Query 017441
Match_columns 371
No_of_seqs 334 out of 1699
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 08:36:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017441.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017441hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0656 G1/S-specific cyclin D 100.0 2.3E-56 5.1E-61 428.0 24.9 288 62-367 42-334 (335)
2 KOG0655 G1/S-specific cyclin E 100.0 4.1E-36 8.9E-41 281.7 18.0 219 60-294 106-337 (408)
3 KOG0653 Cyclin B and related k 100.0 1.9E-31 4.1E-36 266.3 17.4 234 65-310 127-366 (391)
4 COG5024 Cyclin [Cell division 100.0 1E-30 2.2E-35 259.6 12.4 239 53-307 173-414 (440)
5 KOG0654 G2/Mitotic-specific cy 99.9 7.5E-26 1.6E-30 219.5 8.2 214 69-295 107-325 (359)
6 TIGR00569 ccl1 cyclin ccl1. Un 99.9 7.9E-23 1.7E-27 197.0 19.1 191 93-291 53-251 (305)
7 PF00134 Cyclin_N: Cyclin, N-t 99.9 1.6E-22 3.4E-27 170.4 12.3 124 67-196 1-127 (127)
8 KOG0834 CDK9 kinase-activating 99.9 3.6E-22 7.9E-27 192.3 15.7 200 92-296 35-249 (323)
9 KOG0835 Cyclin L [General func 99.9 2.5E-20 5.5E-25 175.7 18.0 195 92-294 19-231 (367)
10 KOG0794 CDK8 kinase-activating 99.8 2.1E-20 4.6E-25 168.6 13.5 192 94-295 39-241 (264)
11 COG5333 CCL1 Cdk activating ki 99.8 1.1E-17 2.3E-22 158.0 14.0 163 93-261 42-209 (297)
12 PRK00423 tfb transcription ini 99.5 2.5E-12 5.5E-17 125.1 22.7 183 95-292 121-304 (310)
13 PF02984 Cyclin_C: Cyclin, C-t 99.4 4.4E-13 9.5E-18 110.9 8.6 104 198-307 1-105 (118)
14 cd00043 CYCLIN Cyclin box fold 99.4 5.3E-13 1.2E-17 103.5 8.5 87 96-188 2-88 (88)
15 KOG2496 Cdk activating kinase 99.4 5.2E-12 1.1E-16 118.8 16.2 155 101-259 61-223 (325)
16 smart00385 CYCLIN domain prese 99.3 3.5E-12 7.7E-17 97.9 7.9 83 101-189 1-83 (83)
17 COG1405 SUA7 Transcription ini 98.9 2.7E-07 5.9E-12 88.5 19.4 185 94-292 95-279 (285)
18 KOG1597 Transcription initiati 98.7 1.8E-06 3.9E-11 81.6 17.7 181 97-293 105-289 (308)
19 PF08613 Cyclin: Cyclin; Inte 98.3 3.5E-06 7.5E-11 73.5 8.9 93 98-195 53-149 (149)
20 smart00385 CYCLIN domain prese 98.2 1.2E-05 2.7E-10 61.0 9.0 81 202-289 1-82 (83)
21 cd00043 CYCLIN Cyclin box fold 98.2 2.4E-05 5.2E-10 60.0 10.2 85 197-288 2-87 (88)
22 KOG4164 Cyclin ik3-1/CABLES [C 98.1 1.2E-06 2.6E-11 85.3 2.8 98 98-198 384-482 (497)
23 KOG1598 Transcription initiati 97.8 0.00035 7.7E-09 71.2 13.2 174 102-289 73-251 (521)
24 PF00382 TFIIB: Transcription 95.8 0.039 8.4E-07 41.6 6.5 60 103-166 1-60 (71)
25 PF00382 TFIIB: Transcription 95.6 0.12 2.7E-06 38.9 8.7 71 204-281 1-71 (71)
26 KOG1674 Cyclin [General functi 94.6 0.11 2.3E-06 48.3 6.9 97 99-198 78-181 (218)
27 PRK00423 tfb transcription ini 92.8 1.3 2.8E-05 43.3 11.3 87 200-293 125-211 (310)
28 PF09080 K-cyclin_vir_C: K cyc 92.0 3.1 6.6E-05 32.8 10.1 94 200-293 4-100 (106)
29 PF09241 Herp-Cyclin: Herpesvi 86.7 13 0.00029 29.0 10.4 95 199-293 3-99 (106)
30 KOG0834 CDK9 kinase-activating 81.2 1.5 3.3E-05 43.0 3.4 89 98-189 154-243 (323)
31 COG1405 SUA7 Transcription ini 77.0 38 0.00082 32.8 11.5 88 199-294 99-187 (285)
32 PF02984 Cyclin_C: Cyclin, C-t 68.3 5.4 0.00012 32.0 3.1 55 100-157 4-58 (118)
33 KOG1597 Transcription initiati 68.0 13 0.00029 35.8 6.0 49 243-294 146-194 (308)
34 PF00134 Cyclin_N: Cyclin, N-t 66.1 69 0.0015 25.9 9.8 68 222-291 52-121 (127)
35 KOG1675 Predicted cyclin [Gene 62.3 10 0.00022 36.9 4.0 99 106-209 200-299 (343)
36 KOG0835 Cyclin L [General func 58.7 37 0.00079 33.5 7.1 60 118-183 162-221 (367)
37 TIGR00569 ccl1 cyclin ccl1. Un 41.2 69 0.0015 31.3 6.1 37 223-259 80-116 (305)
38 PF12550 GCR1_C: Transcription 34.8 1.3E+02 0.0029 23.0 5.8 53 72-127 28-80 (81)
39 PF08613 Cyclin: Cyclin; Inte 21.6 5.1E+02 0.011 22.0 10.1 88 197-290 51-143 (149)
40 COG3474 Cytochrome c2 [Energy 21.2 1.5E+02 0.0032 25.4 4.0 42 61-106 85-130 (135)
No 1
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.3e-56 Score=428.02 Aligned_cols=288 Identities=43% Similarity=0.633 Sum_probs=240.4
Q ss_pred CCCCHHHHHHHHHHHhhcCC--CC-CCCCCchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCC
Q 017441 62 LFWDDNELLSLICKEKKENF--VP-SDPISDEILILARKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKP 138 (371)
Q Consensus 62 ~f~~~e~l~~Ll~~E~~~~~--~~-~~~q~~~i~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p 138 (371)
+.|++|.+.+|+++|.++.| +| ..+++. +++.+|.++++||++||+++++.++|++|||||||||++.+++++.+|
T Consensus 42 ~~~~e~~i~~ll~kEe~~~p~~~~~~~~~~~-~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~ 120 (335)
T KOG0656|consen 42 LLWDERVLANLLEKEEQHNPSLDYFLCVQKL-ILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKP 120 (335)
T ss_pred ccccHHHHHHHHHHHHHhCCCCchhhhcccc-cccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCch
Confidence 78999999999999999988 33 344444 889999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHHHhhcccccCccccchhhccCCCccccHHHHHHHHHHHHHHcCccccCCChhHHHHHHHHHhCCCCccc
Q 017441 139 WMGQLVAVACLSLAAKVDETQVPLLLDLQVKDPKYVFEAKTIQRMELLVLSTLQWRMNPVTPISFFDHIVRRLGLKTHLH 218 (371)
Q Consensus 139 ~~lqLlavaCL~LAaK~eE~~vp~l~dl~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~~~ 218 (371)
|++||+|+|||+||||+||+.+|.+.|++|.+.+|.|++++|+|||++||++|+|+|+++||++|+++|+++++..+...
T Consensus 121 W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~ 200 (335)
T KOG0656|consen 121 WMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNK 200 (335)
T ss_pred HHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccchH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999987777
Q ss_pred HHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCCCHHHHHHHHHHHHHHHhccCCC
Q 017441 219 WEFLYRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNISQDKLKECYLLILELSRGNGSQ 298 (371)
Q Consensus 219 ~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i~~e~l~~C~~~i~el~~~~~~~ 298 (371)
..++.++..+++.+.+|.+|++|+||+||+|++..+...+.+.....+...+..+++++++.+..|+. ..+.
T Consensus 201 ~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~--~~~~------ 272 (335)
T KOG0656|consen 201 HLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD--HFLS------ 272 (335)
T ss_pred HHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh--hhhh------
Confidence 78899999999999999999999999999999999998887666666667888899999999999998 0000
Q ss_pred CCcccccCCCCCCCcccccccccccCCCCCCCC--CCCCCCCCCCCCcccccchhhhccCCCCCeeeeecc
Q 017441 299 NQSCKRKHFPLPGSPSCIIDANFSCDSSNDSWP--AASPFSSPPEPRFKRSRIHVQQMRLPSLTRTFVDVL 367 (371)
Q Consensus 299 ~~~~~~k~~s~p~sP~~V~d~~~s~~s~~~s~~--~~s~~~s~~~~~~kr~~~~~~~~~~~~~~~~~~~~~ 367 (371)
....++.++++.--+.++..-+-. +.++..++++|..|+||.+.++++..+..+..+..+
T Consensus 273 ---------~~~~~~~~~l~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~rr~~~~~~~~~s~~~~~~~~l 334 (335)
T KOG0656|consen 273 ---------KILNSESDCLRGEASNESGEASLRDSSSSSSQSPNSPSLKKRRVSSDKERKQSSPPTEVRDL 334 (335)
T ss_pred ---------hccCCccccccHHHHhhhhcccccccchhccCCCCcccccccccccccccccCCCCcccccc
Confidence 022344455553111111111100 111222223677789999999999998888776654
No 2
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.1e-36 Score=281.67 Aligned_cols=219 Identities=25% Similarity=0.367 Sum_probs=187.7
Q ss_pred CCCCCC--HHHHHHHHHHHhhcCCCCCCCCC-chhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcc-CcccC
Q 017441 60 HDLFWD--DNELLSLICKEKKENFVPSDPIS-DEILILARKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILS-HSFQK 135 (371)
Q Consensus 60 ~~~f~~--~e~l~~Ll~~E~~~~~~~~~~q~-~~i~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~-~~v~~ 135 (371)
+.+-|. .+++..|+.||+.+..+-..+.. -++.++||++++|||++||+-|++.++|+||||.||||||.. ..+.+
T Consensus 106 p~lswgn~~eVW~lM~kkee~~l~~~~~l~qHpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~k 185 (408)
T KOG0655|consen 106 PCLSWGNSKEVWLLMLKKEERYLRDKHFLEQHPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSK 185 (408)
T ss_pred ccccccCHHHHHHHHHccchhhhhhhHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhh
Confidence 445566 48899999999987664333333 337899999999999999999999999999999999999976 46777
Q ss_pred CCCchhHHHHHHHHHHhhcccccCccccchh-hccCCCccccHHHHHHHHHHHHHHcCccccCCChhHHHHHHHHHhCCC
Q 017441 136 DKPWMGQLVAVACLSLAAKVDETQVPLLLDL-QVKDPKYVFEAKTIQRMELLVLSTLQWRMNPVTPISFFDHIVRRLGLK 214 (371)
Q Consensus 136 ~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~ 214 (371)
.+ +||+|+||||||||+||+++|++.+| +|+++.+ +.++|+.||+.||+.|+|++.++|...+|..|+...+.+
T Consensus 186 t~---lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAc--s~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n 260 (408)
T KOG0655|consen 186 TN---LQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGAC--SEDDILTMELIILKALKWELSPITIISWLNVYLQVDALN 260 (408)
T ss_pred hh---HHHhhHHHHHHHHHHhhccCccccceeeeccCcc--chHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcC
Confidence 77 99999999999999999999999999 8998876 799999999999999999999999999999999987654
Q ss_pred Cc--------ccHHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCCCHHHHHHHHH
Q 017441 215 TH--------LHWEFLYRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNISQDKLKECYL 286 (371)
Q Consensus 215 ~~--------~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i~~e~l~~C~~ 286 (371)
+. ...+|++.| .+++.++.|.+.+.|+-++|||||+++.... ....+.+|+.+..|.+|++
T Consensus 261 ~~~k~l~Pq~~~~efiqia-qlLDlc~ldids~~fsYrilaAAal~h~~s~----------e~v~kaSG~~w~~ie~cv~ 329 (408)
T KOG0655|consen 261 DAPKVLLPQYSQEEFIQIA-QLLDLCILDIDSLEFSYRILAAAALCHFTSI----------EVVKKASGLEWDSIEECVD 329 (408)
T ss_pred CCCceeccccchHHHHHHH-HHHHHHHhccccccchHHHHHHHHHHHHhHH----------HHHHHcccccHHHHHHHHH
Confidence 32 225677777 6778888999999999999999999887541 3556789999999999999
Q ss_pred HHHHHHhc
Q 017441 287 LILELSRG 294 (371)
Q Consensus 287 ~i~el~~~ 294 (371)
.|.-+..-
T Consensus 330 wm~Pf~rv 337 (408)
T KOG0655|consen 330 WMVPFVRV 337 (408)
T ss_pred HHHHHHHH
Confidence 99887654
No 3
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=99.97 E-value=1.9e-31 Score=266.33 Aligned_cols=234 Identities=24% Similarity=0.264 Sum_probs=192.7
Q ss_pred CHHHHHHHHHHHhhcCC-CCCCCCCchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHH
Q 017441 65 DDNELLSLICKEKKENF-VPSDPISDEILILARKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQL 143 (371)
Q Consensus 65 ~~e~l~~Ll~~E~~~~~-~~~~~q~~~i~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqL 143 (371)
-++++..+..+|.+..| .|.. +...++..||.++|||+++|+.+|++.++|+++|||++||||+...++..+ +||
T Consensus 127 ~~di~~~l~~~e~~~~p~~~~~-~~~e~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~---lqL 202 (391)
T KOG0653|consen 127 VQDIFEYLRQLELEFLPLSYDI-SQSEIRAKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKK---LQL 202 (391)
T ss_pred HHHHHHHHHHHHHhhCchhhhc-ccccccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHH---hhH
Confidence 36778888888854444 2332 233378899999999999999999999999999999999999998888777 999
Q ss_pred HHHHHHH-HhhcccccCccccchh-hccCCCccccHHHHHHHHHHHHHHcCccccCCChhHHHHHHHHHhCCCCcccHHH
Q 017441 144 VAVACLS-LAAKVDETQVPLLLDL-QVKDPKYVFEAKTIQRMELLVLSTLQWRMNPVTPISFFDHIVRRLGLKTHLHWEF 221 (371)
Q Consensus 144 lavaCL~-LAaK~eE~~vp~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~~~~~~ 221 (371)
+|++||+ ||+|+||..+|.+.|+ +++++. |++++|++||+.||.+|+|++..|||+.||++|++..... ...
T Consensus 203 vgvsalf~IA~K~EE~~~P~v~dlv~isd~~--~s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d----~~~ 276 (391)
T KOG0653|consen 203 VGVSALLSIACKYEEISLPSVEDLVLITDGA--YSREEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYD----IKT 276 (391)
T ss_pred HhHHHHHHHHHhhhhccCCccceeEeeeCCc--cchHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcc----hhH
Confidence 9999966 9999999999999999 676665 5899999999999999999999999999999999987722 233
Q ss_pred HHHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCCCHHHHHHHHHHHHHHHhccCC--CC
Q 017441 222 LYRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNISQDKLKECYLLILELSRGNGS--QN 299 (371)
Q Consensus 222 l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i~~e~l~~C~~~i~el~~~~~~--~~ 299 (371)
.....+++...++|++++.++||.+|+|+++++........ .|...+..++|+...++.+|.+.+..+...... ..
T Consensus 277 ~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~~~~~--~w~~~~~~~sg~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (391)
T KOG0653|consen 277 RTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRMLSKGD--VWSPTLEHYSGYSESYLFECARSLSALSLSSLQNPSL 354 (391)
T ss_pred HHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHhccCC--ccCCCCeeccCCCcHHHHHHHHHHHHHHHHhcccchh
Confidence 44556778888999999999999999999999998876432 588888999999888999999999886655421 12
Q ss_pred Cc-ccccCCCCC
Q 017441 300 QS-CKRKHFPLP 310 (371)
Q Consensus 300 ~~-~~~k~~s~p 310 (371)
+. ..+||.+.+
T Consensus 355 ~~~~~~ky~~~~ 366 (391)
T KOG0653|consen 355 RASVLNKYNSSK 366 (391)
T ss_pred HHHHHHHhcccc
Confidence 22 556775533
No 4
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=99.97 E-value=1e-30 Score=259.63 Aligned_cols=239 Identities=22% Similarity=0.235 Sum_probs=199.0
Q ss_pred CCCccccCCCCCCHHHHHHHHHHHhhcCCCCCCCCCch-hhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccC
Q 017441 53 LPPVLQEHDLFWDDNELLSLICKEKKENFVPSDPISDE-ILILARKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSH 131 (371)
Q Consensus 53 ~~~~~~~~~~f~~~e~l~~Ll~~E~~~~~~~~~~q~~~-i~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~ 131 (371)
.|+++-|. ..+++..|+.+|....|....+.+++ +...||..+|+||.+|+.+|++.++|+++|||++||||++.
T Consensus 173 d~~mv~Ey----~~~Ife~l~k~e~~~lp~~~yl~kq~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~ 248 (440)
T COG5024 173 DPLMVPEY----ASDIFEYLLKLELIDLPNPNYLIKQSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSR 248 (440)
T ss_pred CccchHHH----HHHHHHHHHHHHHHhcCcHHHHhhcchhHHhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccC
Confidence 34555544 67999999999999998432243333 55699999999999999999999999999999999999999
Q ss_pred cccCCCCchhHHHHHHHHHHhhcccccCccccchh-hccCCCccccHHHHHHHHHHHHHHcCccccCCChhHHHHHHHHH
Q 017441 132 SFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDL-QVKDPKYVFEAKTIQRMELLVLSTLQWRMNPVTPISFFDHIVRR 210 (371)
Q Consensus 132 ~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~ 210 (371)
.+.-.+ +||+|++|||||||+||.+.|.+.++ +++++.| +.++|.++|+.+|.+|+|++..|+|..|++++.+.
T Consensus 249 ~v~l~k---~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~--t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka 323 (440)
T COG5024 249 VVSLEK---YQLVGISALFIASKYEEVNCPSIKDLVYATDGAF--TRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKA 323 (440)
T ss_pred cccHHH---HHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccc--cHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhh
Confidence 999888 99999999999999999999999999 6766655 79999999999999999999999999997666654
Q ss_pred hCCCCcccHHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHhC-CCHHHHHHHHHHHH
Q 017441 211 LGLKTHLHWEFLYRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVLN-ISQDKLKECYLLIL 289 (371)
Q Consensus 211 l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~-i~~e~l~~C~~~i~ 289 (371)
-.... .....+.+++..+..+++|.+++||.+|+||++.+++.++..+ |...+..++| |+.+++..+++.+.
T Consensus 324 ~dyd~----~srt~~k~~~e~s~~~~~f~~~~~S~~~aaa~~~s~~~~~~~~---w~~~l~~ySg~y~~~~l~~~~~~~~ 396 (440)
T COG5024 324 SDYDI----FSRTPAKFSSEISPVDYKFIQISPSWCAAAAMYLSRKILSQNQ---WDRTLIHYSGNYTNPDLKPLNESNK 396 (440)
T ss_pred cccch----hhhhhHhhhCCchHhhhhhccCCchHHHHHHHHHHHhhhccCC---CCccccccCCCCCchhHHHHHHHHH
Confidence 33221 1112455677777899999999999999999999999887543 8888989998 99999999999999
Q ss_pred HHHhccCCCCCcccccCC
Q 017441 290 ELSRGNGSQNQSCKRKHF 307 (371)
Q Consensus 290 el~~~~~~~~~~~~~k~~ 307 (371)
+.+.++........+||.
T Consensus 397 ~~l~~~~~~~~~i~~Ky~ 414 (440)
T COG5024 397 ENLQNPSVHHDAIFPKYP 414 (440)
T ss_pred HHhcccchhhhhhhhccc
Confidence 999887543334455554
No 5
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.92 E-value=7.5e-26 Score=219.51 Aligned_cols=214 Identities=23% Similarity=0.303 Sum_probs=184.3
Q ss_pred HHHHHHHHhh-cCC--CC-CCCCCchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHH
Q 017441 69 LLSLICKEKK-ENF--VP-SDPISDEILILARKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLV 144 (371)
Q Consensus 69 l~~Ll~~E~~-~~~--~~-~~~q~~~i~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLl 144 (371)
..++..-|.. ..| +| ..+|.+ +++.||.++|+|.++|++.+++..+++++++++.|||+....+.+.+ +|++
T Consensus 107 ~~~~r~~ei~~~rp~~~~~e~vq~d-~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~~~~k---~ql~ 182 (359)
T KOG0654|consen 107 YNTLRVSDIKSERPLPSKFEFVQAD-ITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEVNKQK---LQLV 182 (359)
T ss_pred hhcccccchhhccCcccceeeeecC-CCcchhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhccCccHHHH---HHHh
Confidence 3344444444 444 45 666777 99999999999999999999999999999999999999999999888 9999
Q ss_pred HHHHHHHhhcccccCccccchh-hccCCCccccHHHHHHHHHHHHHHcCccccCCChhHHHHHHHHHhCCCCcccHHHHH
Q 017441 145 AVACLSLAAKVDETQVPLLLDL-QVKDPKYVFEAKTIQRMELLVLSTLQWRMNPVTPISFFDHIVRRLGLKTHLHWEFLY 223 (371)
Q Consensus 145 avaCL~LAaK~eE~~vp~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~~~~~~l~ 223 (371)
|++|++||+|+||...|.+.++ .+.+.. |+..++.+||..||..|.|.+..||.-.|+..|++.... .....-.
T Consensus 183 g~s~m~I~sk~ee~~~~~~~ef~~itd~t--y~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~~~---~~~~~e~ 257 (359)
T KOG0654|consen 183 GISAMLIASKYEEIKEPRVEEFCYITDNT--YTYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVAQT---PELQVEP 257 (359)
T ss_pred CcccceeeccchhhcchHHHHHHhhhhhh--hHHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhhcc---hhHHHHH
Confidence 9999999999999999999998 665554 478899999999999999999999999999999877654 2223445
Q ss_pred HHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCCCHHHHHHHHHHHHHHHhcc
Q 017441 224 RCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNISQDKLKECYLLILELSRGN 295 (371)
Q Consensus 224 ~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i~~e~l~~C~~~i~el~~~~ 295 (371)
.+.++....+.++.|+.|.||+|||||+++|.-.++ ...|.+.|...+||+.++++.|+..|+ ++.+.
T Consensus 258 ~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~---~~pW~~~L~~~T~y~~edl~~~v~~L~-~~l~~ 325 (359)
T KOG0654|consen 258 LANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLD---FHPWNQTLEDYTGYKAEDLKPCVLDLH-LYLNA 325 (359)
T ss_pred HHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhcc---CCCCchhhHHhhcccHHHHHHHHHHHh-cccCC
Confidence 577888888999999999999999999999998887 345999999999999999999999999 66554
No 6
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.90 E-value=7.9e-23 Score=196.96 Aligned_cols=191 Identities=19% Similarity=0.264 Sum_probs=146.1
Q ss_pred HHHHHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchh-hcc
Q 017441 93 ILARKEVVEWVLRVKAHFG--FTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDL-QVK 169 (371)
Q Consensus 93 ~~~R~~~v~Wi~~v~~~~~--l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl-~v~ 169 (371)
...|..-+.+|.++|.+++ +++.|+++|+.||+||+...++...+ .+++|+|||+||+|+||..+ .+.++ ...
T Consensus 53 ~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~---p~~Ia~tclfLA~KvEE~~~-si~~fv~~~ 128 (305)
T TIGR00569 53 LDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYH---PKIIMLTCVFLACKVEEFNV-SIDQFVGNL 128 (305)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcC---HHHHHHHHHHHHHhccccCc-CHHHHHhhc
Confidence 3689999999999999999 99999999999999999999999777 99999999999999999954 56666 222
Q ss_pred CCCccccHHHHHHHHHHHHHHcCccccCCChhHHHHHHHHHhCCC--C-cccHHHHHHHHHHHHHHhchhhccCCcHHHH
Q 017441 170 DPKYVFEAKTIQRMELLVLSTLQWRMNPVTPISFFDHIVRRLGLK--T-HLHWEFLYRCEHLLLSVIADSRFMCYLPSTL 246 (371)
Q Consensus 170 ~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~--~-~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~I 246 (371)
........++|++||..||++|+|++.+++|+.++..|+..+... . .....+...+..++..++...-++.|+||+|
T Consensus 129 ~~~~~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~I 208 (305)
T TIGR00569 129 KETPLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQI 208 (305)
T ss_pred cCCchhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHH
Confidence 222223568999999999999999999999999999998654311 1 1112344667777777666666888999999
Q ss_pred HHHHHHHHHHhcCCCCccchHHHHHHHhCC--CHHHHHHHHHHHHHH
Q 017441 247 ATATMLHTIQEVEPCNPVEHQNLLMGVLNI--SQDKLKECYLLILEL 291 (371)
Q Consensus 247 AaAai~~a~~~l~~~~~~~~~~~L~~~~~i--~~e~l~~C~~~i~el 291 (371)
|+|||++|.+.++... ++ ......+. +.+.+..-++.|.++
T Consensus 209 AlAAI~lA~~~~~~~l-~~---~~~e~~~~~~~~~~~~~l~~~~~~~ 251 (305)
T TIGR00569 209 ALAAILHTASRAGLNM-ES---YLTEQLSVPGNREELPQLIDIMREL 251 (305)
T ss_pred HHHHHHHHHHHhCCCC-cc---cchhhhcccccHHHHHHHHHHHHHH
Confidence 9999999999887422 11 11234554 556655555555544
No 7
>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). 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 ....
Probab=99.89 E-value=1.6e-22 Score=170.42 Aligned_cols=124 Identities=31% Similarity=0.461 Sum_probs=103.6
Q ss_pred HHHHHHHHHHhhcCC--CCCCCCCchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHH
Q 017441 67 NELLSLICKEKKENF--VPSDPISDEILILARKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLV 144 (371)
Q Consensus 67 e~l~~Ll~~E~~~~~--~~~~~q~~~i~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLl 144 (371)
|++.+|+++|.++.+ .|-..+. .++...|..+++||.+++..+++++.|+++|+.|||||+....+.+.+ ++++
T Consensus 1 ~i~~~~~~~e~~~~~~~~~~~~~~-~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~---~~li 76 (127)
T PF00134_consen 1 DIFRYLLEKELKYKPNPDYLEQQP-EITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSK---LQLI 76 (127)
T ss_dssp HHHHHHHHHHHHTTCCTTHGTGTS-SHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCG---HHHH
T ss_pred CHHHHHHHHHHHHCcCccccccCh-hcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccch---hhhh
Confidence 578999999999875 3333233 488999999999999999999999999999999999999999888777 9999
Q ss_pred HHHHHHHhhcccccCccccchh-hccCCCccccHHHHHHHHHHHHHHcCcccc
Q 017441 145 AVACLSLAAKVDETQVPLLLDL-QVKDPKYVFEAKTIQRMELLVLSTLQWRMN 196 (371)
Q Consensus 145 avaCL~LAaK~eE~~vp~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~ 196 (371)
|+|||+||+|++|..+|.+.++ .+. .+.|+.++|.+||+.||++|+|+++
T Consensus 77 ~~~cl~lA~K~~e~~~~~~~~~~~~~--~~~~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 77 ALACLFLASKMEEDNPPSISDLIRIS--DNTFTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp HHHHHHHHHHHHTSS--HHHHHHHHT--TTSSHHHHHHHHHHHHHHHTTT---
T ss_pred hhhHHHHhhhhhccccchHHHHHHHH--cCCCCHHHHHHHHHHHHHHCCCCcC
Confidence 9999999999999988999998 443 4577999999999999999999985
No 8
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.88 E-value=3.6e-22 Score=192.33 Aligned_cols=200 Identities=22% Similarity=0.291 Sum_probs=167.5
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchh-hccC
Q 017441 92 LILARKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDL-QVKD 170 (371)
Q Consensus 92 ~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl-~v~~ 170 (371)
....|...+.||.+++.++|+++.|+++|+.||+||+...++.... .+.+|++||+||+|+||+ +..+.|+ .+..
T Consensus 35 E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~---~~~vA~sclfLAgKvEet-p~kl~dIi~~s~ 110 (323)
T KOG0834|consen 35 ELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFD---PYTVAASCLFLAGKVEET-PRKLEDIIKVSY 110 (323)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCc---HHHHHHHHHHHHhhcccC-cccHHHHHHHHH
Confidence 3579999999999999999999999999999999999999999888 799999999999999999 5667777 2211
Q ss_pred -----------CCccccHHHHHHHHHHHHHHcCccccCCChhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhcc
Q 017441 171 -----------PKYVFEAKTIQRMELLVLSTLQWRMNPVTPISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFM 239 (371)
Q Consensus 171 -----------~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl 239 (371)
..|.=-++.|+..|+.||++|+|++++-+|+.||..|+..+....+........+..++..++...-++
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL 190 (323)
T KOG0834|consen 111 RYLNPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCL 190 (323)
T ss_pred HHcCcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeE
Confidence 112223688999999999999999999999999999999998766543345566778888888888889
Q ss_pred CCcHHHHHHHHHHHHHHhcCCCCccchHH-HHHHHhC--CCHHHHHHHHHHHHHHHhccC
Q 017441 240 CYLPSTLATATMLHTIQEVEPCNPVEHQN-LLMGVLN--ISQDKLKECYLLILELSRGNG 296 (371)
Q Consensus 240 ~~~PS~IAaAai~~a~~~l~~~~~~~~~~-~L~~~~~--i~~e~l~~C~~~i~el~~~~~ 296 (371)
+|+|..||+|||.+|....+. ....+.. .|+...+ ++.+.+.+.+..+.++|....
T Consensus 191 ~y~p~~IAva~i~lA~~~~~~-~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y~~~~ 249 (323)
T KOG0834|consen 191 QYSPHSIAVACIHLAAKLLGV-ELPSDTDKRWWREFDETVTNELLDDICHEFLDLYEQTP 249 (323)
T ss_pred eecCcEEEeehhhHHHHHcCC-CCCCCcccchhhhhcccCCHHHHHHHHHHHHHHHhhcc
Confidence 999999999999999987764 2222222 5778888 999999999999999997653
No 9
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.85 E-value=2.5e-20 Score=175.66 Aligned_cols=195 Identities=18% Similarity=0.268 Sum_probs=167.6
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchh-hc--
Q 017441 92 LILARKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDL-QV-- 168 (371)
Q Consensus 92 ~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl-~v-- 168 (371)
....|...++||.+.|.-++|++.+.+++..+|-||+...++-+.+ +..+++||++||+|+||. |-.+.|+ .|
T Consensus 19 e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~---~e~vv~ACv~LASKiEE~-Prr~rdVinVFh 94 (367)
T KOG0835|consen 19 EEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHD---FEIVVMACVLLASKIEEE-PRRIRDVINVFH 94 (367)
T ss_pred HHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhcccccccc---HHHHHHHHHHHHhhhccc-cccHhHHHHHHH
Confidence 3568999999999999999999999999999999999999998877 999999999999999998 5555665 22
Q ss_pred --------c-------CCCccccHHHHHHHHHHHHHHcCccccCCChhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHh
Q 017441 169 --------K-------DPKYVFEAKTIQRMELLVLSTLQWRMNPVTPISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVI 233 (371)
Q Consensus 169 --------~-------~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l 233 (371)
. +..+.-.+..+.++|+.||..|+|++++.+|+.++-.|+..+++.++. .+++.++.+...++
T Consensus 95 ~L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~--~l~Q~~wNfmNDsl 172 (367)
T KOG0835|consen 95 YLEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNL--KLLQAAWNFMNDSL 172 (367)
T ss_pred HHHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCch--hHHHHHHHhhhhcc
Confidence 0 011112356789999999999999999999999999999999998876 57888899999999
Q ss_pred chhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCCCHHHHHHHHHHHHHHHhc
Q 017441 234 ADSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNISQDKLKECYLLILELSRG 294 (371)
Q Consensus 234 ~d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i~~e~l~~C~~~i~el~~~ 294 (371)
...-|+.|+|+.||||||++|.+.++.. ....+.|..+++.++++|.+.+-.+..+|..
T Consensus 173 RT~v~vry~pe~iACaciyLaAR~~eIp--Lp~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~ 231 (367)
T KOG0835|consen 173 RTDVFVRYSPESIACACIYLAARNLEIP--LPFQPHWFKAFDTTKREIDEICYRLIPLYKR 231 (367)
T ss_pred ccceeeecCHHHHHHHHHHHHHhhhcCC--CCCCccHHHHcCCcHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999988822 1233467888999999999999999999887
No 10
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.84 E-value=2.1e-20 Score=168.59 Aligned_cols=192 Identities=21% Similarity=0.268 Sum_probs=157.9
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchhh-----c
Q 017441 94 LARKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDLQ-----V 168 (371)
Q Consensus 94 ~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl~-----v 168 (371)
..+--..+.|.++++++++.+.++++|+.||-||+.+.++.... ..|+|.||++||+|+||..+-..+-+. +
T Consensus 39 ~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~---p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L 115 (264)
T KOG0794|consen 39 KLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIE---PRLLAPTCLYLACKVEECPIVHIRLLVNEAKVL 115 (264)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccC---HHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHH
Confidence 34455567799999999999999999999999999999988778 899999999999999998422222220 1
Q ss_pred ------cCCCccccHHHHHHHHHHHHHHcCccccCCChhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhccCCc
Q 017441 169 ------KDPKYVFEAKTIQRMELLVLSTLQWRMNPVTPISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFMCYL 242 (371)
Q Consensus 169 ------~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~ 242 (371)
....+.++.+.|.+||..+|+.|+.-+-+.+|+.-|..++...|..+. ..+..+..+...+....-++-|+
T Consensus 116 ~~~f~~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~---~~l~~~W~ivNDSyr~Dl~Ll~P 192 (264)
T KOG0794|consen 116 KTRFSYWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQ---KLLQLAWSIVNDSYRMDLCLLYP 192 (264)
T ss_pred hhhcccchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccch---hhhhhhHhhhcchhhcceeeecC
Confidence 223445678899999999999999999999999999999999887543 34566777777777777788999
Q ss_pred HHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCCCHHHHHHHHHHHHHHHhcc
Q 017441 243 PSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNISQDKLKECYLLILELSRGN 295 (371)
Q Consensus 243 PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i~~e~l~~C~~~i~el~~~~ 295 (371)
|..||.||++.|+...+.. -.+.|...+.+|.++|.+|++.|.++|..-
T Consensus 193 Ph~IalAcl~Ia~~~~~k~----~~~~w~~el~vD~ekV~~~v~~I~~lYe~w 241 (264)
T KOG0794|consen 193 PHQIALACLYIACVIDEKD----IPKAWFAELSVDMEKVKDIVQEILKLYELW 241 (264)
T ss_pred HHHHHHHHHHHHHhhcCCC----hHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Confidence 9999999999999876643 336777888999999999999999999764
No 11
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=99.75 E-value=1.1e-17 Score=158.00 Aligned_cols=163 Identities=16% Similarity=0.264 Sum_probs=137.7
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhccccc--Cccccchhhc--
Q 017441 93 ILARKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDET--QVPLLLDLQV-- 168 (371)
Q Consensus 93 ~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~--~vp~l~dl~v-- 168 (371)
...|..-..||..+|.+++++..++.+||.||+||+.+..+.... ++-++.||++||+|+||+ ++ .+..+..
T Consensus 42 ~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~---~~~vv~tcv~LA~K~ed~~~~I-~i~~~~~~~ 117 (297)
T COG5333 42 LNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEIS---LYSVVTTCVYLACKVEDTPRDI-SIESFEARD 117 (297)
T ss_pred hhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhccccccc---HHHHHHhheeeeeecccccchh-hHHHHHhhc
Confidence 457777889999999999999999999999999999999988777 999999999999999996 21 1111111
Q ss_pred -cCCCccccHHHHHHHHHHHHHHcCccccCCChhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhccCCcHHHHH
Q 017441 169 -KDPKYVFEAKTIQRMELLVLSTLQWRMNPVTPISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFMCYLPSTLA 247 (371)
Q Consensus 169 -~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IA 247 (371)
......-+++.|..+|..||+.|+|++++++|+.++.+|+..+...+. .+..+.|+.++..++...-++.|+|..||
T Consensus 118 ~~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~--~~~~~~aw~~inDa~~t~~~llypphiIA 195 (297)
T COG5333 118 LWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDK--YKLLQIAWKIINDALRTDLCLLYPPHIIA 195 (297)
T ss_pred cccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccH--HHHHHHHHHHHHhhhhceeeeecChHHHH
Confidence 011223368999999999999999999999999999999998876655 46778899999999888889999999999
Q ss_pred HHHHHHHHHhcCCC
Q 017441 248 TATMLHTIQEVEPC 261 (371)
Q Consensus 248 aAai~~a~~~l~~~ 261 (371)
+||++.|.+.++..
T Consensus 196 ~a~l~ia~~~~~~~ 209 (297)
T COG5333 196 LAALLIACEVLGMP 209 (297)
T ss_pred HHHHHHHHHhcCCc
Confidence 99999999987744
No 12
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.52 E-value=2.5e-12 Score=125.11 Aligned_cols=183 Identities=16% Similarity=0.152 Sum_probs=152.0
Q ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchh-hccCCCc
Q 017441 95 ARKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDL-QVKDPKY 173 (371)
Q Consensus 95 ~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl-~v~~~~~ 173 (371)
.-..+..-|.+++..++++..+.-.|..++.+++....+.... ...+++|||++|+|.++. +-.+.++ .+.
T Consensus 121 ~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs---~~~i~AAclYiACR~~~~-prtl~eI~~~~---- 192 (310)
T PRK00423 121 NLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRS---IEGVVAAALYAACRRCKV-PRTLDEIAEVS---- 192 (310)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCC---HHHHHHHHHHHHHHHcCC-CcCHHHHHHHh----
Confidence 3355667899999999999999999999999999987776656 889999999999999888 5577777 222
Q ss_pred cccHHHHHHHHHHHHHHcCccccCCChhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHHH
Q 017441 174 VFEAKTIQRMELLVLSTLQWRMNPVTPISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFMCYLPSTLATATMLH 253 (371)
Q Consensus 174 ~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~ 253 (371)
..+.++|.+.++.|++.|+.++.+..|.+|+..|...+++.+. +.+.+..++..+....-..+.+|..|||||||+
T Consensus 193 ~v~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~----v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYl 268 (310)
T PRK00423 193 RVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGE----VQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYI 268 (310)
T ss_pred CCCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHH----HHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHH
Confidence 1268999999999999999999999999999999999998753 445666666655444445799999999999999
Q ss_pred HHHhcCCCCccchHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 017441 254 TIQEVEPCNPVEHQNLLMGVLNISQDKLKECYLLILELS 292 (371)
Q Consensus 254 a~~~l~~~~~~~~~~~L~~~~~i~~e~l~~C~~~i~el~ 292 (371)
|....+... -.+.+..++|++...|...++.|.+.+
T Consensus 269 A~~~~g~~~---t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 269 ASLLLGERR---TQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HHHHhCCCC---CHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 998766332 457888999999999999999998855
No 13
>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). 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 ....
Probab=99.43 E-value=4.4e-13 Score=110.91 Aligned_cols=104 Identities=25% Similarity=0.282 Sum_probs=80.2
Q ss_pred CChhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCCC
Q 017441 198 VTPISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNIS 277 (371)
Q Consensus 198 ~Tp~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i~ 277 (371)
|||++||++|++..+. .......+.+++..++.++.|++|+||+||+||+++|+..++.. ..|...+..++|++
T Consensus 1 PTp~~Fl~~~~~~~~~----~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~--~~~~~~l~~~t~~~ 74 (118)
T PF02984_consen 1 PTPYDFLRRFLKISNA----DQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKE--PPWPESLEKLTGYD 74 (118)
T ss_dssp --HHHHHHHHHTSSSH----HHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSS--TCSHHHHHHHHTS-
T ss_pred CcHHHHHHHHHHHcCC----cHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCcc--ccCCccchhhcCCC
Confidence 7999999999553222 22455678889999999999999999999999999999987631 26999999999999
Q ss_pred HHHHHHHHHHHHHHHhccC-CCCCcccccCC
Q 017441 278 QDKLKECYLLILELSRGNG-SQNQSCKRKHF 307 (371)
Q Consensus 278 ~e~l~~C~~~i~el~~~~~-~~~~~~~~k~~ 307 (371)
.++|.+|++.|.+++.+.. ...+..++||.
T Consensus 75 ~~~l~~c~~~i~~~~~~~~~~~~~ai~~Kys 105 (118)
T PF02984_consen 75 KEDLKECIELIQELLSKASNSKLQAIRKKYS 105 (118)
T ss_dssp HHHHHHHHHHHHHHHHHCCGSSCTHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHhcCCccchHHHHHhC
Confidence 9999999999999998643 23344566664
No 14
>cd00043 CYCLIN Cyclin box fold. 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.
Probab=99.43 E-value=5.3e-13 Score=103.51 Aligned_cols=87 Identities=41% Similarity=0.538 Sum_probs=75.2
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchhhccCCCccc
Q 017441 96 RKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDLQVKDPKYVF 175 (371)
Q Consensus 96 R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl~v~~~~~~f 175 (371)
|..+++||.+++..+++++.|.++|+.|+|||+....+.+.+ ++++|+||++||+|+++. ++...++. ....+.
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~---~~~ia~a~l~lA~k~~~~-~~~~~~~~-~~~~~~- 75 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRS---PSLVAAAALYLAAKVEEI-PPWLKDLV-HVTGYA- 75 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCC---hHHHHHHHHHHHHHHcCC-CCCHHHHh-HHhCCC-
Confidence 678899999999999999999999999999999998887555 999999999999999999 77788872 122221
Q ss_pred cHHHHHHHHHHHH
Q 017441 176 EAKTIQRMELLVL 188 (371)
Q Consensus 176 ~~~~I~~mE~~IL 188 (371)
+.++|.+||+.|+
T Consensus 76 ~~~~i~~~e~~il 88 (88)
T cd00043 76 TEEEILRMEKLLL 88 (88)
T ss_pred CHHHHHHHHHHhC
Confidence 7999999999875
No 15
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=99.42 E-value=5.2e-12 Score=118.82 Aligned_cols=155 Identities=16% Similarity=0.302 Sum_probs=112.9
Q ss_pred HHHHHHHHHc--CCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchh-hccCCCccccH
Q 017441 101 EWVLRVKAHF--GFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDL-QVKDPKYVFEA 177 (371)
Q Consensus 101 ~Wi~~v~~~~--~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl-~v~~~~~~f~~ 177 (371)
.-+++.+.+| .+++.++.+|+.||-||+...++.... ...|.+||+++|+|++|.++ .+.++ .-..+.-.-+.
T Consensus 61 ~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~---pk~I~~tc~flA~Kieef~I-SieqFvkn~~~~~~k~~ 136 (325)
T KOG2496|consen 61 LSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYS---PKIIMATCFFLACKIEEFYI-SIEQFVKNMNGRKWKTH 136 (325)
T ss_pred HHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcC---hHHHHHHHHHHHhhhHhhee-cHHHHHhhccCcccccH
Confidence 3344444444 579999999999999999999999888 66799999999999999865 55666 21112223378
Q ss_pred HHHHHHHHHHHHHcCccccCCChhHHHHHHHHHhC----CCCccc-HHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHH
Q 017441 178 KTIQRMELLVLSTLQWRMNPVTPISFFDHIVRRLG----LKTHLH-WEFLYRCEHLLLSVIADSRFMCYLPSTLATATML 252 (371)
Q Consensus 178 ~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~----~~~~~~-~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~ 252 (371)
+.|+..|..+|+.|+|++.+.+|+.-++-|+..+. ...+.. .........++..++...-++-|+||.||+|||+
T Consensus 137 e~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil 216 (325)
T KOG2496|consen 137 EIVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAIL 216 (325)
T ss_pred HHHHhchHHHHHhhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHH
Confidence 99999999999999999999999999998886542 111111 0111112355666665566677999999999997
Q ss_pred HHHHhcC
Q 017441 253 HTIQEVE 259 (371)
Q Consensus 253 ~a~~~l~ 259 (371)
.+....+
T Consensus 217 ~a~~~~~ 223 (325)
T KOG2496|consen 217 HAAGRTG 223 (325)
T ss_pred HHhcccc
Confidence 7754443
No 16
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=99.34 E-value=3.5e-12 Score=97.88 Aligned_cols=83 Identities=37% Similarity=0.492 Sum_probs=70.3
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchhhccCCCccccHHHH
Q 017441 101 EWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDLQVKDPKYVFEAKTI 180 (371)
Q Consensus 101 ~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl~v~~~~~~f~~~~I 180 (371)
+||.+++..+++++++.++|++++|||+....+.+.+ .+++|+||++||+|++|.. |...++. ...++ |+.++|
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~---~~~ia~a~l~lA~k~~~~~-~~~~~~~-~~~~~-~~~~~i 74 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYS---PSLIAAAALYLAAKTEEIP-PWTKELV-HYTGY-FTEEEI 74 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCC---HHHHHHHHHHHHHHHhcCC-CCchhHh-HhhCC-CCHHHH
Confidence 5999999999999999999999999999977666666 9999999999999999985 5556662 12223 689999
Q ss_pred HHHHHHHHH
Q 017441 181 QRMELLVLS 189 (371)
Q Consensus 181 ~~mE~~IL~ 189 (371)
.+||+.||.
T Consensus 75 ~~~~~~il~ 83 (83)
T smart00385 75 LRMEKLLLE 83 (83)
T ss_pred HHHHHHHhC
Confidence 999999874
No 17
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.86 E-value=2.7e-07 Score=88.51 Aligned_cols=185 Identities=15% Similarity=0.193 Sum_probs=151.6
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchhhccCCCc
Q 017441 94 LARKEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDLQVKDPKY 173 (371)
Q Consensus 94 ~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl~v~~~~~ 173 (371)
..-..+..-|-.++..++++..+.-.|..++-+.+...-+.... .+-++++|+++|++.... +..+.++.. ...
T Consensus 95 rnl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRs---ie~v~AA~iY~acR~~~~-prtl~eIa~-a~~- 168 (285)
T COG1405 95 RNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRS---IESVAAACIYAACRINGV-PRTLDEIAK-ALG- 168 (285)
T ss_pred hHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCc---HHHHHHHHHHHHHHHcCC-CccHHHHHH-HHC-
Confidence 34456777888899999999999999999999999887777666 899999999999999887 445555521 122
Q ss_pred cccHHHHHHHHHHHHHHcCccccCCChhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHHH
Q 017441 174 VFEAKTIQRMELLVLSTLQWRMNPVTPISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFMCYLPSTLATATMLH 253 (371)
Q Consensus 174 ~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~ 253 (371)
-++++|.++.+.+...|+=.+.+..|.+|+..|...|++++. ....+..++..+...-.-.+-.|+-+|+||+|+
T Consensus 169 -V~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~----v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~ 243 (285)
T COG1405 169 -VSKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSDE----VRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYL 243 (285)
T ss_pred -CCHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHH----HHHHHHHHHHHHHHhCcccCCCchhHHHHHHHH
Confidence 268999999999999999999999999999999999999853 445666666666555556699999999999999
Q ss_pred HHHhcCCCCccchHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 017441 254 TIQEVEPCNPVEHQNLLMGVLNISQDKLKECYLLILELS 292 (371)
Q Consensus 254 a~~~l~~~~~~~~~~~L~~~~~i~~e~l~~C~~~i~el~ 292 (371)
|....+. ..-+..+..++|++...|..=++.|.+..
T Consensus 244 as~l~~~---~~tq~eva~v~~vtevTIrnrykel~~~~ 279 (285)
T COG1405 244 ASLLLGE---RRTQKEVAKVAGVTEVTIRNRYKELADAL 279 (285)
T ss_pred HHHHhCC---chHHHHHHHHhCCeeeHHHHHHHHHHHhh
Confidence 9987762 23567889999999999999997776644
No 18
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.66 E-value=1.8e-06 Score=81.57 Aligned_cols=181 Identities=15% Similarity=0.178 Sum_probs=138.7
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchhh-ccCCCccc
Q 017441 97 KEVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDLQ-VKDPKYVF 175 (371)
Q Consensus 97 ~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl~-v~~~~~~f 175 (371)
..+..-|..++...+|+....-.|-.+|.++-..+...... ..-+++|||+||+.-++. +..++++. +.. -
T Consensus 105 ~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks---~eai~AAclyiACRq~~~-pRT~kEI~~~an----v 176 (308)
T KOG1597|consen 105 KAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKS---VEALAAACLYIACRQEDV-PRTFKEISAVAN----V 176 (308)
T ss_pred HHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCcc---HHHHHHHHHHHHHHhcCC-CchHHHHHHHHc----C
Confidence 34455577889999999999999999999999666655445 899999999999998877 56677773 322 3
Q ss_pred cHHHHHHHHHHHHHHcCccccCCC--hhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhc-cCCcHHHHHHHHHH
Q 017441 176 EAKTIQRMELLVLSTLQWRMNPVT--PISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRF-MCYLPSTLATATML 252 (371)
Q Consensus 176 ~~~~I~~mE~~IL~~L~w~l~~~T--p~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~f-l~~~PS~IAaAai~ 252 (371)
+.++|-+.=+.|+..|+=.....| .-+|+.+|...|+++.... ..+..+...+ .+..+ .+-.|=.||||+||
T Consensus 177 ~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q----~aA~e~a~ka-~~~~~~~gRsPiSIAAa~IY 251 (308)
T KOG1597|consen 177 SKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQ----EAATEIAEKA-EEMDIRAGRSPISIAAAAIY 251 (308)
T ss_pred CHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHH----HHHHHHHHHH-HHhccccCCCchhHHHHHHH
Confidence 799999999999999997777666 8899999999999887543 2232333222 12222 25789999999999
Q ss_pred HHHHhcCCCCccchHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 017441 253 HTIQEVEPCNPVEHQNLLMGVLNISQDKLKECYLLILELSR 293 (371)
Q Consensus 253 ~a~~~l~~~~~~~~~~~L~~~~~i~~e~l~~C~~~i~el~~ 293 (371)
++....... .-...+..++|+.+..|+.-|+.|.....
T Consensus 252 misqls~~k---kt~keI~~vtgVaE~TIr~sYK~Lyp~~~ 289 (308)
T KOG1597|consen 252 MISQLSDEK---KTQKEIGEVTGVAEVTIRNSYKDLYPHAD 289 (308)
T ss_pred HHHHhccCc---ccHHHHHHHhhhhHHHHHHHHHHHhhchh
Confidence 998765522 24578889999999999999988876544
No 19
>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). 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.
Probab=98.29 E-value=3.5e-06 Score=73.52 Aligned_cols=93 Identities=17% Similarity=0.177 Sum_probs=65.5
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhc---cCcccCCCCchhHHHHHHHHHHhhcccccCccccchh-hccCCCc
Q 017441 98 EVVEWVLRVKAHFGFTALTAILAVNYFDRFIL---SHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDL-QVKDPKY 173 (371)
Q Consensus 98 ~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls---~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl-~v~~~~~ 173 (371)
.+.+|+.++..+-++++.++.+|..|+||+.. ...+. -.+...+-+-++||.+|+|+-+-....-... .+++
T Consensus 53 ~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~-~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~g--- 128 (149)
T PF08613_consen 53 SIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIP-LNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGG--- 128 (149)
T ss_dssp -HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT----STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHT---
T ss_pred cHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccc-cccchhHHHHHHHHHHHHhhcccccccHHHHHhhcC---
Confidence 37889999999999999999999999999998 22222 1234478899999999999954333333444 4432
Q ss_pred cccHHHHHHHHHHHHHHcCccc
Q 017441 174 VFEAKTIQRMELLVLSTLQWRM 195 (371)
Q Consensus 174 ~f~~~~I~~mE~~IL~~L~w~l 195 (371)
++.+++.+||+..|..|+|+|
T Consensus 129 -is~~eln~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 129 -ISLKELNELEREFLKLLDYNL 149 (149)
T ss_dssp -S-HHHHHHHHHHHHHHTTT--
T ss_pred -CCHHHHHHHHHHHHHHCCCcC
Confidence 479999999999999999986
No 20
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.19 E-value=1.2e-05 Score=61.04 Aligned_cols=81 Identities=22% Similarity=0.324 Sum_probs=66.6
Q ss_pred HHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCC-CHHH
Q 017441 202 SFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNI-SQDK 280 (371)
Q Consensus 202 ~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i-~~e~ 280 (371)
+|+..+...++.++ +....+..++...+.+..+..++|+.||+||+++|.+..+.. .|...+..++|+ +.++
T Consensus 1 ~~l~~~~~~~~~~~----~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~---~~~~~~~~~~~~~~~~~ 73 (83)
T smart00385 1 DFLRRVCKALNLDP----ETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIP---PWTKELVHYTGYFTEEE 73 (83)
T ss_pred CHHHHHHHHcCCCH----HHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCC---CCchhHhHhhCCCCHHH
Confidence 36777888887753 455677788888888888999999999999999999877643 377888999999 9999
Q ss_pred HHHHHHHHH
Q 017441 281 LKECYLLIL 289 (371)
Q Consensus 281 l~~C~~~i~ 289 (371)
+.+|.+.|.
T Consensus 74 i~~~~~~il 82 (83)
T smart00385 74 ILRMEKLLL 82 (83)
T ss_pred HHHHHHHHh
Confidence 999998775
No 21
>cd00043 CYCLIN Cyclin box fold. 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.
Probab=98.16 E-value=2.4e-05 Score=60.04 Aligned_cols=85 Identities=22% Similarity=0.274 Sum_probs=71.6
Q ss_pred CCChhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCC
Q 017441 197 PVTPISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNI 276 (371)
Q Consensus 197 ~~Tp~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i 276 (371)
.+++.+|+..+...++.+. .....+..++...+....+..+.|+.||+||+++|.+..+. ..|...+...+++
T Consensus 2 ~~~~~~~l~~~~~~~~~~~----~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~---~~~~~~~~~~~~~ 74 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSP----ETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI---PPWLKDLVHVTGY 74 (88)
T ss_pred cchHHHHHHHHHHHcCCCH----HHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCC---CCCHHHHhHHhCC
Confidence 5789999999999997664 45566777888888888889999999999999999987664 4588899999999
Q ss_pred -CHHHHHHHHHHH
Q 017441 277 -SQDKLKECYLLI 288 (371)
Q Consensus 277 -~~e~l~~C~~~i 288 (371)
+.++|.++.+.|
T Consensus 75 ~~~~~i~~~e~~i 87 (88)
T cd00043 75 ATEEEILRMEKLL 87 (88)
T ss_pred CCHHHHHHHHHHh
Confidence 999999988765
No 22
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=98.14 E-value=1.2e-06 Score=85.33 Aligned_cols=98 Identities=22% Similarity=0.385 Sum_probs=83.6
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchh-hccCCCcccc
Q 017441 98 EVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDL-QVKDPKYVFE 176 (371)
Q Consensus 98 ~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl-~v~~~~~~f~ 176 (371)
.+=.=|.+++...++...|+++|..||.....+..+.+.+ -.|.|-|||.||+||.+..--.++.+ .-.+..+.+.
T Consensus 384 SlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~N---RKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~n 460 (497)
T KOG4164|consen 384 SLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQN---RKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLN 460 (497)
T ss_pred HHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhh---hhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhccc
Confidence 3445588888999999999999999999999999999888 99999999999999987654445555 2245678889
Q ss_pred HHHHHHHHHHHHHHcCccccCC
Q 017441 177 AKTIQRMELLVLSTLQWRMNPV 198 (371)
Q Consensus 177 ~~~I~~mE~~IL~~L~w~l~~~ 198 (371)
+++++..|.-||.+|+|.++.+
T Consensus 461 rrdLia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 461 RRDLIAFEFPVLVALEFALHLP 482 (497)
T ss_pred HHhhhhhhhhHHHhhhhhccCC
Confidence 9999999999999999999865
No 23
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=97.79 E-value=0.00035 Score=71.24 Aligned_cols=174 Identities=16% Similarity=0.138 Sum_probs=132.4
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchh--hccCCCccccHHH
Q 017441 102 WVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDL--QVKDPKYVFEAKT 179 (371)
Q Consensus 102 Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl--~v~~~~~~f~~~~ 179 (371)
-|-+++..+++.. .+-.|.++|---+...-.+... .+.+..+||+|++..|-+. -.+.|+ +... +.-+
T Consensus 73 ~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~---~~~vvasClY~vcR~e~t~-hlliDfS~~Lqv-----~Vy~ 142 (521)
T KOG1598|consen 73 LIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRR---STEVVAACLYLVCRLEKTD-HLLIDFSSYLQV-----SVYD 142 (521)
T ss_pred HHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcc---hHHHHHHHHHHHHHhhCCc-eEEEEeccceEE-----ehhh
Confidence 5888999999999 9999999999888877666656 8999999999999998874 355565 2211 2334
Q ss_pred HHHHHHHHHHHcCcc---ccCCChhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHH
Q 017441 180 IQRMELLVLSTLQWR---MNPVTPISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQ 256 (371)
Q Consensus 180 I~~mE~~IL~~L~w~---l~~~Tp~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~ 256 (371)
+-.+=+.|-..|.-. +..+-|.-|+.+|..++...+.. .+++..+.+++.....|.-..+-+|+-|+-|||+.|++
T Consensus 143 LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~-~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar 221 (521)
T KOG1598|consen 143 LGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKT-EDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAAR 221 (521)
T ss_pred hhHHHHHHHHHhccccccccccCcceeeechhHhhhcCCch-HHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHH
Confidence 555555666667666 77889999999999998776655 47888888999999899999999999999999999999
Q ss_pred hcCCCCccchHHHHHHHhCCCHHHHHHHHHHHH
Q 017441 257 EVEPCNPVEHQNLLMGVLNISQDKLKECYLLIL 289 (371)
Q Consensus 257 ~l~~~~~~~~~~~L~~~~~i~~e~l~~C~~~i~ 289 (371)
..+... -...+..+..+...-+..=+..+.
T Consensus 222 ~h~~~r---si~dIv~vvhV~e~Tl~kRl~Ef~ 251 (521)
T KOG1598|consen 222 MHGFRR---TIGDIAKVVHVCESTLSKRLKEFS 251 (521)
T ss_pred HcCccc---cHHHHHHHHHHhHHHHHHHHHHHh
Confidence 876322 234556666666665555554443
No 24
>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). 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.
Probab=95.76 E-value=0.039 Score=41.61 Aligned_cols=60 Identities=15% Similarity=0.246 Sum_probs=46.8
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchh
Q 017441 103 VLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDL 166 (371)
Q Consensus 103 i~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl 166 (371)
|-++|..++|+..+.-.|..++++-....-....+ ..-++++|+++|++.+.. +..+.++
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~---~~~iaAA~iY~acr~~~~-~~t~~eI 60 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRS---PESIAAACIYLACRLNGV-PRTLKEI 60 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS----HHHHHHHHHHHHHHHTTS-SSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCC---HHHHHHHHHHHHHHHcCC-CcCHHHH
Confidence 45789999999999999999999988776555445 788999999999999876 3355665
No 25
>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). 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.
Probab=95.57 E-value=0.12 Score=38.85 Aligned_cols=71 Identities=13% Similarity=0.156 Sum_probs=48.4
Q ss_pred HHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCCCHHHH
Q 017441 204 FDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNISQDKL 281 (371)
Q Consensus 204 l~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i~~e~l 281 (371)
+..|...+++++ .+.+.+..+...+....-.-+-+|..|||||+|+|.+..+... -...+...+|+++.+|
T Consensus 1 I~r~~~~L~L~~----~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~---t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPE----DVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPR---TLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--H----HHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSS---SHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCH----HHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCc---CHHHHHHHhCCCCCcC
Confidence 356777777765 4556666666665544445678899999999999998876332 4567888889887654
No 26
>KOG1674 consensus Cyclin [General function prediction only]
Probab=94.58 E-value=0.11 Score=48.33 Aligned_cols=97 Identities=14% Similarity=0.184 Sum_probs=68.8
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCc---cc---CCCCch-hHHHHHHHHHHhhcccccCccccchhhccCC
Q 017441 99 VVEWVLRVKAHFGFTALTAILAVNYFDRFILSHS---FQ---KDKPWM-GQLVAVACLSLAAKVDETQVPLLLDLQVKDP 171 (371)
Q Consensus 99 ~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~---v~---~~~p~~-lqLlavaCL~LAaK~eE~~vp~l~dl~v~~~ 171 (371)
+-+++-++..+-+.++.++.+|..|||||..... +. .-+..+ ..-+-++|+.+|+|+.+..- .-...+-..+
T Consensus 78 i~~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~-y~n~~~a~vg 156 (218)
T KOG1674|consen 78 IRQYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVY-YSNAYYAKVG 156 (218)
T ss_pred hHHHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchh-hhHHHHHHhC
Confidence 3456667778888999999999999999998733 11 111223 55578999999999986521 1112211112
Q ss_pred CccccHHHHHHHHHHHHHHcCccccCC
Q 017441 172 KYVFEAKTIQRMELLVLSTLQWRMNPV 198 (371)
Q Consensus 172 ~~~f~~~~I~~mE~~IL~~L~w~l~~~ 198 (371)
. .+.+++..+|+..|..++|++.+.
T Consensus 157 g--l~~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 157 G--LTTDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred C--CChHhhhhhhHHHHhhCCeEEEec
Confidence 2 268899999999999999999875
No 27
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=92.77 E-value=1.3 Score=43.26 Aligned_cols=87 Identities=14% Similarity=0.205 Sum_probs=65.0
Q ss_pred hhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCCCHH
Q 017441 200 PISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNISQD 279 (371)
Q Consensus 200 p~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i~~e 279 (371)
.+..|..+...+++++ .+...+..+...+.....+-+...-.+||||||.|.+.-+.. --...+..++++++.
T Consensus 125 a~~~I~~~~~~L~Lp~----~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~p---rtl~eI~~~~~v~~k 197 (310)
T PRK00423 125 ALSELDRIASQLGLPR----SVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVP---RTLDEIAEVSRVSRK 197 (310)
T ss_pred HHHHHHHHHHHcCCCH----HHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCC---cCHHHHHHHhCCCHH
Confidence 4556777888888775 345566555555544444568888999999999999876632 234677888999999
Q ss_pred HHHHHHHHHHHHHh
Q 017441 280 KLKECYLLILELSR 293 (371)
Q Consensus 280 ~l~~C~~~i~el~~ 293 (371)
+|.++++.|.+.+.
T Consensus 198 ~i~~~~~~l~k~L~ 211 (310)
T PRK00423 198 EIGRCYRFLLRELN 211 (310)
T ss_pred HHHHHHHHHHHHhC
Confidence 99999999988774
No 28
>PF09080 K-cyclin_vir_C: K cyclin, C terminal; InterPro: IPR015164 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). 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 domain adopts a secondary structure consisting of a five alpha-helix cyclin fold. Interaction with cyclin dependent kinases (CDKs) at a PSTAIRE sequence motif within the catalytic cleft of CDK results in the regulation of CDK activity []. ; PDB: 1G3N_C.
Probab=92.01 E-value=3.1 Score=32.81 Aligned_cols=94 Identities=15% Similarity=0.163 Sum_probs=57.9
Q ss_pred hhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhccCCcHHHHHHH-HHHHHHHhcCCCC--ccchHHHHHHHhCC
Q 017441 200 PISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFMCYLPSTLATA-TMLHTIQEVEPCN--PVEHQNLLMGVLNI 276 (371)
Q Consensus 200 p~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaA-ai~~a~~~l~~~~--~~~~~~~L~~~~~i 276 (371)
|.+-+...+-+++.......-+-.+....+-..+.|+.--..+||.||+| |-+++.....|.. ......+|...+|+
T Consensus 4 ~TD~~~~~L~K~~~~~e~L~~~H~~V~~~v~KAiV~P~TG~Lp~SlvaAA~CAL~~~~~~~P~~~~~~~~~~~LA~~~G~ 83 (106)
T PF09080_consen 4 PTDAIGPLLFKSGFTKEQLFAWHSEVVESVHKAIVNPKTGGLPPSLVAAAGCALFSLGAAAPPDTHSGGVVPQLAEALGV 83 (106)
T ss_dssp CHHHHHHHHHHHS-SSTTHHHHHHHHHHHHHHHHCSTTGGGS-HHHHHHHHHHHHS-GGGS--------HHHHHHHHHT-
T ss_pred ccccccHHHHHHcccHHHHHHHHHHHHHHHHHHhcCcccCCCCHHHHHHhhhhhccccccCCCccccccchHHHHHHhCc
Confidence 44555555555554443322222445566777788999999999999998 7777665554332 23356789999999
Q ss_pred CHHHHHHHHHHHHHHHh
Q 017441 277 SQDKLKECYLLILELSR 293 (371)
Q Consensus 277 ~~e~l~~C~~~i~el~~ 293 (371)
+...+....+.+..-.+
T Consensus 84 ~~a~L~AA~E~v~Tt~~ 100 (106)
T PF09080_consen 84 SAATLQAAAESVATTLR 100 (106)
T ss_dssp -HHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHH
Confidence 99999998888876554
No 29
>PF09241 Herp-Cyclin: Herpesviridae viral cyclin; InterPro: IPR015322 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). 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 represents a domain found in a family of viral cyclins that specifically activate CDK6 of host cells to a very high degree []. This domain adopts a helical structure consisting of five alpha-helices, with one helix surrounded by the others.; PDB: 1XO2_A 1JOW_A 2F2C_A 2EUF_A 1BU2_A.
Probab=86.70 E-value=13 Score=28.95 Aligned_cols=95 Identities=12% Similarity=0.087 Sum_probs=68.6
Q ss_pred ChhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcC--CCCccchHHHHHHHhCC
Q 017441 199 TPISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVE--PCNPVEHQNLLMGVLNI 276 (371)
Q Consensus 199 Tp~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~--~~~~~~~~~~L~~~~~i 276 (371)
-..+|+-.....+.++++.-.+....+...+-.++..++..-.+|-.|.|+.++..++.-+ ...+..|...|..++++
T Consensus 3 l~tdflip~c~alkipe~~wpql~e~~s~tickaliqpniall~p~licaggllttiet~ntn~~~wt~yledl~~ilnf 82 (106)
T PF09241_consen 3 LSTDFLIPVCHALKIPEDFWPQLFEATSITICKALIQPNIALLPPCLICAGGLLTTIETDNTNCQPWTCYLEDLSCILNF 82 (106)
T ss_dssp -GGGGHHHHHHHTT--GGGHHHHHHHHHHHHHHHTTSGGGGGS-HHHHHHHHHHHHHHTS-TSSSTCHHHHHHHHHHHTC
T ss_pred chhhhHHHhhhhccCcHHHhHHHHHHHHHHHHHHHcCCCccccCcceeecccceEEEeccCCCCcchhhhHHhhHHHhhc
Confidence 4568888888889888876545555565666667788888899999999999999987543 22344456677788899
Q ss_pred CHHHHHHHHHHHHHHHh
Q 017441 277 SQDKLKECYLLILELSR 293 (371)
Q Consensus 277 ~~e~l~~C~~~i~el~~ 293 (371)
+...++..-+++.+.+.
T Consensus 83 stntirt~kdqv~ea~~ 99 (106)
T PF09241_consen 83 STNTIRTVKDQVSEAFS 99 (106)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHH
Confidence 99999888888877654
No 30
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=81.18 E-value=1.5 Score=43.05 Aligned_cols=89 Identities=18% Similarity=0.186 Sum_probs=51.8
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchh-hccCCCcccc
Q 017441 98 EVVEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDL-QVKDPKYVFE 176 (371)
Q Consensus 98 ~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl-~v~~~~~~f~ 176 (371)
-+++++.++...-+........|-+++-..+...-+-+.. .+-+|++||+||+|+-...+|...+- .-....-..+
T Consensus 154 ~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~---p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt 230 (323)
T KOG0834|consen 154 YLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYS---PHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVT 230 (323)
T ss_pred HHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeec---CcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCC
Confidence 3455555555554444456777777777766654444455 55699999999999977666655443 0001111134
Q ss_pred HHHHHHHHHHHHH
Q 017441 177 AKTIQRMELLVLS 189 (371)
Q Consensus 177 ~~~I~~mE~~IL~ 189 (371)
.+.+..+...+|.
T Consensus 231 ~e~l~~i~~~~l~ 243 (323)
T KOG0834|consen 231 NELLDDICHEFLD 243 (323)
T ss_pred HHHHHHHHHHHHH
Confidence 5555555444443
No 31
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=76.99 E-value=38 Score=32.81 Aligned_cols=88 Identities=14% Similarity=0.180 Sum_probs=59.4
Q ss_pred ChhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhchhhcc-CCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCCC
Q 017441 199 TPISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIADSRFM-CYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNIS 277 (371)
Q Consensus 199 Tp~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~fl-~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i~ 277 (371)
+....+..+...++++.... ..+..+ .....+..++ +=+...++|||+|.|.+..+.. --...+...++++
T Consensus 99 ~a~~~l~~~~~~l~LP~~v~----e~A~~i-yr~a~~~~l~rGRsie~v~AA~iY~acR~~~~p---rtl~eIa~a~~V~ 170 (285)
T COG1405 99 TALEELERIASALGLPESVR----ETAARI-YRKAVDKGLLRGRSIESVAAACIYAACRINGVP---RTLDEIAKALGVS 170 (285)
T ss_pred HHHHHHHHHHHHhCCCchHH----HHHHHH-HHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCC---ccHHHHHHHHCCC
Confidence 45667777777888776543 222222 2223455554 4457889999999999876632 2446778889999
Q ss_pred HHHHHHHHHHHHHHHhc
Q 017441 278 QDKLKECYLLILELSRG 294 (371)
Q Consensus 278 ~e~l~~C~~~i~el~~~ 294 (371)
..++..+++.+......
T Consensus 171 ~kei~rtyr~~~~~L~l 187 (285)
T COG1405 171 KKEIGRTYRLLVRELKL 187 (285)
T ss_pred HHHHHHHHHHHHHhcCC
Confidence 99999999977665443
No 32
>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). 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 ....
Probab=68.32 E-value=5.4 Score=32.01 Aligned_cols=55 Identities=18% Similarity=0.137 Sum_probs=39.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccc
Q 017441 100 VEWVLRVKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDE 157 (371)
Q Consensus 100 v~Wi~~v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE 157 (371)
.+||.......+.+..+..+|-.+++-.+....+-... .-++|+||+++|.++-.
T Consensus 4 ~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~---PS~iAaAai~lA~~~~~ 58 (118)
T PF02984_consen 4 YDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYP---PSVIAAAAILLARKILG 58 (118)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS----HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCC---HHHHHHHHHHHHHHHhC
Confidence 45555553333445678888888888777776666666 77899999999999954
No 33
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=68.00 E-value=13 Score=35.85 Aligned_cols=49 Identities=20% Similarity=0.224 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHhcCCCCccchHHHHHHHhCCCHHHHHHHHHHHHHHHhc
Q 017441 243 PSTLATATMLHTIQEVEPCNPVEHQNLLMGVLNISQDKLKECYLLILELSRG 294 (371)
Q Consensus 243 PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~~i~~e~l~~C~~~i~el~~~ 294 (371)
--.||||||+.|++..+.. .-.+.+..+.++++.+|-+|++.|.+-+..
T Consensus 146 ~eai~AAclyiACRq~~~p---RT~kEI~~~anv~kKEIgr~~K~i~~~l~~ 194 (308)
T KOG1597|consen 146 VEALAAACLYIACRQEDVP---RTFKEISAVANVSKKEIGRCVKLIGEALET 194 (308)
T ss_pred HHHHHHHHHHHHHHhcCCC---chHHHHHHHHcCCHHHHHHHHHHHHHHHhc
Confidence 3468999999999876632 244677888899999999999999886644
No 34
>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). 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 ....
Probab=66.11 E-value=69 Score=25.88 Aligned_cols=68 Identities=13% Similarity=0.013 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHHHHh--CCCHHHHHHHHHHHHHH
Q 017441 222 LYRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLMGVL--NISQDKLKECYLLILEL 291 (371)
Q Consensus 222 l~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~~~~--~i~~e~l~~C~~~i~el 291 (371)
+..+..++...+.........+..+|+||+++|.+.-+.. ..+...+.... .++.+++.+.=..|...
T Consensus 52 ~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~--~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~ 121 (127)
T PF00134_consen 52 LHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDN--PPSISDLIRISDNTFTKKDILEMEREILSA 121 (127)
T ss_dssp HHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS----HHHHHHHHTTTSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccc--cchHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence 3444445555444445678888999999999999876542 12345555555 36777776655555543
No 35
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=62.29 E-value=10 Score=36.86 Aligned_cols=99 Identities=16% Similarity=0.132 Sum_probs=58.9
Q ss_pred HHHHcCCCHHHHHHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccC-ccccchhhccCCCccccHHHHHHHH
Q 017441 106 VKAHFGFTALTAILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQ-VPLLLDLQVKDPKYVFEAKTIQRME 184 (371)
Q Consensus 106 v~~~~~l~~~T~~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~-vp~l~dl~v~~~~~~f~~~~I~~mE 184 (371)
.+....+..+.......|++|-+.-...... |.....+.....++|+|+-... +=...-.++.. .-+.+++..||
T Consensus 200 l~~~~qlta~~aiitL~~~erl~~~~e~~~~-p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlK---d~tveDmNe~E 275 (343)
T KOG1675|consen 200 LFSWAQLTAECDIITLVYAERLLWLAERDPC-PRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILK---DQSVDDMNALE 275 (343)
T ss_pred HhhhhhhhhccchHHHHhhHhhhhHhhcCCC-cchhhhhhhhhheehhhhhhhhhcccHHHHHHHh---hccHhhHHHHH
Confidence 3344445566666677888987765443311 2224444455699999994331 11111112211 12688999999
Q ss_pred HHHHHHcCccccCCChhHHHHHHHH
Q 017441 185 LLVLSTLQWRMNPVTPISFFDHIVR 209 (371)
Q Consensus 185 ~~IL~~L~w~l~~~Tp~~Fl~~fl~ 209 (371)
+.+|+.|+|++++|-. .|..+|..
T Consensus 276 RqfLelLqfNinvp~s-vYAKyYfd 299 (343)
T KOG1675|consen 276 RQFLELLQFNINVPSS-EYAKYYFD 299 (343)
T ss_pred HHHHHHHhhccCccHH-HHHHHHHH
Confidence 9999999999998753 34444443
No 36
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=58.66 E-value=37 Score=33.46 Aligned_cols=60 Identities=20% Similarity=0.297 Sum_probs=36.3
Q ss_pred HHHHHHHHHHhccCcccCCCCchhHHHHHHHHHHhhcccccCccccchhhccCCCccccHHHHHHH
Q 017441 118 ILAVNYFDRFILSHSFQKDKPWMGQLVAVACLSLAAKVDETQVPLLLDLQVKDPKYVFEAKTIQRM 183 (371)
Q Consensus 118 ~lAV~ylDRfls~~~v~~~~p~~lqLlavaCL~LAaK~eE~~vp~l~dl~v~~~~~~f~~~~I~~m 183 (371)
..|-||+.--+-..-+..+. .-.||++|++|||..+|+-.|...... ..+.++..+|...
T Consensus 162 Q~~wNfmNDslRT~v~vry~---pe~iACaciyLaAR~~eIpLp~~P~Wf---~~Fd~~k~eid~i 221 (367)
T KOG0835|consen 162 QAAWNFMNDSLRTDVFVRYS---PESIACACIYLAARNLEIPLPFQPHWF---KAFDTTKREIDEI 221 (367)
T ss_pred HHHHHhhhhccccceeeecC---HHHHHHHHHHHHHhhhcCCCCCCccHH---HHcCCcHHHHHHH
Confidence 33444444433333344455 678999999999999997666555542 1234456666543
No 37
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=41.19 E-value=69 Score=31.31 Aligned_cols=37 Identities=11% Similarity=0.100 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhchhhccCCcHHHHHHHHHHHHHHhcC
Q 017441 223 YRCEHLLLSVIADSRFMCYLPSTLATATMLHTIQEVE 259 (371)
Q Consensus 223 ~~~~~ll~~~l~d~~fl~~~PS~IAaAai~~a~~~l~ 259 (371)
..|..++........++.|.|-.||++|+++|.+.-+
T Consensus 80 aTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE 116 (305)
T TIGR00569 80 GTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE 116 (305)
T ss_pred HHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccc
Confidence 3333344344445567789999999999999987543
No 38
>PF12550 GCR1_C: Transcriptional activator of glycolytic enzymes; InterPro: IPR022210 This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes.
Probab=34.83 E-value=1.3e+02 Score=23.00 Aligned_cols=53 Identities=15% Similarity=0.171 Sum_probs=33.8
Q ss_pred HHHHHhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 017441 72 LICKEKKENFVPSDPISDEILILARKEVVEWVLRVKAHFGFTALTAILAVNYFDRF 127 (371)
Q Consensus 72 Ll~~E~~~~~~~~~~q~~~i~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRf 127 (371)
..+.|+.+......-..+.-+-.-|..+|++|.+++..-|++.+ .|+..+|.+
T Consensus 28 I~~le~~yG~~WR~~~~~~~~y~rRK~Ii~~I~~l~~~~g~~~~---~ai~~le~~ 80 (81)
T PF12550_consen 28 IRSLEKKYGSKWRRDSKERRTYSRRKVIIDFIERLANERGISEE---EAIEILEEI 80 (81)
T ss_pred HHHHHHHhChhhccCcccchhHHHHHHHHHHHHHHHHHcCCCHH---HHHHHHHhc
Confidence 34445565543321122224567899999999999988887765 566666654
No 39
>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). 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.
Probab=21.62 E-value=5.1e+02 Score=22.05 Aligned_cols=88 Identities=13% Similarity=0.037 Sum_probs=47.0
Q ss_pred CCChhHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHhc-----hhhccCCcHHHHHHHHHHHHHHhcCCCCccchHHHHH
Q 017441 197 PVTPISFFDHIVRRLGLKTHLHWEFLYRCEHLLLSVIA-----DSRFMCYLPSTLATATMLHTIQEVEPCNPVEHQNLLM 271 (371)
Q Consensus 197 ~~Tp~~Fl~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~-----d~~fl~~~PS~IAaAai~~a~~~l~~~~~~~~~~~L~ 271 (371)
.++-.+|+..+.+....... .+-.+..++..... ....-.....-+=++|+.+|.+.+... .-+...|.
T Consensus 51 ~i~i~~fl~ri~~~~~~s~~----~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~--~~~n~~~a 124 (149)
T PF08613_consen 51 SISIRDFLSRILKYTQCSPE----CLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDN--TYSNKSWA 124 (149)
T ss_dssp SS-HHHHHHHHHHHTT--HH----HHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS-----HHHHH
T ss_pred CCcHHHHHHHHHHHcCCChH----HHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccc--cccHHHHH
Confidence 34456677777776655432 22222223333222 222345556677888888998887643 23567788
Q ss_pred HHhCCCHHHHHHHHHHHHH
Q 017441 272 GVLNISQDKLKECYLLILE 290 (371)
Q Consensus 272 ~~~~i~~e~l~~C~~~i~e 290 (371)
++.|++..++..-=..++.
T Consensus 125 ~v~gis~~eln~lE~~fL~ 143 (149)
T PF08613_consen 125 KVGGISLKELNELEREFLK 143 (149)
T ss_dssp HHHTS-HHHHHHHHHHHHH
T ss_pred hhcCCCHHHHHHHHHHHHH
Confidence 9999999988764444333
No 40
>COG3474 Cytochrome c2 [Energy production and conversion]
Probab=21.19 E-value=1.5e+02 Score=25.44 Aligned_cols=42 Identities=14% Similarity=0.243 Sum_probs=33.4
Q ss_pred CCCCCHHHHHHHHHHHhhcCCC----CCCCCCchhhHHHHHHHHHHHHHH
Q 017441 61 DLFWDDNELLSLICKEKKENFV----PSDPISDEILILARKEVVEWVLRV 106 (371)
Q Consensus 61 ~~f~~~e~l~~Ll~~E~~~~~~----~~~~q~~~i~~~~R~~~v~Wi~~v 106 (371)
-+-|+++.|...|..=+.+.|. |..+.+ ...|..+|-||...
T Consensus 85 g~vWd~~~L~~fL~~Pkk~vpGTkM~faGlkk----~~dradlIAYLk~~ 130 (135)
T COG3474 85 GIVWDEDNLDEFLTAPKKYVPGTKMAFAGLKK----DQDRADLIAYLKSL 130 (135)
T ss_pred CcccCHHHHHHHHhChhhhCCCcceeecCCCC----HHHHHHHHHHHHhc
Confidence 4679999999999999999983 344443 47999999998754
Done!