Query 045125
Match_columns 342
No_of_seqs 273 out of 1781
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 10:05:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045125.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045125hhsearch_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-46 4.5E-51 351.5 23.5 224 64-295 42-268 (335)
2 KOG0655 G1/S-specific cyclin E 100.0 4E-36 8.8E-41 275.3 20.9 219 66-302 112-336 (408)
3 KOG0653 Cyclin B and related k 100.0 3.2E-35 6.9E-40 287.5 17.5 227 60-304 120-348 (391)
4 COG5024 Cyclin [Cell division 100.0 8.5E-35 1.9E-39 282.4 11.5 229 58-304 172-402 (440)
5 KOG0654 G2/Mitotic-specific cy 100.0 3.8E-30 8.2E-35 243.9 6.4 231 57-304 93-325 (359)
6 PF00134 Cyclin_N: Cyclin, N-t 99.9 3.4E-25 7.4E-30 183.3 11.5 127 69-201 1-127 (127)
7 TIGR00569 ccl1 cyclin ccl1. Un 99.9 4.7E-22 1E-26 187.5 18.1 166 99-270 54-222 (305)
8 KOG0834 CDK9 kinase-activating 99.8 3.9E-20 8.5E-25 174.4 10.9 198 98-304 36-248 (323)
9 KOG0835 Cyclin L [General func 99.8 3.2E-18 7E-23 157.9 17.5 171 96-277 18-210 (367)
10 KOG0794 CDK8 kinase-activating 99.7 6.1E-17 1.3E-21 142.9 12.2 190 100-303 40-240 (264)
11 COG5333 CCL1 Cdk activating ki 99.7 2.6E-16 5.7E-21 145.3 12.5 166 97-274 41-211 (297)
12 PRK00423 tfb transcription ini 99.5 2.6E-12 5.7E-17 122.4 21.6 184 100-301 121-304 (310)
13 cd00043 CYCLIN Cyclin box fold 99.5 2E-13 4.4E-18 104.0 8.0 87 101-193 2-88 (88)
14 PF02984 Cyclin_C: Cyclin, C-t 99.4 1.9E-13 4E-18 111.0 7.0 92 203-304 1-92 (118)
15 smart00385 CYCLIN domain prese 99.4 8.9E-13 1.9E-17 99.4 7.8 83 106-194 1-83 (83)
16 KOG2496 Cdk activating kinase 99.3 1.4E-11 2.9E-16 113.4 10.3 156 105-267 60-221 (325)
17 COG1405 SUA7 Transcription ini 98.7 1.7E-06 3.7E-11 81.2 19.1 185 99-301 95-279 (285)
18 KOG1597 Transcription initiati 98.5 3.3E-06 7.2E-11 78.0 15.6 180 103-301 106-288 (308)
19 PF08613 Cyclin: Cyclin; Inte 98.3 3.2E-06 6.9E-11 72.2 7.8 92 104-200 54-149 (149)
20 cd00043 CYCLIN Cyclin box fold 98.2 1.2E-05 2.7E-10 60.5 9.8 85 202-297 2-87 (88)
21 smart00385 CYCLIN domain prese 98.2 5.4E-06 1.2E-10 61.9 7.7 80 208-298 2-82 (83)
22 KOG4164 Cyclin ik3-1/CABLES [C 98.2 2.5E-07 5.4E-12 88.0 0.0 141 60-203 341-482 (497)
23 KOG1598 Transcription initiati 97.5 0.0023 4.9E-08 64.0 13.8 174 83-270 44-225 (521)
24 PF00382 TFIIB: Transcription 95.7 0.098 2.1E-06 38.5 8.5 70 210-290 2-71 (71)
25 KOG1674 Cyclin [General functi 95.5 0.039 8.5E-07 50.1 6.7 96 105-203 79-181 (218)
26 PF00382 TFIIB: Transcription 95.2 0.12 2.5E-06 38.1 7.2 60 108-171 1-60 (71)
27 PRK00423 tfb transcription ini 93.4 0.92 2E-05 43.4 11.1 88 205-303 125-212 (310)
28 COG1405 SUA7 Transcription ini 84.3 12 0.00027 35.3 10.7 89 204-304 99-188 (285)
29 KOG1597 Transcription initiati 83.8 2.8 6.1E-05 39.4 6.0 50 253-304 146-195 (308)
30 KOG0834 CDK9 kinase-activating 83.0 1.4 3.1E-05 42.3 3.9 92 103-197 154-246 (323)
31 PF02984 Cyclin_C: Cyclin, C-t 81.1 2.6 5.6E-05 33.2 4.3 86 106-197 5-90 (118)
32 KOG1675 Predicted cyclin [Gene 71.4 3.8 8.3E-05 38.8 3.1 98 111-214 200-299 (343)
33 PF00134 Cyclin_N: Cyclin, N-t 68.3 58 0.0013 25.8 9.6 53 247-299 67-120 (127)
34 KOG0835 Cyclin L [General func 56.6 51 0.0011 31.7 7.6 64 122-191 161-224 (367)
35 PF09080 K-cyclin_vir_C: K cyc 52.8 1.1E+02 0.0023 23.7 10.1 89 205-299 4-97 (106)
36 TIGR00569 ccl1 cyclin ccl1. Un 40.2 2.4E+02 0.0052 27.0 9.5 38 233-270 80-117 (305)
37 PF11737 DUF3300: Protein of u 28.9 1.4E+02 0.003 27.5 5.6 54 250-304 60-113 (237)
38 PF08613 Cyclin: Cyclin; Inte 27.0 3.7E+02 0.0081 22.4 8.6 82 202-293 51-137 (149)
39 PF01857 RB_B: Retinoblastoma- 24.4 3.1E+02 0.0067 22.8 6.5 56 105-162 15-71 (135)
40 KOG1925 Rac1 GTPase effector F 22.5 1.2E+02 0.0025 31.1 4.1 70 66-135 547-616 (817)
41 PF12550 GCR1_C: Transcription 20.9 1.7E+02 0.0037 21.8 4.0 34 96-132 47-80 (81)
42 PF14376 Haem_bd: Haem-binding 20.5 2.2E+02 0.0047 23.7 4.9 36 75-110 100-135 (137)
No 1
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.1e-46 Score=351.54 Aligned_cols=224 Identities=50% Similarity=0.743 Sum_probs=201.3
Q ss_pred CCChHHHHHHHHHHHcccCCCCchhhhccCCCCCHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCch
Q 045125 64 PLQSDECLALLLEKECHHLPHNDYLKRLRTGDLDLAARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKV 143 (342)
Q Consensus 64 ~~y~~ei~~~l~~~E~~~~~~~~yl~~~q~~~i~~~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~ 143 (342)
..++++++..|+++|.++.|+.+|...+ +..+++.+|.++++||++|++++++.++|++||+||||||++.+++++.++
T Consensus 42 ~~~~e~~i~~ll~kEe~~~p~~~~~~~~-~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~ 120 (335)
T KOG0656|consen 42 LLWDERVLANLLEKEEQHNPSLDYFLCV-QKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKP 120 (335)
T ss_pred ccccHHHHHHHHHHHHHhCCCCchhhhc-ccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCch
Confidence 5689999999999999999999876665 446888999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHhhhccccCCcccceeeccCCccccHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHcCCCCCCC
Q 045125 144 WMMQLLAVACLSLAAKMEETEVPLCLDLQVGQSKFLFEAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTRKITDDDDDH 223 (342)
Q Consensus 144 ~~lqLlavaCL~IAsK~eE~~~p~~~dl~v~~~~~~~~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~~~~~~~~~~ 223 (342)
|++||+|+|||+||||+||+.+|.+.|+++....|.|.+++|++||+.||++|+|+|+.+||++|+++|+++++..
T Consensus 121 W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~---- 196 (335)
T KOG0656|consen 121 WMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQK---- 196 (335)
T ss_pred HHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcc----
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999887
Q ss_pred CCCcHHHHHHHHHHHHHhhccCccccccCHHHHHHHHHHHHHccCCCCcch---HHHHHHHhcCCCHHHHHHHHH
Q 045125 224 HQTPLRALFCRSIQIITSSIKGIDFLEFKPSEIAAAVAISVTGETKTVVDT---EKAISLLTQHVKKERVLKCIK 295 (342)
Q Consensus 224 ~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~IAaAai~~a~~~~~~~~~w---~~~l~~~~~~~~~~~l~~C~~ 295 (342)
......+...+..+++...+|..|+.|+||+||+|+++.+...+.. .+| ...+..+ .+++++.+..|++
T Consensus 197 -~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~~~~~-l~~~~~~~~~~~~-~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 197 -DHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVSASVDG-LDFREYENNLLSL-LSLSKEKVNRCYD 268 (335)
T ss_pred -cchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHHHhhcc-hhhhhhhHHHHHH-HHhhHHhhhcchh
Confidence 3333667777777888888899999999999999999888876665 333 2345555 6889999999998
No 2
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4e-36 Score=275.35 Aligned_cols=219 Identities=27% Similarity=0.429 Sum_probs=183.8
Q ss_pred ChHHHHHHHHHHHcccCCCCchhhhccCCCCCHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhcc-CcccCCchh
Q 045125 66 QSDECLALLLEKECHHLPHNDYLKRLRTGDLDLAARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSA-YELPKGKVW 144 (342)
Q Consensus 66 y~~ei~~~l~~~E~~~~~~~~yl~~~q~~~i~~~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~-~~~~~~~~~ 144 (342)
-+.+++..|+.||..+.....++.. .++++++||++++|||.+||+.|++.++|+|||+.||||||.. ..+.+..
T Consensus 112 n~~eVW~lM~kkee~~l~~~~~l~q--Hpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~-- 187 (408)
T KOG0655|consen 112 NSKEVWLLMLKKEERYLRDKHFLEQ--HPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTN-- 187 (408)
T ss_pred CHHHHHHHHHccchhhhhhhHHHhh--CCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhh--
Confidence 4689999999999998876677764 7889999999999999999999999999999999999999965 4666666
Q ss_pred hHHHHHHHHHHHHhhhccccCCccccee-eccCCccccHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHcCCCCCC-
Q 045125 145 MMQLLAVACLSLAAKMEETEVPLCLDLQ-VGQSKFLFEAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTRKITDDDDD- 222 (342)
Q Consensus 145 ~lqLlavaCL~IAsK~eE~~~p~~~dl~-v~~~~~~~~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~~~~~~~~~- 222 (342)
|||+|++|||||+|+||++||++.+|+ |+++.+ +.++|++||+.||++|+|++.+.|...+|.-|+.....++..
T Consensus 188 -lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAc--s~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~k 264 (408)
T KOG0655|consen 188 -LQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGAC--SEDDILTMELIILKALKWELSPITIISWLNVYLQVDALNDAPK 264 (408)
T ss_pred -HHHhhHHHHHHHHHHhhccCccccceeeeccCcc--chHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCCCc
Confidence 999999999999999999999999998 888775 999999999999999999999999999999999976554221
Q ss_pred --CCCCcHHHHHHHHHHHH-HhhccCccccccCHHHHHHHHHHHHHccCCCCcchHHHHHHHhcCCCHHHHHHHHHHHHH
Q 045125 223 --HHQTPLRALFCRSIQII-TSSIKGIDFLEFKPSEIAAAVAISVTGETKTVVDTEKAISLLTQHVKKERVLKCIKMMND 299 (342)
Q Consensus 223 --~~~~~~~~l~~~~~~li-l~~l~d~~~l~~~PS~IAaAai~~a~~~~~~~~~w~~~l~~~~~~~~~~~l~~C~~~l~~ 299 (342)
.++.+ +...-..++|+ +|++ +...+.|.-++|||||++.-.. .....+. +|+.+..|.+|+++|.-
T Consensus 265 ~l~Pq~~-~~efiqiaqlLDlc~l-dids~~fsYrilaAAal~h~~s--------~e~v~ka-SG~~w~~ie~cv~wm~P 333 (408)
T KOG0655|consen 265 VLLPQYS-QEEFIQIAQLLDLCIL-DIDSLEFSYRILAAAALCHFTS--------IEVVKKA-SGLEWDSIEECVDWMVP 333 (408)
T ss_pred eeccccc-hHHHHHHHHHHHHHHh-ccccccchHHHHHHHHHHHHhH--------HHHHHHc-ccccHHHHHHHHHHHHH
Confidence 12233 33333344444 5666 9999999999999999876441 2345666 99999999999999987
Q ss_pred HHh
Q 045125 300 SLI 302 (342)
Q Consensus 300 l~~ 302 (342)
+..
T Consensus 334 f~r 336 (408)
T KOG0655|consen 334 FVR 336 (408)
T ss_pred HHH
Confidence 763
No 3
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=3.2e-35 Score=287.46 Aligned_cols=227 Identities=25% Similarity=0.368 Sum_probs=196.4
Q ss_pred ccCCCCChHHHHHHHHHHHcccCCCCchhhhccCCCCCHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCccc
Q 045125 60 LLSLPLQSDECLALLLEKECHHLPHNDYLKRLRTGDLDLAARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELP 139 (342)
Q Consensus 60 ~~~~~~y~~ei~~~l~~~E~~~~~~~~yl~~~q~~~i~~~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~ 139 (342)
.+.+.+|.++|+.+++++|....|...+ . +++.++.+||.++|||+++||.+|++.+||+|+||+++||||++..++
T Consensus 120 ~~~~~ey~~di~~~l~~~e~~~~p~~~~-~--~~~e~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~ 196 (391)
T KOG0653|consen 120 PSMIVEYVQDIFEYLRQLELEFLPLSYD-I--SQSEIRAKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVP 196 (391)
T ss_pred cHHHHHHHHHHHHHHHHHHHhhCchhhh-c--ccccccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhccc
Confidence 3457889999999999999655554444 2 367899999999999999999999999999999999999999998898
Q ss_pred CCchhhHHHHHHHHHH-HHhhhccccCCccccee-eccCCccccHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHcC
Q 045125 140 KGKVWMMQLLAVACLS-LAAKMEETEVPLCLDLQ-VGQSKFLFEAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTRKIT 217 (342)
Q Consensus 140 ~~~~~~lqLlavaCL~-IAsK~eE~~~p~~~dl~-v~~~~~~~~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~~~~ 217 (342)
+.+ +||+|++||| ||+|+||..+|.+.++. ++++. |++++|++||+.||++|+|++..|||+.||++|++...
T Consensus 197 ~~~---lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~--~s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~ 271 (391)
T KOG0653|consen 197 LKK---LQLVGVSALLSIACKYEEISLPSVEDLVLITDGA--YSREEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAAD 271 (391)
T ss_pred HHH---hhHHhHHHHHHHHHhhhhccCCccceeEeeeCCc--cchHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhh
Confidence 888 9999999966 99999999999999996 66655 69999999999999999999999999999999999888
Q ss_pred CCCCCCCCCcHHHHHHHHHHHHHhhccCccccccCHHHHHHHHHHHHHccCCCCcchHHHHHHHhcCCCHHHHHHHHHHH
Q 045125 218 DDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFKPSEIAAAVAISVTGETKTVVDTEKAISLLTQHVKKERVLKCIKMM 297 (342)
Q Consensus 218 ~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~IAaAai~~a~~~~~~~~~w~~~l~~~~~~~~~~~l~~C~~~l 297 (342)
.+ ...+.+.++..++.+ .|+.++.++||.+|+|+++++++.......|...+..+ +|+...++..|...+
T Consensus 272 ~d------~~~~~~~k~~~El~l---~d~~~~~~~~s~~aaa~~~~~~~~~~~~~~w~~~~~~~-sg~~~~~~~~~~~~~ 341 (391)
T KOG0653|consen 272 YD------IKTRTLVKYLLELSL---CDYSMLSIPPSSSAAASFTLALRMLSKGDVWSPTLEHY-SGYSESYLFECARSL 341 (391)
T ss_pred cc------hhHHHHHHHHHHHHH---hhhHHhccCcHHHHHHHHHHHHHHhccCCccCCCCeec-cCCCcHHHHHHHHHH
Confidence 43 333667777777743 39999999999999999999998766633699988888 899888999999999
Q ss_pred HHHHhcC
Q 045125 298 NDSLISG 304 (342)
Q Consensus 298 ~~l~~~~ 304 (342)
..+....
T Consensus 342 ~~~~~~~ 348 (391)
T KOG0653|consen 342 SALSLSS 348 (391)
T ss_pred HHHHHHh
Confidence 8855443
No 4
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=100.00 E-value=8.5e-35 Score=282.38 Aligned_cols=229 Identities=26% Similarity=0.340 Sum_probs=202.8
Q ss_pred CCccCCCCChHHHHHHHHHHHcccCCCCchhhhccCCCCCHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCc
Q 045125 58 DMLLSLPLQSDECLALLLEKECHHLPHNDYLKRLRTGDLDLAARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYE 137 (342)
Q Consensus 58 ~~~~~~~~y~~ei~~~l~~~E~~~~~~~~yl~~~q~~~i~~~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~ 137 (342)
+..+-+++|+.+|+.+|+++|....|.+.|+.+ ++.+...||..+++||.++|..|++.++|+++||+++||||+...
T Consensus 172 ~d~~mv~Ey~~~Ife~l~k~e~~~lp~~~yl~k--q~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~ 249 (440)
T COG5024 172 EDPLMVPEYASDIFEYLLKLELIDLPNPNYLIK--QSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRV 249 (440)
T ss_pred cCccchHHHHHHHHHHHHHHHHHhcCcHHHHhh--cchhHHhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCc
Confidence 356778999999999999999999999999765 777888999999999999999999999999999999999999999
Q ss_pred ccCCchhhHHHHHHHHHHHHhhhccccCCccccee-eccCCccccHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHc
Q 045125 138 LPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQ-VGQSKFLFEAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTRKI 216 (342)
Q Consensus 138 ~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~-v~~~~~~~~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~~~ 216 (342)
++-.+ +||+|++|||||+|+||.+.|.+.+|+ ++++. |+.++|+++|+.+|.+|+|++..|+|..|++++...-
T Consensus 250 v~l~k---~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~--~t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~ 324 (440)
T COG5024 250 VSLEK---YQLVGISALFIASKYEEVNCPSIKDLVYATDGA--FTRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKAS 324 (440)
T ss_pred ccHHH---HHHHHHHHHHHHHhHhHhcCHHHHHHHHHHccc--ccHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhhc
Confidence 99888 999999999999999999999999997 66655 5999999999999999999999999999988776654
Q ss_pred CCCCCCCCCCcHHHHHHHHHHHHHhhccCccccccCHHHHHHHHHHHHHccCCCCcchHHHHHHHhcC-CCHHHHHHHHH
Q 045125 217 TDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFKPSEIAAAVAISVTGETKTVVDTEKAISLLTQH-VKKERVLKCIK 295 (342)
Q Consensus 217 ~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~IAaAai~~a~~~~~~~~~w~~~l~~~~~~-~~~~~l~~C~~ 295 (342)
..+ ...+....+..++ +..++.|.+++||.+||||.+.+++..+. .+|...+..+ +| |+.+++.++.+
T Consensus 325 dyd------~~srt~~k~~~e~---s~~~~~f~~~~~S~~~aaa~~~s~~~~~~-~~w~~~l~~y-Sg~y~~~~l~~~~~ 393 (440)
T COG5024 325 DYD------IFSRTPAKFSSEI---SPVDYKFIQISPSWCAAAAMYLSRKILSQ-NQWDRTLIHY-SGNYTNPDLKPLNE 393 (440)
T ss_pred ccc------hhhhhhHhhhCCc---hHhhhhhccCCchHHHHHHHHHHHhhhcc-CCCCcccccc-CCCCCchhHHHHHH
Confidence 443 2225566666665 34488999999999999999999987776 5699998888 77 99999999999
Q ss_pred HHHHHHhcC
Q 045125 296 MMNDSLISG 304 (342)
Q Consensus 296 ~l~~l~~~~ 304 (342)
.+.+.+...
T Consensus 394 ~~~~~l~~~ 402 (440)
T COG5024 394 SNKENLQNP 402 (440)
T ss_pred HHHHHhccc
Confidence 999988776
No 5
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.96 E-value=3.8e-30 Score=243.91 Aligned_cols=231 Identities=22% Similarity=0.305 Sum_probs=203.3
Q ss_pred CCCccCCCCChHHHHHHHHHHHcc-cCCCCchhhhccCCCCCHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhcc
Q 045125 57 GDMLLSLPLQSDECLALLLEKECH-HLPHNDYLKRLRTGDLDLAARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSA 135 (342)
Q Consensus 57 ~~~~~~~~~y~~ei~~~l~~~E~~-~~~~~~yl~~~q~~~i~~~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~ 135 (342)
+..++.|..|..+|+++++..|.. ..|.++|++++|. ++++.||.++|+|.+++.+.+++..+++|+++++.|||+..
T Consensus 93 ~~dp~~c~~~~~~I~~~~r~~ei~~~rp~~~~~e~vq~-d~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~ 171 (359)
T KOG0654|consen 93 GEDPQMCLKIAAKIYNTLRVSDIKSERPLPSKFEFVQA-DITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSY 171 (359)
T ss_pred ccchHHHHHHHHHHhhcccccchhhccCcccceeeeec-CCCcchhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhcc
Confidence 334567788999999999999999 9999999999864 79999999999999999999999999999999999999999
Q ss_pred CcccCCchhhHHHHHHHHHHHHhhhccccCCccccee-eccCCccccHHHHHHHHHHHHHHcCCccccCChHHHHHHHHH
Q 045125 136 YELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQ-VGQSKFLFEAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTR 214 (342)
Q Consensus 136 ~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~-v~~~~~~~~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~ 214 (342)
..+.+.+ +|++|.+|++||+|+||..+|.+.+|. +.++ .|+..++.+||..||+.|.|.+..||.-.|+..|+.
T Consensus 172 ~~~~~~k---~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~--ty~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~ 246 (359)
T KOG0654|consen 172 KEVNKQK---LQLVGISAMLIASKYEEIKEPRVEEFCYITDN--TYTYWQVLRMEIDILNALTFELVRPTSKTFLRRFLR 246 (359)
T ss_pred CccHHHH---HHHhCcccceeeccchhhcchHHHHHHhhhhh--hhHHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHH
Confidence 9999888 999999999999999999999999995 5554 459999999999999999999999999999999988
Q ss_pred HcCCCCCCCCCCcHHHHHHHHHHHHHhhccCccccccCHHHHHHHHHHHHHccCCCCcchHHHHHHHhcCCCHHHHHHHH
Q 045125 215 KITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFKPSEIAAAVAISVTGETKTVVDTEKAISLLTQHVKKERVLKCI 294 (342)
Q Consensus 215 ~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~IAaAai~~a~~~~~~~~~w~~~l~~~~~~~~~~~l~~C~ 294 (342)
..... ......++.+..++ ++.++.|+.|.||.|||||+++|+-..+ ...|++.|..+ |+|+.++++.|+
T Consensus 247 ~~~~~-----~~~~e~~~~yl~el---sll~~~~l~y~PSliAasAv~lA~~~~~-~~pW~~~L~~~-T~y~~edl~~~v 316 (359)
T KOG0654|consen 247 VAQTP-----ELQVEPLANYLTEL---SLLDYIFLKYLPSLIAASAVFLARLTLD-FHPWNQTLEDY-TGYKAEDLKPCV 316 (359)
T ss_pred hhcch-----hHHHHHHHHHHHHh---hhhhHHHhccChHHHHHHHHHHHHhhcc-CCCCchhhHHh-hcccHHHHHHHH
Confidence 76652 22224455555555 3348889999999999999999997776 47899999999 999999999999
Q ss_pred HHHHHHHhcC
Q 045125 295 KMMNDSLISG 304 (342)
Q Consensus 295 ~~l~~l~~~~ 304 (342)
..|+ ++.+.
T Consensus 317 ~~L~-~~l~~ 325 (359)
T KOG0654|consen 317 LDLH-LYLNA 325 (359)
T ss_pred HHHh-cccCC
Confidence 9999 76654
No 6
>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=99.92 E-value=3.4e-25 Score=183.29 Aligned_cols=127 Identities=37% Similarity=0.551 Sum_probs=111.1
Q ss_pred HHHHHHHHHHcccCCCCchhhhccCCCCCHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHH
Q 045125 69 ECLALLLEKECHHLPHNDYLKRLRTGDLDLAARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQL 148 (342)
Q Consensus 69 ei~~~l~~~E~~~~~~~~yl~~~q~~~i~~~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqL 148 (342)
||+.+|+++|.++.+.+.|++. +++++...|..+++||.+++..+++++.|+++|+.|||||+...++.+.+ +++
T Consensus 1 ~i~~~~~~~e~~~~~~~~~~~~--~~~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~---~~l 75 (127)
T PF00134_consen 1 DIFRYLLEKELKYKPNPDYLEQ--QPEITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSK---LQL 75 (127)
T ss_dssp HHHHHHHHHHHHTTCCTTHGTG--TSSHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCG---HHH
T ss_pred CHHHHHHHHHHHHCcCcccccc--ChhcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccch---hhh
Confidence 6899999999999989999985 55789999999999999999999999999999999999999999888777 999
Q ss_pred HHHHHHHHHhhhccccCCcccceeeccCCccccHHHHHHHHHHHHHHcCCccc
Q 045125 149 LAVACLSLAAKMEETEVPLCLDLQVGQSKFLFEAKTIQRMELLVLSTLKWRMQ 201 (342)
Q Consensus 149 lavaCL~IAsK~eE~~~p~~~dl~v~~~~~~~~~~~I~~mE~~IL~~L~w~l~ 201 (342)
+|++||+||+|++|..+|.+.++. ....+.|++++|.+||+.||++|+|+++
T Consensus 76 i~~~cl~lA~K~~e~~~~~~~~~~-~~~~~~~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 76 IALACLFLASKMEEDNPPSISDLI-RISDNTFTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp HHHHHHHHHHHHHTSS--HHHHHH-HHTTTSSHHHHHHHHHHHHHHHTTT---
T ss_pred hhhhHHHHhhhhhccccchHHHHH-HHHcCCCCHHHHHHHHHHHHHHCCCCcC
Confidence 999999999999999999999995 3335578999999999999999999985
No 7
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.89 E-value=4.7e-22 Score=187.52 Aligned_cols=166 Identities=17% Similarity=0.212 Sum_probs=134.6
Q ss_pred HHHHHHHHHHHHHHHHhC--CChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCccccee-ecc
Q 045125 99 AARQEAVDWIAKVHSHFG--FGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQ-VGQ 175 (342)
Q Consensus 99 ~~R~~~vdWi~~v~~~~~--l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~-v~~ 175 (342)
..|.--+++|.+++.+++ ++..|+++|+.||+||+..+++...+ .+++++||||||+|+||.. .++.++. ...
T Consensus 54 ~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~---p~~Ia~tclfLA~KvEE~~-~si~~fv~~~~ 129 (305)
T TIGR00569 54 DLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYH---PKIIMLTCVFLACKVEEFN-VSIDQFVGNLK 129 (305)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcC---HHHHHHHHHHHHHhccccC-cCHHHHHhhcc
Confidence 678888999999999999 99999999999999999999998777 9999999999999999995 4677774 111
Q ss_pred CCccccHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCccccccCHHH
Q 045125 176 SKFLFEAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFKPSE 255 (342)
Q Consensus 176 ~~~~~~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~ 255 (342)
......+++|++||..||++|+|++.+++|+.++..|+..+....... ... ..+...++.++..++...-++.|+||.
T Consensus 130 ~~~~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~-~~~-~~l~q~a~~~lndsl~Td~~L~y~Ps~ 207 (305)
T TIGR00569 130 ETPLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGL-ENP-EYLRKHADKFLNRTLLTDAYLLYTPSQ 207 (305)
T ss_pred CCchhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccc-cch-HHHHHHHHHHHHHHHcCCceecCCHHH
Confidence 222235699999999999999999999999999999986543221000 111 456777788877666566688899999
Q ss_pred HHHHHHHHHHccCCC
Q 045125 256 IAAAVAISVTGETKT 270 (342)
Q Consensus 256 IAaAai~~a~~~~~~ 270 (342)
||+|||++|.+..+.
T Consensus 208 IAlAAI~lA~~~~~~ 222 (305)
T TIGR00569 208 IALAAILHTASRAGL 222 (305)
T ss_pred HHHHHHHHHHHHhCC
Confidence 999999999987665
No 8
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.82 E-value=3.9e-20 Score=174.38 Aligned_cols=198 Identities=21% Similarity=0.246 Sum_probs=160.7
Q ss_pred HHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCccccee-eccC
Q 045125 98 LAARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQ-VGQS 176 (342)
Q Consensus 98 ~~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~-v~~~ 176 (342)
...|.....||.+++..++++..|+.+|+.|++||+..++..... .+.+|++|||||+|+||. +.++.|+. +...
T Consensus 36 ~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~---~~~vA~sclfLAgKvEet-p~kl~dIi~~s~~ 111 (323)
T KOG0834|consen 36 LRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFD---PYTVAASCLFLAGKVEET-PRKLEDIIKVSYR 111 (323)
T ss_pred HHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCc---HHHHHHHHHHHHhhcccC-cccHHHHHHHHHH
Confidence 578999999999999999999999999999999999999998887 799999999999999998 45666663 1110
Q ss_pred Cc---------cc--cHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccC
Q 045125 177 KF---------LF--EAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKG 245 (342)
Q Consensus 177 ~~---------~~--~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d 245 (342)
.+ .| .++.|+..|+.||++|+|++++-+|+.||..|+..+..+.+. ...++..++.++..+++.
T Consensus 112 ~~~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~-----~~~~a~~Aw~~~nD~~~t 186 (323)
T KOG0834|consen 112 YLNPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENL-----KQPLAQAAWNFVNDSLRT 186 (323)
T ss_pred HcCcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhc-----cccHHHHHHHHhchhhee
Confidence 00 01 268899999999999999999999999999999999988322 135788888888777777
Q ss_pred ccccccCHHHHHHHHHHHHHccCCCC-cchHHH--HHHHhcCCCHHHHHHHHHHHHHHHhcC
Q 045125 246 IDFLEFKPSEIAAAVAISVTGETKTV-VDTEKA--ISLLTQHVKKERVLKCIKMMNDSLISG 304 (342)
Q Consensus 246 ~~~l~~~PS~IAaAai~~a~~~~~~~-~~w~~~--l~~~~~~~~~~~l~~C~~~l~~l~~~~ 304 (342)
.-.++|+|..||+|+|.+|....+.. +.+... +..+-..++.+.|.+....+.++|...
T Consensus 187 ~~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y~~~ 248 (323)
T KOG0834|consen 187 TLCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFLDLYEQT 248 (323)
T ss_pred eeeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHHHHHhhc
Confidence 77899999999999999999654431 222222 333313399999999999999999554
No 9
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.79 E-value=3.2e-18 Score=157.86 Aligned_cols=171 Identities=16% Similarity=0.199 Sum_probs=142.9
Q ss_pred CCHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCccccee-e-
Q 045125 96 LDLAARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQ-V- 173 (342)
Q Consensus 96 i~~~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~-v- 173 (342)
.....|..-++||.+.+.-++|+..+.+++..+|-||+...++-+.+ +..+++||++||+|+||. |-.+.++. |
T Consensus 18 ~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~---~e~vv~ACv~LASKiEE~-Prr~rdVinVF 93 (367)
T KOG0835|consen 18 TEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHD---FEIVVMACVLLASKIEEE-PRRIRDVINVF 93 (367)
T ss_pred hHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhcccccccc---HHHHHHHHHHHHhhhccc-cccHhHHHHHH
Confidence 44578999999999999999999999999999999999999988877 999999999999999997 44555542 1
Q ss_pred ----------------ccCCccccHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHH
Q 045125 174 ----------------GQSKFLFEAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQ 237 (342)
Q Consensus 174 ----------------~~~~~~~~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~ 237 (342)
....+.-.+.++.++|..||+.|+|.+++.+|+.++-.|+..++.. .. ..+.+.+|.
T Consensus 94 h~L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~-----~~--~~l~Q~~wN 166 (367)
T KOG0835|consen 94 HYLEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLP-----PN--LKLLQAAWN 166 (367)
T ss_pred HHHHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCC-----Cc--hhHHHHHHH
Confidence 0111111356799999999999999999999999999999998887 22 467888999
Q ss_pred HHHhhccCccccccCHHHHHHHHHHHHHccCCC----CcchHHH
Q 045125 238 IITSSIKGIDFLEFKPSEIAAAVAISVTGETKT----VVDTEKA 277 (342)
Q Consensus 238 lil~~l~d~~~l~~~PS~IAaAai~~a~~~~~~----~~~w~~~ 277 (342)
+....+...-|..|+|+.||+|||++|.+..++ .++|.+.
T Consensus 167 fmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~ 210 (367)
T KOG0835|consen 167 FMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKA 210 (367)
T ss_pred hhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHH
Confidence 888888888899999999999999999987773 3567543
No 10
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.72 E-value=6.1e-17 Score=142.92 Aligned_cols=190 Identities=24% Similarity=0.227 Sum_probs=150.6
Q ss_pred HHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCccccee-------
Q 045125 100 ARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQ------- 172 (342)
Q Consensus 100 ~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~------- 172 (342)
.+--.-+.|..++.++++...++++|+.||-||+.+.+..... +.|+|.||++||+|+||..+-.++-+.
T Consensus 40 l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~---p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~ 116 (264)
T KOG0794|consen 40 LKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIE---PRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLK 116 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccC---HHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHh
Confidence 3444566788999999999999999999999999999987777 999999999999999998422222221
Q ss_pred ----eccCCccccHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCccc
Q 045125 173 ----VGQSKFLFEAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDF 248 (342)
Q Consensus 173 ----v~~~~~~~~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~ 248 (342)
.....+.+...+|..||..+|+.|+.-+-.-+|+.-|..++...+.. . ..+...++.++..+++..-.
T Consensus 117 ~~f~~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~-----d---~~~l~~~W~ivNDSyr~Dl~ 188 (264)
T KOG0794|consen 117 TRFSYWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGIN-----D---QKLLQLAWSIVNDSYRMDLC 188 (264)
T ss_pred hhcccchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhccc-----c---hhhhhhhHhhhcchhhccee
Confidence 12334456789999999999999999999999999999888876664 1 44567777787777766677
Q ss_pred cccCHHHHHHHHHHHHHccCCCCcchHHHHHHHhcCCCHHHHHHHHHHHHHHHhc
Q 045125 249 LEFKPSEIAAAVAISVTGETKTVVDTEKAISLLTQHVKKERVLKCIKMMNDSLIS 303 (342)
Q Consensus 249 l~~~PS~IAaAai~~a~~~~~~~~~w~~~l~~~~~~~~~~~l~~C~~~l~~l~~~ 303 (342)
+-|+|-.||.||++.|+-..+. +.++.+-.- ...|.+.|.+|++.|-++|..
T Consensus 189 Ll~PPh~IalAcl~Ia~~~~~k--~~~~~w~~e-l~vD~ekV~~~v~~I~~lYe~ 240 (264)
T KOG0794|consen 189 LLYPPHQIALACLYIACVIDEK--DIPKAWFAE-LSVDMEKVKDIVQEILKLYEL 240 (264)
T ss_pred eecCHHHHHHHHHHHHHhhcCC--ChHHHHHHH-HhccHHHHHHHHHHHHHHHHH
Confidence 8899999999999999954333 333443333 489999999999999998854
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=99.68 E-value=2.6e-16 Score=145.28 Aligned_cols=166 Identities=16% Similarity=0.220 Sum_probs=137.3
Q ss_pred CHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccc--cCCcccceeec
Q 045125 97 DLAARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEET--EVPLCLDLQVG 174 (342)
Q Consensus 97 ~~~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~--~~p~~~dl~v~ 174 (342)
+...|.....|+..++.+++++..++.+||.+|+||..+.++.... ++-++.||++||+|+||+ + ..+..+...
T Consensus 41 e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~---~~~vv~tcv~LA~K~ed~~~~-I~i~~~~~~ 116 (297)
T COG5333 41 ELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEIS---LYSVVTTCVYLACKVEDTPRD-ISIESFEAR 116 (297)
T ss_pred hhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhccccccc---HHHHHHhheeeeeecccccch-hhHHHHHhh
Confidence 3467888889999999999999999999999999999999988777 999999999999999995 2 112121111
Q ss_pred ---cCCccccHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCcccccc
Q 045125 175 ---QSKFLFEAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEF 251 (342)
Q Consensus 175 ---~~~~~~~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~ 251 (342)
-....-+++.|..+|..+|+.|+|++.+++|+.++..|+..+... +. ......++.++..+++..-++.|
T Consensus 117 ~~~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~-----~~--~~~~~~aw~~inDa~~t~~~lly 189 (297)
T COG5333 117 DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEK-----DK--YKLLQIAWKIINDALRTDLCLLY 189 (297)
T ss_pred ccccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhc-----cH--HHHHHHHHHHHHhhhhceeeeec
Confidence 012223789999999999999999999999999999999987776 22 56788899999888878888999
Q ss_pred CHHHHHHHHHHHHHccCCCCcch
Q 045125 252 KPSEIAAAVAISVTGETKTVVDT 274 (342)
Q Consensus 252 ~PS~IAaAai~~a~~~~~~~~~w 274 (342)
+|..||+|+++.|....+. +-|
T Consensus 190 pphiIA~a~l~ia~~~~~~-~~~ 211 (297)
T COG5333 190 PPHIIALAALLIACEVLGM-PII 211 (297)
T ss_pred ChHHHHHHHHHHHHHhcCC-ccc
Confidence 9999999999999976544 444
No 12
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.51 E-value=2.6e-12 Score=122.41 Aligned_cols=184 Identities=14% Similarity=0.116 Sum_probs=151.4
Q ss_pred HHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCcccceeeccCCcc
Q 045125 100 ARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQVGQSKFL 179 (342)
Q Consensus 100 ~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~v~~~~~~ 179 (342)
.-.....-|-+++..++++..+.-.|..++.++.....+.... ...++++|||+|+|.++. |-.+.++. ...+
T Consensus 121 ~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs---~~~i~AAclYiACR~~~~-prtl~eI~-~~~~-- 193 (310)
T PRK00423 121 NLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRS---IEGVVAAALYAACRRCKV-PRTLDEIA-EVSR-- 193 (310)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCC---HHHHHHHHHHHHHHHcCC-CcCHHHHH-HHhC--
Confidence 3345567788999999999999999999999999987776666 899999999999999887 46777773 2222
Q ss_pred ccHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCccccccCHHHHHHH
Q 045125 180 FEAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFKPSEIAAA 259 (342)
Q Consensus 180 ~~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~IAaA 259 (342)
.++++|-+.++.|++.|+.++...+|.+|+..|...++.. ..+...+.+++..+....-....+|..||||
T Consensus 194 v~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~---------~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAA 264 (310)
T PRK00423 194 VSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLS---------GEVQKKAIEILQKAKEKGLTSGKGPTGLAAA 264 (310)
T ss_pred CCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCC---------HHHHHHHHHHHHHHHhcCcccCCCHHHHHHH
Confidence 4899999999999999999999999999999999999887 4556666666655543333468999999999
Q ss_pred HHHHHHccCCCCcchHHHHHHHhcCCCHHHHHHHHHHHHHHH
Q 045125 260 VAISVTGETKTVVDTEKAISLLTQHVKKERVLKCIKMMNDSL 301 (342)
Q Consensus 260 ai~~a~~~~~~~~~w~~~l~~~~~~~~~~~l~~C~~~l~~l~ 301 (342)
||++|.+..+. +...+.+... +++++..|...++.|.+.+
T Consensus 265 aIYlA~~~~g~-~~t~keIa~v-~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 265 AIYIASLLLGE-RRTQREVAEV-AGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HHHHHHHHhCC-CCCHHHHHHH-cCCCHHHHHHHHHHHHHHh
Confidence 99999976655 4556677777 8999999999999988754
No 13
>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=99.46 E-value=2e-13 Score=104.02 Aligned_cols=87 Identities=38% Similarity=0.544 Sum_probs=76.7
Q ss_pred HHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCcccceeeccCCccc
Q 045125 101 RQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQVGQSKFLF 180 (342)
Q Consensus 101 R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~v~~~~~~~ 180 (342)
|...++||.+++..++++++|.++|+.++|||+....+.+.+ ++++|++|++||+|++|. ++...++ +....+.
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~---~~~ia~a~l~lA~k~~~~-~~~~~~~-~~~~~~~- 75 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRS---PSLVAAAALYLAAKVEEI-PPWLKDL-VHVTGYA- 75 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCC---hHHHHHHHHHHHHHHcCC-CCCHHHH-hHHhCCC-
Confidence 678899999999999999999999999999999998887666 999999999999999999 7888888 4433322
Q ss_pred cHHHHHHHHHHHH
Q 045125 181 EAKTIQRMELLVL 193 (342)
Q Consensus 181 ~~~~I~~mE~~IL 193 (342)
+.++|.+||+.|+
T Consensus 76 ~~~~i~~~e~~il 88 (88)
T cd00043 76 TEEEILRMEKLLL 88 (88)
T ss_pred CHHHHHHHHHHhC
Confidence 8999999999875
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=99.44 E-value=1.9e-13 Score=111.05 Aligned_cols=92 Identities=23% Similarity=0.339 Sum_probs=70.0
Q ss_pred CChHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCccccccCHHHHHHHHHHHHHccCCCCcchHHHHHHHh
Q 045125 203 ITPFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFKPSEIAAAVAISVTGETKTVVDTEKAISLLT 282 (342)
Q Consensus 203 pTp~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~IAaAai~~a~~~~~~~~~w~~~l~~~~ 282 (342)
|||++||++|++..+.. ..+...+.+++..++.++.|++|+||+||+||+++|+...+..+.|...+..+
T Consensus 1 PTp~~Fl~~~~~~~~~~---------~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~- 70 (118)
T PF02984_consen 1 PTPYDFLRRFLKISNAD---------QEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKL- 70 (118)
T ss_dssp --HHHHHHHHHTSSSHH---------HHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHH-
T ss_pred CcHHHHHHHHHHHcCCc---------HHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhh-
Confidence 89999999995542222 33444444444445559999999999999999999998876546899999998
Q ss_pred cCCCHHHHHHHHHHHHHHHhcC
Q 045125 283 QHVKKERVLKCIKMMNDSLISG 304 (342)
Q Consensus 283 ~~~~~~~l~~C~~~l~~l~~~~ 304 (342)
+++++++|.+|++.|.+++...
T Consensus 71 t~~~~~~l~~c~~~i~~~~~~~ 92 (118)
T PF02984_consen 71 TGYDKEDLKECIELIQELLSKA 92 (118)
T ss_dssp HTS-HHHHHHHHHHHHHHHHHC
T ss_pred cCCCHHHHHHHHHHHHHHHHhc
Confidence 8999999999999999998753
No 15
>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=99.40 E-value=8.9e-13 Score=99.45 Aligned_cols=83 Identities=40% Similarity=0.575 Sum_probs=71.6
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCcccceeeccCCccccHHHH
Q 045125 106 DWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQVGQSKFLFEAKTI 185 (342)
Q Consensus 106 dWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~v~~~~~~~~~~~I 185 (342)
+||.+++..+++++++.++|+.++|||+....+.+.+ .+++|++|++||+|++|.. |...++ ....++ ++.++|
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~---~~~ia~a~l~lA~k~~~~~-~~~~~~-~~~~~~-~~~~~i 74 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYS---PSLIAAAALYLAAKTEEIP-PWTKEL-VHYTGY-FTEEEI 74 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCC---HHHHHHHHHHHHHHHhcCC-CCchhH-hHhhCC-CCHHHH
Confidence 5999999999999999999999999999977776666 9999999999999999986 566676 333333 699999
Q ss_pred HHHHHHHHH
Q 045125 186 QRMELLVLS 194 (342)
Q Consensus 186 ~~mE~~IL~ 194 (342)
.++|+.||.
T Consensus 75 ~~~~~~il~ 83 (83)
T smart00385 75 LRMEKLLLE 83 (83)
T ss_pred HHHHHHHhC
Confidence 999999874
No 16
>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=99.30 E-value=1.4e-11 Score=113.40 Aligned_cols=156 Identities=19% Similarity=0.250 Sum_probs=111.3
Q ss_pred HHHHHHHHHHhC--CChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCcccceeeccCC--ccc
Q 045125 105 VDWIAKVHSHFG--FGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQVGQSK--FLF 180 (342)
Q Consensus 105 vdWi~~v~~~~~--l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~v~~~~--~~~ 180 (342)
..-+++.+..|+ +++.++.+|+.+|-||+-..++.... ...+.+||+|+|+|++|.+ .++.+|. ...+ -.-
T Consensus 60 E~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~---pk~I~~tc~flA~Kieef~-ISieqFv-kn~~~~~~k 134 (325)
T KOG2496|consen 60 ELSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYS---PKIIMATCFFLACKIEEFY-ISIEQFV-KNMNGRKWK 134 (325)
T ss_pred HHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcC---hHHHHHHHHHHHhhhHhhe-ecHHHHH-hhccCcccc
Confidence 334555666665 79999999999999999999887776 8899999999999999986 6777774 2221 223
Q ss_pred cHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHcCCCCCCCCCCcH--HHHHHHHHHHHHhhccCccccccCHHHHHH
Q 045125 181 EAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTRKITDDDDDHHQTPL--RALFCRSIQIITSSIKGIDFLEFKPSEIAA 258 (342)
Q Consensus 181 ~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~~~~~~~~~~~~~~~--~~l~~~~~~lil~~l~d~~~l~~~PS~IAa 258 (342)
+.+.|+..|..+|+.|+|++..-+|+.-++-|+.-+...-... ..+. ..... ...++..++..-.++-|.||.||.
T Consensus 135 ~~e~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~-~n~d~~~~~~d-~~~fl~~~lltDa~lLytPsQIAL 212 (325)
T KOG2496|consen 135 THEIVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPAL-ENPDILRKHDD-SKKFLDRALLTDAYLLYTPSQIAL 212 (325)
T ss_pred cHHHHHhchHHHHHhhhhhheecCCCCchHHHHHHHHHHHHhc-cCHHHHhhhhh-HHHHHHHHHHhccceecChHHHHH
Confidence 7899999999999999999999999998888876443220000 1110 01111 123333343344566799999999
Q ss_pred HHHHHHHcc
Q 045125 259 AVAISVTGE 267 (342)
Q Consensus 259 Aai~~a~~~ 267 (342)
|||+.+...
T Consensus 213 aAil~a~~~ 221 (325)
T KOG2496|consen 213 AAILHAAGR 221 (325)
T ss_pred HHHHHHhcc
Confidence 999777533
No 17
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.71 E-value=1.7e-06 Score=81.25 Aligned_cols=185 Identities=16% Similarity=0.180 Sum_probs=148.8
Q ss_pred HHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCcccceeeccCCc
Q 045125 99 AARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQVGQSKF 178 (342)
Q Consensus 99 ~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~v~~~~~ 178 (342)
+.-..+..-+-.++..++++..+.-.|..++=+.+...-+.... .+-++++|+++|++.... |-.+.++. ...+
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-PRTLDEIA-KALG- 168 (285)
T ss_pred hHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCc---HHHHHHHHHHHHHHHcCC-CccHHHHH-HHHC-
Confidence 34456677788899999999999999999999999888777666 899999999999999887 34555553 2222
Q ss_pred cccHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCccccccCHHHHHH
Q 045125 179 LFEAKTIQRMELLVLSTLKWRMQAITPFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFKPSEIAA 258 (342)
Q Consensus 179 ~~~~~~I~~mE~~IL~~L~w~l~~pTp~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~IAa 258 (342)
.++++|.++.+.+.+.|+=.+.+..|..|+..|...++.+ ..+...+.+++-.+...-.-..=.|+-|||
T Consensus 169 -V~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~---------~~v~~~a~ei~~~~~~~g~~~Gk~P~glAa 238 (285)
T COG1405 169 -VSKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLS---------DEVRRKAIEIVKKAKRAGLTAGKSPAGLAA 238 (285)
T ss_pred -CCHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCC---------HHHHHHHHHHHHHHHHhCcccCCCchhHHH
Confidence 4889999999999999999999999999999999999988 344555566654443333445788999999
Q ss_pred HHHHHHHccCCCCcchHHHHHHHhcCCCHHHHHHHHHHHHHHH
Q 045125 259 AVAISVTGETKTVVDTEKAISLLTQHVKKERVLKCIKMMNDSL 301 (342)
Q Consensus 259 Aai~~a~~~~~~~~~w~~~l~~~~~~~~~~~l~~C~~~l~~l~ 301 (342)
||+++|....+. ...++.+... +++++.-|..=++.|.+..
T Consensus 239 aaiy~as~l~~~-~~tq~eva~v-~~vtevTIrnrykel~~~~ 279 (285)
T COG1405 239 AAIYLASLLLGE-RRTQKEVAKV-AGVTEVTIRNRYKELADAL 279 (285)
T ss_pred HHHHHHHHHhCC-chHHHHHHHH-hCCeeeHHHHHHHHHHHhh
Confidence 999999977665 5677788888 8999999998887776544
No 18
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.55 E-value=3.3e-06 Score=78.00 Aligned_cols=180 Identities=17% Similarity=0.150 Sum_probs=137.2
Q ss_pred HHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCcccceeeccCCccccH
Q 045125 103 EAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQVGQSKFLFEA 182 (342)
Q Consensus 103 ~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~v~~~~~~~~~ 182 (342)
....-|..++...+|+....-.|-.+|-++-..+...... .+-+++|||+||+.-++. |-.++++. .... .++
T Consensus 106 ~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks---~eai~AAclyiACRq~~~-pRT~kEI~--~~an-v~k 178 (308)
T KOG1597|consen 106 AAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKS---VEALAAACLYIACRQEDV-PRTFKEIS--AVAN-VSK 178 (308)
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCcc---HHHHHHHHHHHHHHhcCC-CchHHHHH--HHHc-CCH
Confidence 3344567788999999999999999999999666655444 899999999999999887 45666764 2222 489
Q ss_pred HHHHHHHHHHHHHcCCccccCC--hHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCcccc-ccCHHHHHHH
Q 045125 183 KTIQRMELLVLSTLKWRMQAIT--PFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFL-EFKPSEIAAA 259 (342)
Q Consensus 183 ~~I~~mE~~IL~~L~w~l~~pT--p~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l-~~~PS~IAaA 259 (342)
++|-+.=..|+..|+=.....| .-+|+.+|...+... +.....+.++..... +..+. .-.|=.||||
T Consensus 179 KEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~---------~~~q~aA~e~a~ka~-~~~~~~gRsPiSIAAa 248 (308)
T KOG1597|consen 179 KEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLP---------KSAQEAATEIAEKAE-EMDIRAGRSPISIAAA 248 (308)
T ss_pred HHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCC---------HHHHHHHHHHHHHHH-HhccccCCCchhHHHH
Confidence 9999999999999988777666 889999999999887 333333444433322 33333 3669999999
Q ss_pred HHHHHHccCCCCcchHHHHHHHhcCCCHHHHHHHHHHHHHHH
Q 045125 260 VAISVTGETKTVVDTEKAISLLTQHVKKERVLKCIKMMNDSL 301 (342)
Q Consensus 260 ai~~a~~~~~~~~~w~~~l~~~~~~~~~~~l~~C~~~l~~l~ 301 (342)
+||.+...... ....+.+... +|+.+.-|+.-|+.|....
T Consensus 249 ~IYmisqls~~-kkt~keI~~v-tgVaE~TIr~sYK~Lyp~~ 288 (308)
T KOG1597|consen 249 AIYMISQLSDE-KKTQKEIGEV-TGVAEVTIRNSYKDLYPHA 288 (308)
T ss_pred HHHHHHHhccC-cccHHHHHHH-hhhhHHHHHHHHHHHhhch
Confidence 99999976554 5667788887 9999999999998886543
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=98.26 E-value=3.2e-06 Score=72.21 Aligned_cols=92 Identities=22% Similarity=0.330 Sum_probs=65.6
Q ss_pred HHHHHHHHHHHhCCChhHHHHHHHHHHHHhc---cCcccCCchhhHHHHHHHHHHHHhhhccccCCccccee-eccCCcc
Q 045125 104 AVDWIAKVHSHFGFGPLCSYLTINYLDRFLS---AYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQ-VGQSKFL 179 (342)
Q Consensus 104 ~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs---~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~-v~~~~~~ 179 (342)
+.+|+.++..+-+++++++.+|..|+||+.. ...+.- .+...+-+-++|+.+|+|+-+-....-+.+. ++ +
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~-~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~--g-- 128 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPL-NSSNIHRLFLTALILASKFLDDNTYSNKSWAKVG--G-- 128 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT----STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHH--T--
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhccccccc-ccchhHHHHHHHHHHHHhhcccccccHHHHHhhc--C--
Confidence 7789999999999999999999999999998 222221 1234778889999999999655444444443 32 2
Q ss_pred ccHHHHHHHHHHHHHHcCCcc
Q 045125 180 FEAKTIQRMELLVLSTLKWRM 200 (342)
Q Consensus 180 ~~~~~I~~mE~~IL~~L~w~l 200 (342)
++.+++-+||+..|..|+|+|
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 589999999999999999986
No 20
>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=98.24 E-value=1.2e-05 Score=60.55 Aligned_cols=85 Identities=16% Similarity=0.198 Sum_probs=69.4
Q ss_pred cCChHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCccccccCHHHHHHHHHHHHHccCCCCcchHHHHHHH
Q 045125 202 AITPFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFKPSEIAAAVAISVTGETKTVVDTEKAISLL 281 (342)
Q Consensus 202 ~pTp~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~IAaAai~~a~~~~~~~~~w~~~l~~~ 281 (342)
.|++..|+..+...++.. ......+..++...+....+..++|+.||+||+++|.+..+. +.|.+.+...
T Consensus 2 ~~~~~~~l~~~~~~~~~~---------~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~-~~~~~~~~~~ 71 (88)
T cd00043 2 RPTPLDFLRRVAKALGLS---------PETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI-PPWLKDLVHV 71 (88)
T ss_pred cchHHHHHHHHHHHcCCC---------HHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCC-CCCHHHHhHH
Confidence 578999999999998766 445555666655555566778999999999999999987777 7898888888
Q ss_pred hcCC-CHHHHHHHHHHH
Q 045125 282 TQHV-KKERVLKCIKMM 297 (342)
Q Consensus 282 ~~~~-~~~~l~~C~~~l 297 (342)
+++ +.++|.++...|
T Consensus 72 -~~~~~~~~i~~~e~~i 87 (88)
T cd00043 72 -TGYATEEEILRMEKLL 87 (88)
T ss_pred -hCCCCHHHHHHHHHHh
Confidence 889 999999988765
No 21
>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=98.24 E-value=5.4e-06 Score=61.91 Aligned_cols=80 Identities=19% Similarity=0.270 Sum_probs=63.1
Q ss_pred HHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCccccccCHHHHHHHHHHHHHccCCCCcchHHHHHHHhcCC-C
Q 045125 208 FLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFKPSEIAAAVAISVTGETKTVVDTEKAISLLTQHV-K 286 (342)
Q Consensus 208 Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~IAaAai~~a~~~~~~~~~w~~~l~~~~~~~-~ 286 (342)
|+..+...++.+ ..+...+..++...+.++.+..++|+.||+||+++|++..+. ..|.+.+..+ +++ +
T Consensus 2 ~l~~~~~~~~~~---------~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~-~~~~~~~~~~-~~~~~ 70 (83)
T smart00385 2 FLRRVCKALNLD---------PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEI-PPWTKELVHY-TGYFT 70 (83)
T ss_pred HHHHHHHHcCCC---------HHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcC-CCCchhHhHh-hCCCC
Confidence 666777776665 455666666665566567888999999999999999987776 4698888888 788 9
Q ss_pred HHHHHHHHHHHH
Q 045125 287 KERVLKCIKMMN 298 (342)
Q Consensus 287 ~~~l~~C~~~l~ 298 (342)
.++|.+|...|.
T Consensus 71 ~~~i~~~~~~il 82 (83)
T smart00385 71 EEEILRMEKLLL 82 (83)
T ss_pred HHHHHHHHHHHh
Confidence 999999988764
No 22
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=98.22 E-value=2.5e-07 Score=88.03 Aligned_cols=141 Identities=16% Similarity=0.220 Sum_probs=107.8
Q ss_pred ccCCCCChHHHHHHHHHHHcccCCCCchhhhccCCCCCHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCccc
Q 045125 60 LLSLPLQSDECLALLLEKECHHLPHNDYLKRLRTGDLDLAARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELP 139 (342)
Q Consensus 60 ~~~~~~y~~ei~~~l~~~E~~~~~~~~yl~~~q~~~i~~~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~ 139 (342)
.+.|+.|-.-++.+.+-...+..-+..|-+++-.-.+|...-+-+=.-|.++....++..-|+..|-.||.....+..+.
T Consensus 341 ~l~F~symttvidyVrpsdlKkdmNe~FreKfP~IkLTLSKirSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglis 420 (497)
T KOG4164|consen 341 VLIFSSYMTTVIDYVRPSDLKKDMNETFREKFPHIKLTLSKIRSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLIS 420 (497)
T ss_pred eeEeccccceeEEEechHHHHHHHhHHHHHhCCeeEEeHHHHHHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhh
Confidence 46677777666665554444333334444443333456555555666688999999999999999999999999888888
Q ss_pred CCchhhHHHHHHHHHHHHhhhccccCCccccee-eccCCccccHHHHHHHHHHHHHHcCCccccC
Q 045125 140 KGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQ-VGQSKFLFEAKTIQRMELLVLSTLKWRMQAI 203 (342)
Q Consensus 140 ~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~-v~~~~~~~~~~~I~~mE~~IL~~L~w~l~~p 203 (342)
+.+ -.|.|-|||.+|+||.+.+--.++.+. -.+..+.+++.+++..|.-||.+|+|.|+.|
T Consensus 421 K~N---RKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrrdLia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 421 KQN---RKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRRDLIAFEFPVLVALEFALHLP 482 (497)
T ss_pred hhh---hhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHHhhhhhhhhHHHhhhhhccCC
Confidence 777 899999999999999987666666663 3355678899999999999999999999876
No 23
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=97.49 E-value=0.0023 Score=64.03 Aligned_cols=174 Identities=13% Similarity=0.176 Sum_probs=128.0
Q ss_pred CCCchhhhccCCCC-CHHHHHHHHH----HHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHH
Q 045125 83 PHNDYLKRLRTGDL-DLAARQEAVD----WIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLA 157 (342)
Q Consensus 83 ~~~~yl~~~q~~~i-~~~~R~~~vd----Wi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IA 157 (342)
+...|+..-|.+-- ..+.|...+. -|-+++..++++. .+-.|.++|---++..-.+... .+++-.+||+|+
T Consensus 44 ~~G~~v~~~~~g~~~s~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~---~~~vvasClY~v 119 (521)
T KOG1598|consen 44 AQGQFVRVGQSGAGSSLESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRR---STEVVAACLYLV 119 (521)
T ss_pred cceeEEeccccCCccchHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcc---hHHHHHHHHHHH
Confidence 34455543333222 2344444333 4778999999999 9999999999999888887776 899999999999
Q ss_pred hhhccccCCcccceeeccCCccccHHHHHHHHHHHHHHcCCc---cccCChHHHHHHHHHHcCCCCCCCCCCcHHHHHHH
Q 045125 158 AKMEETEVPLCLDLQVGQSKFLFEAKTIQRMELLVLSTLKWR---MQAITPFSFLDYFTRKITDDDDDHHQTPLRALFCR 234 (342)
Q Consensus 158 sK~eE~~~p~~~dl~v~~~~~~~~~~~I~~mE~~IL~~L~w~---l~~pTp~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~ 234 (342)
+..|-+.+ .+-||. ..- ..+.-++=.+=+.+...|.-. +..+.|.-|+.+|...+... ... +.++..
T Consensus 120 cR~e~t~h-lliDfS-~~L--qv~Vy~LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g-----~~~-~~Vv~~ 189 (521)
T KOG1598|consen 120 CRLEKTDH-LLIDFS-SYL--QVSVYDLGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFG-----DKT-EDVAKT 189 (521)
T ss_pred HHhhCCce-EEEEec-cce--EEehhhhhHHHHHHHHHhccccccccccCcceeeechhHhhhcC-----Cch-HHHHHH
Confidence 99987743 333442 111 124445555666777777777 67789999999999988776 222 668888
Q ss_pred HHHHHHhhccCccccccCHHHHHHHHHHHHHccCCC
Q 045125 235 SIQIITSSIKGIDFLEFKPSEIAAAVAISVTGETKT 270 (342)
Q Consensus 235 ~~~lil~~l~d~~~l~~~PS~IAaAai~~a~~~~~~ 270 (342)
+..++.++.+|+-...=||+-|+-||++.|++..+.
T Consensus 190 a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~ 225 (521)
T KOG1598|consen 190 ATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGF 225 (521)
T ss_pred HHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCc
Confidence 888988888888889999999999999999987665
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=95.74 E-value=0.098 Score=38.49 Aligned_cols=70 Identities=17% Similarity=0.047 Sum_probs=46.1
Q ss_pred HHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCccccccCHHHHHHHHHHHHHccCCCCcchHHHHHHHhcCCCHHH
Q 045125 210 DYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFKPSEIAAAVAISVTGETKTVVDTEKAISLLTQHVKKER 289 (342)
Q Consensus 210 ~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~IAaAai~~a~~~~~~~~~w~~~l~~~~~~~~~~~ 289 (342)
..|...++.. ..+...+.++........-.-.-+|..|||||+++|++..+. +...+.+... .++++..
T Consensus 2 ~r~~~~L~L~---------~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~-~~t~~eIa~~-~~Vs~~t 70 (71)
T PF00382_consen 2 PRICSKLGLP---------EDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGV-PRTLKEIAEA-AGVSEKT 70 (71)
T ss_dssp HHHHHHTT-----------HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTS-SSSHHHHHHH-CTSSHHH
T ss_pred hHHHhHcCCC---------HHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCC-CcCHHHHHHH-hCCCCCc
Confidence 3455555555 566777777765544233334577999999999999988776 5556667776 7887765
Q ss_pred H
Q 045125 290 V 290 (342)
Q Consensus 290 l 290 (342)
|
T Consensus 71 I 71 (71)
T PF00382_consen 71 I 71 (71)
T ss_dssp H
T ss_pred C
Confidence 4
No 25
>KOG1674 consensus Cyclin [General function prediction only]
Probab=95.50 E-value=0.039 Score=50.09 Aligned_cols=96 Identities=16% Similarity=0.246 Sum_probs=68.8
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHhccCc---c---cCCchhh-HHHHHHHHHHHHhhhccccCCcccceeeccCC
Q 045125 105 VDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYE---L---PKGKVWM-MQLLAVACLSLAAKMEETEVPLCLDLQVGQSK 177 (342)
Q Consensus 105 vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~---~---~~~~~~~-lqLlavaCL~IAsK~eE~~~p~~~dl~v~~~~ 177 (342)
-+++.++.++-+.+++++.+|..|||||..+.+ + ..-+.-+ ..-+-++|+.+|+|+.+...-.-.-. ...+
T Consensus 79 ~~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y~n~~~-a~vg- 156 (218)
T KOG1674|consen 79 RQYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYYSNAYY-AKVG- 156 (218)
T ss_pred HHHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchhhhHHHH-HHhC-
Confidence 345667888999999999999999999998733 1 1111122 44578999999999986632212111 1111
Q ss_pred ccccHHHHHHHHHHHHHHcCCccccC
Q 045125 178 FLFEAKTIQRMELLVLSTLKWRMQAI 203 (342)
Q Consensus 178 ~~~~~~~I~~mE~~IL~~L~w~l~~p 203 (342)
..+.+++-.+|+..|..++|++.++
T Consensus 157 -gl~~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 157 -GLTTDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred -CCChHhhhhhhHHHHhhCCeEEEec
Confidence 2478999999999999999999985
No 26
>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=95.15 E-value=0.12 Score=38.07 Aligned_cols=60 Identities=15% Similarity=0.181 Sum_probs=46.0
Q ss_pred HHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCcccce
Q 045125 108 IAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDL 171 (342)
Q Consensus 108 i~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl 171 (342)
|-+++..++++..+.-.|..++++-....-....+ ..-++++|+++|++.+... ....++
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~---~~~iaAA~iY~acr~~~~~-~t~~eI 60 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRS---PESIAAACIYLACRLNGVP-RTLKEI 60 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS----HHHHHHHHHHHHHHHTTSS-SSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCC---HHHHHHHHHHHHHHHcCCC-cCHHHH
Confidence 45689999999999999999999988776655555 8899999999999998663 344444
No 27
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=93.39 E-value=0.92 Score=43.37 Aligned_cols=88 Identities=15% Similarity=0.130 Sum_probs=64.7
Q ss_pred hHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCccccccCHHHHHHHHHHHHHccCCCCcchHHHHHHHhcC
Q 045125 205 PFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFKPSEIAAAVAISVTGETKTVVDTEKAISLLTQH 284 (342)
Q Consensus 205 p~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~IAaAai~~a~~~~~~~~~w~~~l~~~~~~ 284 (342)
.+..|+.+...++.. ..+...+..+.........+-..+.-.+||||+++|++..+. +...+.+..+ ++
T Consensus 125 a~~~I~~~~~~L~Lp---------~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~-prtl~eI~~~-~~ 193 (310)
T PRK00423 125 ALSELDRIASQLGLP---------RSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKV-PRTLDEIAEV-SR 193 (310)
T ss_pred HHHHHHHHHHHcCCC---------HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCC-CcCHHHHHHH-hC
Confidence 445666677777666 566677777665555233345678899999999999998766 5555667766 89
Q ss_pred CCHHHHHHHHHHHHHHHhc
Q 045125 285 VKKERVLKCIKMMNDSLIS 303 (342)
Q Consensus 285 ~~~~~l~~C~~~l~~l~~~ 303 (342)
+++.+|..+++.|.+.+..
T Consensus 194 v~~k~i~~~~~~l~k~L~~ 212 (310)
T PRK00423 194 VSRKEIGRCYRFLLRELNL 212 (310)
T ss_pred CCHHHHHHHHHHHHHHhCC
Confidence 9999999999999887754
No 28
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=84.27 E-value=12 Score=35.30 Aligned_cols=89 Identities=13% Similarity=0.097 Sum_probs=62.3
Q ss_pred ChHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCccccccC-HHHHHHHHHHHHHccCCCCcchHHHHHHHh
Q 045125 204 TPFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFK-PSEIAAAVAISVTGETKTVVDTEKAISLLT 282 (342)
Q Consensus 204 Tp~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~-PS~IAaAai~~a~~~~~~~~~w~~~l~~~~ 282 (342)
+....|..+...++.. ..+...+..+....+ +..++.=| ...++|||++.|++..+. +.....+...
T Consensus 99 ~a~~~l~~~~~~l~LP---------~~v~e~A~~iyr~a~-~~~l~rGRsie~v~AA~iY~acR~~~~-prtl~eIa~a- 166 (285)
T COG1405 99 TALEELERIASALGLP---------ESVRETAARIYRKAV-DKGLLRGRSIESVAAACIYAACRINGV-PRTLDEIAKA- 166 (285)
T ss_pred HHHHHHHHHHHHhCCC---------chHHHHHHHHHHHHh-hcCCCcCCcHHHHHHHHHHHHHHHcCC-CccHHHHHHH-
Confidence 4556666666666665 444455555544444 77776544 788899999999987776 6566667776
Q ss_pred cCCCHHHHHHHHHHHHHHHhcC
Q 045125 283 QHVKKERVLKCIKMMNDSLISG 304 (342)
Q Consensus 283 ~~~~~~~l~~C~~~l~~l~~~~ 304 (342)
.++++.++..++..+......+
T Consensus 167 ~~V~~kei~rtyr~~~~~L~l~ 188 (285)
T COG1405 167 LGVSKKEIGRTYRLLVRELKLK 188 (285)
T ss_pred HCCCHHHHHHHHHHHHHhcCCC
Confidence 7899999999999777666544
No 29
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=83.82 E-value=2.8 Score=39.43 Aligned_cols=50 Identities=24% Similarity=0.355 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHccCCCCcchHHHHHHHhcCCCHHHHHHHHHHHHHHHhcC
Q 045125 253 PSEIAAAVAISVTGETKTVVDTEKAISLLTQHVKKERVLKCIKMMNDSLISG 304 (342)
Q Consensus 253 PS~IAaAai~~a~~~~~~~~~w~~~l~~~~~~~~~~~l~~C~~~l~~l~~~~ 304 (342)
--.|+|||++.|+++.+. +...+.+..+ .++++.+|-+|++.|.+-+..+
T Consensus 146 ~eai~AAclyiACRq~~~-pRT~kEI~~~-anv~kKEIgr~~K~i~~~l~~s 195 (308)
T KOG1597|consen 146 VEALAAACLYIACRQEDV-PRTFKEISAV-ANVSKKEIGRCVKLIGEALETS 195 (308)
T ss_pred HHHHHHHHHHHHHHhcCC-CchHHHHHHH-HcCCHHHHHHHHHHHHHHHhcc
Confidence 346799999999998777 7777888888 8999999999999998765443
No 30
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=82.98 E-value=1.4 Score=42.28 Aligned_cols=92 Identities=16% Similarity=0.155 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCccccee-eccCCcccc
Q 045125 103 EAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQ-VGQSKFLFE 181 (342)
Q Consensus 103 ~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~-v~~~~~~~~ 181 (342)
-+++|+..+-..-+........|.+++...+...-+-..+ .+-+|++|++||+|+-....|...+-. .....-..+
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 4455555555544444456777788887777666555555 788999999999999777655554431 111111147
Q ss_pred HHHHHHHHHHHHHHcC
Q 045125 182 AKTIQRMELLVLSTLK 197 (342)
Q Consensus 182 ~~~I~~mE~~IL~~L~ 197 (342)
.+++..+...+|..+.
T Consensus 231 ~e~l~~i~~~~l~~y~ 246 (323)
T KOG0834|consen 231 NELLDDICHEFLDLYE 246 (323)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 7777777766665543
No 31
>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=81.07 E-value=2.6 Score=33.25 Aligned_cols=86 Identities=19% Similarity=0.185 Sum_probs=50.7
Q ss_pred HHHHHHHHHhCCChhHHHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCcccceeeccCCccccHHHH
Q 045125 106 DWIAKVHSHFGFGPLCSYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQVGQSKFLFEAKTI 185 (342)
Q Consensus 106 dWi~~v~~~~~l~~~T~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~v~~~~~~~~~~~I 185 (342)
+||.......+.+.++..+|-.+++-.+....+-..+ .-++|++|+++|.++-....+-...+ ....+ ++.++|
T Consensus 5 ~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~---PS~iAaAai~lA~~~~~~~~~~~~~l-~~~t~--~~~~~l 78 (118)
T PF02984_consen 5 DFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYP---PSVIAAAAILLARKILGKEPPWPESL-EKLTG--YDKEDL 78 (118)
T ss_dssp HHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS----HHHHHHHHHHHHHHHHHSSTCSHHHH-HHHHT--S-HHHH
T ss_pred HHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCC---HHHHHHHHHHHHHHHhCccccCCccc-hhhcC--CCHHHH
Confidence 4444443323335567778888888777666666666 78999999999999955322222222 11222 377777
Q ss_pred HHHHHHHHHHcC
Q 045125 186 QRMELLVLSTLK 197 (342)
Q Consensus 186 ~~mE~~IL~~L~ 197 (342)
..+=..|.+.+.
T Consensus 79 ~~c~~~i~~~~~ 90 (118)
T PF02984_consen 79 KECIELIQELLS 90 (118)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 766555555443
No 32
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=71.42 E-value=3.8 Score=38.79 Aligned_cols=98 Identities=15% Similarity=0.260 Sum_probs=57.9
Q ss_pred HHHHhCCChhHHHHHHHHHHHHhccCccc-CCchhhHHHHHHHHHHHHhhhccccCCccccee-eccCCccccHHHHHHH
Q 045125 111 VHSHFGFGPLCSYLTINYLDRFLSAYELP-KGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQ-VGQSKFLFEAKTIQRM 188 (342)
Q Consensus 111 v~~~~~l~~~T~~lAv~~lDRfLs~~~~~-~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~-v~~~~~~~~~~~I~~m 188 (342)
.+....+..+..-....|++|-+.-.... .-.+|. .+.....++|+|+-....-.--|.+ |.. ..+.+|+..|
T Consensus 200 l~~~~qlta~~aiitL~~~erl~~~~e~~~~p~~w~--r~~~g~il~sskv~~dqs~wnvdycqIlK---d~tveDmNe~ 274 (343)
T KOG1675|consen 200 LFSWAQLTAECDIITLVYAERLLWLAERDPCPRNWS--RAVLGEILLSSKVYDDQSVWNVDYCEILK---DQSVDDMNAL 274 (343)
T ss_pred HhhhhhhhhccchHHHHhhHhhhhHhhcCCCcchhh--hhhhhhheehhhhhhhhhcccHHHHHHHh---hccHhhHHHH
Confidence 33344444455555567888876543322 222343 3444478999999443211111111 111 1378999999
Q ss_pred HHHHHHHcCCccccCChHHHHHHHHH
Q 045125 189 ELLVLSTLKWRMQAITPFSFLDYFTR 214 (342)
Q Consensus 189 E~~IL~~L~w~l~~pTp~~Fl~~fl~ 214 (342)
|+.+|..|.|+++.|.. .|-.||..
T Consensus 275 ERqfLelLqfNinvp~s-vYAKyYfd 299 (343)
T KOG1675|consen 275 ERQFLELLQFNINVPSS-EYAKYYFD 299 (343)
T ss_pred HHHHHHHHhhccCccHH-HHHHHHHH
Confidence 99999999999998854 35555554
No 33
>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=68.32 E-value=58 Score=25.79 Aligned_cols=53 Identities=11% Similarity=0.029 Sum_probs=33.4
Q ss_pred cccccCHHHHHHHHHHHHHccCCCCcchHHHHHHHh-cCCCHHHHHHHHHHHHH
Q 045125 247 DFLEFKPSEIAAAVAISVTGETKTVVDTEKAISLLT-QHVKKERVLKCIKMMND 299 (342)
Q Consensus 247 ~~l~~~PS~IAaAai~~a~~~~~~~~~w~~~l~~~~-~~~~~~~l~~C~~~l~~ 299 (342)
......+..+|+||+++|.+.....+.+...+.... ..++.+++..--..+.+
T Consensus 67 ~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~ 120 (127)
T PF00134_consen 67 PVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILEMEREILS 120 (127)
T ss_dssp -TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHHHHHHH
T ss_pred ccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 466778889999999999986655344444444441 23677777765544443
No 34
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=56.63 E-value=51 Score=31.73 Aligned_cols=64 Identities=19% Similarity=0.211 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHhccCcccCCchhhHHHHHHHHHHHHhhhccccCCcccceeeccCCccccHHHHHHHHHH
Q 045125 122 SYLTINYLDRFLSAYELPKGKVWMMQLLAVACLSLAAKMEETEVPLCLDLQVGQSKFLFEAKTIQRMELL 191 (342)
Q Consensus 122 ~~lAv~~lDRfLs~~~~~~~~~~~lqLlavaCL~IAsK~eE~~~p~~~dl~v~~~~~~~~~~~I~~mE~~ 191 (342)
+..+-||+.--+-..-..... ...||++|+++|+..+|+-.|..... ... +.+++++|-..=..
T Consensus 161 ~Q~~wNfmNDslRT~v~vry~---pe~iACaciyLaAR~~eIpLp~~P~W-f~~--Fd~~k~eid~ic~~ 224 (367)
T KOG0835|consen 161 LQAAWNFMNDSLRTDVFVRYS---PESIACACIYLAARNLEIPLPFQPHW-FKA--FDTTKREIDEICYR 224 (367)
T ss_pred HHHHHHhhhhccccceeeecC---HHHHHHHHHHHHHhhhcCCCCCCccH-HHH--cCCcHHHHHHHHHH
Confidence 444555555444444444444 67899999999999999655544443 111 22466666544333
No 35
>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=52.81 E-value=1.1e+02 Score=23.71 Aligned_cols=89 Identities=15% Similarity=0.072 Sum_probs=50.2
Q ss_pred hHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhccCccccccCHHHHHHH-HHHHHHccCCCCcc----hHHHHH
Q 045125 205 PFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIKGIDFLEFKPSEIAAA-VAISVTGETKTVVD----TEKAIS 279 (342)
Q Consensus 205 p~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~d~~~l~~~PS~IAaA-ai~~a~~~~~~~~~----w~~~l~ 279 (342)
|.+-+...+-+.... ......+-....+++...+-+..--..+||.|||| |.++.....-..+. .-+.|.
T Consensus 4 ~TD~~~~~L~K~~~~-----~e~L~~~H~~V~~~v~KAiV~P~TG~Lp~SlvaAA~CAL~~~~~~~P~~~~~~~~~~~LA 78 (106)
T PF09080_consen 4 PTDAIGPLLFKSGFT-----KEQLFAWHSEVVESVHKAIVNPKTGGLPPSLVAAAGCALFSLGAAAPPDTHSGGVVPQLA 78 (106)
T ss_dssp CHHHHHHHHHHHS-S-----STTHHHHHHHHHHHHHHHHCSTTGGGS-HHHHHHHHHHHHS-GGGS--------HHHHHH
T ss_pred ccccccHHHHHHccc-----HHHHHHHHHHHHHHHHHHhcCcccCCCCHHHHHHhhhhhccccccCCCccccccchHHHH
Confidence 334445555555544 22224455667777777777999999999999999 66655543322111 122355
Q ss_pred HHhcCCCHHHHHHHHHHHHH
Q 045125 280 LLTQHVKKERVLKCIKMMND 299 (342)
Q Consensus 280 ~~~~~~~~~~l~~C~~~l~~ 299 (342)
.. .|.+..-+..-.+.+..
T Consensus 79 ~~-~G~~~a~L~AA~E~v~T 97 (106)
T PF09080_consen 79 EA-LGVSAATLQAAAESVAT 97 (106)
T ss_dssp HH-HT--HHHHHHHHHHHHH
T ss_pred HH-hCccHHHHHHHHHHHHH
Confidence 55 58888888777776654
No 36
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=40.23 E-value=2.4e+02 Score=26.96 Aligned_cols=38 Identities=11% Similarity=0.081 Sum_probs=25.5
Q ss_pred HHHHHHHHhhccCccccccCHHHHHHHHHHHHHccCCC
Q 045125 233 CRSIQIITSSIKGIDFLEFKPSEIAAAVAISVTGETKT 270 (342)
Q Consensus 233 ~~~~~lil~~l~d~~~l~~~PS~IAaAai~~a~~~~~~ 270 (342)
..+.-++..-.....+..|.|-.||++|+++|.+.-..
T Consensus 80 aTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~ 117 (305)
T TIGR00569 80 GTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEF 117 (305)
T ss_pred HHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhcccc
Confidence 33333333333355667899999999999999975443
No 37
>PF11737 DUF3300: Protein of unknown function (DUF3300); InterPro: IPR021728 This hypothetical bacterial gene product has a long hydrophobic segment and is thus likely to be a membrane protein.
Probab=28.87 E-value=1.4e+02 Score=27.47 Aligned_cols=54 Identities=13% Similarity=0.098 Sum_probs=43.4
Q ss_pred ccCHHHHHHHHHHHHHccCCCCcchHHHHHHHhcCCCHHHHHHHHHHHHHHHhcC
Q 045125 250 EFKPSEIAAAVAISVTGETKTVVDTEKAISLLTQHVKKERVLKCIKMMNDSLISG 304 (342)
Q Consensus 250 ~~~PS~IAaAai~~a~~~~~~~~~w~~~l~~~~~~~~~~~l~~C~~~l~~l~~~~ 304 (342)
..-||+.|++++=-++..+...++|...|..- --.++++|..-++.|++.....
T Consensus 60 ~WDpSVkaL~~fP~VL~~Ms~~l~WTq~LGdA-fl~q~~dVm~aIQ~LR~~A~~~ 113 (237)
T PF11737_consen 60 PWDPSVKALVAFPDVLQMMSDDLDWTQQLGDA-FLAQPQDVMDAIQRLRQRAQAA 113 (237)
T ss_pred CCCHHHHHHHhhHHHHHHHccChHHHHHHHHH-HHhCHHHHHHHHHHHHHHHHHc
Confidence 47799999998877777776668999998654 3578999999999999876543
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=26.99 E-value=3.7e+02 Score=22.38 Aligned_cols=82 Identities=7% Similarity=0.001 Sum_probs=42.6
Q ss_pred cCChHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHhhcc-----CccccccCHHHHHHHHHHHHHccCCCCcchHH
Q 045125 202 AITPFSFLDYFTRKITDDDDDHHQTPLRALFCRSIQIITSSIK-----GIDFLEFKPSEIAAAVAISVTGETKTVVDTEK 276 (342)
Q Consensus 202 ~pTp~~Fl~~fl~~~~~~~~~~~~~~~~~l~~~~~~lil~~l~-----d~~~l~~~PS~IAaAai~~a~~~~~~~~~w~~ 276 (342)
.++..+|+..+.+..... ......+.-++..... ....-...+--+=++|+.+|.+...+..-+++
T Consensus 51 ~i~i~~fl~ri~~~~~~s---------~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~ 121 (149)
T PF08613_consen 51 SISIRDFLSRILKYTQCS---------PECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNK 121 (149)
T ss_dssp SS-HHHHHHHHHHHTT-----------HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HH
T ss_pred CCcHHHHHHHHHHHcCCC---------hHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHH
Confidence 345666777777665554 2222222222222221 12223344556677778888988777666788
Q ss_pred HHHHHhcCCCHHHHHHH
Q 045125 277 AISLLTQHVKKERVLKC 293 (342)
Q Consensus 277 ~l~~~~~~~~~~~l~~C 293 (342)
.+..+ +|++..++..-
T Consensus 122 ~~a~v-~gis~~eln~l 137 (149)
T PF08613_consen 122 SWAKV-GGISLKELNEL 137 (149)
T ss_dssp HHHHH-HTS-HHHHHHH
T ss_pred HHHhh-cCCCHHHHHHH
Confidence 88888 89988887653
No 39
>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=24.37 E-value=3.1e+02 Score=22.84 Aligned_cols=56 Identities=9% Similarity=0.100 Sum_probs=44.2
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHHHHHhcc-CcccCCchhhHHHHHHHHHHHHhhhcc
Q 045125 105 VDWIAKVHSHFGFGPLCSYLTINYLDRFLSA-YELPKGKVWMMQLLAVACLSLAAKMEE 162 (342)
Q Consensus 105 vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~-~~~~~~~~~~lqLlavaCL~IAsK~eE 162 (342)
..-|.++|.+++++++..-.....|+..+.. ..+-++. ++--+-++|+++-+|+..
T Consensus 15 ~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dR--HLDQiilCaiY~i~Kv~~ 71 (135)
T PF01857_consen 15 AVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDR--HLDQIILCAIYGICKVSK 71 (135)
T ss_dssp HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS---HHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcc--hHHHHHHHHHHHHHHhhc
Confidence 3446789999999999888888999998864 3444444 588899999999999965
No 40
>KOG1925 consensus Rac1 GTPase effector FHOS [Signal transduction mechanisms; Cytoskeleton]
Probab=22.45 E-value=1.2e+02 Score=31.14 Aligned_cols=70 Identities=13% Similarity=0.107 Sum_probs=53.4
Q ss_pred ChHHHHHHHHHHHcccCCCCchhhhccCCCCCHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHhcc
Q 045125 66 QSDECLALLLEKECHHLPHNDYLKRLRTGDLDLAARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRFLSA 135 (342)
Q Consensus 66 y~~ei~~~l~~~E~~~~~~~~yl~~~q~~~i~~~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRfLs~ 135 (342)
.-++...+|.+.|++...+.+-+..|..+++.+..|+.+.+|+-+++++.-+-.-+.-.-+|=|+-||.-
T Consensus 547 Df~qL~DNL~qlErrCKaSWe~L~~Iakhe~~p~l~~r~~~fl~~cA~RI~~LKivhrr~~NRfHSFLLy 616 (817)
T KOG1925|consen 547 DFEQLTDNLGQLERRCKASWESLRSIAKHELAPALRARLTHFLDQCARRIAMLKIVHRRVCNRFHSFLLY 616 (817)
T ss_pred cHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567888999999998888888888888899999999999999998887643333333344666666643
No 41
>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=20.95 E-value=1.7e+02 Score=21.85 Aligned_cols=34 Identities=18% Similarity=0.333 Sum_probs=25.8
Q ss_pred CCHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHH
Q 045125 96 LDLAARQEAVDWIAKVHSHFGFGPLCSYLTINYLDRF 132 (342)
Q Consensus 96 i~~~~R~~~vdWi~~v~~~~~l~~~T~~lAv~~lDRf 132 (342)
-...-|..+|++|.++...-|++.+ .|+..+|.+
T Consensus 47 ~~y~rRK~Ii~~I~~l~~~~g~~~~---~ai~~le~~ 80 (81)
T PF12550_consen 47 RTYSRRKVIIDFIERLANERGISEE---EAIEILEEI 80 (81)
T ss_pred hhHHHHHHHHHHHHHHHHHcCCCHH---HHHHHHHhc
Confidence 3457799999999999888777655 567777754
No 42
>PF14376 Haem_bd: Haem-binding domain
Probab=20.54 E-value=2.2e+02 Score=23.69 Aligned_cols=36 Identities=19% Similarity=0.279 Sum_probs=28.7
Q ss_pred HHHHcccCCCCchhhhccCCCCCHHHHHHHHHHHHH
Q 045125 75 LEKECHHLPHNDYLKRLRTGDLDLAARQEAVDWIAK 110 (342)
Q Consensus 75 ~~~E~~~~~~~~yl~~~q~~~i~~~~R~~~vdWi~~ 110 (342)
-..|...+|...|.--+....++.+.|..+++|+-+
T Consensus 100 ~~I~~g~MP~~~Y~~~H~~a~Ls~~ek~~Ll~Wi~~ 135 (137)
T PF14376_consen 100 EVIEDGEMPPPSYTLLHWEAKLSEEEKQALLNWIKE 135 (137)
T ss_pred HHHHcCCCChHHHhhhCCCCCCCHHHHHHHHHHHHH
Confidence 345556788889987666667999999999999975
Done!