Query 035817
Match_columns 365
No_of_seqs 251 out of 1563
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 06:41:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035817.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035817hhsearch_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 2.1E-39 4.6E-44 312.6 20.9 214 11-241 43-268 (335)
2 KOG0655 G1/S-specific cyclin E 100.0 1.3E-33 2.9E-38 266.6 16.7 208 11-248 111-336 (408)
3 KOG0653 Cyclin B and related k 100.0 4.1E-33 8.8E-38 278.9 17.1 217 10-248 124-346 (391)
4 COG5024 Cyclin [Cell division 100.0 2.9E-33 6.4E-38 278.9 14.8 223 6-251 172-403 (440)
5 KOG0654 G2/Mitotic-specific cy 99.9 2.3E-28 5E-33 238.1 7.9 219 10-252 100-327 (359)
6 TIGR00569 ccl1 cyclin ccl1. Un 99.9 1.1E-23 2.4E-28 203.7 16.9 173 64-247 65-252 (305)
7 KOG0834 CDK9 kinase-activating 99.9 7E-24 1.5E-28 205.1 13.5 193 39-252 36-250 (323)
8 PF00134 Cyclin_N: Cyclin, N-t 99.9 4.5E-22 9.8E-27 167.7 10.6 121 15-154 1-127 (127)
9 KOG0835 Cyclin L [General func 99.8 1.1E-19 2.4E-24 172.5 16.1 177 64-249 32-231 (367)
10 KOG0794 CDK8 kinase-activating 99.8 4.4E-20 9.6E-25 167.8 9.3 177 64-251 50-242 (264)
11 COG5333 CCL1 Cdk activating ki 99.8 3.2E-18 7E-23 162.4 12.0 147 64-217 54-210 (297)
12 PRK00423 tfb transcription ini 99.6 2.6E-14 5.6E-19 139.3 20.7 174 64-247 131-304 (310)
13 KOG2496 Cdk activating kinase 99.6 1.7E-14 3.7E-19 136.3 11.2 139 70-214 73-223 (325)
14 PF02984 Cyclin_C: Cyclin, C-t 99.5 8.8E-14 1.9E-18 115.1 8.5 93 156-251 1-93 (118)
15 cd00043 CYCLIN Cyclin box fold 99.4 1.9E-12 4.1E-17 100.3 7.1 77 64-146 11-88 (88)
16 smart00385 CYCLIN domain prese 99.3 4.6E-12 1E-16 97.2 6.5 78 64-147 5-83 (83)
17 COG1405 SUA7 Transcription ini 99.2 1E-09 2.2E-14 105.6 18.9 174 64-247 106-279 (285)
18 KOG1597 Transcription initiati 99.0 3.3E-08 7.2E-13 93.7 16.5 176 64-249 113-290 (308)
19 cd00043 CYCLIN Cyclin box fold 98.5 8.1E-07 1.7E-11 68.4 10.0 85 155-243 2-87 (88)
20 smart00385 CYCLIN domain prese 98.5 4.7E-07 1E-11 69.0 8.5 81 160-244 1-82 (83)
21 PF08613 Cyclin: Cyclin; Inte 98.1 7.8E-06 1.7E-10 71.6 7.3 86 64-153 60-149 (149)
22 KOG4164 Cyclin ik3-1/CABLES [C 97.7 3.7E-05 8.1E-10 75.7 4.4 87 64-156 391-482 (497)
23 KOG1598 Transcription initiati 97.4 0.00099 2.1E-08 68.4 11.0 170 64-244 76-251 (521)
24 PF00382 TFIIB: Transcription 97.0 0.0061 1.3E-07 46.3 8.9 71 162-236 1-71 (71)
25 PF00382 TFIIB: Transcription 96.3 0.013 2.8E-07 44.4 6.3 67 64-136 3-69 (71)
26 PRK00423 tfb transcription ini 94.7 0.13 2.8E-06 50.4 8.3 84 64-153 225-308 (310)
27 KOG1674 Cyclin [General functi 94.5 0.074 1.6E-06 49.6 5.6 93 64-156 84-181 (218)
28 PF00134 Cyclin_N: Cyclin, N-t 88.3 6.5 0.00014 32.2 10.1 85 159-246 35-121 (127)
29 COG1405 SUA7 Transcription ini 88.2 6 0.00013 38.4 11.1 102 142-247 76-185 (285)
30 KOG1597 Transcription initiati 84.7 10 0.00022 36.9 10.4 89 158-251 107-196 (308)
31 KOG1675 Predicted cyclin [Gene 76.2 2.6 5.7E-05 41.1 3.3 89 66-158 201-291 (343)
32 PF02984 Cyclin_C: Cyclin, C-t 74.7 6.2 0.00013 31.7 4.8 75 69-149 14-89 (118)
33 PF09241 Herp-Cyclin: Herpesvi 66.1 64 0.0014 25.5 9.7 91 158-249 4-100 (106)
34 PF09080 K-cyclin_vir_C: K cyc 65.8 68 0.0015 25.7 9.1 70 180-249 29-101 (106)
35 KOG0835 Cyclin L [General func 65.0 18 0.00039 35.8 6.3 61 76-142 161-222 (367)
36 TIGR00569 ccl1 cyclin ccl1. Un 62.8 17 0.00038 35.6 5.9 53 161-214 62-116 (305)
37 KOG0834 CDK9 kinase-activating 55.1 54 0.0012 32.5 7.8 55 159-214 43-97 (323)
38 PF08613 Cyclin: Cyclin; Inte 50.1 1.7E+02 0.0036 25.2 10.7 89 155-246 51-144 (149)
39 PF01302 CAP_GLY: CAP-Gly doma 39.0 16 0.00035 27.6 1.1 19 339-358 39-57 (69)
40 KOG0656 G1/S-specific cyclin D 26.2 2E+02 0.0044 28.6 6.7 56 159-215 82-140 (335)
41 PF07314 DUF1461: Protein of u 22.5 1.5E+02 0.0033 26.5 4.7 48 224-274 40-87 (181)
42 KOG0794 CDK8 kinase-activating 22.4 1.5E+02 0.0033 28.1 4.7 35 180-214 65-99 (264)
43 PF01857 RB_B: Retinoblastoma- 22.2 95 0.0021 26.7 3.2 64 64-131 20-83 (135)
No 1
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.1e-39 Score=312.61 Aligned_cols=214 Identities=27% Similarity=0.418 Sum_probs=193.5
Q ss_pred ccHHHHHHHHHHHHhhhcCCCCCC----CCcChhhhHHHHHHHHHhhhhhhccCcccccccccCCCccHHHHHHHHHHHH
Q 035817 11 AYKEEQFEKYFNVETEWMADEGYA----ESKEVTLRKVAMHVILRSAFWVLLDSFPVQNSKSDKLDAFIPYLAMNIFDRF 86 (365)
Q Consensus 11 ~y~~ei~~~l~~~E~~~~p~~~y~----~~i~~~~R~~~v~wIlr~idWl~~~~~~~~v~~~~~l~~eTl~lAV~~lDRf 86 (365)
-+.++++..|+++|.++.|..+|. ..+.+.+|..+++||+ +|++++++.++|++||+||||||
T Consensus 43 ~~~e~~i~~ll~kEe~~~p~~~~~~~~~~~~~~~~R~~A~~WIl-------------~V~~~~~~~~~~~~LA~NYlDRF 109 (335)
T KOG0656|consen 43 LWDERVLANLLEKEEQHNPSLDYFLCVQKLILSSMRKQALDWIL-------------KVCEEYNFEPLVFLLAMNYLDRF 109 (335)
T ss_pred cccHHHHHHHHHHHHHhCCCCchhhhcccccccHHHHHHHHHHH-------------HHHHHhCCchHHHHHHHHHHHHh
Confidence 577899999999999999998755 4478889999988888 99999999999999999999999
Q ss_pred HhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCC-hhhhhh---ccccCHHHHHHHHHHHHHhcCCccccCChHHHH
Q 035817 87 ISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFS-VPEFLG---KWNLDKDLMLKMELQILRGLKWQMRAVTPICLV 162 (365)
Q Consensus 87 ls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~p-l~dl~~---~~~~t~~~Il~mE~~IL~~L~w~L~~pTp~~FL 162 (365)
++.+.++..|+ |.+||+|+|||+||||+||+.+| +.|++. ++.|.++.|.+||+.||.+|+|+++.+||++|+
T Consensus 110 ls~~~l~k~k~---W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~ 186 (335)
T KOG0656|consen 110 LSSQKLPKDKP---WMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFI 186 (335)
T ss_pred hcccccCCCch---HHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHHHHHHHHHhhccccccCCCchHHH
Confidence 99999998776 99999999999999999999988 578864 589999999999999999999999999999999
Q ss_pred HHHHHHCCCC----hhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHHHHHhhcCCCHHHHHH
Q 035817 163 RFFVEMIPIG----KGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKKILLSRKYVEEEDLET 238 (365)
Q Consensus 163 ~~fl~~l~~~----~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~~L~~~~~~~~~~l~~ 238 (365)
++|+.+++.. +.+..+ +..++..+..+..|++|+||+||+|++..+...+....+......+..+.+++.+.+..
T Consensus 187 ~~fl~ki~~~~~~~~~~~~~-~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~ 265 (335)
T KOG0656|consen 187 DHFLSKISQKDHNKHLFLKH-ASLFLLSVITDIKFLEYPPSVIAAAAILSVSASVDGLDFREYENNLLSLLSLSKEKVNR 265 (335)
T ss_pred HHHHHHcCcccchHHHHHHH-HHHHHHHHhhhhhhhcCChHHHHHHHHHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhc
Confidence 9999999875 456666 89999999999999999999999999999988887665555567788888999999999
Q ss_pred HHH
Q 035817 239 CLD 241 (365)
Q Consensus 239 c~~ 241 (365)
|+.
T Consensus 266 ~~~ 268 (335)
T KOG0656|consen 266 CYD 268 (335)
T ss_pred chh
Confidence 988
No 2
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.3e-33 Score=266.63 Aligned_cols=208 Identities=20% Similarity=0.328 Sum_probs=181.9
Q ss_pred ccHHHHHHHHHHHHhhhcCCCCCC---CCcChhhhHHHHHHHHHhhhhhhccCcccccccccCCCccHHHHHHHHHHHHH
Q 035817 11 AYKEEQFEKYFNVETEWMADEGYA---ESKEVTLRKVAMHVILRSAFWVLLDSFPVQNSKSDKLDAFIPYLAMNIFDRFI 87 (365)
Q Consensus 11 ~y~~ei~~~l~~~E~~~~p~~~y~---~~i~~~~R~~~v~wIlr~idWl~~~~~~~~v~~~~~l~~eTl~lAV~~lDRfl 87 (365)
.-..|++..|..+|..+.....++ ..++++||. |+ +|||+ +||+.++|.+||||||+.||||||
T Consensus 111 gn~~eVW~lM~kkee~~l~~~~~l~qHpdlqp~mRa-----IL--lDWlm------EVCEvykLHRETFyLAvDy~DRyl 177 (408)
T KOG0655|consen 111 GNSKEVWLLMLKKEERYLRDKHFLEQHPDLQPQMRA-----IL--LDWLM------EVCEVYKLHRETFYLAVDYFDRYL 177 (408)
T ss_pred cCHHHHHHHHHccchhhhhhhHHHhhCCCCCHHHHH-----HH--HHHHH------HHHHHHHHhhhHHHHHHHHHHHHH
Confidence 457899999999999998776666 568899999 77 88888 999999999999999999999999
Q ss_pred hcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCC-hhhh--hhccccCHHHHHHHHHHHHHhcCCccccCChHHHHHH
Q 035817 88 SRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFS-VPEF--LGKWNLDKDLMLKMELQILRGLKWQMRAVTPICLVRF 164 (365)
Q Consensus 88 s~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~p-l~dl--~~~~~~t~~~Il~mE~~IL~~L~w~L~~pTp~~FL~~ 164 (365)
... +...| .++||||+||||||||+||+++| +.+| ++++.++.++|++||..||++|+|+|.+.|...||..
T Consensus 178 ~t~-~~v~k----t~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIltmE~iilkal~W~l~PiTii~WL~v 252 (408)
T KOG0655|consen 178 ETQ-VEVSK----TNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDILTMELIILKALKWELSPITIISWLNV 252 (408)
T ss_pred HHH-HHhhh----hhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHHHHHHHHHHHHhcccccceehHHHHHH
Confidence 766 33334 59999999999999999999998 7888 6899999999999999999999999999999999999
Q ss_pred HHHHCCCC------------hhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHHHHHhhcCCC
Q 035817 165 FVEMIPIG------------KGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKKILLSRKYVE 232 (365)
Q Consensus 165 fl~~l~~~------------~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~~L~~~~~~~ 232 (365)
|+.....+ ..+.+ ...++++++.+...+.|.-+.||||||+.-.. .+.+.+.+|+.
T Consensus 253 ylQv~~~n~~~k~l~Pq~~~~efiq--iaqlLDlc~ldids~~fsYrilaAAal~h~~s----------~e~v~kaSG~~ 320 (408)
T KOG0655|consen 253 YLQVDALNDAPKVLLPQYSQEEFIQ--IAQLLDLCILDIDSLEFSYRILAAAALCHFTS----------IEVVKKASGLE 320 (408)
T ss_pred HHHHHhcCCCCceeccccchHHHHH--HHHHHHHHHhccccccchHHHHHHHHHHHHhH----------HHHHHHccccc
Confidence 99987654 11222 45688899999999999999999999987663 25678889999
Q ss_pred HHHHHHHHHHHHHHHH
Q 035817 233 EEDLETCLDETYEKCI 248 (365)
Q Consensus 233 ~~~l~~c~~~l~~l~~ 248 (365)
..+|++|+++|.-+..
T Consensus 321 w~~ie~cv~wm~Pf~r 336 (408)
T KOG0655|consen 321 WDSIEECVDWMVPFVR 336 (408)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999998764
No 3
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.1e-33 Score=278.88 Aligned_cols=217 Identities=21% Similarity=0.279 Sum_probs=190.9
Q ss_pred cccHHHHHHHHHHHHhhhcCCCCCC--CCcChhhhHHHHHHHHHhhhhhhccCcccccccccCCCccHHHHHHHHHHHHH
Q 035817 10 PAYKEEQFEKYFNVETEWMADEGYA--ESKEVTLRKVAMHVILRSAFWVLLDSFPVQNSKSDKLDAFIPYLAMNIFDRFI 87 (365)
Q Consensus 10 ~~y~~ei~~~l~~~E~~~~p~~~y~--~~i~~~~R~~~v~wIlr~idWl~~~~~~~~v~~~~~l~~eTl~lAV~~lDRfl 87 (365)
.+|.++|+.+++.+|....|...+. .+++..||..+ +|||+ +||.+|++.+||+++||+++||||
T Consensus 124 ~ey~~di~~~l~~~e~~~~p~~~~~~~~e~~~~mR~iL-------vdwlv------evh~~F~L~~ETL~LaVnliDRfL 190 (391)
T KOG0653|consen 124 VEYVQDIFEYLRQLELEFLPLSYDISQSEIRAKMRAIL-------VDWLV------EVHEKFGLSPETLYLAVNLIDRFL 190 (391)
T ss_pred HHHHHHHHHHHHHHHHhhCchhhhcccccccHHHHHHH-------HHHHH------HhhhhcCcCHHHHHHHHHHHHHHH
Confidence 6899999999999997555654443 45667899955 55555 999999999999999999999999
Q ss_pred hcCCCCCccCCcccchhhhHHHHHH-HHhhhccCCCC-hhhh--hhccccCHHHHHHHHHHHHHhcCCccccCChHHHHH
Q 035817 88 SRHQLPTVLDHVRDDIVLAANSCLT-LAWKMRDNSFS-VPEF--LGKWNLDKDLMLKMELQILRGLKWQMRAVTPICLVR 163 (365)
Q Consensus 88 s~~~~~~~k~~~~~~lqLiavaCL~-LAsK~eE~~~p-l~dl--~~~~~~t~~~Il~mE~~IL~~L~w~L~~pTp~~FL~ 163 (365)
++..++ +.++||+|++||| ||+|+||..+| +.|+ ++++.|+.++|++||+.||.+|+|++..|||+.||+
T Consensus 191 ~~~~v~------~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il~mE~~il~~L~f~l~~p~~~~FLr 264 (391)
T KOG0653|consen 191 SKVKVP------LKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEILRMEKYILNVLEFDLSVPTPLSFLR 264 (391)
T ss_pred HHhccc------HHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHHHHHHHHHhccCeeecCCchHHHHH
Confidence 998876 3799999999966 99999999888 6776 689999999999999999999999999999999999
Q ss_pred HHHHHCCCChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHHHHHhhcCCCHHHHHHHHHHH
Q 035817 164 FFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKKILLSRKYVEEEDLETCLDET 243 (365)
Q Consensus 164 ~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~~L~~~~~~~~~~l~~c~~~l 243 (365)
+|++....+...... +.++++.+++++.++.++||.+|+|++++++....... .|...+..++|+...++.+|.+.+
T Consensus 265 r~~ka~~~d~~~~~~-~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~~~~~--~w~~~~~~~sg~~~~~~~~~~~~~ 341 (391)
T KOG0653|consen 265 RFLKAADYDIKTRTL-VKYLLELSLCDYSMLSIPPSSSAAASFTLALRMLSKGD--VWSPTLEHYSGYSESYLFECARSL 341 (391)
T ss_pred HHHHhhhcchhHHHH-HHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHhccCC--ccCCCCeeccCCCcHHHHHHHHHH
Confidence 999999876666666 88999999999999999999999999999999886543 588999999999888999999999
Q ss_pred HHHHH
Q 035817 244 YEKCI 248 (365)
Q Consensus 244 ~~l~~ 248 (365)
..+..
T Consensus 342 ~~~~~ 346 (391)
T KOG0653|consen 342 SALSL 346 (391)
T ss_pred HHHHH
Confidence 88543
No 4
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=100.00 E-value=2.9e-33 Score=278.92 Aligned_cols=223 Identities=18% Similarity=0.235 Sum_probs=201.4
Q ss_pred CCCC--cccHHHHHHHHHHHHhhhcCCCCCC---CCcChhhhHHHHHHHHHhhhhhhccCcccccccccCCCccHHHHHH
Q 035817 6 DYPL--PAYKEEQFEKYFNVETEWMADEGYA---ESKEVTLRKVAMHVILRSAFWVLLDSFPVQNSKSDKLDAFIPYLAM 80 (365)
Q Consensus 6 ~~p~--~~y~~ei~~~l~~~E~~~~p~~~y~---~~i~~~~R~~~v~wIlr~idWl~~~~~~~~v~~~~~l~~eTl~lAV 80 (365)
+||+ +||+.+|+.+|+++|....|.++|+ ....+.||..+++||. +||..|++.++|+++||
T Consensus 172 ~d~~mv~Ey~~~Ife~l~k~e~~~lp~~~yl~kq~~~~~~mR~~Lv~wlv-------------evH~~F~llpeTL~lai 238 (440)
T COG5024 172 EDPLMVPEYASDIFEYLLKLELIDLPNPNYLIKQSLYEWSMRSILVDWLV-------------EVHGKFGLLPETLFLAI 238 (440)
T ss_pred cCccchHHHHHHHHHHHHHHHHHhcCcHHHHhhcchhHHhHHHHHHHHHH-------------HhcccccccchHHHHHH
Confidence 4555 7999999999999999999999998 3466789996666666 99999999999999999
Q ss_pred HHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCC-hhhh--hhccccCHHHHHHHHHHHHHhcCCccccCC
Q 035817 81 NIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFS-VPEF--LGKWNLDKDLMLKMELQILRGLKWQMRAVT 157 (365)
Q Consensus 81 ~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~p-l~dl--~~~~~~t~~~Il~mE~~IL~~L~w~L~~pT 157 (365)
+++|||+++..+.. ..+||+|++|||||||+||..+| +.+| ++++.|+.++|+++|+.+|.+|+|++..|+
T Consensus 239 niiDrfLs~~~v~l------~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~ml~~l~f~is~P~ 312 (440)
T COG5024 239 NIIDRFLSSRVVSL------EKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYMLEVLDFNISWPS 312 (440)
T ss_pred HHHHHHhccCcccH------HHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHHHhhhcccccCCCC
Confidence 99999999999984 57999999999999999999998 5676 688999999999999999999999999999
Q ss_pred hHHHHHHHHHHCCCChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHHHHHhhcC-CCHHHH
Q 035817 158 PICLVRFFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKKILLSRKY-VEEEDL 236 (365)
Q Consensus 158 p~~FL~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~~L~~~~~-~~~~~l 236 (365)
|..||+++.+....+-..+.. +.++++.+..++.|.+++||.+||||.+.++..++... |...+..++| |+.+++
T Consensus 313 P~sFLRriSka~dyd~~srt~-~k~~~e~s~~~~~f~~~~~S~~~aaa~~~s~~~~~~~~---w~~~l~~ySg~y~~~~l 388 (440)
T COG5024 313 PMSFLRRISKASDYDIFSRTP-AKFSSEISPVDYKFIQISPSWCAAAAMYLSRKILSQNQ---WDRTLIHYSGNYTNPDL 388 (440)
T ss_pred hHHHHHHHHhhcccchhhhhh-HhhhCCchHhhhhhccCCchHHHHHHHHHHHhhhccCC---CCccccccCCCCCchhH
Confidence 999999998887776555556 88999999999999999999999999999999998654 8899999998 999999
Q ss_pred HHHHHHHHHHHHhcc
Q 035817 237 ETCLDETYEKCIEKK 251 (365)
Q Consensus 237 ~~c~~~l~~l~~~~~ 251 (365)
..+...+.+.+....
T Consensus 389 ~~~~~~~~~~l~~~~ 403 (440)
T COG5024 389 KPLNESNKENLQNPS 403 (440)
T ss_pred HHHHHHHHHHhcccc
Confidence 999999999886654
No 5
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.95 E-value=2.3e-28 Score=238.10 Aligned_cols=219 Identities=21% Similarity=0.249 Sum_probs=198.5
Q ss_pred cccHHHHHHHHHHHHhh-hcCCCCCC----CCcChhhhHHHHHHHHHhhhhhhccCcccccccccCCCccHHHHHHHHHH
Q 035817 10 PAYKEEQFEKYFNVETE-WMADEGYA----ESKEVTLRKVAMHVILRSAFWVLLDSFPVQNSKSDKLDAFIPYLAMNIFD 84 (365)
Q Consensus 10 ~~y~~ei~~~l~~~E~~-~~p~~~y~----~~i~~~~R~~~v~wIlr~idWl~~~~~~~~v~~~~~l~~eTl~lAV~~lD 84 (365)
..|+.+|+++++.-|.. .+|.++|+ .++++.||. |+ +||++ +|++.+++..+|+++++++.|
T Consensus 100 ~~~~~~I~~~~r~~ei~~~rp~~~~~e~vq~d~t~smrg-----il--vdwlv------evsee~r~~~e~l~ls~~~~d 166 (359)
T KOG0654|consen 100 LKIAAKIYNTLRVSDIKSERPLPSKFEFVQADITPSMRG-----IL--VDWLV------EVSEEYRLTFETLYLSVNYRD 166 (359)
T ss_pred HHHHHHHhhcccccchhhccCcccceeeeecCCCcchhh-----hh--hhhhh------HHHHHHHhhhhheeecHHHHH
Confidence 47999999999999999 88998898 679999999 66 77777 999999999999999999999
Q ss_pred HHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCC-hhhh--hhccccCHHHHHHHHHHHHHhcCCccccCChHHH
Q 035817 85 RFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFS-VPEF--LGKWNLDKDLMLKMELQILRGLKWQMRAVTPICL 161 (365)
Q Consensus 85 Rfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~p-l~dl--~~~~~~t~~~Il~mE~~IL~~L~w~L~~pTp~~F 161 (365)
||++...+. +..+|++|++|++||+|+||...| +.+| +.++.|+..++.+||..||..|.|.+..||.-.|
T Consensus 167 rfl~~~~~~------~~k~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~ty~~~qv~~~~~~il~~l~~~~~~pt~~~~ 240 (359)
T KOG0654|consen 167 RFLSYKEVN------KQKLQLVGISAMLIASKYEEIKEPRVEEFCYITDNTYTYWQVLRMEIDILNALTFELVRPTSKTF 240 (359)
T ss_pred HHhccCccH------HHHHHHhCcccceeeccchhhcchHHHHHHhhhhhhhHHHHHHHHHHHHHHHhHHHHhCchHHHH
Confidence 999999888 368999999999999999999888 5676 6889999999999999999999999999999999
Q ss_pred HHHHHHHCCC-ChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHHHHHhhcCCCHHHHHHHH
Q 035817 162 VRFFVEMIPI-GKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKKILLSRKYVEEEDLETCL 240 (365)
Q Consensus 162 L~~fl~~l~~-~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~~L~~~~~~~~~~l~~c~ 240 (365)
+..|+..... ..++... +.++.++++.++.|+.|.||.|||||+++|...++ ...|...|..++||+.+++..|+
T Consensus 241 l~~~~~~~~~~~~~~e~~-~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~---~~pW~~~L~~~T~y~~edl~~~v 316 (359)
T KOG0654|consen 241 LRRFLRVAQTPELQVEPL-ANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLD---FHPWNQTLEDYTGYKAEDLKPCV 316 (359)
T ss_pred HHHHHHhhcchhHHHHHH-HHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhcc---CCCCchhhHHhhcccHHHHHHHH
Confidence 9999887763 3556677 99999999999999999999999999999999887 34699999999999999999999
Q ss_pred HHHHHHHHhccc
Q 035817 241 DETYEKCIEKKI 252 (365)
Q Consensus 241 ~~l~~l~~~~~~ 252 (365)
..|+ ++.+.+.
T Consensus 317 ~~L~-~~l~~~~ 327 (359)
T KOG0654|consen 317 LDLH-LYLNASG 327 (359)
T ss_pred HHHh-cccCCCC
Confidence 9999 5544443
No 6
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.91 E-value=1.1e-23 Score=203.65 Aligned_cols=173 Identities=19% Similarity=0.211 Sum_probs=141.3
Q ss_pred ccccccC--CCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhhhhc----cccCHHH
Q 035817 64 QNSKSDK--LDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEFLGK----WNLDKDL 137 (365)
Q Consensus 64 ~v~~~~~--l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl~~~----~~~t~~~ 137 (365)
++|.+++ ++++|+++|+.||+||+.+.++. ..+.++||+||||||||+||.++++.++... .....++
T Consensus 65 ~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~------~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~~~~~~~~ 138 (305)
T TIGR00569 65 DFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVM------EYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKETPLKALEQ 138 (305)
T ss_pred HHHHHhcCCCCchHHHHHHHHHhHHhccCchh------hcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCCchhhHHH
Confidence 9999999 99999999999999999999988 3689999999999999999999998888543 2346799
Q ss_pred HHHHHHHHHHhcCCccccCChHHHHHHHHHHCCC-------ChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHH
Q 035817 138 MLKMELQILRGLKWQMRAVTPICLVRFFVEMIPI-------GKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTAC 210 (365)
Q Consensus 138 Il~mE~~IL~~L~w~L~~pTp~~FL~~fl~~l~~-------~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~ 210 (365)
|++||..||++|+|++.++||+.++..|+..++. ...+.+. |+.+++.++.+..++.|+||+||+|||++|.
T Consensus 139 Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~-a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~ 217 (305)
T TIGR00569 139 VLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKH-ADKFLNRTLLTDAYLLYTPSQIALAAILHTA 217 (305)
T ss_pred HHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHH-HHHHHHHHHcCCceecCCHHHHHHHHHHHHH
Confidence 9999999999999999999999999999864431 1456677 9999999998888999999999999999999
Q ss_pred HHhCCCcchhhHHHHHhhcCC--CHHHHHHHHHHHHHHH
Q 035817 211 RLLYDDIYEENKKILLSRKYV--EEEDLETCLDETYEKC 247 (365)
Q Consensus 211 ~~l~~~~~~~w~~~L~~~~~~--~~~~l~~c~~~l~~l~ 247 (365)
..++. +.+.. ....... +.+.+...+..|++..
T Consensus 218 ~~~~~-~l~~~---~~e~~~~~~~~~~~~~l~~~~~~~~ 252 (305)
T TIGR00569 218 SRAGL-NMESY---LTEQLSVPGNREELPQLIDIMRELR 252 (305)
T ss_pred HHhCC-CCccc---chhhhcccccHHHHHHHHHHHHHHH
Confidence 98874 32221 1233444 4555555555555543
No 7
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.91 E-value=7e-24 Score=205.11 Aligned_cols=193 Identities=18% Similarity=0.189 Sum_probs=166.3
Q ss_pred hhhhHHHHHHHHHhhhhhhccCcccccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhc
Q 035817 39 VTLRKVAMHVILRSAFWVLLDSFPVQNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMR 118 (365)
Q Consensus 39 ~~~R~~~v~wIlr~idWl~~~~~~~~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~e 118 (365)
...|.+...||. +++.++|+++.|+.+|+.|++||+..+++.. .+.+.+|++|||||+|+|
T Consensus 36 ~~~r~~~~~fI~-------------elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~------~~~~~vA~sclfLAgKvE 96 (323)
T KOG0834|consen 36 LRLRQEGAKFIQ-------------ELGVRLKMPQKTIATAIVIFHRFYMFHSFKK------FDPYTVAASCLFLAGKVE 96 (323)
T ss_pred HHHHHHHHHHHH-------------HHHHHcCCCccchhhhhhhhhhhhhhccccc------CcHHHHHHHHHHHHhhcc
Confidence 456776666776 9999999999999999999999999999982 577999999999999999
Q ss_pred cCCCChhhhhhc-----c--------cc--CHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHHCCCCh----hHHHHH
Q 035817 119 DNSFSVPEFLGK-----W--------NL--DKDLMLKMELQILRGLKWQMRAVTPICLVRFFVEMIPIGK----GIERRT 179 (365)
Q Consensus 119 E~~~pl~dl~~~-----~--------~~--t~~~Il~mE~~IL~~L~w~L~~pTp~~FL~~fl~~l~~~~----~l~~~~ 179 (365)
|+..++.|++.. + .| .++.|+..|+.||++|+|++++-+|+.||..|++.++.+. .+.+.
T Consensus 97 etp~kl~dIi~~s~~~~~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~- 175 (323)
T KOG0834|consen 97 ETPRKLEDIIKVSYRYLNPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQA- 175 (323)
T ss_pred cCcccHHHHHHHHHHHcCcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHH-
Confidence 999999888421 1 11 4789999999999999999999999999999999999874 37777
Q ss_pred HHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHHH-HHhhcC--CCHHHHHHHHHHHHHHHHhccc
Q 035817 180 LNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKKI-LLSRKY--VEEEDLETCLDETYEKCIEKKI 252 (365)
Q Consensus 180 a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~~-L~~~~~--~~~~~l~~c~~~l~~l~~~~~~ 252 (365)
||.++..++....+++|+|.+||+|||++|....+. .++.+... +....+ ++.+++.+.+..+.+++.....
T Consensus 176 Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~-~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y~~~~~ 250 (323)
T KOG0834|consen 176 AWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGV-ELPSDTDKRWWREFDETVTNELLDDICHEFLDLYEQTPQ 250 (323)
T ss_pred HHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCC-CCCCCcccchhhhhcccCCHHHHHHHHHHHHHHHhhccc
Confidence 999999999999999999999999999999988775 44444333 555667 9999999999999999976654
No 8
>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=99.87 E-value=4.5e-22 Score=167.67 Aligned_cols=121 Identities=25% Similarity=0.435 Sum_probs=101.5
Q ss_pred HHHHHHHHHHhhhcCCCCCC---CCcChhhhHHHHHHHHHhhhhhhccCcccccccccCCCccHHHHHHHHHHHHHhcCC
Q 035817 15 EQFEKYFNVETEWMADEGYA---ESKEVTLRKVAMHVILRSAFWVLLDSFPVQNSKSDKLDAFIPYLAMNIFDRFISRHQ 91 (365)
Q Consensus 15 ei~~~l~~~E~~~~p~~~y~---~~i~~~~R~~~v~wIlr~idWl~~~~~~~~v~~~~~l~~eTl~lAV~~lDRfls~~~ 91 (365)
||+++|+++|.++.+.+.|+ +.++...|..+++||. +++..++++++|+++|+.|+|||+.+..
T Consensus 1 ~i~~~~~~~e~~~~~~~~~~~~~~~~~~~~r~~~~~~i~-------------~~~~~~~l~~~~~~~A~~~~dr~~~~~~ 67 (127)
T PF00134_consen 1 DIFRYLLEKELKYKPNPDYLEQQPEITPEMRQIIIDWII-------------ELCQRLKLSPETLHLAIYLFDRFLSKRP 67 (127)
T ss_dssp HHHHHHHHHHHHTTCCTTHGTGTSSHHHHHHHHHHHHHH-------------HHHHHTT-BHHHHHHHHHHHHHHHTTS-
T ss_pred CHHHHHHHHHHHHCcCccccccChhcCHHHHHHHHHHHH-------------HHHHhcccchhHHHHHHHHHHHHHhhcc
Confidence 79999999999998888888 2466788886666666 9999999999999999999999999997
Q ss_pred CCCccCCcccchhhhHHHHHHHHhhhccCCCC-hhhh--hhccccCHHHHHHHHHHHHHhcCCccc
Q 035817 92 LPTVLDHVRDDIVLAANSCLTLAWKMRDNSFS-VPEF--LGKWNLDKDLMLKMELQILRGLKWQMR 154 (365)
Q Consensus 92 ~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~p-l~dl--~~~~~~t~~~Il~mE~~IL~~L~w~L~ 154 (365)
+. +.+++++|+|||+||+|++|..+| +.++ .+++.|++++|.+||+.||++|+|+++
T Consensus 68 ~~------~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 68 VN------RSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp TT------CCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHHHHHHHHTTT---
T ss_pred cc------cchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHHHHHHHHCCCCcC
Confidence 66 368999999999999999999766 6676 356899999999999999999999985
No 9
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.83 E-value=1.1e-19 Score=172.52 Aligned_cols=177 Identities=15% Similarity=0.196 Sum_probs=151.9
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhhhhc-------------
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEFLGK------------- 130 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl~~~------------- 130 (365)
+-+.-++|++.+.+++..+|-||+...++. +.++..++.+|++||+|+||.+..+.|++.-
T Consensus 32 ea~ILL~L~q~a~atgqVLFqRf~~~ks~v------~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~~~~~~ 105 (367)
T KOG0835|consen 32 EAGILLNLPQVAMATGQVLFQRFCYSKSFV------RHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRRESEAA 105 (367)
T ss_pred hhhHhhcCcHHHHHHHHHHHHHHHhccccc------cccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHHhccCc
Confidence 999999999999999999999999999887 3699999999999999999998767665311
Q ss_pred --------cccCHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHHCCCC--hhHHHHHHHHHHHHHccchhccCCCHHH
Q 035817 131 --------WNLDKDLMLKMELQILRGLKWQMRAVTPICLVRFFVEMIPIG--KGIERRTLNEIIIQTQDNISFTRFRPSV 200 (365)
Q Consensus 131 --------~~~t~~~Il~mE~~IL~~L~w~L~~pTp~~FL~~fl~~l~~~--~~l~~~~a~~li~~~l~d~~~l~~~PS~ 200 (365)
+.-.+..+.++|+.||++|||++++.+|+.++-.|+..++.. ..+.+. +|+|.++++....|..|+|+.
T Consensus 106 ~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~l~Q~-~wNfmNDslRT~v~vry~pe~ 184 (367)
T KOG0835|consen 106 EHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLKLLQA-AWNFMNDSLRTDVFVRYSPES 184 (367)
T ss_pred chhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchhHHHH-HHHhhhhccccceeeecCHHH
Confidence 112578899999999999999999999999999999999876 446888 999999999999999999999
Q ss_pred HHHHHHHHHHHHhCCCcchhhHHHHHhhcCCCHHHHHHHHHHHHHHHHh
Q 035817 201 IAASAVLTACRLLYDDIYEENKKILLSRKYVEEEDLETCLDETYEKCIE 249 (365)
Q Consensus 201 IAaAai~lA~~~l~~~~~~~w~~~L~~~~~~~~~~l~~c~~~l~~l~~~ 249 (365)
||+|||++|...++.. ++ .++.|..+.+.++++|.+....+..+|..
T Consensus 185 iACaciyLaAR~~eIp-Lp-~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~ 231 (367)
T KOG0835|consen 185 IACACIYLAARNLEIP-LP-FQPHWFKAFDTTKREIDEICYRLIPLYKR 231 (367)
T ss_pred HHHHHHHHHHhhhcCC-CC-CCccHHHHcCCcHHHHHHHHHHHHHHHHh
Confidence 9999999999988721 11 22345566889999999888888888765
No 10
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.81 E-value=4.4e-20 Score=167.80 Aligned_cols=177 Identities=22% Similarity=0.242 Sum_probs=153.6
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhh-------h--------
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEF-------L-------- 128 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl-------~-------- 128 (365)
.++.++++.+..+++|+.||-||+.+.+.. .-.+.++|.||++||||+||..+....+ +
T Consensus 50 ~lg~~lklRQ~ViATAivY~rRfy~r~S~k------~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~~ 123 (264)
T KOG0794|consen 50 KLGQHLKLRQRVIATAIVYFRRFYLRKSLK------EIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYWP 123 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh------ccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccch
Confidence 899999999999999999999999999977 3689999999999999999986332121 1
Q ss_pred hccccCHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHHCCCC-hhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHH
Q 035817 129 GKWNLDKDLMLKMELQILRGLKWQMRAVTPICLVRFFVEMIPIG-KGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVL 207 (365)
Q Consensus 129 ~~~~~t~~~Il~mE~~IL~~L~w~L~~pTp~~FL~~fl~~l~~~-~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~ 207 (365)
....|..+.|++||..+|+.|++-|.+.+|+.-|..++...+.. .++.+. +|.+++.++....++-|+|..||.|||+
T Consensus 124 e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~~~l~~-~W~ivNDSyr~Dl~Ll~PPh~IalAcl~ 202 (264)
T KOG0794|consen 124 EKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQKLLQL-AWSIVNDSYRMDLCLLYPPHQIALACLY 202 (264)
T ss_pred hhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccchhhhhh-hHhhhcchhhcceeeecCHHHHHHHHHH
Confidence 11456889999999999999999999999999999999999874 568888 9999999999999999999999999999
Q ss_pred HHHHHhCCCcchhhHHHHHhhcCCCHHHHHHHHHHHHHHHHhcc
Q 035817 208 TACRLLYDDIYEENKKILLSRKYVEEEDLETCLDETYEKCIEKK 251 (365)
Q Consensus 208 lA~~~l~~~~~~~w~~~L~~~~~~~~~~l~~c~~~l~~l~~~~~ 251 (365)
+|....+.+. .+.+-....+|.+.+.+|++.+.+++...+
T Consensus 203 Ia~~~~~k~~----~~~w~~el~vD~ekV~~~v~~I~~lYe~wk 242 (264)
T KOG0794|consen 203 IACVIDEKDI----PKAWFAELSVDMEKVKDIVQEILKLYELWK 242 (264)
T ss_pred HHHhhcCCCh----HHHHHHHHhccHHHHHHHHHHHHHHHHHHh
Confidence 9998776543 244455578999999999999999997665
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=99.76 E-value=3.2e-18 Score=162.39 Aligned_cols=147 Identities=20% Similarity=0.296 Sum_probs=130.1
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccC--CCChhhh-----hhc-cccCH
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDN--SFSVPEF-----LGK-WNLDK 135 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~--~~pl~dl-----~~~-~~~t~ 135 (365)
.+|.++++++.|+.+||.+|+||+.+..+. ...++-++.||++||+|+||+ ++.+.-+ .++ ..-++
T Consensus 54 ~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~------e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~sr 127 (297)
T COG5333 54 DLCTRLNLPQTVLATAILFFSRFYLKNSVE------EISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSSR 127 (297)
T ss_pred HHHHhcCCCcchHHHHHHHHHHHHhhcccc------cccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccccH
Confidence 999999999999999999999999999987 368999999999999999994 4443333 222 45589
Q ss_pred HHHHHHHHHHHHhcCCccccCChHHHHHHHHHHCCCCh--hHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHh
Q 035817 136 DLMLKMELQILRGLKWQMRAVTPICLVRFFVEMIPIGK--GIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLL 213 (365)
Q Consensus 136 ~~Il~mE~~IL~~L~w~L~~pTp~~FL~~fl~~l~~~~--~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l 213 (365)
+.|+.+|..||+.|+|++.+++|+..+..|+..+.... ++.+. ||.++..++...-++.|+|..||+||++.|...+
T Consensus 128 ~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~-aw~~inDa~~t~~~llypphiIA~a~l~ia~~~~ 206 (297)
T COG5333 128 ERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQI-AWKIINDALRTDLCLLYPPHIIALAALLIACEVL 206 (297)
T ss_pred HHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHH-HHHHHHhhhhceeeeecChHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999887653 47888 9999999999999999999999999999999987
Q ss_pred CCCc
Q 035817 214 YDDI 217 (365)
Q Consensus 214 ~~~~ 217 (365)
+...
T Consensus 207 ~~~~ 210 (297)
T COG5333 207 GMPI 210 (297)
T ss_pred CCcc
Confidence 7543
No 12
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.63 E-value=2.6e-14 Score=139.34 Aligned_cols=174 Identities=16% Similarity=0.142 Sum_probs=156.8
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhhhhccccCHHHHHHHHH
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEFLGKWNLDKDLMLKMEL 143 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl~~~~~~t~~~Il~mE~ 143 (365)
+++..++++..+.-.|..++.+++....+. ......++++|+|+|+|.++.+.++.++..-...++++|.+.++
T Consensus 131 ~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~r------grs~~~i~AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~ 204 (310)
T PRK00423 131 RIASQLGLPRSVREEAAVIYRKAVEKGLIR------GRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYR 204 (310)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHhcCccc------CCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence 899999999999999999999999886665 25689999999999999999988999996666789999999999
Q ss_pred HHHHhcCCccccCChHHHHHHHHHHCCCChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHH
Q 035817 144 QILRGLKWQMRAVTPICLVRFFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKK 223 (365)
Q Consensus 144 ~IL~~L~w~L~~pTp~~FL~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~ 223 (365)
.|++.|++++...+|.+|+..|...++....+.+. |.+++..+.......+.+|..|||||||+|....+.. ..++
T Consensus 205 ~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~v~~~-A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~---~t~k 280 (310)
T PRK00423 205 FLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKK-AIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGER---RTQR 280 (310)
T ss_pred HHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHH-HHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCC---CCHH
Confidence 99999999999999999999999999999888888 9999998887777789999999999999999876533 3567
Q ss_pred HHHhhcCCCHHHHHHHHHHHHHHH
Q 035817 224 ILLSRKYVEEEDLETCLDETYEKC 247 (365)
Q Consensus 224 ~L~~~~~~~~~~l~~c~~~l~~l~ 247 (365)
.+...+|++...|...++.|...+
T Consensus 281 eIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 281 EVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHh
Confidence 889999999999999999999865
No 13
>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=99.56 E-value=1.7e-14 Score=136.28 Aligned_cols=139 Identities=20% Similarity=0.286 Sum_probs=116.5
Q ss_pred CCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhhhhcc----ccCHHHHHHHHHHH
Q 035817 70 KLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEFLGKW----NLDKDLMLKMELQI 145 (365)
Q Consensus 70 ~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl~~~~----~~t~~~Il~mE~~I 145 (365)
.++++++.+|+.+|-||+...++.. .+.+.|.+||+|+|+|++|.++++.+|..+. .-+.+.|+..|..+
T Consensus 73 ~lp~~Vv~TA~~fFkRffL~nsvme------~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~vLk~E~~l 146 (325)
T KOG2496|consen 73 NLPTSVVSTAIEFFKRFFLENSVME------YSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIVLKYEFLL 146 (325)
T ss_pred CCchHHHHHHHHHHHHHHHhcchhh------cChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHHHhchHHH
Confidence 7899999999999999999999883 5789999999999999999999999986553 37899999999999
Q ss_pred HHhcCCccccCChHHHHHHHHHHCCCC------hhHHHHHH--HHHHHHHccchhccCCCHHHHHHHHHHHHHHHhC
Q 035817 146 LRGLKWQMRAVTPICLVRFFVEMIPIG------KGIERRTL--NEIIIQTQDNISFTRFRPSVIAASAVLTACRLLY 214 (365)
Q Consensus 146 L~~L~w~L~~pTp~~FL~~fl~~l~~~------~~l~~~~a--~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~ 214 (365)
++.|+|+|.+.+|+..++.|+..++.. ..+...+. ..++..++...-++-|.||+||+|||+.|....+
T Consensus 147 lqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a~~~~~ 223 (325)
T KOG2496|consen 147 LQSLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHAAGRTG 223 (325)
T ss_pred HHhhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHHhcccc
Confidence 999999999999999999998866432 22222212 3678888888888999999999999966654443
No 14
>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=99.49 E-value=8.8e-14 Score=115.10 Aligned_cols=93 Identities=23% Similarity=0.305 Sum_probs=78.5
Q ss_pred CChHHHHHHHHHHCCCChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHHHHHhhcCCCHHH
Q 035817 156 VTPICLVRFFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKKILLSRKYVEEED 235 (365)
Q Consensus 156 pTp~~FL~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~~L~~~~~~~~~~ 235 (365)
|||++||++|++..+.+..+... +++++++++.+..|++|+||+||+||+++|+..++.. +.|...+..++|++.++
T Consensus 1 PTp~~Fl~~~~~~~~~~~~~~~~-a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~--~~~~~~l~~~t~~~~~~ 77 (118)
T PF02984_consen 1 PTPYDFLRRFLKISNADQEVRNL-ARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKE--PPWPESLEKLTGYDKED 77 (118)
T ss_dssp --HHHHHHHHHTSSSHHHHHHHH-HHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSS--TCSHHHHHHHHTS-HHH
T ss_pred CcHHHHHHHHHHHcCCcHHHHHH-HHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCcc--ccCCccchhhcCCCHHH
Confidence 79999999997665545667777 9999999999999999999999999999999998631 36999999999999999
Q ss_pred HHHHHHHHHHHHHhcc
Q 035817 236 LETCLDETYEKCIEKK 251 (365)
Q Consensus 236 l~~c~~~l~~l~~~~~ 251 (365)
|.+|++.|.+++....
T Consensus 78 l~~c~~~i~~~~~~~~ 93 (118)
T PF02984_consen 78 LKECIELIQELLSKAS 93 (118)
T ss_dssp HHHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHHhcC
Confidence 9999999999987544
No 15
>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=99.35 E-value=1.9e-12 Score=100.33 Aligned_cols=77 Identities=23% Similarity=0.245 Sum_probs=69.0
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhhhhcccc-CHHHHHHHH
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEFLGKWNL-DKDLMLKME 142 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl~~~~~~-t~~~Il~mE 142 (365)
+++..++++++|.++|+.|+|||+....+. +.+++++|++|++||+|++|..+...++.....+ +.++|.++|
T Consensus 11 ~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~------~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~e 84 (88)
T cd00043 11 RVAKALGLSPETLTLAVNLLDRFLLDYSVL------GRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILRME 84 (88)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHHhcccc------cCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHHHH
Confidence 999999999999999999999999988776 3689999999999999999995567888655566 999999999
Q ss_pred HHHH
Q 035817 143 LQIL 146 (365)
Q Consensus 143 ~~IL 146 (365)
+.|+
T Consensus 85 ~~il 88 (88)
T cd00043 85 KLLL 88 (88)
T ss_pred HHhC
Confidence 9875
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=99.30 E-value=4.6e-12 Score=97.20 Aligned_cols=78 Identities=27% Similarity=0.287 Sum_probs=67.3
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhhhhccc-cCHHHHHHHH
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEFLGKWN-LDKDLMLKME 142 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl~~~~~-~t~~~Il~mE 142 (365)
+++..++++++|.++|+.++|||+....+. +...+++|++|++||+|++|..++..++..-.. |+.++|.++|
T Consensus 5 ~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~------~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~ 78 (83)
T smart00385 5 RVCKALNLDPETLNLAVNLLDRFLSDYKFL------KYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRME 78 (83)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHHHhhcc------cCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHH
Confidence 999999999999999999999999976655 258999999999999999999876777643222 6999999999
Q ss_pred HHHHH
Q 035817 143 LQILR 147 (365)
Q Consensus 143 ~~IL~ 147 (365)
+.||+
T Consensus 79 ~~il~ 83 (83)
T smart00385 79 KLLLE 83 (83)
T ss_pred HHHhC
Confidence 99974
No 17
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.22 E-value=1e-09 Score=105.60 Aligned_cols=174 Identities=17% Similarity=0.192 Sum_probs=156.5
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhhhhccccCHHHHHHHHH
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEFLGKWNLDKDLMLKMEL 143 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl~~~~~~t~~~Il~mE~ 143 (365)
.++..++++....-.|..++-+.+.+.-.. ....+-++++|+++|++....+.++.++......++++|.++.+
T Consensus 106 ~~~~~l~LP~~v~e~A~~iyr~a~~~~l~r------GRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~~kei~rtyr 179 (285)
T COG1405 106 RIASALGLPESVRETAARIYRKAVDKGLLR------GRSIESVAAACIYAACRINGVPRTLDEIAKALGVSKKEIGRTYR 179 (285)
T ss_pred HHHHHhCCCchHHHHHHHHHHHHhhcCCCc------CCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCCHHHHHHHHH
Confidence 788899999999999999998888887766 25689999999999999999988898887665688999999999
Q ss_pred HHHHhcCCccccCChHHHHHHHHHHCCCChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHH
Q 035817 144 QILRGLKWQMRAVTPICLVRFFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKK 223 (365)
Q Consensus 144 ~IL~~L~w~L~~pTp~~FL~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~ 223 (365)
.+...|+=.+.+..|.+|+.+|...|+.+..+... |.+++..+.......+-.|+.|||||||+|....+. ...+.
T Consensus 180 ~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~v~~~-a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~---~~tq~ 255 (285)
T COG1405 180 LLVRELKLKIPPVDPSDYIPRFASKLGLSDEVRRK-AIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGE---RRTQK 255 (285)
T ss_pred HHHHhcCCCCCCCCHHHHHHHHHHHcCCCHHHHHH-HHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCC---chHHH
Confidence 99999999999999999999999999999888888 999999999888888999999999999999987763 34678
Q ss_pred HHHhhcCCCHHHHHHHHHHHHHHH
Q 035817 224 ILLSRKYVEEEDLETCLDETYEKC 247 (365)
Q Consensus 224 ~L~~~~~~~~~~l~~c~~~l~~l~ 247 (365)
.+..++|+++..|+.-++.|.+.+
T Consensus 256 eva~v~~vtevTIrnrykel~~~~ 279 (285)
T COG1405 256 EVAKVAGVTEVTIRNRYKELADAL 279 (285)
T ss_pred HHHHHhCCeeeHHHHHHHHHHHhh
Confidence 999999999999999998887754
No 18
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.95 E-value=3.3e-08 Score=93.73 Aligned_cols=176 Identities=18% Similarity=0.133 Sum_probs=146.8
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhhhhccccCHHHHHHHHH
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEFLGKWNLDKDLMLKMEL 143 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl~~~~~~t~~~Il~mE~ 143 (365)
.++...+|+....-.|-.+|.++-...... .....-+++|||+||+.-++.+..+.++..--..++++|.+.=.
T Consensus 113 ~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lr------Gks~eai~AAclyiACRq~~~pRT~kEI~~~anv~kKEIgr~~K 186 (308)
T KOG1597|consen 113 AMCDRLSLPATIKDRANEIFKLVEDSKLLR------GKSVEALAAACLYIACRQEDVPRTFKEISAVANVSKKEIGRCVK 186 (308)
T ss_pred HHHHHhCCchHHHHHHHHHHHHHHHhhhhc------CccHHHHHHHHHHHHHHhcCCCchHHHHHHHHcCCHHHHHHHHH
Confidence 788899999999999999999998655444 25789999999999999999888899886543499999999999
Q ss_pred HHHHhcCCccccCC--hHHHHHHHHHHCCCChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhh
Q 035817 144 QILRGLKWQMRAVT--PICLVRFFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEEN 221 (365)
Q Consensus 144 ~IL~~L~w~L~~pT--p~~FL~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w 221 (365)
.|+..|+=.+...| ..+|+.+|...+..+.+.... |.++.+.+..-....+-.|=.||||+||++...-+.. -.
T Consensus 187 ~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~a-A~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~k---kt 262 (308)
T KOG1597|consen 187 LIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQEA-ATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEK---KT 262 (308)
T ss_pred HHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHHHH-HHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCc---cc
Confidence 99999998776666 889999999999998777666 7788877754444556889999999999999755422 35
Q ss_pred HHHHHhhcCCCHHHHHHHHHHHHHHHHh
Q 035817 222 KKILLSRKYVEEEDLETCLDETYEKCIE 249 (365)
Q Consensus 222 ~~~L~~~~~~~~~~l~~c~~~l~~l~~~ 249 (365)
++.+..++|+.+..|+..++.|......
T Consensus 263 ~keI~~vtgVaE~TIr~sYK~Lyp~~~~ 290 (308)
T KOG1597|consen 263 QKEIGEVTGVAEVTIRNSYKDLYPHADK 290 (308)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHhhchhh
Confidence 6888999999999999999999876543
No 19
>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=98.54 E-value=8.1e-07 Score=68.38 Aligned_cols=85 Identities=16% Similarity=0.068 Sum_probs=76.7
Q ss_pred cCChHHHHHHHHHHCCCChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHHHHHhhcCC-CH
Q 035817 155 AVTPICLVRFFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKKILLSRKYV-EE 233 (365)
Q Consensus 155 ~pTp~~FL~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~~L~~~~~~-~~ 233 (365)
.+++.+|+..+...++.+..+... |..+++..+....+..+.|+.||+||+++|.+..+. +.|.+.+..++++ +.
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~-A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~---~~~~~~~~~~~~~~~~ 77 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTL-AVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI---PPWLKDLVHVTGYATE 77 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHH-HHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCC---CCCHHHHhHHhCCCCH
Confidence 578999999999999988888888 999999999999999999999999999999987764 5688999999999 99
Q ss_pred HHHHHHHHHH
Q 035817 234 EDLETCLDET 243 (365)
Q Consensus 234 ~~l~~c~~~l 243 (365)
++|..+...+
T Consensus 78 ~~i~~~e~~i 87 (88)
T cd00043 78 EEILRMEKLL 87 (88)
T ss_pred HHHHHHHHHh
Confidence 9999887765
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=98.54 E-value=4.7e-07 Score=69.04 Aligned_cols=81 Identities=16% Similarity=0.123 Sum_probs=71.8
Q ss_pred HHHHHHHHHCCCChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHHHHHhhcCC-CHHHHHH
Q 035817 160 CLVRFFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKKILLSRKYV-EEEDLET 238 (365)
Q Consensus 160 ~FL~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~~L~~~~~~-~~~~l~~ 238 (365)
+|+..+...++.+.++... |.++++.++.+..+.+++|+.||+||+++|.+..+.. .|...+..++|+ +.+++.+
T Consensus 1 ~~l~~~~~~~~~~~~~~~~-a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~---~~~~~~~~~~~~~~~~~i~~ 76 (83)
T smart00385 1 DFLRRVCKALNLDPETLNL-AVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIP---PWTKELVHYTGYFTEEEILR 76 (83)
T ss_pred CHHHHHHHHcCCCHHHHHH-HHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCC---CCchhHhHhhCCCCHHHHHH
Confidence 4788899999988888888 9999999999889999999999999999999887643 488888999999 9999999
Q ss_pred HHHHHH
Q 035817 239 CLDETY 244 (365)
Q Consensus 239 c~~~l~ 244 (365)
|.+.|.
T Consensus 77 ~~~~il 82 (83)
T smart00385 77 MEKLLL 82 (83)
T ss_pred HHHHHh
Confidence 988775
No 21
>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=98.12 E-value=7.8e-06 Score=71.56 Aligned_cols=86 Identities=19% Similarity=0.180 Sum_probs=62.2
Q ss_pred ccccccCCCccHHHHHHHHHHHHHh---cCCCCCccCCcccchhhhHHHHHHHHhhhccCCC-ChhhhhhccccCHHHHH
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFIS---RHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSF-SVPEFLGKWNLDKDLML 139 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls---~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~-pl~dl~~~~~~t~~~Il 139 (365)
++...-+++++|+.+|+.|+||+.. ....... ....+-+-++|+.+|+|+-+... +-..+..-..++.+++.
T Consensus 60 ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~----~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~eln 135 (149)
T PF08613_consen 60 RILKYTQCSPECLILALIYLDRLRQRSRKPNIPLN----SSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKELN 135 (149)
T ss_dssp HHHHHTT--HHHHHHHHHHHHHHHH--H-TT---S----TTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHHHH
T ss_pred HHHHHcCCChHHHHHHHHHHHHHHHhhcccccccc----cchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHHHH
Confidence 8888889999999999999999999 3333322 25677888999999999976543 44555444568999999
Q ss_pred HHHHHHHHhcCCcc
Q 035817 140 KMELQILRGLKWQM 153 (365)
Q Consensus 140 ~mE~~IL~~L~w~L 153 (365)
+||+..|..|+|+|
T Consensus 136 ~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 136 ELEREFLKLLDYNL 149 (149)
T ss_dssp HHHHHHHHHTTT--
T ss_pred HHHHHHHHHCCCcC
Confidence 99999999999986
No 22
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=97.69 E-value=3.7e-05 Score=75.67 Aligned_cols=87 Identities=22% Similarity=0.367 Sum_probs=75.7
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCC-hhhhh----hccccCHHHH
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFS-VPEFL----GKWNLDKDLM 138 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~p-l~dl~----~~~~~t~~~I 138 (365)
+++..-++...|++.|..||.....+..+. | .+.+|.|-|||.+|+|+.+..-. +..++ ....+.+.++
T Consensus 391 ~l~~d~~id~~TVa~AyVYFEKliLkglis--K----~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrrdL 464 (497)
T KOG4164|consen 391 ELGEDCGIDVVTVAMAYVYFEKLILKGLIS--K----QNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRRDL 464 (497)
T ss_pred HhhhccCccceeehhHHHHHHHHHHhhhhh--h----hhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHHhh
Confidence 788899999999999999999999998877 4 47899999999999999976543 55554 3378899999
Q ss_pred HHHHHHHHHhcCCccccC
Q 035817 139 LKMELQILRGLKWQMRAV 156 (365)
Q Consensus 139 l~mE~~IL~~L~w~L~~p 156 (365)
+..|.-||.+|+|.|+++
T Consensus 465 ia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 465 IAFEFPVLVALEFALHLP 482 (497)
T ss_pred hhhhhhHHHhhhhhccCC
Confidence 999999999999999875
No 23
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=97.45 E-value=0.00099 Score=68.40 Aligned_cols=170 Identities=16% Similarity=0.130 Sum_probs=131.1
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhhhhccccCHHHHHHHHH
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEFLGKWNLDKDLMLKMEL 143 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl~~~~~~t~~~Il~mE~ 143 (365)
+++..+++.. .+-.|.++|---+...-.+ ....+.+-.+||+|++..|-+..=+.|+..--..+.-++-.+=+
T Consensus 76 ~~~~~l~l~~-~~~~a~~~~k~a~~~nftk------Gr~~~~vvasClY~vcR~e~t~hlliDfS~~Lqv~Vy~LG~~~l 148 (521)
T KOG1598|consen 76 ELTERLNLGN-KTEVAFNFFKLAPDRNFTK------GRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQVSVYDLGSNFL 148 (521)
T ss_pred HHHHhcCcch-HHHHHHHHHHHHhhCCCCC------CcchHHHHHHHHHHHHHhhCCceEEEEeccceEEehhhhhHHHH
Confidence 8999999999 8899999998888877666 25678899999999999998865555553333356667777778
Q ss_pred HHHHhcCCc---cccCChHHHHHHHHHHCCCC---hhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCc
Q 035817 144 QILRGLKWQ---MRAVTPICLVRFFVEMIPIG---KGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDI 217 (365)
Q Consensus 144 ~IL~~L~w~---L~~pTp~~FL~~fl~~l~~~---~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~ 217 (365)
.|...|.-. +-...|.-|+.+|...+... +++... |..++.....|.-..+-+|+-|.-|||++|....+..
T Consensus 149 ~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~-a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~- 226 (521)
T KOG1598|consen 149 EVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKT-ATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFR- 226 (521)
T ss_pred HHHHHhccccccccccCcceeeechhHhhhcCCchHHHHHH-HHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCcc-
Confidence 888888877 67788999999999887653 456666 8899999999999999999999999999999877632
Q ss_pred chhhHHHHHhhcCCCHHHHHHHHHHHH
Q 035817 218 YEENKKILLSRKYVEEEDLETCLDETY 244 (365)
Q Consensus 218 ~~~w~~~L~~~~~~~~~~l~~c~~~l~ 244 (365)
.-...+..+..+.+..+..-+.++.
T Consensus 227 --rsi~dIv~vvhV~e~Tl~kRl~Ef~ 251 (521)
T KOG1598|consen 227 --RTIGDIAKVVHVCESTLSKRLKEFS 251 (521)
T ss_pred --ccHHHHHHHHHHhHHHHHHHHHHHh
Confidence 2334555555666666555555544
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=97.02 E-value=0.0061 Score=46.29 Aligned_cols=71 Identities=21% Similarity=0.249 Sum_probs=55.5
Q ss_pred HHHHHHHCCCChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHHHHHhhcCCCHHHH
Q 035817 162 VRFFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKKILLSRKYVEEEDL 236 (365)
Q Consensus 162 L~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~~L~~~~~~~~~~l 236 (365)
+..|...++.+..+... |..++..+.......+-+|..+||||||+|.+..+.. --...+...+|+++.+|
T Consensus 1 I~r~~~~L~L~~~v~~~-A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~---~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRER-AKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVP---RTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHH-HHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSS---SSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHH-HHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCC---cCHHHHHHHhCCCCCcC
Confidence 46788888888888888 9999998887777778899999999999999876532 35677888889887764
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=96.32 E-value=0.013 Score=44.44 Aligned_cols=67 Identities=15% Similarity=0.125 Sum_probs=51.8
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhhhhccccCHH
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEFLGKWNLDKD 136 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl~~~~~~t~~ 136 (365)
+++..++|+..+.-.|..++++-....-.. ......++++|+++|++....+.++.++..-...+..
T Consensus 3 r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~------Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~ 69 (71)
T PF00382_consen 3 RICSKLGLPEDVRERAKEIYKKAQERGLLK------GRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEK 69 (71)
T ss_dssp HHHHHTT--HHHHHHHHHHHHHHHHTTTST------TS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHH
T ss_pred HHHhHcCCCHHHHHHHHHHHHHHHHcCCcc------cCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCC
Confidence 678899999999999999999988776554 2468999999999999999998888888543334433
No 26
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=94.75 E-value=0.13 Score=50.44 Aligned_cols=84 Identities=10% Similarity=0.020 Sum_probs=70.8
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhhhhccccCHHHHHHHHH
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEFLGKWNLDKDLMLKMEL 143 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl~~~~~~t~~~Il~mE~ 143 (365)
..+..++++..+.-.|..++.+..... +.. .....-||+||++||++..+...++.++......+...|.+.=+
T Consensus 225 r~~~~L~L~~~v~~~A~~i~~~a~~~~-l~~-----Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~yk 298 (310)
T PRK00423 225 RFASELGLSGEVQKKAIEILQKAKEKG-LTS-----GKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYK 298 (310)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHhcC-ccc-----CCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHH
Confidence 889999999999999999998887654 332 25789999999999999998888888887667889999999999
Q ss_pred HHHHhcCCcc
Q 035817 144 QILRGLKWQM 153 (365)
Q Consensus 144 ~IL~~L~w~L 153 (365)
.|++.|+..+
T Consensus 299 el~~~l~~~~ 308 (310)
T PRK00423 299 ELAEKLDIKI 308 (310)
T ss_pred HHHHHhCccc
Confidence 9999887544
No 27
>KOG1674 consensus Cyclin [General function prediction only]
Probab=94.46 E-value=0.074 Score=49.58 Aligned_cols=93 Identities=20% Similarity=0.163 Sum_probs=67.5
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCC---CCCccCCcccc-hhhhHHHHHHHHhhhccCCC-ChhhhhhccccCHHHH
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQ---LPTVLDHVRDD-IVLAANSCLTLAWKMRDNSF-SVPEFLGKWNLDKDLM 138 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~---~~~~k~~~~~~-lqLiavaCL~LAsK~eE~~~-pl~dl~~~~~~t~~~I 138 (365)
.+..+-+.+++++.+|..|||||..+.+ +...+..+-.+ ..-+-++|+.+|+|+.+... .-.-++.-...+.+++
T Consensus 84 ri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y~n~~~a~vggl~~~el 163 (218)
T KOG1674|consen 84 RIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYYSNAYYAKVGGLTTDEL 163 (218)
T ss_pred HHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchhhhHHHHHHhCCCChHhh
Confidence 6677788899999999999999999733 11000000022 44477899999999986532 2222333467889999
Q ss_pred HHHHHHHHHhcCCccccC
Q 035817 139 LKMELQILRGLKWQMRAV 156 (365)
Q Consensus 139 l~mE~~IL~~L~w~L~~p 156 (365)
..+|...|..++|++.+.
T Consensus 164 n~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 164 NKLELDLLFLLDFRLIIS 181 (218)
T ss_pred hhhhHHHHhhCCeEEEec
Confidence 999999999999999886
No 28
>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=88.29 E-value=6.5 Score=32.24 Aligned_cols=85 Identities=11% Similarity=0.058 Sum_probs=57.8
Q ss_pred HHHHHHHHHHCCCChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCCCcchhhHHHHHhhc--CCCHHHH
Q 035817 159 ICLVRFFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYDDIYEENKKILLSRK--YVEEEDL 236 (365)
Q Consensus 159 ~~FL~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~~L~~~~--~~~~~~l 236 (365)
.+|+......++.+...... |..+++.-+.........+..+|+||+++|.+..... +.+...+...+ .++.+++
T Consensus 35 ~~~i~~~~~~~~l~~~~~~~-A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~--~~~~~~~~~~~~~~~~~~~i 111 (127)
T PF00134_consen 35 IDWIIELCQRLKLSPETLHL-AIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDN--PPSISDLIRISDNTFTKKDI 111 (127)
T ss_dssp HHHHHHHHHHTT-BHHHHHH-HHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS----HHHHHHHHTTTSSHHHHH
T ss_pred HHHHHHHHHhcccchhHHHH-HHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccc--cchHHHHHHHHcCCCCHHHH
Confidence 45666667777766666666 8888887777777888999999999999999877542 23445554444 4677777
Q ss_pred HHHHHHHHHH
Q 035817 237 ETCLDETYEK 246 (365)
Q Consensus 237 ~~c~~~l~~l 246 (365)
...-..+...
T Consensus 112 ~~~E~~iL~~ 121 (127)
T PF00134_consen 112 LEMEREILSA 121 (127)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 6665555543
No 29
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=88.17 E-value=6 Score=38.43 Aligned_cols=102 Identities=12% Similarity=0.117 Sum_probs=75.8
Q ss_pred HHHHHHhcCCccccC--------ChHHHHHHHHHHCCCChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHh
Q 035817 142 ELQILRGLKWQMRAV--------TPICLVRFFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLL 213 (365)
Q Consensus 142 E~~IL~~L~w~L~~p--------Tp~~FL~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l 213 (365)
+..-|+..+.+..+. +.+..+..+...++....+... |..++..++..-..-.-....++|||+|.|....
T Consensus 76 ~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~-A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~ 154 (285)
T COG1405 76 KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRET-AARIYRKAVDKGLLRGRSIESVAAACIYAACRIN 154 (285)
T ss_pred HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHH-HHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHc
Confidence 444455444444444 6677888888888888777777 7777777776655566779999999999999876
Q ss_pred CCCcchhhHHHHHhhcCCCHHHHHHHHHHHHHHH
Q 035817 214 YDDIYEENKKILLSRKYVEEEDLETCLDETYEKC 247 (365)
Q Consensus 214 ~~~~~~~w~~~L~~~~~~~~~~l~~c~~~l~~l~ 247 (365)
+. +.....+...++++..++..+++.+...+
T Consensus 155 ~~---prtl~eIa~a~~V~~kei~rtyr~~~~~L 185 (285)
T COG1405 155 GV---PRTLDEIAKALGVSKKEIGRTYRLLVREL 185 (285)
T ss_pred CC---CccHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 53 34567788889999999999999776654
No 30
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=84.73 E-value=10 Score=36.88 Aligned_cols=89 Identities=16% Similarity=0.175 Sum_probs=63.8
Q ss_pred hHHHHHHHHHHCCCChhHHHHHHHHHHHHHccchhcc-CCCHHHHHHHHHHHHHHHhCCCcchhhHHHHHhhcCCCHHHH
Q 035817 158 PICLVRFFVEMIPIGKGIERRTLNEIIIQTQDNISFT-RFRPSVIAASAVLTACRLLYDDIYEENKKILLSRKYVEEEDL 236 (365)
Q Consensus 158 p~~FL~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l-~~~PS~IAaAai~lA~~~l~~~~~~~w~~~L~~~~~~~~~~l 236 (365)
.+.=+..+...++....+..+ |.++....- +..++ +-.--.|+|||||.|.+..+ .+...+.+..+.+++..+|
T Consensus 107 a~~~I~~m~d~~~Lp~~I~d~-A~~ifk~v~-~~k~lrGks~eai~AAclyiACRq~~---~pRT~kEI~~~anv~kKEI 181 (308)
T KOG1597|consen 107 AFKEITAMCDRLSLPATIKDR-ANEIFKLVE-DSKLLRGKSVEALAAACLYIACRQED---VPRTFKEISAVANVSKKEI 181 (308)
T ss_pred HHHHHHHHHHHhCCchHHHHH-HHHHHHHHH-HhhhhcCccHHHHHHHHHHHHHHhcC---CCchHHHHHHHHcCCHHHH
Confidence 444555666666666666666 777666554 45454 45556899999999998664 3445677788889999999
Q ss_pred HHHHHHHHHHHHhcc
Q 035817 237 ETCLDETYEKCIEKK 251 (365)
Q Consensus 237 ~~c~~~l~~l~~~~~ 251 (365)
-.|++.|.+.++...
T Consensus 182 gr~~K~i~~~l~~s~ 196 (308)
T KOG1597|consen 182 GRCVKLIGEALETSV 196 (308)
T ss_pred HHHHHHHHHHHhccc
Confidence 999999998876543
No 31
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=76.22 E-value=2.6 Score=41.06 Aligned_cols=89 Identities=16% Similarity=0.053 Sum_probs=57.1
Q ss_pred ccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCC--ChhhhhhccccCHHHHHHHHH
Q 035817 66 SKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSF--SVPEFLGKWNLDKDLMLKMEL 143 (365)
Q Consensus 66 ~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~--pl~dl~~~~~~t~~~Il~mE~ 143 (365)
.....+..+.-.....|++|-+--...... + .....+.....++|+|+-.... .+.-.+--...+.+++..|||
T Consensus 201 ~~~~qlta~~aiitL~~~erl~~~~e~~~~-p---~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd~tveDmNe~ER 276 (343)
T KOG1675|consen 201 FSWAQLTAECDIITLVYAERLLWLAERDPC-P---RNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKDQSVDDMNALER 276 (343)
T ss_pred hhhhhhhhccchHHHHhhHhhhhHhhcCCC-c---chhhhhhhhhheehhhhhhhhhcccHHHHHHHhhccHhhHHHHHH
Confidence 334445555556667788887755444321 1 3445555557899999876532 121111113468999999999
Q ss_pred HHHHhcCCccccCCh
Q 035817 144 QILRGLKWQMRAVTP 158 (365)
Q Consensus 144 ~IL~~L~w~L~~pTp 158 (365)
.+|+.|+|++++|..
T Consensus 277 qfLelLqfNinvp~s 291 (343)
T KOG1675|consen 277 QFLELLQFNINVPSS 291 (343)
T ss_pred HHHHHHhhccCccHH
Confidence 999999999998753
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=74.65 E-value=6.2 Score=31.71 Aligned_cols=75 Identities=17% Similarity=0.075 Sum_probs=48.5
Q ss_pred cCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhh-hhhccccCHHHHHHHHHHHHH
Q 035817 69 DKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPE-FLGKWNLDKDLMLKMELQILR 147 (365)
Q Consensus 69 ~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~d-l~~~~~~t~~~Il~mE~~IL~ 147 (365)
.+.+.++..+|-.+++-.+.....-. ...-+||++|+++|.++-....+... +..-..++.++|..+=..|.+
T Consensus 14 ~~~~~~~~~~a~~l~el~l~~~~fl~------~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c~~~i~~ 87 (118)
T PF02984_consen 14 SNADQEVRNLARYLLELSLLDYEFLQ------YPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKECIELIQE 87 (118)
T ss_dssp SSHHHHHHHHHHHHHHHHHHSHHHTT------S-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCcHHHHHHHHHHHHHHHhhccccC------CCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHHHHHHHH
Confidence 34466788888888887776666552 45689999999999999664233322 222235688887776555555
Q ss_pred hc
Q 035817 148 GL 149 (365)
Q Consensus 148 ~L 149 (365)
.+
T Consensus 88 ~~ 89 (118)
T PF02984_consen 88 LL 89 (118)
T ss_dssp HH
T ss_pred HH
Confidence 44
No 33
>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=66.10 E-value=64 Score=25.50 Aligned_cols=91 Identities=12% Similarity=0.035 Sum_probs=65.2
Q ss_pred hHHHHHHHHHHCCCC----hhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhCC--CcchhhHHHHHhhcCC
Q 035817 158 PICLVRFFVEMIPIG----KGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLYD--DIYEENKKILLSRKYV 231 (365)
Q Consensus 158 p~~FL~~fl~~l~~~----~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~~--~~~~~w~~~L~~~~~~ 231 (365)
.-+|+-...+.++.. .++... +.--+..++-.....-.+|-.|.|+.++.....-+. ..|..+.+.+..++++
T Consensus 4 ~tdflip~c~alkipe~~wpql~e~-~s~tickaliqpniall~p~licaggllttiet~ntn~~~wt~yledl~~ilnf 82 (106)
T PF09241_consen 4 STDFLIPVCHALKIPEDFWPQLFEA-TSITICKALIQPNIALLPPCLICAGGLLTTIETDNTNCQPWTCYLEDLSCILNF 82 (106)
T ss_dssp GGGGHHHHHHHTT--GGGHHHHHHH-HHHHHHHHTTSGGGGGS-HHHHHHHHHHHHHHTS-TSSSTCHHHHHHHHHHHTC
T ss_pred hhhhHHHhhhhccCcHHHhHHHHHH-HHHHHHHHHcCCCccccCcceeecccceEEEeccCCCCcchhhhHHhhHHHhhc
Confidence 346777788888776 345555 555666778788888899999999999998865432 2344556777778899
Q ss_pred CHHHHHHHHHHHHHHHHh
Q 035817 232 EEEDLETCLDETYEKCIE 249 (365)
Q Consensus 232 ~~~~l~~c~~~l~~l~~~ 249 (365)
+-..++....++.+.+..
T Consensus 83 stntirt~kdqv~ea~~~ 100 (106)
T PF09241_consen 83 STNTIRTVKDQVSEAFST 100 (106)
T ss_dssp HHHHHHHHHHHHHHHHHT
T ss_pred ccchhhhHHHHHHHHHHh
Confidence 999999998888877643
No 34
>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=65.83 E-value=68 Score=25.68 Aligned_cols=70 Identities=16% Similarity=0.036 Sum_probs=47.5
Q ss_pred HHHHHHHHccchhccCCCHHHHHHH-HHHHHHHHhCCC--cchhhHHHHHhhcCCCHHHHHHHHHHHHHHHHh
Q 035817 180 LNEIIIQTQDNISFTRFRPSVIAAS-AVLTACRLLYDD--IYEENKKILLSRKYVEEEDLETCLDETYEKCIE 249 (365)
Q Consensus 180 a~~li~~~l~d~~~l~~~PS~IAaA-ai~lA~~~l~~~--~~~~w~~~L~~~~~~~~~~l~~c~~~l~~l~~~ 249 (365)
....+..++.+...-..+||.|||| |-++.....-+. ......+.|....|++...+....+.+..-+++
T Consensus 29 V~~~v~KAiV~P~TG~Lp~SlvaAA~CAL~~~~~~~P~~~~~~~~~~~LA~~~G~~~a~L~AA~E~v~Tt~~e 101 (106)
T PF09080_consen 29 VVESVHKAIVNPKTGGLPPSLVAAAGCALFSLGAAAPPDTHSGGVVPQLAEALGVSAATLQAAAESVATTLRE 101 (106)
T ss_dssp HHHHHHHHHCSTTGGGS-HHHHHHHHHHHHS-GGGS--------HHHHHHHHHT--HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCcccCCCCHHHHHHhhhhhccccccCCCccccccchHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 6778888999999999999999998 666665444332 122245688899999999998888887765543
No 35
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=64.97 E-value=18 Score=35.80 Aligned_cols=61 Identities=15% Similarity=0.169 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCC-hhhhhhccccCHHHHHHHH
Q 035817 76 PYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFS-VPEFLGKWNLDKDLMLKME 142 (365)
Q Consensus 76 l~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~p-l~dl~~~~~~t~~~Il~mE 142 (365)
+..|-||+.--+-..-.. +...-.||++|.+||+...|++.| ...+-.-+.+++++|-..=
T Consensus 161 ~Q~~wNfmNDslRT~v~v------ry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic 222 (367)
T KOG0835|consen 161 LQAAWNFMNDSLRTDVFV------RYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEIC 222 (367)
T ss_pred HHHHHHhhhhccccceee------ecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHH
Confidence 566677776655544444 356789999999999999997665 3455455667777775443
No 36
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=62.84 E-value=17 Score=35.60 Aligned_cols=53 Identities=15% Similarity=0.176 Sum_probs=37.0
Q ss_pred HHHHHHHHCC--CChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhC
Q 035817 161 LVRFFVEMIP--IGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLY 214 (365)
Q Consensus 161 FL~~fl~~l~--~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~ 214 (365)
++..+...++ ....+... |..++..-....++..|.|-.||++|+|+|.+.-.
T Consensus 62 ~i~~~~~~lkp~Lpq~viaT-Aivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE 116 (305)
T TIGR00569 62 RLLDFCSAFKPTMPTSVVGT-AIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE 116 (305)
T ss_pred HHHHHHHHhcCCCCchHHHH-HHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccc
Confidence 4444455555 44445454 66666666667778889999999999999997543
No 37
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=55.12 E-value=54 Score=32.50 Aligned_cols=55 Identities=16% Similarity=0.103 Sum_probs=39.6
Q ss_pred HHHHHHHHHHCCCChhHHHHHHHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhC
Q 035817 159 ICLVRFFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLY 214 (365)
Q Consensus 159 ~~FL~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~ 214 (365)
..||......++....-... |..+...-.+...|-.|.|-.+|++||++|.+.-+
T Consensus 43 ~~fI~elg~~L~~~~~ti~t-A~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEe 97 (323)
T KOG0834|consen 43 AKFIQELGVRLKMPQKTIAT-AIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEE 97 (323)
T ss_pred HHHHHHHHHHcCCCccchhh-hhhhhhhhhhhcccccCcHHHHHHHHHHHHhhccc
Confidence 45777777777765333333 55555666667888899999999999999987654
No 38
>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=50.05 E-value=1.7e+02 Score=25.21 Aligned_cols=89 Identities=10% Similarity=0.022 Sum_probs=54.1
Q ss_pred cCChHHHHHHHHHHCCCChhHHHHHHHHHHHHHcc-----chhccCCCHHHHHHHHHHHHHHHhCCCcchhhHHHHHhhc
Q 035817 155 AVTPICLVRFFVEMIPIGKGIERRTLNEIIIQTQD-----NISFTRFRPSVIAASAVLTACRLLYDDIYEENKKILLSRK 229 (365)
Q Consensus 155 ~pTp~~FL~~fl~~l~~~~~l~~~~a~~li~~~l~-----d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~w~~~L~~~~ 229 (365)
..+-.+|+.++.+.........-. |..++..-.. ..........-+=++|+.+|.+.++... .+.+.+..+.
T Consensus 51 ~i~i~~fl~ri~~~~~~s~~~~i~-aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~--~~n~~~a~v~ 127 (149)
T PF08613_consen 51 SISIRDFLSRILKYTQCSPECLIL-ALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNT--YSNKSWAKVG 127 (149)
T ss_dssp SS-HHHHHHHHHHHTT--HHHHHH-HHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS-----HHHHHHHH
T ss_pred CCcHHHHHHHHHHHcCCChHHHHH-HHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhccccc--ccHHHHHhhc
Confidence 345668888888887776555444 4444443222 2223356677889999999999997543 4577888899
Q ss_pred CCCHHHHHHHHHHHHHH
Q 035817 230 YVEEEDLETCLDETYEK 246 (365)
Q Consensus 230 ~~~~~~l~~c~~~l~~l 246 (365)
|++..++..-=..+..+
T Consensus 128 gis~~eln~lE~~fL~~ 144 (149)
T PF08613_consen 128 GISLKELNELEREFLKL 144 (149)
T ss_dssp TS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 99998887665555443
No 39
>PF01302 CAP_GLY: CAP-Gly domain; InterPro: IPR000938 Cytoskeleton-associated proteins (CAP) are made of three distinct parts, an N-terminal section that is most probably globular and contains the CAP-Gly domain, a large central region predicted to be in an alpha-helical coiled-coil conformation and, finally, a short C-terminal globular domain. The CAP-Gly domain is a conserved, glycine-rich domain of about 42 residues found in some CAPs []. Proteins known to contain this domain include restin (also known as cytoplasmic linker protein-170 or CLIP-170), a 160 kDa protein associated with intermediate filaments and that links endocytic vesicles to microtubules; vertebrate dynactin (150 kDa dynein-associated polypeptide; DAP) and Drosophila glued, a major component of activator I; yeast protein BIK1, which seems to be required for the formation or stabilisation of microtubules during mitosis and for spindle pole body fusion during conjugation; yeast protein NIP100 (NIP80); human protein CKAP1/TFCB; Schizosaccharomyces pombe protein alp11 and Caenorhabditis elegans hypothetical protein F53F4.3. The latter proteins contain a N-terminal ubiquitin domain and a C-terminal CAP-Gly domain. The crystal structure of the CAP-Gly domain of C. elegans F53F4.3 protein, solved by single wavelength sulphur-anomalous phasing, revealed a novel protein fold containing three beta-sheets. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove. Residues in the groove are highly conserved as measured from the information content of the aligned sequences. The C-terminal tail of another molecule in the crystal is bound in this groove []. ; PDB: 2CP6_A 2E4H_A 2E3H_A 3E2U_B 2HL3_B 3TQ7_Q 2HKQ_B 2HQH_A 2HKN_B 2HL5_C ....
Probab=39.04 E-value=16 Score=27.55 Aligned_cols=19 Identities=53% Similarity=1.120 Sum_probs=14.6
Q ss_pred CCCCCCCcccccccccccCC
Q 035817 339 PDDPNDGTVEARNYFDLCAP 358 (365)
Q Consensus 339 ~~~~~~~~~~~~~~~~~~~~ 358 (365)
|..-||||+.-+.|| -|+|
T Consensus 39 ~~G~~dGt~~G~rYF-~c~~ 57 (69)
T PF01302_consen 39 PRGKNDGTVKGKRYF-ECPP 57 (69)
T ss_dssp STSSBSSEETTEESS--SST
T ss_pred CCCCCCcEECCEEEe-eeCC
Confidence 345699999999999 4654
No 40
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=26.20 E-value=2e+02 Score=28.64 Aligned_cols=56 Identities=5% Similarity=-0.056 Sum_probs=38.4
Q ss_pred HHHHHHHHHHCCCChhHHHHHHHHHHHHHccchhccCCC---HHHHHHHHHHHHHHHhCC
Q 035817 159 ICLVRFFVEMIPIGKGIERRTLNEIIIQTQDNISFTRFR---PSVIAASAVLTACRLLYD 215 (365)
Q Consensus 159 ~~FL~~fl~~l~~~~~l~~~~a~~li~~~l~d~~~l~~~---PS~IAaAai~lA~~~l~~ 215 (365)
.+|+-...+..+.+....-. |.++++.-+....+-+.+ =-.||+||+.+|.+.-..
T Consensus 82 ~~WIl~V~~~~~~~~~~~~L-A~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~ 140 (335)
T KOG0656|consen 82 LDWILKVCEEYNFEPLVFLL-AMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEET 140 (335)
T ss_pred HHHHHHHHHHhCCchHHHHH-HHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCc
Confidence 44555555544444455555 777788777777777777 557899999999976553
No 41
>PF07314 DUF1461: Protein of unknown function (DUF1461); InterPro: IPR010178 This entry represents a family of highly hydrophobic, uncharacterised predicted integral membrane proteins found almost entirely in low-GC Gram-positive bacteria, although a member is also found in Aquifex aeolicus.
Probab=22.52 E-value=1.5e+02 Score=26.54 Aligned_cols=48 Identities=17% Similarity=0.101 Sum_probs=33.8
Q ss_pred HHHhhcCCCHHHHHHHHHHHHHHHHhcccccccccccccCCCCchhhhhhh
Q 035817 224 ILLSRKYVEEEDLETCLDETYEKCIEKKILLLRDVWFVEKPKLEIGAAEIA 274 (365)
Q Consensus 224 ~L~~~~~~~~~~l~~c~~~l~~l~~~~~~~~~~~~~~~~~P~sp~~v~~~a 274 (365)
.+.+.+|++.+++..-++.|.+++..+....+. .+..|.|+.|+.+.+
T Consensus 40 ~i~~~~gls~~~l~~~~~~l~~YL~~~~~~~l~---~~~~~~s~~g~~Hf~ 87 (181)
T PF07314_consen 40 NIPQVTGLSKEELMKNYDQLIDYLNNPWDDLLK---LPDFPSSKNGLIHFA 87 (181)
T ss_pred CcHHhcCCCHHHHHHHHHHHHHHHCCCcccccc---ccccccChhhhhhHH
Confidence 356678999999999999999999776643211 122567777765543
No 42
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=22.44 E-value=1.5e+02 Score=28.11 Aligned_cols=35 Identities=14% Similarity=0.192 Sum_probs=25.4
Q ss_pred HHHHHHHHccchhccCCCHHHHHHHHHHHHHHHhC
Q 035817 180 LNEIIIQTQDNISFTRFRPSVIAASAVLTACRLLY 214 (365)
Q Consensus 180 a~~li~~~l~d~~~l~~~PS~IAaAai~lA~~~l~ 214 (365)
|.-++...+...++-.+.|-.+|..|+|+|.+.-.
T Consensus 65 AivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE 99 (264)
T KOG0794|consen 65 AIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEE 99 (264)
T ss_pred HHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhh
Confidence 33334444445567889999999999999997654
No 43
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. 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.
Probab=22.21 E-value=95 Score=26.69 Aligned_cols=64 Identities=9% Similarity=0.107 Sum_probs=46.6
Q ss_pred ccccccCCCccHHHHHHHHHHHHHhcCCCCCccCCcccchhhhHHHHHHHHhhhccCCCChhhhhhcc
Q 035817 64 QNSKSDKLDAFIPYLAMNIFDRFISRHQLPTVLDHVRDDIVLAANSCLTLAWKMRDNSFSVPEFLGKW 131 (365)
Q Consensus 64 ~v~~~~~l~~eTl~lAV~~lDRfls~~~~~~~k~~~~~~lqLiavaCL~LAsK~eE~~~pl~dl~~~~ 131 (365)
++|.+++++.+..-..-..|+..+.... ..-+. .++--+-++|+++-+|+....++..+++..|
T Consensus 20 ~LC~~L~l~~~~~~~iwt~fe~~l~~~t-~L~~d---RHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Y 83 (135)
T PF01857_consen 20 DLCERLDLSSDLREKIWTCFEHSLTHHT-ELMKD---RHLDQIILCAIYGICKVSKEELSFKDIIKAY 83 (135)
T ss_dssp HHHHHHTTSTTHHHHHHHHHHHHHHHSG-GGGTT---S-HHHHHHHHHHHHHHHTT-S--HHHHHHHH
T ss_pred HHHHHcCCcHHHHHHHHHHHHHHHHhhH-HHHhc---chHHHHHHHHHHHHHHhhcCCCCHHHHHHHH
Confidence 8899999999988888999999887543 22232 5788888999999999988666667765443
Done!