|||||.||+++    ++...
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~  111 (297)
T COG5333          36 LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPR----DISIE  111 (297)
T ss_pred             cchhhhhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccc----hhhHH
Confidence            55588889999999999999999999999999999999999999999999999999999999999999863    22111


Q ss_pred             HHHHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccH--HHHHHHHHHHHHHhCCccc
Q psy1168         116 CQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHED--QLLALAWRVINDSLRTDVC  193 (229)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~--~i~~~a~~~~~~~~~~~~~  193 (229)
                      +... ++.    .++..+.+++.|+.+|..+|++|+||+.++|||.++..|++++....  ++.+.||.+++|++.+++|
T Consensus       112 ~~~~-~~~----~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~  186 (297)
T COG5333         112 SFEA-RDL----WSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLC  186 (297)
T ss_pred             HHHh-hcc----ccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceee
Confidence            1111 111    23566778999999999999999999999999999999999987654  5999999999999999999


Q ss_pred             ccccHHHHHHHHHHHhcccCccc
Q psy1168         194 LLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       194 l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      +.|+|.+||+||+.+|+..+|..
T Consensus       187 llypphiIA~a~l~ia~~~~~~~  209 (297)
T COG5333         187 LLYPPHIIALAALLIACEVLGMP  209 (297)
T ss_pred             eecChHHHHHHHHHHHHHhcCCc
Confidence            99999999999999999988754

>KOG2496|consensus

Probab=99.96  E-value=2.8e-28  Score=198.52  Aligned_cols=189  Identities=27%  Similarity=0.414  Sum_probs=146.2

Q ss_pred             chh-hhccCCcccHHHHHHhhhc------------C------CCCCCHHHHHHHHHHHHHHHHHHHHhc--CCCHHHHHH
Q psy1168          10 FYP-EWIQQWVLDRQDLIRERKH------------D------LSILSDEEYQKIFIFFANFIQILGEQL--KLRQQVIAT   68 (229)
Q Consensus        10 ~~~-~~~~~w~f~~~~l~~~~~~------------~------~~~~s~~~e~~~r~~~~~~I~~~~~~l--~l~~~~~~~   68 (229)
                      |.. +|++.|+||++||.+.|..            +      -..+.+.++..+-.....-+.+.|+++  ++|..|+.|
T Consensus         2 y~~Ssq~r~W~fte~qL~e~r~~~N~k~i~~~ee~~~~~~~~e~~v~~~ee~tl~k~~E~~l~~f~~k~~p~lp~~Vv~T   81 (325)
T KOG2496|consen    2 YRTSSQYRKWIFTEEQLAERRVDANQKAIQMLEEEAHNLDENEVFVLEAEELTLTKEEELSLVNFYSKFKPNLPTSVVST   81 (325)
T ss_pred             CCcchhhhcccccHHHHHHHHHHHHHHHHHHHHHhccCCCccchhccccccccccHHHHHHHHHHHHHhcCCCchHHHHH
Confidence            445 9999999999999987531            1      112233333333333334445555544  689999999


Q ss_pred             HHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhcccccccchhhHHHHHHHHHHHHH
Q psy1168          69 ATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLE  148 (229)
Q Consensus        69 A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~  148 (229)
                      |+.||+|||..+|.+++++..|++||+|||||++|..+ +++++++...            .+-+...+.|+.+|..+|+
T Consensus        82 A~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~I-SieqFvkn~~------------~~~~k~~e~vLk~E~~llq  148 (325)
T KOG2496|consen   82 AIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYI-SIEQFVKNMN------------GRKWKTHEIVLKYEFLLLQ  148 (325)
T ss_pred             HHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhhee-cHHHHHhhcc------------CcccccHHHHHhchHHHHH
Confidence            99999999999999999999999999999999999985 9999877533            1123457899999999999


Q ss_pred             HcCcceeecCChHHHHHHHHHhCc-------cHHHHHHH--HHHHHHHhCCcccccccHHHHHHHHHHHhcc
Q psy1168         149 NLDCCLIVYQPYRPLLQLVQDIGH-------EDQLLALA--WRVINDSLRTDVCLLYPPYQIAIGECSFSFT  211 (229)
Q Consensus       149 ~L~fdl~~~~P~~~l~~~~~~l~~-------~~~i~~~a--~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~  211 (229)
                      .|+|+|.+.+||+.+..|+.++..       .....+..  ..+++..+.++.++.|+|++||+|||..|..
T Consensus       149 sL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a~~  220 (325)
T KOG2496|consen  149 SLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHAAG  220 (325)
T ss_pred             hhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHHhc
Confidence            999999999999999999987642       12222222  4899999999999999999999999955543

>KOG0656|consensus

Probab=99.92  E-value=3.9e-24  Score=179.77  Aligned_cols=157  Identities=22%  Similarity=0.240  Sum_probs=136.6

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCC---chhHHHHHHHHHhhcccccccchHHHHHHHHH
Q psy1168          42 QKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCID---PLLLAPTCVFLASKVEEFGVISSSRLLSTCQT  118 (229)
Q Consensus        42 ~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~---~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~  118 (229)
                      -.+|..+++||.++|+..++...|...|++|++||+..+++.+.+   .+++|+|||+||+|++|..+|-+.|+....  
T Consensus        75 ~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~--  152 (335)
T KOG0656|consen   75 SSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEY--  152 (335)
T ss_pred             cHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcc--
Confidence            346889999999999999999999999999999999999888888   999999999999999999766777765432  


Q ss_pred             HHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCc----cHHHHHHHHHHHHHHhCCcccc
Q psy1168         119 VVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGH----EDQLLALAWRVINDSLRTDVCL  194 (229)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~----~~~i~~~a~~~~~~~~~~~~~l  194 (229)
                                 .++-...+.|.+||..||.+|+|++...||++|+..|+.+++.    ...+...+..++-......-++
T Consensus       153 -----------~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl  221 (335)
T KOG0656|consen  153 -----------TDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFL  221 (335)
T ss_pred             -----------ccccccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhh
Confidence                       1233458999999999999999999999999999999999987    4677888888888877777899


Q ss_pred             cccHHHHHHHHHHHhcc
Q psy1168         195 LYPPYQIAIGECSFSFT  211 (229)
Q Consensus       195 ~~~P~~IA~aai~~A~~  211 (229)
                      .|+||.||+|++..+..
T Consensus       222 ~y~pSviAaa~~~~v~~  238 (335)
T KOG0656|consen  222 EYPPSVIAAAAILSVSA  238 (335)
T ss_pred             cCChHHHHHHHHHHHHH
Confidence            99999999997755543

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=99.91  E-value=3.9e-23  Score=175.72  Aligned_cols=158  Identities=12%  Similarity=0.137  Sum_probs=144.5

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHH
Q psy1168          41 YQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVV  120 (229)
Q Consensus        41 e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~  120 (229)
                      ++.+ ..+...|.++|..|+||..+..+|..+|++++..+.+++.+...+++||||+|||.++.|+ +++++...+.   
T Consensus       119 er~l-~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~pr-tl~eI~~~~~---  193 (310)
T PRK00423        119 ERNL-AFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPR-TLDEIAEVSR---  193 (310)
T ss_pred             hHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCc-CHHHHHHHhC---
Confidence            4444 4677999999999999999999999999999999999999999999999999999999997 9999876532   


Q ss_pred             HhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHH
Q psy1168         121 KNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQ  200 (229)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~  200 (229)
                                   ..+++|...++.|++.|++++.+.+|++|+.+|+..|+++..+.+.|+.+++++....++.+.+|..
T Consensus       194 -------------v~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~s  260 (310)
T PRK00423        194 -------------VSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTG  260 (310)
T ss_pred             -------------CCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHH
Confidence                         2367888999999999999999999999999999999999999999999999998888999999999


Q ss_pred             HHHHHHHHhcccCccc
Q psy1168         201 IAIGECSFSFTPHVIA  216 (229)
Q Consensus       201 IA~aai~~A~~~~~~~  216 (229)
                      ||+||||+|+..+|..
T Consensus       261 IAAAaIYlA~~~~g~~  276 (310)
T PRK00423        261 LAAAAIYIASLLLGER  276 (310)
T ss_pred             HHHHHHHHHHHHhCCC
Confidence            9999999999988654

>KOG0653|consensus

Probab=99.83  E-value=2.3e-20  Score=163.36  Aligned_cols=161  Identities=19%  Similarity=0.237  Sum_probs=146.2

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHH-HHhhcccccccchHHHHHHHHHHH
Q psy1168          42 QKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVF-LASKVEEFGVISSSRLLSTCQTVV  120 (229)
Q Consensus        42 ~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~-LA~K~ee~~~~~l~~li~~~~~~~  120 (229)
                      .++|...++|+.++..+++|..+|+..|+.+++||+.+..+...+.++++++||| ||||.||...|.+.+++..+.+  
T Consensus       155 ~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~--  232 (391)
T KOG0653|consen  155 AKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDG--  232 (391)
T ss_pred             HHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCC--
Confidence            3689999999999999999999999999999999999988989999999999977 9999999887677887654321  


Q ss_pred             HhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHH
Q psy1168         121 KNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQ  200 (229)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~  200 (229)
                                  ...+++|+.||+.+|.+|+|++.+++|+.|++++.+..+.+......+..+++.++...-.+.++|+.
T Consensus       233 ------------~~s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d~~~~~~~k~~~El~l~d~~~~~~~~s~  300 (391)
T KOG0653|consen  233 ------------AYSREEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYDIKTRTLVKYLLELSLCDYSMLSIPPSS  300 (391)
T ss_pred             ------------ccchHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcchhHHHHHHHHHHHHHhhhHHhccCcHH
Confidence                        13589999999999999999999999999999999999988888999999999999999899999999


Q ss_pred             HHHHHHHHhcccCccc
Q psy1168         201 IAIGECSFSFTPHVIA  216 (229)
Q Consensus       201 IA~aai~~A~~~~~~~  216 (229)
                      +|+|+.+++..++...
T Consensus       301 ~aaa~~~~~~~~~~~~  316 (391)
T KOG0653|consen  301 SAAASFTLALRMLSKG  316 (391)
T ss_pred             HHHHHHHHHHHHhccC
Confidence            9999999999987665

>KOG0655|consensus

Probab=99.81  E-value=7.8e-20  Score=150.69  Aligned_cols=159  Identities=15%  Similarity=0.130  Sum_probs=130.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh-ccccccCCchhHHHHHHHHHhhcccccccchHHHHHH
Q psy1168          37 SDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYA-RNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLST  115 (229)
Q Consensus        37 s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~-~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~  115 (229)
                      .+..+-++|.-..+|+.++|+..+|..+|.+.|+.||+||+. .+.+.+.+.++|+.||||+|+|+||...+++.++..+
T Consensus       137 Hpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyv  216 (408)
T KOG0655|consen  137 HPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYV  216 (408)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeee
Confidence            344455689899999999999999999999999999999987 4567778999999999999999999877788888665


Q ss_pred             HHHHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCcc-----------HHHHHHHHHHH
Q psy1168         116 CQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHE-----------DQLLALAWRVI  184 (229)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~-----------~~i~~~a~~~~  184 (229)
                      .-+              ....++|+.||..||++|+|+|.+.+...++.-|++..+.+           +...-....++
T Consensus       217 TDg--------------Acs~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqiaqlL  282 (408)
T KOG0655|consen  217 TDG--------------ACSEDDILTMELIILKALKWELSPITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIAQLL  282 (408)
T ss_pred             ccC--------------ccchHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCCCceeccccchHHHHHHHHHH
Confidence            322              13478999999999999999999999999999999876542           23333333566


Q ss_pred             HHHhCCcccccccHHHHHHHHHHHh
Q psy1168         185 NDSLRTDVCLLYPPYQIAIGECSFS  209 (229)
Q Consensus       185 ~~~~~~~~~l~~~P~~IA~aai~~A  209 (229)
                      +.+...--++.|+..++||||++--
T Consensus       283 Dlc~ldids~~fsYrilaAAal~h~  307 (408)
T KOG0655|consen  283 DLCILDIDSLEFSYRILAAAALCHF  307 (408)
T ss_pred             HHHHhccccccchHHHHHHHHHHHH
Confidence            6666666688999999999999743

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

Probab=99.79  E-value=4e-18  Score=142.08  Aligned_cols=152  Identities=13%  Similarity=0.132  Sum_probs=141.2

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhcc
Q psy1168          47 FFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNY  126 (229)
Q Consensus        47 ~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~  126 (229)
                      .+...|..++..|+||..+..+|+.+|++.+.++..++....-+++||+|+||+.++.|+ ++.++.....         
T Consensus        99 ~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~pr-tl~eIa~a~~---------  168 (285)
T COG1405          99 TALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPR-TLDEIAKALG---------  168 (285)
T ss_pred             HHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCc-cHHHHHHHHC---------
Confidence            678999999999999999999999999999999999999999999999999999999997 8888876532         


Q ss_pred             cccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHH
Q psy1168         127 AYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGEC  206 (229)
Q Consensus       127 ~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai  206 (229)
                             ..+++|.+..+.+.+.|+-.+....|.+|+.+|+..|+++.++...|..++..+....+..+..|..+|+||+
T Consensus       169 -------V~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaai  241 (285)
T COG1405         169 -------VSKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAI  241 (285)
T ss_pred             -------CCHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHH
Confidence                   2257888999999999999999899999999999999999999999999999999888888999999999999


Q ss_pred             HHhcccCcc
Q psy1168         207 SFSFTPHVI  215 (229)
Q Consensus       207 ~~A~~~~~~  215 (229)
                      |+|+.++++
T Consensus       242 y~as~l~~~  250 (285)
T COG1405         242 YLASLLLGE  250 (285)
T ss_pred             HHHHHHhCC
Confidence            999999874

>KOG1597|consensus

Probab=99.78  E-value=5e-18  Score=138.42  Aligned_cols=165  Identities=16%  Similarity=0.170  Sum_probs=140.8

Q ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhh
Q psy1168          45 FIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKL  124 (229)
Q Consensus        45 r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~  124 (229)
                      ...+...|..+|++++||..+..+|..+|+++...+.+++.....+++||||+||+.++.|+ +++++..+.. +.    
T Consensus       104 ~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~pR-T~kEI~~~an-v~----  177 (308)
T KOG1597|consen  104 LKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDVPR-TFKEISAVAN-VS----  177 (308)
T ss_pred             HHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCc-hHHHHHHHHc-CC----
Confidence            34677899999999999999999999999999999999999999999999999999999997 9999866543 32    


Q ss_pred             cccccccchhhHHHHHHHHHHHHHHcCcceeec--CChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHH
Q psy1168         125 NYAYAQEFPYRTNHILECEFYLLENLDCCLIVY--QPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIA  202 (229)
Q Consensus       125 ~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~--~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA  202 (229)
                                 +++|-+.=..|++.|+-+....  +.-+|+.|||..|++++.+...|..+...+..-+.+-+.+|-+||
T Consensus       178 -----------kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIA  246 (308)
T KOG1597|consen  178 -----------KKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIA  246 (308)
T ss_pred             -----------HHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHH
Confidence                       4566666667777777655544  488999999999999999999999999998888888889999999


Q ss_pred             HHHHHHhcccCc----cccCCcccccCC
Q psy1168         203 IGECSFSFTPHV----IAEVGTLGEVGE  226 (229)
Q Consensus       203 ~aai~~A~~~~~----~~~~~~~~ev~~  226 (229)
                      ||+||+++.+.+    ..+++.+|+|.|
T Consensus       247 Aa~IYmisqls~~kkt~keI~~vtgVaE  274 (308)
T KOG1597|consen  247 AAAIYMISQLSDEKKTQKEIGEVTGVAE  274 (308)
T ss_pred             HHHHHHHHHhccCcccHHHHHHHhhhhH
Confidence            999999999864    334666666655

>COG5024 Cyclin [Cell division and chromosome partitioning]

Probab=99.76  E-value=2.3e-18  Score=150.01  Aligned_cols=163  Identities=17%  Similarity=0.109  Sum_probs=144.5

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHH
Q psy1168          41 YQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVV  120 (229)
Q Consensus        41 e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~  120 (229)
                      +..+|...++||.++-..+++-+.|...|+.+.+||+..+...-...++++++|+|||||+||...+.+.++..++.+. 
T Consensus       209 ~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~-  287 (440)
T COG5024         209 EWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGA-  287 (440)
T ss_pred             HHhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHccc-
Confidence            3389999999999999999999999999999999999998888888999999999999999999876777776654322 


Q ss_pred             HhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHH
Q psy1168         121 KNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQ  200 (229)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~  200 (229)
                                   ..+++++.+|+-+|.+|+|++..+.|..|++++-+.-+-+..-...+.+++.-+....-+..++|+.
T Consensus       288 -------------~t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dyd~~srt~~k~~~e~s~~~~~f~~~~~S~  354 (440)
T COG5024         288 -------------FTRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDYDIFSRTPAKFSSEISPVDYKFIQISPSW  354 (440)
T ss_pred             -------------ccHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhhcccchhhhhhHhhhCCchHhhhhhccCCchH
Confidence                         3489999999999999999999999999999998888877777788888888887777788899999


Q ss_pred             HHHHHHHHhcccCcccc
Q psy1168         201 IAIGECSFSFTPHVIAE  217 (229)
Q Consensus       201 IA~aai~~A~~~~~~~~  217 (229)
                      +|+||.|.|...++-+.
T Consensus       355 ~~aaa~~~s~~~~~~~~  371 (440)
T COG5024         355 CAAAAMYLSRKILSQNQ  371 (440)
T ss_pred             HHHHHHHHHHhhhccCC
Confidence            99999999999886544

>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=99.74  E-value=5e-18  Score=126.16  Aligned_cols=101  Identities=29%  Similarity=0.370  Sum_probs=83.5

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHH
Q psy1168          41 YQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVV  120 (229)
Q Consensus        41 e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~  120 (229)
                      ....|...++||.+++..++++..|.++|+.|+|||+.+.++...+++++++||+++|||++|...+++.+++..+.   
T Consensus        27 ~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~---  103 (127)
T PF00134_consen   27 TPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISD---  103 (127)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTT---
T ss_pred             CHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHc---
Confidence            34677889999999999999999999999999999999999999999999999999999999985457888776531   


Q ss_pred             HhhhcccccccchhhHHHHHHHHHHHHHHcCccee
Q psy1168         121 KNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLI  155 (229)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~  155 (229)
                                 ....++++..+|+.||++|+||++
T Consensus       104 -----------~~~~~~~i~~~E~~iL~~L~f~ln  127 (127)
T PF00134_consen  104 -----------NTFTKKDILEMEREILSALNFDLN  127 (127)
T ss_dssp             -----------TSSHHHHHHHHHHHHHHHTTT---
T ss_pred             -----------CCCCHHHHHHHHHHHHHHCCCCcC
Confidence                       123489999999999999999975

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

>cd00043 CYCLIN Cyclin box fold

Probab=99.47  E-value=3.5e-13  Score=92.73  Aligned_cols=87  Identities=25%  Similarity=0.279  Sum_probs=75.1

Q ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhh
Q psy1168          45 FIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKL  124 (229)
Q Consensus        45 r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~  124 (229)
                      |....+||.++++.++++..+..+|..+++||+..+.+.+++++.+++||+|+|||+++.+ +..+++...+..      
T Consensus         2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~-~~~~~~~~~~~~------   74 (88)
T cd00043           2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIP-PWLKDLVHVTGY------   74 (88)
T ss_pred             cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCC-CCHHHHhHHhCC------
Confidence            3467899999999999999999999999999999999999999999999999999999996 488888665321      


Q ss_pred             cccccccchhhHHHHHHHHHHHH
Q psy1168         125 NYAYAQEFPYRTNHILECEFYLL  147 (229)
Q Consensus       125 ~~~~~~~~~~~~~~i~~~E~~iL  147 (229)
                             .  ..+++..+|..++
T Consensus        75 -------~--~~~~i~~~e~~il   88 (88)
T cd00043          75 -------A--TEEEILRMEKLLL   88 (88)
T ss_pred             -------C--CHHHHHHHHHHhC
Confidence                   0  4788888888764

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.

>KOG0654|consensus

Probab=99.42  E-value=3e-13  Score=115.19  Aligned_cols=162  Identities=18%  Similarity=0.146  Sum_probs=142.1

Q ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHh
Q psy1168          43 KIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKN  122 (229)
Q Consensus        43 ~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~  122 (229)
                      .+|.-.++|..++++..++..++.+.+..+.+||...........+++..+|.++|+|.+|...+.+++++....     
T Consensus       135 smrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~~~~k~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd-----  209 (359)
T KOG0654|consen  135 SMRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEVNKQKLQLVGISAMLIASKYEEIKEPRVEEFCYITD-----  209 (359)
T ss_pred             chhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhccCccHHHHHHHhCcccceeeccchhhcchHHHHHHhhhh-----
Confidence            378889999999999999999999999999999999888888889999999999999999987667777765432     


Q ss_pred             hhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhC-ccHHHHHHHHHHHHHHhCCcccccccHHHH
Q psy1168         123 KLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIG-HEDQLLALAWRVINDSLRTDVCLLYPPYQI  201 (229)
Q Consensus       123 ~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~-~~~~i~~~a~~~~~~~~~~~~~l~~~P~~I  201 (229)
                               ......++..+|..+|..+.|++..++...|+.+|..... ...++..++.++.+.++....++.|.||.|
T Consensus       210 ---------~ty~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~~~~~~~~e~~~~yl~elsll~~~~l~y~PSli  280 (359)
T KOG0654|consen  210 ---------NTYTYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVAQTPELQVEPLANYLTELSLLDYIFLKYLPSLI  280 (359)
T ss_pred             ---------hhhHHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhhcchhHHHHHHHHHHHHhhhhhHHHhccChHHH
Confidence                     2234788999999999999999999999999999987765 567788899999999998888999999999


Q ss_pred             HHHHHHHhcccCccccC
Q psy1168         202 AIGECSFSFTPHVIAEV  218 (229)
Q Consensus       202 A~aai~~A~~~~~~~~~  218 (229)
                      |+||+++|-..++..++
T Consensus       281 AasAv~lA~~~~~~~pW  297 (359)
T KOG0654|consen  281 AASAVFLARLTLDFHPW  297 (359)
T ss_pred             HHHHHHHHHhhccCCCC
Confidence            99999999888774443

>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma

Probab=99.34  E-value=5.1e-12  Score=85.94  Aligned_cols=83  Identities=25%  Similarity=0.418  Sum_probs=70.1

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhccccc
Q psy1168          50 NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYA  129 (229)
Q Consensus        50 ~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~~  129 (229)
                      +||.++++.++++..+..+|..+++|++....+.+++++.+++||+|+|||.+|.++ ...++...+.            
T Consensus         1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~-~~~~~~~~~~------------   67 (83)
T smart00385        1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPP-WTKELVHYTG------------   67 (83)
T ss_pred             CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCC-CchhHhHhhC------------
Confidence            489999999999999999999999999997777789999999999999999999874 7777654321            


Q ss_pred             ccchhhHHHHHHHHHHHHH
Q psy1168         130 QEFPYRTNHILECEFYLLE  148 (229)
Q Consensus       130 ~~~~~~~~~i~~~E~~iL~  148 (229)
                        + ...+++..+|+.+++
T Consensus        68 --~-~~~~~i~~~~~~il~   83 (83)
T smart00385       68 --Y-FTEEEILRMEKLLLE   83 (83)
T ss_pred             --C-CCHHHHHHHHHHHhC
Confidence              0 237889999998873

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

>KOG1598|consensus

Probab=99.12  E-value=2.5e-10  Score=100.73  Aligned_cols=150  Identities=16%  Similarity=0.109  Sum_probs=124.9

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccc--cchHHHHHHHHHHHHhhh
Q psy1168          47 FFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGV--ISSSRLLSTCQTVVKNKL  124 (229)
Q Consensus        47 ~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~--~~l~~li~~~~~~~~~~~  124 (229)
                      .+-..|.+++.+|+++. ++.+|..+|+.-..++-.++.....+.++|+|++|+.+.++.  +...+++++         
T Consensus        69 n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lqv---------  138 (521)
T KOG1598|consen   69 NARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQV---------  138 (521)
T ss_pred             HHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceEE---------
Confidence            45679999999999999 999999999999999999999999999999999999998874  122222221         


Q ss_pred             cccccccchhhHHHHHHHHHHHHHHcCcc---eeecCChHHHHHHHHHhCc---cHHHHHHHHHHHHHHhCCcccccccH
Q psy1168         125 NYAYAQEFPYRTNHILECEFYLLENLDCC---LIVYQPYRPLLQLVQDIGH---EDQLLALAWRVINDSLRTDVCLLYPP  198 (229)
Q Consensus       125 ~~~~~~~~~~~~~~i~~~E~~iL~~L~fd---l~~~~P~~~l~~~~~~l~~---~~~i~~~a~~~~~~~~~~~~~l~~~P  198 (229)
                                ..-++...=..+.+.|.-+   +...+|.-|+.+|...|..   ++++...|..+++.+.++++..+.+|
T Consensus       139 ----------~Vy~LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRP  208 (521)
T KOG1598|consen  139 ----------SVYDLGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRP  208 (521)
T ss_pred             ----------ehhhhhHHHHHHHHHhccccccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence                      1223444445677778877   6778999999999988753   46799999999999999999999999


Q ss_pred             HHHHHHHHHHhcccCccc
Q psy1168         199 YQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       199 ~~IA~aai~~A~~~~~~~  216 (229)
                      +.|+.||+++|+.+||+.
T Consensus       209 sglcGAaLliAar~h~~~  226 (521)
T KOG1598|consen  209 SGLCGAALLIAARMHGFR  226 (521)
T ss_pred             cchhHHHHHHHHHHcCcc
Confidence            999999999999999864

>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=98.96  E-value=4e-09  Score=70.31  Aligned_cols=63  Identities=22%  Similarity=0.345  Sum_probs=55.8

Q ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHH
Q psy1168          52 IQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLST  115 (229)
Q Consensus        52 I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~  115 (229)
                      |.++|+.|+||..+..+|..++++-...+-.++.++..+++||+|+||+.++.++ +++++...
T Consensus         1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~-t~~eIa~~   63 (71)
T PF00382_consen    1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPR-TLKEIAEA   63 (71)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSS-SHHHHHHH
T ss_pred             ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCc-CHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999986 89988654

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.

>KOG4164|consensus

Probab=98.55  E-value=1.9e-07  Score=79.51  Aligned_cols=106  Identities=20%  Similarity=0.317  Sum_probs=86.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHH
Q psy1168          36 LSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLST  115 (229)
Q Consensus        36 ~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~  115 (229)
                      ++....+.++    .-|.+++...++...|+++|.+||.+...++.+.+.+.++.|.|||.||+|++|...-.++.+|..
T Consensus       377 LTLSKirSlK----REMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek  452 (497)
T KOG4164|consen  377 LTLSKIRSLK----REMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEK  452 (497)
T ss_pred             EeHHHHHHHH----HHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHH
Confidence            4444444444    678889999999999999999999999999999999999999999999999998764356677766


Q ss_pred             HHHHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeec
Q psy1168         116 CQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVY  157 (229)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~  157 (229)
                      ....+            ...+.+++..|.-||-+|.|-|.++
T Consensus       453 ~Ee~f------------R~nrrdLia~Ef~VlvaLefaL~~~  482 (497)
T KOG4164|consen  453 LEEQF------------RLNRRDLIAFEFPVLVALEFALHLP  482 (497)
T ss_pred             HHHHh------------cccHHhhhhhhhhHHHhhhhhccCC
Confidence            54433            3448899999999999999988764

>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=98.48  E-value=8.1e-08  Score=69.89  Aligned_cols=59  Identities=22%  Similarity=0.191  Sum_probs=51.0

Q ss_pred             cCChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCcc
Q psy1168         157 YQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       157 ~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      ++|++|+.+|++..+.+.++...|+.+++.++.+..++.|+||.||+||+++|...++.
T Consensus         1 PTp~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~   59 (118)
T PF02984_consen    1 PTPYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGK   59 (118)
T ss_dssp             --HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHS
T ss_pred             CcHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCc
Confidence            58999999997766667889999999999999999999999999999999999998763

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

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=98.24  E-value=7.5e-06  Score=69.97  Aligned_cols=66  Identities=14%  Similarity=0.174  Sum_probs=60.4

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHH
Q psy1168          49 ANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLST  115 (229)
Q Consensus        49 ~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~  115 (229)
                      .++|.++|..|+|+..+..+|..++++........+.+|..+++||+|+||+..+.++ +.+++..+
T Consensus       220 ~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~-t~keIa~v  285 (310)
T PRK00423        220 IDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERR-TQREVAEV  285 (310)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCC-CHHHHHHH
Confidence            4889999999999999999999999999887777899999999999999999999986 88888654

>cd00043 CYCLIN Cyclin box fold

Probab=98.18  E-value=3.6e-06  Score=57.26  Aligned_cols=60  Identities=18%  Similarity=0.159  Sum_probs=55.5

Q ss_pred             ecCChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCcc
Q psy1168         156 VYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       156 ~~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      .++|.+++.+++..++.+.++...|..+++.++....+..++|+.||+||+++|++..+.
T Consensus         2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~   61 (88)
T cd00043           2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI   61 (88)
T ss_pred             cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCC
Confidence            367899999999999999999999999999998877788999999999999999998766

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

>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma

Probab=98.15  E-value=4.1e-06  Score=56.36  Aligned_cols=56  Identities=20%  Similarity=0.220  Sum_probs=50.7

Q ss_pred             HHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         161 RPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       161 ~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      +|+.++++.++.++++...|+.+++.++....+..++|+.||+||+++|++..+..
T Consensus         1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~   56 (83)
T smart00385        1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIP   56 (83)
T ss_pred             CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCC
Confidence            37889999999999999999999999988667778999999999999999988765

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

>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=98.15  E-value=6.5e-06  Score=54.72  Aligned_cols=54  Identities=9%  Similarity=0.095  Sum_probs=46.9

Q ss_pred             HHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         163 LLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       163 l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      +.++++.|++++.+.+.|..+........+.-+.+|..||+||||+|++.++..
T Consensus         1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~   54 (71)
T PF00382_consen    1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVP   54 (71)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSS
T ss_pred             ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCC
Confidence            578999999999999999999999988888889999999999999999988754

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.

>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=98.07  E-value=4.8e-05  Score=58.09  Aligned_cols=91  Identities=20%  Similarity=0.185  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh---c--cccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHh
Q psy1168          48 FANFIQILGEQLKLRQQVIATATVYFKRFYA---R--NSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKN  122 (229)
Q Consensus        48 ~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~---~--~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~  122 (229)
                      ..+|+.++.+..+++..+.-.|..|++|+..   .  ..+.....+-+.++|+.+|.|+-+....+-+....++      
T Consensus        54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~------  127 (149)
T PF08613_consen   54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVG------  127 (149)
T ss_dssp             HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHH------
T ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhc------
Confidence            3478899999999999999999999999988   2  2344566788999999999999876532333322221      


Q ss_pred             hhcccccccchhhHHHHHHHHHHHHHHcCcce
Q psy1168         123 KLNYAYAQEFPYRTNHILECEFYLLENLDCCL  154 (229)
Q Consensus       123 ~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl  154 (229)
                                ....+++-.+|+..|..|+|+|
T Consensus       128 ----------gis~~eln~lE~~fL~~l~~~L  149 (149)
T PF08613_consen  128 ----------GISLKELNELEREFLKLLDYNL  149 (149)
T ss_dssp             ----------TS-HHHHHHHHHHHHHHTTT--
T ss_pred             ----------CCCHHHHHHHHHHHHHHCCCcC
Confidence                      1236789999999999999986

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.

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

Probab=97.19  E-value=0.0016  Score=54.79  Aligned_cols=66  Identities=18%  Similarity=0.179  Sum_probs=58.1

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHH
Q psy1168          49 ANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLST  115 (229)
Q Consensus        49 ~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~  115 (229)
                      .++|.++|+.|+|+..+...|..+.+..-......+.+|.-+|+||+|+|++..+.++ +-+++..+
T Consensus       195 ~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~-tq~eva~v  260 (285)
T COG1405         195 SDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERR-TQKEVAKV  260 (285)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCch-HHHHHHHH
Confidence            3678899999999999999999999999999888899999999999999999999764 55555443

>KOG1597|consensus

Probab=96.94  E-value=0.0051  Score=51.24  Aligned_cols=67  Identities=12%  Similarity=0.169  Sum_probs=60.1

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHH
Q psy1168          48 FANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLST  115 (229)
Q Consensus        48 ~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~  115 (229)
                      ..++|.+.|..|+||..+...|..+-++.-...-..+..|.-|++|++|+++-+.+.++ +.+++..+
T Consensus       203 t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kk-t~keI~~v  269 (308)
T KOG1597|consen  203 TGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKK-TQKEIGEV  269 (308)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcc-cHHHHHHH
Confidence            56899999999999999999999999999888788889999999999999999999764 77777554

>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation

Probab=96.09  E-value=0.05  Score=40.73  Aligned_cols=73  Identities=16%  Similarity=0.139  Sum_probs=55.4

Q ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh--ccccccCCchhHHHHHHHHHhhcccccccchHHHHHHH
Q psy1168          43 KIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYA--RNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTC  116 (229)
Q Consensus        43 ~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~--~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~  116 (229)
                      ++-..+..-|.++|++|+++.......-+.|+..+.  ..-+++.+..-+.+.|+|.-||+..... +.++++..+
T Consensus         9 Kvy~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~-sF~~Ii~~Y   83 (135)
T PF01857_consen    9 KVYKLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEEL-SFKDIIKAY   83 (135)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S---HHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCC-CHHHHHHHH
Confidence            333446677999999999998887777777777765  3456778888999999999999998764 899998764

They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.

>TIGR00569 ccl1 cyclin ccl1

Probab=93.30  E-value=0.21  Score=42.62  Aligned_cols=53  Identities=11%  Similarity=0.100  Sum_probs=45.5

Q ss_pred             HHHHHHHHhC--ccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCc
Q psy1168         162 PLLQLVQDIG--HEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHV  214 (229)
Q Consensus       162 ~l~~~~~~l~--~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~  214 (229)
                      .|..++..++  +++.+.-.|..++...+...-...|+|..||++|+|+|++.-.
T Consensus        62 ~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE  116 (305)
T TIGR00569        62 RLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE  116 (305)
T ss_pred             HHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccc
Confidence            5556677788  8889999999999998887777899999999999999998653

University).

>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=93.21  E-value=0.14  Score=36.50  Aligned_cols=56  Identities=16%  Similarity=0.145  Sum_probs=43.9

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccc
Q psy1168          49 ANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEF  104 (229)
Q Consensus        49 ~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~  104 (229)
                      ..|+....+..+....+...|..+..-......+.++.+-.+|+||+++|.+..+.
T Consensus         4 ~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~   59 (118)
T PF02984_consen    4 YDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGK   59 (118)
T ss_dssp             HHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCc
Confidence            45666665555556678888888888877777888999999999999999999654

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

>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=92.40  E-value=0.51  Score=34.22  Aligned_cols=55  Identities=15%  Similarity=0.000  Sum_probs=45.0

Q ss_pred             HHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCcc
Q psy1168         161 RPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       161 ~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      +++......++++......|..+++..+.........+..+|+||+++|++....
T Consensus        36 ~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~   90 (127)
T PF00134_consen   36 DWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEED   90 (127)
T ss_dssp             HHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhcc
Confidence            4677778888899999999999999887666677888999999999999997644

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 ....

>KOG0835|consensus

Probab=91.10  E-value=0.4  Score=40.87  Aligned_cols=56  Identities=18%  Similarity=0.314  Sum_probs=37.6

Q ss_pred             HHHHHHHhcCCCHHH--HHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccc
Q psy1168          51 FIQILGEQLKLRQQV--IATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGV  106 (229)
Q Consensus        51 ~I~~~~~~l~l~~~~--~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~  106 (229)
                      +|......|++++.-  ...|=+|..--.-..-+..+.+..||+||+|||++..|.|.
T Consensus       144 lii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpL  201 (367)
T KOG0835|consen  144 LIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPL  201 (367)
T ss_pred             HHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCC
Confidence            344444556666543  44444444444444556678999999999999999999764

>KOG1674|consensus

Probab=88.82  E-value=2  Score=34.82  Aligned_cols=92  Identities=21%  Similarity=0.201  Sum_probs=63.5

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHHhhccc---------cccCC-chhHHHHHHHHHhhcccccccchHHHHHHHHHH
Q psy1168          50 NFIQILGEQLKLRQQVIATATVYFKRFYARNS---------LKCID-PLLLAPTCVFLASKVEEFGVISSSRLLSTCQTV  119 (229)
Q Consensus        50 ~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s---------~~~~~-~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~  119 (229)
                      +++.++-+..+....+.-.|.+||+||.....         +.... .+-..++|+-+|+|..+..- --...    +  
T Consensus        80 ~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~-y~n~~----~--  152 (218)
T KOG1674|consen   80 QYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVY-YSNAY----Y--  152 (218)
T ss_pred             HHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchh-hhHHH----H--
Confidence            56677778889999999999999999988521         11223 33468899999999986531 11111    1  


Q ss_pred             HHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeec
Q psy1168         120 VKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVY  157 (229)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~  157 (229)
                       .+-.+        ...+++-.+|..++..++|.+.+.
T Consensus       153 -a~vgg--------l~~~eln~lE~~~l~~~~~~l~i~  181 (218)
T KOG1674|consen  153 -AKVGG--------LTTDELNKLELDLLFLLDFRLIIS  181 (218)
T ss_pred             -HHhCC--------CChHhhhhhhHHHHhhCCeEEEec
Confidence             00001        225666699999999999999886

>KOG0834|consensus

Probab=84.38  E-value=1.5  Score=37.71  Aligned_cols=53  Identities=11%  Similarity=0.072  Sum_probs=43.1

Q ss_pred             HHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccC
Q psy1168         161 RPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPH  213 (229)
Q Consensus       161 ~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~  213 (229)
                      .||......|+..+.-...|..+....+.-.-+-.|+|.++|++|+++|++..
T Consensus        44 ~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvE   96 (323)
T KOG0834|consen   44 KFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVE   96 (323)
T ss_pred             HHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcc
Confidence            46777777888777767777778877777777788999999999999999854

>KOG1598|consensus

Probab=84.23  E-value=2  Score=39.05  Aligned_cols=60  Identities=18%  Similarity=0.271  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHH---HHHHHHhhh
Q psy1168          64 QVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLST---CQTVVKNKL  124 (229)
Q Consensus        64 ~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~---~~~~~~~~~  124 (229)
                      .|.-+|..+..|--.---..+..|--++.|||++||...+.++ ++.+|+.+   +..++++++
T Consensus       185 ~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~r-si~dIv~vvhV~e~Tl~kRl  247 (521)
T KOG1598|consen  185 DVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRR-TIGDIAKVVHVCESTLSKRL  247 (521)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccc-cHHHHHHHHHHhHHHHHHHH
Confidence            4788888887775322223456788999999999999999986 89998764   445555543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	229
3rgf_B	285	Crystal Structure Of Human Cdk8CYCC Length = 285		1e-79
1zp2_A	235	Structure Of The Mediator Subunit Cyclin C Length =		1e-16
1kxu_A	333	Cyclin H, A Positive Regulatory Subunit Of Cdk Acti		2e-12
1jkw_A	323	Structure Of Cyclin Mcs2 Length = 323		3e-12
2i53_A	258	Crystal Structure Of Cyclin K Length = 258		1e-11
2ivx_A	257	Crystal Structure Of Human Cyclin T2 At 1.8 A Resol		3e-08
3tnh_B	259	Cdk9CYCLIN T IN COMPLEX WITH CAN508 Length = 259		6e-06
3mi9_B	266	Crystal Structure Of Hiv-1 Tat Complexed With Human		7e-06
2w2h_A	264	Structural Basis Of Transcription Activation By The		8e-06
2pk2_A	358	Cyclin Box Structure Of The P-Tefb Subunit Cyclin T		8e-06
3blh_B	260	Crystal Structure Of Human Cdk9CYCLINT1 Length = 26		3e-05

>pdb|3RGF|B Chain B, Crystal Structure Of Human Cdk8CYCC Length = 285

Iteration: 1
 Score =  292 bits (748), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 133/188 (70%), Positives = 161/188 (85%)
Query: 17  QWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRF 76
           QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKRF
Sbjct: 15  QWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRF 74
Query: 77  YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT 136
           YAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL++   +V+K + +YA+ +EFPYR 
Sbjct: 75  YARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRM 134
Query: 137 NHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLY 196
           NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLLY
Sbjct: 135 NHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLY 194
Query: 197 PPYQIAIG 204
           PP+ IA+ 
Sbjct: 195 PPFMIALA 202

>pdb|1ZP2|A Chain A, Structure Of The Mediator Subunit Cyclin C Length = 235

Iteration: 1
 Score = 82.8 bits (203), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 56/172 (32%), Positives = 88/172 (51%), Gaps = 10/172 (5%)
Query: 32  DLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFY-ARNSLKCIDPLLL 90
           DL  L      K  I+    +Q  G++L+LRQ+V+ATA V  +R+   +N  K      L
Sbjct: 15  DLESLEPTCLSKDTIYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKGFSLEAL 74
Query: 91  APTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENL 150
             TC++L+ KVEE  V     + + C     N+ N  ++ +     ++I E EF ++  L
Sbjct: 75  VATCIYLSCKVEECPV----HIRTIC-----NEANDLWSLKVKLSRSNISEIEFEIISVL 125
Query: 151 DCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIA 202
           D  LIV+ PY  L Q   D     + L  AW ++NDS  + +CL+  P+Q+A
Sbjct: 126 DAFLIVHHPYTSLEQAFHDGIINQKQLEFAWSIVNDSYASSLCLMAHPHQLA 177

>pdb|1KXU|A Chain A, Cyclin H, A Positive Regulatory Subunit Of Cdk Activating Kinase Length = 333

Iteration: 1
 Score = 68.6 bits (166), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 53/148 (35%), Positives = 70/148 (47%), Gaps = 17/148 (11%)
Query: 63  QQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKN 122
           + V+ TA +YFKRFY  NS+    P ++  TC FLA KV+EF V S           V N
Sbjct: 87  RSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQ--------FVGN 138
Query: 123 KLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIG-------HEDQ 175
                  QE       ILE E  L++ L+  LIV+ PYRP    + D+        + + 
Sbjct: 139 LRESPLGQE--KALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYPILENPEI 196
Query: 176 LLALAWRVINDSLRTDVCLLYPPYQIAI 203
           L   A   +N    TD  LLY P QIA+
Sbjct: 197 LRKTADDFLNRIALTDAYLLYTPSQIAL 224

>pdb|1JKW|A Chain A, Structure Of Cyclin Mcs2 Length = 323

Iteration: 1
 Score = 68.6 bits (166), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 53/148 (35%), Positives = 70/148 (47%), Gaps = 17/148 (11%)
Query: 63  QQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKN 122
           + V+ TA +YFKRFY  NS+    P ++  TC FLA KV+EF V S           V N
Sbjct: 77  RSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQ--------FVGN 128
Query: 123 KLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIG-------HEDQ 175
                  QE       ILE E  L++ L+  LIV+ PYRP    + D+        + + 
Sbjct: 129 LRESPLGQE--KALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYPILENPEI 186
Query: 176 LLALAWRVINDSLRTDVCLLYPPYQIAI 203
           L   A   +N    TD  LLY P QIA+
Sbjct: 187 LRKTADDFLNRIALTDAYLLYTPSQIAL 214

>pdb|2I53|A Chain A, Crystal Structure Of Cyclin K Length = 258

Iteration: 1
 Score = 66.2 bits (160), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/193 (29%), Positives = 91/193 (47%), Gaps = 13/193 (6%)
Query: 18  WVLDRQDLIR--ERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           W  D++DL     +   L   ++  Y++     A FI  +G +L L    +AT  +YF R
Sbjct: 15  WYWDKKDLAHTPSQLEGLDPATEARYRREG---ARFIFDVGTRLGLHYDTLATGIIYFHR 71
Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FY  +S K     +    C+FLA KVEE        ++ T ++++ N + +    + P  
Sbjct: 72  FYMFHSFKQFPRYVTGACCLFLAGKVEE-TPKKCKDIIKTARSLL-NDVQFGQFGDDP-- 127
Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLL----QLVQDIGHEDQLLALAWRVINDSLRTD 191
              ++  E  LL+ +   L V  PY+ LL    QL  D     +L+ +AW  +NDSL T 
Sbjct: 128 KEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTT 187
Query: 192 VCLLYPPYQIAIG 204
           + L + P  IA+ 
Sbjct: 188 LSLQWEPEIIAVA 200

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 45/161 (27%), Positives = 78/161 (48%), Gaps = 12/161 (7%)
Query: 49  ANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFG--- 105
           AN IQ +G++L + Q  I TA VY  RFY  +S    +  +++ T +FLA+KVEE     
Sbjct: 35  ANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKL 94
Query: 106 ---VISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRP 162
              +  +   L   + ++  K + AY Q+    T  ++  E  +L+ L   + +  P+  
Sbjct: 95  EHVIKVAHACLHPLEPLLDTKCD-AYLQQ----TRELVILETIMLQTLGFEITIEHPHTD 149
Query: 163 LLQLVQDIGHEDQLLALAWRVINDSLR-TDVCLLYPPYQIA 202
           +++  Q +     L   ++ +  +SL  T  CL Y P  IA
Sbjct: 150 VVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIA 190

>pdb|3TNH|B Chain B, Cdk9CYCLIN T IN COMPLEX WITH CAN508 Length = 259

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 44/160 (27%), Positives = 72/160 (45%), Gaps = 10/160 (6%)
Query: 49  ANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEE----- 103
           AN +Q +G++L + Q  I TA VY  RFY   S        +AP  +FLA+KVEE     
Sbjct: 42  ANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKL 101
Query: 104 FGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPL 163
             VI  +      Q  + +  + AY Q+       ++  E  +L+ L   L +  P+  +
Sbjct: 102 EHVIKVAHTCLHPQESLPDTRSEAYLQQV----QDLVILESIILQTLGFELTIDHPHTHV 157
Query: 164 LQLVQDIGHEDQLLALAWRVINDSLR-TDVCLLYPPYQIA 202
           ++  Q +     L   ++ +  +SL  T   L Y P  +A
Sbjct: 158 VKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVA 197

>pdb|3MI9|B Chain B, Crystal Structure Of Hiv-1 Tat Complexed With Human P-Tefb Length = 266

Iteration: 1
 Score = 47.4 bits (111), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 44/160 (27%), Positives = 72/160 (45%), Gaps = 10/160 (6%)
Query: 49  ANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEE----- 103
           AN +Q +G++L + Q  I TA VY  RFY   S        +AP  +FLA+KVEE     
Sbjct: 42  ANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKL 101
Query: 104 FGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPL 163
             VI  +      Q  + +  + AY Q+       ++  E  +L+ L   L +  P+  +
Sbjct: 102 EHVIKVAHTCLHPQESLPDTRSEAYLQQ----VQDLVILESIILQTLGFELTIDHPHTHV 157
Query: 164 LQLVQDIGHEDQLLALAWRVINDSLR-TDVCLLYPPYQIA 202
           ++  Q +     L   ++ +  +SL  T   L Y P  +A
Sbjct: 158 VKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVA 197

>pdb|2W2H|A Chain A, Structural Basis Of Transcription Activation By The Cyclin T1-Tat-Tar Rna Complex From Eiav Length = 264

Iteration: 1
 Score = 47.0 bits (110), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 44/160 (27%), Positives = 72/160 (45%), Gaps = 10/160 (6%)
Query: 49  ANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEE----- 103
           AN +Q +G++L + Q  I TA VY  RFY   S        +AP  +FLA+KVEE     
Sbjct: 39  ANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNSVAPAALFLAAKVEEQPKKL 98
Query: 104 FGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPL 163
             VI  +      Q  + +  + AY Q+       ++  E  +L+ L   L +  P+  +
Sbjct: 99  EHVIKVAHTCLHPQESLPDTRSEAYLQQ----VQDLVILESIILQTLGFELTIDHPHTHV 154
Query: 164 LQLVQDIGHEDQLLALAWRVINDSLR-TDVCLLYPPYQIA 202
           ++  Q +     L   ++ +  +SL  T   L Y P  +A
Sbjct: 155 VKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVA 194

>pdb|2PK2|A Chain A, Cyclin Box Structure Of The P-Tefb Subunit Cyclin T1 Derived From A Fusion Complex With Eiav Tat Length = 358

Iteration: 1
 Score = 47.0 bits (110), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 44/160 (27%), Positives = 72/160 (45%), Gaps = 10/160 (6%)
Query: 49  ANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEE----- 103
           AN +Q +G++L + Q  I TA VY  RFY   S        +AP  +FLA+KVEE     
Sbjct: 42  ANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEEQPKKL 101
Query: 104 FGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPL 163
             VI  +      Q  + +  + AY Q+       ++  E  +L+ L   L +  P+  +
Sbjct: 102 EHVIKVAHTCLHPQESLPDTRSEAYLQQV----QDLVILESIILQTLGFELTIDHPHTHV 157
Query: 164 LQLVQDIGHEDQLLALAWRVINDSLR-TDVCLLYPPYQIA 202
           ++  Q +     L   ++ +  +SL  T   L Y P  +A
Sbjct: 158 VKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVA 197

>pdb|3BLH|B Chain B, Crystal Structure Of Human Cdk9CYCLINT1 Length = 260

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 49/195 (25%), Positives = 84/195 (43%), Gaps = 15/195 (7%)
Query: 16  QQWVLDRQDLIRERKHDLSILSDEE--YQKIFIFFANFIQILGEQLKLRQQVIATATVYF 73
           ++W   R+ L         +  D+E  Y++     AN +Q +G++L + Q  I TA VY 
Sbjct: 11  KRWYFTREQLENSPSRRFGVDPDKELSYRQQA---ANLLQDMGQRLNVSQLTINTAIVYM 67
Query: 74  KRFYARNSLKCIDPLLLAPTCVFLASKVEE-----FGVISSSRLLSTCQTVVKNKLNYAY 128
            RFY   S        +AP  +FLA+KVE        VI  +      Q  + +  + AY
Sbjct: 68  HRFYMIQSFTRFPGNSVAPAALFLAAKVEGQPKKLEHVIKVAHTCLHPQESLPDTRSEAY 127
Query: 129 AQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSL 188
            Q+       ++  E  +L+ L   L +  P+  +++  Q +     L   ++ +  +SL
Sbjct: 128 LQQV----QDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSL 183
Query: 189 R-TDVCLLYPPYQIA 202
             T   L Y P  +A
Sbjct: 184 HLTTFSLQYTPPVVA 198

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	229
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	5e-62
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	6e-51
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	7e-51
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	8e-51
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	4e-49
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	4e-45
1f5q_B	252	Gamma herpesvirus cyclin; herpesviral cyclin, cycl	2e-04
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	9e-04

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

 Score =  194 bits (494), Expect = 5e-62
 Identities = 133/189 (70%), Positives = 161/189 (85%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
            QW+LD+QDL++ER+ DL  LS+EEY K+ IFF N IQ LGE LKLRQQVIATATVYFKR
Sbjct: 14  LQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKR 73

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYR 135
           FYAR SLK IDP+L+APTCVFLASKVEEFGV+S++RL++   +V+K + +YA+ +EFPYR
Sbjct: 74  FYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYR 133

Query: 136 TNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL 195
            NHILECEFYLLE +DCCLIVY PYRPLLQ VQD+G ED LL LAWR++ND+ RTD+CLL
Sbjct: 134 MNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLL 193

Query: 196 YPPYQIAIG 204
           YPP+ IA+ 
Sbjct: 194 YPPFMIALA 202

>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 =  165 bits (418), Expect = 6e-51
 Identities = 51/195 (26%), Positives = 82/195 (42%), Gaps = 13/195 (6%)

Query: 16  QQWVLDRQDL--IRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYF 73
             W  D++DL     +   L         +     A FI  +G +L L    +AT  +YF
Sbjct: 13  PCWYWDKKDLAHTPSQLEGLDP---ATEARYRREGARFIFDVGTRLGLHYDTLATGIIYF 69

Query: 74  KRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFP 133
            RFY  +S K     +    C+FLA KVEE       +     +T      +  + Q   
Sbjct: 70  HRFYMFHSFKQFPRYVTGACCLFLAGKVEETPK----KCKDIIKTARSLLNDVQFGQFGD 125

Query: 134 YRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHE----DQLLALAWRVINDSLR 189
                ++  E  LL+ +   L V  PY+ LL+  + +  +     +L+ +AW  +NDSL 
Sbjct: 126 DPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLC 185

Query: 190 TDVCLLYPPYQIAIG 204
           T + L + P  IA+ 
Sbjct: 186 TTLSLQWEPEIIAVA 200

>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 =  167 bits (423), Expect = 7e-51
 Identities = 58/228 (25%), Positives = 87/228 (38%), Gaps = 45/228 (19%)

Query: 5   STQGRFYPEWIQQWVLDRQDLIRERK-------------------HDLSILSDEEYQKIF 45
           S+Q R        W    ++ +   +                   +D   L   E   + 
Sbjct: 5   SSQKR-------HWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLC 57

Query: 46  IFFANFIQILGEQLK--LRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEE 103
            ++   +       K  + + V+ TA +YFKRFY  NS+    P ++  TC FLA KV+E
Sbjct: 58  KYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDE 117

Query: 104 FGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPL 163
           F V        +    V N                ILE E  L++ L+  LIV+ PYRP 
Sbjct: 118 FNV--------SSPQFVGNL--RESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPF 167

Query: 164 LQLVQDIG-------HEDQLLALAWRVINDSLRTDVCLLYPPYQIAIG 204
              + D+        + + L   A   +N    TD  LLY P QIA+ 
Sbjct: 168 EGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALT 215

>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 =  168 bits (425), Expect = 8e-51
 Identities = 45/192 (23%), Positives = 80/192 (41%), Gaps = 5/192 (2%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
           ++W   R+ L         +  D+E        AN +Q +G++L + Q  I TA VY  R
Sbjct: 10  KRWYFTREQLENSPSRRFGVDPDKEL-SYRQQAANLLQDMGQRLNVSQLTINTAIVYMHR 68

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTV--VKNKLNYAYAQEFP 133
           FY   S        +AP  +FLA+KVEE        ++    T    +  L    ++ + 
Sbjct: 69  FYMIQSFTRFPGNSVAPAALFLAAKVEEQPK-KLEHVIKVAHTCLHPQESLPDTRSEAYL 127

Query: 134 YRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLR-TDV 192
            +   ++  E  +L+ L   L +  P+  +++  Q +     L   ++ +  +SL  T  
Sbjct: 128 QQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTF 187

Query: 193 CLLYPPYQIAIG 204
            L Y P  +A  
Sbjct: 188 SLQYTPPVVACV 199

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

 Score =  160 bits (405), Expect = 4e-49
 Identities = 56/190 (29%), Positives = 89/190 (46%), Gaps = 19/190 (10%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
            Q  L           DL  L      K  I+    +Q  G++L+LRQ+V+ATA V  +R
Sbjct: 8   TQLFLST---------DLESLEPTCLSKDTIYQWKVVQTFGDRLRLRQRVLATAIVLLRR 58

Query: 76  FYARNSL-KCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPY 134
           +  + +  K      L  TC++L+ KVEE  V   +         + N+ N  ++ +   
Sbjct: 59  YMLKKNEEKGFSLEALVATCIYLSCKVEECPVHIRT---------ICNEANDLWSLKVKL 109

Query: 135 RTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCL 194
             ++I E EF ++  LD  LIV+ PY  L Q   D     + L  AW ++NDS  + +CL
Sbjct: 110 SRSNISEIEFEIISVLDAFLIVHHPYTSLEQAFHDGIINQKQLEFAWSIVNDSYASSLCL 169

Query: 195 LYPPYQIAIG 204
           +  P+Q+A  
Sbjct: 170 MAHPHQLAYA 179

>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 =  150 bits (379), Expect = 4e-45
 Identities = 45/191 (23%), Positives = 81/191 (42%), Gaps = 3/191 (1%)

Query: 16  QQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKR 75
            +W   R+ L         + +D+E        AN IQ +G++L + Q  I TA VY  R
Sbjct: 3   SRWFFTREQLENTPSRRCGVEADKEL-SCRQQAANLIQEMGQRLNVSQLTINTAIVYMHR 61

Query: 76  FYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAY-AQEFPY 134
           FY  +S    +  +++ T +FLA+KVEE        +      +   +         +  
Sbjct: 62  FYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHACLHPLEPLLDTKCDAYLQ 121

Query: 135 RTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSL-RTDVC 193
           +T  ++  E  +L+ L   + +  P+  +++  Q +     L   ++ +  +SL  T  C
Sbjct: 122 QTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFC 181

Query: 194 LLYPPYQIAIG 204
           L Y P  IA  
Sbjct: 182 LQYKPTVIACV 192

>1f5q_B Gamma herpesvirus cyclin; herpesviral cyclin, cyclin dependent kinase. protein/protein complex, transferase; 2.50A {Murid herpesvirus 4} SCOP: a.74.1.1 a.74.1.1 Length = 252

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 20/150 (13%), Positives = 41/150 (27%), Gaps = 18/150 (12%)

Query: 57  EQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTC 116
           + L+    V   A       +    +   +    A   + +A KV  +  I +++L   C
Sbjct: 61  KDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLC 120

Query: 117 QTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIG----H 172
                     A   +       +L  E   L+ L            +  ++  +      
Sbjct: 121 --------GGATTAD------KLLTLEVKSLDTLSWVADRCLSTDLICYILHIMHAPRED 166

Query: 173 EDQLLALAWRVINDSLRTDVCLLYPPYQIA 202
              +  L    I  +L      +  P  I 
Sbjct: 167 YLNIYNLCRPKIFCALCDGRSAMKRPVLIT 196

>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A Length = 271

 Score = 38.5 bits (90), Expect = 9e-04
 Identities = 28/150 (18%), Positives = 54/150 (36%), Gaps = 18/150 (12%)

Query: 57  EQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTC 116
           E+ K  ++V   A  Y  RF +   +K     LL  TC+F+ASK++E   +++       
Sbjct: 69  EEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAE------ 122

Query: 117 QTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIG----H 172
                         +   R   +L+ E  L+  L   L    P+  +   +  +     +
Sbjct: 123 --------KLCIYTDNSIRPEELLQMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEEN 174

Query: 173 EDQLLALAWRVINDSLRTDVCLLYPPYQIA 202
           +  +   A   +         +  PP  +A
Sbjct: 175 KQIIRKHAQTFVALCATDVKFISNPPSMVA 204

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	229
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	100.0
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	100.0
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	100.0
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	100.0
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	100.0
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	100.0
1c9b_A	207	General transcription factor IIB; protein-DNA comp	100.0
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	99.98
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	99.97
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	99.97
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	99.97
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	99.97
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	99.97
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	99.96
1f5q_B	252	Gamma herpesvirus cyclin; herpesviral cyclin, cycl	99.96
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	99.96
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	99.93
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	99.87
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	98.43
1c9b_A	207	General transcription factor IIB; protein-DNA comp	98.0
2pmi_B	293	PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de	97.82
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	96.71
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	96.68
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	96.07
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	95.17
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	95.03
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	94.22
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	94.17
3m03_A	95	ORC6, origin recognition complex subunit 6; helix	94.02
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	93.55
3h4c_A	260	Transcription factor TFIIB-like; cyclin, transcrip	92.89
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	92.81
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	91.71
4ell_A	411	Retinoblastoma-associated protein; cyclin fold, tu	90.13
2r7g_A	347	PP110, retinoblastoma-associated protein, P105-RB,	89.87
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	89.37
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	89.05
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	88.78
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	88.7
2qdj_A	304	Retinoblastoma-associated protein; cyclin fold, cy	88.35
4elj_A	656	Retinoblastoma-associated protein; cyclin fold, tu	86.64
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	81.79

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

Probab=100.00  E-value=1.1e-50  Score=340.65  Aligned_cols=212  Identities=64%  Similarity=1.128  Sum_probs=198.6

Q ss_pred             cccccchh-hhccCCcccHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccc
Q psy1168           5 STQGRFYP-EWIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLK   83 (229)
Q Consensus         5 ~~~~~~~~-~~~~~w~f~~~~l~~~~~~~~~~~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~   83 (229)
                      +|++|||. +|.++|+||++||++.|+.+.+++++++|+++|..+++||.++|.+|+||+.|.++|++||||||++++++
T Consensus         2 ~m~~~~w~Ss~~~~Wlft~~el~~~~~~~~~~l~~~~e~~~R~~~~~~I~~v~~~l~L~~~t~~tA~~~~~RF~~~~s~~   81 (285)
T 3rgf_B            2 AMAGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLK   81 (285)
T ss_dssp             TTTTCGGGSHHHHHHSCCHHHHHHHHTTGGGTSCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHSCTT
T ss_pred             CccchhhcccccCCcCcCHHHHHHhhhcccccCCHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhCCch
Confidence            79999999 99999999999999999888999999999999999999999999999999999999999999999999999


Q ss_pred             cCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHH
Q psy1168          84 CIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPL  163 (229)
Q Consensus        84 ~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l  163 (229)
                      ++++++|++||||||||+||.+++++++++.++..+.+++.....++++...+++|+.+|+.||++||||+.+++||+|+
T Consensus        82 ~~~~~lva~acLfLA~K~EE~~~~~~~di~~~~~~~~k~~~~~~~~~~~~~~~~~Il~~E~~iL~~L~f~l~v~~P~~fL  161 (285)
T 3rgf_B           82 SIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPL  161 (285)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHCTTTCCSCCCCCHHHHHHHHHHHHHHTTTCCCCCCSHHHH
T ss_pred             hcCHHHHHHHHHHHHHhhhccccccHHHHHHHHHHHHcccccccCchhhHHHHHHHHHHHHHHHHHcCCCeEeCChHHHH
Confidence            99999999999999999999987678999988776666544444456677789999999999999999999999999999


Q ss_pred             HHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         164 LQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       164 ~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      .+|++.++.++++.+.||.++++++.++.|+.|+|+.||+||||+|+.+++.+
T Consensus       162 ~~~~~~l~~~~~~~~~A~~~l~~sl~t~~~l~~~Ps~IAaAaiylA~~~~~~~  214 (285)
T 3rgf_B          162 LQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKD  214 (285)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSSHHHHSCHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHHHccChhhccCHHHHHHHHHHHHHHHcCCC
Confidence            99999999999999999999999999999999999999999999999988753

>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=100.00  E-value=1.2e-42  Score=287.92  Aligned_cols=200  Identities=22%  Similarity=0.298  Sum_probs=179.4

Q ss_pred             ccCCcccHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHH
Q psy1168          15 IQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTC   94 (229)
Q Consensus        15 ~~~w~f~~~~l~~~~~~~~~~~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~ac   94 (229)
                      .++|+||++||+++|+. .+|+++++|.++|..+++||.++|.++++|+.|.++|++||||||+++++++++++++++||
T Consensus         2 ~~~w~~t~e~l~~~ps~-~~g~~~~~e~~~R~~~~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~qlv~~ac   80 (257)
T 2ivx_A            2 SSRWFFTREQLENTPSR-RCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTA   80 (257)
T ss_dssp             CGGGSCCHHHHHSCHHH-HTTCCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHH
T ss_pred             CCCeeecHHHHHhChHh-hcCCCHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhCChhhhCHHHHHHHH
Confidence            47999999999988764 57899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhcccccccchHHHHHHHHHHHHhhhc--ccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCc
Q psy1168          95 VFLASKVEEFGVISSSRLLSTCQTVVKNKLN--YAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGH  172 (229)
Q Consensus        95 l~LA~K~ee~~~~~l~~li~~~~~~~~~~~~--~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~  172 (229)
                      ||||||+||.|+ ++++++.++....++..+  ...++.|...+++|+.+|+.||++||||+.+++|+.|+.+|++.++.
T Consensus        81 L~lA~K~EE~p~-~l~d~~~~~~~~~~~~~~~~~~~~~~y~~~~~~I~~~E~~iL~~L~f~l~~~~P~~fl~~~~~~l~~  159 (257)
T 2ivx_A           81 LFLAAKVEEQAR-KLEHVIKVAHACLHPLEPLLDTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRA  159 (257)
T ss_dssp             HHHHHHHTTCCC-CHHHHHHHHHHHHCTTSCCCCTTSHHHHHHHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHHHTTC
T ss_pred             HHHHhccccCCc-CHHHHHHHHHHHhccCCCCCCcchHHHHHHHHHHHHHHHHHHHHcccceEeeCcHHHHHHHHHHhCC
Confidence            999999999975 999998876654332211  11234566679999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHHHHh-CCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         173 EDQLLALAWRVINDSL-RTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       173 ~~~i~~~a~~~~~~~~-~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      ++++.+.|+.++++++ .++.++.|+|+.||+||+|+|+..+|..
T Consensus       160 ~~~~~~~A~~~~~~sl~~~~~~l~~~Ps~IAaAai~lA~~~~~~~  204 (257)
T 2ivx_A          160 SKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWE  204 (257)
T ss_dssp             CHHHHHHHHHHHHHHHHHCCGGGTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             CcHHHHHHHHHHHhhhhcccHHHcCCHHHHHHHHHHHHHHHhCCC
Confidence            9999999999999998 5889999999999999999999988753

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

Probab=100.00  E-value=1.1e-42  Score=284.48  Aligned_cols=188  Identities=28%  Similarity=0.408  Sum_probs=170.1

Q ss_pred             chh-hhccCCcccHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhcccccc-CCc
Q psy1168          10 FYP-EWIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKC-IDP   87 (229)
Q Consensus        10 ~~~-~~~~~w~f~~~~l~~~~~~~~~~~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~-~~~   87 (229)
                      ||+ +|.++|+||++|+++.|+..    ..  +   |..+++||.++|.+|+||+.|.++|++||||||+++++++ +++
T Consensus         1 ~~~Ss~~~~w~ft~~~l~~~~~~~----~~--~---R~~~~~~i~~v~~~l~L~~~t~~~A~~~~~Rf~~~~~~~~~~~~   71 (235)
T 1zp2_A            1 YWASSQLTQLFLSTDLESLEPTCL----SK--D---TIYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKGFSL   71 (235)
T ss_dssp             -CCCGGGTGGGSCSSCTTSSCCCS----CH--H---HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCSCCCCCH
T ss_pred             CCccCCCCCCccCHHHHHHCCcch----hH--H---HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccccCH
Confidence            789 99999999999999887632    11  1   7899999999999999999999999999999999999999 999


Q ss_pred             hhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHH
Q psy1168          88 LLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLV  167 (229)
Q Consensus        88 ~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~  167 (229)
                      +++++||||||||+||.++ ++++++.++.+..        ++.+...+++|+.+|+.||++||||+.+++|++|+.+|+
T Consensus        72 ~lv~~acL~lA~K~Ee~~~-~l~d~~~~~~~~~--------~~~~~~~~~~I~~~E~~iL~~L~f~l~~~~P~~~l~~~~  142 (235)
T 1zp2_A           72 EALVATCIYLSCKVEECPV-HIRTICNEANDLW--------SLKVKLSRSNISEIEFEIISVLDAFLIVHHPYTSLEQAF  142 (235)
T ss_dssp             HHHHHHHHHHHHHHTTCCC-CHHHHHHHHHTTC--------CCSSCCCHHHHHHHHHHHHHHTTTCCCCCCTHHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCcc-cHHHHHHHHHHHc--------cchhhccHHHHHHHHHHHHHHCCCcEEecChHHHHHHHH
Confidence            9999999999999999986 9999987654321        233455689999999999999999999999999999999


Q ss_pred             HHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCcc
Q psy1168         168 QDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       168 ~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      +.++.++++.+.|+.++++++.++.++.|+|++||+||+|+|+..++.
T Consensus       143 ~~~~~~~~~~~~A~~~l~~s~~~~~~l~~~Ps~IAaAai~lA~~~~~~  190 (235)
T 1zp2_A          143 HDGIINQKQLEFAWSIVNDSYASSLCLMAHPHQLAYAALLISCCNDEN  190 (235)
T ss_dssp             HTTSSCHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHTSCTT
T ss_pred             HHcCCCHHHHHHHHHHHHHHHcCCchhccCHHHHHHHHHHHHHHhcCC
Confidence            999999999999999999999999999999999999999999998875

>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=100.00  E-value=5.9e-42  Score=291.91  Aligned_cols=197  Identities=30%  Similarity=0.461  Sum_probs=166.4

Q ss_pred             chh-hhccCCcccH-HHHHHhhh------------------cCCCCCCHHHHHHHHHHHHHHHHHHHHhcC--CCHHHHH
Q psy1168          10 FYP-EWIQQWVLDR-QDLIRERK------------------HDLSILSDEEYQKIFIFFANFIQILGEQLK--LRQQVIA   67 (229)
Q Consensus        10 ~~~-~~~~~w~f~~-~~l~~~~~------------------~~~~~~s~~~e~~~r~~~~~~I~~~~~~l~--l~~~~~~   67 (229)
                      ||+ +|.++|+||+ ++|++.|.                  ...+++++++|+.+|.++++||.++|.+++  ||+.|.+
T Consensus         2 y~~Stq~~~W~f~~~~~L~~~r~~~n~~~~~~~~~~~~~~~~~~~~lt~eeE~~lr~~~~~~I~ev~~~l~~~Lp~~t~~   81 (323)
T 1jkw_A            2 YHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVG   81 (323)
T ss_dssp             ---------CCCSCHHHHHHHHHHHHHHHHHHHHHTSSSCTTCTTSCCHHHHHHHHHHHHHHHHHHHHHCTTTCCHHHHH
T ss_pred             CCCCccccccccCCHHHHHHHHHHHHHHHHHHHhhccCCCccccCCCCHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH
Confidence            789 9999999995 78886642                  357799999999999999999999999999  9999999


Q ss_pred             HHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhcccccccchhhHHHHHHHHHHHH
Q psy1168          68 TATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLL  147 (229)
Q Consensus        68 ~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL  147 (229)
                      +|++||||||+++++.++++++|++||||||||+||.++ ++++++.....         .+......+++|+.+|+.||
T Consensus        82 tA~~~~~RF~~~~s~~~~~~~lva~acLfLA~K~EE~~~-~l~d~v~~~~~---------~p~~~~~~~~~Il~~E~~iL  151 (323)
T 1jkw_A           82 TACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNV-SSPQFVGNLRE---------SPLGQEKALEQILEYELLLI  151 (323)
T ss_dssp             HHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHTTCCC-CHHHHGGGSSS---------CHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhCChhhcCHHHHHHHHHHHHHhhhcCCC-CHHHHHHHhcc---------ChhhhHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999986 99998653210         00112345899999999999


Q ss_pred             HHcCcceeecCChHHHHHHHHHh-------CccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         148 ENLDCCLIVYQPYRPLLQLVQDI-------GHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       148 ~~L~fdl~~~~P~~~l~~~~~~l-------~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      ++|+|++.+++||+|+.+|+..+       +....+.+.||.++++++.++.|+.|+|++||+||||+|+..+|.+
T Consensus       152 ~~L~f~l~v~~P~~~L~~~l~~l~~~~~~~~~~~~l~~~A~~~l~~sl~t~~~l~~~Ps~IAaAai~lA~~~~~~~  227 (323)
T 1jkw_A          152 QQLNFHLIVHNPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGIT  227 (323)
T ss_dssp             HHTTTCCCCCCSHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHTTSTHHHHSCHHHHHHHHHHHHHHHHSCC
T ss_pred             HHCCCcEEcCChHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHhccHHHcCCHHHHHHHHHHHHHHHcCCC
Confidence            99999999999999999999876       2346789999999999999999999999999999999999987764

>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=100.00  E-value=3.1e-41  Score=279.56  Aligned_cols=199  Identities=26%  Similarity=0.381  Sum_probs=175.3

Q ss_pred             hhccCCcccHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHH
Q psy1168          13 EWIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAP   92 (229)
Q Consensus        13 ~~~~~w~f~~~~l~~~~~~~~~~~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~   92 (229)
                      .+.++|+||++|++++|+. .++++++.|.++|..+++||.++|.++++++.|.++|+.|||||+.++++++++++++++
T Consensus        10 ~~~~~w~~~~~el~~~ps~-~~~~~~~~e~~~R~~~~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~qlv~~   88 (258)
T 2i53_A           10 HTKPCWYWDKKDLAHTPSQ-LEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGA   88 (258)
T ss_dssp             SCSSSCCCCGGGGGGCHHH-HTTCCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHH
T ss_pred             hhccCCccCHHHHHhCchh-hcCCCHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCChhhcCHHHHHH
Confidence            5678899999999887653 568899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcccccccchHHHHHHHHHHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCc
Q psy1168          93 TCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGH  172 (229)
Q Consensus        93 acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~  172 (229)
                      ||||||||+||.++ ++++++.++........   +.......+++|+.+|+.||++|||++.+++|++|+.+|++.++.
T Consensus        89 acL~lA~K~eE~~~-~l~d~~~~~~~~~~~~~---~~~~~~~~~~~i~~~E~~iL~~L~f~l~~~~P~~fl~~~~~~l~~  164 (258)
T 2i53_A           89 CCLFLAGKVEETPK-KCKDIIKTARSLLNDVQ---FGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKG  164 (258)
T ss_dssp             HHHHHHHHHTTCCC-CHHHHHHHHHHHSCHHH---HGGGCSCHHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHHTBCS
T ss_pred             HHHHHHHccccccc-cHHHHHHHHHHHhchhh---hhhhhhhHHHHHHHHHHHHHHHCCCceeccChHHHHHHHHHHhCC
Confidence            99999999999985 99999887654322100   000011247899999999999999999999999999999999987


Q ss_pred             cH----HHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         173 ED----QLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       173 ~~----~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      +.    ++.+.|+.++++++.++.++.|+|+.||+|||++|+..+|.+
T Consensus       165 ~~~~~~~~~~~A~~l~~~s~~~~~~l~~~Ps~IAaAai~lA~~~~~~~  212 (258)
T 2i53_A          165 DKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFE  212 (258)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             CcchHHHHHHHHHHHHHHHHcCCchhccChHHHHHHHHHHHHHHhCCC
Confidence            65    799999999999999999999999999999999999988763

>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=100.00  E-value=1.4e-41  Score=292.93  Aligned_cols=201  Identities=21%  Similarity=0.260  Sum_probs=178.8

Q ss_pred             hhccCCcccHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHH
Q psy1168          13 EWIQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAP   92 (229)
Q Consensus        13 ~~~~~w~f~~~~l~~~~~~~~~~~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~   92 (229)
                      .+.++|+||++||+++|+. .+++++++|..+|..+++||.+++.+|+|++.|+++|++||||||++++++++++++|++
T Consensus         7 ~~~~~wlft~eeL~~~pS~-~dgi~~~~E~~~R~~~v~wI~ev~~~l~L~~~t~~tAv~~~dRFl~~~sv~~~~~qlva~   85 (358)
T 2pk2_A            7 NNNKRWYFTREQLENSPSR-RFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFPGNSVAP   85 (358)
T ss_dssp             -CCSSSSCCSHHHHTCTTH-HHHCCHHHHHHHHHHHHHHHHHHHTTTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHH
T ss_pred             CCCCCceeCHHHHHhChhh-hcCCChHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcccccHHHHHH
Confidence            5679999999999988764 467899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcccccccchHHHHHHHHHHHHhhhc--ccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHh
Q psy1168          93 TCVFLASKVEEFGVISSSRLLSTCQTVVKNKLN--YAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDI  170 (229)
Q Consensus        93 acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~--~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l  170 (229)
                      ||||||||+||.++ ++++++.++....++..+  ...++.|+..+++|+.+|+.||++|+||+.+++|+.|+.+|++.+
T Consensus        86 acLfLA~K~EE~p~-~l~d~v~v~~~~~~~~~~~~~~~~~~y~~~~~~Il~~E~~IL~~L~f~L~v~~P~~fL~~~~~~l  164 (358)
T 2pk2_A           86 AALFLAAKVEEQPK-KLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLV  164 (358)
T ss_dssp             HHHHHHHHHTTCCC-CHHHHHTTHHHHHCSSSCCCCTTSHHHHGGGTGGGTHHHHHHHHTTTCCCCCCTTHHHHHHHHHT
T ss_pred             HHHHHHHhhccCCC-CHHHHHHHHHHHhccccccccccchhhhHHHHHHHHHHHHHHHHcCCceeCCCHHHHHHHHHHHc
Confidence            99999999999985 999998776544332111  112345666789999999999999999999999999999999999


Q ss_pred             CccHHHHHHHHHHHHHHh-CCcccccccHHHHHHHHHHHhcccCcc
Q psy1168         171 GHEDQLLALAWRVINDSL-RTDVCLLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       171 ~~~~~i~~~a~~~~~~~~-~~~~~l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      +.++++.+.||.++++++ .+++++.|+|+.||+||||+|+..++.
T Consensus       165 ~~~~~l~~~A~~ll~~sl~~t~l~l~y~Ps~IAaAAI~lA~~~l~~  210 (358)
T 2pk2_A          165 RASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNW  210 (358)
T ss_dssp             TCCHHHHHHHHHHHHHHTTTSCGGGTSCHHHHTTTTTTTHHHHTTC
T ss_pred             CCCHHHHHHHHHHHHHHHhcCcchhccCHHHHHHHHHHHHHHHhCC
Confidence            999999999999999998 588899999999999999999998875

>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=100.00  E-value=5.9e-32  Score=216.91  Aligned_cols=155  Identities=14%  Similarity=0.211  Sum_probs=145.2

Q ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhh
Q psy1168          45 FIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKL  124 (229)
Q Consensus        45 r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~  124 (229)
                      ...+.++|.++|.+|+||+.|.++|+.|||||+.++++++++++.+++||+|+|||.||.|+ ++++++.++.       
T Consensus         5 l~~a~~~I~~~~~~L~L~~~v~~~A~~~~~r~~~~~~~~~~~~~~v~aaclylAcK~ee~p~-~l~di~~~~~-------   76 (207)
T 1c9b_A            5 MMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPR-TFKEICAVSR-------   76 (207)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTCSTTSCHHHHHHHHHHHHHHHTTCCC-CHHHHHHTSS-------
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcCCCCHHHHHHHHHHHHHHhcCCCC-CHHHHHHHHC-------
Confidence            34789999999999999999999999999999999999999999999999999999999986 9999876532       


Q ss_pred             cccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHH
Q psy1168         125 NYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIG  204 (229)
Q Consensus       125 ~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~a  204 (229)
                               ..++++..+|+.|++.|+|++.+++|+.|+.+|++.+++++++.+.|+.+++++..++++++|+|+.||+|
T Consensus        77 ---------~~~~~i~~~~~~ll~~L~~~l~~~~p~~~l~r~~~~l~l~~~~~~~A~~i~~~~~~~~l~~g~~P~~IAaA  147 (207)
T 1c9b_A           77 ---------ISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAA  147 (207)
T ss_dssp             ---------SCHHHHHHHHHHHHHHTTCCCCCCCTHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHH
T ss_pred             ---------CCHHHHHHHHHHHHHHHCCCcCcCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCccCCCChHHHHHH
Confidence                     23678999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcccCccc
Q psy1168         205 ECSFSFTPHVIA  216 (229)
Q Consensus       205 ai~~A~~~~~~~  216 (229)
                      |+|+|+..+|..
T Consensus       148 aiylA~~~~~~~  159 (207)
T 1c9b_A          148 AIYMASQASAEK  159 (207)
T ss_dssp             HHHHHHHTSSSC
T ss_pred             HHHHHHHHHCCC
Confidence            999999998765

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

Probab=99.98  E-value=5.4e-32  Score=225.28  Aligned_cols=161  Identities=19%  Similarity=0.178  Sum_probs=148.4

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHH
Q psy1168          42 QKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVK  121 (229)
Q Consensus        42 ~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~  121 (229)
                      .++|..+++||.+++.+++++..|.++|+.|+|||++++++.+.+.+++++||+|||||.||...+++++++..+.    
T Consensus        35 ~~~R~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfl~~~~v~~~~lqlv~~acL~iA~K~eE~~~p~~~d~~~~~~----  110 (269)
T 2b9r_A           35 GNMRAILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQNNSVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTD----  110 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHTTSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTC----
T ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcCCCCcHHHhhHHHHHHHHHHHhcccccCccHHHHHHHhc----
Confidence            4688999999999999999999999999999999999999999999999999999999999985458999876531    


Q ss_pred             hhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHH
Q psy1168         122 NKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQI  201 (229)
Q Consensus       122 ~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~I  201 (229)
                                ....+++|++||+.||++|+|++.+++|++|+.+|++.++.+.++...|+.++++++.++.++.|+|+.|
T Consensus       111 ----------~~~~~~eI~~mE~~IL~~L~f~l~~~tp~~fl~~~~~~~~~~~~~~~~a~~l~e~sl~~~~~~~~~Ps~i  180 (269)
T 2b9r_A          111 ----------NTYTKHQIRQMEMKILRALNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFPPSQI  180 (269)
T ss_dssp             ----------SSSCHHHHHHHHHHHHHHTTSCCCCCCHHHHHHHHHHSSCCCHHHHHHHHHHHHHGGGCGGGSSSCTTHH
T ss_pred             ----------CCCCHHHHHHHHHHHHHHcCCccCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhhhcCCHHHH
Confidence                      1234899999999999999999999999999999999999889999999999999999999999999999


Q ss_pred             HHHHHHHhcccCccc
Q psy1168         202 AIGECSFSFTPHVIA  216 (229)
Q Consensus       202 A~aai~~A~~~~~~~  216 (229)
                      |+||+++|...++..
T Consensus       181 AaAai~lA~~~l~~~  195 (269)
T 2b9r_A          181 AAGAFSLALKILDNG  195 (269)
T ss_dssp             HHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHhCCC
Confidence            999999999988765

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

Probab=99.97  E-value=2.5e-32  Score=230.94  Aligned_cols=168  Identities=17%  Similarity=0.191  Sum_probs=148.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHH
Q psy1168          35 ILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLS  114 (229)
Q Consensus        35 ~~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~  114 (229)
                      +.+++-...+|..+++||.+++..++++..|.++|+.|+|||++++++.+.+++++++||+|||||+||...+++++++.
T Consensus        61 ~~q~~i~~~~R~~lvdwl~ev~~~~~l~~~t~~lAv~~lDRfls~~~v~~~~lqLv~~tcL~lAsK~eE~~p~~~~~l~~  140 (306)
T 3g33_B           61 CVQREIKPHMRKMLAYWMLEVCEEQRCEEEVFPLAMNYLDRYLSCVPTRKAQLQLLGAVCMLLASKLRETTPLTIEKLCI  140 (306)
T ss_dssp             TSTTTCCHHHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHCCCCGGGHHHHHHHHHHHHHHHHCSSCCCTTHHHH
T ss_pred             hcCccCCHHHHHHHHHHHHHHHHHhCCcHhHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHhccCCCCCHHHHHH
Confidence            34444455799999999999999999999999999999999999999999999999999999999999986568999876


Q ss_pred             HHHHHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCcc----HHHHHHHHHHHHHHhCC
Q psy1168         115 TCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHE----DQLLALAWRVINDSLRT  190 (229)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~----~~i~~~a~~~~~~~~~~  190 (229)
                      .+.              ....+++|++||+.||++|+|++.+++|++|+.+|++.++..    ..+.+.|+.++++++.+
T Consensus       141 ~~~--------------~~~~~~~i~~mE~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~lsl~d  206 (306)
T 3g33_B          141 YTD--------------HAVSPRQLRDWEVLVLGKLKWDLAAVIAHDFLAFILHRLSLPRDRQALVKKHAQTFLALCATD  206 (306)
T ss_dssp             HTT--------------TSSCHHHHHHHHHHHHHHTTTCCCCCCGGGGHHHHHHTSSCCTTTHHHHHHHHHHHHHHHHHC
T ss_pred             Hhc--------------cCccHHHHHHHHHHHHHHcCCccCCCCHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhh
Confidence            532              123489999999999999999999999999999999998764    23678899999999999


Q ss_pred             cccccccHHHHHHHHHHHhcccCccc
Q psy1168         191 DVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       191 ~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      +.++.|+|+.||+|||++|...++..
T Consensus       207 ~~~l~~~PS~IAaAai~lA~~~l~~~  232 (306)
T 3g33_B          207 YTFAMYPPSMIATGSIGAAVQGLGAC  232 (306)
T ss_dssp             GGGTTSCHHHHHHHHHHHHHHTCC--
T ss_pred             hhhccCCHHHHHHHHHHHHHHHhcCC
Confidence            99999999999999999999988743

>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=99.97  E-value=3.6e-31  Score=218.98  Aligned_cols=161  Identities=16%  Similarity=0.167  Sum_probs=145.0

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHH
Q psy1168          42 QKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVK  121 (229)
Q Consensus        42 ~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~  121 (229)
                      .++|..+++||.+++..++++.+|.++|+.|+|||++++++.+.+.+++++||+|||||+||...+++++++..+.    
T Consensus        48 ~~~R~~lvdwl~ev~~~~~l~~etl~lAv~~~DRfls~~~v~~~~lqLv~~acl~iA~K~eE~~~p~~~d~~~~~~----  123 (257)
T 1g3n_C           48 SHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAA----  123 (257)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTT----
T ss_pred             HHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHccccCCCHHHHHHHHC----
Confidence            4689999999999999999999999999999999999999999999999999999999999974458999876532    


Q ss_pred             hhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccH----HHHHHHHHHHHHHhCCccccccc
Q psy1168         122 NKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHED----QLLALAWRVINDSLRTDVCLLYP  197 (229)
Q Consensus       122 ~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~----~i~~~a~~~~~~~~~~~~~l~~~  197 (229)
                                ....+++|++||+.||++|+|++.+++|++|+.+|++.++.+.    .+.+.|+.+++.++.+..++.|+
T Consensus       124 ----------~~~~~~~i~~mE~~iL~~L~~~l~~~tp~~fl~~~~~~~~~~~~~~~~~~~~a~~~le~~l~d~~~~~~~  193 (257)
T 1g3n_C          124 ----------DSFSRQELIDQEKELLEKLAWRTEAVLATDVTSFLLLKLVGGSQHLDFWHHEVNTLITKALVDPLTGSLP  193 (257)
T ss_dssp             ----------TCSCHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHHHHSCSSTTHHHHHHHHHHHHHHHHTSTTGGGSC
T ss_pred             ----------CCCCHHHHHHHHHHHHHHCCCcCCCCCHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhCcchhCcC
Confidence                      1234899999999999999999999999999999999998653    34678999999999999999999


Q ss_pred             HHHHHHHHHHHhcccCccc
Q psy1168         198 PYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       198 P~~IA~aai~~A~~~~~~~  216 (229)
                      |+.||+||+++|...++.+
T Consensus       194 PS~iAaAai~lA~~~l~~~  212 (257)
T 1g3n_C          194 ASIISAAGCALLVPANVIP  212 (257)
T ss_dssp             HHHHHHHHHHHHCCGGGSC
T ss_pred             HHHHHHHHHHHHHHHhCCC
Confidence            9999999999999988753

>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=99.97  E-value=9.1e-32  Score=222.93  Aligned_cols=160  Identities=21%  Similarity=0.199  Sum_probs=145.1

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHH
Q psy1168          42 QKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVK  121 (229)
Q Consensus        42 ~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~  121 (229)
                      .++|..+++||.+++..++++..|.++|+.|+|||++++++.+.+.+++++||+|||||.||...+++++++..+.    
T Consensus        36 ~~~R~~lvdwl~~v~~~~~l~~~tl~lAv~~lDRfls~~~v~~~~lqlv~~acl~iA~K~ee~~~~~~~d~~~i~~----  111 (260)
T 2cch_B           36 NSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITD----  111 (260)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTT----
T ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccCCCCHHHHhHHHHHHHHHHHHhcccCCCCHHHHHHHHc----
Confidence            4689999999999999999999999999999999999999999999999999999999999994359999976532    


Q ss_pred             hhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccH-HHHHHHHHHHHHHhCCcc-cccccHH
Q psy1168         122 NKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHED-QLLALAWRVINDSLRTDV-CLLYPPY  199 (229)
Q Consensus       122 ~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~-~i~~~a~~~~~~~~~~~~-~l~~~P~  199 (229)
                                ....+++|++||+.||++|+|++.+++|++|+.+|++.++.+. .+.+.|+.++++++.+.. ++.|+|+
T Consensus       112 ----------~~~~~~~i~~mE~~iL~~L~~~l~~~tp~~fl~~~~~~l~~~~~~~~~~a~~l~e~sl~~~~~~~~~~Ps  181 (260)
T 2cch_B          112 ----------DTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPS  181 (260)
T ss_dssp             ----------SSSCHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHH
T ss_pred             ----------CCcCHHHHHHHHHHHHHHcCCccCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHhHHHHhCCCHH
Confidence                      1234899999999999999999999999999999999998765 899999999999987776 9999999


Q ss_pred             HHHHHHHHHhcccCcc
Q psy1168         200 QIAIGECSFSFTPHVI  215 (229)
Q Consensus       200 ~IA~aai~~A~~~~~~  215 (229)
                      .||+||+++|+..++.
T Consensus       182 ~iAaAai~lA~~~~~~  197 (260)
T 2cch_B          182 VIAGAAFHLALYTVTG  197 (260)
T ss_dssp             HHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHhCC
Confidence            9999999999987764

>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=99.97  E-value=2.9e-31  Score=219.22  Aligned_cols=163  Identities=16%  Similarity=0.174  Sum_probs=144.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHH
Q psy1168          38 DEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQ  117 (229)
Q Consensus        38 ~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~  117 (229)
                      ++-..++|...++||.+++..++++..|.++|+.|+|||++++++.+.+.+++++||+|||||+||...+++++++..+.
T Consensus        45 ~~i~~~~R~~lvdwl~~v~~~~~l~~etl~lAv~~~DRfls~~~v~~~~lqLv~~acl~iA~K~eE~~~p~~~d~~~~~~  124 (254)
T 2f2c_A           45 TEVTVDNRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSC  124 (254)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSCCCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHSTTC-
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHHccCCcCHHHccHHHHHHHHHHHHhcccCCCCHHHHHHHhC
Confidence            33345689999999999999999999999999999999999999999999999999999999999964458999865432


Q ss_pred             HHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccHH----HHHHHHHHHHHHhCCccc
Q psy1168         118 TVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQ----LLALAWRVINDSLRTDVC  193 (229)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~~----i~~~a~~~~~~~~~~~~~  193 (229)
                      +              ...+++|++||+.||++|+|++.+++|++|+.+|++.++.+.+    +.+.|+.+++.++.+..+
T Consensus       125 ~--------------~~~~~~i~~mE~~IL~~L~~~l~~~tp~~fl~~~~~~~~~~~~~~~~~~~~a~~ll~~~l~d~~~  190 (254)
T 2f2c_A          125 D--------------CFTNLELINQEKDILEALKWDTEAVLATDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNI  190 (254)
T ss_dssp             ----------------CCHHHHHHHHHHHHHHTTTCCCCCCGGGSHHHHHHHTTCCGGGHHHHHHHHHHHHHHHTTSGGG
T ss_pred             C--------------CCCHHHHHHHHHHHHHHCCCcCCCCCHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHcCcch
Confidence            1              2348999999999999999999999999999999999987543    467899999999999999


Q ss_pred             ccccHHHHHHHHHHHhcccCc
Q psy1168         194 LLYPPYQIAIGECSFSFTPHV  214 (229)
Q Consensus       194 l~~~P~~IA~aai~~A~~~~~  214 (229)
                      +.|+|+.||+||+++|...++
T Consensus       191 ~~~~PS~iAaAai~la~~~~~  211 (254)
T 2f2c_A          191 ALLSPGLICAGGLLTTIETDN  211 (254)
T ss_dssp             TTSCHHHHHHHHHHHHHHTTC
T ss_pred             hccCHHHHHHHHHHHHHHhcC
Confidence            999999999999999998753

>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=99.97  E-value=1.9e-30  Score=216.22  Aligned_cols=160  Identities=19%  Similarity=0.270  Sum_probs=142.7

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHH
Q psy1168          42 QKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVK  121 (229)
Q Consensus        42 ~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~  121 (229)
                      .++|..+++||.+++.+++++..|.++|+.|+|||++++++.+.+.+++++||+|||||+||...+++++++..+.    
T Consensus        54 ~~~R~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~v~~~~lqlv~~acL~iAsK~EE~~p~~~~~~~~~~~----  129 (271)
T 2w96_A           54 PSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTD----  129 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHTTSCCCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTT----
T ss_pred             HHHHHHHHHHHHHHHHHHCCchhHHHHHHHHHHHhCCcCCcCHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHhc----
Confidence            4588999999999999999999999999999999999999999999999999999999999983248999876421    


Q ss_pred             hhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccHH----HHHHHHHHHHHHhCCccccccc
Q psy1168         122 NKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHEDQ----LLALAWRVINDSLRTDVCLLYP  197 (229)
Q Consensus       122 ~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~~----i~~~a~~~~~~~~~~~~~l~~~  197 (229)
                                ....+++|++||+.||++|+|++.+++|++|+.+|++.++.+.+    +.+.|+.+++++..+..++.|+
T Consensus       130 ----------~~~~~~eI~~mE~~IL~~L~~~l~~~tp~~fl~~~~~~l~~~~~~~~~~~~~a~~~l~~~~~d~~~~~~~  199 (271)
T 2w96_A          130 ----------NSIRPEELLQMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNP  199 (271)
T ss_dssp             ----------TSSCHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHTSTHHHHSC
T ss_pred             ----------CCCCHHHHHHHHHHHHHHCCCccCCCCHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHHHhhhhhhccC
Confidence                      12358999999999999999999999999999999999987644    3467999999998888899999


Q ss_pred             HHHHHHHHHHHhcccCcc
Q psy1168         198 PYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       198 P~~IA~aai~~A~~~~~~  215 (229)
                      |+.||+|||++|...++.
T Consensus       200 PS~iAaAai~lA~~~l~~  217 (271)
T 2w96_A          200 PSMVAAGSVVAAVQGLNL  217 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCc
Confidence            999999999999987764

>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=99.96  E-value=8.4e-29  Score=197.48  Aligned_cols=158  Identities=11%  Similarity=0.151  Sum_probs=145.4

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHH
Q psy1168          41 YQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVV  120 (229)
Q Consensus        41 e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~  120 (229)
                      |+.+ ..++++|.++|.+|+||+.+..+|..||+||+..+.++++++..+++||+|+|||.++.|+ +++|+..++.   
T Consensus         6 er~l-~~a~~~I~~~~~~L~L~~~v~~~A~~l~~~~~~~~~~~gr~~~~vaaAclylAcr~~~~p~-~l~di~~~~~---   80 (200)
T 1ais_B            6 ERNL-AFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPR-TLDEIADIAR---   80 (200)
T ss_dssp             --CH-HHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTTTTTTCCHHHHHHHHHHHHHHHHTCCC-CHHHHHHHTT---
T ss_pred             HHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHHHHcCCCC-CHHHHHHHHC---
Confidence            4444 4799999999999999999999999999999999999999999999999999999999986 9999977532   


Q ss_pred             HhhhcccccccchhhHHHHHHHHHHHHHHcCcceee--cCChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccH
Q psy1168         121 KNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIV--YQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPP  198 (229)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~--~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P  198 (229)
                                   ..+.+|..+|+.+++.|||++.+  .+|+.|+.+|++.+++++++.+.|+.+++++..++++.+++|
T Consensus        81 -------------v~~~~i~~~~~~l~~~L~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~~~~gr~P  147 (200)
T 1ais_B           81 -------------VDKKEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSP  147 (200)
T ss_dssp             -------------SCHHHHHHHHHHHHHHTTCCTTTTCCCGGGGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCH
T ss_pred             -------------CCHHHHHHHHHHHHHHhcccCCcCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCcccCCCH
Confidence                         23688999999999999999999  999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcccCccc
Q psy1168         199 YQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       199 ~~IA~aai~~A~~~~~~~  216 (229)
                      +.||+||||+|+..+|..
T Consensus       148 ~~iAaAaly~A~~~~~~~  165 (200)
T 1ais_B          148 AGLVAAALYIASLLEGEK  165 (200)
T ss_dssp             HHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHhCCC
Confidence            999999999999998754

>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=99.96  E-value=1.6e-28  Score=201.99  Aligned_cols=160  Identities=12%  Similarity=0.133  Sum_probs=141.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHH
Q psy1168          37 SDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTC  116 (229)
Q Consensus        37 s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~  116 (229)
                      +++-..++|...++||.+++..++++++|.++|+.|+|||++++++...+.+++++||+|||+|+||...+++++++..+
T Consensus        41 q~~i~~~~R~~lvdWl~ev~~~~~l~~eT~~lAv~~lDRfLs~~~v~~~~lqLvg~tcl~iAsK~eE~~p~~~~~l~~~~  120 (252)
T 1f5q_B           41 DQHFTSQYRKVLTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLC  120 (252)
T ss_dssp             HHHHHCSHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHh
Confidence            34445678999999999999999999999999999999999999999999999999999999999998656889987643


Q ss_pred             HHHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccH----HHHHHHHHHHHHHhCCcc
Q psy1168         117 QTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHED----QLLALAWRVINDSLRTDV  192 (229)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~----~i~~~a~~~~~~~~~~~~  192 (229)
                      .              ....+++|++||+.||++|+|++.++||++|+.+|++.++.+.    .+...|..+++.++.+.-
T Consensus       121 ~--------------~~yt~~~i~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~~~~~~~~~~~~~~~a~~~l~~~l~d~~  186 (252)
T 1f5q_B          121 G--------------GATTADKLLTLEVKSLDTLSWVADRCLSTDLICYILHIMHAPREDYLNIYNLCRPKIFCALCDGR  186 (252)
T ss_dssp             C--------------TTCCHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCHH
T ss_pred             C--------------CCCCHHHHHHHHHHHHHHCCCccCCCCHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHHHhchh
Confidence            2              2234899999999999999999999999999999999987653    366788999999988888


Q ss_pred             cccccHHHHHHHHHHHhc
Q psy1168         193 CLLYPPYQIAIGECSFSF  210 (229)
Q Consensus       193 ~l~~~P~~IA~aai~~A~  210 (229)
                      ++.|+||.||+||+..+.
T Consensus       187 ~l~~~PS~iAaaa~~~~l  204 (252)
T 1f5q_B          187 SAMKRPVLITLACMHLTM  204 (252)
T ss_dssp             HHTSCHHHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHh
Confidence            999999999999976664

>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=99.96  E-value=1.6e-28  Score=205.59  Aligned_cols=156  Identities=17%  Similarity=0.166  Sum_probs=136.2

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhc-cccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHH
Q psy1168          42 QKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYAR-NSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVV  120 (229)
Q Consensus        42 ~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~-~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~  120 (229)
                      .++|..+++||.+++.+++++..|.++|+.|+|||+++ +++.+.+.+++++||+|||||+||...+++++++..+.   
T Consensus        47 ~~~R~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~~v~~~~lqlv~~acL~iA~K~eE~~~p~l~~~~~i~~---  123 (283)
T 1w98_B           47 PKMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTD---  123 (283)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTT---
T ss_pred             HHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcccCCCcHHHHHHHHc---
Confidence            35889999999999999999999999999999999998 68999999999999999999999985458999876421   


Q ss_pred             HhhhcccccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHhCccH-----------HHHHHHHHHHHHHhC
Q psy1168         121 KNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQDIGHED-----------QLLALAWRVINDSLR  189 (229)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~l~~~~-----------~i~~~a~~~~~~~~~  189 (229)
                                 ....+++|++||+.||++|+|++.+++|++|+.+|++.++.++           .....+..+++.++.
T Consensus       124 -----------~~~~~~ei~~mE~~IL~~L~~~l~~~tp~~fL~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~llelsl~  192 (283)
T 1w98_B          124 -----------GACSGDEILTMELMIMKALKWRLSPLTIVSWLNVYMQVAYLNDLHEVLLPQYPQQIFIQIAELLDLCVL  192 (283)
T ss_dssp             -----------TSSCHHHHHHHHHHHHHHTTTCCCCCCHHHHHHHHHHHHTCCSSCCSSSCCSCHHHHHHHHHHHHHHHH
T ss_pred             -----------CCCCHHHHHHHHHHHHHHcCCcCCCCCHHHHHHHHHHHhccCchhhHHHHhhhHHHHHHHHHHHHHHHh
Confidence                       1234899999999999999999999999999999999876431           233456678899988


Q ss_pred             CcccccccHHHHHHHHHHHhcc
Q psy1168         190 TDVCLLYPPYQIAIGECSFSFT  211 (229)
Q Consensus       190 ~~~~l~~~P~~IA~aai~~A~~  211 (229)
                      +..++.|+|+.||+||+++|+.
T Consensus       193 d~~~l~~~PS~iAaAai~la~~  214 (283)
T 1w98_B          193 DVDCLEFPYGILAASALYHFSS  214 (283)
T ss_dssp             SGGGGGSCHHHHHHHHHHHTSC
T ss_pred             hhhhhcCCHHHHHHHHHHHHHC
Confidence            8889999999999999999975

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

Probab=99.93  E-value=1.4e-26  Score=198.74  Aligned_cols=154  Identities=13%  Similarity=0.032  Sum_probs=80.8

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhc
Q psy1168          46 IFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLN  125 (229)
Q Consensus        46 ~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~  125 (229)
                      ..+...|.++|..|+||..+..+|..||+|++..+.+++++...+++||||+|||.++.|+ +++++..++.        
T Consensus       127 ~~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~~~~~~~~kgr~~~~vaaAclyiAcR~e~~pr-tl~ei~~~~~--------  197 (345)
T 3k7a_M          127 QAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVAR-TFKEIQSLIH--------  197 (345)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHTHHHHHHHHHSSSCSSCCCCSHHHHTTTTTTTSBTTBSSC-CHHHHHHSSS--------
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCcHHHHHHHHHHHHHHHcCCCc-cHHHHHHHHC--------
Confidence            4678999999999999999999999999999999999999999999999999999999996 9999876532        


Q ss_pred             ccccccchhhHHHHHHHHHHHHHHcC------------cceeecCChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCccc
Q psy1168         126 YAYAQEFPYRTNHILECEFYLLENLD------------CCLIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVC  193 (229)
Q Consensus       126 ~~~~~~~~~~~~~i~~~E~~iL~~L~------------fdl~~~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~  193 (229)
                              ..+++|.++++.|++.|+            |++.+.+|++|+.+|++.|+++.++.+.|+.+++++..++++
T Consensus       198 --------v~~keIgr~~~~l~~~L~~~~~~~~~~~~~~~~~~~~p~~~i~Rf~~~L~l~~~v~~~A~~i~~~~~~~~l~  269 (345)
T 3k7a_M          198 --------VKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAEYTAKKCKEIKEI  269 (345)
T ss_dssp             --------CCSHHHHHHHHHHHHHHTCC----------------------------------------------------
T ss_pred             --------CCHHHHHHHHHHHHHHHhhhhccccccccccccCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhchh
Confidence                    236789999999999998            999999999999999999999999999999999999999999


Q ss_pred             ccccHHHHHHHHHHHhcccCccc
Q psy1168         194 LLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       194 l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      .+++|+.||+||||+|+.+++..
T Consensus       270 ~Gr~P~~IAaAaIylAa~~~~~~  292 (345)
T 3k7a_M          270 AGKSPITIAVVSIYLNILLFQIP  292 (345)
T ss_dssp             -----------------------
T ss_pred             cCCCHHHHHHHHHHHHHHHHCCC
Confidence            99999999999999999998754

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

Probab=99.87  E-value=1.7e-22  Score=173.00  Aligned_cols=153  Identities=13%  Similarity=0.032  Sum_probs=79.0

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhc
Q psy1168          46 IFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLN  125 (229)
Q Consensus        46 ~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~  125 (229)
                      ..+...|.++|..|+||..+..+|..+|++++..+.+++.....+++||||+|||.++.|+ +++++..++.        
T Consensus       127 ~~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~a~~~~~~rGrs~e~vaAAclYiACR~~~~pr-tl~eI~~~~~--------  197 (345)
T 4bbr_M          127 QAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVAR-TFKEIQSLIH--------  197 (345)
T ss_dssp             THHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCTTTTTCCHHHHHHHHHHHHHHHTCCBC-CHHHHHHHHT--------
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHhcCCCc-cHHHHHHHhC--------
Confidence            4577899999999999999999999999999999999999999999999999999999997 9999877532        


Q ss_pred             ccccccchhhHHHHHHHHHHHHHHcCcc------------eeecCChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCccc
Q psy1168         126 YAYAQEFPYRTNHILECEFYLLENLDCC------------LIVYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVC  193 (229)
Q Consensus       126 ~~~~~~~~~~~~~i~~~E~~iL~~L~fd------------l~~~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~  193 (229)
                              ..+++|.+..+.|.+.|+..            +...+|.+|+.+|+..|+++.++.+.|+.+++.+....+.
T Consensus       198 --------v~~keigr~~k~l~~~L~l~~~~~~~~~~~~~~~~~~p~~~i~Rf~s~L~l~~~v~~~A~~i~~~~~~~~i~  269 (345)
T 4bbr_M          198 --------VKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAEYTAKKCKEIKEI  269 (345)
T ss_dssp             --------CCTTHHHHHHHHHHHCC-------------------------------------------------------
T ss_pred             --------CCHHHHHHHHHHHHHHhCccccccccccccccCCCCCHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcccc
Confidence                    12577888889999999864            6778999999999999999999999999999999999999


Q ss_pred             ccccHHHHHHHHHHHhcccCcc
Q psy1168         194 LLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       194 l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      .+.+|..||+||||+|+.+++.
T Consensus       270 ~GR~P~~IAAAaIylAa~l~g~  291 (345)
T 4bbr_M          270 AGKSPITIAVVSIYLNILLFQI  291 (345)
T ss_dssp             ----------------------
T ss_pred             cCCChHHHHHHHHHHHHHHhCC
Confidence            9999999999999999998864

>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=98.43  E-value=1.2e-06  Score=69.02  Aligned_cols=89  Identities=16%  Similarity=0.203  Sum_probs=74.1

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhcccc
Q psy1168          49 ANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAY  128 (229)
Q Consensus        49 ~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~  128 (229)
                      ..+|.++|+.|+++..+..+|..++++........+++|..+++||+|+||+..+.++ +.+++..++.           
T Consensus       109 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~~~~gr~P~~iAaAaly~A~~~~~~~~-t~~ei~~~~~-----------  176 (200)
T 1ais_B          109 TDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKR-TQREVAEVAR-----------  176 (200)
T ss_dssp             GGGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHHHHHHHHTTCCC-CHHHHHHHHT-----------
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHhCCCC-CHHHHHHHhC-----------
Confidence            3788999999999999999999999999988888899999999999999999999875 8888866532           


Q ss_pred             cccchhhHHHHHHHHHHHHHHcCcce
Q psy1168         129 AQEFPYRTNHILECEFYLLENLDCCL  154 (229)
Q Consensus       129 ~~~~~~~~~~i~~~E~~iL~~L~fdl  154 (229)
                           ....+|...-..+.+.||.++
T Consensus       177 -----vs~~ti~~~~~~l~~~l~~~~  197 (200)
T 1ais_B          177 -----VTEVTVRNRYKELVEKLKIKV  197 (200)
T ss_dssp             -----CCHHHHHHHHHHHHHHHTCCC
T ss_pred             -----CCHHHHHHHHHHHHHHcCCCC
Confidence                 124566677777778887654

>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=98.00  E-value=3.1e-05  Score=61.09  Aligned_cols=66  Identities=17%  Similarity=0.217  Sum_probs=58.4

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHH
Q psy1168          49 ANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLST  115 (229)
Q Consensus        49 ~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~  115 (229)
                      ..+|.++++.|+++..+..+|..++.+-+...-..++.|..||+||+|+||+..+.++ +.+++..+
T Consensus       103 ~~~l~r~~~~l~l~~~~~~~A~~i~~~~~~~~l~~g~~P~~IAaAaiylA~~~~~~~~-~~~~i~~~  168 (207)
T 1c9b_A          103 GDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKR-TQKEIGDI  168 (207)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHHHTSSSCC-CHHHHHHH
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHCCCC-CHHHHHHH
Confidence            4778899999999999999999999999887778899999999999999999998875 77777544

>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=97.82  E-value=0.00018  Score=59.27  Aligned_cols=103  Identities=15%  Similarity=0.089  Sum_probs=77.8

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHHhhcc---ccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhcc
Q psy1168          50 NFIQILGEQLKLRQQVIATATVYFKRFYARN---SLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNY  126 (229)
Q Consensus        50 ~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~---s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~  126 (229)
                      +|+.++.+.-+++..+.-.|.+|++|+..+.   .+.....+-+.++|+.+|+|+-+....+-+....+. +        
T Consensus        79 ~Yl~RI~k~t~ls~~~ll~ALvYLdRL~~~~p~~~l~~~nvHRLlLtALmlAsK~ldD~~ysN~~wAkVg-G--------  149 (293)
T 2pmi_B           79 NYFIRLTKFSSLEHCVLMTSLYYIDLLQTVYPDFTLNSLTAHRFLLTATTVATKGLCDSFSTNAHYAKVG-G--------  149 (293)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHHHHHHHCTTCCCSTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHH-T--------
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHHHhhCCCCccCCchHHHHHHHHHHHHHHhccccccChhHhhhcc-C--------
Confidence            6788888899999999999999999998743   234567888999999999999887543434433321 1        


Q ss_pred             cccccchhhHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHH
Q psy1168         127 AYAQEFPYRTNHILECEFYLLENLDCCLIVYQPYRPLLQLVQD  169 (229)
Q Consensus       127 ~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~~~P~~~l~~~~~~  169 (229)
                             ...+++-.+|+..|..|+|++.+. +..|...+...
T Consensus       150 -------isl~ELN~LE~eFL~lLdf~L~V~-~ee~~~cy~E~  184 (293)
T 2pmi_B          150 -------VRCHELNILENDFLKRVNYRIIPR-DHNITLCSIEQ  184 (293)
T ss_dssp             -------SCHHHHHHHHHHHHHTTTTCCSCC-TTHHHHHHHHS
T ss_pred             -------cCHHHHHHHHHHHHHHcCCceeeC-HHHHHHHHHHH
Confidence                   236889999999999999999876 44565544443

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

Probab=96.71  E-value=0.00025  Score=60.37  Aligned_cols=67  Identities=16%  Similarity=0.217  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHH
Q psy1168          48 FANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLST  115 (229)
Q Consensus        48 ~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~  115 (229)
                      ..++|.++|.+|+++..+..+|..+.++.....-..+..|.-||+||||+||+..+.++ +.+++..+
T Consensus       235 p~~~i~Rf~s~L~l~~~v~~~A~~i~~~~~~~~i~~GR~P~~IAAAaIylAa~l~g~~~-t~~eIa~v  301 (345)
T 4bbr_M          235 NLTYIPRFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPI-TAAKVGQT  301 (345)
T ss_dssp             --------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcccccCCChHHHHHHHHHHHHHHhCCCC-CHHHHHHH
Confidence            44789999999999999999999999998877667789999999999999999998764 77776554

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

Probab=96.68  E-value=0.00027  Score=60.18  Aligned_cols=66  Identities=17%  Similarity=0.236  Sum_probs=0.0

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHH
Q psy1168          49 ANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLST  115 (229)
Q Consensus        49 ~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~  115 (229)
                      ..+|.++|..|+++..+..+|..+.++.....-..++.|..||+||||+|++..+.++ +.+++..+
T Consensus       236 ~~~i~Rf~~~L~l~~~v~~~A~~i~~~~~~~~l~~Gr~P~~IAaAaIylAa~~~~~~~-t~~eIa~~  301 (345)
T 3k7a_M          236 LTYIPRFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPI-TAAKVGQT  301 (345)
T ss_dssp             -------------------------------------------------------------------
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhchhcCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHH
Confidence            4788899999999999999999999999877777889999999999999999987764 56666443

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

Probab=96.07  E-value=0.014  Score=46.70  Aligned_cols=55  Identities=15%  Similarity=0.054  Sum_probs=48.4

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccc
Q psy1168          50 NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEF  104 (229)
Q Consensus        50 ~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~  104 (229)
                      +++.+.++.++++..+...|..+...-+....+.++.|..||+||+|+|++..+.
T Consensus       136 ~~l~~~~~~~~~~~~~~~~A~~~l~~s~~~~~~l~~~Ps~IAaAai~lA~~~~~~  190 (235)
T 1zp2_A          136 TSLEQAFHDGIINQKQLEFAWSIVNDSYASSLCLMAHPHQLAYAALLISCCNDEN  190 (235)
T ss_dssp             HHHHHHHHTTSSCHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHTSCTT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCchhccCHHHHHHHHHHHHHHhcCC
Confidence            5677777788999999999999999988777788899999999999999998764

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

Probab=95.17  E-value=0.021  Score=47.09  Aligned_cols=56  Identities=13%  Similarity=0.178  Sum_probs=48.2

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhccccc
Q psy1168          50 NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFG  105 (229)
Q Consensus        50 ~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~  105 (229)
                      +++.++++.++.+..+...|..+...-+....+-.+.|..||+||+|+|++..+.+
T Consensus       159 ~fL~~~~~~l~~~~~~~~~A~~~l~~sl~t~~~l~~~Ps~IAaAaiylA~~~~~~~  214 (285)
T 3rgf_B          159 RPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKD  214 (285)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSHHHHSCHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHHHccChhhccCHHHHHHHHHHHHHHHcCCC
Confidence            56777788888888999999999998887777778999999999999999987653

>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=95.03  E-value=0.048  Score=43.98  Aligned_cols=56  Identities=18%  Similarity=0.297  Sum_probs=47.6

Q ss_pred             HHHHHHHHhcCCCH----HHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhccccc
Q psy1168          50 NFIQILGEQLKLRQ----QVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFG  105 (229)
Q Consensus        50 ~~I~~~~~~l~l~~----~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~  105 (229)
                      +++.++++.++.+.    .+...|..+...-+....+..+.|..||+||+++|++..+.+
T Consensus       153 ~fl~~~~~~l~~~~~~~~~~~~~A~~l~~~s~~~~~~l~~~Ps~IAaAai~lA~~~~~~~  212 (258)
T 2i53_A          153 QFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFE  212 (258)
T ss_dssp             HHHHHHHHTBCSCHHHHHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHhCCCcchHHHHHHHHHHHHHHHHcCCchhccChHHHHHHHHHHHHHHhCCC
Confidence            57778888899887    578888888888887777888999999999999999987653

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

Probab=94.22  E-value=0.1  Score=42.37  Aligned_cols=56  Identities=14%  Similarity=0.122  Sum_probs=48.1

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhccccc
Q psy1168          50 NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFG  105 (229)
Q Consensus        50 ~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~  105 (229)
                      +|+.+.++.++++..+...|..+...-+....+.++.|..+|+||+++|++..+.+
T Consensus       140 ~fl~~~~~~~~~~~~~~~~a~~l~e~sl~~~~~~~~~Ps~iAaAai~lA~~~l~~~  195 (269)
T 2b9r_A          140 HFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFPPSQIAAGAFSLALKILDNG  195 (269)
T ss_dssp             HHHHHHHHSSCCCHHHHHHHHHHHHHGGGCGGGSSSCTTHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhhhcCCHHHHHHHHHHHHHHHhCCC
Confidence            56777888899999988889888888877777888999999999999999987654

>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=94.17  E-value=0.11  Score=41.82  Aligned_cols=56  Identities=5%  Similarity=-0.078  Sum_probs=49.8

Q ss_pred             hHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCcc
Q psy1168         160 YRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       160 ~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      .+++......+++++++...|..++...+.....-.+++..+|+||+++|++....
T Consensus        35 ~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~qlv~~acL~lA~K~EE~   90 (257)
T 2ivx_A           35 ANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQ   90 (257)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhCChhhhCHHHHHHHHHHHHhccccC
Confidence            36788888999999999999999999988777778899999999999999998765

>3m03_A ORC6, origin recognition complex subunit 6; helix turn helix, DNA binding protein, origin recognition CO DNA replication; HET: MES; 2.50A {Homo sapiens}

Probab=94.02  E-value=0.11  Score=35.23  Aligned_cols=61  Identities=15%  Similarity=0.204  Sum_probs=44.8

Q ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHHhhcc-----ccccCCchhHHHHHHHHHhhcccccccchHHHHH
Q psy1168          52 IQILGEQLKLRQQVIATATVYFKRFYARN-----SLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLS  114 (229)
Q Consensus        52 I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~-----s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~  114 (229)
                      |.++|..++++. +...|..++++|=..-     .-.+.+.-.+.+||+|.|||.....+ +-..++.
T Consensus         6 v~dLcVqfgc~e-~~~~a~~lL~~Yk~~l~~~~~~~~D~s~P~f~aaA~~~acr~~K~kV-dK~KL~~   71 (95)
T 3m03_A            6 IRDLAVQFSCIE-AVNMASKILKSYESSLPQTQQVDLDLSRPLFTSAALLSACKILKLKV-DKNKMVA   71 (95)
T ss_dssp             HHHHHHHHTCGG-GHHHHHHHHHHHHTTSCHHHHHHCCTTSHHHHHHHHHHHHHHTTCCC-CHHHHHH
T ss_pred             HHHHHHHhCCHH-HHHHHHHHHHHHHHHhHHHhhccccccccHHHHHHHHHHHHHHccCC-CHHHHHH
Confidence            678999999988 6677889999985431     11245566788899999999988764 5455544

>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=93.55  E-value=0.13  Score=42.98  Aligned_cols=55  Identities=11%  Similarity=0.116  Sum_probs=48.5

Q ss_pred             HHHHHHHHHhC--ccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCcc
Q psy1168         161 RPLLQLVQDIG--HEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       161 ~~l~~~~~~l~--~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      .+|..++..++  +++.+...|..++...+.....-.++|..||+||+|+|++...+
T Consensus        62 ~~I~ev~~~l~~~Lp~~t~~tA~~~~~RF~~~~s~~~~~~~lva~acLfLA~K~EE~  118 (323)
T 1jkw_A           62 KRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEF  118 (323)
T ss_dssp             HHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhhCChhhcCHHHHHHHHHHHHHhhhcC
Confidence            45677888888  99999999999999988877778899999999999999998765

>3h4c_A Transcription factor TFIIB-like; cyclin, transcription factor TFIIB repeat; 2.30A {Trypanosoma brucei brucei}

Probab=92.89  E-value=0.38  Score=37.29  Aligned_cols=65  Identities=12%  Similarity=0.183  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhcc---ccccCCchhHHHHHHHHHhhcccccccchHHHH
Q psy1168          48 FANFIQILGEQLKLRQQVIATATVYFKRFYARN---SLKCIDPLLLAPTCVFLASKVEEFGVISSSRLL  113 (229)
Q Consensus        48 ~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~---s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li  113 (229)
                      +.+.|+.+.++-++|..++..|+.+-+.|.-.+   .-+-.+++.|++||+.+|+--...|+ ++.++-
T Consensus        15 M~nclr~L~kKs~~~eaVL~~AieLar~fvg~rR~rgqRvE~q~dVAAAc~miAae~~~~Pi-plaE~r   82 (260)
T 3h4c_A           15 MLNCMRGLHKKAVLPEPVLDRGIELARAFVGGRRARGQRVERQPDVAAACLMIAAEEAQQPL-PLAEVR   82 (260)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHHHTTCCC-CHHHHH
T ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHHHhhhhhhhcccccccHHHHHHHHHHHHHHcCCCc-cHHHHH
Confidence            346678899999999999999999999997543   22335688999999999999888885 777763

>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=92.81  E-value=0.16  Score=43.20  Aligned_cols=56  Identities=9%  Similarity=-0.011  Sum_probs=48.8

Q ss_pred             hHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCcc
Q psy1168         160 YRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       160 ~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      .++|......+++.+++...|..++...+.....-.+++..||+||+|+|++....
T Consensus        42 v~wI~ev~~~l~L~~~t~~tAv~~~dRFl~~~sv~~~~~qlva~acLfLA~K~EE~   97 (358)
T 2pk2_A           42 ANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEEQ   97 (358)
T ss_dssp             HHHHHHHHTTTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHhhccC
Confidence            45677778888899999999999999988777777899999999999999998765

>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=91.71  E-value=0.51  Score=37.96  Aligned_cols=57  Identities=12%  Similarity=-0.058  Sum_probs=44.5

Q ss_pred             HHHHHHHHHhcCCCH-HHHHHHHHHHHHHhhccc-cccCCchhHHHHHHHHHhhccccc
Q psy1168          49 ANFIQILGEQLKLRQ-QVIATATVYFKRFYARNS-LKCIDPLLLAPTCVFLASKVEEFG  105 (229)
Q Consensus        49 ~~~I~~~~~~l~l~~-~~~~~A~~~~~Rf~~~~s-~~~~~~~~v~~acl~LA~K~ee~~  105 (229)
                      .+|+.++++.++.+. .+...|..+...-+.... +.++.|..+|+||+++|++..+.+
T Consensus       140 ~~fl~~~~~~l~~~~~~~~~~a~~l~e~sl~~~~~~~~~~Ps~iAaAai~lA~~~~~~~  198 (260)
T 2cch_B          140 NQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQ  198 (260)
T ss_dssp             HHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHHHHHhHHHHhCCCHHHHHHHHHHHHHHHhCCC
Confidence            367888888888876 677777777776554444 678999999999999999987654

>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor, cell cycle; 1.98A {Homo sapiens}

Probab=90.13  E-value=1.4  Score=37.89  Aligned_cols=74  Identities=9%  Similarity=0.084  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHhh--ccccccCCchhHHHHHHHHHhhcccccccchHHHHHHH
Q psy1168          42 QKIFIFFANFIQILGEQLKLRQ-QVIATATVYFKRFYA--RNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTC  116 (229)
Q Consensus        42 ~~~r~~~~~~I~~~~~~l~l~~-~~~~~A~~~~~Rf~~--~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~  116 (229)
                      +++-..+..-|.++|++|+++. +....--+.|+..+.  ..-+++.|..-+.+.|+|.-||+..... +.++|+..+
T Consensus       276 rKvy~LAa~Rl~~LC~~L~~~~~~l~~~IWt~fe~~l~~~teLm~dRHLDQiiLCsiY~i~Kv~~~~~-tFk~Ii~~Y  352 (411)
T 4ell_A          276 KKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDL-KFKIIVTAY  352 (411)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHTTTCCC-CHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHhhhHhhccccHHHHHHHHHHHHHhhccCCC-CHHHHHHHH
Confidence            3444457778999999998765 333333344444443  3456788899999999999999998764 899998754

>2r7g_A PP110, retinoblastoma-associated protein, P105-RB, RB; retinoblastoma protein, E2F displacement, transcription repressor; 1.67A {Homo sapiens} SCOP: a.74.1.3 a.74.1.3 PDB: 1n4m_A 3pom_A 1gh6_B 1gux_A 1o9k_A 1ad6_A 1gux_B 1o9k_B

Probab=89.87  E-value=1.5  Score=36.95  Aligned_cols=74  Identities=9%  Similarity=0.084  Sum_probs=54.5

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHhh--ccccccCCchhHHHHHHHHHhhcccccccchHHHHHHH
Q psy1168          42 QKIFIFFANFIQILGEQLKLRQ-QVIATATVYFKRFYA--RNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTC  116 (229)
Q Consensus        42 ~~~r~~~~~~I~~~~~~l~l~~-~~~~~A~~~~~Rf~~--~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~  116 (229)
                      +++-..+..-+.++|++|+++. ......-+.|...+.  ..-+++.|..-+.+.|+|.-||+..... +.++++..+
T Consensus       212 rKvy~La~~Rl~~LC~~L~~~~~~~~~~iWt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~-tF~~Ii~~Y  288 (347)
T 2r7g_A          212 KKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDL-KFKIIVTAY  288 (347)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHHTTCCC-CHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHhChHhhcCCcHHHHHHHHHHHHHHhcCCCC-CHHHHHHHH
Confidence            3444446677999999998765 344445555655554  3466788999999999999999998764 999998764

>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=89.37  E-value=2  Score=34.22  Aligned_cols=53  Identities=13%  Similarity=0.266  Sum_probs=38.9

Q ss_pred             HHHHHHHHhcCCCHHH----HHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcc
Q psy1168          50 NFIQILGEQLKLRQQV----IATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVE  102 (229)
Q Consensus        50 ~~I~~~~~~l~l~~~~----~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~e  102 (229)
                      +|+...++.++.+..+    ...|..++..-.....+..+.|..+|+||+++|.+..
T Consensus       154 ~fl~~~~~~~~~~~~~~~~~~~~a~~ll~~~l~d~~~~~~~PS~iAaAai~la~~~~  210 (254)
T 2f2c_A          154 DFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNIALLSPGLICAGGLLTTIETD  210 (254)
T ss_dssp             GSHHHHHHHTTCCGGGHHHHHHHHHHHHHHHTTSGGGTTSCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHcCcchhccCHHHHHHHHHHHHHHhc
Confidence            4566666777777654    3356666665555556778999999999999999985

>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=89.05  E-value=0.66  Score=37.55  Aligned_cols=54  Identities=13%  Similarity=0.111  Sum_probs=38.9

Q ss_pred             HHHHHHHHhcCCCHHHH----HHHHHHHHHHhhccccccCCchhHHHHHHHHHhhccc
Q psy1168          50 NFIQILGEQLKLRQQVI----ATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEE  103 (229)
Q Consensus        50 ~~I~~~~~~l~l~~~~~----~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee  103 (229)
                      +|+..+.+.++++..+.    ..|..++..-.....+.++.|..+|+||+++|++..+
T Consensus       159 ~fl~~~~~~l~~~~~~~~~~~~~a~~~l~~~~~d~~~~~~~PS~iAaAai~lA~~~l~  216 (271)
T 2w96_A          159 DFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNPPSMVAAGSVVAAVQGLN  216 (271)
T ss_dssp             HHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHTSTHHHHSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCchHHHHHHHHHHHHHHHHHhhhhhhccCHHHHHHHHHHHHHHHhC
Confidence            66777788888887653    3455555544334445678999999999999997653

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

Probab=88.78  E-value=2.6  Score=34.75  Aligned_cols=55  Identities=15%  Similarity=0.183  Sum_probs=39.8

Q ss_pred             HHHHHHHHhcCCCHH----HHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccc
Q psy1168          50 NFIQILGEQLKLRQQ----VIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEF  104 (229)
Q Consensus        50 ~~I~~~~~~l~l~~~----~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~  104 (229)
                      +|+..+.+.++.+..    +...|..++..-+....+..+.|..||+||+++|.+.-+.
T Consensus       173 ~fl~~~l~~l~~~~~~~~~~~~~a~~~l~lsl~d~~~l~~~PS~IAaAai~lA~~~l~~  231 (306)
T 3g33_B          173 DFLAFILHRLSLPRDRQALVKKHAQTFLALCATDYTFAMYPPSMIATGSIGAAVQGLGA  231 (306)
T ss_dssp             GGHHHHHHTSSCCTTTHHHHHHHHHHHHHHHHHCGGGTTSCHHHHHHHHHHHHHHTCC-
T ss_pred             HHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhhhhhccCCHHHHHHHHHHHHHHHhcC
Confidence            456666677776543    3455666666656666777899999999999999997664

>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=88.70  E-value=0.54  Score=37.74  Aligned_cols=55  Identities=7%  Similarity=-0.013  Sum_probs=39.9

Q ss_pred             HHHHHHHHhcCCCHHH----HHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccc
Q psy1168          50 NFIQILGEQLKLRQQV----IATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEF  104 (229)
Q Consensus        50 ~~I~~~~~~l~l~~~~----~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~  104 (229)
                      +|+...++.++.+..+    ...|..++..-.....+..+.|..+|+||+++|.+..+.
T Consensus       153 ~fl~~~~~~~~~~~~~~~~~~~~a~~~le~~l~d~~~~~~~PS~iAaAai~lA~~~l~~  211 (257)
T 1g3n_C          153 DVTSFLLLKLVGGSQHLDFWHHEVNTLITKALVDPLTGSLPASIISAAGCALLVPANVI  211 (257)
T ss_dssp             HHHHHHHHHHSCSSTTHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHCCGGGS
T ss_pred             HHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhCcchhCcCHHHHHHHHHHHHHHHhCC
Confidence            5566666667766543    345666666655556677899999999999999998763

>2qdj_A Retinoblastoma-associated protein; cyclin fold, cyclin wedge, antitumor protein; 2.00A {Homo sapiens}

Probab=88.35  E-value=1  Score=37.33  Aligned_cols=65  Identities=15%  Similarity=0.133  Sum_probs=46.8

Q ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHHhhcc---ccccCCchhHHHHHHHHHhhcccccccchHHHHHHH
Q psy1168          52 IQILGEQLKLRQQVIATATVYFKRFYARN---SLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTC  116 (229)
Q Consensus        52 I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~---s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~  116 (229)
                      ..++|+.|+++..|...|...|++.-..-   +...-+....-.||||.||...+..-.++.++++.+
T Consensus         6 F~~lC~~Lnld~~~~~~Aw~~~~~~~~~~~~~~~~~~~~~~~w~acLY~a~~~~~~n~vsLt~LLr~~   73 (304)
T 2qdj_A            6 FTALCQKLKIPDHVRERAWLTWEKVSSVDGVLGGYIQKKKELWGICIFIAAVDLDEMSFTFTELQKNI   73 (304)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHC----------CHHHHHHHHHHHHHHHHTCCCSCHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCCccchHHHHHHhHHHHhhccCCCcCcHHHHHHHc
Confidence            45789999999999999999999976531   122234555666779999987666556899988764

>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens}

Probab=86.64  E-value=3.8  Score=37.47  Aligned_cols=75  Identities=9%  Similarity=0.089  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHhh--ccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHH
Q psy1168          42 QKIFIFFANFIQILGEQLKLRQ-QVIATATVYFKRFYA--RNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQ  117 (229)
Q Consensus        42 ~~~r~~~~~~I~~~~~~l~l~~-~~~~~A~~~~~Rf~~--~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~  117 (229)
                      +++-..+..-|.++|++|+++. ......-+.|+..+.  ..-+++.|..-+++.|+|.-||+..... +.++|+..+.
T Consensus       521 rKvy~LAa~Rl~~LC~~L~~~~~~i~~~IWt~fe~~l~~~t~L~~dRHLDQiilCsiY~icKv~~~~l-tFk~Ii~~Yr  598 (656)
T 4elj_A          521 KKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDL-KFKIIVTAYK  598 (656)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHHHHHCGGGSTTSCHHHHHHHHHHHHHHHTTCCC-CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhccCCc-CHHHHHHHHH
Confidence            4554557788999999998774 344455556666554  3466788999999999999999998764 9999988643

>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=81.79  E-value=2.1  Score=34.85  Aligned_cols=55  Identities=13%  Similarity=0.032  Sum_probs=43.8

Q ss_pred             HHHHHHHHHhCccHHHHHHHHHHHHHHhCC-cccccccHHHHHHHHHHHhcccCcc
Q psy1168         161 RPLLQLVQDIGHEDQLLALAWRVINDSLRT-DVCLLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       161 ~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~-~~~l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      +++......+++..+...+|..+++..+.. ...-......+|+||+++|++....
T Consensus        55 ~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~~v~~~~lqlv~~acL~iA~K~eE~  110 (283)
T 1w98_B           55 DWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEI  110 (283)
T ss_dssp             HHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCS
T ss_pred             HHHHHHHHHhCCCccHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhccc
Confidence            456666777788899999999999887654 3445788999999999999997654

---

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	229
d2i53a1	144	a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens)	3e-23
d1jkwa1	151	a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo s	4e-23
d2ivxa1	143	a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens)	2e-22
d1jkwa2	126	a.74.1.1 (A:162-287) Cyclin H (mcs2) {Human (Homo	3e-13
d2i53a2	110	a.74.1.1 (A:158-267) Cyclin K {Human (Homo sapiens	1e-11
d2ivxa2	113	a.74.1.1 (A:150-262) Cyclin-T2 {Human (Homo sapien	2e-11
d1f5qb1	141	a.74.1.1 (B:6-146) Viral cyclin {Murine herpesviru	1e-05
d1g3nc1	132	a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma	2e-04
d1bu2a1	127	a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saim	4e-04
d1w98b2	140	a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human	5e-04
d1aisb1	98	a.74.1.2 (B:1108-1205) Transcription factor IIB (T	0.001
d2cchb1	128	a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [T	0.004

>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 = 89.3 bits (221), Expect = 3e-23
 Identities = 35/143 (24%), Positives = 57/143 (39%), Gaps = 9/143 (6%)

Query: 16  QQWVLDRQDLIR--ERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYF 73
             W  D++DL     +   L   ++  Y++       FI  +G +L L    +AT  +YF
Sbjct: 9   PCWYWDKKDLAHTPSQLEGLDPATEARYRREGA---RFIFDVGTRLGLHYDTLATGIIYF 65

Query: 74  KRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFP 133
            RFY  +S K     +    C+FLA KVEE       +     +T      +  + Q   
Sbjct: 66  HRFYMFHSFKQFPRYVTGACCLFLAGKVEETPK----KCKDIIKTARSLLNDVQFGQFGD 121

Query: 134 YRTNHILECEFYLLENLDCCLIV 156
                ++  E  LL+ +   L V
Sbjct: 122 DPKEEVMVLERILLQTIKFDLQV 144

>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 = 88.9 bits (220), Expect = 4e-23
 Identities = 36/128 (28%), Positives = 53/128 (41%), Gaps = 12/128 (9%)

Query: 32  DLSILSDEEYQKIFIFFANFIQILGEQLK--LRQQVIATATVYFKRFYARNSLKCIDPLL 89
           D   L   E   +  ++   +       K  + + V+ TA +YFKRFY  NS+    P +
Sbjct: 34  DPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRI 93

Query: 90  LAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLEN 149
           +  TC FLA KV+EF V S   +                          ILE E  L++ 
Sbjct: 94  IMLTCAFLACKVDEFNVSSPQFV----------GNLRESPLGQEKALEQILEYELLLIQQ 143

Query: 150 LDCCLIVY 157
           L+  LIV+
Sbjct: 144 LNFHLIVH 151

>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 = 87.4 bits (216), Expect = 2e-22
 Identities = 31/144 (21%), Positives = 60/144 (41%), Gaps = 6/144 (4%)

Query: 16  QQWVLDRQDLIR--ERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYF 73
            +W   R+ L     R+  +    +   ++      N IQ +G++L + Q  I TA VY 
Sbjct: 3   SRWFFTREQLENTPSRRCGVEADKELSCRQQAA---NLIQEMGQRLNVSQLTINTAIVYM 59

Query: 74  KRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLN-YAYAQEF 132
            RFY  +S    +  +++ T +FLA+KVEE        +      +   +         +
Sbjct: 60  HRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHACLHPLEPLLDTKCDAY 119

Query: 133 PYRTNHILECEFYLLENLDCCLIV 156
             +T  ++  E  +L+ L   + +
Sbjct: 120 LQQTRELVILETIMLQTLGFEITI 143

>d1jkwa2 a.74.1.1 (A:162-287) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Length = 126

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

 Score = 62.2 bits (151), Expect = 3e-13
 Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 7/53 (13%)

Query: 159 PYRPLLQLVQDI-------GHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIG 204
           PYRP    + D+        + + L   A   +N    TD  LLY P QIA+ 
Sbjct: 2   PYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALT 54

>d2i53a2 a.74.1.1 (A:158-267) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Length = 110

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

 Score = 57.6 bits (139), Expect = 1e-11
 Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 4/51 (7%)

Query: 158 QPYRPLLQLVQDIGHE----DQLLALAWRVINDSLRTDVCLLYPPYQIAIG 204
            PY+ LL+  + +  +     +L+ +AW  +NDSL T + L + P  IA+ 
Sbjct: 2   HPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVA 52

>d2ivxa2 a.74.1.1 (A:150-262) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Length = 113

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

 Score = 56.8 bits (137), Expect = 2e-11
 Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 158 QPYRPLLQLVQDIGHEDQLLALAWRVINDSLR-TDVCLLYPPYQIAIG 204
            P+  +++  Q +     L   ++ +  +SL  T  CL Y P  IA  
Sbjct: 2   HPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACV 49

>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Length = 141

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

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 19/144 (13%), Positives = 38/144 (26%), Gaps = 29/144 (20%)

Query: 23  QDLIRERKHDLSILSDEEYQKIFIFFAN---------------FIQILGEQLKLRQQVIA 67
             L+ E      I   E      +   N               ++  + + L+    V  
Sbjct: 7   SSLLNEEDCRQMIYRSEREHDARMVGVNVDQHFTSQYRKVLTTWMFCVCKDLRQDNNVFP 66

Query: 68  TATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYA 127
            A       +    +   +    A   + +A KV  +  I +++L   C           
Sbjct: 67  LAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLCGGA-------- 118

Query: 128 YAQEFPYRTNHILECEFYLLENLD 151
                    + +L  E   L+ L 
Sbjct: 119 ------TTADKLLTLEVKSLDTLS 136

>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]} Length = 132

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

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 18/102 (17%), Positives = 33/102 (32%), Gaps = 14/102 (13%)

Query: 50  NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISS 109
            ++  + ++  L   V+A A     R      +           C+ +ASK+     IS+
Sbjct: 41  TWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPIST 100

Query: 110 SRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLD 151
           S L                     +    +++ E  LLE L 
Sbjct: 101 SSLCYAAA--------------DSFSRQELIDQEKELLEKLA 128

>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} Length = 127

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

 Score = 37.2 bits (86), Expect = 4e-04
 Identities = 14/95 (14%), Positives = 29/95 (30%), Gaps = 14/95 (14%)

Query: 57  EQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTC 116
           E  +L + V   +     R+  +          +   CV + SK+     ++ S+L    
Sbjct: 43  ESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLS 102

Query: 117 QTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLD 151
                            +    ++  E  +LE L 
Sbjct: 103 CDC--------------FTNLELINQEKDILEALK 123

>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]} Length = 140

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

 Score = 36.9 bits (85), Expect = 5e-04
 Identities = 18/106 (16%), Positives = 39/106 (36%), Gaps = 15/106 (14%)

Query: 50  NFIQILGEQLKLRQQVIATATVYFKRFYARN-SLKCIDPLLLAPTCVFLASKVEEFGVIS 108
           +++  + E  KL ++    A  +F R+ A   ++      L+  + +F+A+K+EE     
Sbjct: 48  DWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPK 107

Query: 109 SSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCL 154
             +                         + IL  E  +++ L   L
Sbjct: 108 LHQFAYVTDGA--------------CSGDEILTMELMIMKALKWRL 139

>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 98

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]

 Score = 34.8 bits (80), Expect = 0.001
 Identities = 9/55 (16%), Positives = 23/55 (41%)

Query: 50  NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEF 104
           + +  +  QLKL + V   A   ++    +  ++      +   CV+ A ++ + 
Sbjct: 7   SELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKV 61

>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Length = 128

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

 Score = 34.2 bits (78), Expect = 0.004
 Identities = 22/105 (20%), Positives = 39/105 (37%), Gaps = 14/105 (13%)

Query: 50  NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISS 109
           +++  +GE+ KL+ + +  A  Y  RF +  S+      L+    + LASK EE      
Sbjct: 36  DWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEV 95

Query: 110 SRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCL 154
           +  +                    Y    +L  E  +L+ L   L
Sbjct: 96  AEFVYITD--------------DTYTKKQVLRMEHLVLKVLTFDL 126

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	229
d2ivxa1	143	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	100.0
d2i53a1	144	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	99.97
d1jkwa1	151	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	99.94
d1bu2a1	127	Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}	99.77
d2cchb1	128	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	99.76
d1g3nc1	132	Viral cyclin {Kaposi's sarcoma-associated herpesvi	99.76
d1f5qb1	141	Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]	99.75
d1w98b2	140	G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax	99.74
d2ivxa2	113	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	99.42
d2i53a2	110	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	99.38
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	99.25
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	99.16
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	99.04
d1jkwa2	126	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	98.98
d1vola2	109	Transcription factor IIB (TFIIB), core domain {Hum	98.81
d1vola2	109	Transcription factor IIB (TFIIB), core domain {Hum	98.5
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	98.44
d2cchb2	124	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	98.22
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	97.98
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	97.84
d2ivxa2	113	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	97.07
d2i53a2	110	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	96.26
d2ivxa1	143	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	95.7
d2i53a1	144	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	95.42
d1jkwa1	151	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	94.18
d2r7ga2	142	Retinoblastoma tumor suppressor domains {Human (Ho	92.93
d1w98b1	130	G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax	90.73
d1bu2a1	127	Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}	90.47
d2cchb1	128	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	88.8
d1g3nc1	132	Viral cyclin {Kaposi's sarcoma-associated herpesvi	87.62
d1f5qb1	141	Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]	87.03
d1jkwa2	126	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	86.62
d1w98b2	140	G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax	84.41

>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=100.00  E-value=6.4e-33  Score=208.32  Aligned_cols=140  Identities=22%  Similarity=0.335  Sum_probs=123.7

Q ss_pred             ccCCcccHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHH
Q psy1168          15 IQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTC   94 (229)
Q Consensus        15 ~~~w~f~~~~l~~~~~~~~~~~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~ac   94 (229)
                      .++|+||++|++++|+. .+|++.++|..+|..+++||.++|.+|++|..|+++|++||||||+++++.++++++|++||
T Consensus         2 ~~~w~~t~~~l~~~pS~-~~gi~~~~E~~~R~~~~~~i~~~~~~l~l~~~t~~~A~~l~~Rf~~~~s~~~~~~~~va~ac   80 (143)
T d2ivxa1           2 SSRWFFTREQLENTPSR-RCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTA   80 (143)
T ss_dssp             CGGGSCCHHHHHSCHHH-HTTCCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHH
T ss_pred             CCCCCCCHHHHHhCccc-ccCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCccccCHHHHHHHH
Confidence            47999999999998874 57899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhcccccccchHHHHHHHHHHHHhhhc--ccccccchhhHHHHHHHHHHHHHHcCcceee
Q psy1168          95 VFLASKVEEFGVISSSRLLSTCQTVVKNKLN--YAYAQEFPYRTNHILECEFYLLENLDCCLIV  156 (229)
Q Consensus        95 l~LA~K~ee~~~~~l~~li~~~~~~~~~~~~--~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~  156 (229)
                      +|||||+||+++ ++++++.++....++..+  ...++++..++++|+.+|+.||++||||++|
T Consensus        81 l~LA~K~eE~~~-~~~~ii~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~Fdl~V  143 (143)
T d2ivxa1          81 LFLAAKVEEQAR-KLEHVIKVAHACLHPLEPLLDTKCDAYLQQTRELVILETIMLQTLGFEITI  143 (143)
T ss_dssp             HHHHHHHTTCCC-CHHHHHHHHHHHHCTTSCCCCTTSHHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             HHHHHHhccccc-cHHHHHHHHHHHhcccchhhhhchhhhHHHHHHHHHHHHHHHHHcCCeeeC
Confidence            999999999986 999999886654433211  1224567778999999999999999999975

>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=99.97  E-value=2.9e-32  Score=204.87  Aligned_cols=137  Identities=26%  Similarity=0.364  Sum_probs=121.7

Q ss_pred             ccCCcccHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHH
Q psy1168          15 IQQWVLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTC   94 (229)
Q Consensus        15 ~~~w~f~~~~l~~~~~~~~~~~s~~~e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~ac   94 (229)
                      ..+|+||++|++++|+. .+|++++.|..+|..+++||.++|.+|++|..|.++|+.|||||+.++++..++++++++||
T Consensus         8 ~~~w~fs~~~l~~tps~-~~~i~~~~E~~~R~~~~~~i~~~~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~~lva~ac   86 (144)
T d2i53a1           8 KPCWYWDKKDLAHTPSQ-LEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACC   86 (144)
T ss_dssp             SSSCCCCGGGGGGCHHH-HTTCCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHH
T ss_pred             CCCCCcCHHHHHhChhh-hcCCChHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhhCcccchhHHHHHHHH
Confidence            34899999999998875 36899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhcccccccchHHHHHHHHHHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceee
Q psy1168          95 VFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIV  156 (229)
Q Consensus        95 l~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~  156 (229)
                      ||||||+||+++ ++++++.++....++..   .++.+..++++|+.+|+.||++||||+.|
T Consensus        87 l~LA~K~eE~~~-~l~~vi~~~~~~~~~~~---~~~~~~~~~~~i~~~E~~iL~~L~Fdl~V  144 (144)
T d2i53a1          87 LFLAGKVEETPK-KCKDIIKTARSLLNDVQ---FGQFGDDPKEEVMVLERILLQTIKFDLQV  144 (144)
T ss_dssp             HHHHHHHTTCCC-CHHHHHHHHHHHSCHHH---HGGGCSCHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             HHHHHHhhcccc-cHHHHHHHHHHHhhhhh---hhhhchhhHHHHHHHHHHHHHHCCCeeeC
Confidence            999999999986 99999988765543221   23455667899999999999999999975

>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=99.94  E-value=3.6e-27  Score=178.11  Aligned_cols=130  Identities=32%  Similarity=0.525  Sum_probs=109.7

Q ss_pred             Cccc-HHHHHHhhh------------------cCCCCCCHHHHHHHHHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHH
Q psy1168          18 WVLD-RQDLIRERK------------------HDLSILSDEEYQKIFIFFANFIQILGEQLK--LRQQVIATATVYFKRF   76 (229)
Q Consensus        18 w~f~-~~~l~~~~~------------------~~~~~~s~~~e~~~r~~~~~~I~~~~~~l~--l~~~~~~~A~~~~~Rf   76 (229)
                      |+|+ +++|...+.                  ....++++++|..+|.+++++|.++|..++  +|+.|.++|++|||||
T Consensus         1 W~F~~~~~l~~lr~~~n~~~~~~~~~~~~~~~~~~~~l~~~ee~~l~~~~~~~l~~~~~~~k~~l~~~~~~tA~~~~~RF   80 (151)
T d1jkwa1           1 WTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRF   80 (151)
T ss_dssp             CCCSCHHHHHHHHHHHHHHHHHHHHHTSSSCTTCTTSCCHHHHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHH
T ss_pred             CcCCCHHHHHHHHHHHHHHHHHHHHhhcccCcccccCCCHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHH
Confidence            9995 456776531                  245689999999999999999999999876  9999999999999999


Q ss_pred             hhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhcccccccchhhHHHHHHHHHHHHHHcCcceee
Q psy1168          77 YARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLIV  156 (229)
Q Consensus        77 ~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~~  156 (229)
                      |+++++.+++++++++||||||||+||+++ ++++++......         ..++...+++|+.+|..||++|+|||.|
T Consensus        81 ~~~~s~~~~~~~li~~acl~LA~K~ee~~~-~~~~~~~~~~~~---------~~~~~~~~~~i~~~E~~iL~~L~f~L~V  150 (151)
T d1jkwa1          81 YLNNSVMEYHPRIIMLTCAFLACKVDEFNV-SSPQFVGNLRES---------PLGQEKALEQILEYELLLIQQLNFHLIV  150 (151)
T ss_dssp             GGGSCTTTSCHHHHHHHHHHHHHHHTTCCC-CHHHHGGGSSSC---------HHHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             hhcCccccccHHHHHHHHHHHHHHHcccCC-CHHHHHHHHHhh---------cccccccHHHHHHHHHHHHHHcCCeeee
Confidence            999999999999999999999999999985 888886543211         1234456899999999999999999976


Q ss_pred             c
Q psy1168         157 Y  157 (229)
Q Consensus       157 ~  157 (229)
                      +
T Consensus       151 h  151 (151)
T d1jkwa1         151 H  151 (151)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.77  E-value=3.8e-19  Score=129.59  Aligned_cols=100  Identities=15%  Similarity=0.208  Sum_probs=89.6

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHH
Q psy1168          42 QKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVK  121 (229)
Q Consensus        42 ~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~  121 (229)
                      ..+|...++|+.++|..++++.+|.+.|+.|+|||++...+...+.+++|+||+++|+|++|...+++++++..+.    
T Consensus        28 ~~~R~~lidWl~~v~~~~~l~~eTl~lAv~llDryl~~~~i~~~~lqLi~~tcL~IAsK~ee~~~~~l~~l~~~~~----  103 (127)
T d1bu2a1          28 VDNRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSC----  103 (127)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSCCCTTTHHHHHHHHHHHHHHHSSSSCCCHHHHHHTTT----
T ss_pred             HHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHc----
Confidence            3478889999999999999999999999999999999999999999999999999999999987678999876542    


Q ss_pred             hhhcccccccchhhHHHHHHHHHHHHHHcCccee
Q psy1168         122 NKLNYAYAQEFPYRTNHILECEFYLLENLDCCLI  155 (229)
Q Consensus       122 ~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~  155 (229)
                                ....++++.++|+.||.+|+||+.
T Consensus       104 ----------~~~t~~ei~~mE~~IL~~L~~dl~  127 (127)
T d1bu2a1         104 ----------DCFTNLELINQEKDILEALKWDTE  127 (127)
T ss_dssp             ----------TSSCHHHHHHHHHHHHHHTTTCCC
T ss_pred             ----------CCCCHHHHHHHHHHHHHHcCCCCC
Confidence                      123488999999999999999974

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

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

Probab=99.76  E-value=6.2e-19  Score=128.76  Aligned_cols=99  Identities=22%  Similarity=0.311  Sum_probs=88.7

Q ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHh
Q psy1168          43 KIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKN  122 (229)
Q Consensus        43 ~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~  122 (229)
                      .+|...++||.+++..++++..|.++|+.|+|||++..++...+.+++++||++||+|++|...+++++++..+.     
T Consensus        29 ~~R~~li~W~~~v~~~~~l~~~t~~lAv~llDr~l~~~~i~~~~~qLi~~~cl~iAsK~ee~~~~~l~~l~~~~~-----  103 (128)
T d2cchb1          29 SMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITD-----  103 (128)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTT-----
T ss_pred             HHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcccCCchHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHc-----
Confidence            468889999999999999999999999999999999999988899999999999999999987678999876532     


Q ss_pred             hhcccccccchhhHHHHHHHHHHHHHHcCccee
Q psy1168         123 KLNYAYAQEFPYRTNHILECEFYLLENLDCCLI  155 (229)
Q Consensus       123 ~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~  155 (229)
                               ....++++.++|..||++|+||+.
T Consensus       104 ---------~~~t~~~i~~mE~~IL~~L~~~l~  127 (128)
T d2cchb1         104 ---------DTYTKKQVLRMEHLVLKVLTFDLA  127 (128)
T ss_dssp             ---------SSSCHHHHHHHHHHHHHHTTTCCC
T ss_pred             ---------CCCCHHHHHHHHHHHHHHCCCeec
Confidence                     123489999999999999999985

>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=99.76  E-value=7.6e-19  Score=128.88  Aligned_cols=99  Identities=18%  Similarity=0.245  Sum_probs=88.6

Q ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHh
Q psy1168          43 KIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKN  122 (229)
Q Consensus        43 ~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~  122 (229)
                      .+|...++|+.+++..++++.+|.+.|+.|+|||+++.++...+.+++|+||+++|+|++|...+++++++..+.+    
T Consensus        34 ~~R~~lidWl~~v~~~~~l~~et~~lAv~llDrfls~~~v~~~~lqLia~tcl~iAsK~ee~~~~~~~~l~~~~~~----  109 (132)
T d1g3nc1          34 HMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAAD----  109 (132)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTT----
T ss_pred             HHHHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCcccCcHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHcC----
Confidence            3788899999999999999999999999999999999999988999999999999999999866688998765431    


Q ss_pred             hhcccccccchhhHHHHHHHHHHHHHHcCccee
Q psy1168         123 KLNYAYAQEFPYRTNHILECEFYLLENLDCCLI  155 (229)
Q Consensus       123 ~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~  155 (229)
                                ...++++.++|..||++|+|++.
T Consensus       110 ----------~~t~~ei~~mE~~IL~~L~w~l~  132 (132)
T d1g3nc1         110 ----------SFSRQELIDQEKELLEKLAWRTE  132 (132)
T ss_dssp             ----------CSCHHHHHHHHHHHHHHTTTCCC
T ss_pred             ----------CCCHHHHHHHHHHHHHHcCCcCC
Confidence                      23489999999999999999974

>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=99.75  E-value=9.6e-19  Score=129.68  Aligned_cols=101  Identities=14%  Similarity=0.204  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHH
Q psy1168          41 YQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVV  120 (229)
Q Consensus        41 e~~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~  120 (229)
                      -..+|...++|+.+++..++++.+|.+.|+.|++||++...+...+.+++++||+++|+|++|...+++.+++..+.+  
T Consensus        40 t~~~R~~lvdWm~~v~~~~~l~~etl~lAv~llDrfls~~~i~~~~lqL~a~tcL~IAsK~ee~~~~~~~~l~~~~~~--  117 (141)
T d1f5qb1          40 TSQYRKVLTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLCGG--  117 (141)
T ss_dssp             HCSHHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHCT--
T ss_pred             CHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHhcC--
Confidence            356899999999999999999999999999999999999999999999999999999999999876788888765431  


Q ss_pred             HhhhcccccccchhhHHHHHHHHHHHHHHcCccee
Q psy1168         121 KNKLNYAYAQEFPYRTNHILECEFYLLENLDCCLI  155 (229)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~  155 (229)
                                  ...++++..||..||++|+|+++
T Consensus       118 ------------~yt~~ei~~mE~~IL~~L~w~~~  140 (141)
T d1f5qb1         118 ------------ATTADKLLTLEVKSLDTLSWVAD  140 (141)
T ss_dssp             ------------TCCHHHHHHHHHHHHHHTTTCCC
T ss_pred             ------------CCCHHHHHHHHHHHHHHCCccCC
Confidence                        13489999999999999999875

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

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

Probab=99.74  E-value=2.7e-18  Score=127.23  Aligned_cols=99  Identities=19%  Similarity=0.273  Sum_probs=86.4

Q ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhc-cccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHH
Q psy1168          43 KIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYAR-NSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVK  121 (229)
Q Consensus        43 ~~r~~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~-~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~  121 (229)
                      ++|...++||.+++..++++.+|.++|+.|+|||+.. ..+...+.+++++||++||+|++|...+++++++..+.+   
T Consensus        41 ~~R~~lidW~~~v~~~~~l~~et~~lAv~llDryl~~~~~v~~~~lqL~a~acL~IAsK~ee~~~~~~~~l~~~~~~---  117 (140)
T d1w98b2          41 KMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDG---  117 (140)
T ss_dssp             HHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTT---
T ss_pred             HHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhccccccHHHHhHHHHHHHHHHHHHcccCCCCHHHHHHHHcC---
Confidence            4788999999999999999999999999999999974 456777899999999999999999776789998764321   


Q ss_pred             hhhcccccccchhhHHHHHHHHHHHHHHcCccee
Q psy1168         122 NKLNYAYAQEFPYRTNHILECEFYLLENLDCCLI  155 (229)
Q Consensus       122 ~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~fdl~  155 (229)
                                 ...++++.++|..||++|+|+++
T Consensus       118 -----------~~t~~ei~~mE~~IL~~L~~~Ln  140 (140)
T d1w98b2         118 -----------ACSGDEILTMELMIMKALKWRLS  140 (140)
T ss_dssp             -----------SSCHHHHHHHHHHHHHHTTTCCC
T ss_pred             -----------CCCHHHHHHHHHHHHHHCCCcCC
Confidence                       23489999999999999999974

>d2ivxa2 a.74.1.1 (A:150-262) 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=99.42  E-value=7.8e-14  Score=98.45  Aligned_cols=60  Identities=20%  Similarity=0.227  Sum_probs=57.0

Q ss_pred             cCChHHHHHHHHHhCccHHHHHHHHHHHHHHhC-CcccccccHHHHHHHHHHHhcccCccc
Q psy1168         157 YQPYRPLLQLVQDIGHEDQLLALAWRVINDSLR-TDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       157 ~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~-~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      +|||.|+..|++.++.++++.+.||.++||+++ |++|+.|+|..||+|||++|+++++++
T Consensus         1 eHPhk~ll~~~k~l~~~~~l~q~AW~~lnDs~r~T~lcL~~~P~~IA~a~I~LA~~~~~~~   61 (113)
T d2ivxa2           1 EHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWE   61 (113)
T ss_dssp             CCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCGGGTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCcHHHHHHHHHhCCChHHHHHHHHHHHHHhccCCeeeecCcHHHHHHHHHHHHHHhCCC
Confidence            589999999999999999999999999999997 899999999999999999999988764

>d2i53a2 a.74.1.1 (A:158-267) 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=99.38  E-value=1.9e-13  Score=96.49  Aligned_cols=60  Identities=27%  Similarity=0.454  Sum_probs=55.5

Q ss_pred             cCChHHHHHHHHHhCcc----HHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         157 YQPYRPLLQLVQDIGHE----DQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       157 ~~P~~~l~~~~~~l~~~----~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      +|||+|+..|++.++..    +++.+.||.++||+++|++|+.|+|..||+|||++|+..++++
T Consensus         1 eHP~~~L~~~~~~l~~~~~~~~~l~q~AW~~lNDs~rT~lcL~~~P~~IA~a~I~lA~~~~~~~   64 (110)
T d2i53a2           1 EHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFE   64 (110)
T ss_dssp             CCHHHHHHHHHHTBCSCHHHHHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCcHHHHHHHHHhcCccccchHHHHHHHHHHHHHhcCCchhccCcHHHHHHHHHHHHHHhCCC
Confidence            48999999999999865    4699999999999999999999999999999999999988764

>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=99.25  E-value=2.9e-11  Score=82.69  Aligned_cols=92  Identities=16%  Similarity=0.271  Sum_probs=80.1

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhcc
Q psy1168          47 FFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNY  126 (229)
Q Consensus        47 ~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~  126 (229)
                      .+.+.|.++|+.|+||..+..+|..+|++....+..++..+..+++||+|+||+.++.|+ +++++...+          
T Consensus         4 ~a~~~I~~~~~~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~~~~i~AA~iY~acr~~~~p~-t~~eIa~~~----------   72 (95)
T d1vola1           4 NAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGVPR-TFKEICAVS----------   72 (95)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTCCCTTSCHHHHHHHHHHHHHHHTTCCC-CHHHHHTTT----------
T ss_pred             HHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCChHHHHHHHHHHHHHHcCCCC-CHHHHHHHh----------
Confidence            356889999999999999999999999999999999999999999999999999999996 888886532          


Q ss_pred             cccccchhhHHHHHHHHHHHHHHcCccee
Q psy1168         127 AYAQEFPYRTNHILECEFYLLENLDCCLI  155 (229)
Q Consensus       127 ~~~~~~~~~~~~i~~~E~~iL~~L~fdl~  155 (229)
                            .....++....+.+.+.|+.+++
T Consensus        73 ------~i~~~~i~k~~k~i~~~L~~~v~   95 (95)
T d1vola1          73 ------RISKKEIGRCFKLILKALETSVD   95 (95)
T ss_dssp             ------CSCHHHHHHHHHHHHHHTTCCCC
T ss_pred             ------CCCHHHHHHHHHHHHHHHCCcCC
Confidence                  23367788888899999988763

>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=99.16  E-value=1.4e-10  Score=79.68  Aligned_cols=89  Identities=15%  Similarity=0.213  Sum_probs=78.0

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhcc
Q psy1168          47 FFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNY  126 (229)
Q Consensus        47 ~~~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~  126 (229)
                      .+...|.++|+.|+||..+..+|..+|++....+..++..+..+++||+|+||+.++.|+ +++|+...+.         
T Consensus         4 ~a~~~I~~~~~~L~L~~~i~~~A~~i~k~~~~~~~~~g~~~~~iaaA~iY~Acr~~~~~~-t~~eIa~~~~---------   73 (98)
T d1aisb1           4 FALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPR-TLDEIADIAR---------   73 (98)
T ss_dssp             HHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTTTTTTCCHHHHHHHHHHHHHHHHTCCC-CHHHHHHHTT---------
T ss_pred             HHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHHHHHHHHHcCCCC-CHHHHHHHHC---------
Confidence            466789999999999999999999999999999988999999999999999999999996 8999876532         


Q ss_pred             cccccchhhHHHHHHHHHHHHHHcCc
Q psy1168         127 AYAQEFPYRTNHILECEFYLLENLDC  152 (229)
Q Consensus       127 ~~~~~~~~~~~~i~~~E~~iL~~L~f  152 (229)
                             ....++....+.+++.|+.
T Consensus        74 -------is~~ti~k~yk~i~~~L~l   92 (98)
T d1aisb1          74 -------VDKKEIGRSYRFIARNLNL   92 (98)
T ss_dssp             -------SCHHHHHHHHHHHHHHTTC
T ss_pred             -------CCHHHHHHHHHHHHHHcCC
Confidence                   2367788888889888873

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

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

Probab=99.04  E-value=6.9e-10  Score=75.66  Aligned_cols=89  Identities=16%  Similarity=0.191  Sum_probs=75.8

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhhccccc
Q psy1168          50 NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYA  129 (229)
Q Consensus        50 ~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~~~~~~~~~~~~~~  129 (229)
                      +||.++|..|+||..+...|..++++.....-..+..+..+++||+|+||+.++.++ +++++..++.            
T Consensus         5 d~I~R~~~~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~vaAA~iY~a~r~~~~~~-t~~eIa~~~~------------   71 (95)
T d1aisb2           5 DYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKR-TQREVAEVAR------------   71 (95)
T ss_dssp             GGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHHHHHHHHTTCCC-CHHHHHHHHT------------
T ss_pred             HHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCcHHhHHHHHHHHHHHHcCCCc-CHHHHHHHHC------------
Confidence            689999999999999999999999999998889999999999999999999999986 8898876542            


Q ss_pred             ccchhhHHHHHHHHHHHHHHcCccee
Q psy1168         130 QEFPYRTNHILECEFYLLENLDCCLI  155 (229)
Q Consensus       130 ~~~~~~~~~i~~~E~~iL~~L~fdl~  155 (229)
                          .....|...-..+.+.|+..+.
T Consensus        72 ----vs~~tI~~~yk~l~~~l~~~~p   93 (95)
T d1aisb2          72 ----VTEVTVRNRYKELVEKLKIKVP   93 (95)
T ss_dssp             ----CCHHHHHHHHHHHHHHHTCCCC
T ss_pred             ----CCHHHHHHHHHHHHHHhCCCCC
Confidence                1245566677777888877653

>d1jkwa2 a.74.1.1 (A:162-287) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.98  E-value=2.2e-10  Score=82.15  Aligned_cols=59  Identities=32%  Similarity=0.390  Sum_probs=53.1

Q ss_pred             CChHHHHHHHHHhC-------ccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         158 QPYRPLLQLVQDIG-------HEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       158 ~P~~~l~~~~~~l~-------~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      |||+.+..++.++.       ..+.+.+.||.++||+++|++|+.|+|++||+||+++|+..++++
T Consensus         1 HPyRpl~g~l~dl~~~~~~~~~~~~l~~~a~~~lnds~~Td~~l~y~P~qIalaal~~a~~~~~~~   66 (126)
T d1jkwa2           1 NPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGIT   66 (126)
T ss_dssp             CSHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHTTSTHHHHSCHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCccHHHHHHHHHHhccCcCCHHHHHHHHHHHHHHHHcCCeeeeeCHHHHHHHHHHHHHHHcCCC
Confidence            79999999997763       247899999999999999999999999999999999999988764

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

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

Probab=98.81  E-value=6.2e-09  Score=72.61  Aligned_cols=67  Identities=16%  Similarity=0.217  Sum_probs=62.3

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccccccchHHHHHHH
Q psy1168          49 ANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTC  116 (229)
Q Consensus        49 ~~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~  116 (229)
                      .++|.++|.+|+||..+..+|..++++....+-..+..+..+++||+|+||+.++.++ +++++..++
T Consensus         5 ~d~i~Rf~s~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~iaAa~iY~a~r~~~~~~-t~~eIa~~~   71 (109)
T d1vola2           5 GDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKR-TQKEIGDIA   71 (109)
T ss_dssp             GGTHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHHHTSSSCC-CHHHHHHHH
T ss_pred             HHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCCHHHHHHHHHHHHHHHcCCCC-CHHHHHHHH
Confidence            4789999999999999999999999999999999999999999999999999999986 899986654

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

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

Probab=98.50  E-value=8.2e-08  Score=66.70  Aligned_cols=60  Identities=8%  Similarity=0.042  Sum_probs=56.0

Q ss_pred             cCChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         157 YQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       157 ~~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      .+|.+|+.+|+..|+++..+.+.|..+...+....+.-+.+|..+|+||||+|+...|..
T Consensus         2 i~~~d~i~Rf~s~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~iaAa~iY~a~r~~~~~   61 (109)
T d1vola2           2 ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEK   61 (109)
T ss_dssp             CCGGGTHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHHHTSSSC
T ss_pred             CCHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCCHHHHHHHHHHHHHHHcCCC
Confidence            579999999999999999999999999999988888899999999999999999988754

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

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

Probab=98.44  E-value=1.5e-07  Score=63.71  Aligned_cols=59  Identities=7%  Similarity=0.117  Sum_probs=54.9

Q ss_pred             CChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         158 QPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       158 ~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      .|-+|+.+|+..|++++.+.+.|..+........+.-+.+|..+|+||||+|+..+|..
T Consensus         2 ~P~d~I~R~~~~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~vaAA~iY~a~r~~~~~   60 (95)
T d1aisb2           2 KPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEK   60 (95)
T ss_dssp             CGGGGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHHHHHHHHTTCC
T ss_pred             CHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCcHHhHHHHHHHHHHHHcCCC
Confidence            58999999999999999999999999999888888889999999999999999988754

>d2cchb2 a.74.1.1 (B:309-432) 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=98.22  E-value=2.2e-07  Score=65.93  Aligned_cols=61  Identities=20%  Similarity=0.037  Sum_probs=52.1

Q ss_pred             cCChHHHHHHH-HHhCccHHHHHHHHHHHHHHhCC-cccccccHHHHHHHHHHHhcccCcccc
Q psy1168         157 YQPYRPLLQLV-QDIGHEDQLLALAWRVINDSLRT-DVCLLYPPYQIAIGECSFSFTPHVIAE  217 (229)
Q Consensus       157 ~~P~~~l~~~~-~~l~~~~~i~~~a~~~~~~~~~~-~~~l~~~P~~IA~aai~~A~~~~~~~~  217 (229)
                      |+|+.|+.+|. +..+.+.++..+|.++++.++.+ +.++.|+||.||+|||++|...+|..+
T Consensus         1 PT~~~FL~ry~~~~~~~d~~~~~la~Yl~ElsLl~~~~~l~~~PS~lAaaai~lar~~l~~~~   63 (124)
T d2cchb2           1 PTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQS   63 (124)
T ss_dssp             CCHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHHHHHHHHHHHHSCC
T ss_pred             CchhHHHHHHHHHHccCcHHHHHHHHHHHHHHHHhHHHHHccChHHHHHHHHHHHHHHhCCCC
Confidence            58899999875 45556788999999999999987 479999999999999999988877643

>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=97.98  E-value=5.3e-06  Score=55.69  Aligned_cols=59  Identities=5%  Similarity=0.013  Sum_probs=53.8

Q ss_pred             CChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         158 QPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       158 ~P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      +++..|.+++..+++++.+.+.|..+...+....+.-+.+|..+|+||||+|++.++..
T Consensus         4 ~a~~~I~~~~~~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~~~~i~AA~iY~acr~~~~p   62 (95)
T d1vola1           4 NAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGVP   62 (95)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTCCCTTSCHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCChHHHHHHHHHHHHHHcCCC
Confidence            35778999999999999999999999999988888889999999999999999988753

>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=97.84  E-value=1.3e-05  Score=54.04  Aligned_cols=57  Identities=7%  Similarity=-0.020  Sum_probs=52.5

Q ss_pred             ChHHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCcc
Q psy1168         159 PYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       159 P~~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      ++..|.++++.+++++.+.+.|..+...+......-+.+|..+|+||||+|++.++.
T Consensus         5 a~~~I~~~~~~L~L~~~i~~~A~~i~k~~~~~~~~~g~~~~~iaaA~iY~Acr~~~~   61 (98)
T d1aisb1           5 ALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKV   61 (98)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTTTTTTCCHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHHHHHHHHHcCC
Confidence            567789999999999999999999999999888888999999999999999998765

>d2ivxa2 a.74.1.1 (A:150-262) 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=97.07  E-value=0.00087  Score=45.90  Aligned_cols=57  Identities=12%  Similarity=0.151  Sum_probs=48.5

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHHhh-ccccccCCchhHHHHHHHHHhhcccccc
Q psy1168          50 NFIQILGEQLKLRQQVIATATVYFKRFYA-RNSLKCIDPLLLAPTCVFLASKVEEFGV  106 (229)
Q Consensus        50 ~~I~~~~~~l~l~~~~~~~A~~~~~Rf~~-~~s~~~~~~~~v~~acl~LA~K~ee~~~  106 (229)
                      .++.+.++.++.+.++..+|-.+.+-.+. ..-.-.+.++.||+||++||+|..+.+.
T Consensus         5 k~ll~~~k~l~~~~~l~q~AW~~lnDs~r~T~lcL~~~P~~IA~a~I~LA~~~~~~~~   62 (113)
T d2ivxa2           5 TDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEI   62 (113)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCGGGTSCHHHHHHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHHhccCCeeeecCcHHHHHHHHHHHHHHhCCCC
Confidence            46778888899999999999999999875 5555779999999999999999876653

>d2i53a2 a.74.1.1 (A:158-267) 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=96.26  E-value=0.0061  Score=41.22  Aligned_cols=55  Identities=18%  Similarity=0.298  Sum_probs=44.5

Q ss_pred             HHHHHHHhcCCCH----HHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhccccc
Q psy1168          51 FIQILGEQLKLRQ----QVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFG  105 (229)
Q Consensus        51 ~I~~~~~~l~l~~----~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~~  105 (229)
                      ++.+..+.|+...    .+..+|-.+.+-.|...-.-.+.++.||+||++||+|..+.+
T Consensus         6 ~L~~~~~~l~~~~~~~~~l~q~AW~~lNDs~rT~lcL~~~P~~IA~a~I~lA~~~~~~~   64 (110)
T d2i53a2           6 FLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFE   64 (110)
T ss_dssp             HHHHHHHTBCSCHHHHHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHhcCccccchHHHHHHHHHHHHHhcCCchhccCcHHHHHHHHHHHHHHhCCC
Confidence            4556666776664    467888899998888777788999999999999999998765

>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=95.70  E-value=0.012  Score=41.47  Aligned_cols=54  Identities=6%  Similarity=-0.056  Sum_probs=48.2

Q ss_pred             HHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCc
Q psy1168         161 RPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHV  214 (229)
Q Consensus       161 ~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~  214 (229)
                      +++......++++......|..+++..+...-+-.++|..||+||+++|++...
T Consensus        36 ~~i~~~~~~l~l~~~t~~~A~~l~~Rf~~~~s~~~~~~~~va~acl~LA~K~eE   89 (143)
T d2ivxa1          36 NLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE   89 (143)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHhcc
Confidence            578888889999999999999999998877777889999999999999999753

>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=95.42  E-value=0.018  Score=40.56  Aligned_cols=54  Identities=11%  Similarity=0.018  Sum_probs=48.1

Q ss_pred             HHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCc
Q psy1168         161 RPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHV  214 (229)
Q Consensus       161 ~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~  214 (229)
                      +++......++++......|..+++..+...-...+.|..||+||+++|++...
T Consensus        42 ~~i~~~~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~~lva~acl~LA~K~eE   95 (144)
T d2i53a1          42 RFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEE   95 (144)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHHHhhCcccchhHHHHHHHHHHHHHHhhc
Confidence            577888889999999999999999998877777889999999999999999754

>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=94.18  E-value=0.057  Score=38.16  Aligned_cols=53  Identities=11%  Similarity=0.107  Sum_probs=44.0

Q ss_pred             HHHHHHHHh--CccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCc
Q psy1168         162 PLLQLVQDI--GHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHV  214 (229)
Q Consensus       162 ~l~~~~~~l--~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~  214 (229)
                      .+..++..+  ++++.+...|..++...+.......+.|..||+||+++|++...
T Consensus        53 ~l~~~~~~~k~~l~~~~~~tA~~~~~RF~~~~s~~~~~~~li~~acl~LA~K~ee  107 (151)
T d1jkwa1          53 RLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDE  107 (151)
T ss_dssp             HHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHccCCCHHHHHHHHHHHHHHhhcCccccccHHHHHHHHHHHHHHHcc
Confidence            344556654  36789999999999998888888899999999999999999764

>d2r7ga2 a.74.1.3 (A:644-785) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=92.93  E-value=0.32  Score=33.82  Aligned_cols=73  Identities=10%  Similarity=0.078  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHhh--ccccccCCchhHHHHHHHHHhhcccccccchHHHHHHH
Q psy1168          43 KIFIFFANFIQILGEQLKLRQ-QVIATATVYFKRFYA--RNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTC  116 (229)
Q Consensus        43 ~~r~~~~~~I~~~~~~l~l~~-~~~~~A~~~~~Rf~~--~~s~~~~~~~~v~~acl~LA~K~ee~~~~~l~~li~~~  116 (229)
                      ++-..+..-|..+|++|++.. ++....-.+|+..+.  ..-+.+.+..-+.+.|+|..||+..... +.++++..+
T Consensus        10 Kvy~La~~Rl~~LC~~L~~~~~~l~~~Iw~~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~-~F~~Ii~~Y   85 (142)
T d2r7ga2          10 KVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDL-KFKIIVTAY   85 (142)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHHTTCCC-CHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHHHHhHHHHhccchhHHHHHHHHHHHHhccCCC-CHHHHHHHH
Confidence            333346667999999997753 333333344444443  3456678888899999999999988764 899988764

>d1w98b1 a.74.1.1 (B:228-357) 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=90.73  E-value=0.31  Score=33.20  Aligned_cols=52  Identities=13%  Similarity=-0.008  Sum_probs=37.6

Q ss_pred             CChHHHHHHHHHhCc-----------cHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHh
Q psy1168         158 QPYRPLLQLVQDIGH-----------EDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFS  209 (229)
Q Consensus       158 ~P~~~l~~~~~~l~~-----------~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A  209 (229)
                      |+...+.-|++....           +....-.+-.+++.+..+--++.|+.+.|||||+|--
T Consensus         3 T~~~WLn~YmQl~~~~~~~~~l~Pqys~~~fiq~aqLLDLC~LDi~sl~fsYsvLAAaAl~h~   65 (130)
T d1w98b1           3 TIVSWLNVYMQVAYLNDLHEVLLPQYPQQIFIQIAELLDLCVLDVDCLEFPYGILAASALYHF   65 (130)
T ss_dssp             CHHHHHHHHHHHHTCCSSCCSSSCCSCHHHHHHHHHHHHHHHHSGGGGGSCHHHHHHHHHHHT
T ss_pred             chhHHHHHHHHHHhcCCccceecCCCCHHHHHHHHHHHHHHHhhhhhhcCchHHHHHHHHHHc
Confidence            445556666655432           3455556667888888888899999999999999843

>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=90.47  E-value=0.33  Score=32.97  Aligned_cols=56  Identities=7%  Similarity=0.025  Sum_probs=44.1

Q ss_pred             HHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         161 RPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       161 ~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      +++...+..+++..+....|..+++..+...-.-.-.-..+|++|+++|++.....
T Consensus        36 dWl~~v~~~~~l~~eTl~lAv~llDryl~~~~i~~~~lqLi~~tcL~IAsK~ee~~   91 (127)
T d1bu2a1          36 TWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVK   91 (127)
T ss_dssp             HHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSCCCTTTHHHHHHHHHHHHHHHSSSS
T ss_pred             HHHHHHHHHHCCChHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHhcC
Confidence            56677777888888999999999998665444445667899999999999986543

>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=88.80  E-value=0.27  Score=33.40  Aligned_cols=56  Identities=14%  Similarity=0.034  Sum_probs=42.0

Q ss_pred             HHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         161 RPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       161 ~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      +++......++++.+....|..+++..+...-...-....+|++|+++|++.....
T Consensus        36 ~W~~~v~~~~~l~~~t~~lAv~llDr~l~~~~i~~~~~qLi~~~cl~iAsK~ee~~   91 (128)
T d2cchb1          36 DWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIY   91 (128)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCSS
T ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHHhcccCCchHHHHHHHHHHHHHHHHHHhcc
Confidence            45666777888888999999999887654333334557789999999999976543

>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=87.62  E-value=0.52  Score=32.13  Aligned_cols=56  Identities=11%  Similarity=0.027  Sum_probs=40.8

Q ss_pred             HHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         161 RPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       161 ~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      +++...+..+++..+....|..+++..+...-.-.-.=..+|++|+++|++.....
T Consensus        41 dWl~~v~~~~~l~~et~~lAv~llDrfls~~~v~~~~lqLia~tcl~iAsK~ee~~   96 (132)
T d1g3nc1          41 TWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLT   96 (132)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHHHHHHHCSS
T ss_pred             HHHHHHHHHhCCCcchHHHHHHHHHHHcCcccCcHHHHHHHHHHHHHHHHHhcccC
Confidence            45666677788888999999999988664333323345679999999999976543

>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=87.03  E-value=0.41  Score=33.12  Aligned_cols=56  Identities=7%  Similarity=0.019  Sum_probs=42.1

Q ss_pred             HHHHHHHHHhCccHHHHHHHHHHHHHHhCCcccccccHHHHHHHHHHHhcccCccc
Q psy1168         161 RPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIGECSFSFTPHVIA  216 (229)
Q Consensus       161 ~~l~~~~~~l~~~~~i~~~a~~~~~~~~~~~~~l~~~P~~IA~aai~~A~~~~~~~  216 (229)
                      +++...+..+++..+....|..+++..+.....-......+|++|+++|++.....
T Consensus        49 dWm~~v~~~~~l~~etl~lAv~llDrfls~~~i~~~~lqL~a~tcL~IAsK~ee~~  104 (141)
T d1f5qb1          49 TWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYM  104 (141)
T ss_dssp             HHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHCSS
T ss_pred             HHHHHHHHHHCCChHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHhcC
Confidence            46666777788888888888888887654333445667889999999999986543

>d1jkwa2 a.74.1.1 (A:162-287) 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=86.62  E-value=3.2  Score=27.78  Aligned_cols=55  Identities=16%  Similarity=0.203  Sum_probs=40.3

Q ss_pred             HHHHHHHHh---cCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHhhcccc
Q psy1168          50 NFIQILGEQ---LKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEF  104 (229)
Q Consensus        50 ~~I~~~~~~---l~l~~~~~~~A~~~~~Rf~~~~s~~~~~~~~v~~acl~LA~K~ee~  104 (229)
                      .++.++...   +.-+......|-.+++.-+.....-.|.|..|++||+++|++....
T Consensus         8 g~l~dl~~~~~~~~~~~~l~~~a~~~lnds~~Td~~l~y~P~qIalaal~~a~~~~~~   65 (126)
T d1jkwa2           8 GFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGI   65 (126)
T ss_dssp             HHHHHHHHHCTTCCCHHHHHHHHHHHHHHHTTSTHHHHSCHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHhccCcCCHHHHHHHHHHHHHHHHcCCeeeeeCHHHHHHHHHHHHHHHcCC
Confidence            444444333   2334567778888888887777777789999999999999998754

>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=84.41  E-value=1.1  Score=30.64  Aligned_cols=55  Identities=11%  Similarity=0.017  Sum_probs=40.8

Q ss_pred             HHHHHHHHHhCccHHHHHHHHHHHHHHhC-CcccccccHHHHHHHHHHHhcccCcc
Q psy1168         161 RPLLQLVQDIGHEDQLLALAWRVINDSLR-TDVCLLYPPYQIAIGECSFSFTPHVI  215 (229)
Q Consensus       161 ~~l~~~~~~l~~~~~i~~~a~~~~~~~~~-~~~~l~~~P~~IA~aai~~A~~~~~~  215 (229)
                      +++...+..++++.+....|..+++..+. ......-.-..+|++|+++|++....
T Consensus        48 dW~~~v~~~~~l~~et~~lAv~llDryl~~~~~v~~~~lqL~a~acL~IAsK~ee~  103 (140)
T d1w98b2          48 DWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEI  103 (140)
T ss_dssp             HHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCS
T ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHHHhccccccHHHHhHHHHHHHHHHHHHccc
Confidence            45667778888899999999999987543 22222334578999999999997643